From 87f706dfaaa603670448110758ac66d4786314ea Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Thu, 10 Jan 2019 10:17:24 +0100 Subject: [PATCH 1/5] CPack stub to generate RPM, DEB, etc Added the first necessary files allowing to generate all kind of packages for the future. Currently not much testing is present. --- CMakeLists.txt | 16 ++++++ cmake/CPackOptions.cmake.in | 33 ++++++++++++ cmake/musrfit-root6.spec.in | 101 ++++++++++++++++++++++++++++++++++++ cmake/welcome.txt | 1 + 4 files changed, 151 insertions(+) create mode 100644 cmake/CPackOptions.cmake.in create mode 100644 cmake/musrfit-root6.spec.in create mode 100644 cmake/welcome.txt diff --git a/CMakeLists.txt b/CMakeLists.txt index 43149c13..a16e7959 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -315,4 +315,20 @@ message("") message("-------------------------------------------------------------------------") message("") +#--- cpack specific info ...................................................... +file(TO_NATIVE_PATH ${PROJECT_SOURCE_DIR} PROJECT_SOURCE_DIR_NATIVE) +file(TO_NATIVE_PATH ${PROJECT_BINARY_DIR} PROJECT_BINARY_DIR_NATIVE) +string(REPLACE "\\" "\\\\" PROJECT_SOURCE_DIR_NATIVE_D ${PROJECT_SOURCE_DIR_NATIVE}) +string(REPLACE "\\" "\\\\" PROJECT_BINARY_DIR_NATIVE_D ${PROJECT_BINARY_DIR_NATIVE}) + +configure_file(${CMAKE_SOURCE_DIR}/cmake/CPackOptions.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/CPackOptions.cmake @ONLY) +set (CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/CPackOptions.cmake") +#set (CPACK_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks +#set (CPACK_SOURCE_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks +if (UNIX) +# set (CPACK_GENERATOR ${CPACK_GENERATOR};RPM) +endif () +# Include of CPack must always be last +include(CPack) + #--- end ---------------------------------------------------------------------- diff --git a/cmake/CPackOptions.cmake.in b/cmake/CPackOptions.cmake.in new file mode 100644 index 00000000..4a7c278b --- /dev/null +++ b/cmake/CPackOptions.cmake.in @@ -0,0 +1,33 @@ +# musrfit - cpack + +include(CPackComponent) + +set (CPACK_PACKAGE_NAME "musrfit-root6") +set (CPACK_PACKAGE_VENDOR "Paul Scherrer Institute - LMU - LEM") +set (CPACK_PACKAGE_DIRECTOR "@CMAKE_CURRENT_BINARY_DIR@/pack") +set (CPACK_PACKAGE_VERSION_MAJOR "@PROJECT_VERSION_MAJOR@") +set (CPACK_PACKAGE_VERSION_MINOR "@PROJECT_VERSION_MINOR@") +set (CPACK_PACKAGE_VERSION_PATCH "@PROJECT_VERSION_PATCH@") +set (CPACK_PACKAGE_CONTACT "") +set (CPACK_PACKAGE_DESCRIPTION_FILE "@PROJECT_SOURCE_DIR@/README.md") +set (CPACK_PACKAGE_DESCRIPTION_SUMMARY "musrfit - muSR data analysis package") +set (CPACK_PACKAGE_HOMEPAGE_URL "http://lmu.web.psi.ch/musrfit/user/html/index.html") +set (CPACK_PACKAGE_CHECKSUM "MD5") +set (CPACK_RESOURCE_FILE_LICENSE "@PROJECT_SOURCE_DIR@/COPYING") +set (CPACK_RESOURCE_FILE_README "@PROJECT_SOURCE_DIR@/README.md") +set (CPACK_RESOURCE_FILE_WELCOME "@PROJECT_SOURCE_DIR@/cmake/welcome.txt") + +# we do not have any absolute paths, so do not need DESTDIR +set (CPACK_SET_DESTDIR "OFF") +set (CPACK_PACKAGE_RELOCATABLE "true") + +if (${CPACK_GENERATOR} STREQUAL "RPM") + set (CPACK_RPM_FILE_NAME "RPM-DEFAULT") + set (CPACK_RPM_PACKAGE_RELEASE "1") + set (CPACK_RPM_PACKAGE_LICENSE "@PROJECT_SOURCE_DIR@/COPYING") + set (CPACK_RPM_PACKAGE_VENDOR "Paul Scherrer Institute - LMU - LEM") +endif () + +if (${CPACK_GENERATOR} STREQUAL "DEB") + # to be populated yet +endif () diff --git a/cmake/musrfit-root6.spec.in b/cmake/musrfit-root6.spec.in new file mode 100644 index 00000000..da5f7054 --- /dev/null +++ b/cmake/musrfit-root6.spec.in @@ -0,0 +1,101 @@ +Name: musrfit-root6 +Version: 1.4 +Release: 1%{?dist} +Summary: musrfit - muSR data analysis package + +License: GPLv2 +URL: http://lmu.web.psi.ch/musrfit/user/html/index.html +Source0: https://gitlab.psi.ch/nemu/musrfit/repository/%{name}-%{version}.tar.gz + +BuildRequires: cmake +BuildRequires: libtool +BuildRequires: gcc +BuildRequires: make +BuildRequires: hdf-devel hdf5-devel +BuildRequires: mxml-devel +BuildRequires: fftw3-devel +BuildRequires: boost-devel +BuildRequires: gsl-devel +BuildRequires: libxml2-devel +BuildRequires: root +BuildRequires: root-io-xml +BuildRequires: root-mathmore +BuildRequires: root-minuit2 +BuildRequires: qt5-qtbase-devel qt5-qtsvg-devel