Reorganizing analysis of correlation functions.
authorDavid van der Spoel <spoel@xray.bmc.uu.se>
Wed, 21 May 2014 14:38:25 +0000 (16:38 +0200)
committerGerrit Code Review <gerrit@gerrit.gromacs.org>
Tue, 14 Oct 2014 18:16:34 +0000 (20:16 +0200)
commit106ca9e645d05a79a01fdd27446794439e197685
treee6d6c58f9d9fc7d3153abb52ae2895dd8c0116bd
parentf8857af5fa730ac83b9172279765fbc2c0aa8a4a
Reorganizing analysis of correlation functions.

Moved routines computing correlation functions and
fitting to those in a special subdirectory not
dependent on gmxana. The autocorrelation now functions
as it should (previously there were issues with long
time correlations).

Replaced Levenberg-Marquardt algorithm by another implementation
from http://apps.jcns.fz-juelich.de/doku/sc/lmfit,
under a FreeBSD license. This code is in src/external/lmfit.

Added Doxygen comments to all headers.

Fixed wordcount algorithm in xvgr.c

The routines many_auto_correl and many_cross_correl
are optimized using OpenMP.

Change-Id: Ifbe003437db36e35d606cd942bb38deeef86ea64
69 files changed:
COPYING
cmake/legacy_and_external.supp
src/external/lmfit/README [new file with mode: 0644]
src/external/lmfit/lmcurve.c [new file with mode: 0644]
src/external/lmfit/lmcurve.h [new file with mode: 0644]
src/external/lmfit/lmmin.c [new file with mode: 0644]
src/external/lmfit/lmmin.h [new file with mode: 0644]
src/external/lmfit/lmstruct.h [new file with mode: 0644]
src/gromacs/CMakeLists.txt
src/gromacs/correlationfunctions/CMakeLists.txt [new file with mode: 0644]
src/gromacs/correlationfunctions/autocorr.c [moved from src/gromacs/gmxana/autocorr.c with 72% similarity]
src/gromacs/correlationfunctions/autocorr.h [new file with mode: 0644]
src/gromacs/correlationfunctions/crosscorr.c [new file with mode: 0644]
src/gromacs/correlationfunctions/crosscorr.h [new file with mode: 0644]
src/gromacs/correlationfunctions/expfit.c [new file with mode: 0644]
src/gromacs/correlationfunctions/expfit.h [new file with mode: 0644]
src/gromacs/correlationfunctions/integrate.c [new file with mode: 0644]
src/gromacs/correlationfunctions/integrate.h [new file with mode: 0644]
src/gromacs/correlationfunctions/manyautocorrelation.c [new file with mode: 0644]
src/gromacs/correlationfunctions/manyautocorrelation.h [new file with mode: 0644]
src/gromacs/correlationfunctions/polynomials.c [moved from src/gromacs/gmxana/polynomials.c with 79% similarity]
src/gromacs/correlationfunctions/polynomials.h [moved from src/gromacs/gmxana/correl.h with 70% similarity]
src/gromacs/correlationfunctions/tests/CMakeLists.txt [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/autocorr.cpp [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/correlationdataset.cpp [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/correlationdataset.h [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/expfit.cpp [new file with mode: 0755]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacCos.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacNormal.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacP0.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacP1.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacP2.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacP3.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacP4.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacRcross.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/AutocorrTest_EacVector.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERF.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnERREST.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP1.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP2.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP3.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP5.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP7.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnEXP9.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnPRES.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/refdata/ExpfitTest_EffnVAC.xml [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/testCOS3.xvg [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/testEXP.xvg [new file with mode: 0644]
src/gromacs/correlationfunctions/tests/testINVEXP.xvg [new file with mode: 0755]
src/gromacs/correlationfunctions/tests/testPRES.xvg [new file with mode: 0644]
src/gromacs/fileio/xvgr.cpp
src/gromacs/gmxana/correl.c [deleted file]
src/gromacs/gmxana/expfit.c [deleted file]
src/gromacs/gmxana/gmx_analyze.c
src/gromacs/gmxana/gmx_angle.c
src/gromacs/gmxana/gmx_chi.c
src/gromacs/gmxana/gmx_densorder.cpp
src/gromacs/gmxana/gmx_dielectric.c
src/gromacs/gmxana/gmx_dipoles.cpp
src/gromacs/gmxana/gmx_dos.c
src/gromacs/gmxana/gmx_energy.c
src/gromacs/gmxana/gmx_gyrate.c
src/gromacs/gmxana/gmx_hbond.c
src/gromacs/gmxana/gmx_rdf.c
src/gromacs/gmxana/gmx_rotacf.c
src/gromacs/gmxana/gmx_tcaf.c
src/gromacs/gmxana/gmx_velacc.c
src/gromacs/gmxana/gstat.h
src/gromacs/gmxana/levenmar.c [deleted file]