update of doku for the dks6 branch.

This commit is contained in:
suter_a 2021-10-06 15:24:00 +02:00
parent 54f6fb62b3
commit dd02b07c56
34 changed files with 1786 additions and 1370 deletions

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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 3b34bde782d0a2e964b32bc698e5a292
tags: 645f666f9bcd5a90fca523b33c5a78b7

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#---------------------------------------------------
# get compilation flags from root-config
ROOTCFLAGS = $(shell $(ROOTSYS)/bin/root-config --cflags)
#---------------------------------------------------
OS = LINUX
CXX = g++
CXXFLAGS = -O3 -Wall -Wno-trigraphs -fPIC
LOCALINCLUDE = .
ROOTINCLUDE = $(ROOTSYS)/include
INCLUDES = -I$(LOCALINCLUDE) -I$(ROOTINCLUDE)
LD = g++
LDFLAGS =
SOFLAGS = -O -shared
# the output from the root-config script:
CXXFLAGS += $(ROOTCFLAGS)
LDFLAGS +=
# some definitions: headers (used to generate *Dict* stuff), sources, objects,...
OBJS =
OBJS += TMyFunction.o TMyLibraryDict.o
SHLIB = libTMyLibrary.so
# make the shared lib:
#
all: $(SHLIB)
$(SHLIB): $(OBJS)
@echo "---> Building shared library $(SHLIB) ..."
/bin/rm -f $(SHLIB)
$(LD) $(OBJS) $(SOFLAGS) -o $(SHLIB)
@echo "done"
# clean up: remove all object file (and core files)
# semicolon needed to tell make there is no source
# for this target!
#
clean:; @rm -f $(OBJS) *Dict* core*
@echo "---> removing $(OBJS)"
#
$(OBJS): %.o: %.cpp
$(CXX) $(INCLUDES) $(CXXFLAGS) -c $<
# Generate the ROOT CINT dictionary
TMyLibraryDict.cpp: TMyFunction.h TMyLibraryLinkDef.h
@echo "Generating dictionary $@..."
rootcint -f $@ -c -p -I$(ROOTINCLUDE) $^
install: all
@echo "Installing shared lib: libTApproximation.so"
ifeq ($(OS),LINUX)
cp -pv $(SHLIB) $(ROOTSYS)/lib
cp -pv $(LOCALINCLUDE)/*.h $(ROOTSYS)/include
endif

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371
doc/html/_static/haiku.css Normal file
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/*
* haiku.css_t
* ~~~~~~~~~~~
*
* Sphinx stylesheet -- haiku theme.
*
* Adapted from http://haiku-os.org/docs/Haiku-doc.css.
* Original copyright message:
*
* Copyright 2008-2009, Haiku. All rights reserved.
* Distributed under the terms of the MIT License.
*
* Authors:
* Francois Revol <revol@free.fr>
* Stephan Assmus <superstippi@gmx.de>
* Braden Ewing <brewin@gmail.com>
* Humdinger <humdingerb@gmail.com>
*
* :copyright: Copyright 2007-2014 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
@import url("basic.css");
html {
margin: 0px;
padding: 0px;
background: #FFF url(bg-page.png) top left repeat-x;
}
body {
line-height: 1.5;
margin: auto;
padding: 0px;
font-family: "DejaVu Sans", Arial, Helvetica, sans-serif;
min-width: 59em;
max-width: 70em;
color: #333333;
}
div.footer {
padding: 8px;
font-size: 11px;
text-align: center;
letter-spacing: 0.5px;
}
/* link colors and text decoration */
a:link {
font-weight: bold;
text-decoration: none;
color: #dc3c01;
}
a:visited {
font-weight: bold;
text-decoration: none;
color: #892601;
}
a:hover, a:active {
text-decoration: underline;
color: #ff4500;
}
/* Some headers act as anchors, don't give them a hover effect */
h1 a:hover, a:active {
text-decoration: none;
color: #0c3762;
}
h2 a:hover, a:active {
text-decoration: none;
color: #0c3762;
}
h3 a:hover, a:active {
text-decoration: none;
color: #0c3762;
}
h4 a:hover, a:active {
text-decoration: none;
color: #0c3762;
}
a.headerlink {
color: #a7ce38;
padding-left: 5px;
}
a.headerlink:hover {
color: #a7ce38;
}
/* basic text elements */
div.content {
margin-top: 20px;
margin-left: 40px;
margin-right: 40px;
margin-bottom: 50px;
font-size: 0.9em;
}
/* heading and navigation */
div.header {
position: relative;
left: 0px;
top: 0px;
height: 85px;
/* background: #eeeeee; */
padding: 0 40px;
}
div.header h1 {
font-size: 1.6em;
font-weight: normal;
letter-spacing: 1px;
color: #0c3762;
border: 0;
margin: 0;
padding-top: 15px;
}
div.header h1 a {
