update of the docu.
This commit is contained in:
parent
72dd9dea65
commit
f22b16876f
@ -1,4 +1,4 @@
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# Sphinx build info version 1
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# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 4e935cd35ad4b5e15fdb7bfc2da9495e
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config: 429dcaf60d751fc64b55c07d7174ea6f
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tags: 645f666f9bcd5a90fca523b33c5a78b7
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BIN
doc/html/_static/ajax-loader.gif
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@ -4,7 +4,7 @@
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*
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* Sphinx stylesheet -- basic theme.
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*
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* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
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* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
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* :license: BSD, see LICENSE for details.
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*
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*/
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@ -52,6 +52,8 @@ div.sphinxsidebar {
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width: 230px;
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margin-left: -100%;
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font-size: 90%;
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word-wrap: break-word;
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overflow-wrap : break-word;
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}
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div.sphinxsidebar ul {
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@ -80,13 +82,21 @@ div.sphinxsidebar input {
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}
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div.sphinxsidebar #searchbox input[type="text"] {
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width: 170px;
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float: left;
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width: 80%;
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padding: 0.25em;
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box-sizing: border-box;
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}
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div.sphinxsidebar #searchbox input[type="submit"] {
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width: 30px;
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float: left;
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width: 20%;
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border-left: none;
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padding: 0.25em;
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box-sizing: border-box;
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}
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img {
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border: 0;
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max-width: 100%;
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@ -124,6 +134,8 @@ ul.keywordmatches li.goodmatch a {
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table.contentstable {
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width: 90%;
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margin-left: auto;
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margin-right: auto;
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}
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table.contentstable p.biglink {
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@ -151,9 +163,14 @@ table.indextable td {
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vertical-align: top;
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}
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table.indextable dl, table.indextable dd {
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table.indextable ul {
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margin-top: 0;
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margin-bottom: 0;
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list-style-type: none;
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}
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table.indextable > tbody > tr > td > ul {
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padding-left: 0em;
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}
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table.indextable tr.pcap {
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@ -185,8 +202,27 @@ div.genindex-jumpbox {
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padding: 0.4em;
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}
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/* -- domain module index --------------------------------------------------- */
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table.modindextable td {
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padding: 2px;
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border-collapse: collapse;
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}
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/* -- general body styles --------------------------------------------------- */
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div.body {
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min-width: 450px;
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max-width: 800px;
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}
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div.body p, div.body dd, div.body li, div.body blockquote {
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-moz-hyphens: auto;
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-ms-hyphens: auto;
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-webkit-hyphens: auto;
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hyphens: auto;
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}
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a.headerlink {
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visibility: hidden;
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}
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@ -197,7 +233,10 @@ h3:hover > a.headerlink,
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h4:hover > a.headerlink,
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h5:hover > a.headerlink,
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h6:hover > a.headerlink,
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dt:hover > a.headerlink {
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dt:hover > a.headerlink,
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caption:hover > a.headerlink,
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p.caption:hover > a.headerlink,
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div.code-block-caption:hover > a.headerlink {
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visibility: visible;
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}
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@ -209,10 +248,6 @@ div.body td {
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text-align: left;
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}
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.field-list ul {
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padding-left: 1em;
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}
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.first {
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margin-top: 0 !important;
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}
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@ -314,6 +349,18 @@ table.docutils {
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border-collapse: collapse;
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}
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table.align-center {
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margin-left: auto;
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margin-right: auto;
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}
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table caption span.caption-number {
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font-style: italic;
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}
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table caption span.caption-text {
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}
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table.docutils td, table.docutils th {
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padding: 1px 8px 1px 5px;
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border-top: 0;
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@ -322,10 +369,6 @@ table.docutils td, table.docutils th {
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border-bottom: 1px solid #aaa;
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}
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table.field-list td, table.field-list th {
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border: 0 !important;
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}
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table.footnote td, table.footnote th {
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border: 0 !important;
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}
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@ -344,6 +387,46 @@ table.citation td {
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border-bottom: none;
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}
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/* -- figures --------------------------------------------------------------- */
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div.figure {
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margin: 0.5em;
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padding: 0.5em;
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}
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div.figure p.caption {
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padding: 0.3em;
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}
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div.figure p.caption span.caption-number {
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font-style: italic;
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}
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div.figure p.caption span.caption-text {
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}
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/* -- field list styles ----------------------------------------------------- */
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table.field-list td, table.field-list th {
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border: 0 !important;
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}
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.field-list ul {
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margin: 0;
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padding-left: 1em;
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}
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.field-list p {
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margin: 0;
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}
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.field-name {
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-moz-hyphens: manual;
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-ms-hyphens: manual;
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-webkit-hyphens: manual;
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hyphens: manual;
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}
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/* -- other body styles ----------------------------------------------------- */
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ol.arabic {
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@ -384,28 +467,27 @@ dd {
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margin-left: 30px;
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}
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dt:target, .highlighted {
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dt:target, span.highlighted {
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background-color: #fbe54e;
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}
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rect.highlighted {
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fill: #fbe54e;
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}
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dl.glossary dt {
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font-weight: bold;
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font-size: 1.1em;
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}
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.field-list ul {
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margin: 0;
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padding-left: 1em;
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}
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.field-list p {
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margin: 0;
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}
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.optional {
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font-size: 1.3em;
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}
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.sig-paren {
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font-size: larger;
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}
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.versionmodified {
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font-style: italic;
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}
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@ -456,6 +538,13 @@ pre {
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overflow-y: hidden; /* fixes display issues on Chrome browsers */
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}
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span.pre {
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-moz-hyphens: none;
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-ms-hyphens: none;
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-webkit-hyphens: none;
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hyphens: none;
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}
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td.linenos pre {
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padding: 5px 0px;
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border: 0;
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@ -471,22 +560,51 @@ table.highlighttable td {
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padding: 0 0.5em 0 0.5em;
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}
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tt.descname {
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div.code-block-caption {
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padding: 2px 5px;
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font-size: small;
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}
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div.code-block-caption code {
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background-color: transparent;
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}
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div.code-block-caption + div > div.highlight > pre {
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margin-top: 0;
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}
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div.code-block-caption span.caption-number {
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padding: 0.1em 0.3em;
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font-style: italic;
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}
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div.code-block-caption span.caption-text {
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}
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div.literal-block-wrapper {
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padding: 1em 1em 0;
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}
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div.literal-block-wrapper div.highlight {
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margin: 0;
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}
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code.descname {
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background-color: transparent;
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font-weight: bold;
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font-size: 1.2em;
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}
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tt.descclassname {
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code.descclassname {
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background-color: transparent;
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}
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tt.xref, a tt {
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code.xref, a code {
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background-color: transparent;
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font-weight: bold;
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}
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h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
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h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
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background-color: transparent;
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}
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@ -518,6 +636,16 @@ span.eqno {
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float: right;
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}
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span.eqno a.headerlink {
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position: relative;
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left: 0px;
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z-index: 1;
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}
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div.math:hover a.headerlink {
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visibility: visible;
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}
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/* -- printout stylesheet --------------------------------------------------- */
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@media print {
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1
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1
doc/html/_static/css/badge_only.css
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@ -0,0 +1 @@
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.fa:before{-webkit-font-smoothing:antialiased}.clearfix{*zoom:1}.clearfix:before,.clearfix:after{display:table;content:""}.clearfix:after{clear:both}@font-face{font-family:FontAwesome;font-weight:normal;font-style:normal;src:url("../fonts/fontawesome-webfont.eot");src:url("../fonts/fontawesome-webfont.eot?#iefix") format("embedded-opentype"),url("../fonts/fontawesome-webfont.woff") format("woff"),url("../fonts/fontawesome-webfont.ttf") format("truetype"),url("../fonts/fontawesome-webfont.svg#FontAwesome") format("svg")}.fa:before{display:inline-block;font-family:FontAwesome;font-style:normal;font-weight:normal;line-height:1;text-decoration:inherit}a .fa{display:inline-block;text-decoration:inherit}li .fa{display:inline-block}li .fa-large:before,li .fa-large:before{width:1.875em}ul.fas{list-style-type:none;margin-left:2em;text-indent:-0.8em}ul.fas li .fa{width:.8em}ul.fas li .fa-large:before,ul.fas li .fa-large:before{vertical-align:baseline}.fa-book:before{content:""}.icon-book:before{content:""}.fa-caret-down:before{content:""}.icon-caret-down:before{content:""}.fa-caret-up:before{content:""}.icon-caret-up:before{content:""}.fa-caret-left:before{content:""}.icon-caret-left:before{content:""}.fa-caret-right:before{content:""}.icon-caret-right:before{content:""}.rst-versions{position:fixed;bottom:0;left:0;width:300px;color:#fcfcfc;background:#1f1d1d;font-family:"Lato","proxima-nova","Helvetica Neue",Arial,sans-serif;z-index:400}.rst-versions a{color:#2980B9;text-decoration:none}.rst-versions .rst-badge-small{display:none}.rst-versions .rst-current-version{padding:12px;background-color:#272525;display:block;text-align:right;font-size:90%;cursor:pointer;color:#27AE60;*zoom:1}.rst-versions .rst-current-version:before,.rst-versions .rst-current-version:after{display:table;content:""}.rst-versions .rst-current-version:after{clear:both}.rst-versions .rst-current-version .fa{color:#fcfcfc}.rst-versions .rst-current-version .fa-book{float:left}.rst-versions .rst-current-version .icon-book{float:left}.rst-versions .rst-current-version.rst-out-of-date{background-color:#E74C3C;color:#fff}.rst-versions .rst-current-version.rst-active-old-version{background-color:#F1C40F;color:#000}.rst-versions.shift-up{height:auto;max-height:100%}.rst-versions.shift-up .rst-other-versions{display:block}.rst-versions .rst-other-versions{font-size:90%;padding:12px;color:gray;display:none}.rst-versions .rst-other-versions hr{display:block;height:1px;border:0;margin:20px 0;padding:0;border-top:solid 1px #413d3d}.rst-versions .rst-other-versions dd{display:inline-block;margin:0}.rst-versions .rst-other-versions dd a{display:inline-block;padding:6px;color:#fcfcfc}.rst-versions.rst-badge{width:auto;bottom:20px;right:20px;left:auto;border:none;max-width:300px}.rst-versions.rst-badge .icon-book{float:none}.rst-versions.rst-badge .fa-book{float:none}.rst-versions.rst-badge.shift-up .rst-current-version{text-align:right}.rst-versions.rst-badge.shift-up .rst-current-version .fa-book{float:left}.rst-versions.rst-badge.shift-up .rst-current-version .icon-book{float:left}.rst-versions.rst-badge .rst-current-version{width:auto;height:30px;line-height:30px;padding:0 6px;display:block;text-align:center}@media screen and (max-width: 768px){.rst-versions{width:85%;display:none}.rst-versions.shift{display:block}}
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*
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* Sphinx JavaScript utilities for all documentation.
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*
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* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
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* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
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* :license: BSD, see LICENSE for details.
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*
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*/
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@ -45,7 +45,7 @@ jQuery.urlencode = encodeURIComponent;
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* it will always return arrays of strings for the value parts.
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*/
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jQuery.getQueryParameters = function(s) {
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if (typeof s == 'undefined')
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if (typeof s === 'undefined')
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s = document.location.search;
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var parts = s.substr(s.indexOf('?') + 1).split('&');
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var result = {};
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@ -66,31 +66,81 @@ jQuery.getQueryParameters = function(s) {
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* span elements with the given class name.
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*/
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jQuery.fn.highlightText = function(text, className) {
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function highlight(node) {
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if (node.nodeType == 3) {
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function highlight(node, addItems) {
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if (node.nodeType === 3) {
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var val = node.nodeValue;
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var pos = val.toLowerCase().indexOf(text);
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if (pos >= 0 && !jQuery(node.parentNode).hasClass(className)) {
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var span = document.createElement("span");
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span.className = className;
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if (pos >= 0 &&
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!jQuery(node.parentNode).hasClass(className) &&
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!jQuery(node.parentNode).hasClass("nohighlight")) {
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var span;
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var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
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if (isInSVG) {
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span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
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} else {
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span = document.createElement("span");
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span.className = className;
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}
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span.appendChild(document.createTextNode(val.substr(pos, text.length)));
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node.parentNode.insertBefore(span, node.parentNode.insertBefore(
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document.createTextNode(val.substr(pos + text.length)),
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node.nextSibling));
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node.nodeValue = val.substr(0, pos);
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if (isInSVG) {
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var bbox = span.getBBox();
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var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
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rect.x.baseVal.value = bbox.x;
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rect.y.baseVal.value = bbox.y;
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rect.width.baseVal.value = bbox.width;
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rect.height.baseVal.value = bbox.height;
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rect.setAttribute('class', className);
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var parentOfText = node.parentNode.parentNode;
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addItems.push({
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"parent": node.parentNode,
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}
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}
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else if (!jQuery(node).is("button, select, textarea")) {
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jQuery.each(node.childNodes, function() {
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highlight(this);
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highlight(this, addItems);
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});
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}
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}
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return this.each(function() {
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highlight(this);
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var addItems = [];
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var result = this.each(function() {
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highlight(this, addItems);
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});
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for (var i = 0; i < addItems.length; ++i) {
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jQuery(addItems[i].parent).before(addItems[i].target);
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}
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return result;
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};
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/*
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* backward compatibility for jQuery.browser
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* This will be supported until firefox bug is fixed.
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*/
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if (!jQuery.browser) {
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jQuery.uaMatch = function(ua) {
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ua = ua.toLowerCase();
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var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
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/(webkit)[ \/]([\w.]+)/.exec(ua) ||
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/(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
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/(msie) ([\w.]+)/.exec(ua) ||
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ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
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[];
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return {
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browser: match[ 1 ] || "",
|
||||
version: match[ 2 ] || "0"
|
||||
};
|
||||
};
|
||||
jQuery.browser = {};
|
||||
jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Small JavaScript module for the documentation.
|
||||
*/
|
||||
@ -100,27 +150,28 @@ var Documentation = {
|
||||
this.fixFirefoxAnchorBug();
|
||||
this.highlightSearchWords();
|
||||
this.initIndexTable();
|
||||
|
||||
},
|
||||
|
||||
/**
|
||||
* i18n support
|
||||
*/
|
||||
TRANSLATIONS : {},
|
||||
PLURAL_EXPR : function(n) { return n == 1 ? 0 : 1; },
|
||||
PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; },
|
||||
LOCALE : 'unknown',
|
||||
|
||||
// gettext and ngettext don't access this so that the functions
|
||||
// can safely bound to a different name (_ = Documentation.gettext)
|
||||
gettext : function(string) {
|
||||
var translated = Documentation.TRANSLATIONS[string];
|
||||
if (typeof translated == 'undefined')
|
||||
if (typeof translated === 'undefined')
|
||||
return string;
|
||||
return (typeof translated == 'string') ? translated : translated[0];
|
||||
return (typeof translated === 'string') ? translated : translated[0];
|
||||
},
|
||||
|
||||
ngettext : function(singular, plural, n) {
|
||||
var translated = Documentation.TRANSLATIONS[singular];
|
||||
if (typeof translated == 'undefined')
|
||||
if (typeof translated === 'undefined')
|
||||
return (n == 1) ? singular : plural;
|
||||
return translated[Documentation.PLURALEXPR(n)];
|
||||
},
|
||||
@ -152,6 +203,7 @@ var Documentation = {
|
||||
|
||||
/**
|
||||
* workaround a firefox stupidity
|
||||
* see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075
|
||||
*/
|
||||
fixFirefoxAnchorBug : function() {
|
||||
if (document.location.hash && $.browser.mozilla)
|
||||
@ -190,7 +242,7 @@ var Documentation = {
|
||||
var src = $(this).attr('src');
|
||||
var idnum = $(this).attr('id').substr(7);
|
||||
$('tr.cg-' + idnum).toggle();
|
||||
if (src.substr(-9) == 'minus.png')
|
||||
if (src.substr(-9) === 'minus.png')
|
||||
$(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
|
||||
else
|
||||
$(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
|
||||
@ -222,11 +274,34 @@ var Documentation = {
|
||||
var path = document.location.pathname;
|
||||
var parts = path.split(/\//);
|
||||
$.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
|
||||
if (this == '..')
|
||||
if (this === '..')
|
||||
parts.pop();
|
||||
});
|
||||
var url = parts.join('/');
|
||||
return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
|
||||
},
|
||||
|
||||
initOnKeyListeners: function() {
|
||||
$(document).keyup(function(event) {
|
||||
var activeElementType = document.activeElement.tagName;
|
||||
// don't navigate when in search box or textarea
|
||||
if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
|
||||
switch (event.keyCode) {
|
||||
case 37: // left
|
||||
var prevHref = $('link[rel="prev"]').prop('href');
|
||||
if (prevHref) {
|
||||
window.location.href = prevHref;
|
||||
return false;
|
||||
}
|
||||
case 39: // right
|
||||
var nextHref = $('link[rel="next"]').prop('href');
|
||||
if (nextHref) {
|
||||
window.location.href = nextHref;
|
||||
return false;
|
||||
}
|
||||
}
|
||||
}
|
||||
});
|
||||
}
|
||||
};
|
||||
|
||||
|
||||
@ -1,12 +1,9 @@
|
||||
var DOCUMENTATION_OPTIONS = {
|
||||
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
|
||||
VERSION: '1.7.6',
|
||||
VERSION: '1.8.2',
|
||||
LANGUAGE: 'None',
|
||||
COLLAPSE_INDEX: false,
|
||||
BUILDER: 'html',
|
||||
FILE_SUFFIX: '.html',
|
||||
LINK_SUFFIX: '.html',
|
||||
HAS_SOURCE: true,
|
||||
SOURCELINK_SUFFIX: '.txt',
|
||||
NAVIGATION_WITH_KEYS: false
|
||||
SOURCELINK_SUFFIX: '.txt'
|
||||
};
|
||||
BIN
doc/html/_static/down-pressed.png
Normal file
BIN
doc/html/_static/down-pressed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 222 B |
BIN
doc/html/_static/down.png
Normal file
BIN
doc/html/_static/down.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 202 B |
Binary file not shown.
|
Before Width: | Height: | Size: 392 B After Width: | Height: | Size: 286 B |
BIN
doc/html/_static/fonts/Inconsolata-Bold.ttf
Normal file
BIN
doc/html/_static/fonts/Inconsolata-Bold.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/Inconsolata-Regular.ttf
Normal file
BIN
doc/html/_static/fonts/Inconsolata-Regular.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/Lato-Bold.ttf
Normal file
BIN
doc/html/_static/fonts/Lato-Bold.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/Lato-BoldItalic.ttf
Normal file
BIN
doc/html/_static/fonts/Lato-BoldItalic.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/Lato-Italic.ttf
Normal file
BIN
doc/html/_static/fonts/Lato-Italic.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/Lato-Regular.ttf
Normal file
BIN
doc/html/_static/fonts/Lato-Regular.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/RobotoSlab-Bold.ttf
Normal file
BIN
doc/html/_static/fonts/RobotoSlab-Bold.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/RobotoSlab-Regular.ttf
Normal file
BIN
doc/html/_static/fonts/RobotoSlab-Regular.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/fontawesome-webfont.eot
Normal file
BIN
doc/html/_static/fonts/fontawesome-webfont.eot
Normal file
Binary file not shown.
2671
doc/html/_static/fonts/fontawesome-webfont.svg
Normal file
2671
doc/html/_static/fonts/fontawesome-webfont.svg
Normal file
File diff suppressed because it is too large
Load Diff
|
After Width: | Height: | Size: 434 KiB |
BIN
doc/html/_static/fonts/fontawesome-webfont.ttf
Normal file
BIN
doc/html/_static/fonts/fontawesome-webfont.ttf
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/fontawesome-webfont.woff
Normal file
BIN
doc/html/_static/fonts/fontawesome-webfont.woff
Normal file
Binary file not shown.
BIN
doc/html/_static/fonts/fontawesome-webfont.woff2
Normal file
BIN
doc/html/_static/fonts/fontawesome-webfont.woff2
Normal file
Binary file not shown.
@ -16,7 +16,7 @@
|
||||
* Braden Ewing <brewin@gmail.com>
|
||||
* Humdinger <humdingerb@gmail.com>
|
||||
*
|
||||
* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
|
||||
* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
|
||||
* :license: BSD, see LICENSE for details.
|
||||
*
|
||||
*/
|
||||
@ -307,7 +307,7 @@ td {
|
||||
vertical-align: top;
|
||||
}
|
||||
|
||||
tt {
|
||||
code {
|
||||
background-color: #e2e2e2;
|
||||
font-size: 1.0em;
|
||||
font-family: monospace;
|
||||
@ -369,3 +369,8 @@ div.viewcode-block:target {
|
||||
margin: -1px -10px;
|
||||
padding: 0 12px;
|
||||
}
|
||||
|
||||
/* math display */
|
||||
div.math p {
|
||||
text-align: center;
|
||||
}
|
||||
File diff suppressed because it is too large
Load Diff
6
doc/html/_static/jquery.js
vendored
6
doc/html/_static/jquery.js
vendored
File diff suppressed because one or more lines are too long
4
doc/html/_static/js/modernizr.min.js
vendored
Normal file
4
doc/html/_static/js/modernizr.min.js
vendored
Normal file
File diff suppressed because one or more lines are too long
1
doc/html/_static/js/theme.js
Normal file
1
doc/html/_static/js/theme.js
Normal file
@ -0,0 +1 @@
|
||||
require=function r(s,a,l){function c(i,n){if(!a[i]){if(!s[i]){var e="function"==typeof require&&require;if(!n&&e)return e(i,!0);if(u)return u(i,!0);var t=new Error("Cannot find module '"+i+"'");throw t.code="MODULE_NOT_FOUND",t}var o=a[i]={exports:{}};s[i][0].call(o.exports,function(n){var e=s[i][1][n];return c(e||n)},o,o.exports,r,s,a,l)}return a[i].exports}for(var u="function"==typeof require&&require,n=0;n<l.length;n++)c(l[n]);return c}({"sphinx-rtd-theme":[function(n,e,i){var jQuery="undefined"!=typeof window?window.jQuery:n("jquery");e.exports.ThemeNav={navBar:null,win:null,winScroll:!1,winResize:!1,linkScroll:!1,winPosition:0,winHeight:null,docHeight:null,isRunning:!1,enable:function(e){var i=this;"undefined"==typeof withStickNav&&(e=!0),i.isRunning||(i.isRunning=!0,jQuery(function(n){i.init(n),i.reset(),i.win.on("hashchange",i.reset),e&&i.win.on("scroll",function(){i.linkScroll||i.winScroll||(i.winScroll=!0,requestAnimationFrame(function(){i.onScroll()}))}),i.win.on("resize",function(){i.winResize||(i.winResize=!0,requestAnimationFrame(function(){i.onResize()}))}),i.onResize()}))},enableSticky:function(){this.enable(!0)},init:function(i){i(document);var t=this;this.navBar=i("div.wy-side-scroll:first"),this.win=i(window),i(document).on("click","[data-toggle='wy-nav-top']",function(){i("[data-toggle='wy-nav-shift']").toggleClass("shift"),i("[data-toggle='rst-versions']").toggleClass("shift")}).on("click",".wy-menu-vertical .current ul li a",function(){var n=i(this);i("[data-toggle='wy-nav-shift']").removeClass("shift"),i("[data-toggle='rst-versions']").toggleClass("shift"),t.toggleCurrent(n),t.hashChange()}).on("click","[data-toggle='rst-current-version']",function(){i("[data-toggle='rst-versions']").toggleClass("shift-up")}),i("table.docutils:not(.field-list,.footnote,.citation)").wrap("<div class='wy-table-responsive'></div>"),i("table.docutils.footnote").wrap("<div class='wy-table-responsive footnote'></div>"),i("table.docutils.citation").wrap("<div class='wy-table-responsive citation'></div>"),i(".wy-menu-vertical ul").not(".simple").siblings("a").each(function(){var e=i(this);expand=i('<span class="toctree-expand"></span>'),expand.on("click",function(n){return t.toggleCurrent(e),n.stopPropagation(),!1}),e.prepend(expand)})},reset:function(){var n=encodeURI(window.location.hash)||"#";try{var e=$(".wy-menu-vertical"),i=e.find('[href="'+n+'"]');if(0===i.length){var t=$('.document [id="'+n.substring(1)+'"]').closest("div.section");0===(i=e.find('[href="#'+t.attr("id")+'"]')).length&&(i=e.find('[href="#"]'))}0<i.length&&($(".wy-menu-vertical .current").removeClass("current"),i.addClass("current"),i.closest("li.toctree-l1").addClass("current"),i.closest("li.toctree-l1").parent().addClass("current"),i.closest("li.toctree-l1").addClass("current"),i.closest("li.toctree-l2").addClass("current"),i.closest("li.toctree-l3").addClass("current"),i.closest("li.toctree-l4").addClass("current"))}catch(o){console.log("Error expanding nav for anchor",o)}},onScroll:function(){this.winScroll=!1;var n=this.win.scrollTop(),e=n+this.winHeight,i=this.navBar.scrollTop()+(n-this.winPosition);n<0||e>this.docHeight||(this.navBar.scrollTop(i),this.winPosition=n)},onResize:function(){this.winResize=!1,this.winHeight=this.win.height(),this.docHeight=$(document).height()},hashChange:function(){this.linkScroll=!0,this.win.one("hashchange",function(){this.linkScroll=!1})},toggleCurrent:function(n){var e=n.closest("li");e.siblings("li.current").removeClass("current"),e.siblings().find("li.current").removeClass("current"),e.find("> ul li.current").removeClass("current"),e.toggleClass("current")}},"undefined"!=typeof window&&(window.SphinxRtdTheme={Navigation:e.exports.ThemeNav,StickyNav:e.exports.ThemeNav}),function(){for(var r=0,n=["ms","moz","webkit","o"],e=0;e<n.length&&!window.requestAnimationFrame;++e)window.requestAnimationFrame=window[n[e]+"RequestAnimationFrame"],window.cancelAnimationFrame=window[n[e]+"CancelAnimationFrame"]||window[n[e]+"CancelRequestAnimationFrame"];window.requestAnimationFrame||(window.requestAnimationFrame=function(n,e){var i=(new Date).getTime(),t=Math.max(0,16-(i-r)),o=window.setTimeout(function(){n(i+t)},t);return r=i+t,o}),window.cancelAnimationFrame||(window.cancelAnimationFrame=function(n){clearTimeout(n)})}()},{jquery:"jquery"}]},{},["sphinx-rtd-theme"]);
|
||||
@ -1,297 +0,0 @@
|
||||
/*
|
||||
* language_data.js
|
||||
* ~~~~~~~~~~~~~~~~
|
||||
*
|
||||
* This script contains the language-specific data used by searchtools.js,
|
||||
* namely the list of stopwords, stemmer, scorer and splitter.
|
||||
*
|
||||
* :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
|
||||
* :license: BSD, see LICENSE for details.
|
||||
*
|
||||
*/
|
||||
|
||||
var stopwords = ["a","and","are","as","at","be","but","by","for","if","in","into","is","it","near","no","not","of","on","or","such","that","the","their","then","there","these","they","this","to","was","will","with"];
|
||||
|
||||
|
||||
/* Non-minified version JS is _stemmer.js if file is provided */
|
||||
/**
|
||||
* Porter Stemmer
|
||||
*/
|
||||
var Stemmer = function() {
|
||||
|
||||
var step2list = {
|
||||
ational: 'ate',
|
||||
tional: 'tion',
|
||||
enci: 'ence',
|
||||
anci: 'ance',
|
||||
izer: 'ize',
|
||||
bli: 'ble',
|
||||
alli: 'al',
|
||||
entli: 'ent',
|
||||
eli: 'e',
|
||||
ousli: 'ous',
|
||||
ization: 'ize',
|
||||
ation: 'ate',
|
||||
ator: 'ate',
|
||||
alism: 'al',
|
||||
iveness: 'ive',
|
||||
fulness: 'ful',
|
||||
ousness: 'ous',
|
||||
aliti: 'al',
|
||||
iviti: 'ive',
|
||||
biliti: 'ble',
|
||||
logi: 'log'
|
||||
};
|
||||
|
||||
var step3list = {
|
||||
icate: 'ic',
|
||||
ative: '',
|
||||
alize: 'al',
|
||||
iciti: 'ic',
|
||||
ical: 'ic',
|
||||
ful: '',
|
||||
ness: ''
|
||||
};
|
||||
|
||||
var c = "[^aeiou]"; // consonant
|
||||
var v = "[aeiouy]"; // vowel
|
||||
var C = c + "[^aeiouy]*"; // consonant sequence
|
||||
var V = v + "[aeiou]*"; // vowel sequence
|
||||
|
||||
var mgr0 = "^(" + C + ")?" + V + C; // [C]VC... is m>0
|
||||
var meq1 = "^(" + C + ")?" + V + C + "(" + V + ")?$"; // [C]VC[V] is m=1
|
||||
var mgr1 = "^(" + C + ")?" + V + C + V + C; // [C]VCVC... is m>1
|
||||
var s_v = "^(" + C + ")?" + v; // vowel in stem
|
||||
|
||||
this.stemWord = function (w) {
|
||||
var stem;
|
||||
var suffix;
|
||||
var firstch;
|
||||
var origword = w;
|
||||
|
||||
if (w.length < 3)
|
||||
return w;
|
||||
|
||||
var re;
|
||||
var re2;
|
||||
var re3;
|
||||
var re4;
|
||||
|
||||
firstch = w.substr(0,1);
|
||||
if (firstch == "y")
|
||||
w = firstch.toUpperCase() + w.substr(1);
|
||||
|
||||
// Step 1a
|
||||
re = /^(.+?)(ss|i)es$/;
|
||||
re2 = /^(.+?)([^s])s$/;
|
||||
|
||||
if (re.test(w))
|
||||
w = w.replace(re,"$1$2");
|
||||
else if (re2.test(w))
|
||||
w = w.replace(re2,"$1$2");
|
||||
|
||||
// Step 1b
|
||||
re = /^(.+?)eed$/;
|
||||
re2 = /^(.+?)(ed|ing)$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
re = new RegExp(mgr0);
|
||||
if (re.test(fp[1])) {
|
||||
re = /.$/;
|
||||
w = w.replace(re,"");
|
||||
}
|
||||
}
|
||||
else if (re2.test(w)) {
|
||||
var fp = re2.exec(w);
|
||||
stem = fp[1];
|
||||
re2 = new RegExp(s_v);
|
||||
if (re2.test(stem)) {
|
||||
w = stem;
|
||||
re2 = /(at|bl|iz)$/;
|
||||
re3 = new RegExp("([^aeiouylsz])\\1$");
|
||||
re4 = new RegExp("^" + C + v + "[^aeiouwxy]$");
|
||||
if (re2.test(w))
|
||||
w = w + "e";
|
||||
else if (re3.test(w)) {
|
||||
re = /.$/;
|
||||
w = w.replace(re,"");
|
||||
}
|
||||
else if (re4.test(w))
|
||||
w = w + "e";
|
||||
}
|
||||
}
|
||||
|
||||
// Step 1c
|
||||
re = /^(.+?)y$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
stem = fp[1];
|
||||
re = new RegExp(s_v);
|
||||
if (re.test(stem))
|
||||
w = stem + "i";
|
||||
}
|
||||
|
||||
// Step 2
|
||||
re = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
stem = fp[1];
|
||||
suffix = fp[2];
|
||||
re = new RegExp(mgr0);
|
||||
if (re.test(stem))
|
||||
w = stem + step2list[suffix];
|
||||
}
|
||||
|
||||
// Step 3
|
||||
re = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
stem = fp[1];
|
||||
suffix = fp[2];
|
||||
re = new RegExp(mgr0);
|
||||
if (re.test(stem))
|
||||
w = stem + step3list[suffix];
|
||||
}
|
||||
|
||||
// Step 4
|
||||
re = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;
|
||||
re2 = /^(.+?)(s|t)(ion)$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
stem = fp[1];
|
||||
re = new RegExp(mgr1);
|
||||
if (re.test(stem))
|
||||
w = stem;
|
||||
}
|
||||
else if (re2.test(w)) {
|
||||
var fp = re2.exec(w);
|
||||
stem = fp[1] + fp[2];
|
||||
re2 = new RegExp(mgr1);
|
||||
if (re2.test(stem))
|
||||
w = stem;
|
||||
}
|
||||
|
||||
// Step 5
|
||||
re = /^(.+?)e$/;
|
||||
if (re.test(w)) {
|
||||
var fp = re.exec(w);
|
||||
stem = fp[1];
|
||||
re = new RegExp(mgr1);
|
||||
re2 = new RegExp(meq1);
|
||||
re3 = new RegExp("^" + C + v + "[^aeiouwxy]$");
|
||||
if (re.test(stem) || (re2.test(stem) && !(re3.test(stem))))
|
||||
w = stem;
|
||||
}
|
||||
re = /ll$/;
|
||||
re2 = new RegExp(mgr1);
|
||||
if (re.test(w) && re2.test(w)) {
|
||||
re = /.$/;
|
||||
w = w.replace(re,"");
|
||||
}
|
||||
|
||||
// and turn initial Y back to y
|
||||
if (firstch == "y")
|
||||
w = firstch.toLowerCase() + w.substr(1);
|
||||
return w;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
var splitChars = (function() {
|
||||
var result = {};
|
||||
var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
|
||||
1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
|
||||
2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
|
||||
2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
|
||||
3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
|
||||
3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
|
||||
4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
|
||||
8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
|
||||
11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
|
||||
43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
|
||||
var i, j, start, end;
|
||||
for (i = 0; i < singles.length; i++) {
|
||||
result[singles[i]] = true;
|
||||
}
|
||||
var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
|
||||
[722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
|
||||
[1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
|
||||
[1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
|
||||
[1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
|
||||
[2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
|
||||
[2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
|
||||
[2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
|
||||
[2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
|
||||
[2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
|
||||
[2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
|
||||
[2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
|
||||
[3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
|
||||
[3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
|
||||
[3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
|
||||
[3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
|
||||
[3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
|
||||
[3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
|
||||
[4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
|
||||
[4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
|
||||
[4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
|
||||
[4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
|
||||
[5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
|
||||
[6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
|
||||
[6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
|
||||
[6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
|
||||
[6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
|
||||
[7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
|
||||
[7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
|
||||
[8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
|
||||
[8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
|
||||
[8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
|
||||
[10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
|
||||
[11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
|
||||
[12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
|
||||
[12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
|
||||
[12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
|
||||
[19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
|
||||
[42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
|
||||
[42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
|
||||
[43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
|
||||
[43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
|
||||
[43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
|
||||
[43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
|
||||
[44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
|
||||
[57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
|
||||
[64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
|
||||
[65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
|
||||
[65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
|
||||
for (i = 0; i < ranges.length; i++) {
|
||||
start = ranges[i][0];
|
||||
end = ranges[i][1];
|
||||
for (j = start; j <= end; j++) {
|
||||
result[j] = true;
|
||||
}
|
||||
}
|
||||
return result;
|
||||
})();
|
||||
|
||||
function splitQuery(query) {
|
||||
var result = [];
|
||||
var start = -1;
|
||||
for (var i = 0; i < query.length; i++) {
|
||||
if (splitChars[query.charCodeAt(i)]) {
|
||||
if (start !== -1) {
|
||||
result.push(query.slice(start, i));
|
||||
start = -1;
|
||||
}
|
||||
} else if (start === -1) {
|
||||
start = i;
|
||||
}
|
||||
}
|
||||
if (start !== -1) {
|
||||
result.push(query.slice(start));
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 199 B After Width: | Height: | Size: 90 B |
@ -1,245 +0,0 @@
|
||||
/*
|
||||
* nature.css_t
|
||||
* ~~~~~~~~~~~~
|
||||
*
|
||||
* Sphinx stylesheet -- nature theme.
|
||||
*
|
||||
* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
|
||||
* :license: BSD, see LICENSE for details.
|
||||
*
|
||||
*/
|
||||
|
||||
@import url("basic.css");
|
||||
|
||||
/* -- page layout ----------------------------------------------------------- */
|
||||
|
||||
body {
|
||||
font-family: Arial, sans-serif;
|
||||
font-size: 100%;
|
||||
background-color: #111;
|
||||
color: #555;
|
||||
margin: 0;
|
||||
padding: 0;
|
||||
}
|
||||
|
||||
div.documentwrapper {
|
||||
float: left;
|
||||
width: 100%;
|
||||
}
|
||||
|
||||
div.bodywrapper {
|
||||
margin: 0 0 0 230px;
|
||||
}
|
||||
|
||||
hr {
|
||||
border: 1px solid #B1B4B6;
|
||||
}
|
||||
|
||||
div.document {
|
||||
background-color: #eee;
|
||||
}
|
||||
|
||||
div.body {
|
||||
background-color: #ffffff;
|
||||
color: #3E4349;
|
||||
padding: 0 30px 30px 30px;
|
||||
font-size: 0.9em;
|
||||
}
|
||||
|
||||
div.footer {
|
||||
color: #555;
|
||||
width: 100%;
|
||||
padding: 13px 0;
|
||||
text-align: center;
|
||||
font-size: 75%;
|
||||
}
|
||||
|
||||
div.footer a {
|
||||
color: #444;
|
||||
text-decoration: underline;
|
||||
}
|
||||
|
||||
div.related {
|
||||
background-color: #6BA81E;
|
||||
line-height: 32px;
|
||||
color: #fff;
|
||||
text-shadow: 0px 1px 0 #444;
|
||||
font-size: 0.9em;
|
||||
}
|
||||
|
||||
div.related a {
|
||||
color: #E2F3CC;
|
||||
}
|
||||
|
||||
div.sphinxsidebar {
|
||||
font-size: 0.75em;
|
||||
line-height: 1.5em;
|
||||
}
|
||||
|
||||
div.sphinxsidebarwrapper{
|
||||
padding: 20px 0;
|
||||
}
|
||||
|
||||
div.sphinxsidebar h3,
|
||||
div.sphinxsidebar h4 {
|
||||
font-family: Arial, sans-serif;
|
||||
color: #222;
|
||||
font-size: 1.2em;
|
||||
font-weight: normal;
|
||||
margin: 0;
|
||||
padding: 5px 10px;
|
||||
background-color: #ddd;
|
||||
text-shadow: 1px 1px 0 white
|
||||
}
|
||||
|
||||
div.sphinxsidebar h4{
|
||||
font-size: 1.1em;
|
||||
}
|
||||
|
||||
div.sphinxsidebar h3 a {
|
||||
color: #444;
|
||||
}
|
||||
|
||||
|
||||
div.sphinxsidebar p {
|
||||
color: #888;
|
||||
padding: 5px 20px;
|
||||
}
|
||||
|
||||
div.sphinxsidebar p.topless {
|
||||
}
|
||||
|
||||
div.sphinxsidebar ul {
|
||||
margin: 10px 20px;
|
||||
padding: 0;
|
||||
color: #000;
|
||||
}
|
||||
|
||||
div.sphinxsidebar a {
|
||||
color: #444;
|
||||
}
|
||||
|
||||
div.sphinxsidebar input {
|
||||
border: 1px solid #ccc;
|
||||
font-family: sans-serif;
|
||||
font-size: 1em;
|
||||
}
|
||||
|
||||
div.sphinxsidebar input[type=text]{
|
||||
margin-left: 20px;
|
||||
}
|
||||
|
||||
/* -- body styles ----------------------------------------------------------- */
|
||||
|
||||
a {
|
||||
color: #005B81;
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
a:hover {
|
||||
color: #E32E00;
|
||||
text-decoration: underline;
|
||||
}
|
||||
|
||||
div.body h1,
|
||||
div.body h2,
|
||||
div.body h3,
|
||||
div.body h4,
|
||||
div.body h5,
|
||||
div.body h6 {
|
||||
font-family: Arial, sans-serif;
|
||||
background-color: #BED4EB;
|
||||
font-weight: normal;
|
||||
color: #212224;
|
||||
margin: 30px 0px 10px 0px;
|
||||
padding: 5px 0 5px 10px;
|
||||
text-shadow: 0px 1px 0 white
|
||||
}
|
||||
|
||||
div.body h1 { border-top: 20px solid white; margin-top: 0; font-size: 200%; }
|
||||
div.body h2 { font-size: 150%; background-color: #C8D5E3; }
|
||||
div.body h3 { font-size: 120%; background-color: #D8DEE3; }
|
||||
div.body h4 { font-size: 110%; background-color: #D8DEE3; }
|
||||
div.body h5 { font-size: 100%; background-color: #D8DEE3; }
|
||||
div.body h6 { font-size: 100%; background-color: #D8DEE3; }
|
||||
|
||||
a.headerlink {
|
||||
color: #c60f0f;
|
||||
font-size: 0.8em;
|
||||
padding: 0 4px 0 4px;
|
||||
text-decoration: none;
|
||||
}
|
||||
|
||||
a.headerlink:hover {
|
||||
background-color: #c60f0f;
|
||||
color: white;
|
||||
}
|
||||
|
||||
div.body p, div.body dd, div.body li {
|
||||
line-height: 1.5em;
|
||||
}
|
||||
|
||||
div.admonition p.admonition-title + p {
|
||||
display: inline;
|
||||
}
|
||||
|
||||
div.highlight{
|
||||
background-color: white;
|
||||
}
|
||||
|
||||
div.note {
|
||||
background-color: #eee;
|
||||
border: 1px solid #ccc;
|
||||
}
|
||||
|
||||
div.seealso {
|
||||
background-color: #ffc;
|
||||
border: 1px solid #ff6;
|
||||
}
|
||||
|
||||
div.topic {
|
||||
background-color: #eee;
|
||||
}
|
||||
|
||||
div.warning {
|
||||
background-color: #ffe4e4;
|
||||
border: 1px solid #f66;
|
||||
}
|
||||
|
||||
p.admonition-title {
|
||||
display: inline;
|
||||
}
|
||||
|
||||
p.admonition-title:after {
|
||||
content: ":";
|
||||
}
|
||||
|
||||
pre {
|
||||
padding: 10px;
|
||||
background-color: White;
|
||||
color: #222;
|
||||
line-height: 1.2em;
|
||||
border: 1px solid #C6C9CB;
|
||||
font-size: 1.1em;
|
||||
margin: 1.5em 0 1.5em 0;
|
||||
-webkit-box-shadow: 1px 1px 1px #d8d8d8;
|
||||
-moz-box-shadow: 1px 1px 1px #d8d8d8;
|
||||
}
|
||||
|
||||
tt {
|
||||
background-color: #ecf0f3;
|
||||
color: #222;
|
||||
/* padding: 1px 2px; */
|
||||
font-size: 1.1em;
|
||||
font-family: monospace;
|
||||
}
|
||||
|
||||
.viewcode-back {
|
||||
font-family: Arial, sans-serif;
|
||||
}
|
||||
|
||||
div.viewcode-block:target {
|
||||
background-color: #f4debf;
|
||||
border-top: 1px solid #ac9;
|
||||
border-bottom: 1px solid #ac9;
|
||||
}
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 199 B After Width: | Height: | Size: 90 B |
@ -2,14 +2,15 @@
|
||||
* searchtools.js_t
|
||||
* ~~~~~~~~~~~~~~~~
|
||||
*
|
||||
* Sphinx JavaScript utilties for the full-text search.