qt5-qtwebkit-devel +BuildRequires: nexus +Requires: hdf hdf5 +Requires: mxml +Requires: fftw3 +Requires: gsl +Requires: boost-devel +Requires: libxml2 +Requires: root +Requires: root-io-xml +Requires: root-mathmore +Requires: root-minuit2 +Requires: qt5-qtbase qt5-qtsvg qt5-qtwebkit +Requires: nexus + +%description +This is a data analysis package to analyze time differential muSR and beta-NMR data. Currently it allows the following things: +- setting up most commonly used fitting functions for muSR and beta-NMR +- fitting data, including global fits +- showing the fit results and the residuals +- showing the Fourier transform of the data +- extracting easily the fitting parameters to be used in other programs (gnuplot, qtiplot/origin, ...) +- allows to generate fitting input files for follow-up runs +- allows to generate global fitting input files based on a single run template +- allows to implement more sophisticated user functions (e.g. GL vortex lattice, Meissner screening including low-energy muon stopping profiles) + +Currently supported platforms: +- Linux +- Mac OS X +- Windows - not really, only for the very brave ones + + +%prep +%setup -q -n %{name}-%{version} + + +%build +##æs35 ./autogen.sh +# DOCDIR is needed to be set here. BMWlibs still makes troubles +%cmake -DASlibs=1 -DBMWlbis=1 -Dnexus=1 DOCDIR=$RPM_BUILD_ROOT/usr/share/doc/musrfit +%cmake --build ./ --clean-first -- -j8 +##æs35 %configure --enable-ASlibs --enable-BMWlibs --enable-NeXus DOCDIR=$RPM_BUILD_ROOT/usr/share/doc/musrfit +##æs35 %make_build + + +%install +# INSTALL_ROOT is needed for Qt applications +rm -rf $RPM_BUILD_ROOT +%make_install INSTALL_ROOT=%{buildroot} + +%files +%_prefix/bin/any2many +%_prefix/bin/dump_header +%_prefix/bin/msr2data +%_prefix/bin/msr2msr +%_prefix/bin/mupp +%_prefix/bin/mupp_plot +%_prefix/bin/musredit +%_prefix/bin/musrfit +%_prefix/bin/musrFT +%_prefix/bin/musrRootValidation +%_prefix/bin/musrStep +%_prefix/bin/musrt0 +%_prefix/bin/musrview +%_prefix/bin/musrWiz +%_prefix/bin/write_musrRoot_runHeader +%_prefix/include/* +%_prefix/lib64/* +%license COPYING +%doc %_prefix/share/doc/musrfit + + + +%changelog +* Thu Dec 20 2018 Andreas Suter - 1.4-1 +- adopted to cmake +* Wed Oct 25 2017 Andreas Suter - 1.2-1 +- first spec file for musrfit-root6 diff --git a/cmake/welcome.txt b/cmake/welcome.txt new file mode 100644 index 00000000..c8836b44 --- /dev/null +++ b/cmake/welcome.txt @@ -0,0 +1 @@ +Welcome to the musrfit package From d634fd2ce614133cdaf5b5448bef4ce1cd0e1942 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Mon, 14 Jan 2019 11:19:19 +0100 Subject: [PATCH 2/5] CPack/CMake for musrfit more tweaks towards musrfit rpm --- CMakeLists.txt | 2 +- cmake/CPackOptions.cmake.in | 7 ++++++- cmake/ChangeLogRPM | 2 ++ 3 files changed, 9 insertions(+), 2 deletions(-) create mode 100644 cmake/ChangeLogRPM diff --git a/CMakeLists.txt b/CMakeLists.txt index a16e7959..c0bc9da6 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -326,7 +326,7 @@ set (CPACK_PROJECT_CONFIG_FILE "${PROJECT_BINARY_DIR}/CPackOptions.cmake") #set (CPACK_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks #set (CPACK_SOURCE_GENERATOR TGZ) # not use ZIP on UNIX as problem with symlinks if (UNIX) -# set (CPACK_GENERATOR ${CPACK_GENERATOR};RPM) + set (CPACK_GENERATOR ${CPACK_GENERATOR};RPM) endif () # Include of CPack must always be last include(CPack) diff --git a/cmake/CPackOptions.cmake.in b/cmake/CPackOptions.cmake.in index 4a7c278b..7654ae58 100644 --- a/cmake/CPackOptions.cmake.in +++ b/cmake/CPackOptions.cmake.in @@ -17,15 +17,20 @@ set (CPACK_RESOURCE_FILE_LICENSE "@PROJECT_SOURCE_DIR@/COPYING") set (CPACK_RESOURCE_FILE_README "@PROJECT_SOURCE_DIR@/README.md") set (CPACK_RESOURCE_FILE_WELCOME "@PROJECT_SOURCE_DIR@/cmake/welcome.txt") +set (CPACK_RPM_EXCLUDE_FROM_AUTO_FILELIST_ADDITION "@CMAKE_INSTALL_PREFIX@;@CMAKE_INSTALL_PREFIX@/bin;@CMAKE_INSTALL_PREFIX@/include;@CMAKE_INSTALL_PREFIX@/share;@CMAKE_INSTALL_PREFIX@/lib64;@CMAKE_INSTALL_PREFIX@/lib;@CMAKE_INSTALL_PREFIX@/pkgconfig") + # we do not have any absolute paths, so do not need DESTDIR set (CPACK_SET_DESTDIR "OFF") set (CPACK_PACKAGE_RELOCATABLE "true") if (${CPACK_GENERATOR} STREQUAL "RPM") + set(CPACK_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@") + set(CPACK_PACKAGING_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@") set (CPACK_RPM_FILE_NAME "RPM-DEFAULT") set (CPACK_RPM_PACKAGE_RELEASE "1") - set (CPACK_RPM_PACKAGE_LICENSE "@PROJECT_SOURCE_DIR@/COPYING") + set (CPACK_RPM_PACKAGE_LICENSE "GPLv2") set (CPACK_RPM_PACKAGE_VENDOR "Paul Scherrer Institute - LMU - LEM") + set (CPACK_RPM_CHANGELOG_FILE "@PROJECT_SOURCE_DIR@/cmake/ChangeLogRPM") endif () if (${CPACK_GENERATOR} STREQUAL "DEB") diff --git a/cmake/ChangeLogRPM b/cmake/ChangeLogRPM new file mode 100644 index 00000000..eb75b666 --- /dev/null +++ b/cmake/ChangeLogRPM @@ -0,0 +1,2 @@ +* Mon Jan 14 2019 Andreas Suter - 1.4.0-1 +- first cpack/cmake version From c7e35dfdff845deb829c2e26d5930ac8462773ed Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Fri, 18 Jan 2019 10:35:26 +0100 Subject: [PATCH 3/5] Make so far undocumented functions ifgk and ifll public and at the same time properly normalize them. --- src/classes/PTheory.cpp | 8 ++++---- src/include/PTheory.h | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/classes/PTheory.cpp b/src/classes/PTheory.cpp index cfa21852..49b1bc18 100644 --- a/src/classes/PTheory.cpp +++ b/src/classes/PTheory.cpp @@ -2115,14 +2115,14 @@ Double_t PTheory::InternalFieldGK(register Double_t t, const PDoubleVector& para tt = t-val[5]; Double_t result = 0.0; - Double_t nu_t = val[1]*tt; + Double_t w_t = TWO_PI*val[1]*tt; Double_t rateLF = TMath::Power(val[3]*tt, val[4]); Double_t rate2 = val[2]*val[2]*tt*tt; // (sigma t)^2 if (val[1] < 0.01) { // internal field frequency is approaching zero result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(1.0-rate2)*TMath::Exp(-0.5*rate2); } else { - result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(TMath::Cos(nu_t)-val[2]*val[2]*tt/val[1]*TMath::Sin(nu_t))*TMath::Exp(-0.5*rate2); + result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(TMath::Cos(w_t)-val[2]*val[2]*tt/(TWO_PI*val[1])*TMath::Sin(w_t))*TMath::Exp(-0.5*rate2); } return result; @@ -2167,14 +2167,14 @@ Double_t PTheory::InternalFieldLL(register Double_t t, const PDoubleVector& para tt = t-val[5]; Double_t result = 0.0; - Double_t nu_t = val[1]*tt; + Double_t w_t = TWO_PI*val[1]*tt; Double_t rateLF = TMath::Power(val[3]*tt, val[4]); Double_t a_t = val[2]*tt; // a t if (val[1] < 0.01) { // internal field frequency is approaching zero result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(1.0-a_t)*TMath::Exp(-a_t); } else { - result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(TMath::Cos(nu_t)-val[3]/val[1]*TMath::Sin(nu_t))*TMath::Exp(-a_t); + result = (1.0-val[0])*TMath::Exp(-rateLF) + val[0]*(TMath::Cos(w_t)-val[3]/(TWO_PI*val[1])*TMath::Sin(w_t))*TMath::Exp(-a_t); } return result; diff --git a/src/include/PTheory.h b/src/include/PTheory.h index 528d7f09..085f20d7 100644 --- a/src/include/PTheory.h +++ b/src/include/PTheory.h @@ -196,7 +196,7 @@ static PTheoDataBase fgTheoDataBase[THEORY_MAX] = { "internFldGK", "ifgk", "(fraction frequency Trate Lrate beta)", "(fraction frequency Trate Lrate beta tshift)"}, {THEORY_INTERNAL_FIELD_LARKIN, THEORY_PARAM_INTERNAL_FIELD_LARKIN, false, - "internFldLL", "ifll", "(fraction frequency Trate Lrate)", "(fraction frequency Trate Lrate tshift)"}, + "internFldLL", "ifll", "(fraction frequency Trate Lrate beta)", "(fraction frequency Trate Lrate beta tshift)"}, {THEORY_BESSEL, THEORY_PARAM_BESSEL, false, "bessel", "b", "(phase frequency)", "(phase frequency tshift)"}, From 75a2a9b3f3cf1ecbc49840964ef65194d49b2932 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Mon, 21 Jan 2019 13:35:13 +0100 Subject: [PATCH 4/5] update version information. --- CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index c0bc9da6..f6b17c1a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,7 +1,7 @@ # - musrfit cmake_minimum_required(VERSION 3.6) -project(musrfit VERSION 1.4.0 LANGUAGES C CXX) +project(musrfit VERSION 1.4.1 LANGUAGES C CXX) #--- musrfit specific options ------------------------------------------------- option(nexus "build optional NeXus support. Needed for ISIS" OFF) From 32220f754d44796d39e2e441da1edfe04e7f8e64 Mon Sep 17 00:00:00 2001 From: Andreas Suter Date: Mon, 21 Jan 2019 13:36:15 +0100 Subject: [PATCH 5/5] Docu update Added information about the not yet documented functions for internal fields with Gaussian/Lorentzian