font-weight: normal;
color: #0c3762;
}
div.header h2 {
font-size: 1.3em;
font-weight: normal;
letter-spacing: 1px;
text-transform: uppercase;
color: #aaa;
border: 0;
margin-top: -3px;
padding: 0;
}
div.header img.rightlogo {
float: right;
}
div.title {
font-size: 1.3em;
font-weight: bold;
color: #0c3762;
border-bottom: dotted thin #e0e0e0;
margin-bottom: 25px;
}
div.topnav {
/* background: #e0e0e0; */
}
div.topnav p {
margin-top: 0;
margin-left: 40px;
margin-right: 40px;
margin-bottom: 0px;
text-align: right;
font-size: 0.8em;
}
div.bottomnav {
background: #eeeeee;
}
div.bottomnav p {
margin-right: 40px;
text-align: right;
font-size: 0.8em;
}
a.uplink {
font-weight: normal;
}
/* contents box */
table.index {
margin: 0px 0px 30px 30px;
padding: 1px;
border-width: 1px;
border-style: dotted;
border-color: #e0e0e0;
}
table.index tr.heading {
background-color: #e0e0e0;
text-align: center;
font-weight: bold;
font-size: 1.1em;
}
table.index tr.index {
background-color: #eeeeee;
}
table.index td {
padding: 5px 20px;
}
table.index a:link, table.index a:visited {
font-weight: normal;
text-decoration: none;
color: #dc3c01;
}
table.index a:hover, table.index a:active {
text-decoration: underline;
color: #ff4500;
}
/* Haiku User Guide styles and layout */
/* Rounded corner boxes */
/* Common declarations */
div.admonition {
-webkit-border-radius: 10px;
-khtml-border-radius: 10px;
-moz-border-radius: 10px;
border-radius: 10px;
border-style: dotted;
border-width: thin;
border-color: #dcdcdc;
padding: 10px 15px 10px 15px;
margin-bottom: 15px;
margin-top: 15px;
}
div.note {
padding: 10px 15px 10px 80px;
background: #e4ffde url(alert_info_32.png) 15px 15px no-repeat;
min-height: 42px;
}
div.warning {
padding: 10px 15px 10px 80px;
background: #fffbc6 url(alert_warning_32.png) 15px 15px no-repeat;
min-height: 42px;
}
div.seealso {
background: #e4ffde;
}
/* More layout and styles */
h1 {
font-size: 1.3em;
font-weight: bold;
color: #0c3762;
border-bottom: dotted thin #e0e0e0;
margin-top: 30px;
}
h2 {
font-size: 1.2em;
font-weight: normal;
color: #0c3762;
border-bottom: dotted thin #e0e0e0;
margin-top: 30px;
}
h3 {
font-size: 1.1em;
font-weight: normal;
color: #0c3762;
margin-top: 30px;
}
h4 {
font-size: 1.0em;
font-weight: normal;
color: #0c3762;
margin-top: 30px;
}
p {
text-align: justify;
}
p.last {
margin-bottom: 0;
}
ol {
padding-left: 20px;
}
ul {
padding-left: 5px;
margin-top: 3px;
}
li {
line-height: 1.3;
}
div.content ul > li {
-moz-background-clip:border;
-moz-background-inline-policy:continuous;
-moz-background-origin:padding;
background: transparent url(bullet_orange.png) no-repeat scroll left 0.45em;
list-style-image: none;
list-style-type: none;
padding: 0 0 0 1.666em;
margin-bottom: 3px;
}
td {
vertical-align: top;
}
tt {
background-color: #e2e2e2;
font-size: 1.0em;
font-family: monospace;
}
pre {
border-color: #0c3762;
border-style: dotted;
border-width: thin;
margin: 0 0 12px 0;
padding: 0.8em;
background-color: #f0f0f0;
}
hr {
border-top: 1px solid #ccc;
border-bottom: 0;
border-right: 0;
border-left: 0;
margin-bottom: 10px;
margin-top: 20px;
}
/* printer only pretty stuff */
@media print {
.noprint {
display: none;
}
/* for acronyms we want their definitions inlined at print time */
acronym[title]:after {
font-size: small;
content: " (" attr(title) ")";
font-style: italic;
}
/* and not have mozilla dotted underline */
acronym {
border: none;
}
div.topnav, div.bottomnav, div.header, table.index {
display: none;
}
div.content {
margin: 0px;
padding: 0px;
}
html {
background: #FFF;
}
}
.viewcode-back {
font-family: "DejaVu Sans", Arial, Helvetica, sans-serif;
}
div.viewcode-block:target {
background-color: #f4debf;
border-top: 1px solid #ac9;
border-bottom: 1px solid #ac9;
margin: -1px -10px;
padding: 0 12px;
}

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/*
* websupport.js
* ~~~~~~~~~~~~~
*
* sphinx.websupport utilties for all documentation.