|
||||
* Sphinx JavaScript utilities for the full-text search.
|
||||
*
|
||||
* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
|
||||
* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
|
||||
* :license: BSD, see LICENSE for details.
|
||||
*
|
||||
*/
|
||||
|
||||
|
||||
/* Non-minified version JS is _stemmer.js if file is provided */
|
||||
/**
|
||||
* Porter Stemmer
|
||||
*/
|
||||
@ -225,6 +226,106 @@ var Scorer = {
|
||||
};
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
var splitChars = (function() {
|
||||
var result = {};
|
||||
var singles = [96, 180, 187, 191, 215, 247, 749, 885, 903, 907, 909, 930, 1014, 1648,
|
||||
1748, 1809, 2416, 2473, 2481, 2526, 2601, 2609, 2612, 2615, 2653, 2702,
|
||||
2706, 2729, 2737, 2740, 2857, 2865, 2868, 2910, 2928, 2948, 2961, 2971,
|
||||
2973, 3085, 3089, 3113, 3124, 3213, 3217, 3241, 3252, 3295, 3341, 3345,
|
||||
3369, 3506, 3516, 3633, 3715, 3721, 3736, 3744, 3748, 3750, 3756, 3761,
|
||||
3781, 3912, 4239, 4347, 4681, 4695, 4697, 4745, 4785, 4799, 4801, 4823,
|
||||
4881, 5760, 5901, 5997, 6313, 7405, 8024, 8026, 8028, 8030, 8117, 8125,
|
||||
8133, 8181, 8468, 8485, 8487, 8489, 8494, 8527, 11311, 11359, 11687, 11695,
|
||||
11703, 11711, 11719, 11727, 11735, 12448, 12539, 43010, 43014, 43019, 43587,
|
||||
43696, 43713, 64286, 64297, 64311, 64317, 64319, 64322, 64325, 65141];
|
||||
var i, j, start, end;
|
||||
for (i = 0; i < singles.length; i++) {
|
||||
result[singles[i]] = true;
|
||||
}
|
||||
var ranges = [[0, 47], [58, 64], [91, 94], [123, 169], [171, 177], [182, 184], [706, 709],
|
||||
[722, 735], [741, 747], [751, 879], [888, 889], [894, 901], [1154, 1161],
|
||||
[1318, 1328], [1367, 1368], [1370, 1376], [1416, 1487], [1515, 1519], [1523, 1568],
|
||||
[1611, 1631], [1642, 1645], [1750, 1764], [1767, 1773], [1789, 1790], [1792, 1807],
|
||||
[1840, 1868], [1958, 1968], [1970, 1983], [2027, 2035], [2038, 2041], [2043, 2047],
|
||||
[2070, 2073], [2075, 2083], [2085, 2087], [2089, 2307], [2362, 2364], [2366, 2383],
|
||||
[2385, 2391], [2402, 2405], [2419, 2424], [2432, 2436], [2445, 2446], [2449, 2450],
|
||||
[2483, 2485], [2490, 2492], [2494, 2509], [2511, 2523], [2530, 2533], [2546, 2547],
|
||||
[2554, 2564], [2571, 2574], [2577, 2578], [2618, 2648], [2655, 2661], [2672, 2673],
|
||||
[2677, 2692], [2746, 2748], [2750, 2767], [2769, 2783], [2786, 2789], [2800, 2820],
|
||||
[2829, 2830], [2833, 2834], [2874, 2876], [2878, 2907], [2914, 2917], [2930, 2946],
|
||||
[2955, 2957], [2966, 2968], [2976, 2978], [2981, 2983], [2987, 2989], [3002, 3023],
|
||||
[3025, 3045], [3059, 3076], [3130, 3132], [3134, 3159], [3162, 3167], [3170, 3173],
|
||||
[3184, 3191], [3199, 3204], [3258, 3260], [3262, 3293], [3298, 3301], [3312, 3332],
|
||||
[3386, 3388], [3390, 3423], [3426, 3429], [3446, 3449], [3456, 3460], [3479, 3481],
|
||||
[3518, 3519], [3527, 3584], [3636, 3647], [3655, 3663], [3674, 3712], [3717, 3718],
|
||||
[3723, 3724], [3726, 3731], [3752, 3753], [3764, 3772], [3774, 3775], [3783, 3791],
|
||||
[3802, 3803], [3806, 3839], [3841, 3871], [3892, 3903], [3949, 3975], [3980, 4095],
|
||||
[4139, 4158], [4170, 4175], [4182, 4185], [4190, 4192], [4194, 4196], [4199, 4205],
|
||||
[4209, 4212], [4226, 4237], [4250, 4255], [4294, 4303], [4349, 4351], [4686, 4687],
|
||||
[4702, 4703], [4750, 4751], [4790, 4791], [4806, 4807], [4886, 4887], [4955, 4968],
|
||||
[4989, 4991], [5008, 5023], [5109, 5120], [5741, 5742], [5787, 5791], [5867, 5869],
|
||||
[5873, 5887], [5906, 5919], [5938, 5951], [5970, 5983], [6001, 6015], [6068, 6102],
|
||||
[6104, 6107], [6109, 6111], [6122, 6127], [6138, 6159], [6170, 6175], [6264, 6271],
|
||||
[6315, 6319], [6390, 6399], [6429, 6469], [6510, 6511], [6517, 6527], [6572, 6592],
|
||||
[6600, 6607], [6619, 6655], [6679, 6687], [6741, 6783], [6794, 6799], [6810, 6822],
|
||||
[6824, 6916], [6964, 6980], [6988, 6991], [7002, 7042], [7073, 7085], [7098, 7167],
|
||||
[7204, 7231], [7242, 7244], [7294, 7400], [7410, 7423], [7616, 7679], [7958, 7959],
|
||||
[7966, 7967], [8006, 8007], [8014, 8015], [8062, 8063], [8127, 8129], [8141, 8143],
|
||||
[8148, 8149], [8156, 8159], [8173, 8177], [8189, 8303], [8306, 8307], [8314, 8318],
|
||||
[8330, 8335], [8341, 8449], [8451, 8454], [8456, 8457], [8470, 8472], [8478, 8483],
|
||||
[8506, 8507], [8512, 8516], [8522, 8525], [8586, 9311], [9372, 9449], [9472, 10101],
|
||||
[10132, 11263], [11493, 11498], [11503, 11516], [11518, 11519], [11558, 11567],
|
||||
[11622, 11630], [11632, 11647], [11671, 11679], [11743, 11822], [11824, 12292],
|
||||
[12296, 12320], [12330, 12336], [12342, 12343], [12349, 12352], [12439, 12444],
|
||||
[12544, 12548], [12590, 12592], [12687, 12689], [12694, 12703], [12728, 12783],
|
||||
[12800, 12831], [12842, 12880], [12896, 12927], [12938, 12976], [12992, 13311],
|
||||
[19894, 19967], [40908, 40959], [42125, 42191], [42238, 42239], [42509, 42511],
|
||||
[42540, 42559], [42592, 42593], [42607, 42622], [42648, 42655], [42736, 42774],
|
||||
[42784, 42785], [42889, 42890], [42893, 43002], [43043, 43055], [43062, 43071],
|
||||
[43124, 43137], [43188, 43215], [43226, 43249], [43256, 43258], [43260, 43263],
|
||||
[43302, 43311], [43335, 43359], [43389, 43395], [43443, 43470], [43482, 43519],
|
||||
[43561, 43583], [43596, 43599], [43610, 43615], [43639, 43641], [43643, 43647],
|
||||
[43698, 43700], [43703, 43704], [43710, 43711], [43715, 43738], [43742, 43967],
|
||||
[44003, 44015], [44026, 44031], [55204, 55215], [55239, 55242], [55292, 55295],
|
||||
[57344, 63743], [64046, 64047], [64110, 64111], [64218, 64255], [64263, 64274],
|
||||
[64280, 64284], [64434, 64466], [64830, 64847], [64912, 64913], [64968, 65007],
|
||||
[65020, 65135], [65277, 65295], [65306, 65312], [65339, 65344], [65371, 65381],
|
||||
[65471, 65473], [65480, 65481], [65488, 65489], [65496, 65497]];
|
||||
for (i = 0; i < ranges.length; i++) {
|
||||
start = ranges[i][0];
|
||||
end = ranges[i][1];
|
||||
for (j = start; j <= end; j++) {
|
||||
result[j] = true;
|
||||
}
|
||||
}
|
||||
return result;
|
||||
})();
|
||||
|
||||
function splitQuery(query) {
|
||||
var result = [];
|
||||
var start = -1;
|
||||
for (var i = 0; i < query.length; i++) {
|
||||
if (splitChars[query.charCodeAt(i)]) {
|
||||
if (start !== -1) {
|
||||
result.push(query.slice(start, i));
|
||||
start = -1;
|
||||
}
|
||||
} else if (start === -1) {
|
||||
start = i;
|
||||
}
|
||||
}
|
||||
if (start !== -1) {
|
||||
result.push(query.slice(start));
|
||||
}
|
||||
return result;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Search Module
|
||||
*/
|
||||
@ -323,7 +424,7 @@ var Search = {
|
||||
var searchterms = [];
|
||||
var excluded = [];
|
||||
var hlterms = [];
|
||||
var tmp = query.split(/\s+/);
|
||||
var tmp = splitQuery(query);
|
||||
var objectterms = [];
|
||||
for (i = 0; i < tmp.length; i++) {
|
||||
if (tmp[i] !== "") {
|
||||
@ -337,6 +438,10 @@ var Search = {
|
||||
}
|
||||
// stem the word
|
||||
var word = stemmer.stemWord(tmp[i].toLowerCase());
|
||||
// prevent stemmer from cutting word smaller than two chars
|
||||
if(word.length < 3 && tmp[i].length >= 3) {
|
||||
word = tmp[i];
|
||||
}
|
||||
var toAppend;
|
||||
// select the correct list
|
||||
if (word[0] == '-') {
|
||||
@ -373,8 +478,7 @@ var Search = {
|
||||
}
|
||||
|
||||
// lookup as search terms in fulltext
|
||||
results = results.concat(this.performTermsSearch(searchterms, excluded, terms, Scorer.term))
|
||||
.concat(this.performTermsSearch(searchterms, excluded, titleterms, Scorer.title));
|
||||
results = results.concat(this.performTermsSearch(searchterms, excluded, terms, titleterms));
|
||||
|
||||
// let the scorer override scores with a custom scoring function
|
||||
if (Scorer.score) {
|
||||
@ -435,11 +539,15 @@ var Search = {
|
||||
displayNextItem();
|
||||
});
|
||||
} else if (DOCUMENTATION_OPTIONS.HAS_SOURCE) {
|
||||
$.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[0] + '.txt',
|
||||
var suffix = DOCUMENTATION_OPTIONS.SOURCELINK_SUFFIX;
|
||||
if (suffix === undefined) {
|
||||
suffix = '.txt';
|
||||
}
|
||||
$.ajax({url: DOCUMENTATION_OPTIONS.URL_ROOT + '_sources/' + item[5] + (item[5].slice(-suffix.length) === suffix ? '' : suffix),
|
||||
dataType: "text",
|
||||
complete: function(jqxhr, textstatus) {
|
||||
var data = jqxhr.responseText;
|
||||
if (data !== '') {
|
||||
if (data !== '' && data !== undefined) {
|
||||
listItem.append(Search.makeSearchSummary(data, searchterms, hlterms));
|
||||
}
|
||||
Search.output.append(listItem);
|
||||
@ -474,6 +582,7 @@ var Search = {
|
||||
*/
|
||||
performObjectSearch : function(object, otherterms) {
|
||||
var filenames = this._index.filenames;
|
||||
var docnames = this._index.docnames;
|
||||
var objects = this._index.objects;
|
||||
var objnames = this._index.objnames;
|
||||
var titles = this._index.titles;
|
||||
@ -527,7 +636,7 @@ var Search = {
|
||||
} else {
|
||||
score += Scorer.objPrioDefault;
|
||||
}
|
||||
results.push([filenames[match[0]], fullname, '#'+anchor, descr, score]);
|
||||
results.push([docnames[match[0]], fullname, '#'+anchor, descr, score, filenames[match[0]]]);
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -538,23 +647,48 @@ var Search = {
|
||||
/**
|
||||
* search for full-text terms in the index
|
||||
*/
|
||||
performTermsSearch : function(searchterms, excluded, terms, score) {
|
||||
performTermsSearch : function(searchterms, excluded, terms, titleterms) {
|
||||
var docnames = this._index.docnames;
|
||||
var filenames = this._index.filenames;
|
||||
var titles = this._index.titles;
|
||||
|
||||
var i, j, file, files;
|
||||
var i, j, file;
|
||||
var fileMap = {};
|
||||
var scoreMap = {};
|
||||
var results = [];
|
||||
|
||||
// perform the search on the required terms
|
||||
for (i = 0; i < searchterms.length; i++) {
|
||||
var word = searchterms[i];
|
||||
var files = [];
|
||||
var _o = [
|
||||
{files: terms[word], score: Scorer.term},
|
||||
{files: titleterms[word], score: Scorer.title}
|
||||
];
|
||||
|
||||
// no match but word was a required one
|
||||
if ((files = terms[word]) === undefined)
|
||||
if ($u.every(_o, function(o){return o.files === undefined;})) {
|
||||
break;
|
||||
if (files.length === undefined) {
|
||||
files = [files];
|
||||
}
|
||||
// found search word in contents
|
||||
$u.each(_o, function(o) {
|
||||
var _files = o.files;
|
||||
if (_files === undefined)
|
||||
return
|
||||
|
||||
if (_files.length === undefined)
|
||||
_files = [_files];
|
||||
files = files.concat(_files);
|
||||
|
||||
// set score for the word in each file to Scorer.term
|
||||
for (j = 0; j < _files.length; j++) {
|
||||
file = _files[j];
|
||||
if (!(file in scoreMap))
|
||||
scoreMap[file] = {}
|
||||
scoreMap[file][word] = o.score;
|
||||
}
|
||||
});
|
||||
|
||||
// create the mapping
|
||||
for (j = 0; j < files.length; j++) {
|
||||
file = files[j];
|
||||
@ -576,7 +710,9 @@ var Search = {
|
||||
// ensure that none of the excluded terms is in the search result
|
||||
for (i = 0; i < excluded.length; i++) {
|
||||
if (terms[excluded[i]] == file ||
|
||||
$u.contains(terms[excluded[i]] || [], file)) {
|
||||
titleterms[excluded[i]] == file ||
|
||||
$u.contains(terms[excluded[i]] || [], file) ||
|
||||
$u.contains(titleterms[excluded[i]] || [], file)) {
|
||||
valid = false;
|
||||
break;
|
||||
}
|
||||
@ -584,7 +720,10 @@ var Search = {
|
||||
|
||||
// if we have still a valid result we can add it to the result list
|
||||
if (valid) {
|
||||
results.push([filenames[file], titles[file], '', null, score]);
|
||||
// select one (max) score for the file.
|
||||
// for better ranking, we should calculate ranking by using words statistics like basic tf-idf...
|
||||
var score = $u.max($u.map(fileMap[file], function(w){return scoreMap[file][w]}));
|
||||
results.push([docnames[file], titles[file], '', null, score, filenames[file]]);
|
||||
}
|
||||
}
|
||||
return results;
|
||||
@ -594,7 +733,7 @@ var Search = {
|
||||
* helper function to return a node containing the
|
||||
* search summary for a given text. keywords is a list
|
||||
* of stemmed words, hlwords is the list of normal, unstemmed
|
||||
* words. the first one is used to find the occurance, the
|
||||
* words. the first one is used to find the occurrence, the
|
||||
* latter for highlighting it.
|
||||
*/
|
||||
makeSearchSummary : function(text, keywords, hlwords) {
|
||||
|
||||
BIN
doc/html/_static/up-pressed.png
Normal file
BIN
doc/html/_static/up-pressed.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 214 B |
BIN
doc/html/_static/up.png
Normal file
BIN
doc/html/_static/up.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 203 B |
808
doc/html/_static/websupport.js
Normal file
808
doc/html/_static/websupport.js
Normal file
@ -0,0 +1,808 @@
|
||||
/*
|
||||
* websupport.js
|
||||
* ~~~~~~~~~~~~~
|
||||
*
|
||||
* sphinx.websupport utilities for all documentation.
|
||||
*
|
||||
* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
|
||||
* :license: BSD, see LICENSE for details.
|
||||
*
|
||||
*/
|
||||
|
||||
(function($) {
|
||||
$.fn.autogrow = function() {
|
||||
return this.each(function() {
|
||||
var textarea = this;
|
||||
|
||||
$.fn.autogrow.resize(textarea);
|
||||
|
||||
$(textarea)
|
||||
.focus(function() {
|
||||
textarea.interval = setInterval(function() {
|
||||
$.fn.autogrow.resize(textarea);
|
||||
}, 500);
|
||||
})
|
||||
.blur(function() {
|
||||
clearInterval(textarea.interval);
|
||||
});
|
||||
});
|
||||
};
|
||||
|
||||
$.fn.autogrow.resize = function(textarea) {
|
||||
var lineHeight = parseInt($(textarea).css('line-height'), 10);
|
||||
var lines = textarea.value.split('\n');
|
||||
var columns = textarea.cols;
|
||||
var lineCount = 0;
|
||||
$.each(lines, function() {
|
||||
lineCount += Math.ceil(this.length / columns) || 1;
|
||||
});
|
||||
var height = lineHeight * (lineCount + 1);
|
||||
$(textarea).css('height', height);
|
||||
};
|
||||
})(jQuery);
|
||||
|
||||
(function($) {
|
||||
var comp, by;
|
||||
|
||||
function init() {
|
||||
initEvents();
|
||||
initComparator();
|
||||
}
|
||||
|
||||
function initEvents() {
|
||||
$(document).on("click", 'a.comment-close', function(event) {
|
||||
event.preventDefault();
|
||||
hide($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.vote', function(event) {
|
||||
event.preventDefault();
|
||||
handleVote($(this));
|
||||
});
|
||||
$(document).on("click", 'a.reply', function(event) {
|
||||
event.preventDefault();
|
||||
openReply($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.close-reply', function(event) {
|
||||
event.preventDefault();
|
||||
closeReply($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.sort-option', function(event) {
|
||||
event.preventDefault();
|
||||
handleReSort($(this));
|
||||
});
|
||||
$(document).on("click", 'a.show-proposal', function(event) {
|
||||
event.preventDefault();
|
||||
showProposal($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.hide-proposal', function(event) {
|
||||
event.preventDefault();
|
||||
hideProposal($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.show-propose-change', function(event) {
|
||||
event.preventDefault();
|
||||
showProposeChange($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.hide-propose-change', function(event) {
|
||||
event.preventDefault();
|
||||
hideProposeChange($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.accept-comment', function(event) {
|
||||
event.preventDefault();
|
||||
acceptComment($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.delete-comment', function(event) {
|
||||
event.preventDefault();
|
||||
deleteComment($(this).attr('id').substring(2));
|
||||
});
|
||||
$(document).on("click", 'a.comment-markup', function(event) {
|
||||
event.preventDefault();
|
||||
toggleCommentMarkupBox($(this).attr('id').substring(2));
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Set comp, which is a comparator function used for sorting and
|
||||
* inserting comments into the list.
|
||||
*/
|
||||
function setComparator() {
|
||||
// If the first three letters are "asc", sort in ascending order
|
||||
// and remove the prefix.
|
||||
if (by.substring(0,3) == 'asc') {
|
||||
var i = by.substring(3);
|
||||
comp = function(a, b) { return a[i] - b[i]; };
|
||||
} else {
|
||||
// Otherwise sort in descending order.
|
||||
comp = function(a, b) { return b[by] - a[by]; };
|
||||
}
|
||||
|
||||
// Reset link styles and format the selected sort option.
|
||||
$('a.sel').attr('href', '#').removeClass('sel');
|
||||
$('a.by' + by).removeAttr('href').addClass('sel');
|
||||
}
|
||||
|
||||
/**
|
||||
* Create a comp function. If the user has preferences stored in
|
||||
* the sortBy cookie, use those, otherwise use the default.
|
||||
*/
|
||||
function initComparator() {
|
||||
by = 'rating'; // Default to sort by rating.
|
||||
// If the sortBy cookie is set, use that instead.
|
||||
if (document.cookie.length > 0) {
|
||||
var start = document.cookie.indexOf('sortBy=');
|
||||
if (start != -1) {
|
||||
start = start + 7;
|
||||
var end = document.cookie.indexOf(";", start);
|
||||
if (end == -1) {
|
||||
end = document.cookie.length;
|
||||
by = unescape(document.cookie.substring(start, end));
|
||||
}
|
||||
}
|
||||
}
|
||||
setComparator();
|
||||
}
|
||||
|
||||
/**
|
||||
* Show a comment div.
|
||||
*/
|
||||
function show(id) {
|
||||
$('#ao' + id).hide();
|
||||
$('#ah' + id).show();
|
||||
var context = $.extend({id: id}, opts);
|
||||
var popup = $(renderTemplate(popupTemplate, context)).hide();
|
||||
popup.find('textarea[name="proposal"]').hide();
|
||||
popup.find('a.by' + by).addClass('sel');
|
||||
var form = popup.find('#cf' + id);
|
||||
form.submit(function(event) {
|
||||
event.preventDefault();
|
||||
addComment(form);
|
||||
});
|
||||
$('#s' + id).after(popup);
|
||||
popup.slideDown('fast', function() {
|
||||
getComments(id);
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Hide a comment div.
|
||||
*/
|
||||
function hide(id) {
|
||||
$('#ah' + id).hide();
|
||||
$('#ao' + id).show();
|
||||
var div = $('#sc' + id);
|
||||
div.slideUp('fast', function() {
|
||||
div.remove();
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Perform an ajax request to get comments for a node
|
||||
* and insert the comments into the comments tree.
|
||||
*/
|
||||
function getComments(id) {
|
||||
$.ajax({
|
||||
type: 'GET',
|
||||
url: opts.getCommentsURL,
|
||||
data: {node: id},
|
||||
success: function(data, textStatus, request) {
|
||||
var ul = $('#cl' + id);
|
||||
var speed = 100;
|
||||
$('#cf' + id)
|
||||
.find('textarea[name="proposal"]')
|
||||
.data('source', data.source);
|
||||
|
||||
if (data.comments.length === 0) {
|
||||
ul.html('<li>No comments yet.</li>');
|
||||
ul.data('empty', true);
|
||||
} else {
|
||||
// If there are comments, sort them and put them in the list.
|
||||
var comments = sortComments(data.comments);
|
||||
speed = data.comments.length * 100;
|
||||
appendComments(comments, ul);
|
||||
ul.data('empty', false);
|
||||
}
|
||||
$('#cn' + id).slideUp(speed + 200);
|
||||
ul.slideDown(speed);
|
||||
},
|
||||
error: function(request, textStatus, error) {
|
||||
showError('Oops, there was a problem retrieving the comments.');
|
||||
},
|
||||
dataType: 'json'
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Add a comment via ajax and insert the comment into the comment tree.
|
||||
*/
|
||||
function addComment(form) {
|
||||
var node_id = form.find('input[name="node"]').val();
|
||||
var parent_id = form.find('input[name="parent"]').val();
|
||||
var text = form.find('textarea[name="comment"]').val();
|
||||
var proposal = form.find('textarea[name="proposal"]').val();
|
||||
|
||||
if (text == '') {
|
||||
showError('Please enter a comment.');
|
||||
return;
|
||||
}
|
||||
|
||||
// Disable the form that is being submitted.
|
||||
form.find('textarea,input').attr('disabled', 'disabled');
|
||||
|
||||
// Send the comment to the server.
|
||||
$.ajax({
|
||||
type: "POST",
|
||||
url: opts.addCommentURL,
|
||||
dataType: 'json',
|
||||
data: {
|
||||
node: node_id,
|
||||
parent: parent_id,
|
||||
text: text,
|
||||
proposal: proposal
|
||||
},
|
||||
success: function(data, textStatus, error) {
|
||||
// Reset the form.
|
||||
if (node_id) {
|
||||
hideProposeChange(node_id);
|
||||
}
|
||||
form.find('textarea')
|
||||
.val('')
|
||||
.add(form.find('input'))
|
||||
.removeAttr('disabled');
|
||||
var ul = $('#cl' + (node_id || parent_id));
|
||||
if (ul.data('empty')) {
|
||||
$(ul).empty();
|
||||
ul.data('empty', false);
|
||||
}
|
||||
insertComment(data.comment);
|
||||
var ao = $('#ao' + node_id);
|
||||
ao.find('img').attr({'src': opts.commentBrightImage});
|
||||
if (node_id) {
|
||||
// if this was a "root" comment, remove the commenting box
|
||||
// (the user can get it back by reopening the comment popup)
|
||||
$('#ca' + node_id).slideUp();
|
||||
}
|
||||
},
|
||||
error: function(request, textStatus, error) {
|
||||
form.find('textarea,input').removeAttr('disabled');
|
||||
showError('Oops, there was a problem adding the comment.');
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively append comments to the main comment list and children
|
||||
* lists, creating the comment tree.
|
||||
*/
|
||||
function appendComments(comments, ul) {
|
||||
$.each(comments, function() {
|
||||
var div = createCommentDiv(this);
|
||||
ul.append($(document.createElement('li')).html(div));
|
||||
appendComments(this.children, div.find('ul.comment-children'));
|
||||
// To avoid stagnating data, don't store the comments children in data.
|
||||
this.children = null;
|
||||
div.data('comment', this);
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* After adding a new comment, it must be inserted in the correct
|
||||
* location in the comment tree.
|
||||
*/
|
||||
function insertComment(comment) {
|
||||
var div = createCommentDiv(comment);
|
||||
|
||||
// To avoid stagnating data, don't store the comments children in data.
|
||||
comment.children = null;
|
||||
div.data('comment', comment);
|
||||
|
||||
var ul = $('#cl' + (comment.node || comment.parent));
|
||||
var siblings = getChildren(ul);
|
||||
|
||||
var li = $(document.createElement('li'));
|
||||
li.hide();
|
||||
|
||||
// Determine where in the parents children list to insert this comment.
|
||||
for(var i=0; i < siblings.length; i++) {
|
||||
if (comp(comment, siblings[i]) <= 0) {
|
||||
$('#cd' + siblings[i].id)
|
||||
.parent()
|
||||
.before(li.html(div));
|
||||
li.slideDown('fast');
|
||||
return;
|
||||
}
|
||||
}
|
||||
|
||||
// If we get here, this comment rates lower than all the others,
|
||||
// or it is the only comment in the list.
|
||||
ul.append(li.html(div));
|
||||
li.slideDown('fast');
|
||||
}
|
||||
|
||||
function acceptComment(id) {
|
||||
$.ajax({
|
||||
type: 'POST',
|
||||
url: opts.acceptCommentURL,
|
||||
data: {id: id},
|
||||
success: function(data, textStatus, request) {
|
||||
$('#cm' + id).fadeOut('fast');
|
||||
$('#cd' + id).removeClass('moderate');
|
||||
},
|
||||
error: function(request, textStatus, error) {
|
||||
showError('Oops, there was a problem accepting the comment.');
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
function deleteComment(id) {
|
||||
$.ajax({
|
||||
type: 'POST',
|
||||
url: opts.deleteCommentURL,
|
||||
data: {id: id},
|
||||
success: function(data, textStatus, request) {
|
||||
var div = $('#cd' + id);
|
||||
if (data == 'delete') {
|
||||
// Moderator mode: remove the comment and all children immediately
|
||||
div.slideUp('fast', function() {
|
||||
div.remove();
|
||||
});
|
||||
return;
|
||||
}
|
||||
// User mode: only mark the comment as deleted
|
||||
div
|
||||
.find('span.user-id:first')
|
||||
.text('[deleted]').end()
|
||||
.find('div.comment-text:first')
|
||||
.text('[deleted]').end()
|
||||
.find('#cm' + id + ', #dc' + id + ', #ac' + id + ', #rc' + id +
|
||||
', #sp' + id + ', #hp' + id + ', #cr' + id + ', #rl' + id)
|
||||
.remove();
|
||||
var comment = div.data('comment');
|
||||
comment.username = '[deleted]';
|
||||
comment.text = '[deleted]';
|
||||
div.data('comment', comment);
|
||||
},
|
||||
error: function(request, textStatus, error) {
|
||||
showError('Oops, there was a problem deleting the comment.');
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
function showProposal(id) {
|
||||
$('#sp' + id).hide();
|
||||
$('#hp' + id).show();
|
||||
$('#pr' + id).slideDown('fast');
|
||||
}
|
||||
|
||||
function hideProposal(id) {
|
||||
$('#hp' + id).hide();
|
||||
$('#sp' + id).show();
|
||||
$('#pr' + id).slideUp('fast');
|
||||
}
|
||||
|
||||
function showProposeChange(id) {
|
||||
$('#pc' + id).hide();
|
||||
$('#hc' + id).show();
|
||||
var textarea = $('#pt' + id);
|
||||
textarea.val(textarea.data('source'));
|
||||
$.fn.autogrow.resize(textarea[0]);
|
||||
textarea.slideDown('fast');
|
||||
}
|
||||
|
||||
function hideProposeChange(id) {
|
||||
$('#hc' + id).hide();
|
||||
$('#pc' + id).show();
|
||||
var textarea = $('#pt' + id);
|
||||
textarea.val('').removeAttr('disabled');
|
||||
textarea.slideUp('fast');
|
||||
}
|
||||
|
||||
function toggleCommentMarkupBox(id) {
|
||||
$('#mb' + id).toggle();
|
||||
}
|
||||
|
||||
/** Handle when the user clicks on a sort by link. */
|
||||
function handleReSort(link) {
|
||||
var classes = link.attr('class').split(/\s+/);
|
||||
for (var i=0; i<classes.length; i++) {
|
||||
if (classes[i] != 'sort-option') {
|
||||
by = classes[i].substring(2);
|
||||
}
|
||||
}
|
||||
setComparator();
|
||||
// Save/update the sortBy cookie.
|
||||
var expiration = new Date();
|
||||
expiration.setDate(expiration.getDate() + 365);
|
||||
document.cookie= 'sortBy=' + escape(by) +
|
||||
';expires=' + expiration.toUTCString();
|
||||
$('ul.comment-ul').each(function(index, ul) {
|
||||
var comments = getChildren($(ul), true);
|
||||
comments = sortComments(comments);
|
||||
appendComments(comments, $(ul).empty());
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Function to process a vote when a user clicks an arrow.
|
||||
*/
|
||||
function handleVote(link) {
|
||||
if (!opts.voting) {
|
||||
showError("You'll need to login to vote.");
|
||||
return;
|
||||
}
|
||||
|
||||
var id = link.attr('id');
|
||||
if (!id) {
|
||||
// Didn't click on one of the voting arrows.
|
||||
return;
|
||||
}
|
||||
// If it is an unvote, the new vote value is 0,
|
||||
// Otherwise it's 1 for an upvote, or -1 for a downvote.
|
||||
var value = 0;
|
||||
if (id.charAt(1) != 'u') {
|
||||
value = id.charAt(0) == 'u' ? 1 : -1;
|
||||
}
|
||||
// The data to be sent to the server.
|
||||
var d = {
|
||||
comment_id: id.substring(2),
|
||||
value: value
|
||||
};
|
||||
|
||||
// Swap the vote and unvote links.
|
||||
link.hide();
|
||||
$('#' + id.charAt(0) + (id.charAt(1) == 'u' ? 'v' : 'u') + d.comment_id)
|
||||
.show();
|
||||
|
||||
// The div the comment is displayed in.
|
||||
var div = $('div#cd' + d.comment_id);
|
||||
var data = div.data('comment');
|
||||
|
||||
// If this is not an unvote, and the other vote arrow has
|
||||
// already been pressed, unpress it.
|
||||
if ((d.value !== 0) && (data.vote === d.value * -1)) {
|
||||
$('#' + (d.value == 1 ? 'd' : 'u') + 'u' + d.comment_id).hide();
|
||||
$('#' + (d.value == 1 ? 'd' : 'u') + 'v' + d.comment_id).show();
|
||||
}
|
||||
|
||||
// Update the comments rating in the local data.
|
||||
data.rating += (data.vote === 0) ? d.value : (d.value - data.vote);
|
||||
data.vote = d.value;
|
||||
div.data('comment', data);
|
||||
|
||||
// Change the rating text.
|
||||
div.find('.rating:first')
|
||||
.text(data.rating + ' point' + (data.rating == 1 ? '' : 's'));
|
||||
|
||||
// Send the vote information to the server.
|
||||
$.ajax({
|
||||
type: "POST",
|
||||
url: opts.processVoteURL,
|
||||
data: d,
|
||||
error: function(request, textStatus, error) {
|
||||
showError('Oops, there was a problem casting that vote.');
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Open a reply form used to reply to an existing comment.
|
||||
*/
|
||||
function openReply(id) {
|
||||
// Swap out the reply link for the hide link
|
||||
$('#rl' + id).hide();
|
||||
$('#cr' + id).show();
|
||||
|
||||
// Add the reply li to the children ul.
|
||||
var div = $(renderTemplate(replyTemplate, {id: id})).hide();
|
||||
$('#cl' + id)
|
||||
.prepend(div)
|
||||
// Setup the submit handler for the reply form.
|
||||
.find('#rf' + id)
|
||||
.submit(function(event) {
|
||||
event.preventDefault();
|
||||
addComment($('#rf' + id));
|
||||
closeReply(id);
|
||||
})
|
||||
.find('input[type=button]')
|
||||
.click(function() {
|
||||
closeReply(id);
|
||||
});
|
||||
div.slideDown('fast', function() {
|
||||
$('#rf' + id).find('textarea').focus();
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Close the reply form opened with openReply.
|
||||
*/
|
||||
function closeReply(id) {
|
||||
// Remove the reply div from the DOM.
|
||||
$('#rd' + id).slideUp('fast', function() {
|
||||
$(this).remove();
|
||||
});
|
||||
|
||||
// Swap out the hide link for the reply link
|
||||
$('#cr' + id).hide();
|
||||
$('#rl' + id).show();
|
||||
}
|
||||
|
||||
/**
|
||||
* Recursively sort a tree of comments using the comp comparator.
|
||||
*/
|
||||
function sortComments(comments) {
|
||||
comments.sort(comp);
|
||||
$.each(comments, function() {
|
||||
this.children = sortComments(this.children);
|
||||
});
|
||||
return comments;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the children comments from a ul. If recursive is true,
|
||||
* recursively include childrens' children.
|
||||
*/
|
||||
function getChildren(ul, recursive) {
|
||||
var children = [];
|
||||
ul.children().children("[id^='cd']")
|
||||
.each(function() {
|
||||
var comment = $(this).data('comment');
|
||||
if (recursive)
|
||||
comment.children = getChildren($(this).find('#cl' + comment.id), true);
|
||||
children.push(comment);
|
||||
});
|
||||
return children;
|
||||
}
|
||||
|
||||
/** Create a div to display a comment in. */
|
||||
function createCommentDiv(comment) {
|
||||
if (!comment.displayed && !opts.moderator) {
|
||||
return $('<div class="moderate">Thank you! Your comment will show up '
|
||||
+ 'once it is has been approved by a moderator.</div>');
|
||||
}
|
||||
// Prettify the comment rating.
|
||||
comment.pretty_rating = comment.rating + ' point' +
|
||||
(comment.rating == 1 ? '' : 's');
|
||||
// Make a class (for displaying not yet moderated comments differently)
|
||||
comment.css_class = comment.displayed ? '' : ' moderate';
|
||||
// Create a div for this comment.
|
||||
var context = $.extend({}, opts, comment);
|
||||
var div = $(renderTemplate(commentTemplate, context));
|
||||
|
||||
// If the user has voted on this comment, highlight the correct arrow.
|
||||
if (comment.vote) {
|
||||
var direction = (comment.vote == 1) ? 'u' : 'd';
|
||||
div.find('#' + direction + 'v' + comment.id).hide();
|
||||
div.find('#' + direction + 'u' + comment.id).show();
|
||||
}
|
||||
|
||||
if (opts.moderator || comment.text != '[deleted]') {
|
||||
div.find('a.reply').show();
|
||||
if (comment.proposal_diff)
|
||||
div.find('#sp' + comment.id).show();
|
||||
if (opts.moderator && !comment.displayed)
|
||||
div.find('#cm' + comment.id).show();
|
||||
if (opts.moderator || (opts.username == comment.username))
|
||||
div.find('#dc' + comment.id).show();
|
||||
}
|
||||
return div;
|
||||
}
|
||||
|
||||
/**
|
||||
* A simple template renderer. Placeholders such as <%id%> are replaced
|
||||
* by context['id'] with items being escaped. Placeholders such as <#id#>
|
||||
* are not escaped.
|
||||
*/
|
||||
function renderTemplate(template, context) {
|
||||
var esc = $(document.createElement('div'));
|
||||
|
||||
function handle(ph, escape) {
|
||||
var cur = context;
|
||||
$.each(ph.split('.'), function() {
|
||||
cur = cur[this];
|
||||
});
|
||||
return escape ? esc.text(cur || "").html() : cur;
|
||||
}
|
||||
|
||||
return template.replace(/<([%#])([\w\.]*)\1>/g, function() {
|
||||
return handle(arguments[2], arguments[1] == '%' ? true : false);
|
||||
});
|
||||
}
|
||||
|
||||
/** Flash an error message briefly. */
|
||||
function showError(message) {
|
||||
$(document.createElement('div')).attr({'class': 'popup-error'})
|
||||
.append($(document.createElement('div'))
|
||||
.attr({'class': 'error-message'}).text(message))
|
||||
.appendTo('body')
|
||||
.fadeIn("slow")
|
||||
.delay(2000)
|
||||
.fadeOut("slow");
|
||||
}
|
||||
|
||||
/** Add a link the user uses to open the comments popup. */
|
||||
$.fn.comment = function() {
|
||||
return this.each(function() {
|
||||
var id = $(this).attr('id').substring(1);
|
||||
var count = COMMENT_METADATA[id];
|
||||
var title = count + ' comment' + (count == 1 ? '' : 's');
|
||||
var image = count > 0 ? opts.commentBrightImage : opts.commentImage;
|
||||
var addcls = count == 0 ? ' nocomment' : '';
|
||||
$(this)
|
||||
.append(
|
||||
$(document.createElement('a')).attr({
|
||||
href: '#',
|
||||
'class': 'sphinx-comment-open' + addcls,
|
||||
id: 'ao' + id
|
||||
})
|
||||
.append($(document.createElement('img')).attr({
|
||||
src: image,
|
||||
alt: 'comment',
|
||||
title: title
|
||||
}))
|
||||
.click(function(event) {
|
||||
event.preventDefault();
|
||||
show($(this).attr('id').substring(2));
|
||||
})
|
||||
)
|
||||
.append(
|
||||
$(document.createElement('a')).attr({
|
||||
href: '#',
|
||||
'class': 'sphinx-comment-close hidden',
|
||||
id: 'ah' + id
|
||||
})
|
||||
.append($(document.createElement('img')).attr({
|
||||
src: opts.closeCommentImage,
|
||||
alt: 'close',
|
||||
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<span id="acknowledgment"></span><span id="index-0"></span><h1>Acknowledgements<a class="headerlink" href="#acknowledgements" title="Permalink to this headline">¶</a></h1>
|
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<dl class="docutils">
|
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<dt><strong>Bastian M. Wojek</strong></dt>
|
||||
<dd>I am very much indebted to BMW for his rigorous testing of <tt class="docutils literal"><span class="pre">musrfit</span></tt>, his many useful suggestions, contributions, and for the
|
||||
largest part of the user manual of <tt class="docutils literal"><span class="pre">musrfit</span></tt> which makes it accessible to a broader audience! Many thanks Bastian!</dd>
|
||||
<dd>I am very much indebted to BMW for his rigorous testing of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>, his many useful suggestions, contributions, and for the
|
||||
largest part of the user manual of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> which makes it accessible to a broader audience! Many thanks Bastian!</dd>
|
||||
<dt><strong>Uldis Locans</strong></dt>
|
||||
<dd>I am very much indebted to Uldis work on <a class="reference internal" href="setup-dks.html#setup-dks"><em>DKS</em></a> enabling the GPU support for <tt class="docutils literal"><span class="pre">musrfit</span></tt>. His kind, calm, and
|
||||
<dd>I am very much indebted to Uldis work on <a class="reference internal" href="setup-dks.html#setup-dks"><span class="std std-ref">DKS</span></a> enabling the GPU support for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>. His kind, calm, and
|
||||
extremely competent way to deal with his projects as well as to deal with the chaos of physicists way to think is admirable. Many thanks Uldis!</dd>
|
||||
<dt><strong>Zaher Salman</strong></dt>
|
||||
<dd>Thanks for his beta-NMR and web-interface contributions to <tt class="docutils literal"><span class="pre">musrfit</span></tt>!</dd>
|
||||
<dd>Thanks for his beta-NMR and web-interface contributions to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>!</dd>
|
||||
<dt><strong>Robert Scheuermann</strong></dt>
|
||||
<dd>Thanks for his constant contructive input on <tt class="docutils literal"><span class="pre">musrfit</span></tt>!</dd>
|
||||
<dd>Thanks for his constant contructive input on <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>!</dd>
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<span id="index-0"></span><h1>any2many - a Universal μSR-file-format converter<a class="headerlink" href="#any2many-a-universal-mgrsr-file-format-converter" title="Permalink to this headline">¶</a></h1>
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<p><tt class="docutils literal"><span class="pre">any2many</span></tt> allows to convert most μSR-file-formats from one to the other.