broadening. --- doc/html/_sources/user-manual.txt | 32 +++++++---- doc/html/acknowledgement.html | 12 ++--- doc/html/any2many.html | 12 ++--- doc/html/bugtracking.html | 12 ++--- doc/html/cite.html | 12 ++--- doc/html/genindex.html | 12 ++--- doc/html/index.html | 14 ++--- doc/html/msr2data.html | 12 ++--- doc/html/mupp.html | 12 ++--- doc/html/musr-root.html | 12 ++--- doc/html/musredit.html | 12 ++--- doc/html/objects.inv | Bin 1904 -> 1908 bytes doc/html/search.html | 12 ++--- doc/html/searchindex.js | 2 +- doc/html/setup-dks.html | 12 ++--- doc/html/setup-standard.html | 12 ++--- doc/html/tutorial.html | 14 ++--- doc/html/user-libs.html | 16 +++--- doc/html/user-manual.html | 86 +++++++++++++++++++++--------- 19 files changed, 176 insertions(+), 132 deletions(-) diff --git a/doc/html/_sources/user-manual.txt b/doc/html/_sources/user-manual.txt index 3ebcd7be..2f675eeb 100644 --- a/doc/html/_sources/user-manual.txt +++ b/doc/html/_sources/user-manual.txt @@ -656,33 +656,39 @@ spinGlass spg :math:`\lambda (\mu \mathrm{s}^{-1})`, \ :math:`\fra rdAnisoHf rahf :math:`\nu` (MHz), \ :math:`\frac{1}{6} (1-\nu t/2) \exp(-\nu t/2) +` [#n7]_ :math:`\lambda (\mu \mathrm{s}^{-1})` :math:`+ \frac{1}{3} (1 - \nu t/4) \exp(-\frac{\nu t + 2.44949 \lambda t}{4})` TFieldCos tf :math:`\varphi (^\circ), \nu` (MHz) :math:`\cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right)` -internFld if :math:`\alpha (1), \varphi (^\circ)`, \ :math:`\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(\lambda_{\rm T}t) +` +internFld if :math:`\alpha (1), \varphi (^\circ)`, \ :math:`\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +` :math:`\nu` (MHz), \ :math:`+ (1-\alpha) \exp(-\lambda_{\rm L} t)` :math:`\lambda_{\rm T} (\mu \mathrm{s}^{-1})`,\ :math:`\lambda_{\rm L} (\mu \mathrm{s}^{-1})` Bessel b :math:`\varphi (^\circ), \nu` (MHz) :math:`j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right)` -internbsl ib :math:`\alpha (1), \varphi (^\circ)`, \ :math:`\alpha j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(\lambda_{\rm T}t) +` +internbsl ib :math:`\alpha (1), \varphi (^\circ)`, \ :math:`\alpha j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +` :math:`\nu` (MHz), \ :math:`+ (1-\alpha) \exp(-\lambda_{\rm L} t)` :math:`\lambda_{\rm T} (\mu \mathrm{s}^{-1})`,\ :math:`\lambda_{\rm L} (\mu \mathrm{s}^{-1})` +internFldGK ifgk :math:`\alpha (1), \nu` (MHz), \ :math:`\alpha\left[\cos(2\pi\nu t)-\frac{\sigma^2 t}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-\sigma^2 t^2/2)+` + :math:`\sigma (\mu \mathrm{s}^{-1})`, \ :math:`+ (1-\alpha) \exp(-(\lambda t)^\beta)` [#n8]_ + :math:`\lambda (\mu\mathrm{s}^{-1}), \beta (1)` +internFldLL ifll :math:`\alpha (1), \nu` (MHz), \ :math:`\alpha\left[\cos(2\pi\nu t)-\frac{a}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-a t)+` + :math:`a (\mu \mathrm{s}^{-1})`, \ :math:`+ (1-\alpha) \exp(-(\lambda t)^\beta)` [#n9]_ + :math:`\lambda (\mu\mathrm{s}^{-1}), \beta (1)` abragam ab :math:`\sigma (\mu \mathrm{s}^{-1})`, \ :math:`\exp\left[-\frac{\sigma^2}{\gamma^2} (e^{-\gamma t} - 1 + \gamma t)\right]` :math:`\gamma` (MHz) -skewedGss skg :math:`\varphi (^\circ), \nu` (MHz) \ :math:`\frac{\sigma_{-}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{-}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) + \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{-} t}{\sqrt{2}}\right)\right\} +` [#n8]_ +skewedGss skg :math:`\varphi (^\circ), \nu` (MHz) \ :math:`\frac{\sigma_{-}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{-}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) + \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{-} t}{\sqrt{2}}\right)\right\} +` [#n10]_ :math:`\sigma_{+} (\mu \mathrm{s}^{-1})`, \ :math:`+ \frac{\sigma_{+}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{+}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) - \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{+} t}{\sqrt{2}}\right)\right\}` :math:`\sigma_{-} (\mu \mathrm{s}^{-1})` -staticNKZF snkzf :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`\frac{1}{3} + \frac{2}{3}\left(\frac{1}{1+R_b^2\Delta_0^2 t^2}\right)^{3/2} \left(1 - \frac{\Delta_0^2 t^2}{1+R_b^2\Delta_0^2 t^2}\right) \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2\Delta_0^2 t^2)}\right]` [#n9]_ +staticNKZF