*
* :copyright: Copyright 2007-2014 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() {
$('a.comment-close').live("click", function(event) {
event.preventDefault();
hide($(this).attr('id').substring(2));
});
$('a.vote').live("click", function(event) {
event.preventDefault();
handleVote($(this));
});
$('a.reply').live("click", function(event) {
event.preventDefault();
openReply($(this).attr('id').substring(2));
});
$('a.close-reply').live("click", function(event) {
event.preventDefault();
closeReply($(this).attr('id').substring(2));
});
$('a.sort-option').live("click", function(event) {
event.preventDefault();
handleReSort($(this));
});
$('a.show-proposal').live("click", function(event) {
event.preventDefault();
showProposal($(this).attr('id').substring(2));
});
$('a.hide-proposal').live("click", function(event) {
event.preventDefault();
hideProposal($(this).attr('id').substring(2));
});
$('a.show-propose-change').live("click", function(event) {
event.preventDefault();
showProposeChange($(this).attr('id').substring(2));
});
$('a.hide-propose-change').live("click", function(event) {
event.preventDefault();
hideProposeChange($(this).attr('id').substring(2));
});
$('a.accept-comment').live("click", function(event) {
event.preventDefault();
acceptComment($(this).attr('id').substring(2));
});
$('a.delete-comment').live("click", function(event) {
event.preventDefault();
deleteComment($(this).attr('id').substring(2));
});
$('a.comment-markup').live("click", function(event) {
event.preventDefault();
toggleCommentMarkupBox($(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(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,
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return $('<div class="moderate">Thank you! Your comment will show up '
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<a href="#" id="dv<%id%>" class="vote" title="vote down">\
<img src="<%downArrow%>" id="da<%id%>" />\
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<a href="#" id="du<%id%>" class="un vote" title="vote down">\
<img src="<%downArrowPressed%>" />\
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<div class="comment-content">\
<p class="tagline comment">\
<span class="user-id"><%username%></span>\
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<span id="cm<%id%>" class="moderation hidden">\
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<pre class="proposal" id="pr<%id%>">\
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</div>';
var replyTemplate = '\
<li>\
<div class="reply-div" id="rd<%id%>">\
<form id="rf<%id%>">\
<textarea name="comment" cols="80"></textarea>\
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<input type="button" value="Cancel" />\
<input type="hidden" name="parent" value="<%id%>" />\
<input type="hidden" name="node" value="" />\
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</li>';
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init();
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});
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document.location.hash = '#s' + anchor.substring(9);
}
});

View File

@ -6,15 +6,15 @@
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@ -601,73 +598,21 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
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<li><a class="reference internal" href="#">Documentation of user libs (user functions)</a><ul>
<li><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><a class="reference internal" href="#nonlocal-superconductivity-related-meissner-screening-functions-as-libs">Nonlocal superconductivity related Meissner screening functions (AS libs)</a></li>
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@ -65,23 +62,28 @@
<dl class="docutils">
<dt><strong>&lt;msr-file&gt;</strong></dt>
<dd>filename of the msr input file defining all the details needed for performing a fit to a specified set of data. This is the only mandatory parameter.</dd>
<dt><strong>-k, - -keep-mn2-output</strong></dt>
<dt><strong>-k, &#8211;keep-mn2-output</strong></dt>
<dd>selects the option for keeping the output of <tt class="docutils literal"><span class="pre">MINUIT2</span></tt> including the correlation coefficients between different parameters and renaming the files <tt class="docutils literal"><span class="pre">MINUIT2.OUTPUT</span></tt> and <tt class="docutils literal"><span class="pre">MINUIT2.root</span></tt> to <tt class="docutils literal"><span class="pre">&lt;msr_file_without_extension&gt;-mn2.output</span></tt> and <tt class="docutils literal"><span class="pre">&lt;msr_file_without_extension&gt;-mn2.root</span></tt>, respectively, <em>e.g.</em> <tt class="docutils literal"><span class="pre">&lt;msr_file&gt;</span></tt> = <tt class="docutils literal"><span class="pre">8472.msr</span></tt> will result in <tt class="docutils literal"><span class="pre">8472-mn2.output</span></tt>, <tt class="docutils literal"><span class="pre">8472-mn2.root</span></tt>.</dd>