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<li class="toctree-l1 current"><a class="current reference internal" href="#">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
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<span id="cite"></span><span id="index-0"></span><h1>How to Cite <tt class="docutils literal"><span class="pre">musrfit</span></tt>?<a class="headerlink" href="#how-to-cite-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<p>Since quite some effort is going into the development and maintenance of the <tt class="docutils literal"><span class="pre">musrfit</span></tt> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath</p>
|
||||
<span id="cite"></span><span id="index-0"></span><h1>How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?<a class="headerlink" href="#how-to-cite-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<p>Since quite some effort is going into the development and maintenance of the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath</p>
|
||||
<blockquote>
|
||||
<div><ul class="simple">
|
||||
<li>A. Suter, B.M. Wojek, “Musrfit: A Free Platform-Independent Framework for μSR Data Analysis”, Physics Procedia <strong>30</strong>, 69 (2012). <a class="reference external" href="http://dx.doi.org/10.1016/j.phpro.2012.04.042">http://dx.doi.org/10.1016/j.phpro.2012.04.042</a></li>
|
||||
<li>A. Suter, B.M. Wojek, “Musrfit: A Free Platform-Independent Framework for μSR Data Analysis”, Physics Procedia <strong>30</strong>, 69 (2012). <a class="reference external" href="http://dx.doi.org/10.1016/j.phpro.2012.04.042">http://dx.doi.org/10.1016/j.phpro.2012.04.042</a></li>
|
||||
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|
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|
||||
<p>The GPU high speed <tt class="docutils literal"><span class="pre">musrfit</span></tt> version is utilizing <tt class="docutils literal"><span class="pre">DKS</span></tt>. In case you are using this version, please also add the following citations</p>
|
||||
<p>The GPU high speed <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> version is utilizing <code class="docutils literal notranslate"><span class="pre">DKS</span></code>. In case you are using this version, please also add the following citations</p>
|
||||
<blockquote>
|
||||
<div><ul class="simple">
|
||||
<li>A. Adelmann, U. Locans, A. Suter, “The Dynamic Kernel Scheduler—Part 1”, Computer Physics Communications <strong>207</strong>, 83 (2016). <a class="reference external" href="https://doi.org/10.1016/j.cpc.2016.05.013">https://doi.org/10.1016/j.cpc.2016.05.013</a></li>
|
||||
<li>U. Locans, <em>et al.</em>, “Real-time computation of parameter fitting and image reconstruction using graphical processing units”, Computer Physics Communications <strong>215</strong>, 71 (2017). <a class="reference external" href="https://doi.org/10.1016/j.cpc.2017.02.007">https://doi.org/10.1016/j.cpc.2017.02.007</a></li>
|
||||
<li>U.Locans and A.Suter, “Musrfit – Real Time Parameter Fitting Using GPUs”, JPS Conf. Proc. <em>21</em>, 011051 (2018). <a class="reference external" href="http://dx.doi.org/10.7566/JPSCP.21.011051">http://dx.doi.org/10.7566/JPSCP.21.011051</a></li>
|
||||
<li>A. Adelmann, U. Locans, A. Suter, “The Dynamic Kernel Scheduler—Part 1”, Computer Physics Communications <strong>207</strong>, 83 (2016). <a class="reference external" href="https://doi.org/10.1016/j.cpc.2016.05.013">https://doi.org/10.1016/j.cpc.2016.05.013</a></li>
|
||||
<li>U. Locans, <em>et al.</em>, “Real-time computation of parameter fitting and image reconstruction using graphical processing units”, Computer Physics Communications <strong>215</strong>, 71 (2017). <a class="reference external" href="https://doi.org/10.1016/j.cpc.2017.02.007">https://doi.org/10.1016/j.cpc.2017.02.007</a></li>
|
||||
<li>U.Locans and A.Suter, “Musrfit – Real Time Parameter Fitting Using GPUs”, JPS Conf. Proc. <em>21</em>, 011051 (2018). <a class="reference external" href="http://dx.doi.org/10.7566/JPSCP.21.011051">http://dx.doi.org/10.7566/JPSCP.21.011051</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
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<h1>Welcome to the musrfit documentation!<a class="headerlink" href="#welcome-to-the-musrfit-documentation" title="Permalink to this headline">¶</a></h1>
|
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<div class="toctree-wrapper compound">
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <tt class="docutils literal"><span class="pre">musrfit</span></tt>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <tt class="docutils literal"><span class="pre">musrfit</span></tt></a><ul>
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a><ul>
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<li class="toctree-l2"><a class="reference internal" href="tutorial.html#single-histogram-fit-tutorial">Single-histogram-fit tutorial</a></li>
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<li class="toctree-l2"><a class="reference internal" href="tutorial.html#asymmtery-fit-tutorial">Asymmtery-fit tutorial</a></li>
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@ -69,7 +181,7 @@
|
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<li class="toctree-l2"><a class="reference internal" href="user-libs.html#functions-to-analyze-bgr-nmr-data-bnmr-libs">Functions to analyze β-NMR data (BNMR libs)</a></li>
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|
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a><ul>
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="setup-standard.html#supported-operating-systems-and-software-requirements">Supported Operating Systems and Software Requirements</a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s</a><ul>
|
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<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a Tesla K40c (NVIDIA)</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a AMD Graphic Card (Radeon R9 390X)</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-macos-for-opencl-support">Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for macOS for OpenCL support</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a Tesla K40c (NVIDIA)</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a AMD Graphic Card (Radeon R9 390X)</a></li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="setup-dks.html#setting-up-musrfit-dks-for-macos-for-opencl-support">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for macOS for OpenCL support</a></li>
|
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</ul>
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</li>
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<li class="toctree-l1"><a class="reference internal" href="musredit.html"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a><ul>
|
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<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a><ul>
|
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<li class="toctree-l2"><a class="reference internal" href="musredit.html#introduction">Introduction</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="musredit.html#available-executable-configuration-files-and-their-basic-usage">Available Executable, Configuration Files and their Basic Usage</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="musredit.html#musredit-features">musredit Features</a></li>
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@ -97,7 +209,7 @@
|
||||
<li class="toctree-l2"><a class="reference internal" href="mupp.html#the-usage-summary">The Usage Summary</a></li>
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<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr Files</a><ul>
|
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<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a><ul>
|
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<li class="toctree-l2"><a class="reference internal" href="msr2data.html#basic-types-of-usage">Basic Types of Usage</a></li>
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|
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<li class="toctree-l2"><a class="reference internal" href="msr2data.html#the-global-mode">The Global Mode</a></li>
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@ -127,27 +239,77 @@
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<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#basic-types-of-usage">Basic Types of Usage</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#run-list-file-structure">Run List File Structure</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#the-graphical-user-interface-for-msr2data-provided-by-musredit">The Graphical User Interface for msr2data Provided by musredit</a></li>
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<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
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<div class="section" id="msr2data-a-program-for-automatically-processing-multiple-musrfit-msr-files">
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<span id="msr2data"></span><span id="index-0"></span><h1>msr2data - A Program for Automatically Processing Multiple <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr Files<a class="headerlink" href="#msr2data-a-program-for-automatically-processing-multiple-musrfit-msr-files" title="Permalink to this headline">¶</a></h1>
|
||||
<p><tt class="docutils literal"><span class="pre">msr2data</span></tt> (originally written by B. M. Wojek) is a program implemented in <tt class="docutils literal"><span class="pre">C++</span></tt>. Its purpose is
|
||||
to process multiple msr files (input files for <tt class="docutils literal"><span class="pre">musrfit</span></tt>) with the same parameters and summarize the fitting
|
||||
<span id="msr2data"></span><span id="index-0"></span><h1>msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files<a class="headerlink" href="#msr2data-a-program-for-automatically-processing-multiple-musrfit-msr-files" title="Permalink to this headline">¶</a></h1>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">msr2data</span></code> (originally written by B. M. Wojek) is a program implemented in <code class="docutils literal notranslate"><span class="pre">C++</span></code>. Its purpose is
|
||||
to process multiple msr files (input files for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>) with the same parameters and summarize the fitting
|
||||
results either in a <em>TRIUMF DB</em> <a class="footnote-reference" href="#f1" id="id1">[1]</a> or a <em>column ASCII</em> file. This allows essentially to</p>
|
||||
<ol class="arabic simple">
|
||||
<li>Collect the fit parameters.</li>
|
||||
@ -60,60 +185,60 @@ results either in a <em>TRIUMF DB</em> <a class="footnote-reference" href="#f1"
|
||||
<colgroup><col class="label" /><col /></colgroup>
|
||||
<tbody valign="top">
|
||||
<tr><td class="label"><a class="fn-backref" href="#id1">[1]</a></td><td>For an abridged description of this format see <a class="reference external" href="http://musr.org/xyfit/dbformat.html">here</a>. The DB files
|
||||
produced by <tt class="docutils literal"><span class="pre">msr2data</span></tt> can be viewed for instance with <a class="reference internal" href="mupp.html#mupp"><em>mupp</em></a> or μView <a class="reference external" href="http://musr.org/muview/">see here</a>, however,
|
||||
they are not completely backward-compatible to the original <tt class="docutils literal"><span class="pre">db</span> <span class="pre">language</span></tt> since the parameter names can be longer than five or
|
||||
produced by <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> can be viewed for instance with <a class="reference internal" href="mupp.html#mupp"><span class="std std-ref">mupp</span></a> or μView <a class="reference external" href="http://musr.org/muview/">see here</a>, however,
|
||||
they are not completely backward-compatible to the original <code class="docutils literal notranslate"><span class="pre">db</span> <span class="pre">language</span></code> since the parameter names can be longer than five or
|
||||
six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the
|
||||
parameter names in the msr files!</td></tr>
|
||||
</tbody>
|
||||
</table>
|
||||
<div class="section" id="basic-types-of-usage">
|
||||
<span id="msr2data-basic-usage"></span><h2>Basic Types of Usage<a class="headerlink" href="#basic-types-of-usage" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Apart from numerous <a class="reference internal" href="#msr2data-opt-param"><em>optional parameters</em></a> that might be set, in principle there are four different ways of calling <tt class="docutils literal"><span class="pre">msr2data</span></tt>.
|
||||
<p>Apart from numerous <a class="reference internal" href="#msr2data-opt-param"><span class="std std-ref">optional parameters</span></a> that might be set, in principle there are four different ways of calling <code class="docutils literal notranslate"><span class="pre">msr2data</span></code>.
|
||||
These differ in how the list of runs which should be processed is supplied:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong>msr2data <run> <extension> [optional parameters]</strong></dt>
|
||||
<dd>A single run number.</dd>
|
||||
<dt><strong>msr2data <firstRunNo> <lastRunNo> <extension> [optional parameters]</strong></dt>
|
||||
<dd>An interval of run numbers is specified through the first and the last run number. The condition <tt class="docutils literal"><span class="pre"><firstRunNo></span></tt> < <tt class="docutils literal"><span class="pre"><lastRunNo></span></tt> is not necessary.</dd>
|
||||
<dd>An interval of run numbers is specified through the first and the last run number. The condition <code class="docutils literal notranslate"><span class="pre"><firstRunNo></span></code> < <code class="docutils literal notranslate"><span class="pre"><lastRunNo></span></code> is not necessary.</dd>
|
||||
<dt><strong>msr2data [ <runList> ] <extension> [optional parameters]</strong></dt>
|
||||
<dd><p class="first">Where <tt class="docutils literal"><span class="pre"><runList></span></tt> is one or a combination of the following:</p>
|
||||
<dd><p class="first">Where <code class="docutils literal notranslate"><span class="pre"><runList></span></code> is one or a combination of the following:</p>
|
||||
<ol class="last arabic simple">
|
||||
<li><tt class="docutils literal"><span class="pre"><run0>,</span> <span class="pre"><run1>,</span> <span class="pre"><run2>,</span> <span class="pre">...</span> <span class="pre"><runN></span></tt> : run numbers, <em>e.g.</em> 123 124,</li>
|
||||
<li><tt class="docutils literal"><span class="pre"><run0>-<runN></span></tt> : a range, <em>e.g.</em> 123-125 -> 123 124 125,</li>
|
||||
<li><tt class="docutils literal"><span class="pre"><run0>:<runN>:<step></span></tt> : a sequence, <em>e.g.</em> 123:127:2 -> 123 125 127. <tt class="docutils literal"><span class="pre"><step></span></tt> has to be a positive integer.</li>
|
||||
<li>A <tt class="docutils literal"><span class="pre"><runList></span></tt> can also combine (1)-(3), <em>e.g.</em> 123 128-130 133, etc.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre"><run0>,</span> <span class="pre"><run1>,</span> <span class="pre"><run2>,</span> <span class="pre">...</span> <span class="pre"><runN></span></code> : run numbers, <em>e.g.</em> 123 124,</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre"><run0>-<runN></span></code> : a range, <em>e.g.</em> 123-125 -> 123 124 125,</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre"><run0>:<runN>:<step></span></code> : a sequence, <em>e.g.</em> 123:127:2 -> 123 125 127. <code class="docutils literal notranslate"><span class="pre"><step></span></code> has to be a positive integer.</li>
|
||||
<li>A <code class="docutils literal notranslate"><span class="pre"><runList></span></code> can also combine (1)-(3), <em>e.g.</em> 123 128-130 133, etc.</li>
|
||||
</ol>
|
||||
</dd>
|
||||
<dt><strong>msr2data <runListFileName> <extension> [optional parameters]</strong></dt>
|
||||
<dd>An ASCII file containing a list of run numbers and optional external parameters is passed to <tt class="docutils literal"><span class="pre">msr2data</span></tt>. For the structure of the ASCII file
|
||||
see <a class="reference internal" href="#run-list-file-structure"><em>below</em></a>.</dd>
|
||||
<dd>An ASCII file containing a list of run numbers and optional external parameters is passed to <code class="docutils literal notranslate"><span class="pre">msr2data</span></code>. For the structure of the ASCII file
|
||||
see <a class="reference internal" href="#run-list-file-structure"><span class="std std-ref">below</span></a>.</dd>
|
||||
</dl>
|
||||
<p>All four basic types of calling <tt class="docutils literal"><span class="pre">msr2data</span></tt> contain the <em>mandatory</em> file-name <tt class="docutils literal"><span class="pre"><extension></span></tt> passed right after the list of runs. The meaning of
|
||||
this <tt class="docutils literal"><span class="pre"><extension></span></tt> should become clear after giving examples for all four cases:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> _tf_h13
|
||||
<p>All four basic types of calling <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> contain the <em>mandatory</em> file-name <code class="docutils literal notranslate"><span class="pre"><extension></span></code> passed right after the list of runs. The meaning of
|
||||
this <code class="docutils literal notranslate"><span class="pre"><extension></span></code> should become clear after giving examples for all four cases:</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> _tf_h13
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>generates the DB file <tt class="docutils literal"><span class="pre">out.db</span></tt> (can be changed by using the -o option) from <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt>.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8474</span> _tf_h13
|
||||
<p>generates the DB file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> (can be changed by using the -o option) from <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code>.</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8474</span> _tf_h13
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>generates the DB file <tt class="docutils literal"><span class="pre">out.db</span></tt> (can be changed by using the -o option) from <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8473_tf_h13.msr</span></tt>, and <tt class="docutils literal"><span class="pre">8474_tf_h13.msr</span></tt>.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8472</span> <span class="m">8470</span><span class="o">]</span> _tf_h13
|
||||
<p>generates the DB file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> (can be changed by using the -o option) from <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8473_tf_h13.msr</span></code>, and <code class="docutils literal notranslate"><span class="pre">8474_tf_h13.msr</span></code>.</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8472</span> <span class="m">8470</span><span class="o">]</span> _tf_h13
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>generates the DB file <tt class="docutils literal"><span class="pre">out.db</span></tt> (can be changed by using the -o option) from <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt> and <tt class="docutils literal"><span class="pre">8470_tf_h13.msr</span></tt>.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8470</span>:8474:2<span class="o">]</span> _tf_h13
|
||||
<p>generates the DB file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> (can be changed by using the -o option) from <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code> and <code class="docutils literal notranslate"><span class="pre">8470_tf_h13.msr</span></code>.</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8470</span>:8474:2<span class="o">]</span> _tf_h13
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>generates the DB file <tt class="docutils literal"><span class="pre">out.db</span></tt> (can be changed by using the -o option) from <tt class="docutils literal"><span class="pre">8470_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt>, and <tt class="docutils literal"><span class="pre">8474_tf_h13.msr</span></tt>.</p>
|
||||
<p>generates the DB file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> (can be changed by using the -o option) from <code class="docutils literal notranslate"><span class="pre">8470_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code>, and <code class="docutils literal notranslate"><span class="pre">8474_tf_h13.msr</span></code>.</p>
|
||||
<div class="section" id="run-list-file-structure">
|
||||
<span id="id2"></span><h3>Run List File Structure<a class="headerlink" href="#run-list-file-structure" title="Permalink to this headline">¶</a></h3>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data run.list _tf_h13
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data run.list _tf_h13
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>generates the DB file <tt class="docutils literal"><span class="pre">out.db</span></tt> (can be changed by using the -o option) from all runs listed in the ASCII file <tt class="docutils literal"><span class="pre">run.list</span></tt> in the working directory.
|
||||
In this file it is also possible to include <em>external</em> parameters which should be put in the resulting DB file. The structure of the <tt class="docutils literal"><span class="pre">run.list</span></tt> is the following:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>RUN VAR1 VAR2 VAR3 ...
|
||||
<p>generates the DB file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> (can be changed by using the -o option) from all runs listed in the ASCII file <code class="docutils literal notranslate"><span class="pre">run.list</span></code> in the working directory.
|
||||
In this file it is also possible to include <em>external</em> parameters which should be put in the resulting DB file. The structure of the <code class="docutils literal notranslate"><span class="pre">run.list</span></code> is the following:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>RUN VAR1 VAR2 VAR3 ...
|
||||
8460 200 27.1 46.2 ...
|
||||
8472 205 27.1 46.3 ...
|
||||
8453 210 27.2 45.9 ...
|
||||
@ -123,18 +248,18 @@ In this file it is also possible to include <em>external</em> parameters which s
|
||||
</pre></div>
|
||||
</div>
|
||||
<p><em>The first not commented and not empty line determines the parameter names and labels and has to be present!</em></p>
|
||||
<p>It is allowed to add comments (with a preceding ‘#’) or empty lines to the run-list file.</p>
|
||||
<p>It is allowed to add comments (with a preceding ‘#’) or empty lines to the run-list file.</p>
|
||||
<p>The following should be mentioned together with the above examples:</p>
|
||||
<ul>
|
||||
<li><p class="first">The output files in the examples above are only newly created if they did <em>not</em> exist before invoking <tt class="docutils literal"><span class="pre">msr2data</span></tt>.
|
||||
<li><p class="first">The output files in the examples above are only newly created if they did <em>not</em> exist before invoking <code class="docutils literal notranslate"><span class="pre">msr2data</span></code>.
|
||||
If the files were already present the msr file data would be appended!</p>
|
||||
</li>
|
||||
<li><p class="first">If the files have been newly created, also the DB file header is written. If the files were present before, only
|
||||
the data blocks are appended. The output of the header can either be forced or completely suppressed with the <tt class="docutils literal"><span class="pre">header</span></tt>
|
||||
and <tt class="docutils literal"><span class="pre">noheader</span></tt> options as shall be seen later.</p>
|
||||
the data blocks are appended. The output of the header can either be forced or completely suppressed with the <code class="docutils literal notranslate"><span class="pre">header</span></code>
|
||||
and <code class="docutils literal notranslate"><span class="pre">noheader</span></code> options as shall be seen later.</p>
|
||||
</li>
|
||||
<li><p class="first">If the <tt class="docutils literal"><span class="pre">musrfit</span></tt> output files do not have an <tt class="docutils literal"><span class="pre"><extension></span></tt> as specified above like <tt class="docutils literal"><span class="pre">8472.msr</span></tt> one has to call <tt class="docutils literal"><span class="pre">msr2data</span></tt> like in the following example:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8460</span> <span class="s2">""</span>
|
||||
<li><p class="first">If the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> output files do not have an <code class="docutils literal notranslate"><span class="pre"><extension></span></code> as specified above like <code class="docutils literal notranslate"><span class="pre">8472.msr</span></code> one has to call <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> like in the following example:</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8460</span> <span class="s2">""</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</li>
|
||||
@ -143,7 +268,7 @@ and <tt class="docutils literal"><span class="pre">noheader</span></tt> options
|
||||
</div>
|
||||
<div class="section" id="optional-parameters">
|
||||
<span id="msr2data-opt-param"></span><h2>Optional Parameters<a class="headerlink" href="#optional-parameters" title="Permalink to this headline">¶</a></h2>
|
||||
<p>As mentioned already above there are some optional parameters which change the behavior of <tt class="docutils literal"><span class="pre">msr2data</span></tt> and can be passed in any order. Here is a complete list:</p>
|
||||
<p>As mentioned already above there are some optional parameters which change the behavior of <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> and can be passed in any order. Here is a complete list:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong>data</strong></dt>
|
||||
<dd>The output file format is changed to a simple column ASCII file (default output file name: out.dat).</dd>
|
||||
@ -153,79 +278,79 @@ and <tt class="docutils literal"><span class="pre">noheader</span></tt> options
|
||||
<dd>Force the output of the file header even if the output file was present before.</dd>
|
||||
<dt><strong>noheader</strong></dt>
|
||||
<dd>The output of the file header is suppressed—also if the output file is newly created.
|
||||
If either both or none of the header options are given, <tt class="docutils literal"><span class="pre">msr2data</span></tt> writes the file header only to new files
|
||||
If either both or none of the header options are given, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> writes the file header only to new files
|
||||
and it solely appends the data blocks to an existing output file assuming that the header is present already.</dd>
|
||||
<dt><strong>nosummary</strong></dt>
|
||||
<dd>There will be no attempt to read additional information like the temperature or the applied magnetic field from
|
||||
the data files even if these information were present there.</dd>
|
||||
<dt><strong>paramList <param></strong></dt>
|
||||
<dd>option used to select the parameters which shall be exported. <tt class="docutils literal"><span class="pre"><param></span></tt> is a list of parameter numbers to be exported.
|
||||
Allowed lists are: <tt class="docutils literal"><span class="pre"><startNo>-<endNo></span></tt>, <em>e.g.</em> <tt class="docutils literal"><span class="pre">1-16</span></tt> will export parameters 1 to 16. Space separated numbers, <em>e.g.:</em> <tt class="docutils literal"><span class="pre">1</span> <span class="pre">3</span> <span class="pre">5</span></tt>.
|
||||
A combination of both is possible, <em>e.g.</em> <tt class="docutils literal"><span class="pre">1-16</span> <span class="pre">19</span> <span class="pre">31</span> <span class="pre">62</span></tt>, and so on.</dd>
|
||||
<dd>option used to select the parameters which shall be exported. <code class="docutils literal notranslate"><span class="pre"><param></span></code> is a list of parameter numbers to be exported.
|
||||
Allowed lists are: <code class="docutils literal notranslate"><span class="pre"><startNo>-<endNo></span></code>, <em>e.g.</em> <code class="docutils literal notranslate"><span class="pre">1-16</span></code> will export parameters 1 to 16. Space separated numbers, <em>e.g.:</em> <code class="docutils literal notranslate"><span class="pre">1</span> <span class="pre">3</span> <span class="pre">5</span></code>.
|
||||
A combination of both is possible, <em>e.g.</em> <code class="docutils literal notranslate"><span class="pre">1-16</span> <span class="pre">19</span> <span class="pre">31</span> <span class="pre">62</span></code>, and so on.</dd>
|
||||
<dt><strong>-o<outputFileName>, -o <outputFileName></strong></dt>
|
||||
<dd>The processed data will be written to the file <tt class="docutils literal"><span class="pre"><outputFileName></span></tt> instead of the default <tt class="docutils literal"><span class="pre">out.db</span></tt> or <tt class="docutils literal"><span class="pre">out.dat</span></tt>.
|
||||
If <tt class="docutils literal"><span class="pre"><outputFileName></span></tt> is equal to none (case-insensitive) the parameter data are not appended to any output file.</dd>
|
||||
<dd>The processed data will be written to the file <code class="docutils literal notranslate"><span class="pre"><outputFileName></span></code> instead of the default <code class="docutils literal notranslate"><span class="pre">out.db</span></code> or <code class="docutils literal notranslate"><span class="pre">out.dat</span></code>.
|
||||
If <code class="docutils literal notranslate"><span class="pre"><outputFileName></span></code> is equal to none (case-insensitive) the parameter data are not appended to any output file.</dd>
|
||||
<dt><strong>fit</strong></dt>
|
||||
<dd>Additionally to the final data collection <tt class="docutils literal"><span class="pre">msr2data</span></tt> will invoke <tt class="docutils literal"><span class="pre">musrfit</span></tt> to fit the specified runs.
|
||||
<dd>Additionally to the final data collection <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> will invoke <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> to fit the specified runs.
|
||||
All msr files are assumed to be present, none is newly generated!</dd>
|
||||
<dt><strong>fit-<template>[!]</strong></dt>
|
||||
<dd>Additionally to the final data collection <tt class="docutils literal"><span class="pre">msr2data</span></tt> will generate msr files for the runs specified in the list
|
||||
of runs and invoke <a class="reference internal" href="user-manual.html#musrfit"><em>musrfit</em></a> for performing fits of the data. As template for the first run the file
|
||||
<tt class="docutils literal"><span class="pre"><template><extension>.msr</span></tt> (or if not available: <tt class="docutils literal"><span class="pre"><template><extension>.mlog</span></tt>) is used; the subsequent input
|
||||
files will be created using the msr output of the last processed runs (“chain fit”). However, if for all runs only
|
||||
the given template should be used one has to append an exclamation mark (<strong>!</strong>) to the <tt class="docutils literal"><span class="pre"><template></span></tt>.</dd>
|
||||
<dd>Additionally to the final data collection <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> will generate msr files for the runs specified in the list
|
||||
of runs and invoke <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a> for performing fits of the data. As template for the first run the file
|
||||
<code class="docutils literal notranslate"><span class="pre"><template><extension>.msr</span></code> (or if not available: <code class="docutils literal notranslate"><span class="pre"><template><extension>.mlog</span></code>) is used; the subsequent input
|
||||
files will be created using the msr output of the last processed runs (“chain fit”). However, if for all runs only
|
||||
the given template should be used one has to append an exclamation mark (<strong>!</strong>) to the <code class="docutils literal notranslate"><span class="pre"><template></span></code>.</dd>
|
||||
<dt><strong>msr-<template></strong></dt>
|
||||
<dd>The same as <tt class="docutils literal"><span class="pre">fit-<template>[!]</span></tt>, <em>without</em> calling <tt class="docutils literal"><span class="pre">musrfit</span></tt> and the final data collection, <em>i.e.</em> only the msr files for the given runs are generated.</dd>
|
||||
<dd>The same as <code class="docutils literal notranslate"><span class="pre">fit-<template>[!]</span></code>, <em>without</em> calling <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> and the final data collection, <em>i.e.</em> only the msr files for the given runs are generated.</dd>
|
||||
<dt><strong>-k</strong></dt>
|
||||
<dd>If specified together with the <tt class="docutils literal"><span class="pre">fit-<template></span></tt> option, the <a class="reference internal" href="user-manual.html#musrfit"><em>- -keep-mn2-output</em></a> option is passed to <tt class="docutils literal"><span class="pre">musrfit</span></tt>.
|
||||
<dd>If specified together with the <code class="docutils literal notranslate"><span class="pre">fit-<template></span></code> option, the <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">- -keep-mn2-output</span></a> option is passed to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>.
|
||||
In the case no fits should be done, this option is ignored.</dd>
|
||||
<dt><strong>-t</strong></dt>
|
||||
<dd>In case this option is given additionally to the <tt class="docutils literal"><span class="pre">fit-<template></span> <span class="pre">option</span></tt>, <tt class="docutils literal"><span class="pre">musrfit</span></tt> is called with
|
||||
the <a class="reference internal" href="user-manual.html#musrfit"><em>- -title-from-data-file</em></a> option. If no fitting is done, this option is ignored.</dd>
|
||||
<dd>In case this option is given additionally to the <code class="docutils literal notranslate"><span class="pre">fit-<template></span> <span class="pre">option</span></code>, <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is called with
|
||||
the <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">- -title-from-data-file</span></a> option. If no fitting is done, this option is ignored.</dd>
|
||||
</dl>
|
||||
<p><strong>Examples:</strong></p>
|
||||
<p>In order to illustrate the usage of these parameters a few examples with explanations are given below:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8400</span> <span class="m">8460</span> _tf_h13 -oABC.db fit-8472
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8400</span> <span class="m">8460</span> _tf_h13 -oABC.db fit-8472
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Using <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt> as first template, <tt class="docutils literal"><span class="pre">msr2data</span></tt> generates subsequent msr input files <tt class="docutils literal"><span class="pre">8400_tf_h13.msr</span></tt> through <tt class="docutils literal"><span class="pre">8460_tf_h13.msr</span></tt>,
|
||||
calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> to perform a fit of these files and collects the results of the fits together with the DB header in the new file <tt class="docutils literal"><span class="pre">ABC.db</span></tt>.
|
||||
Additionally, some information about external parameters like the temperature will be passed to <tt class="docutils literal"><span class="pre">ABC.db</span></tt> if it is present in the data files.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8500</span> <span class="m">8502</span>-8504 <span class="m">8507</span><span class="o">]</span> _zf fit-8472 noheader nosummary -o DEF.db
|
||||
<p>Using <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code> as first template, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> generates subsequent msr input files <code class="docutils literal notranslate"><span class="pre">8400_tf_h13.msr</span></code> through <code class="docutils literal notranslate"><span class="pre">8460_tf_h13.msr</span></code>,
|
||||
calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> to perform a fit of these files and collects the results of the fits together with the DB header in the new file <code class="docutils literal notranslate"><span class="pre">ABC.db</span></code>.
|
||||
Additionally, some information about external parameters like the temperature will be passed to <code class="docutils literal notranslate"><span class="pre">ABC.db</span></code> if it is present in the data files.</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8500</span> <span class="m">8502</span>-8504 <span class="m">8507</span><span class="o">]</span> _zf fit-8472 noheader nosummary -o DEF.db
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Using <tt class="docutils literal"><span class="pre">8472_zf.msr</span></tt> as first template, <tt class="docutils literal"><span class="pre">msr2data</span></tt> generates subsequent msr input files <tt class="docutils literal"><span class="pre">8500_zf.msr</span></tt>, <tt class="docutils literal"><span class="pre">8502_zf.msr</span></tt>, <tt class="docutils literal"><span class="pre">8503_zf.msr</span></tt>,
|
||||
<tt class="docutils literal"><span class="pre">8504_zf.msr</span></tt>, and <tt class="docutils literal"><span class="pre">8507_zf.msr</span></tt>, calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> to perform a fit of these files and collects the results of the fits in the file <tt class="docutils literal"><span class="pre">DEF.db</span></tt>
|
||||
<p>Using <code class="docutils literal notranslate"><span class="pre">8472_zf.msr</span></code> as first template, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> generates subsequent msr input files <code class="docutils literal notranslate"><span class="pre">8500_zf.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8502_zf.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8503_zf.msr</span></code>,
|
||||
<code class="docutils literal notranslate"><span class="pre">8504_zf.msr</span></code>, and <code class="docutils literal notranslate"><span class="pre">8507_zf.msr</span></code>, calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> to perform a fit of these files and collects the results of the fits in the file <code class="docutils literal notranslate"><span class="pre">DEF.db</span></code>
|
||||
<em>without</em> writing the DB file header or attempting to read additional information from the data files.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8595</span> <span class="m">8585</span> <span class="s2">""</span> noheader fit-8472! -oGHI.dat data nosummary -k
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8595</span> <span class="m">8585</span> <span class="s2">""</span> noheader fit-8472! -oGHI.dat data nosummary -k
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Using <tt class="docutils literal"><span class="pre">8472.msr</span></tt> as template for all runs, <tt class="docutils literal"><span class="pre">msr2data</span></tt> generates the msr input files <tt class="docutils literal"><span class="pre">8595.msr</span></tt> through <tt class="docutils literal"><span class="pre">8585.msr</span></tt>, calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> with
|
||||
the option <tt class="docutils literal"><span class="pre">--keep-mn2-ouput</span></tt> to perform a fit of these files and collects the results of the fits in the column-structured ASCII file <tt class="docutils literal"><span class="pre">GHI.dat</span></tt>
|
||||
<p>Using <code class="docutils literal notranslate"><span class="pre">8472.msr</span></code> as template for all runs, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> generates the msr input files <code class="docutils literal notranslate"><span class="pre">8595.msr</span></code> through <code class="docutils literal notranslate"><span class="pre">8585.msr</span></code>, calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> with
|
||||
the option <code class="docutils literal notranslate"><span class="pre">--keep-mn2-ouput</span></code> to perform a fit of these files and collects the results of the fits in the column-structured ASCII file <code class="docutils literal notranslate"><span class="pre">GHI.dat</span></code>
|
||||
<em>without</em> writing any file header or attempting to read additional information from the data files.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8475</span> <span class="s2">""</span> fit -o none
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8475</span> <span class="s2">""</span> fit -o none
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Take the <em>given</em> msr files <tt class="docutils literal"><span class="pre">8472.msr</span></tt> through <tt class="docutils literal"><span class="pre">8475.msr</span></tt> and call <tt class="docutils literal"><span class="pre">musrfit</span></tt> <em>without</em> finally summarizing the results.</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8475</span> _tf_h13 msr-8471!
|
||||
<p>Take the <em>given</em> msr files <code class="docutils literal notranslate"><span class="pre">8472.msr</span></code> through <code class="docutils literal notranslate"><span class="pre">8475.msr</span></code> and call <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> <em>without</em> finally summarizing the results.</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8472</span> <span class="m">8475</span> _tf_h13 msr-8471!
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Using <tt class="docutils literal"><span class="pre">8471_tf_h13.msr</span></tt> as template for all runs, <tt class="docutils literal"><span class="pre">msr2data</span></tt> generates the msr input files <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt> through <tt class="docutils literal"><span class="pre">8475_tf_h13.msr</span></tt>.
|
||||
<p>Using <code class="docutils literal notranslate"><span class="pre">8471_tf_h13.msr</span></code> as template for all runs, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> generates the msr input files <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code> through <code class="docutils literal notranslate"><span class="pre">8475_tf_h13.msr</span></code>.
|
||||
<em>No fitting will be performed and no DB or ASCII output will be generated!</em></p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8472</span> <span class="m">8475</span>-8479<span class="o">]</span> _tf_h13 paramList <span class="m">1</span>-16 data -o bestData.dat
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="o">[</span><span class="m">8472</span> <span class="m">8475</span>-8479<span class="o">]</span> _tf_h13 paramList <span class="m">1</span>-16 data -o bestData.dat
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Will collect the parameters 1 to 16 from the msr-files <tt class="docutils literal"><span class="pre">8472_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8475_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8476_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8477_tf_h13.msr</span></tt>, <tt class="docutils literal"><span class="pre">8478_tf_h13.msr</span></tt>,
|
||||
and <tt class="docutils literal"><span class="pre">8479_tf_h13.msr</span></tt> and write these parameters into a column like output file <tt class="docutils literal"><span class="pre">bestData.dat</span></tt>.</p>
|
||||
<p>Will collect the parameters 1 to 16 from the msr-files <code class="docutils literal notranslate"><span class="pre">8472_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8475_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8476_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8477_tf_h13.msr</span></code>, <code class="docutils literal notranslate"><span class="pre">8478_tf_h13.msr</span></code>,
|
||||
and <code class="docutils literal notranslate"><span class="pre">8479_tf_h13.msr</span></code> and write these parameters into a column like output file <code class="docutils literal notranslate"><span class="pre">bestData.dat</span></code>.</p>
|
||||
</div>
|
||||
<div class="section" id="the-global-mode">
|
||||
<span id="index-1"></span><h2>The Global Mode<a class="headerlink" href="#the-global-mode" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Apart from all the options described <a class="reference internal" href="#msr2data-opt-param"><em>above</em></a> there is another program option: <strong>global</strong>.
|
||||
This option changes the general behavior of <tt class="docutils literal"><span class="pre">msr2data</span></tt> in that way that instead of processing one msr file for each
|
||||
<p>Apart from all the options described <a class="reference internal" href="#msr2data-opt-param"><span class="std std-ref">above</span></a> there is another program option: <strong>global</strong>.
|
||||
This option changes the general behavior of <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> in that way that instead of processing one msr file for each
|
||||
run it combines all specified runs in <em>one single msr file</em> with the possibility to define common parameters for all
|
||||
runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured
|
||||
ASCII file that single msr file is read and the parameters valid for each run are extracted. The global option can be
|
||||
used in conjunction with any of the described invocations of <tt class="docutils literal"><span class="pre">msr2data</span></tt> and together with all options stated <a class="reference internal" href="#msr2data-opt-param"><em>above</em></a>.</p>
|
||||
used in conjunction with any of the described invocations of <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> and together with all options stated <a class="reference internal" href="#msr2data-opt-param"><span class="std std-ref">above</span></a>.</p>
|
||||
<div class="section" id="file-generation">
|
||||
<h3>File Generation<a class="headerlink" href="#file-generation" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this
|
||||
@ -233,48 +358,48 @@ purpose a single-run template containing information about common and run-specif
|
||||
parameters are identified through their parameter names:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong>run-specific parameters</strong></dt>
|
||||
<dd>these parameters are tagged with the current run number in the format <tt class="docutils literal"><span class="pre">%0Xu</span></tt>, <em>i.e.</em> <tt class="docutils literal"><span class="pre">X</span></tt> digits with leading zeros,
|
||||
at the end of the parameter name, <em>e.g.</em> for a 4-digit-formatted run number <tt class="docutils literal"><span class="pre">alpha0123</span></tt> if the run number was 123 or
|
||||
for a 8-digit-formatted run number <tt class="docutils literal"><span class="pre">alpha00123456</span></tt> if the run number was 123456. <tt class="docutils literal"><span class="pre">X</span></tt> has to be at least 4.</dd>
|
||||
<dd>these parameters are tagged with the current run number in the format <code class="docutils literal notranslate"><span class="pre">%0Xu</span></code>, <em>i.e.</em> <code class="docutils literal notranslate"><span class="pre">X</span></code> digits with leading zeros,
|
||||
at the end of the parameter name, <em>e.g.</em> for a 4-digit-formatted run number <code class="docutils literal notranslate"><span class="pre">alpha0123</span></code> if the run number was 123 or
|
||||
for a 8-digit-formatted run number <code class="docutils literal notranslate"><span class="pre">alpha00123456</span></code> if the run number was 123456. <code class="docutils literal notranslate"><span class="pre">X</span></code> has to be at least 4.</dd>
|
||||
<dt><strong>common parameters</strong></dt>
|
||||
<dd>all parameters that are not run specific</dd>
|
||||
</dl>
|
||||
<p>The <a class="reference internal" href="user-manual.html#msr-fitparameter-block"><em>FITPARAMETER block</em></a> of an exemplary template file <tt class="docutils literal"><span class="pre">8472_example.msr</span></tt> could therefore look like:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 Phase 35.8359 -3.94496 3.93749
|
||||
2 Asy8472 0.04501 -0.00208 0.00211 0 0.33
|
||||
3 Field 143.212 -0.27960 0.27885 100 200
|
||||
4 Rate8472 0.14245 -0.02501 0.02279 0 1
|
||||
<p>The <a class="reference internal" href="user-manual.html#msr-fitparameter-block"><span class="std std-ref">FITPARAMETER block</span></a> of an exemplary template file <code class="docutils literal notranslate"><span class="pre">8472_example.msr</span></code> could therefore look like:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FITPARAMETER</span>
|
||||
<span class="c1"># No Name Value Step Pos_Error Boundaries</span>
|
||||
<span class="mi">1</span> <span class="n">Phase</span> <span class="mf">35.8359</span> <span class="o">-</span><span class="mf">3.94496</span> <span class="mf">3.93749</span>
|
||||
<span class="mi">2</span> <span class="n">Asy8472</span> <span class="mf">0.04501</span> <span class="o">-</span><span class="mf">0.00208</span> <span class="mf">0.00211</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||||
<span class="mi">3</span> <span class="n">Field</span> <span class="mf">143.212</span> <span class="o">-</span><span class="mf">0.27960</span> <span class="mf">0.27885</span> <span class="mi">100</span> <span class="mi">200</span>
|
||||
<span class="mi">4</span> <span class="n">Rate8472</span> <span class="mf">0.14245</span> <span class="o">-</span><span class="mf">0.02501</span> <span class="mf">0.02279</span> <span class="mi">0</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here the parameters <strong>2</strong> and <strong>4</strong> would be treated as <em>run-specific</em> whereas the parameters <strong>1</strong> and <strong>3</strong> would be <em>common</em> to the original and all newly added runs.</p>
|
||||
<p>Normally, within the template file there should <em>not</em> appear explicitly any run-specific parameters in the <a class="reference internal" href="user-manual.html#msr-theory-block"><em>THEORY</em></a> and
|
||||
<a class="reference internal" href="user-manual.html#msr-functions-block"><em>FUNCTIONS</em></a> blocks. If however, those parameters are met, <tt class="docutils literal"><span class="pre">msr2data</span></tt> will try to substitute them by mapped parameters
|
||||
and add them accordingly to the map contained in each <a class="reference internal" href="user-manual.html#msr-run-block"><em>RUN block</em></a>.</p>
|
||||
<p>When <tt class="docutils literal"><span class="pre">msr2data</span></tt> is called to generate a global msr file, <em>e.g.</em></p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example msr-8472 global
|
||||
<p>Normally, within the template file there should <em>not</em> appear explicitly any run-specific parameters in the <a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">THEORY</span></a> and
|
||||
<a class="reference internal" href="user-manual.html#msr-functions-block"><span class="std std-ref">FUNCTIONS</span></a> blocks. If however, those parameters are met, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> will try to substitute them by mapped parameters
|
||||
and add them accordingly to the map contained in each <a class="reference internal" href="user-manual.html#msr-run-block"><span class="std std-ref">RUN block</span></a>.</p>
|
||||
<p>When <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> is called to generate a global msr file, <em>e.g.</em></p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example msr-8472 global
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>a new msr file <tt class="docutils literal"><span class="pre">8471+global_example.msr</span></tt> is created. As can be seen in the example, the name of the global msr file always starts with the
|
||||
first specified run number followed by the <tt class="docutils literal"><span class="pre">+global</span></tt> identifier and the template <tt class="docutils literal"><span class="pre"><extension></span></tt>. The example’s global FITPARAMETER block would be:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
<p>a new msr file <code class="docutils literal notranslate"><span class="pre">8471+global_example.msr</span></code> is created. As can be seen in the example, the name of the global msr file always starts with the
|
||||
first specified run number followed by the <code class="docutils literal notranslate"><span class="pre">+global</span></code> identifier and the template <code class="docutils literal notranslate"><span class="pre"><extension></span></code>. The example’s global FITPARAMETER block would be:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FITPARAMETER</span>
|
||||
<span class="c1"># No Name Value Step Pos_Error Boundaries</span>
|
||||
|
||||
# Common parameters for all runs
|
||||
<span class="c1"># Common parameters for all runs</span>
|
||||
|
||||
1 Phase 35.8359 -3.94496 3.93749
|
||||
2 Field 143.212 -0.27960 0.27885 100 200
|
||||
<span class="mi">1</span> <span class="n">Phase</span> <span class="mf">35.8359</span> <span class="o">-</span><span class="mf">3.94496</span> <span class="mf">3.93749</span>
|
||||
<span class="mi">2</span> <span class="n">Field</span> <span class="mf">143.212</span> <span class="o">-</span><span class="mf">0.27960</span> <span class="mf">0.27885</span> <span class="mi">100</span> <span class="mi">200</span>
|
||||
|
||||
# Specific parameters for run 8471
|
||||
<span class="c1"># Specific parameters for run 8471</span>
|
||||
|
||||
3 Asy8471 0.04501 -0.00208 0.00211 0 0.33
|
||||
4 Rate8471 0.14245 -0.02501 0.02279 0 1
|
||||
<span class="mi">3</span> <span class="n">Asy8471</span> <span class="mf">0.04501</span> <span class="o">-</span><span class="mf">0.00208</span> <span class="mf">0.00211</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||||
<span class="mi">4</span> <span class="n">Rate8471</span> <span class="mf">0.14245</span> <span class="o">-</span><span class="mf">0.02501</span> <span class="mf">0.02279</span> <span class="mi">0</span> <span class="mi">1</span>
|
||||
|
||||
# Specific parameters for run 8470
|
||||
<span class="c1"># Specific parameters for run 8470</span>
|
||||
|
||||
5 Asy8470 0.04501 -0.00208 0.00211 0 0.33
|
||||
6 Rate8470 0.14245 -0.02501 0.02279 0 1
|
||||
<span class="mi">5</span> <span class="n">Asy8470</span> <span class="mf">0.04501</span> <span class="o">-</span><span class="mf">0.00208</span> <span class="mf">0.00211</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||||
<span class="mi">6</span> <span class="n">Rate8470</span> <span class="mf">0.14245</span> <span class="o">-</span><span class="mf">0.02501</span> <span class="mf">0.02279</span> <span class="mi">0</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>This shows that the fit parameters are reorganized in a way that the common parameters appear at the beginning of the parameter list and they are
|
||||
@ -289,7 +414,7 @@ created — for each run as many as found for the template run.</p>
|
||||
<div class="section" id="parameter-extraction">
|
||||
<span id="index-2"></span><h3>Parameter Extraction<a class="headerlink" href="#parameter-extraction" title="Permalink to this headline">¶</a></h3>
|
||||
<p>After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a DB or column-structured ASCII file;
|
||||
as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a class="reference internal" href="#run-list-file-structure"><em>run-list file</em></a>.