snkzf :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`\frac{1}{3} + \frac{2}{3}\left(\frac{1}{1+R_b^2\Delta_0^2 t^2}\right)^{3/2} \left(1 - \frac{\Delta_0^2 t^2}{1+R_b^2\Delta_0^2 t^2}\right) \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2\Delta_0^2 t^2)}\right]` [#n11]_ :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)` -staticNKTF snktf :math:`\varphi (^\circ), \nu` (MHz), \ :math:`\sqrt{\frac{1}{1+R_b^2 \Delta_0^2 t^2}} \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2 \Delta_0^2 t^2)}\right] \cos(2\pi\nu t + \varphi)` see [11] +staticNKTF snktf :math:`\varphi (^\circ), \nu` (MHz), \ :math:`\sqrt{\frac{1}{1+R_b^2 \Delta_0^2 t^2}} \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2 \Delta_0^2 t^2)}\right] \cos(2\pi\nu t + \varphi)` see [13] :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)` -dynamicNKZF dnkzf :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`\sqrt{\frac{1}{1+4 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{2\Delta_0^2 \Theta(t)}{1+4 R_b^2 \Delta_0^2 \Theta(t)}\right]`, see [11] +dynamicNKZF dnkzf :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`\sqrt{\frac{1}{1+4 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{2\Delta_0^2 \Theta(t)}{1+4 R_b^2 \Delta_0^2 \Theta(t)}\right]`, see [13] :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`, \ :math:`\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}` :math:`\nu_c` (MHz) -dynamicNKTF dnktf :math:`\varphi (^\circ), \nu` (MHz), \ :math:`\sqrt{\frac{1}{1+2 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{\Delta_0^2 \Theta(t)}{1+2 R_b^2 \Delta_0^2 \Theta(t)}\right] \cos(2\pi\nu t + \varphi)`, see [11] +dynamicNKTF dnktf :math:`\varphi (^\circ), \nu` (MHz), \ :math:`\sqrt{\frac{1}{1+2 R_b^2 \Delta_0^2 \Theta(t)}} \exp\left[-\frac{\Delta_0^2 \Theta(t)}{1+2 R_b^2 \Delta_0^2 \Theta(t)}\right] \cos(2\pi\nu t + \varphi)`, see [13] :math:`\Delta_0 (\mu \mathrm{s}^{-1})`, \ :math:`\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}` :math:`R_b = \Delta_{\rm GbG}/\Delta_0 (1)`, \ :math:`\nu_c` (MHz) -muMinusExpTF mmsetf :math:`N_0 (1), \tau (\mu \mathrm{s}^{-1})`, \ :math:`N_0 \exp(-t/\tau) \left[ 1 + A \exp(-\lambda t) \cos(2 \pi \nu t + \varphi) \right]` [#n10]_ +muMinusExpTF mmsetf :math:`N_0 (1), \tau (\mu \mathrm{s}^{-1})`, \ :math:`N_0 \exp(-t/\tau) \left[ 1 + A \exp(-\lambda t) \cos(2 \pi \nu t + \varphi) \right]` [#n12]_ :math:`A (1), \lambda (\mu \mathrm{s}^{-1})`, \ :math:`\varphi (^\circ), \nu` (MHz) polynom p :math:`t_0 ([t]), a_0 (1)`, \ :math:`\sum_{k=0}^n a_k (t-t_0)^k` @@ -700,12 +706,16 @@ polynom p :math:`t_0 ([t]), a_0 (1)`, \ :math:`\sum .. [#n5] R.S. Hayano *et al.*, Phys. Rev. B **20**, 850 (1979)., P. Dalmas de Réotier and A. Yaouanc, J. Phys.: Condens. Matter **4**, 4533 (1992). -- **not** DKS ready. .. [#n6] `M.R. Crook `_ and R. Cywinski, J. Phys.: Condens. Matter **9** 1149 (1997). .. [#n7] `R.E. Turner `_ and D.R. Harshman, Phys. Rev. B **34**, 4467 (1986). -.. [#n8] `see memo `_ -- **not** DKS ready. -.. [#n9] `D.R. Noakes `_ and G.M. Kalvius, Phys. Rev. B **56**, 2352 (1997); +.. [#n8] `E.I. Kornilov `_ and V.Yu. Pomjakushin, Physics Letters A **153**, 364, (1991). + In the original work, :math:`\alpha=2/3,\, \lambda=0,\, \beta=1`. If you find values strongly deviating from these values you should question your analysis approach. +.. [#n9] `M.I. Larkin `_ *et al.*, Physica B: Condensed Matter **289-290**, 153 (2000). + In the original work, :math:`\alpha=2/3,\, \lambda=0,\, \beta=1`. If you find values strongly deviating from these values you should question your analysis approach. +.. [#n10] `see memo `_ -- **not** DKS ready. +.. [#n11] `D.R. Noakes `_ and G.M. Kalvius, Phys. Rev. B **56**, 2352 (1997); A. Yaouanc and P. Dalmas de Réotier "Muon Spin Rotation, Relaxation, and Resonance" Oxford Scientific Publication; simplifying the original formulae by eliminating :math:`\Delta_{\rm eff}` via the identity :math:`\Delta_{\rm eff}^2 = (1+R_b^2)\Delta_0`. -.. [#n10] This function is explicit for :math:`\mu^-`! Do not try to use it for :math:`\mu^+`! +.. [#n12] This function is explicit for :math:`\mu^-`! Do not try to use it for :math:`\mu^+`! .. _msr-map-intro: diff --git a/doc/html/acknowledgement.html b/doc/html/acknowledgement.html index 74b21a92..7ec06c40 100644 --- a/doc/html/acknowledgement.html +++ b/doc/html/acknowledgement.html @@ -6,7 +6,7 @@ - Acknowledgements — musrfit 1.4.0 documentation + Acknowledgements — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