<dt><strong>-c, - -chisq-only</strong></dt>
<dt><strong>-c, &#8211;chisq-only</strong></dt>
<dd>Instead of fitting the model, <tt class="docutils literal"><span class="pre">musrfit</span></tt> calculates <span class="math">\(\chi^2\)</span> or max. log-likelihood, maxLH, only once and sends the result to the standard output if called with this option. This is <em>e.g.</em> useful for the adjustment of the initial values of the fit parameters.</dd>
<dt><strong>-t, - -title-from-data-file</strong></dt>
<dt><strong>-t, &#8211;title-from-data-file</strong></dt>
<dd>If this option is given <tt class="docutils literal"><span class="pre">musrfit</span></tt> will replace the title in the <tt class="docutils literal"><span class="pre">&lt;msr_file&gt;</span></tt> by the run title in the data file of the first run appearing in a RUN block. In case there is no run title in the data file no substitution is done.</dd>
<dt><strong>-e, - -estimateN0</strong></dt>
<dt><strong>-e, &#8211;estimateN0</strong></dt>
<dd>estimate <span class="math">\(N_0\)</span> for single histogram fits.</dd>
<dt><strong>-p, - -per-run-block-chisq</strong></dt>
<dt><strong>-p, &#8211;per-run-block-chisq</strong></dt>
<dd>will write per run block chisq/maxLH into the msr-file.</dd>
<dt><strong>- -dump &lt;type&gt;</strong></dt>
<dt><strong>-n, &#8211;no-of-cores-avail</strong></dt>
<dd>print out how many cores are available (only vaild for OpenMP)</dd>
<dt><strong>-u, &#8211;use-no-of-threads &lt;number&gt;</strong></dt>
<dd>&lt;number&gt;: number of threads to be used (OpenMP). Needs to be &lt;= max. number of cores.
If OpenMP is enable, the maximal number of cores is used, if it is not limited by this option.</dd>
<dt><strong>&#8211;dump &lt;type&gt;</strong></dt>
<dd>is writing a data file with the fit data and the theory; &lt;type&gt; can be ascii (data in columns) or root (data in ROOT histograms).</dd>
<dt><strong>- -timeout &lt;timeout_tag&gt;</strong></dt>
<dt><strong>&#8211;timeout &lt;timeout_tag&gt;</strong></dt>
<dd>overwrites the predefined timeout of 3600 sec. &lt;timeout_tag&gt; <span class="math">\(\leq\)</span> 0 means the timeout facility is not enabled. &lt;timeout_tag&gt; &gt; 0, <em>e.g.</em> <tt class="docutils literal"><span class="pre">nn</span></tt> will set the timeout to <tt class="docutils literal"><span class="pre">nn</span></tt> (sec). If during a fit this timeout is reached, <tt class="docutils literal"><span class="pre">musrfit</span></tt> will terminate. This is used to prevent orphan <tt class="docutils literal"><span class="pre">musrfit</span></tt> processes to jam the system.</dd>
<dt><strong>- -help</strong></dt>
<dt><strong>&#8211;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>
<dt><strong>&#8211;version</strong></dt>
<dd>prints the version number of <tt class="docutils literal"><span class="pre">musrfit</span></tt></dd>
</dl>
<p>If called with a msr input file, <em>e.g.</em></p>
@ -101,22 +103,22 @@
<dl class="docutils">
<dt><strong>&lt;msr_file&gt;</strong></dt>
<dd>name of the msr input or output file to be displayed. This is the only mandatory parameter.</dd>
<dt><strong>- -help</strong></dt>
<dt><strong>&#8211;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>
<dt><strong>&#8211;version</strong></dt>
<dd>prints the version number of <tt class="docutils literal"><span class="pre">musrview</span></tt>.</dd>
<dt><strong>-f, - -fourier</strong></dt>
<dt><strong>-f, &#8211;fourier</strong></dt>
<dd>will directly present the Fourier transform of the &lt;msr_file&gt; with Fourier options as defined in the &lt;msr_file&gt;.</dd>
<dt><strong>-a, - -avg</strong></dt>
<dt><strong>-a, &#8211;avg</strong></dt>
<dd>will directly present the averaged data/Fourier of the &lt;msr_file&gt;.</dd>
<dt><strong>-1, - -one_to_one</strong></dt>
<dt><strong>-1, &#8211;one_to_one</strong></dt>
<dd>calculate the theory points <em>only</em> at the data points.</dd>
<dt><strong>- -&lt;graphic_format_extension&gt;</strong></dt>
<dt><strong>&#8211;&lt;graphic_format_extension&gt;</strong></dt>
<dd>will produce a graphics output file without starting a ROOT session. The filename is based on the name of the &lt;msr_file&gt;, <em>e.g.</em> 8472.msr will result in 8472_0.png.