|
||||
as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a class="reference internal" href="#run-list-file-structure"><span class="std std-ref">run-list file</span></a>.
|
||||
In order to reach this goal the global msr file has to obey certain rules:</p>
|
||||
<ul class="simple">
|
||||
<li>The order of the parameters has to match the one described above, meaning the common parameters are listed first followed by
|
||||
@ -297,35 +422,35 @@ the same number of parameters specific to each run tagged by the according run n
|
||||
having the same order as the specified list of runs.</li>
|
||||
<li>The RUN blocks have to be ordered according to the list of runs to be processed.</li>
|
||||
</ul>
|
||||
<p>Following these rules – which is achieved most easily by generating the global msr file using <tt class="docutils literal"><span class="pre">msr2data</span></tt> as shown above – the parameters can be extracted <em>e.g.</em> like</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example global data -o globalFit.dat
|
||||
<p>Following these rules – which is achieved most easily by generating the global msr file using <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> as shown above – the parameters can be extracted <em>e.g.</em> like</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example global data -o globalFit.dat
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>This will read in the file <tt class="docutils literal"><span class="pre">8471+global_example.msr</span></tt>, extract for each run all relevant parameters from the msr file as well as
|
||||
from the according data files (if available) and append all of them in columns to the ASCII file <tt class="docutils literal"><span class="pre">globalFit.dat</span></tt>.</p>
|
||||
<p>This will read in the file <code class="docutils literal notranslate"><span class="pre">8471+global_example.msr</span></code>, extract for each run all relevant parameters from the msr file as well as
|
||||
from the according data files (if available) and append all of them in columns to the ASCII file <code class="docutils literal notranslate"><span class="pre">globalFit.dat</span></code>.</p>
|
||||
</div>
|
||||
<div class="section" id="the-extended-global-mode">
|
||||
<span id="index-3"></span><h3>The Extended Global Mode<a class="headerlink" href="#the-extended-global-mode" title="Permalink to this headline">¶</a></h3>
|
||||
<p>If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first;
|
||||
afterwards the run-specific parameters of these single-run msr files are collected into the global msr file. In special cases this might be useful
|
||||
to obtain a better set of starting values for the parameters, however, in most cases it will not replace the “manual review” of the generated global
|
||||
to obtain a better set of starting values for the parameters, however, in most cases it will not replace the “manual review” of the generated global
|
||||
input file. The option is activated by choosing the keyword <strong>global+</strong>. For example</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example global+ msr-8472
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> _example global+ msr-8472
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here, <tt class="docutils literal"><span class="pre">8472_example.msr</span></tt> is first used as template to generate the file <tt class="docutils literal"><span class="pre">8471-OneRunFit_example.msr</span></tt>, then <tt class="docutils literal"><span class="pre">musrfit</span></tt> is called for it, the result
|
||||
is used to generate <tt class="docutils literal"><span class="pre">8470-OneRunFit_example.msr</span></tt> and <tt class="docutils literal"><span class="pre">musrfit</span></tt> is called for that file. Finally, the global fit file <tt class="docutils literal"><span class="pre">8471+global_example.msr</span></tt> is
|
||||
produced — including the fit results of the <tt class="docutils literal"><span class="pre">OneRunFit</span></tt> files for the run-specific parameters.</p>
|
||||
<p>Here, <code class="docutils literal notranslate"><span class="pre">8472_example.msr</span></code> is first used as template to generate the file <code class="docutils literal notranslate"><span class="pre">8471-OneRunFit_example.msr</span></code>, then <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is called for it, the result
|
||||
is used to generate <code class="docutils literal notranslate"><span class="pre">8470-OneRunFit_example.msr</span></code> and <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is called for that file. Finally, the global fit file <code class="docutils literal notranslate"><span class="pre">8471+global_example.msr</span></code> is
|
||||
produced — including the fit results of the <code class="docutils literal notranslate"><span class="pre">OneRunFit</span></code> files for the run-specific parameters.</p>
|
||||
<p>By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the fit option
|
||||
explained before). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.
|
||||
The single run msr files are <em>not</em> deleted at the moment. The information contained in them might be useful for some people. Of course the data can also
|
||||
be collected by <tt class="docutils literal"><span class="pre">msr2data</span></tt>. <em>E.g.</em> in order to produce a DB file <tt class="docutils literal"><span class="pre">OneRunFits.db</span></tt> one could call</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> -OneRunFit_example -o OneRunFits.db
|
||||
be collected by <code class="docutils literal notranslate"><span class="pre">msr2data</span></code>. <em>E.g.</em> in order to produce a DB file <code class="docutils literal notranslate"><span class="pre">OneRunFits.db</span></code> one could call</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">8471</span> <span class="m">8470</span> -OneRunFit_example -o OneRunFits.db
|
||||
</pre></div>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Please be aware that the program in this mode <em>always</em> generates new single-run msr files and <em>always</em> calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> for them. In case there are
|
||||
<p class="last">Please be aware that the program in this mode <em>always</em> generates new single-run msr files and <em>always</em> calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> for them. In case there are
|
||||
already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure
|
||||
the file integrity and correct parameter order within these files.</p>
|
||||
</div>
|
||||
@ -335,54 +460,104 @@ the file integrity and correct parameter order within these files.</p>
|
||||
<h2>Known Limitations<a class="headerlink" href="#known-limitations" title="Permalink to this headline">¶</a></h2>
|
||||
<ul class="simple">
|
||||
<li>The indexing run number of the msr file has to be at the begin of every filename.</li>
|
||||
<li>Within the data file name the <tt class="docutils literal"><span class="pre">RUN#</span></tt> has the format <tt class="docutils literal"><span class="pre">%0Xu</span></tt>, <em>i.e.</em> <tt class="docutils literal"><span class="pre">X</span></tt> digits with leading zeros, and has to be the rightmost number given in this
|
||||
format in the file name. <tt class="docutils literal"><span class="pre">X</span></tt> has to be at least 4. The highest treatable run number is <span class="math">\(2^{32}-1 = 4294967295\)</span>.</li>
|
||||
<li>In order to keep <tt class="docutils literal"><span class="pre">msr2data</span></tt> working properly the msr files should only contain <em>one</em> STATISTIC block at the end of the file and <em>one</em> FITPARAMETER block
|
||||
right after the TITLE — <tt class="docutils literal"><span class="pre">musrfit</span></tt> itself allows to have more creative msr files...</li>
|
||||
<li>The msr-file generation from a template takes only care of runs given on the <em>first</em> line of a <tt class="docutils literal"><span class="pre">RUN</span> <span class="pre">block</span></tt>. <a class="reference internal" href="user-manual.html#msr-addrun"><em>ADDRUN</em></a> statements are simply
|
||||
copied! Since this is most probably <em>not</em> what one likes to do, it is suggested <em>not</em> to use the <tt class="docutils literal"><span class="pre">fit-<template></span></tt> and <tt class="docutils literal"><span class="pre">msr-<template></span></tt> options if
|
||||
<li>Within the data file name the <code class="docutils literal notranslate"><span class="pre">RUN#</span></code> has the format <code class="docutils literal notranslate"><span class="pre">%0Xu</span></code>, <em>i.e.</em> <code class="docutils literal notranslate"><span class="pre">X</span></code> digits with leading zeros, and has to be the rightmost number given in this
|
||||
format in the file name. <code class="docutils literal notranslate"><span class="pre">X</span></code> has to be at least 4. The highest treatable run number is <span class="math notranslate nohighlight">\(2^{32}-1 = 4294967295\)</span>.</li>
|
||||
<li>In order to keep <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> working properly the msr files should only contain <em>one</em> STATISTIC block at the end of the file and <em>one</em> FITPARAMETER block
|
||||
right after the TITLE — <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> itself allows to have more creative msr files…</li>
|
||||
<li>The msr-file generation from a template takes only care of runs given on the <em>first</em> line of a <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">block</span></code>. <a class="reference internal" href="user-manual.html#msr-addrun"><span class="std std-ref">ADDRUN</span></a> statements are simply
|
||||
copied! Since this is most probably <em>not</em> what one likes to do, it is suggested <em>not</em> to use the <code class="docutils literal notranslate"><span class="pre">fit-<template></span></code> and <code class="docutils literal notranslate"><span class="pre">msr-<template></span></code> options if
|
||||
ADDRUN statements were present in the template file.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">msr2data</span></tt> will write only up to two successive empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file,
|
||||
<li><code class="docutils literal notranslate"><span class="pre">msr2data</span></code> will write only up to two successive empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file,
|
||||
these are not copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div class="section" id="the-graphical-user-interface-for-msr2data-provided-by-musredit">
|
||||
<h2>The Graphical User Interface for msr2data Provided by musredit<a class="headerlink" href="#the-graphical-user-interface-for-msr2data-provided-by-musredit" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="musredit.html#musredit-sec"><em>musredit</em></a>, designed especially for the manipulation of <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr files and graphical front ends to <tt class="docutils literal"><span class="pre">musrfit</span></tt>, offer an almost
|
||||
self-explanatory graphical user interface to <tt class="docutils literal"><span class="pre">msr2data</span></tt> depicted below:</p>
|
||||
<img src="_images/msr2data-GUI.svg" /><ol class="arabic simple">
|
||||
<li>and 2. Choose one of the ways to specify your list of runs as described under <a class="reference internal" href="#msr2data-basic-usage"><em>basic usage</em></a>.</li>
|
||||
<p><a class="reference internal" href="musredit.html#musredit-sec"><span class="std std-ref">musredit</span></a>, designed especially for the manipulation of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr files and graphical front ends to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>, offer an almost
|
||||
self-explanatory graphical user interface to <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> depicted below:</p>
|
||||
<img alt="_images/msr2data-GUI.svg" src="_images/msr2data-GUI.svg" /><ol class="arabic simple">
|
||||
<li>and 2. Choose one of the ways to specify your list of runs as described under <a class="reference internal" href="#msr2data-basic-usage"><span class="std std-ref">basic usage</span></a>.</li>
|
||||
</ol>
|
||||
<ol class="arabic simple" start="3">
|
||||
<li>Give the file extension here, <em>e.g.</em> <tt class="docutils literal"><span class="pre">_zf</span></tt> for files like <tt class="docutils literal"><span class="pre">8472_zf.msr</span></tt>. If the files do not have an extension this
|
||||
field stays empty. <tt class="docutils literal"><span class="pre">musredit</span></tt> takes care of passing the “” to <tt class="docutils literal"><span class="pre">msr2data</span></tt> as mentioned above.</li>
|
||||
<li>Activates the <tt class="docutils literal"><span class="pre">fit-<template></span></tt> option if <tt class="docutils literal"><span class="pre"><template></span></tt> is entered. In case the option <tt class="docutils literal"><span class="pre">Chain</span> <span class="pre">Fit</span></tt> is <em>not</em> set the
|
||||
<li>Give the file extension here, <em>e.g.</em> <code class="docutils literal notranslate"><span class="pre">_zf</span></code> for files like <code class="docutils literal notranslate"><span class="pre">8472_zf.msr</span></code>. If the files do not have an extension this
|
||||
field stays empty. <code class="docutils literal notranslate"><span class="pre">musredit</span></code> takes care of passing the “” to <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> as mentioned above.</li>
|
||||
<li>Activates the <code class="docutils literal notranslate"><span class="pre">fit-<template></span></code> option if <code class="docutils literal notranslate"><span class="pre"><template></span></code> is entered. In case the option <code class="docutils literal notranslate"><span class="pre">Chain</span> <span class="pre">Fit</span></code> is <em>not</em> set the
|
||||
given template will be used for the input-file generation for all runs to be fitted — otherwise the output of the first
|
||||
fit serves as template for the second and so on. The template field stays empty if <em>no</em> fits should be performed!</li>
|
||||
<li>Activates the <tt class="docutils literal"><span class="pre">-o</span> <span class="pre"><outputFileName></span></tt> option if <tt class="docutils literal"><span class="pre"><outputFileName></span></tt> is entered. If nothing is entered the default output file <tt class="docutils literal"><span class="pre">out.db</span></tt> or <tt class="docutils literal"><span class="pre">out.dat</span></tt> is used.</li>
|
||||
<li>Activates the <code class="docutils literal notranslate"><span class="pre">-o</span> <span class="pre"><outputFileName></span></code> option if <code class="docutils literal notranslate"><span class="pre"><outputFileName></span></code> is entered. If nothing is entered the default output file <code class="docutils literal notranslate"><span class="pre">out.db</span></code> or <code class="docutils literal notranslate"><span class="pre">out.dat</span></code> is used.</li>
|
||||
</ol>
|
||||
<p>The options tags correspond essentially to the description in <a class="reference internal" href="#msr2data-opt-param"><em>optional parameters</em></a>.</p>
|
||||
<p>The options tags correspond essentially to the description in <a class="reference internal" href="#msr2data-opt-param"><span class="std std-ref">optional parameters</span></a>.</p>
|
||||
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|
||||
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|
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|
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|
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|
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«  <a href="mupp.html">mupp - μSR Parameter Plotter</a>
|
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|
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|
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|
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<h2 class="heading"><span>mupp - μSR Parameter Plotter</span></h2>
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
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<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">mupp - μSR Parameter Plotter</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#the-graphical-user-interface">The Graphical User Interface</a><ul>
|
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<li class="toctree-l3"><a class="reference internal" href="#define-variable-dialog">Define Variable Dialog</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#the-scripting-interface">The Scripting Interface</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#the-usage-summary">The Usage Summary</a></li>
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|
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<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
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«  <a href="musredit.html"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a>
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  ::  
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  ::  
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<a href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr Files</a>  »
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<div class="section" id="mupp-mgrsr-parameter-plotter">
|
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<span id="mupp"></span><span id="index-0"></span><h1>mupp - μSR Parameter Plotter<a class="headerlink" href="#mupp-mgrsr-parameter-plotter" title="Permalink to this headline">¶</a></h1>
|
||||
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> is a little helper program which allows to quickly plot a collection of msr-file parameters,
|
||||
as for instance generated by <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>. It can handle <tt class="docutils literal"><span class="pre">db</span></tt>- and <tt class="docutils literal"><span class="pre">dat</span></tt>-files.
|
||||
Also a collection of <tt class="docutils literal"><span class="pre">msr</span></tt>-files can be invoked. <tt class="docutils literal"><span class="pre">mupp</span></tt> is heavily inspired by μView (see
|
||||
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> is a little helper program which allows to quickly plot a collection of msr-file parameters,
|
||||
as for instance generated by <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>. It can handle <code class="docutils literal notranslate"><span class="pre">db</span></code>- and <code class="docutils literal notranslate"><span class="pre">dat</span></code>-files.
|
||||
Also a collection of <code class="docutils literal notranslate"><span class="pre">msr</span></code>-files can be invoked. <code class="docutils literal notranslate"><span class="pre">mupp</span></code> is heavily inspired by μView (see
|
||||
<a class="reference external" href="http://musr.org/muview/">here</a>).</p>
|
||||
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> can be operated from within as graphical user interface or via a command line scripting interface.
|
||||
The <tt class="docutils literal"><span class="pre">mupp</span></tt> GUI can be invoked either directly from the command line or from within <a class="reference internal" href="musredit.html#musredit-sec"><em>musredit</em></a>.</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> can be operated from within as graphical user interface or via a command line scripting interface.
|
||||
The <code class="docutils literal notranslate"><span class="pre">mupp</span></code> GUI can be invoked either directly from the command line or from within <a class="reference internal" href="musredit.html#musredit-sec"><span class="std std-ref">musredit</span></a>.</p>
|
||||
<p>Each collection bundles a number of runs, where a run is a single μSR measurement.
|
||||
A run is analyzed by a number of parameters (defined in the msr-files), and complemented by
|
||||
additional physical parameters as the temperature, magnetic field, implantation energy, etc.
|
||||
@ -62,56 +180,56 @@ Hence parameters can be seen as vectors and can be plot against each other.</p>
|
||||
<div class="section" id="the-graphical-user-interface">
|
||||
<span id="index-1"></span><h2>The Graphical User Interface<a class="headerlink" href="#the-graphical-user-interface" title="Permalink to this headline">¶</a></h2>
|
||||
<p>A typical setting could look like this</p>
|
||||
<img src="_images/mupp-gui-0.svg" /><ol class="arabic">
|
||||
<li><p class="first">shows the list of loaded collections. A collection is defined as <tt class="docutils literal"><span class="pre">db</span></tt>- or <tt class="docutils literal"><span class="pre">dat</span></tt>-file (typically the
|
||||
output from <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>). If you call the open-dialog and select a collection of
|
||||
<tt class="docutils literal"><span class="pre">msr</span></tt>-files, <tt class="docutils literal"><span class="pre">mupp</span></tt> will call <tt class="docutils literal"><span class="pre">msr2data</span></tt> and tries to generate a collection on-the-fly.</p>
|
||||
<img alt="_images/mupp-gui-0.svg" src="_images/mupp-gui-0.svg" /><ol class="arabic">
|
||||
<li><p class="first">shows the list of loaded collections. A collection is defined as <code class="docutils literal notranslate"><span class="pre">db</span></code>- or <code class="docutils literal notranslate"><span class="pre">dat</span></code>-file (typically the
|
||||
output from <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>). If you call the open-dialog and select a collection of
|
||||
<code class="docutils literal notranslate"><span class="pre">msr</span></code>-files, <code class="docutils literal notranslate"><span class="pre">mupp</span></code> will call <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> and tries to generate a collection on-the-fly.</p>
|
||||
</li>
|
||||
<li><p class="first">in this list, the data-tags of the currently selected collection is presented. The data-tags can be
|
||||
directly dragged over to the <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis list. Another way is to select the data-tag
|
||||
wished and click <tt class="docutils literal"><span class="pre">add</span> <span class="pre">X</span></tt> to add the selected data-tag to the <tt class="docutils literal"><span class="pre">x</span></tt>-axis list. Analogous it is done
|
||||
for the <tt class="docutils literal"><span class="pre">y</span></tt>-axis.</p>
|
||||
directly dragged over to the <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list. Another way is to select the data-tag
|
||||
wished and click <code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">X</span></code> to add the selected data-tag to the <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list. Analogous it is done
|
||||
for the <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">x</span></tt>-axis list. The labels are followed by <tt class="docutils literal"><span class="pre">(-X-)</span></tt> where the number <tt class="docutils literal"><span class="pre">X</span></tt> corresponds to the
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list. The labels are followed by <code class="docutils literal notranslate"><span class="pre">(-X-)</span></code> where the number <code class="docutils literal notranslate"><span class="pre">X</span></code> corresponds to the
|
||||
selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">y</span></tt>-axis list. The labels are followed by <tt class="docutils literal"><span class="pre">(-X-)</span></tt> where the number <tt class="docutils literal"><span class="pre">X</span></tt> corresponds to the
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list. The labels are followed by <code class="docutils literal notranslate"><span class="pre">(-X-)</span></code> where the number <code class="docutils literal notranslate"><span class="pre">X</span></code> corresponds to the
|
||||
selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">add</span> <span class="pre">X</span></tt> allows to add the currently selected data-tag to the <tt class="docutils literal"><span class="pre">x</span></tt>-axis list.</p>
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">X</span></code> allows to add the currently selected data-tag to the <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">add</span> <span class="pre">Y</span></tt> allows to add the currently selected data-tag to the <tt class="docutils literal"><span class="pre">y</span></tt>-axis list.</p>
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">Y</span></code> allows to add the currently selected data-tag to the <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">remove</span> <span class="pre">X</span></tt> will remove the selected <tt class="docutils literal"><span class="pre">x</span></tt>-axis tag.</p>
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">remove</span> <span class="pre">X</span></code> will remove the selected <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis tag.</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">remove</span> <span class="pre">Y</span></tt> will remove the selected <tt class="docutils literal"><span class="pre">y</span></tt>-axis tag.</p>
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">remove</span> <span class="pre">Y</span></code> will remove the selected <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis tag.</p>
|
||||
</li>
|
||||
<li><p class="first">Often one would like to compare trends of different settings. In the above example each collections
|
||||
holds an energy scans for a given temperature. Each collection is measured at a different temperature.
|
||||
Now, instead of adding <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis tags for each collection, you can do the following:
|
||||
you add <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis data-tags for the first collection. Afterwards you select all the other
|
||||
collections of interest and click on <tt class="docutils literal"><span class="pre">Add</span> <span class="pre">Ditto</span></tt>. <tt class="docutils literal"><span class="pre">mupp</span></tt> will then add the corresponding
|
||||
<tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis data-tags accordingly. This is less error prone and quicker!</p>
|
||||
Now, instead of adding <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis tags for each collection, you can do the following:
|
||||
you add <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis data-tags for the first collection. Afterwards you select all the other
|
||||
collections of interest and click on <code class="docutils literal notranslate"><span class="pre">Add</span> <span class="pre">Ditto</span></code>. <code class="docutils literal notranslate"><span class="pre">mupp</span></code> will then add the corresponding
|
||||
<code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis data-tags accordingly. This is less error prone and quicker!</p>
|
||||
</li>
|
||||
<li><p class="first">Clicking the <tt class="docutils literal"><span class="pre">Plot</span></tt> button will invoke <tt class="docutils literal"><span class="pre">mupp_plot</span></tt> (a <tt class="docutils literal"><span class="pre">ROOT</span></tt> based application) which will
|
||||
<li><p class="first">Clicking the <code class="docutils literal notranslate"><span class="pre">Plot</span></code> button will invoke <code class="docutils literal notranslate"><span class="pre">mupp_plot</span></code> (a <code class="docutils literal notranslate"><span class="pre">ROOT</span></code> based application) which will
|
||||
present the data, as shown here</p>
|
||||
<a class="reference internal image-reference" href="_images/mupp-plot-0.svg"><img height="600px" src="_images/mupp-plot-0.svg" /></a>
|
||||
<a class="reference internal image-reference" href="_images/mupp-plot-0.svg"><img alt="_images/mupp-plot-0.svg" height="600px" src="_images/mupp-plot-0.svg" /></a>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">Remove</span> <span class="pre">Collection</span></tt>: will remove the selected collection</p>
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">Remove</span> <span class="pre">Collection</span></code>: will remove the selected collection</p>
|
||||
</li>
|
||||
<li><p class="first"><tt class="docutils literal"><span class="pre">Refresh</span> <span class="pre">Collection</span></tt>: will reload the collection (<tt class="docutils literal"><span class="pre">db</span></tt>- or <tt class="docutils literal"><span class="pre">dat</span></tt>-file). This is often useful
|
||||
<li><p class="first"><code class="docutils literal notranslate"><span class="pre">Refresh</span> <span class="pre">Collection</span></code>: will reload the collection (<code class="docutils literal notranslate"><span class="pre">db</span></code>- or <code class="docutils literal notranslate"><span class="pre">dat</span></code>-file). This is often useful
|
||||
during beamtime where the collection is growing run-by-run.</p>
|
||||
</li>
|
||||
<li><p class="first">Command history window.</p>
|
||||
</li>
|
||||
<li><p class="first">This is the script command line. Currently it allows to perform the tasks without mouse gambling.
|
||||
In the future much more commands are planed. See the <tt class="docutils literal"><span class="pre">Help</span> <span class="pre">/</span> <span class="pre">Cmd's</span></tt> for the currently available
|
||||
In the future much more commands are planed. See the <code class="docutils literal notranslate"><span class="pre">Help</span> <span class="pre">/</span> <span class="pre">Cmd's</span></code> for the currently available
|
||||
commands.</p>
|
||||
</li>
|
||||
</ol>
|
||||
<div class="section" id="define-variable-dialog">
|
||||
<h3>Define Variable Dialog<a class="headerlink" href="#define-variable-dialog" title="Permalink to this headline">¶</a></h3>
|
||||
<img src="_images/mupp-add-var.svg" /><ol class="arabic simple">
|
||||
<img alt="_images/mupp-add-var.svg" src="_images/mupp-add-var.svg" /><ol class="arabic simple">
|
||||
<li>Variable text edit window.</li>
|
||||
<li>Collection link window.</li>
|
||||
<li>Shows the parameters of the selected collection.</li>
|
||||
@ -121,54 +239,54 @@ commands.</p>
|
||||
<p>A variable defined here is a mathematical expression defined by parameters of loaded collections.
|
||||
Since a parameter also has an associated error, also newly defined variables <strong>always</strong> need
|
||||
to be defined together with a corresponding error variable. If the name of a variable is defined
|
||||
as <tt class="docutils literal"><span class="pre">SigmaSC_10</span></tt> (see the above snapshot), the error variable need to be named as <tt class="docutils literal"><span class="pre">SigmaSC_10Err</span></tt>.</p>
|
||||
<p>Currently the following mathematical functions are defined: <tt class="docutils literal"><span class="pre">max</span></tt>, <tt class="docutils literal"><span class="pre">min</span></tt>, <tt class="docutils literal"><span class="pre">abs</span></tt>, <tt class="docutils literal"><span class="pre">sin</span></tt>, <tt class="docutils literal"><span class="pre">cos</span></tt>,
|
||||
<tt class="docutils literal"><span class="pre">tan</span></tt>, <tt class="docutils literal"><span class="pre">exp</span></tt>, <tt class="docutils literal"><span class="pre">log</span></tt>, <tt class="docutils literal"><span class="pre">ln</span></tt>, <tt class="docutils literal"><span class="pre">pow</span></tt>.</p>
|
||||
as <code class="docutils literal notranslate"><span class="pre">SigmaSC_10</span></code> (see the above snapshot), the error variable need to be named as <code class="docutils literal notranslate"><span class="pre">SigmaSC_10Err</span></code>.</p>
|
||||
<p>Currently the following mathematical functions are defined: <code class="docutils literal notranslate"><span class="pre">max</span></code>, <code class="docutils literal notranslate"><span class="pre">min</span></code>, <code class="docutils literal notranslate"><span class="pre">abs</span></code>, <code class="docutils literal notranslate"><span class="pre">sin</span></code>, <code class="docutils literal notranslate"><span class="pre">cos</span></code>,
|
||||
<code class="docutils literal notranslate"><span class="pre">tan</span></code>, <code class="docutils literal notranslate"><span class="pre">exp</span></code>, <code class="docutils literal notranslate"><span class="pre">log</span></code>, <code class="docutils literal notranslate"><span class="pre">ln</span></code>, <code class="docutils literal notranslate"><span class="pre">pow</span></code>.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-scripting-interface">
|
||||
<span id="index-2"></span><h2>The Scripting Interface<a class="headerlink" href="#the-scripting-interface" title="Permalink to this headline">¶</a></h2>
|
||||
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> can also be operated in a scripting like manner. The use cases are plot updates during run time,
|
||||
or web-based interaction which requests figures. A script is invoked by the command line option <tt class="docutils literal"><span class="pre">-s</span></tt> (see
|
||||
<a class="reference internal" href="#mupp-usage"><em>mupp command line summary</em></a>. Currently the following scripting commands are available:</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> can also be operated in a scripting like manner. The use cases are plot updates during run time,
|
||||
or web-based interaction which requests figures. A script is invoked by the command line option <code class="docutils literal notranslate"><span class="pre">-s</span></code> (see
|
||||
<a class="reference internal" href="#mupp-usage"><span class="std std-ref">mupp command line summary</span></a>. Currently the following scripting commands are available:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong>loadPath <dir></strong></dt>
|
||||
<dd>set the load path to <tt class="docutils literal"><span class="pre"><dir></span></tt>. Bash variables like $HOME are accepted. This is the path where to look for collection files (<tt class="docutils literal"><span class="pre">db</span></tt>- and <tt class="docutils literal"><span class="pre">dat</span></tt>-files).</dd>
|
||||
<dd>set the load path to <code class="docutils literal notranslate"><span class="pre"><dir></span></code>. Bash variables like $HOME are accepted. This is the path where to look for collection files (<code class="docutils literal notranslate"><span class="pre">db</span></code>- and <code class="docutils literal notranslate"><span class="pre">dat</span></code>-files).</dd>
|
||||
<dt><strong>load <coll></strong></dt>
|
||||
<dd>will load the collection <tt class="docutils literal"><span class="pre"><coll></span></tt>.</dd>
|
||||
<dd>will load the collection <code class="docutils literal notranslate"><span class="pre"><coll></span></code>.</dd>
|
||||
<dt><strong>selectAll</strong></dt>
|
||||
<dd>will select all loaded collections. This means every plot of variable x/y will be carried out to <em>ALL</em> collections.</dd>
|
||||
<dt><strong>select <nn></strong></dt>
|
||||
<dd>selects collection <tt class="docutils literal"><span class="pre"><nn></span></tt>, where <tt class="docutils literal"><span class="pre"><nn></span></tt> is either the <em>number</em> of the collections, or its <em>name</em>, <em>e.g.</em>
|
||||
<dd>selects collection <code class="docutils literal notranslate"><span class="pre"><nn></span></code>, where <code class="docutils literal notranslate"><span class="pre"><nn></span></code> is either the <em>number</em> of the collections, or its <em>name</em>, <em>e.g.</em>
|
||||
select YBCO-40nm-T5K-FC150mT-Escan.db.</dd>
|
||||
<dt><strong>x <label></strong></dt>
|
||||
<dd>add <tt class="docutils literal"><span class="pre"><label></span></tt> as a <em>x</em>-variable. Only <em>one</em> is allowed.</dd>
|
||||
<dd>add <code class="docutils literal notranslate"><span class="pre"><label></span></code> as a <em>x</em>-variable. Only <em>one</em> is allowed.</dd>
|
||||
<dt><strong>y <label(s)></strong></dt>
|
||||
<dd>add <tt class="docutils literal"><span class="pre"><label(s)></span></tt> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</dd>
|
||||
<dd>add <code class="docutils literal notranslate"><span class="pre"><label(s)></span></code> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</dd>
|
||||
<dt><strong>norm</strong></dt>
|
||||
<dd>this will normalize all the <em>y</em>-variables by their maximum.</dd>
|
||||
<dt><strong>savePath <dir></strong></dt>
|
||||
<dd>set the save path to <tt class="docutils literal"><span class="pre"><dir></span></tt>. The place where the macros, and/or the plot output will be saved.</dd>
|
||||
<dd>set the save path to <code class="docutils literal notranslate"><span class="pre"><dir></span></code>. The place where the macros, and/or the plot output will be saved.</dd>
|
||||
<dt><strong>plot <fln></strong></dt>
|
||||
<dd>where <tt class="docutils literal"><span class="pre"><fln></span></tt> is the file name with extension under which the plot should be saved.</dd>
|
||||
<dd>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name with extension under which the plot should be saved.</dd>
|
||||
<dt><strong>macro <fln></strong></dt>
|
||||
<dd>where <tt class="docutils literal"><span class="pre"><fln></span></tt> is the file name under which the root macro should be saved.</dd>
|
||||
<dd>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name under which the root macro should be saved.</dd>
|
||||
<dt><strong>var <var_name> = <expr></strong></dt>
|
||||
<dd><p class="first">defines a variable.
|
||||
<expr> is a mathematical expression where collection variables are addressed
|
||||
via the ‘$’, e.g. <tt class="docutils literal"><span class="pre">dataT</span></tt> is addressed by <tt class="docutils literal"><span class="pre">$dataT</span></tt>, etc. An example:</p>
|
||||
<p><tt class="docutils literal"><span class="pre">var</span> <span class="pre">invT</span> <span class="pre">=</span> <span class="pre">1000.0</span> <span class="pre">/</span> <span class="pre">$dataT</span></tt></p>
|
||||
via the ‘$’, e.g. <code class="docutils literal notranslate"><span class="pre">dataT</span></code> is addressed by <code class="docutils literal notranslate"><span class="pre">$dataT</span></code>, etc. An example:</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invT</span> <span class="pre">=</span> <span class="pre">1000.0</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
|
||||
<p>Each variable has to be accompanied by its error variable. An error variable
|
||||
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|
||||
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|
||||
For the above example the error variable is</p>
|
||||
<p class="last"><tt class="docutils literal"><span class="pre">var</span> <span class="pre">invTErr</span> <span class="pre">=</span> <span class="pre">$invT</span> <span class="pre">*</span> <span class="pre">$dataTErr</span> <span class="pre">/</span> <span class="pre">$dataT</span></tt></p>
|
||||
<p class="last"><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invTErr</span> <span class="pre">=</span> <span class="pre">$invT</span> <span class="pre">*</span> <span class="pre">$dataTErr</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
|
||||
</dd>
|
||||
<dt><strong>col <nn> : <var_name></strong></dt>
|
||||
<dd>links <var_name> to the collection <nn>, where <nn> is the number of the
|
||||
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|
||||
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|
||||
<p>An example script file <tt class="docutils literal"><span class="pre">sigmaSC-vs-temp.txt</span></tt> might look like this:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span># This is a comment
|
||||
<p>An example script file <code class="docutils literal notranslate"><span class="pre">sigmaSC-vs-temp.txt</span></code> might look like this:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># This is a comment
|
||||
# Script: sigmaSC-vs-temp.txt
|
||||
|
||||
loadPath ./
|
||||
@ -216,7 +334,7 @@ macro SigmaSCVsTemp.C
|
||||
</div>
|
||||
<div class="section" id="the-usage-summary">
|
||||
<span id="mupp-usage"></span><span id="index-3"></span><h2>The Usage Summary<a class="headerlink" href="#the-usage-summary" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>usage: mupp [OPTIONS] [[--path <fit-param-path>] <fit-param-file-names>]
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>usage: mupp [OPTIONS] [[--path <fit-param-path>] <fit-param-file-names>]
|
||||
|
||||
OPTIONS:
|
||||
-h, --help: this help
|
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@ -263,23 +381,73 @@ SCRIPT COMMANDS:
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«  <a href="musredit.html"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a>
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#introduction">Introduction</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#available-executable-configuration-files-and-their-basic-usage">Available Executable, Configuration Files and their Basic Usage</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#musredit-musrgui">musredit (musrgui)</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#musredit-startup-xml">musredit_startup.xml</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#musredit-features">musredit Features</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#id1">musrWiz</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#musrwiz-introduction">musrWiz-Introduction</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-theory">musrWiz - Theory</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-functions">musrWiz - Functions</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-maps">musrWiz - Maps</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-fit-parameters">musrWiz - Fit Parameters</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-fit-info">musrWiz - Fit Info</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#musrwiz-create">musrWiz - Create</a></li>
|
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<li class="toctree-l2"><a class="reference internal" href="#musrstep">musrStep</a></li>
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<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
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<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
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<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
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<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
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«  <a href="setup-dks.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s</a>
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  ::  
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<div class="section" id="musredit-the-gui-based-interface-to-musrfit">
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<span id="musredit-sec"></span><span id="index-0"></span><h1><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt><a class="headerlink" href="#musredit-the-gui-based-interface-to-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<span id="musredit-sec"></span><span id="index-0"></span><h1><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code><a class="headerlink" href="#musredit-the-gui-based-interface-to-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="introduction">
|
||||
<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2>
|
||||
<p><tt class="docutils literal"><span class="pre">musredit</span></tt> is an editor which also provide a graphical user interface to the programs contained in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> suite and are intended
|
||||
to help the user handle <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr files. It is implemented in <tt class="docutils literal"><span class="pre">C++</span></tt> and use the <a class="reference external" href="https://qt.io">Qt</a> framework. <tt class="docutils literal"><span class="pre">musredit</span></tt> is based on Qt 4.6, Qt 5.6 (or above), or Qt6.x.
|
||||
The Qt 5.6 and Qt 6.x version of <tt class="docutils literal"><span class="pre">musredit</span></tt> will be actively developed, whereas the Qt 4.x version will only get bug fixing and eventually will be dropped.
|
||||
On this documentation page only the features related to <tt class="docutils literal"><span class="pre">musrfit</span></tt> are described — the basic editor functions which should be self-explanatory are <em>not</em>.
|
||||
<tt class="docutils literal"><span class="pre">musrgui</span></tt> is an outdated early version of <tt class="docutils literal"><span class="pre">musredit</span></tt> and will not described anymore. If still in use, the user is urged to switch to <tt class="docutils literal"><span class="pre">musredit</span></tt>.</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">musredit</span></code> is an editor which also provide a graphical user interface to the programs contained in the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> suite and are intended
|
||||
to help the user handle <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr files. It is implemented in <code class="docutils literal notranslate"><span class="pre">C++</span></code> and use the <a class="reference external" href="https://qt.io">Qt</a> framework. <code class="docutils literal notranslate"><span class="pre">musredit</span></code> is based on Qt 4.6, Qt 5.6 (or above), or Qt6.x.
|
||||
The Qt 5.6 and Qt 6.x version of <code class="docutils literal notranslate"><span class="pre">musredit</span></code> will be actively developed, whereas the Qt 4.x version will only get bug fixing and eventually will be dropped.
|
||||
On this documentation page only the features related to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> are described — the basic editor functions which should be self-explanatory are <em>not</em>.