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    • © Copyright 2018, Andreas Suter. - Last updated on Nov 13, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.
    diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js index cda51a40..058381e2 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ -Search.setIndex({filenames:["acknowledgement","any2many","bugtracking","cite","index","msr2data","mupp","musr-root","musredit","setup-dks","setup-standard","tutorial","user-libs","user-manual"],titles:["Acknowledgements","any2many - a Universal \u03bcSR-file-format converter","Bugtracking","How to Cite musrfit?","Welcome to the musrfit documentation!","msr2data - A Program for Automatically Processing Multiple musrfit msr Files","mupp - \u03bcSR Parameter Plotter","MusrRoot - an Extensible Open File Format for \u03bcSR","musredit: the GUI Based Interface to musrfit","Setting up musrfit / DKS: High Speed Fitting with GPU’s","Setting up musrfit on Different Platforms","Tutorial for musrfit","Documentation of user libs (user functions)","User 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13],execut:[8,13],configur:[8,13],musrgui:[8,10],musredit_startup:8,xml:[8,12,13],featur:8,musrwiz:8,theori:[8,13],"function":[8,12,13],map:[8,13],fit:[8,9,13,11],info:8,creat:8,musrstep:8,set:[9,10],high:9,speed:9,gpu:[9,13],tesla:9,k40c:9,nvidia:9,driver:9,instal:[9,10],cuda:9,via:[9,10],automak:[9,10],cmake:[9,10],amd:9,card:9,radeon:9,"390x":9,app:9,softwar:[9,10],develop:9,kit:9,sdk:9,enabl:[9,13],opencl:[9,13],support:[9,13,10],maco:[9,10],differ:10,platform:10,oper:10,system:10,restrict:10,gnu:10,linux:10,nexu:10,build:10,last:10,step:10,obsol:10,check:10,window:10,cygwin:10,potenti:10,problem:10,mac:10,macport:10,packag:10,from:10,sourc:10,environ:10,variabl:10,fink:10,obsolet:10,tutori:11,singl:[13,11],histogram:[13,11],determin:11,data:[12,11],rang:11,musrt0:[13,11],model:[12,11],view:11,musrview:[13,11],further:11,asymmteri:11,lib:12,meissner:12,profil:12,vortex:12,lattic:12,relat:12,bmw:12,libfitpofb:12,dimension:12,london:12,state:12,isotrop:12,superconductor:12,bulk:12,field:12,distribut:12,mix:12,startup:12,nonloc:12,superconduct:12,screen:12,analyz:12,"\u03b2":12,nmr:12,bnmr:12,libbnmr:12,liblineprofil:12,manual:13,kei:13,shortcut:13,musrft:13,msr2msr:13,dump_head:13,musrfit_startup:13,descript:13,titl:13,fitparamet:13,block:13,command:13,fourier:13,plot:13,statist:13,rrf:13,asymmetri:13,neg:13,muon:13,non:13,without:13,object:13,access:13,technic:13,framework:13},envversion:43}) \ No newline at end of file diff --git a/doc/html/setup-dks.html b/doc/html/setup-dks.html index fcec2311..bd141748 100644 --- a/doc/html/setup-dks.html +++ b/doc/html/setup-dks.html @@ -6,7 +6,7 @@ - Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.4.0 documentation + Setting up musrfit / DKS: High Speed Fitting with GPU’s — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • @@ -354,12 +354,12 @@ The only thing you need DKS previous | -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • © Copyright 2018, Andreas Suter. - Last updated on Oct 15, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.
    diff --git a/doc/html/setup-standard.html b/doc/html/setup-standard.html index c9df2538..e64c9cb0 100644 --- a/doc/html/setup-standard.html +++ b/doc/html/setup-standard.html @@ -6,7 +6,7 @@ - Setting up musrfit on Different Platforms — musrfit 1.4.0 documentation + Setting up musrfit on Different Platforms — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • @@ -1481,12 +1481,12 @@ $ musrview test-histo-ROOT-NPP.msr
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • © Copyright 2018, Andreas Suter. - Last updated on Oct 15, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.
    diff --git a/doc/html/tutorial.html b/doc/html/tutorial.html index 9c39cb34..14bc3db4 100644 --- a/doc/html/tutorial.html +++ b/doc/html/tutorial.html @@ -6,7 +6,7 @@ - Tutorial for musrfit — musrfit 1.4.0 documentation + Tutorial for musrfit — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • @@ -132,7 +132,7 @@ TFieldCos map1 fun2 (phase frequency)