Supported values for <tt class="docutils literal"><span class="pre">&lt;graphic_format_extension&gt;</span></tt> are <em>eps</em>, <em>pdf</em>, <em>gif</em>, <em>jpg</em>, <em>png</em>, <em>svg</em>, <em>xpm</em>, and, <em>root</em>.</dd>
<dt><strong>- -ascii</strong></dt>
<dt><strong>&#8211;ascii</strong></dt>
<dd>will generate an ascii dump of the data and theory as plotted.</dd>
<dt><strong>- -timeout &lt;timeout&gt;</strong></dt>
<dt><strong>&#8211;timeout &lt;timeout&gt;</strong></dt>
<dd>&lt;timeout&gt; given in seconds after which <tt class="docutils literal"><span class="pre">musrview</span></tt> terminates. If &lt;timeout&gt; <span class="math">\(\leq\)</span> 0, no timeout will take place. Default for &lt;timeout&gt; is 0.</dd>
</dl>
<p>If called with a msr file and the <tt class="docutils literal"><span class="pre">--&lt;graphic_format_extension&gt;</span></tt> option, <em>e.g.</em></p>
@ -175,55 +177,55 @@ Supported values for <tt class="docutils literal"><span class="pre">&lt;graphic_
<dd><dl class="first last docutils">
<dt><strong>&lt;msr_files&gt;</strong></dt>
<dd>msr-file name(s). These msr-files are used for the Fourier transform. It can be a list of msr-files, <em>e.g.</em> <tt class="docutils literal"><span class="pre">musrFT</span> <span class="pre">3110.msr</span> <span class="pre">3111.msr</span></tt></dd>
<dt><strong>-df, - -data-file &lt;data-file&gt;</strong></dt>
<dt><strong>-df, &#8211;data-file &lt;data-file&gt;</strong></dt>
<dd>This allows to feed only μSR data file(s) to perform the Fourier transform. Since the extended &lt;msr-file&gt; information are missing, they will need to be provided by to options, or <tt class="docutils literal"><span class="pre">musrFT</span></tt> tries to guess, based on <a class="reference internal" href="#musrfit-startup"><em>musrfit_startup.xml</em></a> settings.</dd>
</dl>
</dd>
<dt><strong>Options</strong></dt>
<dd><dl class="first last docutils">
<dt><strong>- -help</strong></dt>
<dt><strong>&#8211;help</strong></dt>
<dd>display a help and exit.</dd>
<dt><strong>- -version</strong></dt>
<dt><strong>&#8211;version</strong></dt>
<dd>output version information and exit.</dd>
<dt><strong>-g, - -graphic-format &lt;graphic-format-extension&gt;</strong></dt>
<dt><strong>-g, &#8211;graphic-format &lt;graphic-format-extension&gt;</strong></dt>
<dd>will produce a graphic-output-file without starting a root session. The name is based either on the &lt;msr-file&gt; or the &lt;data-file&gt;, <em>e.g.</em> <tt class="docutils literal"><span class="pre">3310.msr</span> <span class="pre">-&gt;</span> <span class="pre">3310_0.png</span></tt>. Supported graphic-format-extension: <em>eps</em>, <em>pdf</em>, <em>gif</em>, <em>jpg</em>, <em>png</em>, <em>svg</em>, <em>xpm</em>, and <em>root</em>.</dd>
<dt><strong>- -dump &lt;fln&gt;</strong></dt>
<dt><strong>&#8211;dump &lt;fln&gt;</strong></dt>
<dd>rather than starting a root session and showing Fourier graphs of the data, it will output the Fourier data in an ascii file &lt;fln&gt;.</dd>
<dt><strong>-br, - -background-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dt><strong>-br, &#8211;background-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dd>background interval used to estimate the background to be subtracted before the Fourier transform. &lt;start&gt;, &lt;end&gt; to be given in bins.</dd>
<dt><strong>-bg, - -background</strong></dt>
<dt><strong>-bg, &#8211;background</strong></dt>
<dd>gives the background explicit for each histogram.</dd>
<dt><strong>-fo, - -fourier-option &lt;fopt&gt;</strong></dt>
<dt><strong>-fo, &#8211;fourier-option &lt;fopt&gt;</strong></dt>
<dd>&lt;fopt&gt; can be &#8216;<em>real</em>&#8216;, &#8216;<em>imag</em>&#8216;, &#8216;<em>real+imag</em>&#8216;, &#8216;<em>power</em>&#8216;, or &#8216;<em>phase</em>&#8216;. If this is not defined (neither on the command line nor in the <a class="reference internal" href="#musrfit-startup"><em>musrfit_startup.xml</em></a>) &#8216;<em>power</em>&#8216; will be used.</dd>
<dt><strong>-ap, - -apodization &lt;val&gt;</strong></dt>
<dt><strong>-ap, &#8211;apodization &lt;val&gt;</strong></dt>