|
||||
<code class="docutils literal notranslate"><span class="pre">musrgui</span></code> is an outdated early version of <code class="docutils literal notranslate"><span class="pre">musredit</span></code> and will not described anymore. If still in use, the user is urged to switch to <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Before going on using <tt class="docutils literal"><span class="pre">musredit</span></tt> it is strongly recommended to read the <a class="reference internal" href="user-manual.html#user-manual"><em>manual of musrfit</em></a> first!</p>
|
||||
<p class="last">Before going on using <code class="docutils literal notranslate"><span class="pre">musredit</span></code> it is strongly recommended to read the <a class="reference internal" href="user-manual.html#user-manual"><span class="std std-ref">manual of musrfit</span></a> first!</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="available-executable-configuration-files-and-their-basic-usage">
|
||||
<h2>Available Executable, Configuration Files and their Basic Usage<a class="headerlink" href="#available-executable-configuration-files-and-their-basic-usage" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="section" id="musredit-musrgui">
|
||||
<h3>musredit (musrgui)<a class="headerlink" href="#musredit-musrgui" title="Permalink to this headline">¶</a></h3>
|
||||
<p><tt class="docutils literal"><span class="pre">musredit</span></tt> (<tt class="docutils literal"><span class="pre">musrgui</span></tt>) is the editor executable. If called from within a shell it accepts a few optional parameters:</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">musredit</span></code> (<code class="docutils literal notranslate"><span class="pre">musrgui</span></code>) is the editor executable. If called from within a shell it accepts a few optional parameters:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong><msr-files></strong></dt>
|
||||
<dd>File names of the msr files that should be opened in separate editor tabs on startup of <tt class="docutils literal"><span class="pre">musredit</span></tt>.</dd>
|
||||
<dd>File names of the msr files that should be opened in separate editor tabs on startup of <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</dd>
|
||||
<dt><strong>- -help</strong></dt>
|
||||
<dd>Displays a small help notice in the shell explaining the basic usage of the program.</dd>
|
||||
<dt><strong>- -version</strong></dt>
|
||||
<dd>Prints the version number of <tt class="docutils literal"><span class="pre">musredit</span></tt>.</dd>
|
||||
<dd>Prints the version number of <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</dd>
|
||||
</dl>
|
||||
<p>If called without any parameters an empty editor window opens.</p>
|
||||
</div>
|
||||
<div class="section" id="musredit-startup-xml">
|
||||
<span id="index-1"></span><h3>musredit_startup.xml<a class="headerlink" href="#musredit-startup-xml" title="Permalink to this headline">¶</a></h3>
|
||||
<p><tt class="docutils literal"><span class="pre">musredit_startup.xml</span></tt> is the configuration file located under <tt class="docutils literal"><span class="pre">$HOME\.musrfit\musredit</span></tt>. It is also possible to have another version
|
||||
<p><code class="docutils literal notranslate"><span class="pre">musredit_startup.xml</span></code> is the configuration file located under <code class="docutils literal notranslate"><span class="pre">$HOME\.musrfit\musredit</span></code>. It is also possible to have another version
|
||||
of this file in the working directory which then will be used!</p>
|
||||
<p>In this file the following <tt class="docutils literal"><span class="pre">XML</span></tt> tags are allowed to define settings and might proof useful for all users of <tt class="docutils literal"><span class="pre">musredit</span></tt>:</p>
|
||||
<p>In this file the following <code class="docutils literal notranslate"><span class="pre">XML</span></code> tags are allowed to define settings and might proof useful for all users of <code class="docutils literal notranslate"><span class="pre">musredit</span></code>:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong><general></general></strong></dt>
|
||||
<dd><p class="first">set the default paths to executable and files in this environment</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><exec_path>PATH_TO_EXEC</exec_path></strong></dt>
|
||||
<dd>set the path <tt class="docutils literal"><span class="pre">PATH_TO_EXEC</span></tt> where the executable <tt class="docutils literal"><span class="pre">musrfit</span></tt>, <tt class="docutils literal"><span class="pre">musrview</span></tt>, <tt class="docutils literal"><span class="pre">musrt0</span></tt>, etc. can be found (inside the <tt class="docutils literal"><span class="pre"><general></span></tt> environment)</dd>
|
||||
<dd>set the path <code class="docutils literal notranslate"><span class="pre">PATH_TO_EXEC</span></code> where the executable <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>, <code class="docutils literal notranslate"><span class="pre">musrview</span></code>, <code class="docutils literal notranslate"><span class="pre">musrt0</span></code>, etc. can be found (inside the <code class="docutils literal notranslate"><span class="pre"><general></span></code> environment)</dd>
|
||||
<dt><strong><default_save_path>SAVE_PATH</default_save_path></strong></dt>
|
||||
<dd>specify the path <tt class="docutils literal"><span class="pre">SAVE_PATH</span></tt> where <tt class="docutils literal"><span class="pre">musredit</span></tt> point by default when opening and saving msr files (inside the <tt class="docutils literal"><span class="pre"><general></span></tt> environment). Default is the current directory.</dd>
|
||||
<dd>specify the path <code class="docutils literal notranslate"><span class="pre">SAVE_PATH</span></code> where <code class="docutils literal notranslate"><span class="pre">musredit</span></code> point by default when opening and saving msr files (inside the <code class="docutils literal notranslate"><span class="pre"><general></span></code> environment). Default is the current directory.</dd>
|
||||
<dt><strong><msr_default_file_path>MSR_DEF_PATH</msr_default_file_path></strong></dt>
|
||||
<dd>set the path <tt class="docutils literal"><span class="pre">MSR_DEF_PATH</span></tt> where the default msr files provided by <tt class="docutils literal"><span class="pre">musredit</span></tt> are stored (inside the <tt class="docutils literal"><span class="pre"><general></span></tt> environment)</dd>
|
||||
<dd>set the path <code class="docutils literal notranslate"><span class="pre">MSR_DEF_PATH</span></code> where the default msr files provided by <code class="docutils literal notranslate"><span class="pre">musredit</span></code> are stored (inside the <code class="docutils literal notranslate"><span class="pre"><general></span></code> environment)</dd>
|
||||
<dt><strong><timeout>3600</timeout></strong></dt>
|
||||
<dd>timeout in seconds after which <a class="reference internal" href="user-manual.html#musrview"><em>musrview</em></a> canvas will automatically quit. A value of 0 or
|
||||
a negative number will keep the <tt class="docutils literal"><span class="pre">musrview</span></tt> canvas open without self-determination.</dd>
|
||||
<dd>timeout in seconds after which <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a> canvas will automatically quit. A value of 0 or
|
||||
a negative number will keep the <code class="docutils literal notranslate"><span class="pre">musrview</span></code> canvas open without self-determination.</dd>
|
||||
<dt><strong><keep_minuit2_output>y/n</keep_minuit2_output></strong></dt>
|
||||
<dd>flag indicating if the <tt class="docutils literal"><span class="pre">MINUIT2</span></tt> output shall be kept per msr-file (‘y’) or only for the current msr-file (‘n’).</dd>
|
||||
<dd>flag indicating if the <code class="docutils literal notranslate"><span class="pre">MINUIT2</span></code> output shall be kept per msr-file (‘y’) or only for the current msr-file (‘n’).</dd>
|
||||
<dt><strong><dump_ascii>y/n</dump_ascii></strong></dt>
|
||||
<dd>flag indicating if <tt class="docutils literal"><span class="pre">musrfit</span></tt> shall dump fit data into ascii format. See help of <a class="reference internal" href="user-manual.html#musrfit"><em>musrfit</em></a>.</dd>
|
||||
<dd>flag indicating if <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> shall dump fit data into ascii format. See help of <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a>.</dd>
|
||||
<dt><strong><dump_root>y/n</dump_root></strong></dt>
|
||||
<dd>flag indicating if <tt class="docutils literal"><span class="pre">musrfit</span></tt> shall dump fit data into root format. See help of <a class="reference internal" href="user-manual.html#musrfit"><em>musrfit</em></a>.</dd>
|
||||
<dd>flag indicating if <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> shall dump fit data into root format. See help of <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a>.</dd>
|
||||
<dt><strong><title_from_data_file>y/n</title_from_data_file></strong></dt>
|
||||
<dd>specify if <tt class="docutils literal"><span class="pre">musrfit</span></tt> should be called with the <tt class="docutils literal"><span class="pre">-t</span></tt> option by default (inside the <tt class="docutils literal"><span class="pre"><general></span></tt> environment)</dd>
|
||||
<dd>specify if <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> should be called with the <code class="docutils literal notranslate"><span class="pre">-t</span></code> option by default (inside the <code class="docutils literal notranslate"><span class="pre"><general></span></code> environment)</dd>
|
||||
<dt><strong><chisq_pre_run_block>y/n</chisq_pre_run_block></strong></dt>
|
||||
<dd>flag indicating if per-run chisq shall be written into the msr-output-file.</dd>
|
||||
<dt><strong><estimate_n0>y/n</estimate_n0></strong></dt>
|
||||
<dd>flag indicating if for a single histogram fit <span class="math">\(N_0\)</span> shall be estimated before the fit procedure starts.</dd>
|
||||
<dd>flag indicating if for a single histogram fit <span class="math notranslate nohighlight">\(N_0\)</span> shall be estimated before the fit procedure starts.</dd>
|
||||
<dt><strong><musrview_show_fourier>y/n</musrview_show_fourier></strong></dt>
|
||||
<dd>flag indicating if <tt class="docutils literal"><span class="pre">musrview</span></tt> will directly present the Fourier transform rather than the time domain data.</dd>
|
||||
<dd>flag indicating if <code class="docutils literal notranslate"><span class="pre">musrview</span></code> will directly present the Fourier transform rather than the time domain data.</dd>
|
||||
<dt><strong><musrview_show_avg>y/n</musrview_show_avg></strong></dt>
|
||||
<dd>flag indicating if <tt class="docutils literal"><span class="pre">musrview</span></tt> will directly present averaged data, typically used for Fourier power spectra.</dd>
|
||||
<dd>flag indicating if <code class="docutils literal notranslate"><span class="pre">musrview</span></code> will directly present averaged data, typically used for Fourier power spectra.</dd>
|
||||
<dt><strong><enable_musrt0>y/n</enable_musrt0></strong></dt>
|
||||
<dd>specify if <a class="reference internal" href="user-manual.html#musrt0"><em>musrt0</em></a> can be called from within <tt class="docutils literal"><span class="pre">musredit</span></tt> (inside the <tt class="docutils literal"><span class="pre"><general></span></tt> environment)</dd>
|
||||
<dd>specify if <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a> can be called from within <code class="docutils literal notranslate"><span class="pre">musredit</span></code> (inside the <code class="docutils literal notranslate"><span class="pre"><general></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
<dt><strong><font_settings></font_settings></strong></dt>
|
||||
<dd><p class="first">set the default font in this environment</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><font_name>FONT</font_name></strong></dt>
|
||||
<dd>specify the name of the font <tt class="docutils literal"><span class="pre">FONT</span></tt> to be used by default in <tt class="docutils literal"><span class="pre">musredit</span></tt> (inside the <tt class="docutils literal"><span class="pre"><font_settings></span></tt> environment)</dd>
|
||||
<dd>specify the name of the font <code class="docutils literal notranslate"><span class="pre">FONT</span></code> to be used by default in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> (inside the <code class="docutils literal notranslate"><span class="pre"><font_settings></span></code> environment)</dd>
|
||||
<dt><strong><font_size>N</font_size></strong></dt>
|
||||
<dd>specify the size <tt class="docutils literal"><span class="pre">N</span></tt> of the font to be used by default in <tt class="docutils literal"><span class="pre">musredit</span></tt> (inside the <tt class="docutils literal"><span class="pre"><font_settings></span></tt> environment)</dd>
|
||||
<dd>specify the size <code class="docutils literal notranslate"><span class="pre">N</span></code> of the font to be used by default in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> (inside the <code class="docutils literal notranslate"><span class="pre"><font_settings></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
<dt><strong><msr_file_defaults></msr_file_defaults></strong></dt>
|
||||
<dd><p class="first">put the default settings for newly created msr files in this environment</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><beamline>BL</beamline></strong></dt>
|
||||
<dd>set the name of the muon beamline <tt class="docutils literal"><span class="pre">BL</span></tt> here (inside a <tt class="docutils literal"><span class="pre"><msr_file_defaults></span></tt> environment)</dd>
|
||||
<dd>set the name of the muon beamline <code class="docutils literal notranslate"><span class="pre">BL</span></code> here (inside a <code class="docutils literal notranslate"><span class="pre"><msr_file_defaults></span></code> environment)</dd>
|
||||
<dt><strong><institute>INST</institute></strong></dt>
|
||||
<dd>set the name of the facility <tt class="docutils literal"><span class="pre">INST</span></tt> where the beamline <tt class="docutils literal"><span class="pre">BL</span></tt> is located. Valid settings are <tt class="docutils literal"><span class="pre">PSI</span></tt>, <tt class="docutils literal"><span class="pre">RAL</span></tt>, <tt class="docutils literal"><span class="pre">JPARC</span></tt>, and <tt class="docutils literal"><span class="pre">TRIUMF</span></tt> (inside a <tt class="docutils literal"><span class="pre"><msr_file_defaults></span></tt> environment)</dd>
|
||||
<dd>set the name of the facility <code class="docutils literal notranslate"><span class="pre">INST</span></code> where the beamline <code class="docutils literal notranslate"><span class="pre">BL</span></code> is located. Valid settings are <code class="docutils literal notranslate"><span class="pre">PSI</span></code>, <code class="docutils literal notranslate"><span class="pre">RAL</span></code>, <code class="docutils literal notranslate"><span class="pre">JPARC</span></code>, and <code class="docutils literal notranslate"><span class="pre">TRIUMF</span></code> (inside a <code class="docutils literal notranslate"><span class="pre"><msr_file_defaults></span></code> environment)</dd>
|
||||
<dt><strong><file_format>FF</file_format></strong></dt>
|
||||
<dd>specify the default data file format <tt class="docutils literal"><span class="pre">FF</span></tt> here. Valid formats are <tt class="docutils literal"><span class="pre">NEXUS</span></tt>, <tt class="docutils literal"><span class="pre">MUSR-ROOT</span></tt>, <tt class="docutils literal"><span class="pre">ROOT-NPP</span></tt>, <tt class="docutils literal"><span class="pre">ROOT-PPC</span></tt>, <tt class="docutils literal"><span class="pre">PSI-BIN</span></tt>, <tt class="docutils literal"><span class="pre">PSI-MDU</span></tt>, <tt class="docutils literal"><span class="pre">MDU-ASCII</span></tt>, <tt class="docutils literal"><span class="pre">WKM</span></tt>, <tt class="docutils literal"><span class="pre">MUD</span></tt>, <tt class="docutils literal"><span class="pre">ASCII</span></tt>, and <tt class="docutils literal"><span class="pre">DB</span></tt> (inside a <tt class="docutils literal"><span class="pre"><msr_file_defaults></span></tt> environment)</dd>
|
||||
<dd>specify the default data file format <code class="docutils literal notranslate"><span class="pre">FF</span></code> here. Valid formats are <code class="docutils literal notranslate"><span class="pre">NEXUS</span></code>, <code class="docutils literal notranslate"><span class="pre">MUSR-ROOT</span></code>, <code class="docutils literal notranslate"><span class="pre">ROOT-NPP</span></code>, <code class="docutils literal notranslate"><span class="pre">ROOT-PPC</span></code>, <code class="docutils literal notranslate"><span class="pre">PSI-BIN</span></code>, <code class="docutils literal notranslate"><span class="pre">PSI-MDU</span></code>, <code class="docutils literal notranslate"><span class="pre">MDU-ASCII</span></code>, <code class="docutils literal notranslate"><span class="pre">WKM</span></code>, <code class="docutils literal notranslate"><span class="pre">MUD</span></code>, <code class="docutils literal notranslate"><span class="pre">ASCII</span></code>, and <code class="docutils literal notranslate"><span class="pre">DB</span></code> (inside a <code class="docutils literal notranslate"><span class="pre"><msr_file_defaults></span></code> environment)</dd>
|
||||
<dt><strong><lifetime_correction>y/n</lifetime_correction></strong></dt>
|
||||
<dd>choose if by default the <tt class="docutils literal"><span class="pre">lifetimecorrection</span></tt> option should be set (inside a <tt class="docutils literal"><span class="pre"><msr_file_defaults></span></tt> environment)</dd>
|
||||
<dd>choose if by default the <code class="docutils literal notranslate"><span class="pre">lifetimecorrection</span></code> option should be set (inside a <code class="docutils literal notranslate"><span class="pre"><msr_file_defaults></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
<dt><strong><msr2data_defaults></msr2data_defaults></strong></dt>
|
||||
<dd><p class="first">define the default options for calling <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a> in this environment; the options set here are ticked by default in the graphical interface of <tt class="docutils literal"><span class="pre">musredit</span></tt>.</p>
|
||||
<dd><p class="first">define the default options for calling <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a> in this environment; the options set here are ticked by default in the graphical interface of <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><chain_fit>y/n</chain_fit></strong></dt>
|
||||
<dd>(un)set the chain fit (!) option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the chain fit (!) option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><write_data_header>y/n</write_data_header></strong></dt>
|
||||
<dd>(un)set the noheader option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the noheader option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><ignore_data_header_info>y/n</ignore_data_header_info></strong></dt>
|
||||
<dd>(un)set the nosummary option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the nosummary option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><keep_minuit2_output>y/n</keep_minuit2_output></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">-k</span></tt> option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">-k</span></code> option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><write_column_data>y/n</write_column_data></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">data</span></tt> option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">data</span></code> option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><create_msr_file_only>y/n</create_msr_file_only></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">msr</span></tt> option in case a template run is specified (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">msr</span></code> option in case a template run is specified (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><fit_only>y/n</fit_only></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">fit</span></tt> option in case no template run is specified (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">fit</span></code> option in case no template run is specified (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><global>y/n</global></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">global</span></tt> option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">global</span></code> option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><global_plus>y/n</global_plus></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">global+</span></tt> option (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">global+</span></code> option (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><recreate_data_file>y/n</recreate_data_file></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">musredit</span></tt> option for recreating the output file (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">musredit</span></code> option for recreating the output file (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
<dt><strong><open_file_after_fitting>y/n</open_file_after_fitting></strong></dt>
|
||||
<dd>(un)set the <tt class="docutils literal"><span class="pre">musredit</span></tt> option for opening msr files after fitting (inside a <tt class="docutils literal"><span class="pre"><msr2data_defaults></span></tt> environment)</dd>
|
||||
<dd>(un)set the <code class="docutils literal notranslate"><span class="pre">musredit</span></code> option for opening msr files after fitting (inside a <code class="docutils literal notranslate"><span class="pre"><msr2data_defaults></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<p>Additionally, there are some settings defined in this XML file which should be only changed by experienced users who like to add new features to <tt class="docutils literal"><span class="pre">musredit</span></tt>:</p>
|
||||
<p>Additionally, there are some settings defined in this XML file which should be only changed by experienced users who like to add new features to <code class="docutils literal notranslate"><span class="pre">musredit</span></code>:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong><help_section></help_section></strong></dt>
|
||||
<dd><p class="first">define various help messages in this environment</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><musr_web_X>LINK</musr_web_X></strong></dt>
|
||||
<dd>define the <tt class="docutils literal"><span class="pre">LINK</span></tt> to the help page <tt class="docutils literal"><span class="pre">musr_web_X</span></tt>, where <tt class="docutils literal"><span class="pre">X</span></tt> is <tt class="docutils literal"><span class="pre">main</span></tt>, <tt class="docutils literal"><span class="pre">title</span></tt>, <tt class="docutils literal"><span class="pre">parameters</span></tt>, <tt class="docutils literal"><span class="pre">theory</span></tt>, <tt class="docutils literal"><span class="pre">functions</span></tt>, <tt class="docutils literal"><span class="pre">run</span></tt>,
|
||||
<tt class="docutils literal"><span class="pre">command</span></tt>, <tt class="docutils literal"><span class="pre">fourier</span></tt>, <tt class="docutils literal"><span class="pre">plot</span></tt>, <tt class="docutils literal"><span class="pre">statistics</span></tt>, <tt class="docutils literal"><span class="pre">msr2data</span></tt>, or <tt class="docutils literal"><span class="pre">musrFT</span></tt> (inside a <tt class="docutils literal"><span class="pre"><help_section></span></tt> environment)</dd>
|
||||
<dd>define the <code class="docutils literal notranslate"><span class="pre">LINK</span></code> to the help page <code class="docutils literal notranslate"><span class="pre">musr_web_X</span></code>, where <code class="docutils literal notranslate"><span class="pre">X</span></code> is <code class="docutils literal notranslate"><span class="pre">main</span></code>, <code class="docutils literal notranslate"><span class="pre">title</span></code>, <code class="docutils literal notranslate"><span class="pre">parameters</span></code>, <code class="docutils literal notranslate"><span class="pre">theory</span></code>, <code class="docutils literal notranslate"><span class="pre">functions</span></code>, <code class="docutils literal notranslate"><span class="pre">run</span></code>,
|
||||
<code class="docutils literal notranslate"><span class="pre">command</span></code>, <code class="docutils literal notranslate"><span class="pre">fourier</span></code>, <code class="docutils literal notranslate"><span class="pre">plot</span></code>, <code class="docutils literal notranslate"><span class="pre">statistics</span></code>, <code class="docutils literal notranslate"><span class="pre">msr2data</span></code>, or <code class="docutils literal notranslate"><span class="pre">musrFT</span></code> (inside a <code class="docutils literal notranslate"><span class="pre"><help_section></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
<dt><strong><func_pixmap_path>PIX_PATH</func_pixmap_path></strong></dt>
|
||||
<dd>set the path <tt class="docutils literal"><span class="pre">PIX_PATH</span></tt> to LaTeX pixmaps visualizing the various supported theory functions</dd>
|
||||
<dd>set the path <code class="docutils literal notranslate"><span class="pre">PIX_PATH</span></code> to LaTeX pixmaps visualizing the various supported theory functions</dd>
|
||||
<dt><strong><theory_functions></theory_functions></strong></dt>
|
||||
<dd><p class="first">define the functions for a msr file’s <a class="reference internal" href="user-manual.html#msr-theory-block"><em>THEORY block</em></a> according to the correct syntax in this environment</p>
|
||||
<dd><p class="first">define the functions for a msr file’s <a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">THEORY block</span></a> according to the correct syntax in this environment</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><func></func></strong></dt>
|
||||
<dd><p class="first">specify a function here (inside a <tt class="docutils literal"><span class="pre"><theory_functions></span></tt> environment)</p>
|
||||
<dd><p class="first">specify a function here (inside a <code class="docutils literal notranslate"><span class="pre"><theory_functions></span></code> environment)</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><name>NAME</name></strong></dt>
|
||||
<dd>the <tt class="docutils literal"><span class="pre">NAME</span></tt> of the function in the msr file (inside a <tt class="docutils literal"><span class="pre"><func></span></tt> environment)</dd>
|
||||
<dd>the <code class="docutils literal notranslate"><span class="pre">NAME</span></code> of the function in the msr file (inside a <code class="docutils literal notranslate"><span class="pre"><func></span></code> environment)</dd>
|
||||
<dt><strong><comment>COMMENT</comment></strong></dt>
|
||||
<dd>description of the used parameters (inside a <tt class="docutils literal"><span class="pre"><func></span></tt> environment)</dd>
|
||||
<dd>description of the used parameters (inside a <code class="docutils literal notranslate"><span class="pre"><func></span></code> environment)</dd>
|
||||
<dt><strong><label>LABEL</label></strong></dt>
|
||||
<dd><tt class="docutils literal"><span class="pre">LABEL</span></tt> of the function in the <tt class="docutils literal"><span class="pre">musredit</span></tt> menu (inside a <tt class="docutils literal"><span class="pre"><func></span></tt> environment)</dd>
|
||||
<dd><code class="docutils literal notranslate"><span class="pre">LABEL</span></code> of the function in the <code class="docutils literal notranslate"><span class="pre">musredit</span></code> menu (inside a <code class="docutils literal notranslate"><span class="pre"><func></span></code> environment)</dd>
|
||||
<dt><strong><pixmap>PIXMAP</pixmap></strong></dt>
|
||||
<dd>LaTeX picture used to describe the function and stored in the <tt class="docutils literal"><span class="pre">PIX_PATH</span></tt> (inside a <tt class="docutils literal"><span class="pre"><func></span></tt> environment)</dd>
|
||||
<dd>LaTeX picture used to describe the function and stored in the <code class="docutils literal notranslate"><span class="pre">PIX_PATH</span></code> (inside a <code class="docutils literal notranslate"><span class="pre"><func></span></code> environment)</dd>
|
||||
<dt><strong><params>N</params></strong></dt>
|
||||
<dd>number of parameters <tt class="docutils literal"><span class="pre">N</span></tt> used by the function (inside a <tt class="docutils literal"><span class="pre"><func></span></tt> environment)</dd>
|
||||
<dd>number of parameters <code class="docutils literal notranslate"><span class="pre">N</span></code> used by the function (inside a <code class="docutils literal notranslate"><span class="pre"><func></span></code> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<p>An example of the <tt class="docutils literal"><span class="pre">musredit_startup.xml</span></tt> looks like:</p>
|
||||
<div class="highlight-xml"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||||
<p>An example of the <code class="docutils literal notranslate"><span class="pre">musredit_startup.xml</span></code> looks like:</p>
|
||||
<div class="highlight-xml notranslate"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||||
<span class="nt"><musredit_startup</span> <span class="na">xmlns=</span><span class="s">"http://lmu.web.psi.ch/musrfit/user/MUSR/MusrGui.html"</span><span class="nt">></span>
|
||||
<span class="nt"><comment></span>
|
||||
This is handling default setting parameters for the musredit.
|
||||
@ -282,105 +412,105 @@ a negative number will keep the <tt class="docutils literal"><span class="pre">m
|
||||
</div>
|
||||
<div class="section" id="musredit-features">
|
||||
<span id="index-2"></span><h2>musredit Features<a class="headerlink" href="#musredit-features" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The features of <tt class="docutils literal"><span class="pre">musrfit</span></tt> which can be accessed by the graphical front ends <tt class="docutils literal"><span class="pre">musredit</span></tt> will be described in the following. All functions
|
||||
<p>The features of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> which can be accessed by the graphical front ends <code class="docutils literal notranslate"><span class="pre">musredit</span></code> will be described in the following. All functions
|
||||
can either be called by choosing them from the <em>MusrFit menu</em>, by clicking the respective button in the <em>MusrFit bar</em>, or by using a <em>keyboard shortcut</em>.</p>
|
||||
<p><strong>musrWiz</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrWiz.svg" /><p><tt class="docutils literal"><span class="pre">musrWiz</span></tt> is a helper programs which allows to create a msr-file from scratch without too much a priori knowledge. For details see <a class="reference internal" href="#musrwiz"><em>musrWiz</em></a>.</p>
|
||||
<div><img alt="_images/musrWiz.svg" src="_images/musrWiz.svg" /><p><code class="docutils literal notranslate"><span class="pre">musrWiz</span></code> is a helper programs which allows to create a msr-file from scratch without too much a priori knowledge. For details see <a class="reference internal" href="#musrwiz"><span class="std std-ref">musrWiz</span></a>.</p>
|
||||
</div></blockquote>
|
||||
<p id="musrwiz"><span id="index-3"></span><strong>Calculate Chisq</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrchisq.svg" /><p>Calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> with the option <tt class="docutils literal"><span class="pre">-c</span></tt>, <em>i.e.</em> calculates the <span class="math">\(\chi^2\)</span> or log max-likelihood for the active msr file tab. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+C</span></tt>.
|
||||
<div><img alt="_images/musrchisq.svg" src="_images/musrchisq.svg" /><p>Calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> with the option <code class="docutils literal notranslate"><span class="pre">-c</span></code>, <em>i.e.</em> calculates the <span class="math notranslate nohighlight">\(\chi^2\)</span> or log max-likelihood for the active msr file tab. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+C</span></code>.
|
||||
The equivalent call on the command line would be</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrfit -c <msr-file>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrfit -c <msr-file>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div></blockquote>
|
||||
<p><strong>Fit</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrfit.svg" /><p>Calls <tt class="docutils literal"><span class="pre">musrfit</span></tt> for fitting of the active msr file in the currently active tab. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+F</span></tt>.
|
||||
<div><img alt="_images/musrfit.svg" src="_images/musrfit.svg" /><p>Calls <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> for fitting of the active msr file in the currently active tab. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+F</span></code>.
|
||||
The equivalent call on the command line could look like</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrfit <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrfit <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The optional parameters may be chosen under <a class="reference internal" href="#musredit-prefs"><em>Preferences</em></a>. For further information refer to the manual of <a class="reference internal" href="user-manual.html#user-manual"><em>musrfit</em></a>.</p>
|
||||
<p>The optional parameters may be chosen under <a class="reference internal" href="#musredit-prefs"><span class="std std-ref">Preferences</span></a>. For further information refer to the manual of <a class="reference internal" href="user-manual.html#user-manual"><span class="std std-ref">musrfit</span></a>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>Swap Msr <-> Mlog</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrswap.svg" /><p>Swap the msr and mlog files. <em>E.g.</em>, for a file called <tt class="docutils literal"><span class="pre">8472_zf.msr</span></tt>, this is copied to <tt class="docutils literal"><span class="pre">8472_zf.mlog</span></tt> and vice versa. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+S</span></tt>.</p>
|
||||
<div><img alt="_images/musrswap.svg" src="_images/musrswap.svg" /><p>Swap the msr and mlog files. <em>E.g.</em>, for a file called <code class="docutils literal notranslate"><span class="pre">8472_zf.msr</span></code>, this is copied to <code class="docutils literal notranslate"><span class="pre">8472_zf.mlog</span></code> and vice versa. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+S</span></code>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>Set Steps</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrStep.svg" /><p><tt class="docutils literal"><span class="pre">musrStep</span></tt> allows to adjust the step size, <em>i.e.</em> the initial steps for the fitter. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+P</span></tt>.</p>
|
||||
<div><img alt="_images/musrStep.svg" src="_images/musrStep.svg" /><p><code class="docutils literal notranslate"><span class="pre">musrStep</span></code> allows to adjust the step size, <em>i.e.</em> the initial steps for the fitter. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+P</span></code>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>Msr2Data</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/msr2data.svg" /><p>Opens a graphical interface to the <tt class="docutils literal"><span class="pre">msr2data</span></tt> program described in detail in its <a class="reference internal" href="msr2data.html#msr2data"><em>own manual</em></a>. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+2</span></tt>.</p>
|
||||
<div><img alt="_images/msr2data.svg" src="_images/msr2data.svg" /><p>Opens a graphical interface to the <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> program described in detail in its <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">own manual</span></a>. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+2</span></code>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>mupp</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/mupp.svg" /><p>Application which allows to plot <tt class="docutils literal"><span class="pre">*.db</span></tt> and <tt class="docutils literal"><span class="pre">*.dat</span></tt> parameter files. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+U</span></tt>.
|
||||
For a detailed description see the <a class="reference internal" href="mupp.html#mupp"><em>mupp docu</em></a>.</p>
|
||||
<div><img alt="_images/mupp.svg" src="_images/mupp.svg" /><p>Application which allows to plot <code class="docutils literal notranslate"><span class="pre">*.db</span></code> and <code class="docutils literal notranslate"><span class="pre">*.dat</span></code> parameter files. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+U</span></code>.
|
||||
For a detailed description see the <a class="reference internal" href="mupp.html#mupp"><span class="std std-ref">mupp docu</span></a>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>View</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrview.svg" /><p>Calls <tt class="docutils literal"><span class="pre">musrview</span></tt> from the active tab of <tt class="docutils literal"><span class="pre">musredit</span></tt>. For more details see the <a class="reference internal" href="user-manual.html#musrview"><em>musrview</em></a> docu. Shortcut-key: <tt class="docutils literal"><span class="pre">Alt+V</span></tt>.
|
||||
<div><img alt="_images/musrview.svg" src="_images/musrview.svg" /><p>Calls <code class="docutils literal notranslate"><span class="pre">musrview</span></code> from the active tab of <code class="docutils literal notranslate"><span class="pre">musredit</span></code>. For more details see the <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a> docu. Shortcut-key: <code class="docutils literal notranslate"><span class="pre">Alt+V</span></code>.
|
||||
The equivalent call on the command line could look like</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrview <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrview <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div></blockquote>
|
||||
<p><strong>T0</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrt0-icon.svg" /><p>Calls <tt class="docutils literal"><span class="pre">musrt0</span></tt> which allows to set the <tt class="docutils literal"><span class="pre">T0</span></tt> values for all the runs. For more details see the <a class="reference internal" href="user-manual.html#musrt0"><em>musrt0</em></a> docu.
|
||||
<div><img alt="_images/musrt0-icon.svg" src="_images/musrt0-icon.svg" /><p>Calls <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> which allows to set the <code class="docutils literal notranslate"><span class="pre">T0</span></code> values for all the runs. For more details see the <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a> docu.
|
||||
The equivalent call on the command line could look like</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrt0 <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrt0 <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div></blockquote>
|
||||
<p><strong>Raw Fourier</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrFT.svg" /><p>Calls <tt class="docutils literal"><span class="pre">musrFT</span></tt> which allows to perform a Fourier transform of the raw data. For more details see the <a class="reference internal" href="user-manual.html#musrft"><em>musrFT</em></a> docu.
|
||||
<div><img alt="_images/musrFT.svg" src="_images/musrFT.svg" /><p>Calls <code class="docutils literal notranslate"><span class="pre">musrFT</span></code> which allows to perform a Fourier transform of the raw data. For more details see the <a class="reference internal" href="user-manual.html#musrft"><span class="std std-ref">musrFT</span></a> docu.
|
||||
The equivalent call on the command line could look like</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrFT <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrFT <msr-file> <span class="o">[</span>optional parameters<span class="o">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div></blockquote>
|
||||
<p id="musredit-prefs"><strong>Preferences</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrprefs.svg" /><p>Opens a window in which the optional parameters that should be passed to musrfit can be chosen.
|
||||
For further information refer to the manual of <a class="reference internal" href="user-manual.html#musrfit"><em>musrfit</em></a>.</p>
|
||||
<div><img alt="_images/musrprefs.svg" src="_images/musrprefs.svg" /><p>Opens a window in which the optional parameters that should be passed to musrfit can be chosen.
|
||||
For further information refer to the manual of <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a>.</p>
|
||||
</div></blockquote>
|
||||
<p><strong>Dump Header</strong></p>
|
||||
<blockquote>
|
||||
<div><img src="_images/musrdump.svg" /><p>Opens a file dialog which allows to select a μSR data file. When this file can be read, the run header info is dumped into a dialog window.
|
||||
Essentially this calls <tt class="docutils literal"><span class="pre">dump_header</span></tt> internally.</p>
|
||||
<div><img alt="_images/musrdump.svg" src="_images/musrdump.svg" /><p>Opens a file dialog which allows to select a μSR data file. When this file can be read, the run header info is dumped into a dialog window.
|
||||
Essentially this calls <code class="docutils literal notranslate"><span class="pre">dump_header</span></code> internally.</p>
|
||||
</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="id1">
|
||||
<h2>musrWiz<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
|
||||
<p><tt class="docutils literal"><span class="pre">musrWiz</span></tt> is a helper program which allows to easily create the necessary msr-file needed as an input for <tt class="docutils literal"><span class="pre">musrfit</span></tt>.
|
||||
<tt class="docutils literal"><span class="pre">musrWiz</span></tt> is still in it’s early stage; not all options are already implemented and here and there you will likely find some bugs.
|
||||
From <tt class="docutils literal"><span class="pre">musredit</span></tt> it can be accessed via the MusrFit menu or the wand</p>
|
||||
<img src="_images/musredit-musrWiz.svg" /><p>The <tt class="docutils literal"><span class="pre">musrWiz</span></tt> GUI is organized in a couple of different dialogues which some information needs to be provided by the user.
|
||||
<p><code class="docutils literal notranslate"><span class="pre">musrWiz</span></code> is a helper program which allows to easily create the necessary msr-file needed as an input for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>.
|
||||
<code class="docutils literal notranslate"><span class="pre">musrWiz</span></code> is still in it’s early stage; not all options are already implemented and here and there you will likely find some bugs.
|
||||
From <code class="docutils literal notranslate"><span class="pre">musredit</span></code> it can be accessed via the MusrFit menu or the wand</p>
|
||||
<img alt="_images/musredit-musrWiz.svg" src="_images/musredit-musrWiz.svg" /><p>The <code class="docutils literal notranslate"><span class="pre">musrWiz</span></code> GUI is organized in a couple of different dialogues which some information needs to be provided by the user.
|
||||
In the following these different dialogues will be discussed briefly.</p>
|
||||
<div class="section" id="musrwiz-introduction">
|
||||
<span id="index-4"></span><h3>musrWiz-Introduction<a class="headerlink" href="#musrwiz-introduction" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The introduction dialogue</p>
|
||||
<img src="_images/musrWiz-Intro.svg" /><ol class="arabic simple">
|
||||
<img alt="_images/musrWiz-Intro.svg" src="_images/musrWiz-Intro.svg" /><ol class="arabic simple">
|
||||
<li>an explicit msr-file name can be provided here. More often the msr-file name is generated out of the run number.</li>
|
||||
<li>year of the run data.</li>
|
||||
<li>run number. If no explicit msr-file is provided, the run number together with fit type and type of measurement will be used to generate the msr-file name.</li>
|
||||
<li>from the pull down menu the institute (for which a necessary <tt class="docutils literal"><span class="pre">xml</span></tt>-file is provided) has to be choosen.</li>
|
||||
<li>from the pull down menu the institute (for which a necessary <code class="docutils literal notranslate"><span class="pre">xml</span></code>-file is provided) has to be choosen.</li>
|
||||
<li>from the pull down menu the the instrument can be chosen.</li>
|
||||
<li>the fit type has to be chosen. Possible fit types are: <tt class="docutils literal"><span class="pre">Single</span> <span class="pre">Histo</span></tt> / <tt class="docutils literal"><span class="pre">Single</span> <span class="pre">Histo</span> <span class="pre">RRF</span></tt> / <tt class="docutils literal"><span class="pre">Asymmetry</span></tt> / <tt class="docutils literal"><span class="pre">Asymmetry</span> <span class="pre">RRF</span></tt> / <tt class="docutils literal"><span class="pre">Mu</span> <span class="pre">Minus</span></tt> / <tt class="docutils literal"><span class="pre">None</span> <span class="pre">muSR</span></tt></li>
|
||||
<li>type of measurement is essentially needed for the grouping of the detectors. Possible are: <tt class="docutils literal"><span class="pre">ZF</span></tt> for zero field measurements / <tt class="docutils literal"><span class="pre">TF</span></tt> for transverse field measurements / <tt class="docutils literal"><span class="pre">LF</span></tt> for longitudinal field measurements.
|
||||
<li>the fit type has to be chosen. Possible fit types are: <code class="docutils literal notranslate"><span class="pre">Single</span> <span class="pre">Histo</span></code> / <code class="docutils literal notranslate"><span class="pre">Single</span> <span class="pre">Histo</span> <span class="pre">RRF</span></code> / <code class="docutils literal notranslate"><span class="pre">Asymmetry</span></code> / <code class="docutils literal notranslate"><span class="pre">Asymmetry</span> <span class="pre">RRF</span></code> / <code class="docutils literal notranslate"><span class="pre">Mu</span> <span class="pre">Minus</span></code> / <code class="docutils literal notranslate"><span class="pre">None</span> <span class="pre">muSR</span></code></li>
|
||||
<li>type of measurement is essentially needed for the grouping of the detectors. Possible are: <code class="docutils literal notranslate"><span class="pre">ZF</span></code> for zero field measurements / <code class="docutils literal notranslate"><span class="pre">TF</span></code> for transverse field measurements / <code class="docutils literal notranslate"><span class="pre">LF</span></code> for longitudinal field measurements.
|
||||
Depending on the choice and instrument some additional question might be asked, <em>e.g.</em> which magnet has been used.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">T0</span></tt>‘s: this last menu defines from where to get the t0’s. The options are: <tt class="docutils literal"><span class="pre">from</span> <span class="pre">data</span> <span class="pre">file</span></tt>, <em>i.e.</em> the t0 are assumed to be correctly set
|
||||
in the provided data file <tt class="docutils literal"><span class="pre">call</span> <span class="pre">musrT0</span></tt>, <em>i.e.</em> after the msr-file is generated, <tt class="docutils literal"><span class="pre">musrt0</span></tt> will be called which allows the user to find the
|
||||
proper t0 from the prompt peak <tt class="docutils literal"><span class="pre">enter</span> <span class="pre">here</span></tt> will provide a pop-up menu where the t0 parameter can be given explicitly.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">T0</span></code>’s: this last menu defines from where to get the t0’s. The options are: <code class="docutils literal notranslate"><span class="pre">from</span> <span class="pre">data</span> <span class="pre">file</span></code>, <em>i.e.</em> the t0 are assumed to be correctly set
|
||||
in the provided data file <code class="docutils literal notranslate"><span class="pre">call</span> <span class="pre">musrT0</span></code>, <em>i.e.</em> after the msr-file is generated, <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> will be called which allows the user to find the
|
||||
proper t0 from the prompt peak <code class="docutils literal notranslate"><span class="pre">enter</span> <span class="pre">here</span></code> will provide a pop-up menu where the t0 parameter can be given explicitly.</li>
|
||||
</ol>
|
||||
<p>If all this information have been provided <tt class="docutils literal"><span class="pre">Next></span></tt> will lead you the the theory dialogue.</p>
|
||||
<p>If all this information have been provided <code class="docutils literal notranslate"><span class="pre">Next></span></code> will lead you the the theory dialogue.</p>
|
||||
</div>
|
||||
<div class="section" id="musrwiz-theory">
|
||||
<span id="index-5"></span><h3>musrWiz - Theory<a class="headerlink" href="#musrwiz-theory" title="Permalink to this headline">¶</a></h3>
|
||||
@ -390,59 +520,59 @@ proper t0 from the prompt peak <tt class="docutils literal"><span class="pre">en
|
||||
within the template almost everything is already pre-defined. The disadvantage is that you are not free in setting
|
||||
up your theory function as you would like to have.</li>
|
||||
<li>freely write your theory function. The advantage here is that you can customize your theory function at your needs.
|
||||
This will come at the cost that you also will need to define <tt class="docutils literal"><span class="pre">maps</span></tt>, <tt class="docutils literal"><span class="pre">functions</span></tt>, etc. yourself. The good thing
|
||||
This will come at the cost that you also will need to define <code class="docutils literal notranslate"><span class="pre">maps</span></code>, <code class="docutils literal notranslate"><span class="pre">functions</span></code>, etc. yourself. The good thing
|
||||
though is that at the very end you can save this as a template for future re-use.</li>
|
||||
</ol>
|
||||
<p>First the template path will be described. The theory dialogue looks like this</p>
|
||||
<img src="_images/musrWiz-Theory.svg" /><ol class="arabic simple">
|
||||
<img alt="_images/musrWiz-Theory.svg" src="_images/musrWiz-Theory.svg" /><ol class="arabic simple">
|
||||
<li>This is a text edit field were you can enter the theory fit function as you would like to have it. In the example
|
||||
given the theory reads <span class="math">\(p1 \exp(-p2\, t) \cos(2 \pi\, f1 + m1)\)</span>, where <tt class="docutils literal"><span class="pre">pX</span></tt> stands for parameter, <tt class="docutils literal"><span class="pre">fX</span></tt> for function,
|
||||
<tt class="docutils literal"><span class="pre">mX</span></tt> for map, and <tt class="docutils literal"><span class="pre">X</span></tt> for the corresponding number.</li>
|
||||
<li>The <tt class="docutils literal"><span class="pre">Clear</span> <span class="pre">All</span></tt> button will clear whatever you entered in the text field above.</li>
|
||||
given the theory reads <span class="math notranslate nohighlight">\(p1 \exp(-p2\, t) \cos(2 \pi\, f1 + m1)\)</span>, where <code class="docutils literal notranslate"><span class="pre">pX</span></code> stands for parameter, <code class="docutils literal notranslate"><span class="pre">fX</span></code> for function,
|
||||
<code class="docutils literal notranslate"><span class="pre">mX</span></code> for map, and <code class="docutils literal notranslate"><span class="pre">X</span></code> for the corresponding number.</li>
|
||||
<li>The <code class="docutils literal notranslate"><span class="pre">Clear</span> <span class="pre">All</span></code> button will clear whatever you entered in the text field above.</li>
|
||||
<li>This pull-down menu allows to select a theory function which will be added to the text field above by pressing
|
||||
the <tt class="docutils literal"><span class="pre">Add</span></tt> button. Pre defined theory function starting with a <tt class="docutils literal"><span class="pre">T</span></tt> are templates rather than only theory function strings.</li>
|
||||
<li>The <tt class="docutils literal"><span class="pre">Add</span></tt> button is used to add the chosen theory function / template from the pull-down menu to its left.</li>
|
||||
<li>The <tt class="docutils literal"><span class="pre">Check</span></tt> button is used to make a syntactical check of whatever is written in the text edit field.</li>
|
||||
the <code class="docutils literal notranslate"><span class="pre">Add</span></code> button. Pre defined theory function starting with a <code class="docutils literal notranslate"><span class="pre">T</span></code> are templates rather than only theory function strings.</li>
|
||||
<li>The <code class="docutils literal notranslate"><span class="pre">Add</span></code> button is used to add the chosen theory function / template from the pull-down menu to its left.</li>
|
||||
<li>The <code class="docutils literal notranslate"><span class="pre">Check</span></code> button is used to make a syntactical check of whatever is written in the text edit field.</li>
|
||||
</ol>
|
||||
</div>
|
||||
<div class="section" id="musrwiz-functions">
|
||||
<span id="index-6"></span><h3>musrWiz - Functions<a class="headerlink" href="#musrwiz-functions" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In the Functions dialogue all the necessary functions can be entered. A function operates <em>only</em> on fitting parameters.