    The THEORY block is used to define a fit-parameter-dependent theory function used to model -the decay asymmetry. Different predefined and user-defined +the decay asymmetry. Different predefined and user-defined functions can be combined here. Theory lines following each other are multiplied and the + sign is used to add different (here: two) signal contributions. The numbers are the parameter numbers according to the FITPARAMETER block. map and fun are used to refer to @@ -443,12 +443,12 @@ For a complete description please refer to the manuals of previous | -

  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • © Copyright 2018, Andreas Suter. - Last updated on Oct 15, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.
    diff --git a/doc/html/user-libs.html b/doc/html/user-libs.html index 8f159925..5dddef1f 100644 --- a/doc/html/user-libs.html +++ b/doc/html/user-libs.html @@ -6,7 +6,7 @@ - Documentation of user libs (user functions) — musrfit 1.4.0 documentation + Documentation of user libs (user functions) — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • @@ -58,7 +58,7 @@

    libFitPofB

    Introduction

    -

    libFitPofB is a collection of C++ classes using the musrfit user-functions +

    libFitPofB is a collection of C++ classes using the musrfit user-functions interface in order to facilitate the usage in conjunction with musrfit. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions \(p(B)\) which lead to the muon-spin depolarization functions

    @@ -372,7 +372,7 @@ The expected name of the RGE

    Functions to analyze β-NMR data (BNMR libs)

    -

    This is a collection of C++ classes using the musrfit user-functions +

    This is a collection of C++ classes using the musrfit user-functions interface in order to facilitate the usage in conjunction with musrfit. It consists of two libraries:

    © Copyright 2018, Andreas Suter. - Last updated on Oct 15, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.
    diff --git a/doc/html/user-manual.html b/doc/html/user-manual.html index 3a9261c9..25a0005f 100644 --- a/doc/html/user-manual.html +++ b/doc/html/user-manual.html @@ -6,7 +6,7 @@ - User manual — musrfit 1.4.0 documentation + User manual — musrfit 1.4.1 documentation @@ -14,7 +14,7 @@ - + @@ -41,7 +41,7 @@
  • previous |
    • -
  • musrfit 1.4.0 documentation »
    • +
  • musrfit 1.4.1 documentation »
    • @@ -584,7 +584,7 @@ in case a \(\chi^2\) single-histogram fit is done, als - + name @@ -721,7 +721,7 @@ in case a \(\chi^2\) single-histogram fit is done, als if \(\alpha (1), \varphi (^\circ)\), \(\nu\) (MHz), \(\lambda_{\rm T} (\mu \mathrm{s}^{-1})\),\(\lambda_{\rm L} (\mu \mathrm{s}^{-1})\)
    -
    \(\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(\lambda_{\rm T}t) +\)
    +
    \(\alpha \cos\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +\)
    \(+ (1-\alpha) \exp(-\lambda_{\rm L} t)\)
    @@ -737,12 +737,32 @@ in case a \(\chi^2\) single-histogram fit is done, als ib \(\alpha (1), \varphi (^\circ)\), \(\nu\) (MHz), \(\lambda_{\rm T} (\mu \mathrm{s}^{-1})\),\(\lambda_{\rm L} (\mu \mathrm{s}^{-1})\)
    -
    \(\alpha j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(\lambda_{\rm T}t) +\)
    +
    \(\alpha j_0\left(2\pi\nu t + \frac{\pi \varphi}{180}\right) \exp(-\lambda_{\rm T}t) +\)
    \(+ (1-\alpha) \exp(-\lambda_{\rm L} t)\)
      +internFldGK +ifgk +\(\alpha (1), \nu\) (MHz), \(\sigma (\mu \mathrm{s}^{-1})\), \(\lambda (\mu\mathrm{s}^{-1}), \beta (1)\) +
    +
    \(\alpha\left[\cos(2\pi\nu t)-\frac{\sigma^2 t}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-\sigma^2 t^2/2)+\)
    +
    \(+ (1-\alpha) \exp(-(\lambda t)^\beta)\)
    +
    + +[10] + +internFldLL +ifll +\(\alpha (1), \nu\) (MHz), \(a (\mu \mathrm{s}^{-1})\), \(\lambda (\mu\mathrm{s}^{-1}), \beta (1)\) +
    +
    \(\alpha\left[\cos(2\pi\nu t)-\frac{a}{2\pi\nu}\sin(2\pi\nu t)\right]\exp(-a t)+\)
    +
    \(+ (1-\alpha) \exp(-(\lambda t)^\beta)\)
    +
    + +[11] + abragam ab \(\sigma (\mu \mathrm{s}^{-1})\), \(\gamma\) (MHz) @@ -757,19 +777,19 @@ in case a \(\chi^2\) single-histogram fit is done, als
    \(+ \frac{\sigma_{+}}{\sigma_{+}+\sigma_{-}} \exp\left[\frac{\sigma_{+}^2 t^2}{2}\right] \left\{\cos(2\pi\nu t + \frac{\pi\varphi}{180}) - \sin(2\pi\nu t + \frac{\pi\varphi}{180}) \mathrm{Erfi}\left(\frac{\sigma_{+} t}{\sqrt{2}}\right)\right\}\)
    -[10] +[12] staticNKZF snkzf \(\Delta_0 (\mu \mathrm{s}^{-1})\), \(R_b = \Delta_{\rm GbG}/\Delta_0 (1)\) \(\frac{1}{3} + \frac{2}{3}\left(\frac{1}{1+R_b^2\Delta_0^2 t^2}\right)^{3/2} \left(1 - \frac{\Delta_0^2 t^2}{1+R_b^2\Delta_0^2 t^2}\right) \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2\Delta_0^2 t^2)}\right]\) -[11] +[13] staticNKTF snktf \(\varphi (^\circ), \nu\) (MHz), \(\Delta_0 (\mu \mathrm{s}^{-1})\), \(R_b = \Delta_{\rm GbG}/\Delta_0 (1)\) \(\sqrt{\frac{1}{1+R_b^2 \Delta_0^2 t^2}} \exp\left[-\frac{\Delta_0^2 t^2}{2(1+R_b^2 \Delta_0^2 t^2)}\right] \cos(2\pi\nu t + \varphi)\) -see [11] +see [13] dynamicNKZF dnkzf @@ -779,7 +799,7 @@ in case a \(\chi^2\) single-histogram fit is done, als
    \(\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}\)
    -see [11] +see [13] dynamicNKTF dnktf @@ -789,13 +809,13 @@ in case a \(\chi^2\) single-histogram fit is done, als
    \(\Theta(t) = \frac{\exp(-\nu_c t) -1 -\nu_c t}{\nu_c^2}\)
    -see [11] +see [13] muMinusExpTF mmsetf \(N_0 (1), \tau (\mu \mathrm{s}^{-1})\), \(A (1), \lambda (\mu \mathrm{s}^{-1})\), \(\varphi (^\circ), \nu\) (MHz) \(N_0 \exp(-t/\tau) \left[ 1 + A \exp(-\lambda t) \cos(2 \pi \nu t + \varphi) \right]\) -[12] +[14] polynom p @@ -853,22 +873,36 @@ in case a \(\chi^2\) single-histogram fit is done, als - +
    [10]see memo – not DKS ready.
    [10]E.I. Kornilov and V.Yu. Pomjakushin, Physics Letters A 153, 364, (1991). +In the original work, \(\alpha=2/3,\, \lambda=0,\, \beta=1\). If you find values strongly deviating from these values you should question your analysis approach.
    - +
    [11]D.R. Noakes and G.M. Kalvius, Phys. Rev. B 56, 2352 (1997); -A. Yaouanc and P. Dalmas de Réotier “Muon Spin Rotation, Relaxation, and Resonance” Oxford Scientific Publication; -simplifying the original formulae by eliminating \(\Delta_{\rm eff}\) via the identity -\(\Delta_{\rm eff}^2 = (1+R_b^2)\Delta_0\).
    [11]M.I. Larkin et al., Physica B: Condensed Matter 289-290, 153 (2000). +In the original work, \(\alpha=2/3,\, \lambda=0,\, \beta=1\). If you find values strongly deviating from these values you should question your analysis approach.
    - + + +
    [12]This function is explicit for \(\mu^-\)! Do not try to use it for \(\mu^+\)!
    [12]see memo – not DKS ready.
    + + + + + +
    [13]D.R. Noakes and G.M. Kalvius, Phys. Rev. B 56, 2352 (1997); +A. Yaouanc and P. Dalmas de Réotier “Muon Spin Rotation, Relaxation, and Resonance” Oxford Scientific Publication; +simplifying the original formulae by eliminating \(\Delta_{\rm eff}\) via the identity +\(\Delta_{\rm eff}^2 = (1+R_b^2)\Delta_0\).
    + + + +
    [14]This function is explicit for \(\mu^-\)! Do not try to use it for \(\mu^+\)!
    @@ -901,7 +935,7 @@ Whereas the theory is operating on the parameters and the time, functions curren

    User Functions

    In the case complicated and not predefined functions are needed to fit data, musrfit offers the possibility to implement external functions and introduce them to musrfit through the ROOT dictionary mechanism. The detailed rules these user-defined functions have to obey will be discussed -in the according section. Here only the syntax for the msr file is provided. To call a user function in the THEORY block the +in the according section. Here only the syntax for the msr file is provided. To call a user function in the THEORY block the keyword userFcn is used. It is followed by the name of the shared library which holds the C++ class where the function is implemented and the name of the class. Finally, all parameters are given in the order needed by the class. Of course it is also possible to use mapped parameters or functions instead of specifying the parameters directly.

    @@ -1732,7 +1766,7 @@ If enabled in the XML
    -

    Fit Types

    +

    Fit Types

    Single Histogram Fit (fit type 0)

    The single-histogram fit (fit type 0) is used to fit a function directly to the raw data using

    @@ -1843,8 +1877,8 @@ the single histogram RRF fit apply: if you not urgently need it: do not

    The same applies for the plot with plot type 8.

    -
    -

    User Functions

    +
    +

    User Functions

    musrfit offers the possibility to plug-in user-defined functions implemented in C++ classes to the fitting and plotting routines. In order to do so, basically two things are needed:

    @@ -2154,7 +2188,7 @@ In case this cannot be ensured, the parallelization can be disabled by ̵
  • Non-μSR Fit (fit type 8)
    • -
  • User Functions
    • © Copyright 2018, Andreas Suter. - Last updated on Nov 13, 2018. + Last updated on Jan 21, 2019. Created using Sphinx 1.2.3.