<dd>&lt;val&gt; can be either &#8216;<em>none</em>&#8216;, &#8216;<em>weak</em>&#8216;, &#8216;<em>medium</em>&#8216;, &#8216;<em>strong</em>&#8216;. Default will be &#8216;<em>none</em>&#8216;.</dd>
<dt><strong>-fp, - -fourier-power &lt;N&gt;</strong></dt>
<dt><strong>-fp, &#8211;fourier-power &lt;N&gt;</strong></dt>
<dd>&lt;N&gt; being the Fourier power, i.e. <tt class="docutils literal"><span class="pre">2^&lt;N&gt;</span></tt> used for zero padding. Default is -1, i.e. <em>no</em> zero padding will be performed.</dd>
<dt><strong>-u, - -units &lt;units&gt;</strong></dt>
<dt><strong>-u, &#8211;units &lt;units&gt;</strong></dt>
<dd>&lt;units&gt; is used to define the abscissa of the Fourier transform. One may choose between the fields (<em>Gauss</em>) or (<em>Tesla</em>), the frequency (<em>MHz</em>), and the angular-frequency domain (<em>Mc/s</em>). Default will be &#8216;<em>MHz</em>&#8216;.</dd>
<dt><strong>-ph, - -phase &lt;val&gt;</strong></dt>
<dt><strong>-ph, &#8211;phase &lt;val&gt;</strong></dt>
<dd>defines the initial phase &lt;val&gt;. This only is of concern for &#8216;<em>real</em>&#8216;, &#8216;<em>imag</em>&#8216;, and &#8216;<em>real+imag</em>&#8216;. Default will be 0.0.</dd>
<dt><strong>-fr, - -fourier-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dt><strong>-fr, &#8211;fourier-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dd>Fourier range. &lt;start&gt;, &lt;end&gt; are interpreted in the units given. Default will be -1.0 for both which means, take the full Fourier range.</dd>
<dt><strong>-tr, - -time-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dt><strong>-tr, &#8211;time-range &lt;start&gt; &lt;end&gt;</strong></dt>
<dd>time domain range to be used for Fourier transform. &lt;start&gt;, &lt;end&gt; are to be given in (μs). If nothing is provided, the full time range found in the data file(s) will be used.</dd>
<dt><strong>- -histo &lt;list&gt;</strong></dt>
<dt><strong>&#8211;histo &lt;list&gt;</strong></dt>
<dd>give the &lt;list&gt; of histograms to be used for the Fourier transform. <em>E.g.</em> <tt class="docutils literal"><span class="pre">musrFT</span> <span class="pre">-df</span> <span class="pre">lem15_his_01234.root</span> <span class="pre">--histo</span> <span class="pre">1</span> <span class="pre">3</span></tt>, will only be needed together with the option <tt class="docutils literal"><span class="pre">--data-file</span></tt>. If multiple data files are given, &lt;list&gt; will apply to all data-files given. If <tt class="docutils literal"><span class="pre">--histo</span></tt> is not given, <em>all</em> histos of a data file will be used. &lt;list&gt; can be anything like: 2 3 6, or 2-17, or 1-6 9, etc.</dd>
<dt><strong>-a, - -average</strong></dt>
<dt><strong>-a, &#8211;average</strong></dt>
<dd>show the average of all <strong>ALL</strong> Fourier transformed data.</dd>
<dt><strong>-ad, - -average-per-data-set</strong></dt>
<dt><strong>-ad, &#8211;average-per-data-set</strong></dt>
<dd>show the average of <strong>per-data-set</strong> Fourier transformed data.</dd>
<dt><strong>- -t0 &lt;list&gt;</strong></dt>
<dd>A list of t0&#8217;s can be provided. This in conjunction with <tt class="docutils literal"><span class="pre">--data-file</span></tt> and <tt class="docutils literal"><span class="pre">--fourier-option</span> <span class="pre">real</span></tt> allows to get the proper initial phase if t0&#8217;s are known. If a single t0 for multiple histos is given, it is assume, that this t0 is common to <em>all</em> histos. Example: <tt class="docutils literal"><span class="pre">musrFT</span> <span class="pre">-df</span> <span class="pre">lem15_his_01234.root</span> <span class="pre">-fo</span> <span class="pre">real</span> <span class="pre">--t0</span> <span class="pre">2750</span> <span class="pre">--histo</span> <span class="pre">1</span> <span class="pre">3</span></tt>.</dd>
<dt><strong>-pa, - -packing &lt;N&gt;</strong></dt>
<dt><strong>-pa, &#8211;packing &lt;N&gt;</strong></dt>
<dd>if &lt;N&gt; (an integer), the time domain data will first be packed/rebinned by &lt;N&gt;.</dd>
<dt><strong>- -title &lt;title&gt;</strong></dt>
<dt><strong>&#8211;title &lt;title&gt;</strong></dt>
<dd>give a global title for the plot.</dd>