|
||||
This is different to the theory function which operates on the fitting parameters and the time. The dialogue looks like this</p>
|
||||
<img src="_images/musrWiz-Functions.svg" /><ol class="arabic simple">
|
||||
<img alt="_images/musrWiz-Functions.svg" src="_images/musrWiz-Functions.svg" /><ol class="arabic simple">
|
||||
<li>a text edit field in which the various needed functions can be entered. In case a template theory is used, the appropriate function should be shown here and <em>no</em> editing will be needed here.</li>
|
||||
<li>pressing <tt class="docutils literal"><span class="pre">Show</span> <span class="pre">Theory</span></tt> button will pop-up a little window showing the previously entered theory function. This is handy when defining its own theory, <em>i.e.</em> not working with a template.</li>
|
||||
<li>pressing <code class="docutils literal notranslate"><span class="pre">Show</span> <span class="pre">Theory</span></code> button will pop-up a little window showing the previously entered theory function. This is handy when defining its own theory, <em>i.e.</em> not working with a template.</li>
|
||||
</ol>
|
||||
<img src="_images/musrWiz-Functions-and-Theory.svg" /></div>
|
||||
<img alt="_images/musrWiz-Functions-and-Theory.svg" src="_images/musrWiz-Functions-and-Theory.svg" /></div>
|
||||
<div class="section" id="musrwiz-maps">
|
||||
<span id="index-7"></span><h3>musrWiz - Maps<a class="headerlink" href="#musrwiz-maps" title="Permalink to this headline">¶</a></h3>
|
||||
<img src="_images/musrWiz-Maps.svg" /><p>The map dialogue will list the maps previously used in the theory and functions blocks/dialogues before. Again, if a template is used, nothing needs to be entered here.</p>
|
||||
<img alt="_images/musrWiz-Maps.svg" src="_images/musrWiz-Maps.svg" /><p>The map dialogue will list the maps previously used in the theory and functions blocks/dialogues before. Again, if a template is used, nothing needs to be entered here.</p>
|
||||
<ol class="arabic simple">
|
||||
<li>The <tt class="docutils literal"><span class="pre">Show</span> <span class="pre">Theory</span></tt> button allows to show the currently defined theory and the functions.</li>
|
||||
<li>The <code class="docutils literal notranslate"><span class="pre">Show</span> <span class="pre">Theory</span></code> button allows to show the currently defined theory and the functions.</li>
|
||||
</ol>
|
||||
</div>
|
||||
<div class="section" id="musrwiz-fit-parameters">
|
||||
<span id="index-8"></span><h3>musrWiz - Fit Parameters<a class="headerlink" href="#musrwiz-fit-parameters" title="Permalink to this headline">¶</a></h3>
|
||||
<img src="_images/musrWiz-FitParam.svg" /><p>In the fit parameter dialogue all parameter names can be defined. Furthermore the starting values for the parameters, the step
|
||||
<img alt="_images/musrWiz-FitParam.svg" src="_images/musrWiz-FitParam.svg" /><p>In the fit parameter dialogue all parameter names can be defined. Furthermore the starting values for the parameters, the step
|
||||
(initial step size for the parameter fit), and any boundaries can be defined here.</p>
|
||||
<ol class="arabic simple">
|
||||
<li>The <tt class="docutils literal"><span class="pre">Show</span> <span class="pre">Theory</span></tt> button allows to show the currently defined theory and the functions.</li>
|
||||
<li>The <code class="docutils literal notranslate"><span class="pre">Show</span> <span class="pre">Theory</span></code> button allows to show the currently defined theory and the functions.</li>
|
||||
</ol>
|
||||
</div>
|
||||
<div class="section" id="musrwiz-fit-info">
|
||||
<span id="index-9"></span><h3>musrWiz - Fit Info<a class="headerlink" href="#musrwiz-fit-info" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Collects all the <tt class="docutils literal"><span class="pre">musrfit</span></tt> and <tt class="docutils literal"><span class="pre">MINUIT2</span></tt> specific fit commands.</p>
|
||||
<img src="_images/musrWiz-FitInfo.svg" /><ol class="arabic simple">
|
||||
<p>Collects all the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> and <code class="docutils literal notranslate"><span class="pre">MINUIT2</span></code> specific fit commands.</p>
|
||||
<img alt="_images/musrWiz-FitInfo.svg" src="_images/musrWiz-FitInfo.svg" /><ol class="arabic simple">
|
||||
<li>allows to define the time fit range (start time, end time).</li>
|
||||
<li>packing defines how many bins of the original data shall be combined (added, also called re-binning).</li>
|
||||
<li>in this text field to fitting commands are given (see the <tt class="docutils literal"><span class="pre">MINUIT</span></tt> and <a class="reference internal" href="user-manual.html#msr-commands-block"><em>musrfit</em></a> manual for details).</li>
|
||||
<li>in this text field to fitting commands are given (see the <code class="docutils literal notranslate"><span class="pre">MINUIT</span></code> and <a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">musrfit</span></a> manual for details).</li>
|
||||
</ol>
|
||||
</div>
|
||||
<div class="section" id="musrwiz-create">
|
||||
<span id="index-10"></span><h3>musrWiz - Create<a class="headerlink" href="#musrwiz-create" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Collects the last necessary information before creating the msr-file.</p>
|
||||
<img src="_images/musrWiz-Create.svg" /><ol class="arabic simple">
|
||||
<li>shows the path where the msr-file will be saved. If you would like to save it somewhere else press the <tt class="docutils literal"><span class="pre">Save</span> <span class="pre">As</span> <span class="pre">(msr-file</span> <span class="pre">path)</span></tt> button.</li>
|
||||
<img alt="_images/musrWiz-Create.svg" src="_images/musrWiz-Create.svg" /><ol class="arabic simple">
|
||||
<li>shows the path where the msr-file will be saved. If you would like to save it somewhere else press the <code class="docutils literal notranslate"><span class="pre">Save</span> <span class="pre">As</span> <span class="pre">(msr-file</span> <span class="pre">path)</span></code> button.</li>
|
||||
<li>pressing this button will allow you to find the path where to save the msr-file.</li>
|
||||
<li>pressing this button will save to current configuration as a template for future re-use.</li>
|
||||
</ol>
|
||||
@ -450,50 +580,100 @@ This is different to the theory function which operates on the fitting parameter
|
||||
</div>
|
||||
<div class="section" id="musrstep">
|
||||
<span id="index-11"></span><h2>musrStep<a class="headerlink" href="#musrstep" title="Permalink to this headline">¶</a></h2>
|
||||
<p><tt class="docutils literal"><span class="pre">musrStep</span></tt> is a little helper program which allows to reset the initial step size. This sometimes comes very handy if working on an instrument
|
||||
<p><code class="docutils literal notranslate"><span class="pre">musrStep</span></code> is a little helper program which allows to reset the initial step size. This sometimes comes very handy if working on an instrument
|
||||
with many detectors after a fit slightly went wrong leaving you with a far too small initial step size for further iterations. To edit all the steps
|
||||
individually is tedious and error prone. Here <tt class="docutils literal"><span class="pre">musrStep</span></tt> can help.</p>
|
||||
<img src="_images/musrStep-GUI.svg" /><p>When invoking <tt class="docutils literal"><span class="pre">musrStep</span></tt> the above dialogue will popup</p>
|
||||
individually is tedious and error prone. Here <code class="docutils literal notranslate"><span class="pre">musrStep</span></code> can help.</p>
|
||||
<img alt="_images/musrStep-GUI.svg" src="_images/musrStep-GUI.svg" /><p>When invoking <code class="docutils literal notranslate"><span class="pre">musrStep</span></code> the above dialogue will popup</p>
|
||||
<ol class="arabic simple">
|
||||
<li>shows the relevant parts of the FITPARAMETER block. The only editable column is step.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Check</span> <span class="pre">Specific</span></tt> will popup a dialogue where a template string can be entered, <em>e.g.</em> <tt class="docutils literal"><span class="pre">Asym</span></tt>. As a result all fit parameters containing the template string will be selected.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Check</span> <span class="pre">All</span></tt> will select all fit parameters.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Uncheck</span> <span class="pre">All</span></tt> will unselect all fit parameters.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Modify</span> <span class="pre">Automatic</span></tt> will change all the step values automatically. It basically sets all the step sizes to 1% of
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Check</span> <span class="pre">Specific</span></code> will popup a dialogue where a template string can be entered, <em>e.g.</em> <code class="docutils literal notranslate"><span class="pre">Asym</span></code>. As a result all fit parameters containing the template string will be selected.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Check</span> <span class="pre">All</span></code> will select all fit parameters.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Uncheck</span> <span class="pre">All</span></code> will unselect all fit parameters.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Modify</span> <span class="pre">Automatic</span></code> will change all the step values automatically. It basically sets all the step sizes to 1% of
|
||||
the corresponding fit parameter value, except the phases where the step will be set to a value of 5 degrees.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Modify</span> <span class="pre">Selected</span></tt> will start the dialogue shown beneath. Follow the description there.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Save&Quit</span></tt> will save the current step values, close the dialogue and reload the modified msr-file.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Cancel</span></tt> will cancel the <tt class="docutils literal"><span class="pre">musrStep</span></tt> dialogue without modifying anything.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Modify</span> <span class="pre">Selected</span></code> will start the dialogue shown beneath. Follow the description there.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Save&Quit</span></code> will save the current step values, close the dialogue and reload the modified msr-file.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Cancel</span></code> will cancel the <code class="docutils literal notranslate"><span class="pre">musrStep</span></code> dialogue without modifying anything.</li>
|
||||
</ol>
|
||||
<img src="_images/musrStep-Modify-Selected.svg" /><p>When clicking on <tt class="docutils literal"><span class="pre">Modify</span> <span class="pre">Selected</span></tt> the above dialogue will be presented. It allows to manipulate all selected fit parameter step values according to the following rules</p>
|
||||
<img alt="_images/musrStep-Modify-Selected.svg" src="_images/musrStep-Modify-Selected.svg" /><p>When clicking on <code class="docutils literal notranslate"><span class="pre">Modify</span> <span class="pre">Selected</span></code> the above dialogue will be presented. It allows to manipulate all selected fit parameter step values according to the following rules</p>
|
||||
<ol class="arabic simple">
|
||||
<li><tt class="docutils literal"><span class="pre">Scale</span> <span class="pre">by</span> <span class="pre">Factor</span></tt> will scale the step value by the factor given in the field (2). If the <tt class="docutils literal"><span class="pre">Absolute</span> <span class="pre">Value</span></tt> check box is selected, rather than scaling the factor value will be used to modify the step value.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Scale</span> <span class="pre">by</span> <span class="pre">Factor</span></code> will scale the step value by the factor given in the field (2). If the <code class="docutils literal notranslate"><span class="pre">Absolute</span> <span class="pre">Value</span></code> check box is selected, rather than scaling the factor value will be used to modify the step value.</li>
|
||||
<li>scaling factor or absolute value to modify the step values of the selected fit parameters.</li>
|
||||
<li>checking the <tt class="docutils literal"><span class="pre">Absolute</span> <span class="pre">Value</span></tt> check box will change the meaning from <em>Scale by Factor</em> to <em>Copy Factor Value</em>.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Scale</span> <span class="pre">Automatically</span></tt> will modify the step values of the selected fit parameters according to the rules described before.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">Cancel</span></tt> will cancel the dialogue.</li>
|
||||
<li>checking the <code class="docutils literal notranslate"><span class="pre">Absolute</span> <span class="pre">Value</span></code> check box will change the meaning from <em>Scale by Factor</em> to <em>Copy Factor Value</em>.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Scale</span> <span class="pre">Automatically</span></code> will modify the step values of the selected fit parameters according to the rules described before.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">Cancel</span></code> will cancel the dialogue.</li>
|
||||
</ol>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
<div class="bottomnav">
|
||||
</div>
|
||||
|
||||
<p>
|
||||
«  <a href="setup-dks.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s</a>
|
||||
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a><ul>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a Tesla K40c (NVIDIA)</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#driver-installation-for-the-tesla-k40c">Driver Installation for the Tesla K40c</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#installation-of-cuda">Installation of CUDA</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#installation-of-dks">Installation of DKS</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#installation-of-musrfit-for-dks">Installation of musrfit for DKS</a><ul>
|
||||
<li class="toctree-l4"><a class="reference internal" href="#install-via-cmake">Install via cmake</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a AMD Graphic Card (Radeon R9 390X)</a><ul>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x">Driver Installation for an AMD Graphic Card, <em>e.g.</em> Radeon R9 390X</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#amd-app-software-development-kit-sdk-to-enable-opencl-support">AMD APP Software Development Kit (SDK) to enable <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> support</a></li>
|
||||
<li class="toctree-l3"><a class="reference internal" href="#installation-of-dks-and-musrfit">Installation of DKS and musrfit</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l2"><a class="reference internal" href="#setting-up-musrfit-dks-for-macos-for-opencl-support">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for macOS for OpenCL support</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
|
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</ul>
|
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«  <a href="setup-standard.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a>
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  ::  
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  ::  
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<a href="musredit.html"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a>  »
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<li>Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</li>
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<div class="section" id="setting-up-musrfit-dks-high-speed-fitting-with-gpu-s">
|
||||
<span id="setup-dks"></span><span id="index-0"></span><h1>Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> / <tt class="docutils literal"><span class="pre">DKS</span></tt>: High Speed Fitting with GPU’s<a class="headerlink" href="#setting-up-musrfit-dks-high-speed-fitting-with-gpu-s" title="Permalink to this headline">¶</a></h1>
|
||||
<p>In the years 2016/2017 we explored ways to speed up current fitting frameworks, especially <tt class="docutils literal"><span class="pre">musrfit.</span></tt>
|
||||
This allows now to analyze histogram sets of high field spectrometers like <tt class="docutils literal"><span class="pre">HAL-9500</span></tt> at PSI without
|
||||
<span id="setup-dks"></span><span id="index-0"></span><h1>Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s<a class="headerlink" href="#setting-up-musrfit-dks-high-speed-fitting-with-gpu-s" title="Permalink to this headline">¶</a></h1>
|
||||
<p>In the years 2016/2017 we explored ways to speed up current fitting frameworks, especially <code class="docutils literal notranslate"><span class="pre">musrfit.</span></code>
|
||||
This allows now to analyze histogram sets of high field spectrometers like <code class="docutils literal notranslate"><span class="pre">HAL-9500</span></code> at PSI without
|
||||
the <em>error-prone</em> RRF fitting (see U. Locans and A. Suter,
|
||||
<a class="reference external" href="http://dx.doi.org/10.7566/JPSCP.21.011051">musrfit - Real Time Parameter Fitting Using GPU</a>, and the
|
||||
Memo from A. Suter, “Rotating Reference Frame Fits”, in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> source code). At the same time
|
||||
Memo from A. Suter, “Rotating Reference Frame Fits”, in the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> source code). At the same time
|
||||
it can help to speed-up elaborate global fits tremendously, and dealing properly with muonium. It also
|
||||
allows Apple macOS users to speed up their fitting code on the CPU. Currently it is not straight forward
|
||||
to get <tt class="docutils literal"><span class="pre">musrfit</span></tt> multi-threaded under macOS since Apple doesn’t be default support <tt class="docutils literal"><span class="pre">OpenMP</span></tt>. <tt class="docutils literal"><span class="pre">DKS</span></tt>
|
||||
enables <tt class="docutils literal"><span class="pre">musrfit</span></tt> to utilize <tt class="docutils literal"><span class="pre">OpenCL</span></tt> instead which is present on macOS by default.</p>
|
||||
to get <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> multi-threaded under macOS since Apple doesn’t be default support <code class="docutils literal notranslate"><span class="pre">OpenMP</span></code>. <code class="docutils literal notranslate"><span class="pre">DKS</span></code>
|
||||
enables <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> to utilize <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> instead which is present on macOS by default.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Before you run into the shop to buy a gamer graphic card or a Tesla card, make sure that you have an
|
||||
@ -65,35 +194,35 @@ appropriate server with a sufficiently strong power supply!</p>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">However, the current <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> version doesn’t yet support all theory functions on the GPU.
|
||||
In case the theory function is not yet available for the GPU, <tt class="docutils literal"><span class="pre">musrfit</span></tt> will fall back to the CPU implementation.</p>
|
||||
<p class="last">However, the current <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> version doesn’t yet support all theory functions on the GPU.
|
||||
In case the theory function is not yet available for the GPU, <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> will fall back to the CPU implementation.</p>
|
||||
</div>
|
||||
<p>Conceptually the setup of <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> is as following:</p>
|
||||
<p>Conceptually the setup of <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> is as following:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>install the latest hardware driver for your graphic card.</li>
|
||||
<li>install the GPU SDK which enables number crunching (<tt class="docutils literal"><span class="pre">CUDA</span></tt> for NVIDIA, <tt class="docutils literal"><span class="pre">OpenCL</span></tt> for AMD)</li>
|
||||
<li>install <tt class="docutils literal"><span class="pre">DKS</span></tt></li>
|
||||
<li>install the <tt class="docutils literal"><span class="pre">musrfit</span></tt> version which is <tt class="docutils literal"><span class="pre">DKS</span></tt> ready</li>
|
||||
<li>install the GPU SDK which enables number crunching (<code class="docutils literal notranslate"><span class="pre">CUDA</span></code> for NVIDIA, <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> for AMD)</li>
|
||||
<li>install <code class="docutils literal notranslate"><span class="pre">DKS</span></code></li>
|
||||
<li>install the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> version which is <code class="docutils literal notranslate"><span class="pre">DKS</span></code> ready</li>
|
||||
</ol>
|
||||
<p>In the following the description for the installation of <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for the following systems will be discussed in some more detail:</p>
|
||||
<p>In the following the description for the installation of <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for the following systems will be discussed in some more detail:</p>
|
||||
<ul class="simple">
|
||||
<li>NVIDIA Tesla K40c</li>
|
||||
<li>AMD Graphic Card (Radeon R9 390X)</li>
|
||||
<li>macOS in order to get <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support</li>
|
||||
<li>macOS in order to get <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> support</li>
|
||||
</ul>
|
||||
<p>The usage of <tt class="docutils literal"><span class="pre">musrfit</span></tt> with GPU acceleration and <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support is described in the
|
||||
<a class="reference internal" href="user-manual.html#user-manual"><em>User manual of the μSR data analysis software musrfit</em></a>. The additional
|
||||
<tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> are found <a class="reference internal" href="user-manual.html#msr-commands-block-dks"><em>here</em></a>.</p>
|
||||
<p>The usage of <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> with GPU acceleration and <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> support is described in the
|
||||
<a class="reference internal" href="user-manual.html#user-manual"><span class="std std-ref">User manual of the μSR data analysis software musrfit</span></a>. The additional
|
||||
<code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> are found <a class="reference internal" href="user-manual.html#msr-commands-block-dks"><span class="std std-ref">here</span></a>.</p>
|
||||
<div class="section" id="setting-up-musrfit-dks-for-a-tesla-k40c-nvidia">
|
||||
<span id="index-1"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a Tesla K40c (NVIDIA)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="index-1"></span><h2>Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a Tesla K40c (NVIDIA)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-tesla-k40c-nvidia" title="Permalink to this headline">¶</a></h2>
|
||||
<p>It is assumed that the Tesla K40c is already physically installed on your system. For now I only
|
||||
will discuss to set it up for a Linux based system. In order to check that your operating systems
|
||||
see the card, enter the following command in the terminal:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep NVIDIA
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep NVIDIA
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The response should look something like</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>05:00.0 3D controller: NVIDIA Corporation GK110BGL [Tesla K40c] (rev a1)
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">05</span><span class="p">:</span><span class="mf">00.0</span> <span class="mi">3</span><span class="n">D</span> <span class="n">controller</span><span class="p">:</span> <span class="n">NVIDIA</span> <span class="n">Corporation</span> <span class="n">GK110BGL</span> <span class="p">[</span><span class="n">Tesla</span> <span class="n">K40c</span><span class="p">]</span> <span class="p">(</span><span class="n">rev</span> <span class="n">a1</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>which means that the OS physically recognizes your card.</p>
|
||||
@ -101,25 +230,25 @@ see the card, enter the following command in the terminal:</p>
|
||||
<h3>Driver Installation for the Tesla K40c<a class="headerlink" href="#driver-installation-for-the-tesla-k40c" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Next, you will need to download and install the driver for your card. Select the proper operating system,
|
||||
card, etc. from the <a class="reference external" href="http://www.nvidia.com/Download/index.aspx?lang=en-us">NVIDIA download center</a>. At PSI
|
||||
we are running currently Red Hat Enterprise Linux 7.x (RHEL) for which we will get a <tt class="docutils literal"><span class="pre">rpm</span></tt> (something like
|
||||
<tt class="docutils literal"><span class="pre">nvidia-diag-driver-local-repo-rhel7-375.66-1.x86_64.rpm</span></tt>). Install it and make sure there is no conflict
|
||||
we are running currently Red Hat Enterprise Linux 7.x (RHEL) for which we will get a <code class="docutils literal notranslate"><span class="pre">rpm</span></code> (something like
|
||||
<code class="docutils literal notranslate"><span class="pre">nvidia-diag-driver-local-repo-rhel7-375.66-1.x86_64.rpm</span></code>). Install it and make sure there is no conflict
|
||||
with the nouveau driver of the system.</p>
|
||||
</div>
|
||||
<div class="section" id="installation-of-cuda">
|
||||
<span id="index-2"></span><h3>Installation of CUDA<a class="headerlink" href="#installation-of-cuda" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Download the <a class="reference external" href="https://developer.nvidia.com/cuda-downloads">CUDA SDK</a> form NVIDIA for your system. Again,
|
||||
for the RHEL 7.x this is an <tt class="docutils literal"><span class="pre">rpm</span></tt>. After the installation of the rpm you should reboot your machine.
|
||||
Afterwards you are ready for the installation of <tt class="docutils literal"><span class="pre">DKS</span></tt>.</p>
|
||||
for the RHEL 7.x this is an <code class="docutils literal notranslate"><span class="pre">rpm</span></code>. After the installation of the rpm you should reboot your machine.
|
||||
Afterwards you are ready for the installation of <code class="docutils literal notranslate"><span class="pre">DKS</span></code>.</p>
|
||||
</div>
|
||||
<div class="section" id="installation-of-dks">
|
||||
<span id="index-3"></span><h3>Installation of DKS<a class="headerlink" href="#installation-of-dks" title="Permalink to this headline">¶</a></h3>
|
||||
<p>For the following list of commands the <tt class="docutils literal"><span class="pre">'$'</span></tt> will be given as the command prompt. <em>Do not enter it!</em>
|
||||
Also some comments will be added starting with a <tt class="docutils literal"><span class="pre">'#'</span></tt> which can be omitted. They are only there to
|
||||
explain what is going on. <tt class="docutils literal"><span class="pre">DKS</span></tt> stands for Dynamical Kernel Scheduler and provides a thin interface
|
||||
allowing host applications to incorporate GPU’s and other hardware accelerators.</p>
|
||||
<p>Details can be found in the papers listed <a class="reference internal" href="cite.html#cite"><em>here</em></a>, or on the <a class="reference external" href="https://gitlab.psi.ch/uldis_l/DKS/wikis/home">DKS wiki page</a>.</p>
|
||||
<p>For the following list of commands the <code class="docutils literal notranslate"><span class="pre">'$'</span></code> will be given as the command prompt. <em>Do not enter it!</em>
|
||||
Also some comments will be added starting with a <code class="docutils literal notranslate"><span class="pre">'#'</span></code> which can be omitted. They are only there to
|
||||
explain what is going on. <code class="docutils literal notranslate"><span class="pre">DKS</span></code> stands for Dynamical Kernel Scheduler and provides a thin interface
|
||||
allowing host applications to incorporate GPU’s and other hardware accelerators.</p>
|
||||
<p>Details can be found in the papers listed <a class="reference internal" href="cite.html#cite"><span class="std std-ref">here</span></a>, or on the <a class="reference external" href="https://gitlab.psi.ch/uldis_l/DKS/wikis/home">DKS wiki page</a>.</p>
|
||||
<p>In brief the installation should be something like this:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="c1"># go to whatever directory you would like to clone/install DKS</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># go to whatever directory you would like to clone/install DKS</span>
|
||||
<span class="c1"># For macOS DKS will likely to got to $HOME/Applications to be consistent with the musrfit docu for macOS</span>
|
||||
$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps
|
||||
$ git clone https://gitlab.psi.ch/uldis_l/DKS.git
|
||||
@ -131,16 +260,16 @@ $ cmake --build ./ --clean-first
|
||||
$ make install
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Since <tt class="docutils literal"><span class="pre">DKS</span></tt> is installed in a non-standard path, a couple of additional small steps are required.
|
||||
<p>Since <code class="docutils literal notranslate"><span class="pre">DKS</span></code> is installed in a non-standard path, a couple of additional small steps are required.
|
||||
This will be different for Linux compared to macOS.</p>
|
||||
<p>For <strong>Linux:</strong></p>
|
||||
<p>add the <tt class="docutils literal"><span class="pre">DKS</span></tt> library path to <tt class="docutils literal"><span class="pre">/etc/ld.so.conf.d/musrfit-x86_64.conf</span></tt> and execute as super user</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/ldconfig
|
||||
<p>add the <code class="docutils literal notranslate"><span class="pre">DKS</span></code> library path to <code class="docutils literal notranslate"><span class="pre">/etc/ld.so.conf.d/musrfit-x86_64.conf</span></code> and execute as super user</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ /sbin/ldconfig
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>For <strong>macOS:</strong></p>
|
||||
<p>add the <tt class="docutils literal"><span class="pre">DKS</span></tt> path to <tt class="docutils literal"><span class="pre">$HOME/.profile</span></tt>:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">DKS</span><span class="o">=</span><span class="nv">$HOME</span>/Applications/DKS/exec
|
||||
<p>add the <code class="docutils literal notranslate"><span class="pre">DKS</span></code> path to <code class="docutils literal notranslate"><span class="pre">$HOME/.profile</span></code>:</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span> <span class="nv">DKS</span><span class="o">=</span><span class="nv">$HOME</span>/Applications/DKS/exec
|
||||
<span class="nb">export</span> <span class="nv">LD_LIBRARY_PATH</span><span class="o">=</span><span class="nv">$DKS</span>/lib:<span class="nv">$LD_LIBRARY_PATH</span>
|
||||
|
||||
launchctl setenv DKS <span class="nv">$DKS</span>
|
||||
@ -150,10 +279,10 @@ launchctl setenv LD_LIBRARY_PATH <span class="nv">$LD_LIBRARY_PATH</span>
|
||||
</div>
|
||||
<div class="section" id="installation-of-musrfit-for-dks">
|
||||
<span id="musrfit-dks-install"></span><h3>Installation of musrfit for DKS<a class="headerlink" href="#installation-of-musrfit-for-dks" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Most of the installation steps are the same as described for <tt class="docutils literal"><span class="pre">musrfit</span></tt> without GPU support.
|
||||
Here only the differences are explained. First checkout <tt class="docutils literal"><span class="pre">musrfit</span></tt>, then you will need to
|
||||
<p>Most of the installation steps are the same as described for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> without GPU support.
|
||||
Here only the differences are explained. First checkout <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>, then you will need to
|
||||
switch the working branch which is done by</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ <span class="nb">cd</span> <span class="nv">$HOME</span>/Apps/musrfit
|
||||
$ git checkout dks6
|
||||
</pre></div>
|
||||
</div>
|
||||
@ -162,19 +291,19 @@ $ git checkout dks6
|
||||
<p>There is on more configuration switch</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong>-Ddks=<value></strong></dt>
|
||||
<dd>it allows to enable/disable <tt class="docutils literal"><span class="pre">DKS</span></tt> support. The default is <tt class="docutils literal"><span class="pre"><value>=1</span></tt>, <em>i.e.</em> enabled. To disable use <tt class="docutils literal"><span class="pre"><value>=0</span></tt>.</dd>
|
||||
<dd>it allows to enable/disable <code class="docutils literal notranslate"><span class="pre">DKS</span></code> support. The default is <code class="docutils literal notranslate"><span class="pre"><value>=1</span></code>, <em>i.e.</em> enabled. To disable use <code class="docutils literal notranslate"><span class="pre"><value>=0</span></code>.</dd>
|
||||
</dl>
|
||||
<p>For a typical setup on a RHEL or macOS system it could look like this</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -DASlibs<span class="o">=</span><span class="m">1</span> -DBMWlibs<span class="o">=</span><span class="m">1</span> -Dnexus<span class="o">=</span><span class="m">1</span> -Ddks<span class="o">=</span><span class="m">1</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ cmake ../ -DCMAKE_INSTALL_PREFIX<span class="o">=</span><span class="nv">$ROOTSYS</span> -DASlibs<span class="o">=</span><span class="m">1</span> -DBMWlibs<span class="o">=</span><span class="m">1</span> -Dnexus<span class="o">=</span><span class="m">1</span> -Ddks<span class="o">=</span><span class="m">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>After</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ cmake --build ./ --clean-first -- -j8
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ cmake --build ./ --clean-first -- -j8
|
||||
$ make install
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>and updating the shared library lookup table (<em>only</em> needed for Linux)</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/ldconfig <span class="c1"># as superuser / root</span>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ /sbin/ldconfig <span class="c1"># as superuser / root</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>you are done with the setup.</p>
|
||||
@ -182,7 +311,7 @@ $ make install
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x">
|
||||
<span id="index-4"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for a AMD Graphic Card (Radeon R9 390X)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x" title="Permalink to this headline">¶</a></h2>
|
||||
<span id="index-4"></span><h2>Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for a AMD Graphic Card (Radeon R9 390X)<a class="headerlink" href="#setting-up-musrfit-dks-for-a-amd-graphic-card-radeon-r9-390x" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="section" id="driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x">
|
||||
<h3>Driver Installation for an AMD Graphic Card, <em>e.g.</em> Radeon R9 390X<a class="headerlink" href="#driver-installation-for-an-amd-graphic-card-e-g-radeon-r9-390x" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This will depend slightly on the AMD Card and operating system. Here I will summaries how it was done
|
||||
@ -190,85 +319,135 @@ on a RHEL (Linux) system using a Radeon R9 390X.</p>
|
||||
<p>It is assumed that the Radeon R9 390X is already physically installed on your system. For now I only
|
||||
will discuss to set it up for a Linux based system. In order to check that your operating systems see
|
||||
the card, enter the following command in the terminal:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep AMD
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ lspci <span class="p">|</span> grep AMD
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The response should look something like</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>84:00.0 VGA compatible controller: Advanced Micro Devices, Inc. [AMD/ATI] Hawaii XT / Grenada XT [Radeon R9 290X/390X] (rev 80)
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">84</span><span class="p">:</span><span class="mf">00.0</span> <span class="n">VGA</span> <span class="n">compatible</span> <span class="n">controller</span><span class="p">:</span> <span class="n">Advanced</span> <span class="n">Micro</span> <span class="n">Devices</span><span class="p">,</span> <span class="n">Inc</span><span class="o">.</span> <span class="p">[</span><span class="n">AMD</span><span class="o">/</span><span class="n">ATI</span><span class="p">]</span> <span class="n">Hawaii</span> <span class="n">XT</span> <span class="o">/</span> <span class="n">Grenada</span> <span class="n">XT</span> <span class="p">[</span><span class="n">Radeon</span> <span class="n">R9</span> <span class="mi">290</span><span class="n">X</span><span class="o">/</span><span class="mi">390</span><span class="n">X</span><span class="p">]</span> <span class="p">(</span><span class="n">rev</span> <span class="mi">80</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>which means that the OS physically recognizes your card.</p>
|
||||
<p>For RHEL7.x the AMDGPU-PRO driver should be used. It can be downloaded from <a class="reference external" href="http://support.amd.com/en-us/kb-articles/Pages/AMDGPU-PRO-RedHat-Install.aspx">AMD</a>. Unpack the driver</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ tar -Jxvf amdgpu-pro-17.10-414273.tar.xz
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ tar -Jxvf amdgpu-pro-17.10-414273.tar.xz
|
||||
$ <span class="nb">cd</span> amdgpu-pro-17.10-414273
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Install the driver as root</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ./amdgpu-pro-install --compute -y
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./amdgpu-pro-install --compute -y
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here I assume that the AMD graphic card is only used for computation. You need to add the following command
|
||||
in order that the user <strong>blabla</strong> (change this to the appropriate user name) can access the GPU (otherwise
|
||||
only root works):</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ /sbin/usermod -a -G video blabla
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ /sbin/usermod -a -G video blabla
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Reboot the machine.</p>
|
||||
</div>
|
||||
<div class="section" id="amd-app-software-development-kit-sdk-to-enable-opencl-support">
|
||||
<h3>AMD APP Software Development Kit (SDK) to enable <tt class="docutils literal"><span class="pre">OpenCL</span></tt> support<a class="headerlink" href="#amd-app-software-development-kit-sdk-to-enable-opencl-support" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>AMD APP Software Development Kit (SDK) to enable <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> support<a class="headerlink" href="#amd-app-software-development-kit-sdk-to-enable-opencl-support" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The AMD APP Software Development Kit (SDK) is a complete development platform created by AMD to allow you to
|
||||
quickly and easily develop applications accelerated by AMD APP technology. The SDK provides samples, documentation,
|
||||
and other materials to quickly get you started leveraging accelerated compute using <tt class="docutils literal"><span class="pre">OpenCL</span></tt> or <tt class="docutils literal"><span class="pre">C++</span> <span class="pre">AMP</span></tt> in your
|
||||
<tt class="docutils literal"><span class="pre">C/C++</span></tt> applications.</p>
|
||||
and other materials to quickly get you started leveraging accelerated compute using <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> or <code class="docutils literal notranslate"><span class="pre">C++</span> <span class="pre">AMP</span></code> in your
|
||||
<code class="docutils literal notranslate"><span class="pre">C/C++</span></code> applications.</p>
|
||||
<p>Download the AMD APP SDK 3.0 from <a class="reference external" href="http://developer.amd.com/tools-and-sdks/opencl-zone/amd-accelerated-parallel-processing-app-sdk/">AMD-SDK</a>.</p>
|
||||
<p>Extract the installer</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ tar -xvjf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ tar -xvjf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Run the installer</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>This will install the AMD APP SDK to <tt class="docutils literal"><span class="pre">/opt/AMDAPPSDK-3.0/</span></tt> where you can find the <tt class="docutils literal"><span class="pre">OpenCL</span></tt> include
|
||||
<p>This will install the AMD APP SDK to <code class="docutils literal notranslate"><span class="pre">/opt/AMDAPPSDK-3.0/</span></code> where you can find the <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code> include
|
||||
and library files, as well as documentation and sample code. The install guide for AMD OpenCL SDK can
|
||||
be found at <a class="reference external" href="http://developer.amd.com/wordpress/media/2012/10/AMD_APP_SDK_InstallationNotes.pdf">AMD SDK Installation Notes</a>.</p>
|
||||
</div>
|
||||
<div class="section" id="installation-of-dks-and-musrfit">
|
||||
<h3>Installation of DKS and musrfit<a class="headerlink" href="#installation-of-dks-and-musrfit" title="Permalink to this headline">¶</a></h3>
|
||||
<p>To install <tt class="docutils literal"><span class="pre">DKS</span></tt> and <tt class="docutils literal"><span class="pre">musrfit</span></tt> follow the instructions <a class="reference internal" href="#musrfit-dks-install"><em>above</em></a>.</p>
|
||||
<p>To install <code class="docutils literal notranslate"><span class="pre">DKS</span></code> and <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> follow the instructions <a class="reference internal" href="#musrfit-dks-install"><span class="std std-ref">above</span></a>.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="setting-up-musrfit-dks-for-macos-for-opencl-support">
|
||||
<span id="index-5"></span><h2>Setting up <tt class="docutils literal"><span class="pre">musrfit/DKS</span></tt> for macOS for OpenCL support<a class="headerlink" href="#setting-up-musrfit-dks-for-macos-for-opencl-support" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Since Apple is not providing an out-of-the-box <tt class="docutils literal"><span class="pre">OpenMP</span></tt> support on their macOS compiler framework (Xcode),
|
||||
typically <tt class="docutils literal"><span class="pre">musrfit</span></tt> is just running <em>single threaded</em>. Here <tt class="docutils literal"><span class="pre">DKS</span></tt> can help since it delivers <tt class="docutils literal"><span class="pre">OpenCL</span></tt>
|
||||
support which is present on macOS. Hence, if you would like to run <tt class="docutils literal"><span class="pre">musrfit</span></tt> multi-threaded the easiest
|
||||
way is to use <tt class="docutils literal"><span class="pre">DKS</span></tt>.</p>
|
||||
<span id="index-5"></span><h2>Setting up <code class="docutils literal notranslate"><span class="pre">musrfit/DKS</span></code> for macOS for OpenCL support<a class="headerlink" href="#setting-up-musrfit-dks-for-macos-for-opencl-support" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Since Apple is not providing an out-of-the-box <code class="docutils literal notranslate"><span class="pre">OpenMP</span></code> support on their macOS compiler framework (Xcode),
|
||||
typically <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is just running <em>single threaded</em>. Here <code class="docutils literal notranslate"><span class="pre">DKS</span></code> can help since it delivers <code class="docutils literal notranslate"><span class="pre">OpenCL</span></code>
|
||||
support which is present on macOS. Hence, if you would like to run <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> multi-threaded the easiest
|
||||
way is to use <code class="docutils literal notranslate"><span class="pre">DKS</span></code>.</p>
|
||||
<p>Since there is no graphic card involved, you do not need any graphic card driver of additional SDK.
|
||||
The only thing you need <tt class="docutils literal"><span class="pre">DKS</span></tt> and the proper <tt class="docutils literal"><span class="pre">musrfit</span></tt> version.</p>
|
||||
<p>The installation instruction for <tt class="docutils literal"><span class="pre">DKS/musrfit</span></tt> can be found <a class="reference internal" href="#musrfit-dks-install"><em>here</em></a>.</p>
|
||||
The only thing you need <code class="docutils literal notranslate"><span class="pre">DKS</span></code> and the proper <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> version.</p>
|
||||
<p>The installation instruction for <code class="docutils literal notranslate"><span class="pre">DKS/musrfit</span></code> can be found <a class="reference internal" href="#musrfit-dks-install"><span class="std std-ref">here</span></a>.</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
<div class="bottomnav">
|
||||
</div>
|
||||
|
||||
<p>
|
||||
«  <a href="setup-standard.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a>
|
||||
  ::  
|
||||
<a class="uplink" href="index.html">Contents</a>
|
||||
  ::  
|
||||
<a href="musredit.html"><tt class="docutils literal"><span class="pre">musredit</span></tt>: the GUI Based Interface to <tt class="docutils literal"><span class="pre">musrfit</span></tt></a>  »
|
||||
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||||
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||||
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||||
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||||
|
||||
<a href="musredit.html" class="btn btn-neutral float-right" title="musredit: the GUI Based Interface to musrfit" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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||||
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||||
|
||||
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<span>musrfit 1.8.0 documentation</span></a></h1>
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<h2 class="heading"><span>Tutorial for musrfit</span></h2>
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
|
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#single-histogram-fit-tutorial">Single-histogram-fit tutorial</a><ul>
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<li class="toctree-l3"><a class="reference internal" href="#the-msr-file">The msr file</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#determine-t0-and-the-data-range-using-musrt0">Determine t0 and the data range using musrt0</a></li>
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<li class="toctree-l3"><a class="reference internal" href="#fit-the-model-to-the-data-using-musrfit">Fit the model to the data using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#view-the-data-and-the-fit-using-musrview">View the data and the fit using <code class="docutils literal notranslate"><span class="pre">musrview</span></code></a></li>
|
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<li class="toctree-l3"><a class="reference internal" href="#process-multiple-msr-files-using-msr2data">Process multiple msr files using <code class="docutils literal notranslate"><span class="pre">msr2data</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#further-reading">Further reading</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#asymmtery-fit-tutorial">Asymmtery-fit tutorial</a></li>
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<li class="toctree-l1"><a class="reference internal" href="user-manual.html">User manual</a></li>
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<li class="toctree-l1"><a class="reference internal" href="user-libs.html">Documentation of user libs (user functions)</a></li>
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<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
|
||||
<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
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«  <a href="cite.html">How to Cite <tt class="docutils literal"><span class="pre">musrfit</span></tt>?</a>
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  ::  
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<div class="section" id="tutorial-for-musrfit">
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<span id="index-0"></span><h1>Tutorial for <tt class="docutils literal"><span class="pre">musrfit</span></tt><a class="headerlink" href="#tutorial-for-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<span id="index-0"></span><h1>Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code><a class="headerlink" href="#tutorial-for-musrfit" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="single-histogram-fit-tutorial">
|
||||
<h2>Single-histogram-fit tutorial<a class="headerlink" href="#single-histogram-fit-tutorial" title="Permalink to this headline">¶</a></h2>
|
||||
<p>The μSR-data-analysis process using musrfit is based on so-called msr files. These files contain all
|
||||
information needed for the analysis such as names of the data files, a theory function, fit and plot parameters,
|
||||
and so on. It is the idea of this page to explain the basic use of an msr file and the different programs
|
||||
of the <tt class="docutils literal"><span class="pre">musrfit</span></tt> suite using the example of a single-histogram fit to time-differential transverse-field
|
||||
μSR data. For a complete description of all options please refer to the <a class="reference internal" href="user-manual.html#user-manual"><em>manual</em></a>.</p>
|
||||
of the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> suite using the example of a single-histogram fit to time-differential transverse-field
|
||||
μSR data. For a complete description of all options please refer to the <a class="reference internal" href="user-manual.html#user-manual"><span class="std std-ref">manual</span></a>.</p>
|
||||
<p>The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in
|
||||
the <a class="reference external" href="https://www.psi.ch/smus/gps">GPS spectrometer</a> at <a class="reference external" href="https://www.psi.ch">PSI</a> using the “transverse geometry”.
|
||||
the <a class="reference external" href="https://www.psi.ch/smus/gps">GPS spectrometer</a> at <a class="reference external" href="https://www.psi.ch">PSI</a> using the “transverse geometry”.
|
||||
In this geometry the muon spin is rotated about 50° up and the field is applied parallel to the muon momentum.