<dt><strong>- -create-msr-file &lt;fln&gt;</strong></dt>
<dt><strong>&#8211;create-msr-file &lt;fln&gt;</strong></dt>
<dd>creates a msr-file based on the command line options provided. This will help on the way to a full fitting model.</dd>
<dt><strong>-lc, - -lifetimecorrection &lt;fudge&gt;</strong></dt>
<dt><strong>-lc, &#8211;lifetimecorrection &lt;fudge&gt;</strong></dt>
<dd>try to eliminate the muon life time decay. Only makes sense for low transverse fields. &lt;fudge&gt; is a tweaking factor (scaling factor for the estimated t0) and should be kept around 1.0.</dd>
<dt><strong>- -timeout &lt;timeout&gt;</strong></dt>
<dt><strong>&#8211;timeout &lt;timeout&gt;</strong></dt>
<dd>&lt;timeout&gt; given in seconds after which <tt class="docutils literal"><span class="pre">musrFT</span></tt> terminates. If &lt;timeout&gt; <span class="math">\(\leq\)</span> 0, no timeout will take place. Default &lt;timeout&gt; is 3600 sec.</dd>
</dl>
</dd>
@ -277,13 +279,13 @@ Supported values for <tt class="docutils literal"><span class="pre">&lt;graphic_
<dl class="docutils">
<dt><strong>&lt;msr_file&gt;</strong></dt>
<dd>name of an msr file.</dd>
<dt><strong>-g, - -getT0FromPromptPeak [&lt;firstGoodBinOffset&gt;]</strong></dt>
<dt><strong>-g, &#8211;getT0FromPromptPeak [&lt;firstGoodBinOffset&gt;]</strong></dt>
<dd>tries to estimate t0 from the prompt peak (maximum entry) in each histogram and writes the corresponding values to the t0 lines in the <a class="reference internal" href="#msr-run-block"><em>RUN blocks</em></a> of the msr file. If an optional number &lt;firstGoodBinOffset&gt; is given, the lower limit of the data range will be set to t0 + &lt;firstGoodBinOffset&gt;.</dd>
<dt><strong>- -timeout &lt;timeout&gt;</strong></dt>
<dt><strong>&#8211;timeout &lt;timeout&gt;</strong></dt>
<dd>&lt;timeout&gt; given in seconds after which musrview terminates. If &lt;timeout&gt; <span class="math">\(\leq\)</span> 0, no timeout will take place. Default for &lt;timeout&gt; is 0.</dd>
<dt><strong>- -help</strong></dt>
<dt><strong>&#8211;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>
<dt><strong>&#8211;version</strong></dt>
<dd>prints the version number of musrt0.</dd>
</dl>
<p>The interactive mode of <tt class="docutils literal"><span class="pre">musrt0</span></tt> is started if the program is called with a sole msr-file argument, <em>e.g.</em></p>
@ -327,7 +329,7 @@ Supported values for <tt class="docutils literal"><span class="pre">&lt;graphic_
<dd>input WKM msr file (mandatory first parameter).</dd>
<dt><strong>&lt;msr_file_out&gt;</strong></dt>
<dd>converted output musrfit msr file (mandatory second parameter).</dd>
<dt><strong>- -help</strong></dt>
<dt><strong>&#8211;help</strong></dt>
<dd>displays a small help notice in the shell explaining the basic usage of the program.</dd>
</dl>
<p>A typical example then looks like:</p>
@ -410,13 +412,13 @@ Supported values for <tt class="docutils literal"><span class="pre">&lt;graphic_
<span id="index-9"></span><h3>dump_header<a class="headerlink" href="#dump-header" title="Permalink to this headline"></a></h3>
<p><tt class="docutils literal"><span class="pre">dump_header</span></tt> is a little program which tries to read a μSR data file and sends the relevant information (required header info, start of the histos, etc.) to the standard output. Currently the following μSR data file formats are supported: <em>MusrROOT</em>, <em>ROOT</em> (old LEM format), <em>PSI-BIN</em>, <em>PSI-MDU</em>, <em>NeXus</em> (IDF1 and IDF2), <em>MUD</em>, and <em>WKM</em>.</p>
<dl class="docutils">
<dt><strong>-rn, - -runNo &lt;runNo&gt;</strong></dt>
<dt><strong>-rn, &#8211;runNo &lt;runNo&gt;</strong></dt>
<dd>run number of the header to be dumped.</dd>
<dt><strong>-fn, - -fileName &lt;fileName&gt;</strong></dt>
<dt><strong>-fn, &#8211;fileName &lt;fileName&gt;</strong></dt>
<dd>muSR data file name.</dd>
<dt><strong>-ff, - -fileFormat &lt;fileFormat&gt;</strong></dt>
<dt><strong>-ff, &#8211;fileFormat &lt;fileFormat&gt;</strong></dt>
<dd>where &lt;fileFormat&gt; is one of the above listed ones.</dd>
<dt><strong>-y, - -year &lt;year&gt;</strong></dt>
<dt><strong>-y, &#8211;year &lt;year&gt;</strong></dt>