|
||||
Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.</p>
|
||||
<p>To analyze these data (in a simple way) one starts out from the msr file <tt class="docutils literal"><span class="pre">3110_tutorial.msr</span></tt> provided together
|
||||
with the source-code distribution in the sub-directory <tt class="docutils literal"><span class="pre">doc/examples/</span></tt>. This ASCII file can be edited using any
|
||||
text editor. For convenience the editor <tt class="docutils literal"><span class="pre">musredit</span></tt> is provided which offer some msr-file-specific functionalities
|
||||
<p>To analyze these data (in a simple way) one starts out from the msr file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> provided together
|
||||
with the source-code distribution in the sub-directory <code class="docutils literal notranslate"><span class="pre">doc/examples/</span></code>. This ASCII file can be edited using any
|
||||
text editor. For convenience the editor <code class="docutils literal notranslate"><span class="pre">musredit</span></code> is provided which offer some msr-file-specific functionalities
|
||||
and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is
|
||||
open within <tt class="docutils literal"><span class="pre">musredit</span></tt>.</p>
|
||||
open within <code class="docutils literal notranslate"><span class="pre">musredit</span></code>.</p>
|
||||
<div class="section" id="the-msr-file">
|
||||
<h3>The msr file<a class="headerlink" href="#the-msr-file" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The msr file itself is divided into different blocks; a full description of the format can be found <a class="reference internal" href="user-manual.html#msr-file-format"><em>here</em></a>.
|
||||
In the file <tt class="docutils literal"><span class="pre">3110_tutorial.msr</span></tt> these blocks are successively:</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-title-block"><em>The title</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>sample XYZ
|
||||
<p>The msr file itself is divided into different blocks; a full description of the format can be found <a class="reference internal" href="user-manual.html#msr-file-format"><span class="std std-ref">here</span></a>.
|
||||
In the file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> these blocks are successively:</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-title-block"><span class="std std-ref">The title</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">sample</span> <span class="n">XYZ</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>A descriptive title of the file.</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-fitparameter-block"><em>The FITPARAMETER block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>FITPARAMETER
|
||||
# No Name Value Step Pos_Error Boundaries
|
||||
1 NormUp 4500 5 none 0 none
|
||||
2 BgUp 200 1 none 0 none
|
||||
3 PhaseUp 15 1 none
|
||||
<p><a class="reference internal" href="user-manual.html#msr-fitparameter-block"><span class="std std-ref">The FITPARAMETER block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FITPARAMETER</span>
|
||||
<span class="c1"># No Name Value Step Pos_Error Boundaries</span>
|
||||
<span class="mi">1</span> <span class="n">NormUp</span> <span class="mi">4500</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">2</span> <span class="n">BgUp</span> <span class="mi">200</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">3</span> <span class="n">PhaseUp</span> <span class="mi">15</span> <span class="mi">1</span> <span class="n">none</span>
|
||||
|
||||
4 NormDown 4500 5 none 0 none
|
||||
5 BgDown 200 1 none 0 none
|
||||
6 PhaseDown 195 1 none
|
||||
<span class="mi">4</span> <span class="n">NormDown</span> <span class="mi">4500</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">5</span> <span class="n">BgDown</span> <span class="mi">200</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">6</span> <span class="n">PhaseDown</span> <span class="mi">195</span> <span class="mi">1</span> <span class="n">none</span>
|
||||
|
||||
7 NormRight 600 5 none 0 none
|
||||
8 BgRight 40 1 none 0 none
|
||||
9 PhaseRight 285 1 none
|
||||
<span class="mi">7</span> <span class="n">NormRight</span> <span class="mi">600</span> <span class="mi">5</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">8</span> <span class="n">BgRight</span> <span class="mi">40</span> <span class="mi">1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">9</span> <span class="n">PhaseRight</span> <span class="mi">285</span> <span class="mi">1</span> <span class="n">none</span>
|
||||
|
||||
10 AsymSig1 0.17 0.01 none 0 0.33
|
||||
11 RateSig1 2.5 0.1 none 0 none
|
||||
12 FieldSig1 100 1 none
|
||||
<span class="mi">10</span> <span class="n">AsymSig1</span> <span class="mf">0.17</span> <span class="mf">0.01</span> <span class="n">none</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||||
<span class="mi">11</span> <span class="n">RateSig1</span> <span class="mf">2.5</span> <span class="mf">0.1</span> <span class="n">none</span> <span class="mi">0</span> <span class="n">none</span>
|
||||
<span class="mi">12</span> <span class="n">FieldSig1</span> <span class="mi">100</span> <span class="mi">1</span> <span class="n">none</span>
|
||||
|
||||
13 AsymSig2 0.02 0.01 none 0 0.33
|
||||
14 RateSig2 0.5 0.1 none
|
||||
15 FieldSig2 150 1 none
|
||||
<span class="mi">13</span> <span class="n">AsymSig2</span> <span class="mf">0.02</span> <span class="mf">0.01</span> <span class="n">none</span> <span class="mi">0</span> <span class="mf">0.33</span>
|
||||
<span class="mi">14</span> <span class="n">RateSig2</span> <span class="mf">0.5</span> <span class="mf">0.1</span> <span class="n">none</span>
|
||||
<span class="mi">15</span> <span class="n">FieldSig2</span> <span class="mi">150</span> <span class="mi">1</span> <span class="n">none</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The list of parameters used in the theory function to describe the set of data.
|
||||
Each parameter has a number, a name, an initial value and an initial step (for
|
||||
the fitting process). If a parameter should be fixed, the initial step is set
|
||||
to 0. After a fit (see below), this block contains the determined parameter values
|
||||
and uncertainties (in the <tt class="docutils literal"><span class="pre">Step</span></tt> column). If asymmetric errors are determined, these
|
||||
will be listed in the <tt class="docutils literal"><span class="pre">Step</span></tt> column (negative) and the <tt class="docutils literal"><span class="pre">Pos_Error</span></tt> column (positive).
|
||||
and uncertainties (in the <code class="docutils literal notranslate"><span class="pre">Step</span></code> column). If asymmetric errors are determined, these
|
||||
will be listed in the <code class="docutils literal notranslate"><span class="pre">Step</span></code> column (negative) and the <code class="docutils literal notranslate"><span class="pre">Pos_Error</span></code> column (positive).
|
||||
Optionally, lower and upper boundaries for the parameters can be specified as
|
||||
shown above.</p>
|
||||
<p>The meaning of the parameters above is explained in the following:</p>
|
||||
<p>Since a <a class="reference internal" href="user-manual.html#single-histogram-fit"><em>single-histogram fit</em></a> should be done, some
|
||||
<p>Since a <a class="reference internal" href="user-manual.html#single-histogram-fit"><span class="std std-ref">single-histogram fit</span></a> should be done, some
|
||||
histogram-specific parameters are needed. These are a normalization constant (parameter 1),
|
||||
a parameter describing the background of uncorrelated events (parameter 2) and the initial
|
||||
phase of the spin precession with respect to the detector (parameter 3). As stated above,
|
||||
there are three histograms containing useful information (“Up”, “Down”, “Right”); hence,
|
||||
there are three histograms containing useful information (“Up”, “Down”, “Right”); hence,
|
||||
this set of parameters has to be present for each of them (parameters 1–9).
|
||||
The remaining parameters are used to model the decay asymmetry which is assumed to be equal
|
||||
for all histograms. In this example one has two signals (<em>e.g.</em> from the sample and the
|
||||
sample holder), each with an amplitude (parameters 10 and 13), a depolarization rate
|
||||
(parameters 11 and 14) and a mean field (here given in Gauss, parameters 12 and 15).</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-theory-block"><em>The THEORY block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>THEORY
|
||||
asymmetry 10
|
||||
simplExpo 11 (rate)
|
||||
TFieldCos map1 fun1 (phase frequency)
|
||||
+
|
||||
asymmetry 13
|
||||
simpleGss 14 (rate)
|
||||
TFieldCos map1 fun2 (phase frequency)
|
||||
<p><a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">The THEORY block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">THEORY</span>
|
||||
<span class="n">asymmetry</span> <span class="mi">10</span>
|
||||
<span class="n">simplExpo</span> <span class="mi">11</span> <span class="p">(</span><span class="n">rate</span><span class="p">)</span>
|
||||
<span class="n">TFieldCos</span> <span class="n">map1</span> <span class="n">fun1</span> <span class="p">(</span><span class="n">phase</span> <span class="n">frequency</span><span class="p">)</span>
|
||||
<span class="o">+</span>
|
||||
<span class="n">asymmetry</span> <span class="mi">13</span>
|
||||
<span class="n">simpleGss</span> <span class="mi">14</span> <span class="p">(</span><span class="n">rate</span><span class="p">)</span>
|
||||
<span class="n">TFieldCos</span> <span class="n">map1</span> <span class="n">fun2</span> <span class="p">(</span><span class="n">phase</span> <span class="n">frequency</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The THEORY block is used to define a fit-parameter-dependent theory function used to model
|
||||
the decay asymmetry. Different <a class="reference internal" href="user-manual.html#msr-theory-block"><em>predefined</em></a> and <a class="reference internal" href="user-manual.html#id38"><em>user-defined</em></a>
|
||||
the decay asymmetry. Different <a class="reference internal" href="user-manual.html#msr-theory-block"><span class="std std-ref">predefined</span></a> and <a class="reference internal" href="user-manual.html#id38"><span class="std std-ref">user-defined</span></a>
|
||||
functions can be combined here. Theory lines following each other are <em>multiplied</em> and the <strong>+</strong> sign
|
||||
is used to add different (here: two) signal contributions. The numbers are the parameter numbers
|
||||
according to the <tt class="docutils literal"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></tt>. <tt class="docutils literal"><span class="pre">map</span></tt> and <tt class="docutils literal"><span class="pre">fun</span></tt> are used to refer to
|
||||
according to the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code>. <code class="docutils literal notranslate"><span class="pre">map</span></code> and <code class="docutils literal notranslate"><span class="pre">fun</span></code> are used to refer to
|
||||
histogram-dependent parameters and to interrelate fit parameters, respectively (see below).</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-functions-block"><em>The FUNCTIONS block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">FUNCTIONS</span>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-functions-block"><span class="std std-ref">The FUNCTIONS block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FUNCTIONS</span>
|
||||
<span class="n">fun1</span> <span class="o">=</span> <span class="n">gamma_mu</span> <span class="o">*</span> <span class="n">par12</span>
|
||||
<span class="n">fun2</span> <span class="o">=</span> <span class="n">gamma_mu</span> <span class="o">*</span> <span class="n">par15</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>Here functions interrelating different fit parameters and predefined constants can be defined for
|
||||
the use in the <tt class="docutils literal"><span class="pre">THEORY</span> <span class="pre">block</span></tt>. In the example, the functions are used to calculate the
|
||||
muon-spin-precession frequencies for the given fields [<span class="math">\(\nu = \gamma_\mu B / (2\pi)\)</span>]. One
|
||||
the use in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code>. In the example, the functions are used to calculate the
|
||||
muon-spin-precession frequencies for the given fields [<span class="math notranslate nohighlight">\(\nu = \gamma_\mu B / (2\pi)\)</span>]. One
|
||||
function is used for each signal. Altogether, the theory function defined above is
|
||||
<span class="math">\(A(t) = p_{10} e^{-p_{11} t} \cos(\varphi_i \pi/180 + \gamma_\mu p_{12} t) + p_{13} e^{-(p_{14} t)^2/2} \cos(\varphi_i \pi/180 + \gamma_\mu p_{15} t)\)</span>, where the <em>p</em> are the parameters in the <tt class="docutils literal"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></tt> and <span class="math">\(\varphi_i = p_3, p_6, p_9\)</span>
|
||||
<span class="math notranslate nohighlight">\(A(t) = p_{10} e^{-p_{11} t} \cos(\varphi_i \pi/180 + \gamma_\mu p_{12} t) + p_{13} e^{-(p_{14} t)^2/2} \cos(\varphi_i \pi/180 + \gamma_\mu p_{15} t)\)</span>, where the <em>p</em> are the parameters in the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code> and <span class="math notranslate nohighlight">\(\varphi_i = p_3, p_6, p_9\)</span>
|
||||
depending on the histogram as shall be seen later.</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-run-block"><em>The RUN block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN (name beamline institute data-file-format)
|
||||
fittype 0 (single histogram fit)
|
||||
norm 1
|
||||
backgr.fit 2
|
||||
map 3 0 0 0 0 0 0 0 0 0
|
||||
forward 3
|
||||
data 1 8000
|
||||
t0 1
|
||||
fit 0 4.9
|
||||
packing 20
|
||||
<p><a class="reference internal" href="user-manual.html#msr-run-block"><span class="std std-ref">The RUN block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">RUN</span> <span class="n">data</span><span class="o">/</span><span class="n">deltat_pta_gps_3110</span> <span class="n">PIM3</span> <span class="n">PSI</span> <span class="n">PSI</span><span class="o">-</span><span class="n">BIN</span> <span class="p">(</span><span class="n">name</span> <span class="n">beamline</span> <span class="n">institute</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span><span class="o">-</span><span class="nb">format</span><span class="p">)</span>
|
||||
<span class="n">fittype</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histogram</span> <span class="n">fit</span><span class="p">)</span>
|
||||
<span class="n">norm</span> <span class="mi">1</span>
|
||||
<span class="n">backgr</span><span class="o">.</span><span class="n">fit</span> <span class="mi">2</span>
|
||||
<span class="nb">map</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
<span class="n">forward</span> <span class="mi">3</span>
|
||||
<span class="n">data</span> <span class="mi">1</span> <span class="mi">8000</span>
|
||||
<span class="n">t0</span> <span class="mi">1</span>
|
||||
<span class="n">fit</span> <span class="mi">0</span> <span class="mf">4.9</span>
|
||||
<span class="n">packing</span> <span class="mi">20</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The RUN blocks are used to collect information on the data to be analyzed. Specifically, these are:</p>
|
||||
<blockquote>
|
||||
<div><div class="highlight-python"><div class="highlight"><pre><span></span>RUN data/deltat_pta_gps_3110 PIM3 PSI PSI-BIN (name beamline institute data-file-format)
|
||||
<div><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">RUN</span> <span class="n">data</span><span class="o">/</span><span class="n">deltat_pta_gps_3110</span> <span class="n">PIM3</span> <span class="n">PSI</span> <span class="n">PSI</span><span class="o">-</span><span class="n">BIN</span> <span class="p">(</span><span class="n">name</span> <span class="n">beamline</span> <span class="n">institute</span> <span class="n">data</span><span class="o">-</span><span class="n">file</span><span class="o">-</span><span class="nb">format</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The path to the data file and the file format (NEXUS, ROOT-NPP, ROOT-PPC, PSI-BIN, PSI-MDU, WKM, MUD, MDU-ASCII).</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>fittype 0 (single histogram fit)
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fittype</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histogram</span> <span class="n">fit</span><span class="p">)</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the fit type (0 = single-histogram fit)</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>norm 1
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">norm</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the number of the fit parameter representing the normalization constant</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>backgr.fit 2
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">backgr</span><span class="o">.</span><span class="n">fit</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the number of the fit parameter representing the background</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>map 3 0 0 0 0 0 0 0 0 0
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">map</span> <span class="mi">3</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the definition of the <strong>maps</strong> used in the <tt class="docutils literal"><span class="pre">THEORY</span> <span class="pre">block</span></tt> — RUN-block-specific
|
||||
<p>the definition of the <strong>maps</strong> used in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code> — RUN-block-specific
|
||||
parameters are given here; in this example, <strong>map1</strong> is substituted by <strong>parameter 3</strong>
|
||||
in the <tt class="docutils literal"><span class="pre">THEORY</span> <span class="pre">block</span></tt> for this RUN block and <strong>map2</strong>, <strong>map3</strong>, and so on are undefined.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>forward 3
|
||||
in the <code class="docutils literal notranslate"><span class="pre">THEORY</span> <span class="pre">block</span></code> for this RUN block and <strong>map2</strong>, <strong>map3</strong>, and so on are undefined.</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">forward</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the histogram number; in this example 3 corresponds to the histogram of the “Up” positron counter</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>data 1 8000
|
||||
<p>the histogram number; in this example 3 corresponds to the histogram of the “Up” positron counter</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">data</span> <span class="mi">1</span> <span class="mi">8000</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>start and end bins of the range containing useful data in the histogram (to be adjusted, <em>e.g.</em> by using <tt class="docutils literal"><span class="pre">musrt0</span></tt>, see below)</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>t0 1
|
||||
<p>start and end bins of the range containing useful data in the histogram (to be adjusted, <em>e.g.</em> by using <code class="docutils literal notranslate"><span class="pre">musrt0</span></code>, see below)</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">t0</span> <span class="mi">1</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>histogram bin corresponding to the time zero (muon implantation time) (to be adjusted, <em>e.g.</em> by <tt class="docutils literal"><span class="pre">musrt0</span></tt>, see below)</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>fit 0 4.9
|
||||
<p>histogram bin corresponding to the time zero (muon implantation time) (to be adjusted, <em>e.g.</em> by <code class="docutils literal notranslate"><span class="pre">musrt0</span></code>, see below)</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fit</span> <span class="mi">0</span> <span class="mf">4.9</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>start and end times (in μs) defining the fit range. <em>In case the fit range
|
||||
exceeds the range of useful data (specified above using the data tag), eventually
|
||||
this data range is used as fit range.</em></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>packing 20
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">packing</span> <span class="mi">20</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the packing of the histograms (in histogram bins)</p>
|
||||
<p>Since the data of three histograms is to be analyzed, the file contains not only one but
|
||||
three RUN blocks — each defining the histogram-specific information following the example given above.</p>
|
||||
</div></blockquote>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-commands-block"><em>The COMMAND block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span><span class="n">COMMANDS</span>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">The COMMAND block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">COMMANDS</span>
|
||||
<span class="n">MINIMIZE</span>
|
||||
<span class="n">MINOS</span>
|
||||
<span class="n">SAVE</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>In the <tt class="docutils literal"><span class="pre">COMMANDS</span> <span class="pre">block</span></tt>, a sequence of operations that should be performed is defined.
|
||||
Here, the requested operations are the minimization of <span class="math">\(\chi^2\)</span> (MINIMIZE), the
|
||||
<p>In the <code class="docutils literal notranslate"><span class="pre">COMMANDS</span> <span class="pre">block</span></code>, a sequence of operations that should be performed is defined.
|
||||
Here, the requested operations are the minimization of <span class="math notranslate nohighlight">\(\chi^2\)</span> (MINIMIZE), the
|
||||
calculation of <em>asymmetric errors</em> (MINOS) as well as saving the found parameter values
|
||||
and uncertainties to the msr file (SAVE). A full description of the possible commands can
|
||||
be found <a class="reference internal" href="user-manual.html#msr-commands-block"><em>here</em></a>.</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-fourier-block"><em>The FOURIER block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>FOURIER
|
||||
units Gauss # units either 'Gauss', 'MHz', or 'Mc/s'
|
||||
fourier_power 10
|
||||
apodization WEAK # NONE, WEAK, MEDIUM, STRONG
|
||||
plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
|
||||
phase par3
|
||||
range 0.0 600.0
|
||||
be found <a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">here</span></a>.</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-fourier-block"><span class="std std-ref">The FOURIER block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FOURIER</span>
|
||||
<span class="n">units</span> <span class="n">Gauss</span> <span class="c1"># units either 'Gauss', 'MHz', or 'Mc/s'</span>
|
||||
<span class="n">fourier_power</span> <span class="mi">10</span>
|
||||
<span class="n">apodization</span> <span class="n">WEAK</span> <span class="c1"># NONE, WEAK, MEDIUM, STRONG</span>
|
||||
<span class="n">plot</span> <span class="n">POWER</span> <span class="c1"># REAL, IMAG, REAL_AND_IMAG, POWER, PHASE</span>
|
||||
<span class="n">phase</span> <span class="n">par3</span>
|
||||
<span class="nb">range</span> <span class="mf">0.0</span> <span class="mf">600.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The <tt class="docutils literal"><span class="pre">FOURIER</span> <span class="pre">block</span></tt> is used to define basic settings for the Fourier transform available
|
||||
in <a class="reference internal" href="user-manual.html#musrview"><em>musrview</em></a>. These are:</p>
|
||||
<p>The <code class="docutils literal notranslate"><span class="pre">FOURIER</span> <span class="pre">block</span></code> is used to define basic settings for the Fourier transform available
|
||||
in <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a>. These are:</p>
|
||||
<blockquote>
|
||||
<div><div class="highlight-python"><div class="highlight"><pre><span></span>units Gauss # units either 'Gauss', 'MHz', or 'Mc/s'
|
||||
<div><div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">Gauss</span> <span class="c1"># units either 'Gauss', 'MHz', or 'Mc/s'</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the units of the Fourier domain</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>fourier_power 10
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">fourier_power</span> <span class="mi">10</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the number of data points used for the discrete transform, here <span class="math">\(2^{10}=1024\)</span>.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>apodization WEAK # NONE, WEAK, MEDIUM, STRONG
|
||||
<p>the number of data points used for the discrete transform, here <span class="math notranslate nohighlight">\(2^{10}=1024\)</span>.</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">apodization</span> <span class="n">WEAK</span> <span class="c1"># NONE, WEAK, MEDIUM, STRONG</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the <a class="reference internal" href="user-manual.html#msr-fourier-block-apodization"><em>apodization</em></a> to be used</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>plot POWER # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE
|
||||
<p>the <a class="reference internal" href="user-manual.html#msr-fourier-block-apodization"><span class="std std-ref">apodization</span></a> to be used</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">plot</span> <span class="n">POWER</span> <span class="c1"># REAL, IMAG, REAL_AND_IMAG, POWER, PHASE</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>what should be plotted (real part, imaginary part, and so on)</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>phase par3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">phase</span> <span class="n">par3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the initial phase of the input data is given here in degrees. Optionally, a phase parameter
|
||||
from the <tt class="docutils literal"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></tt> can be given, here <strong>par3</strong> takes the value of <strong>parameter 3</strong>.</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>range 0.0 600.0
|
||||
from the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span> <span class="pre">block</span></code> can be given, here <strong>par3</strong> takes the value of <strong>parameter 3</strong>.</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nb">range</span> <span class="mf">0.0</span> <span class="mf">600.0</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>the start and end points of the range of the Fourier transform in the units specified above</p>
|
||||
</div></blockquote>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-plot-block"><em>The PLOT block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>PLOT 0 (single histo plot)
|
||||
runs 1 2
|
||||
range 0 4 -0.2 0.2
|
||||
<p><a class="reference internal" href="user-manual.html#msr-plot-block"><span class="std std-ref">The PLOT block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PLOT</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histo</span> <span class="n">plot</span><span class="p">)</span>
|
||||
<span class="n">runs</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
<span class="nb">range</span> <span class="mi">0</span> <span class="mi">4</span> <span class="o">-</span><span class="mf">0.2</span> <span class="mf">0.2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The <tt class="docutils literal"><span class="pre">PLOT</span> <span class="pre">block</span></tt> defines which data (corresponding to the given RUN blocks) is plotted when
|
||||
<a class="reference internal" href="user-manual.html#musrview"><em>musrview</em></a> is called. In the given example, a canvas would be drawn containing
|
||||
the (life-time-corrected) data of the first two <tt class="docutils literal"><span class="pre">RUN</span> <span class="pre">blocks</span></tt> (“Up” and “Down” positron counters).
|
||||
<p>The <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> defines which data (corresponding to the given RUN blocks) is plotted when
|
||||
<a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a> is called. In the given example, a canvas would be drawn containing
|
||||
the (life-time-corrected) data of the first two <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">blocks</span></code> (“Up” and “Down” positron counters).
|
||||
The abscissa would range from 0 to 4 μs, the axis of ordinates from -0.2 to 0.2.
|
||||
It is possible to define more than one <tt class="docutils literal"><span class="pre">PLOT</span> <span class="pre">block</span></tt>. Each <tt class="docutils literal"><span class="pre">PLOT</span> <span class="pre">block</span></tt> corresponds to a
|
||||
separate canvas. Therefore, the second <tt class="docutils literal"><span class="pre">PLOT</span> <span class="pre">block</span></tt> in the file</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>PLOT 0 (single histo plot)
|
||||
runs 3
|
||||
use_fit_ranges
|
||||
It is possible to define more than one <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code>. Each <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> corresponds to a
|
||||
separate canvas. Therefore, the second <code class="docutils literal notranslate"><span class="pre">PLOT</span> <span class="pre">block</span></code> in the file</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">PLOT</span> <span class="mi">0</span> <span class="p">(</span><span class="n">single</span> <span class="n">histo</span> <span class="n">plot</span><span class="p">)</span>
|
||||
<span class="n">runs</span> <span class="mi">3</span>
|
||||
<span class="n">use_fit_ranges</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>produces an additional window containing the (not life-time-corrected) data of the third <tt class="docutils literal"><span class="pre">RUN</span> <span class="pre">block</span></tt>
|
||||
(“Right” positron counter). The abscissa ranges from 0 to 4.9 μs (according to the fit range given
|
||||
in the <tt class="docutils literal"><span class="pre">RUN</span> <span class="pre">block</span></tt>).</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-statistic-block"><em>The STATISTIC block</em></a></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>STATISTIC --- 2011-07-09 10:58:44
|
||||
chisq = 1348.1764, NDF = 1146, chisq/NDF = 1.176419
|
||||
<p>produces an additional window containing the (not life-time-corrected) data of the third <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">block</span></code>
|
||||
(“Right” positron counter). The abscissa ranges from 0 to 4.9 μs (according to the fit range given
|
||||
in the <code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">block</span></code>).</p>
|
||||
<p><a class="reference internal" href="user-manual.html#msr-statistic-block"><span class="std std-ref">The STATISTIC block</span></a></p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">STATISTIC</span> <span class="o">---</span> <span class="mi">2011</span><span class="o">-</span><span class="mi">07</span><span class="o">-</span><span class="mi">09</span> <span class="mi">10</span><span class="p">:</span><span class="mi">58</span><span class="p">:</span><span class="mi">44</span>
|
||||
<span class="n">chisq</span> <span class="o">=</span> <span class="mf">1348.1764</span><span class="p">,</span> <span class="n">NDF</span> <span class="o">=</span> <span class="mi">1146</span><span class="p">,</span> <span class="n">chisq</span><span class="o">/</span><span class="n">NDF</span> <span class="o">=</span> <span class="mf">1.176419</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>This block is the last block of a msr file. It contains some information on the fit: the
|
||||
date and time as well as the absolute and normalized values of <span class="math">\(\chi^2\)</span> and the
|
||||
date and time as well as the absolute and normalized values of <span class="math notranslate nohighlight">\(\chi^2\)</span> and the
|
||||
number of degrees of freedom in the fit.
|
||||
These information only have a meaning if the fitting procedure has been executed at
|
||||
least once and the fit has converged!</p>
|
||||
@ -293,9 +415,9 @@ least once and the fit has converged!</p>
|
||||
<div class="section" id="determine-t0-and-the-data-range-using-musrt0">
|
||||
<h3>Determine t0 and the data range using musrt0<a class="headerlink" href="#determine-t0-and-the-data-range-using-musrt0" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Before the given model can be fitted to the data, the data ranges and time zeros of the different
|
||||
<tt class="docutils literal"><span class="pre">RUN</span> <span class="pre">blocks</span></tt> have to be set correctly. This can be achieved using <a class="reference internal" href="user-manual.html#musrt0"><em>musrt0</em></a>.
|
||||
Starting this program by selecting the <tt class="docutils literal"><span class="pre">musrt0</span></tt> button in <tt class="docutils literal"><span class="pre">musredit</span></tt> or calling from a terminal</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrt0 3110_tutorial.msr
|
||||
<code class="docutils literal notranslate"><span class="pre">RUN</span> <span class="pre">blocks</span></code> have to be set correctly. This can be achieved using <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a>.
|
||||
Starting this program by selecting the <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> button in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or calling from a terminal</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrt0 3110_tutorial.msr
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>opens an interactive window plotting the data of the first RUN block:</p>
|
||||
@ -310,65 +432,65 @@ when the cursor is found at a suitable location:</p>
|
||||
<img alt="_images/tutorial-musrt0-2.png" src="_images/tutorial-musrt0-2.png" />
|
||||
<p>After all lines have been adjusted for the first histogram, one can go on to the second by pressing <strong>q</strong>.
|
||||
This procedure is repeated until all ranges have been set correctly. When finished with the last histogram
|
||||
the new t0 and data-range values will be written to the msr file. A full description of <tt class="docutils literal"><span class="pre">musrt0</span></tt> can be
|
||||
found <a class="reference internal" href="user-manual.html#musrt0"><em>here</em></a>.</p>
|
||||
the new t0 and data-range values will be written to the msr file. A full description of <code class="docutils literal notranslate"><span class="pre">musrt0</span></code> can be
|
||||
found <a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">here</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="fit-the-model-to-the-data-using-musrfit">
|
||||
<h3>Fit the model to the data using <tt class="docutils literal"><span class="pre">musrfit</span></tt><a class="headerlink" href="#fit-the-model-to-the-data-using-musrfit" title="Permalink to this headline">¶</a></h3>
|
||||
<h3>Fit the model to the data using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code><a class="headerlink" href="#fit-the-model-to-the-data-using-musrfit" title="Permalink to this headline">¶</a></h3>
|
||||
<p>Now that the basics of the msr file have been introduced and the necessary adjustments have been done one
|
||||
can proceed with fitting the specified model to the data. This is done by selecting the <tt class="docutils literal"><span class="pre">musrfit</span></tt> icon
|
||||
in <tt class="docutils literal"><span class="pre">musredit</span></tt> or calling from a terminal</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrfit 3110_tutorial.msr
|
||||
can proceed with fitting the specified model to the data. This is done by selecting the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> icon
|
||||
in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or calling from a terminal</p>
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrfit 3110_tutorial.msr
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>After the fitting procedure has finished the msr file is updated and contains the newly determined values
|
||||
of the fit parameters.</p>
|
||||
</div>
|
||||
<div class="section" id="view-the-data-and-the-fit-using-musrview">
|
||||
<h3>View the data and the fit using <tt class="docutils literal"><span class="pre">musrview</span></tt><a class="headerlink" href="#view-the-data-and-the-fit-using-musrview" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The data and the corresponding fit can be visualized by choosing the <tt class="docutils literal"><span class="pre">musrview</span></tt> icon in <tt class="docutils literal"><span class="pre">musredit</span></tt> or
|
||||
<h3>View the data and the fit using <code class="docutils literal notranslate"><span class="pre">musrview</span></code><a class="headerlink" href="#view-the-data-and-the-fit-using-musrview" title="Permalink to this headline">¶</a></h3>
|
||||
<p>The data and the corresponding fit can be visualized by choosing the <code class="docutils literal notranslate"><span class="pre">musrview</span></code> icon in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> or
|
||||
calling from a terminal</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ musrview 3110_tutorial.msr
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ musrview 3110_tutorial.msr
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>This creates the windows according to the given PLOT blocks in the msr file:</p>
|
||||
<img alt="_images/tutorial-musrview-1.png" src="_images/tutorial-musrview-1.png" />
|
||||
<p>The basic features of <tt class="docutils literal"><span class="pre">musrview</span></tt> can be found in the <tt class="docutils literal"><span class="pre">Musrfit</span> <span class="pre">menu</span></tt>. They include:</p>
|
||||
<p>The basic features of <code class="docutils literal notranslate"><span class="pre">musrview</span></code> can be found in the <code class="docutils literal notranslate"><span class="pre">Musrfit</span> <span class="pre">menu</span></code>. They include:</p>
|
||||
<ul class="simple">
|
||||
<li>export the shown data and the model to an ASCII file with comma-separated values</li>
|
||||
<li>presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)</li>
|
||||
<li>calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), <em>e.g.</em> for
|
||||
the asymmetry of the “Up” and “Down” detectors:</li>
|
||||
the asymmetry of the “Up” and “Down” detectors:</li>
|
||||
</ul>
|
||||
<img alt="_images/tutorial-musrview-FT.png" src="_images/tutorial-musrview-FT.png" />
|
||||
</div>
|
||||
<div class="section" id="process-multiple-msr-files-using-msr2data">
|
||||
<h3>Process multiple msr files using <tt class="docutils literal"><span class="pre">msr2data</span></tt><a class="headerlink" href="#process-multiple-msr-files-using-msr2data" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This short introduction is concluded by calling attention to the program <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>.
|
||||
As the name indicates the main purpose of this program is to extract the <tt class="docutils literal"><span class="pre">FITPARAMETER</span></tt> block
|
||||
<h3>Process multiple msr files using <code class="docutils literal notranslate"><span class="pre">msr2data</span></code><a class="headerlink" href="#process-multiple-msr-files-using-msr2data" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This short introduction is concluded by calling attention to the program <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>.
|
||||
As the name indicates the main purpose of this program is to extract the <code class="docutils literal notranslate"><span class="pre">FITPARAMETER</span></code> block
|
||||
information from multiple msr files with the same structure and to summarize them in a single
|
||||
ASCII file (either in <tt class="docutils literal"><span class="pre">TRIUMF</span> <span class="pre">DB</span></tt> format or simple columns). However, as described in detail
|
||||
ASCII file (either in <code class="docutils literal notranslate"><span class="pre">TRIUMF</span> <span class="pre">DB</span></code> format or simple columns). However, as described in detail
|
||||
in the manual, it is not only possible to collect data from msr files but also to create new
|
||||
msr files from a template and to process these files using <tt class="docutils literal"><span class="pre">musrfit</span></tt> on the fly.</p>
|
||||
msr files from a template and to process these files using <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on the fly.</p>
|
||||
<p>Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced
|
||||
above for run <strong>3110</strong> (<em>e.g.</em> in the case one has done measurements at different temperatures) one can
|
||||
use the file <tt class="docutils literal"><span class="pre">3110_tutorial.msr</span></tt> as template, generate the files <tt class="docutils literal"><span class="pre">3111_tutorial.msr</span></tt> through
|
||||
<tt class="docutils literal"><span class="pre">3114_tutorial.msr</span></tt> with the corresponding updates in the RUN blocks, call for each one <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||||
use the file <code class="docutils literal notranslate"><span class="pre">3110_tutorial.msr</span></code> as template, generate the files <code class="docutils literal notranslate"><span class="pre">3111_tutorial.msr</span></code> through
|
||||
<code class="docutils literal notranslate"><span class="pre">3114_tutorial.msr</span></code> with the corresponding updates in the RUN blocks, call for each one <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>
|
||||
and finally summarize the FITPARAMETER block information of all processed files in an ASCII output
|
||||
file <tt class="docutils literal"><span class="pre">tutorial-T-dependence.dat</span></tt> (simple columns). If further information on the temperature or the
|
||||
file <code class="docutils literal notranslate"><span class="pre">tutorial-T-dependence.dat</span></code> (simple columns). If further information on the temperature or the
|
||||
applied field is available in the data files these will be included as well in the resulting ASCII file.
|
||||
From the terminal this would be done as follows:</p>
|
||||
<div class="highlight-bash"><div class="highlight"><pre><span></span>$ msr2data <span class="m">3110</span> <span class="m">3114</span> _tutorial fit-3110 -o tutorial-T-dependence.dat data
|
||||
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$ msr2data <span class="m">3110</span> <span class="m">3114</span> _tutorial fit-3110 -o tutorial-T-dependence.dat data
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>To achieve the same in <tt class="docutils literal"><span class="pre">musredit</span></tt> (in this snapshot in the <em>dark theme</em>) one selects the <tt class="docutils literal"><span class="pre">msr2data</span></tt> icon and fills the form accordingly:</p>
|
||||
<p>To achieve the same in <code class="docutils literal notranslate"><span class="pre">musredit</span></code> (in this snapshot in the <em>dark theme</em>) one selects the <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> icon and fills the form accordingly:</p>
|
||||
<img alt="_images/tutorial-musredit-msr2data.png" src="_images/tutorial-musredit-msr2data.png" />
|
||||
</div>
|
||||
<div class="section" id="further-reading">
|
||||
<h3>Further reading<a class="headerlink" href="#further-reading" title="Permalink to this headline">¶</a></h3>
|
||||
<p>This page only summarizes the very basic features and options of the programs contained in the <tt class="docutils literal"><span class="pre">musrfit</span></tt> suite.
|
||||
For a complete description please refer to the manuals of <a class="reference internal" href="user-manual.html#musrfit"><em>musrfit</em></a> (including <a class="reference internal" href="user-manual.html#musrview"><em>musrview</em></a>,
|
||||
<a class="reference internal" href="user-manual.html#musrt0"><em>musrt0</em></a>, and <a class="reference internal" href="user-manual.html#musrft"><em>musrFT</em></a>), <a class="reference internal" href="mupp.html#mupp"><em>mupp</em></a>, <a class="reference internal" href="musredit.html#musredit-sec"><em>musredit</em></a>, and <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>.</p>
|
||||
<p>This page only summarizes the very basic features and options of the programs contained in the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> suite.
|
||||
For a complete description please refer to the manuals of <a class="reference internal" href="user-manual.html#musrfit"><span class="std std-ref">musrfit</span></a> (including <a class="reference internal" href="user-manual.html#musrview"><span class="std std-ref">musrview</span></a>,
|
||||
<a class="reference internal" href="user-manual.html#musrt0"><span class="std std-ref">musrt0</span></a>, and <a class="reference internal" href="user-manual.html#musrft"><span class="std std-ref">musrFT</span></a>), <a class="reference internal" href="mupp.html#mupp"><span class="std std-ref">mupp</span></a>, <a class="reference internal" href="musredit.html#musredit-sec"><span class="std std-ref">musredit</span></a>, and <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="asymmtery-fit-tutorial">
|
||||
@ -378,23 +500,73 @@ For a complete description please refer to the manuals of <a class="reference in
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
<div class="bottomnav">
|
||||
</div>
|
||||
|
||||
<p>
|
||||
«  <a href="cite.html">How to Cite <tt class="docutils literal"><span class="pre">musrfit</span></tt>?</a>
|
||||
  ::  
|
||||
<a class="uplink" href="index.html">Contents</a>
|
||||
  ::  
|
||||
<a href="user-manual.html">User manual</a>  »
|
||||
</p>
|
||||
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|
||||
<footer>
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||||
|
||||
</div>
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||||
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<a href="user-manual.html" class="btn btn-neutral float-right" title="User manual" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
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||||
© Copyright 2022, Andreas Suter.
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||||
Last updated on May 29, 2022.
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||||
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
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||||
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|
||||
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||||
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||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
||||
<p>
|
||||
© Copyright 2022, Andreas Suter.
|
||||
Last updated on Dec 12, 2022.
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||||
|
||||
</p>
|
||||
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|
||||
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
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<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Documentation of user libs (user functions)</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#meissner-profiles-vortex-lattice-related-functions-bmw-libs">Meissner-Profiles / Vortex-Lattice related functions (BMW libs)</a><ul>
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<li class="toctree-l4"><a class="reference internal" href="#le-mgrsr">LE-μSR</a></li>
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<li class="toctree-l4"><a class="reference internal" href="#bulk-mgrsr">Bulk μSR</a></li>
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<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
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<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
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<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
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<div class="section" id="documentation-of-user-libs-user-functions">
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<span id="user-libs"></span><span id="index-0"></span><h1>Documentation of user libs (user functions)<a class="headerlink" href="#documentation-of-user-libs-user-functions" title="Permalink to this headline">¶</a></h1>
|
||||
@ -55,22 +189,22 @@
|
||||
<span id="index-2"></span><h3>libFitPofB<a class="headerlink" href="#libfitpofb" title="Permalink to this headline">¶</a></h3>
|
||||
<div class="section" id="introduction">
|
||||
<h4>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h4>
|
||||
<p><tt class="docutils literal"><span class="pre">libFitPofB</span></tt> is a collection of <tt class="docutils literal"><span class="pre">C++</span></tt> classes using the <tt class="docutils literal"><span class="pre">musrfit</span></tt> <a class="reference internal" href="user-manual.html#id38"><em>user-functions</em></a>
|
||||
interface in order to facilitate the usage in conjunction with <tt class="docutils literal"><span class="pre">musrfit</span></tt>. The classes contained in this
|
||||
<p><code class="docutils literal notranslate"><span class="pre">libFitPofB</span></code> is a collection of <code class="docutils literal notranslate"><span class="pre">C++</span></code> classes using the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> <a class="reference internal" href="user-manual.html#id38"><span class="std std-ref">user-functions</span></a>
|
||||
interface in order to facilitate the usage in conjunction with <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>. The classes contained in this
|
||||
library generally implement calculations of one-dimensional static magnetic field distributions
|
||||
<span class="math">\(p(B)\)</span> which lead to the muon-spin depolarization functions</p>
|
||||
<div class="math">
|
||||
<span class="math notranslate nohighlight">\(p(B)\)</span> which lead to the muon-spin depolarization functions</p>
|
||||
<div class="math notranslate nohighlight">
|
||||
\[{\cal P}(t) = \int p(B) \cos(\gamma_\mu B t + \varphi) dB,\]</div>
|
||||
<p>where <span class="math">\(\gamma_\mu = 2 \pi \times 135.54\)</span> MHz/T is the gyromagnetic ratio of the muon and <span class="math">\(\varphi\)</span>
|
||||
<p>where <span class="math notranslate nohighlight">\(\gamma_\mu = 2 \pi \times 135.54\)</span> MHz/T is the gyromagnetic ratio of the muon and <span class="math notranslate nohighlight">\(\varphi\)</span>
|
||||
is the initial phase of the muon spins with respect to the positron detector. At the moment the only available
|
||||
implementations deal with field distributions measured in local isotropic superconductors, either by means of
|
||||
low-energy μSR (see <a class="reference external" href="https://www.psi.ch/smus/lem">https://www.psi.ch/smus/lem</a>) in the Meissner state or by bulk μSR in the mixed state.
|
||||
In the following the basic usage of the library in <tt class="docutils literal"><span class="pre">musrfit</span></tt> is explained—the calculations by themselves are only
|
||||
In the following the basic usage of the library in <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> is explained—the calculations by themselves are only
|
||||
outlined. For further information please refer to the original literature and/or the source code of the implementation.</p>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">In order to supply certain information needed for the calculations but not suited to be stored in the <tt class="docutils literal"><span class="pre">musrfit</span></tt>
|
||||
msr files an <tt class="docutils literal"><span class="pre">XML</span></tt> configuration file in the working directory is used. For details, see below.</p>
|
||||
<p class="last">In order to supply certain information needed for the calculations but not suited to be stored in the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>
|
||||
msr files an <code class="docutils literal notranslate"><span class="pre">XML</span></code> configuration file in the working directory is used. For details, see below.</p>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
@ -79,16 +213,16 @@ is the best way to do efficient Fourier transforms for a given machine before th
|
||||
repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once
|
||||
obtained information in an external file and just load it the next time this information is needed
|
||||
(<a class="reference external" href="http://fftw.org/fftw3_doc/Wisdom.html">wisdom handling</a>). In case this feature shall be used, a valid wisdom
|
||||
file has to be specified in the <tt class="docutils literal"><span class="pre">XML</span></tt> file.</p>
|
||||
file has to be specified in the <code class="docutils literal notranslate"><span class="pre">XML</span></code> file.</p>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">The model functions described in the following do generally <em>not behave nicely</em> in conjunction with <tt class="docutils literal"><span class="pre">MINUIT</span></tt>
|
||||
<p class="last">The model functions described in the following do generally <em>not behave nicely</em> in conjunction with <code class="docutils literal notranslate"><span class="pre">MINUIT</span></code>
|
||||
function minimizations (or maximizations). The analysis process at the moment in most cases involves some
|
||||
tedious trial-and-error procedure, where the displayed MINUIT information as always deserves attention.
|
||||
This is especially true if small effects should be analyzed (<em>e.g.</em> small diamagnetic shifts in superconductors).
|
||||
The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also
|
||||
the use of the fit option of <tt class="docutils literal"><span class="pre">msr2data</span></tt> <em>cannot</em> be advised.</p>
|
||||
the use of the fit option of <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> <em>cannot</em> be advised.</p>
|
||||
</div>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
@ -100,44 +234,44 @@ an acknowledgment of the use of the library is appreciated.</p>
|
||||
<h4>LE-μSR<a class="headerlink" href="#le-mgrsr" title="Permalink to this headline">¶</a></h4>
|
||||
<div class="section" id="one-dimensional-london-model-for-the-meissner-state-of-isotropic-superconductors">
|
||||
<span id="index-3"></span><h5>One-dimensional London model for the Meissner state of isotropic superconductors<a class="headerlink" href="#one-dimensional-london-model-for-the-meissner-state-of-isotropic-superconductors" title="Permalink to this headline">¶</a></h5>
|
||||
<p>The models for analyzing LE-μSR data assume the magnetic induction <span class="math">\(B(z)\)</span> to vary only in the
|
||||
<p>The models for analyzing LE-μSR data assume the magnetic induction <span class="math notranslate nohighlight">\(B(z)\)</span> to vary only in the
|
||||
dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[p(B) = n(z) \left| \frac{dB(z)}{dz} \right|^{-1}\]</div>
|
||||
<p>where <span class="math">\(n(z)\)</span> is the muon implantation profile simulated by <tt class="docutils literal"><span class="pre">TRIM.SP</span></tt>.</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(n(z)\)</span> is the muon implantation profile simulated by <code class="docutils literal notranslate"><span class="pre">TRIM.SP</span></code>.</p>
|
||||
<p>Assuming an array of <em>N</em> isotropic local superconductors with a total thickness <em>d</em> in the Meissner state
|
||||
the magnetic induction is given by solving the 1D London equation</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[\frac{\partial^2}{\partial z^2}B_i(z) = \frac{1}{\lambda_i^2}B_i(z)\]</div>
|
||||
<p>for each layer <em>i</em> taking into account the boundary conditions (F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34)</p>
|
||||
<div class="math">
|
||||
\[B_1(0) = B_N(d) = \mu_0H\]\[B_i(d_i) = B_{i+1}(d_i)\]\[\lambda_i^2B_i'(z)\Big\vert_{z=d_i} = \lambda_{i+1}^2B_{i+1}'(z)\Big\vert_{z=d_i},\]</div>
|
||||
<p>where the <span class="math">\(d_i\)</span> specify the interfaces between two adjacent layers and <span class="math">\(\lambda_i\)</span> is
|
||||
the magnetic field penetration depth in the constituent <span class="math">\(i\)</span>.</p>
|
||||
<div class="math notranslate nohighlight">
|
||||
\[ \begin{align}\begin{aligned}B_1(0) = B_N(d) = \mu_0H\\B_i(d_i) = B_{i+1}(d_i)\\\lambda_i^2B_i'(z)\Big\vert_{z=d_i} = \lambda_{i+1}^2B_{i+1}'(z)\Big\vert_{z=d_i},\end{aligned}\end{align} \]</div>
|
||||
<p>where the <span class="math notranslate nohighlight">\(d_i\)</span> specify the interfaces between two adjacent layers and <span class="math notranslate nohighlight">\(\lambda_i\)</span> is
|
||||
the magnetic field penetration depth in the constituent <span class="math notranslate nohighlight">\(i\)</span>.</p>
|
||||
<p>The calculation of the field distribution has been set up for a superconducting half-space as well
|
||||
as superconducting thin films with up to three superconducting layers with different penetration depths.
|
||||
The muon-spin depolarization functions are calculated using the following lines in the <tt class="docutils literal"><span class="pre">THEORY</span></tt> block
|
||||
of a <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr file:</p>
|
||||
The muon-spin depolarization functions are calculated using the following lines in the <code class="docutils literal notranslate"><span class="pre">THEORY</span></code> block
|
||||
of a <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr file:</p>
|
||||
<p id="index-4"><strong>Superconducting half-space</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TLondon1DHS 1 2 3 4 5
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TLondon1DHS</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>phase (deg)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><em>XML startup</em></a> file (keV)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><span class="std std-ref">XML startup</span></a> file (keV)</li>
|
||||
<li>applied field (G)</li>
|
||||
<li>thickness of the dead layer (nm)</li>
|
||||
<li>magnetic field penetration depth (nm)</li>
|
||||
</ol>
|
||||
<p id="index-5"><strong>Superconducting thin film (one layer)</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TLondon1D1L 1 2 3 4 5 6 [a b]
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TLondon1D1L</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">6</span> <span class="p">[</span><span class="n">a</span> <span class="n">b</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The mandatory parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>phase (deg)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><em>XML startup</em></a> file (keV)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><span class="std std-ref">XML startup</span></a> file (keV)</li>
|
||||
<li>applied field (G)</li>
|
||||
<li>thickness of the dead layer (nm)</li>
|
||||
<li>thickness of the actually superconducting layer (nm)</li>
|
||||
@ -149,13 +283,13 @@ of a <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr file
|
||||
<li>fraction f<sub>s</sub> of muons in the substrate contributing to the signal (0 ≤ f<sub>s</sub> ≤ 1)</li>
|
||||
</ol>
|
||||
<p id="index-6"><strong>Superconducting thin-film bilayer heterostructure</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 [a b c]
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TLondon1D2L</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="p">[</span><span class="n">a</span> <span class="n">b</span> <span class="n">c</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The mandatory parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>phase (deg)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><em>XML startup</em></a> file (keV)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><span class="std std-ref">XML startup</span></a> file (keV)</li>
|
||||
<li>applied field (G)</li>
|
||||
<li>thickness of the dead layer (nm)</li>
|
||||
<li>thickness of the actually superconducting first layer (nm)</li>
|
||||
@ -170,13 +304,13 @@ of a <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr file
|
||||
<li>fraction f<sub>s</sub> of muons in the substrate contributing to the signal (0 ≤ f<sub>s</sub> ≤ 1)</li>
|
||||
</ol>
|
||||
<p id="index-7"><strong>Superconducting thin-film trilayer heterostructure</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 [a b c d]
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TLondon1D3L</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mi">5</span> <span class="mi">6</span> <span class="mi">7</span> <span class="mi">8</span> <span class="mi">9</span> <span class="mi">10</span> <span class="p">[</span><span class="n">a</span> <span class="n">b</span> <span class="n">c</span> <span class="n">d</span><span class="p">]</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The mandatory parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>phase (deg)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><em>XML startup</em></a> file (keV)</li>
|
||||
<li>muon implantation energy as specified in the <a class="reference internal" href="#bmwlibs-xml"><span class="std std-ref">XML startup</span></a> file (keV)</li>
|
||||
<li>applied field (G)</li>
|
||||
<li>thickness of the dead layer (nm)</li>
|
||||
<li>thickness of the actually superconducting first layer (nm)</li>
|
||||
@ -202,32 +336,32 @@ of a <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr file
|
||||
<p>When investigating superconductors in the mixed state by means of conventional μSR a
|
||||
two-dimensional flux-line lattice is probed randomly by the muons. The spatial field
|
||||
distributions within such an ordered lattice are modeled using the Fourier series</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[B(\mathbf{r}) = \langle B \rangle \sum\limits_{\mathbf{K}}B_{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r}),\]</div>
|
||||
<p>where <span class="math">\(\mathbf{r}=(x,y)\)</span>, <strong>K</strong> are the reciprocal lattice vectors of a two-dimensional
|
||||
vortex lattice and the <span class="math">\(B_{\mathbf{K}}\)</span> are the Fourier coefficients depending on the
|
||||
magnetic penetration depth <span class="math">\(\lambda\)</span> and the superconducting coherence length <span class="math">\(\xi\)</span>.
|
||||
The <span class="math">\(B_{\mathbf{K}}\)</span> for some specific models are as follows:</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(\mathbf{r}=(x,y)\)</span>, <strong>K</strong> are the reciprocal lattice vectors of a two-dimensional
|
||||
vortex lattice and the <span class="math notranslate nohighlight">\(B_{\mathbf{K}}\)</span> are the Fourier coefficients depending on the
|
||||
magnetic penetration depth <span class="math notranslate nohighlight">\(\lambda\)</span> and the superconducting coherence length <span class="math notranslate nohighlight">\(\xi\)</span>.
|
||||
The <span class="math notranslate nohighlight">\(B_{\mathbf{K}}\)</span> for some specific models are as follows:</p>
|
||||
<p><strong>London model with Gaussian cutoff</strong> (E.H. Brandt, <a class="reference external" href="http://dx.doi.org/10.1007/BF00683568">J. Low Temp. Phys. 73, 355 (1988)</a>.)</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}\]</div>
|
||||
<p><strong>Modified London model</strong> (T.M. Riseman <em>et al.</em>, <a class="reference external" href="http://dx.doi.org/10.1103/PhysRevB.52.10569">Phys. Rev. B 52, 10569 (1995)</a>.)</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[B_{\mathbf{K}} = \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)},\]</div>
|
||||
<p>where <span class="math">\(b = \langle B \rangle / (\mu_0 H_{\rm c2})\)</span>.</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(b = \langle B \rangle / (\mu_0 H_{\rm c2})\)</span>.</p>
|
||||
<p><strong>Analytical Ginzburg-Landau model</strong> ( A. Yaouanc, P. Dalmas de Réotier and E.H. Brandt, <a class="reference external" href="http://dx.doi.org/10.1103/PhysRevB.55.11107">Phys. Rev. B 55, 11107 (1997)</a>)</p>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[B_{\mathbf{K}} = \frac{f_{\infty}K_1\left(\frac{\xi_v}{\lambda}\sqrt{f_{\infty}^2+\lambda^2K^2}\right)}{K_1\left(\frac{\xi_v}{\lambda}f_{\infty}\right)\sqrt{f_{\infty}^2+\lambda^2K^2}},\]</div>
|
||||
<p>where <span class="math">\(f_{\infty} = 1 - b^4,~\xi_v = \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}\)</span> and
|
||||
<span class="math">\(K_1\)</span> is a modified Bessel function.</p>
|
||||
<p>Apart from the mentioned analytic models the <strong>numerical Ginzburg-Landau model</strong> (<a class="reference external" href="http://dx.doi.org/10.1103/PhysRevB.68.054506">E.H. Brandt, Phys. Rev. B 68, 054506 (2003).</a>) is available. In this case <span class="math">\(B(\mathbf{r})\)</span> is obtained by an iterative minimization of the free energy of the vortex lattice.</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(f_{\infty} = 1 - b^4,~\xi_v = \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}\)</span> and
|
||||
<span class="math notranslate nohighlight">\(K_1\)</span> is a modified Bessel function.</p>
|
||||
<p>Apart from the mentioned analytic models the <strong>numerical Ginzburg-Landau model</strong> (<a class="reference external" href="http://dx.doi.org/10.1103/PhysRevB.68.054506">E.H. Brandt, Phys. Rev. B 68, 054506 (2003).</a>) is available. In this case <span class="math notranslate nohighlight">\(B(\mathbf{r})\)</span> is obtained by an iterative minimization of the free energy of the vortex lattice.</p>
|
||||
<p><strong>Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</strong></p>
|
||||
<p>At the moment, the calculation of the field distribution has been implemented for <em>triangular</em> flux-line lattices.
|
||||
The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through
|
||||
the <a class="reference internal" href="#bmwlibs-xml"><em>XML startup</em></a>.
|
||||
The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <tt class="docutils literal"><span class="pre">musrfit</span></tt> msr file:</p>
|
||||
the <a class="reference internal" href="#bmwlibs-xml"><span class="std std-ref">XML startup</span></a>.
|
||||
The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr file:</p>
|
||||
<p id="index-9"><strong>2D triangular vortex lattice, London model with Gaussian cutoff</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TBulkTriVortexLondon 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TBulkTriVortexLondon</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
@ -238,7 +372,7 @@ The muon-spin depolarization functions finally are calculated using the followin
|
||||
<li>Ginzburg-Landau coherence length (nm)</li>
|
||||
</ol>
|
||||
<p id="index-10"><strong>2D triangular vortex lattice, modified London model</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TBulkTriVortexML 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TBulkTriVortexML</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
@ -249,7 +383,7 @@ The muon-spin depolarization functions finally are calculated using the followin
|
||||
<li>Ginzburg-Landau coherence length (nm)</li>
|
||||
</ol>
|
||||
<p id="index-11"><strong>2D triangular vortex lattice, analytic Ginzburg-Landau model</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TBulkTriVortexAGL 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TBulkTriVortexAGL</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
@ -260,7 +394,7 @@ The muon-spin depolarization functions finally are calculated using the followin
|
||||
<li>Ginzburg-Landau coherence length (nm)</li>
|
||||
</ol>
|
||||
<p id="index-12"><strong>2D triangular vortex lattice, numerical Ginzburg-Landau model</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libFitPofB TBulkTriVortexNGL 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libFitPofB</span> <span class="n">TBulkTriVortexNGL</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
@ -272,36 +406,36 @@ The muon-spin depolarization functions finally are calculated using the followin
|
||||
</ol>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">In order to improve the convergence of <tt class="docutils literal"><span class="pre">MIGRAD</span></tt> it has proven useful to use the log-likelihood
|
||||
maximization instead of the <span class="math">\(\chi^2\)</span> minimization routines and to choose sufficiently large
|
||||
initial steps for the parameters. Calling <tt class="docutils literal"><span class="pre">MINOS</span></tt> in conjunction with these functions is futile.</p>
|
||||
<p class="last">In order to improve the convergence of <code class="docutils literal notranslate"><span class="pre">MIGRAD</span></code> it has proven useful to use the log-likelihood
|
||||
maximization instead of the <span class="math notranslate nohighlight">\(\chi^2\)</span> minimization routines and to choose sufficiently large
|
||||
initial steps for the parameters. Calling <code class="docutils literal notranslate"><span class="pre">MINOS</span></code> in conjunction with these functions is futile.</p>
|
||||
</div>
|
||||
<p>Therefore, the <a class="reference internal" href="user-manual.html#msr-commands-block"><em>COMMANDS block</em></a> of the msr file could look like:</p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>COMMANDS
|
||||
STRATEGY 2
|
||||
MAX_LIKELIHOOD
|
||||
MIGRAD
|
||||
HESSE
|
||||
SAVE
|
||||
<p>Therefore, the <a class="reference internal" href="user-manual.html#msr-commands-block"><span class="std std-ref">COMMANDS block</span></a> of the msr file could look like:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">COMMANDS</span>
|
||||
<span class="n">STRATEGY</span> <span class="mi">2</span>
|
||||
<span class="n">MAX_LIKELIHOOD</span>
|
||||
<span class="n">MIGRAD</span>
|
||||
<span class="n">HESSE</span>
|
||||
<span class="n">SAVE</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="the-xml-startup-file">
|
||||
<span id="bmwlibs-xml"></span><span id="index-13"></span><h4>The XML startup file<a class="headerlink" href="#the-xml-startup-file" title="Permalink to this headline">¶</a></h4>
|
||||
<p><tt class="docutils literal"><span class="pre">BMW_startup.xml</span></tt> is a configuration file located in the working directory. In this file some settings
|
||||
<p><code class="docutils literal notranslate"><span class="pre">BMW_startup.xml</span></code> is a configuration file located in the working directory. In this file some settings
|
||||
like the time and field resolution of the calculations as well as the present muon implantation profiles
|
||||
for a LE-μSR analysis have to be defined. The following XML tags are allowed to define settings:</p>
|
||||
<dl class="docutils">
|
||||
<dt><strong><debug>ONE_OR_ZERO</debug></strong></dt>
|
||||
<dd>activate the debugging output of the settings read from the XML file by setting 1, deactivate it with 0.</dd>
|
||||
<dt><strong><wisdom>PATH_TO_FILE</wisdom></strong></dt>
|
||||
<dd>specify the <tt class="docutils literal"><span class="pre">PATH_TO_FILE</span></tt> to an <a class="reference external" href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom">FFTW3 wisdom file</a>
|
||||
that should be used; if the <tt class="docutils literal"><span class="pre">PATH_TO_FILE</span></tt> is invalid, no <tt class="docutils literal"><span class="pre">FFTW3</span></tt> wisdom will be used.</dd>
|
||||
<dd>specify the <code class="docutils literal notranslate"><span class="pre">PATH_TO_FILE</span></code> to an <a class="reference external" href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom">FFTW3 wisdom file</a>
|
||||
that should be used; if the <code class="docutils literal notranslate"><span class="pre">PATH_TO_FILE</span></code> is invalid, no <code class="docutils literal notranslate"><span class="pre">FFTW3</span></code> wisdom will be used.</dd>
|
||||
<dt><strong><delta_t>ResT</delta_t></strong></dt>
|
||||
<dd>set the time resolution <tt class="docutils literal"><span class="pre">ResT</span></tt> for the calculated depolarization function in microseconds.</dd>
|
||||
<dd>set the time resolution <code class="docutils literal notranslate"><span class="pre">ResT</span></code> for the calculated depolarization function in microseconds.</dd>
|
||||
<dt><strong><delta_B>ResB</delta_B></strong></dt>
|
||||
<dd>set the field resolution <tt class="docutils literal"><span class="pre">ResB</span></tt> for the calculated field distribution in Gauss.</dd>
|
||||
<dd>set the field resolution <code class="docutils literal notranslate"><span class="pre">ResB</span></code> for the calculated field distribution in Gauss.</dd>
|
||||
<dt><strong><VortexLattice></VortexLattice></strong></dt>
|
||||
<dd><p class="first">set the parameters used for the calculation of the spatial field distribution of a vortex lattice.</p>
|
||||
<dl class="last docutils">
|
||||
@ -314,25 +448,25 @@ vortex lattice are calculated (inside a <strong><VortexLattice></strong> e
|
||||
<dd><p class="first">set the parameters used for the calculation of LE-μSR field distributions</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><data_path>DATA_PATH_PREFIX</data_path></strong></dt>
|
||||
<dd>specify the <tt class="docutils literal"><span class="pre">DATA_PATH_PREFIX</span></tt> to the <tt class="docutils literal"><span class="pre">TRIM.SP</span></tt> implantation profiles (inside a <strong><LEM></strong> environment)</dd>
|
||||
<dd>specify the <code class="docutils literal notranslate"><span class="pre">DATA_PATH_PREFIX</span></code> to the <code class="docutils literal notranslate"><span class="pre">TRIM.SP</span></code> implantation profiles (inside a <strong><LEM></strong> environment)</dd>
|
||||
<dt><strong><N_theory>N_THEORY</N_theory></strong></dt>
|
||||
<dd>specify the number of points <strong>N_THEORY</strong> for which <em>B(z)</em> is calculated (inside a <strong><LEM></strong> environment)
|
||||
The specification of this number is not needed if the calculation of the inverse of <em>B(z)</em> is implemented!</dd>
|
||||
<dt><strong><energy_list></energy_list></strong></dt>
|
||||
<dd><p class="first">set the energies for which <tt class="docutils literal"><span class="pre">TRIM.SP</span></tt> implantation profiles are available (inside a <strong><LEM></strong> environment)</p>
|
||||
<dd><p class="first">set the energies for which <code class="docutils literal notranslate"><span class="pre">TRIM.SP</span></code> implantation profiles are available (inside a <strong><LEM></strong> environment)</p>
|
||||
<dl class="last docutils">
|
||||
<dt><strong><energy_label>LABEL</energy_label></strong></dt>
|
||||
<dd>specify the <strong>LABEL</strong> within the file name of a available <tt class="docutils literal"><span class="pre">TRIM.SP</span></tt> <tt class="docutils literal"><span class="pre">RGE</span></tt> file (inside a <strong><energy_list></strong> environment)
|
||||
The expected name of the <tt class="docutils literal"><span class="pre">RGE</span></tt> file will be: <tt class="docutils literal"><span class="pre">DATA_PATH_PREFIX</span> <span class="pre">+</span> <span class="pre">LABEL</span> <span class="pre">+</span> <span class="pre">.rge</span></tt></dd>
|
||||
<dd>specify the <strong>LABEL</strong> within the file name of a available <code class="docutils literal notranslate"><span class="pre">TRIM.SP</span></code> <code class="docutils literal notranslate"><span class="pre">RGE</span></code> file (inside a <strong><energy_list></strong> environment)
|
||||
The expected name of the <code class="docutils literal notranslate"><span class="pre">RGE</span></code> file will be: <code class="docutils literal notranslate"><span class="pre">DATA_PATH_PREFIX</span> <span class="pre">+</span> <span class="pre">LABEL</span> <span class="pre">+</span> <span class="pre">.rge</span></code></dd>
|
||||
<dt><strong><energy>E</energy></strong></dt>
|
||||
<dd>specify the muon energy <em>E</em> (in keV) belonging to the <tt class="docutils literal"><span class="pre">TRIM.SP</span></tt> <tt class="docutils literal"><span class="pre">RGE</span></tt> file given above (inside a <strong><energy_list></strong> environment)</dd>
|
||||
<dd>specify the muon energy <em>E</em> (in keV) belonging to the <code class="docutils literal notranslate"><span class="pre">TRIM.SP</span></code> <code class="docutils literal notranslate"><span class="pre">RGE</span></code> file given above (inside a <strong><energy_list></strong> environment)</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
</dd>
|
||||
</dl>
|
||||
<p>An example XML file looks as follows:</p>
|
||||
<div class="highlight-xml"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||||
<div class="highlight-xml notranslate"><div class="highlight"><pre><span></span><span class="cp"><?xml version="1.0" encoding="UTF-8"?></span>
|
||||
<span class="nt"><BMW></span>
|
||||
<span class="nt"><debug></span>0<span class="nt"></debug></span>
|
||||
<span class="nt"><wisdom></span>/home/user/WordsOfWisdom.dat<span class="nt"></wisdom></span>
|
||||
@ -365,69 +499,69 @@ The expected name of the <tt class="docutils literal"><span class="pre">RGE</spa
|
||||
</div>
|
||||
<div class="section" id="nonlocal-superconductivity-related-meissner-screening-functions-as-libs">
|
||||
<h2>Nonlocal superconductivity related Meissner screening functions (AS libs)<a class="headerlink" href="#nonlocal-superconductivity-related-meissner-screening-functions-as-libs" title="Permalink to this headline">¶</a></h2>
|
||||
<p>To be written yet ...</p>
|
||||
<p>To be written yet …</p>
|
||||
</div>
|
||||
<div class="section" id="functions-to-analyze-bgr-nmr-data-bnmr-libs">
|
||||
<span id="bnmr-libs"></span><span id="index-14"></span><h2>Functions to analyze β-NMR data (BNMR libs)<a class="headerlink" href="#functions-to-analyze-bgr-nmr-data-bnmr-libs" title="Permalink to this headline">¶</a></h2>
|
||||
<p>This is a collection of <tt class="docutils literal"><span class="pre">C++</span></tt> classes using the <tt class="docutils literal"><span class="pre">musrfit</span></tt> <a class="reference internal" href="user-manual.html#id38"><em>user-functions</em></a>
|
||||
interface in order to facilitate the usage in conjunction with <tt class="docutils literal"><span class="pre">musrfit</span></tt>. It consists of two libraries:</p>
|
||||
<p>This is a collection of <code class="docutils literal notranslate"><span class="pre">C++</span></code> classes using the <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> <a class="reference internal" href="user-manual.html#id38"><span class="std std-ref">user-functions</span></a>
|
||||
interface in order to facilitate the usage in conjunction with <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>. It consists of two libraries:</p>
|
||||
<ul class="simple">
|
||||
<li><tt class="docutils literal"><span class="pre">libBNMR</span></tt> contains functions to fit spin lattice relaxation (SLR) data.</li>
|
||||
<li><tt class="docutils literal"><span class="pre">libLineProfile</span></tt> contains functions to fit resonance lineshapes.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">libBNMR</span></code> contains functions to fit spin lattice relaxation (SLR) data.</li>
|
||||
<li><code class="docutils literal notranslate"><span class="pre">libLineProfile</span></code> contains functions to fit resonance lineshapes.</li>
|
||||
</ul>
|
||||
<div class="admonition note">
|
||||
<p class="first admonition-title">Note</p>
|
||||
<p class="last">Currently it is recommended to read in the data in ASCII format as a non-μSR fit <a class="reference internal" href="user-manual.html#non-musr-fit"><em>(fit type 8)</em></a>.</p>
|
||||
<p class="last">Currently it is recommended to read in the data in ASCII format as a non-μSR fit <a class="reference internal" href="user-manual.html#non-musr-fit"><span class="std std-ref">(fit type 8)</span></a>.</p>
|
||||
</div>
|
||||
<div class="section" id="libbnmr">
|
||||
<span id="index-15"></span><h3>libBNMR<a class="headerlink" href="#libbnmr" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In β-NMR the SLR is usually measured by implanting a pulse of <span class="math">\(^8\)</span>Li with a length <span class="math">\(t_0\)</span> into the sample.
|
||||
The asymmetry is measured both during the pulse and afterwards. For a a general spin relaxation function <span class="math">\(f(t)\)</span> the time evolution of the asymmetry is then given by [<a class="reference external" href="http://dx.doi.org/10.1103/PhysRevLett.96.147601">Z. Salman, et al., PRL 96, 147601 (2006)</a>]:</p>
|
||||
<div class="math" id="slr">
|
||||
<p>In β-NMR the SLR is usually measured by implanting a pulse of <span class="math notranslate nohighlight">\(^8\)</span>Li with a length <span class="math notranslate nohighlight">\(t_0\)</span> into the sample.
|
||||
The asymmetry is measured both during the pulse and afterwards. For a a general spin relaxation function <span class="math notranslate nohighlight">\(f(t)\)</span> the time evolution of the asymmetry is then given by [<a class="reference external" href="http://dx.doi.org/10.1103/PhysRevLett.96.147601">Z. Salman, et al., PRL 96, 147601 (2006)</a>]:</p>
|
||||
<div class="math notranslate nohighlight" id="slr">
|
||||
<span id="index-16"></span>\[\begin{split}P(t) = \left\{\begin{matrix}
|
||||
\frac{\int_0^t e^{-(t-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^t e^{-t'/\tau_{\mathrm{Li}}}dt' } & t\leq t_0\\[6pt]
|
||||
\frac{\int_0^{t_0}e^{-(t_0-t')/\tau_{\mathrm{Li}}}f(t-t')dt'}{\int_0^{t_0}e^{-t'/\tau_{\mathrm{Li}}}dt'} & t> t_0,
|
||||
\end{matrix}\right.\end{split}\]</div>
|
||||
<p>where <span class="math">\(\tau_{\mathrm{Li}}=1.21\)</span>s is the <span class="math">\(^8\)</span>Li lifetime.</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(\tau_{\mathrm{Li}}=1.21\)</span>s is the <span class="math notranslate nohighlight">\(^8\)</span>Li lifetime.</p>
|
||||
<div class="section" id="functions">
|
||||
<h4>Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h4>
|
||||
<p>The <tt class="docutils literal"><span class="pre">libBNMR</span></tt> library currently contains the following functions:</p>
|
||||
<p>The <code class="docutils literal notranslate"><span class="pre">libBNMR</span></code> library currently contains the following functions:</p>
|
||||
<p id="index-17"><strong>Exponential relaxation</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libBNMR ExpRlx 1 2
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libBNMR</span> <span class="n">ExpRlx</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>pulse length <span class="math">\(t_0\)</span> (s)</li>
|
||||
<li>relaxation rate <span class="math">\(\lambda\)</span> (s<span class="math">\(^{-1}\)</span>)</li>
|
||||
<li>pulse length <span class="math notranslate nohighlight">\(t_0\)</span> (s)</li>
|
||||
<li>relaxation rate <span class="math notranslate nohighlight">\(\lambda\)</span> (s<span class="math notranslate nohighlight">\(^{-1}\)</span>)</li>
|
||||
</ol>
|
||||
<p>This function implements <span class="math">\(f(t)=e^{-\lambda t}\)</span>.</p>
|
||||
<p>This function implements <span class="math notranslate nohighlight">\(f(t)=e^{-\lambda t}\)</span>.</p>
|
||||
<p id="index-18"><strong>Stretched exponential relaxation</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libBNMR SExpRlx 1 2 3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libBNMR</span> <span class="n">SExpRlx</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>pulse length <span class="math">\(t_0\)</span> (s)</li>
|
||||
<li>relaxation rate <span class="math">\(\lambda\)</span> (s<span class="math">\(^{-1}\)</span>)</li>
|
||||
<li>stretching exponent <span class="math">\(\beta\)</span></li>
|
||||
<li>pulse length <span class="math notranslate nohighlight">\(t_0\)</span> (s)</li>
|
||||
<li>relaxation rate <span class="math notranslate nohighlight">\(\lambda\)</span> (s<span class="math notranslate nohighlight">\(^{-1}\)</span>)</li>
|
||||
<li>stretching exponent <span class="math notranslate nohighlight">\(\beta\)</span></li>
|
||||
</ol>
|
||||
<p>This function implements <span class="math">\(f(t)=e^{-(\lambda t)^{\beta}}\)</span>.</p>
|
||||
<p>This function implements <span class="math notranslate nohighlight">\(f(t)=e^{-(\lambda t)^{\beta}}\)</span>.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="liblineprofile">
|
||||
<span id="index-19"></span><h3>libLineProfile<a class="headerlink" href="#liblineprofile" title="Permalink to this headline">¶</a></h3>
|
||||
<p>In addition to some simple line shapes <tt class="docutils literal"><span class="pre">libLineProfile</span></tt> contains functions to fit chemical shift anisotropies in the powder average.
|
||||
<p>In addition to some simple line shapes <code class="docutils literal notranslate"><span class="pre">libLineProfile</span></code> contains functions to fit chemical shift anisotropies in the powder average.
|
||||
Their functional form can be found in <a class="reference external" href="http://dx.doi.org/10.1007/978-3-642-68756-3_2">M. Mehring, Principles of High Resolution NMR in Solids (Springer 1983)</a>.</p>
|
||||
<p>For an axially symmetric interaction it is given by:</p>
|
||||
<div class="math" id="iax">
|
||||
<div class="math notranslate nohighlight" id="iax">
|
||||
<span id="index-20"></span>\[\begin{split}I_{\mathrm ax}(f)=\left\{\begin{matrix} \frac{1}{2\sqrt{(f_\parallel-f_\perp)(f-f_\perp)}}& f\in(f_\perp,f_\parallel)\cup(f_\parallel,f_\perp)\\[6pt] 0 & \text{otherwise}\end{matrix} \right.\end{split}\]</div>
|
||||
<p>where <span class="math">\(f_\parallel\)</span> and <span class="math">\(f_\perp\)</span> are the frequencies that would be observed if the field is oriented paralell or perpendicular to the symmetry axis, respectively.</p>
|
||||
<p>where <span class="math notranslate nohighlight">\(f_\parallel\)</span> and <span class="math notranslate nohighlight">\(f_\perp\)</span> are the frequencies that would be observed if the field is oriented paralell or perpendicular to the symmetry axis, respectively.</p>
|
||||
<div class="line-block">
|
||||
<div class="line">In case of a completely anisotropic interaction, the powder average can be described by the frequencies along the three principle axis <span class="math">\(f_1,f_2,f_3\)</span>.</div>
|
||||
<div class="line">Assume without loss of generality that <span class="math">\(f_1<f_2<f_3\)</span>, then</div>
|
||||
<div class="line">In case of a completely anisotropic interaction, the powder average can be described by the frequencies along the three principle axis <span class="math notranslate nohighlight">\(f_1,f_2,f_3\)</span>.</div>
|
||||
<div class="line">Assume without loss of generality that <span class="math notranslate nohighlight">\(f_1<f_2<f_3\)</span>, then</div>
|
||||
</div>
|
||||
<div class="math" id="ianiso">
|
||||
<div class="math notranslate nohighlight" id="ianiso">
|
||||
<span id="index-21"></span>\[\begin{split}I(f)&=\left\{\begin{matrix}
|
||||
\frac{K(m)}{\pi\sqrt{(f-f_1)(f_3-f_2)}},& f_3\geq f>f_2 \\[9pt]
|
||||
\frac{K(m)}{\pi\sqrt{(f_3-f)(f_2-f_1)}},& f_2>f\geq f_1\\[9pt]
|
||||
@ -440,180 +574,230 @@ m&=\left\{\begin{matrix}
|
||||
\end{matrix} \right. \\
|
||||
\\
|
||||
K(m)&=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\end{split}\]</div>
|
||||
<p><span class="math">\(K(m)\)</span> is the complete elliptic integral of the first kind.</p>
|
||||
<p><span class="math notranslate nohighlight">\(K(m)\)</span> is the complete elliptic integral of the first kind.</p>
|
||||
<div class="section" id="id1">
|
||||
<h4>Functions<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h4>
|
||||
<p>The <tt class="docutils literal"><span class="pre">libLineProfile</span></tt> library currently contains the following functions:</p>
|
||||
<p>The <code class="docutils literal notranslate"><span class="pre">libLineProfile</span></code> library currently contains the following functions:</p>
|
||||
<p id="index-22"><strong>Gaussian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineGauss 1 2
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">LineGauss</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>center of the line <span class="math">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math">\(\sigma\)</span></li>
|
||||
<li>center of the line <span class="math notranslate nohighlight">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math notranslate nohighlight">\(\sigma\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is 1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)=e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}}\]</div>
|
||||
<p id="index-23"><strong>Lorentzian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineLorentzian 1 2
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">LineLorentzian</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>center of the line <span class="math">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math">\(w\)</span></li>
|
||||
<li>center of the line <span class="math notranslate nohighlight">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math notranslate nohighlight">\(w\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is 1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= \frac{w^2}{4(f-f_0)^2+w^2}\]</div>
|
||||
<p id="index-24"><strong>Laplacian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineLaplace 1 2
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">LineLaplace</span> <span class="mi">1</span> <span class="mi">2</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>center of the line <span class="math">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math">\(w\)</span></li>
|
||||
<li>center of the line <span class="math notranslate nohighlight">\(f_0\)</span></li>
|
||||
<li>FWHM of the line <span class="math notranslate nohighlight">\(w\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is 1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)=e^{-2\ln 2 \left|\frac{f-f_0}{w}\right|}\]</div>
|
||||
<p id="index-25"><strong>Skewed Lorentzian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineSkewLorentzian 1 2 3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">LineSkewLorentzian</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>center of the line <span class="math">\(f_0\)</span></li>
|
||||
<li>width of the line <span class="math">\(w\)</span></li>
|
||||
<li>skewness parameter <span class="math">\(a\)</span></li>
|
||||
<li>center of the line <span class="math notranslate nohighlight">\(f_0\)</span></li>
|
||||
<li>width of the line <span class="math notranslate nohighlight">\(w\)</span></li>
|
||||
<li>skewness parameter <span class="math notranslate nohighlight">\(a\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is 1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= \frac{w w_a}{4(f-f_0)^2+w_a^2}, \quad w_a=\frac{2w}{1+e^{a(f-f_0)}}\]</div>
|
||||
<p id="index-26"><strong>Skewed Lorentzian 2</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile LineSkewLorentzian2 1 2 3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">LineSkewLorentzian2</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>center of the line <span class="math">\(f_0\)</span></li>
|
||||
<li>width left of the center <span class="math">\(w_1\)</span></li>
|
||||
<li>width right of the center <span class="math">\(w_2\)</span></li>
|
||||
<li>center of the line <span class="math notranslate nohighlight">\(f_0\)</span></li>
|
||||
<li>width left of the center <span class="math notranslate nohighlight">\(w_1\)</span></li>
|
||||
<li>width right of the center <span class="math notranslate nohighlight">\(w_2\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is 1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[\begin{split}A(f)= \left\{\begin{matrix}\frac{{w_1}^2}{4{(f-f_0)}^2+{w_1}^2},&f\leq f_0\\[9pt] \frac{{w_2}^2}{4{(f-f_0)}^2+{w_2}^2},&f>f_0\end{matrix}\right.\end{split}\]</div>
|
||||
<p id="index-27"><strong>Powder average of an axially symmetric interaction convoluted with a Lorentzian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAxialLor 1 2 3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">PowderLineAxialLor</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>frequency for the field oriented paralell to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
|
||||
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
|
||||
<li>FWHM of the Lorentzian <span class="math">\(w\)</span></li>
|
||||
<li>frequency for the field oriented paralell to the symmetry axis <span class="math notranslate nohighlight">\(f_\parallel\)</span></li>
|
||||
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math notranslate nohighlight">\(f_\parallel\)</span></li>
|
||||
<li>FWHM of the Lorentzian <span class="math notranslate nohighlight">\(w\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
|
||||
<div class="line">The height of the peak is <span class="math notranslate nohighlight">\(\sim\)</span>1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= I_{\mathrm ax}(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)\]</div>
|
||||
<p>with <span class="math">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><em>above</em></a>.</p>
|
||||
<p>with <span class="math notranslate nohighlight">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><span class="std std-ref">above</span></a>.</p>
|
||||
<p id="index-28"><strong>Powder average of an axially symmetric interaction convoluted with a Gaussian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAxialGss 1 2 3
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">PowderLineAxialGss</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li>frequency for the field oriented paralell to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
|
||||
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math">\(f_\parallel\)</span></li>
|
||||
<li>FWHM of the Gaussian <span class="math">\(\sigma\)</span></li>
|
||||
<li>frequency for the field oriented paralell to the symmetry axis <span class="math notranslate nohighlight">\(f_\parallel\)</span></li>
|
||||
<li>frequency for the field oriented perpendicular to the symmetry axis <span class="math notranslate nohighlight">\(f_\parallel\)</span></li>
|
||||
<li>FWHM of the Gaussian <span class="math notranslate nohighlight">\(\sigma\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
|
||||
<div class="line">The height of the peak is <span class="math notranslate nohighlight">\(\sim\)</span>1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= I_{\mathrm ax}(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)\]</div>
|
||||
<p>with <span class="math">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><em>above</em></a>.</p>
|
||||
<p>with <span class="math notranslate nohighlight">\(I_{\mathrm ax}(f)\)</span> defined <a class="reference internal" href="#iax"><span class="std std-ref">above</span></a>.</p>
|
||||
<p id="index-29"><strong>Powder average of an anisotropic interaction convoluted with a Lorentzian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAsymLor 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">PowderLineAsymLor</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li><span class="math">\(f_1\)</span></li>
|
||||
<li><span class="math">\(f_1\)</span></li>
|
||||
<li><span class="math">\(f_3\)</span> frequencies along the principal axes</li>
|
||||
<li>FWHM of the Lorentzian <span class="math">\(w\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_1\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_1\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_3\)</span> frequencies along the principal axes</li>
|
||||
<li>FWHM of the Lorentzian <span class="math notranslate nohighlight">\(w\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
|
||||
<div class="line">The height of the peak is <span class="math notranslate nohighlight">\(\sim\)</span>1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= I(f)\circledast\left( \frac{w^2}{4f^2+w^2} \right)\]</div>
|
||||
<p>with <span class="math">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><em>above</em></a>. Note that <span class="math">\(f_1<f_2<f_3\)</span> is not required by the code.</p>
|
||||
<p>with <span class="math notranslate nohighlight">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><span class="std std-ref">above</span></a>. Note that <span class="math notranslate nohighlight">\(f_1<f_2<f_3\)</span> is not required by the code.</p>
|
||||
<p id="index-30"><strong>Powder average of an anisotropic interaction convoluted with a Gaussian</strong></p>
|
||||
<div class="highlight-python"><div class="highlight"><pre><span></span>userFcn libLineProfile PowderLineAsymGss 1 2 3 4
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">userFcn</span> <span class="n">libLineProfile</span> <span class="n">PowderLineAsymGss</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">4</span>
|
||||
</pre></div>
|
||||
</div>
|
||||
<p>The parameters are:</p>
|
||||
<ol class="arabic simple">
|
||||
<li><span class="math">\(f_1\)</span></li>
|
||||
<li><span class="math">\(f_1\)</span></li>
|
||||
<li><span class="math">\(f_3\)</span> frequencies along the principal axes</li>
|
||||
<li>FWHM of the Gaussian <span class="math">\(\sigma\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_1\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_1\)</span></li>
|
||||
<li><span class="math notranslate nohighlight">\(f_3\)</span> frequencies along the principal axes</li>
|
||||
<li>FWHM of the Gaussian <span class="math notranslate nohighlight">\(\sigma\)</span></li>
|
||||
</ol>
|
||||
<div class="line-block">
|
||||
<div class="line">The height of the peak is <span class="math">\(\sim\)</span>1.</div>
|
||||
<div class="line">The height of the peak is <span class="math notranslate nohighlight">\(\sim\)</span>1.</div>
|
||||
<div class="line">The functional form is given by</div>
|
||||
</div>
|
||||
<div class="math">
|
||||
<div class="math notranslate nohighlight">
|
||||
\[A(f)= I(f)\circledast\left( e^{-\frac{4\ln 2 (f-f_0)^2}{ \sigma^2}} \right)\]</div>
|
||||
<p>with <span class="math">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><em>above</em></a>. Note that <span class="math">\(f_1<f_2<f_3\)</span> is not required by the code.</p>
|
||||
<p>with <span class="math notranslate nohighlight">\(I(f)\)</span> defined <a class="reference internal" href="#ianiso"><span class="std std-ref">above</span></a>. Note that <span class="math notranslate nohighlight">\(f_1<f_2<f_3\)</span> is not required by the code.</p>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
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|
||||
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|
||||
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|
||||
|
||||
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|
||||
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|
||||
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|
||||
<a class="uplink" href="index.html">Contents</a>
|
||||
  ::  
|
||||
<a href="setup-standard.html">Setting up <tt class="docutils literal"><span class="pre">musrfit</span></tt> on Different Platforms</a>  »
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Last updated on May 29, 2022.
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|
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|
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|
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© Copyright 2022, Andreas Suter.
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Last updated on Dec 12, 2022.
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