<dd>&lt;year&gt; has to be a 4 digit value, <em>e.g.</em> 2005, if provided it is used to generate the file name for the given &lt;runNo&gt;, otherwise the current year is used. If a file name is given, this option has no effect.</dd>
<dt><strong>-s, &#8211;summary</strong></dt>
<dd>this option is used for LE-μSR data sets only. It will, additionally to the header information, print the summary file content.</dd>
@ -2602,106 +2604,21 @@ here:</p>
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<h3><a href="index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">User manual</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#available-executables-configuration-files-and-their-basic-usage">Available Executables, Configuration Files and their Basic Usage</a><ul>
<li><a class="reference internal" href="#musrfit">musrfit</a></li>
<li><a class="reference internal" href="#musrview">musrview</a></li>
<li><a class="reference internal" href="#musrft">musrFT</a></li>
<li><a class="reference internal" href="#musrt0">musrt0</a></li>
<li><a class="reference internal" href="#msr2msr">msr2msr</a></li>
<li><a class="reference internal" href="#msr2data">msr2data</a></li>
<li><a class="reference internal" href="#any2many">any2many</a></li>
<li><a class="reference internal" href="#dump-header">dump_header</a></li>
<li><a class="reference internal" href="#musrfit-startup-xml">musrfit_startup.xml</a></li>
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<li><a class="reference internal" href="#description-of-the-msr-file-format">Description of the msr File Format</a><ul>
<li><a class="reference internal" href="#the-title">The Title</a></li>
<li><a class="reference internal" href="#the-fitparameter-block">The FITPARAMETER Block</a></li>
<li><a class="reference internal" href="#the-theory-block">The THEORY Block</a></li>
<li><a class="reference internal" href="#the-functions-block">The FUNCTIONS Block</a></li>
<li><a class="reference internal" href="#the-global-block">The GLOBAL Block</a></li>
<li><a class="reference internal" href="#the-run-block">The RUN Block</a></li>
<li><a class="reference internal" href="#the-commands-block">The COMMANDS Block</a></li>
<li><a class="reference internal" href="#the-fourier-block">The FOURIER Block</a></li>
<li><a class="reference internal" href="#the-plot-block">The PLOT Block</a></li>
<li><a class="reference internal" href="#the-statistic-block">The STATISTIC Block</a></li>
</ul>
</li>
<li><a class="reference internal" href="#fit-types">Fit Types</a><ul>
<li><a class="reference internal" href="#single-histogram-fit-fit-type-0">Single Histogram Fit (fit type 0)</a></li>
<li><a class="reference internal" href="#single-histogram-rrf-fit-fit-type-1">Single Histogram RRF Fit (fit type 1)</a></li>
<li><a class="reference internal" href="#asymmetry-fit-fit-type-2">Asymmetry Fit (fit type 2)</a></li>
<li><a class="reference internal" href="#asymmetry-rrf-fit-fit-type-3">Asymmetry RRF Fit (fit type 3)</a></li>
<li><a class="reference internal" href="#negative-muon-mgrsr-fit-fit-type-4">Negative Muon μSR Fit (fit type 4)</a></li>
<li><a class="reference internal" href="#beta-nmr-asymmetry-fit-fit-type-5">beta-NMR Asymmetry Fit (fit type 5)</a></li>
<li><a class="reference internal" href="#non-mgrsr-fit-fit-type-8">Non-μSR Fit (fit type 8)</a></li>
</ul>
</li>
<li><a class="reference internal" href="#id38">User Functions</a><ul>
<li><a class="reference internal" href="#user-function-without-global-user-function-object-access">User Function without global user-function-object access</a></li>
<li><a class="reference internal" href="#user-function-with-global-user-function-object-access">User Function with global user-function-object access</a></li>
<li><a class="reference internal" href="#rge-file-handler-for-low-energy-mgrsr">rge-file handler for Low-Energy μSR</a></li>
</ul>
</li>
<li><a class="reference internal" href="#technical-description-of-the-musrfit-framework">Technical Description of the musrfit framework</a></li>
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Last updated on Aug 06, 2021.
Last updated on Oct 06, 2021.
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