New analysis tool to compute the free volume and total volume.
authorDavid van der Spoel <spoel@xray.bmc.uu.se>
Thu, 28 Mar 2013 16:25:38 +0000 (17:25 +0100)
committerGerrit Code Review <gerrit@gerrit.gromacs.org>
Fri, 14 Jun 2013 11:40:06 +0000 (13:40 +0200)
commit13d8138935594153868d73aac6404cdd41482964
tree3f20cbc30ba6b5f0531f25b1b33af4af994ed248
parent58df55650cc675d95af2966a432f04594069eb2f
New analysis tool to compute the free volume and total volume.

Works with selections, such that the freevolume in a box containing
a subset of all atoms can be computed.
Added excessive comments so that others can use this as a reference
for implementing analysis tools as well.
Added a test system as well, but this is somewhat tricky due to
real precision and the Monte Carlo algorithm.
literature reference.
valgrind.

Change-Id: I2acb48b829c9495e399c60e9dc927662e2958d69
13 files changed:
src/gromacs/gmxlib/rmpbc.c
src/gromacs/gmxlib/tpxio.c
src/gromacs/gmxlib/typedefs.c
src/gromacs/legacyheaders/vec.h
src/gromacs/trajectoryanalysis/modules.cpp
src/gromacs/trajectoryanalysis/modules/freevolume.cpp [new file with mode: 0644]
src/gromacs/trajectoryanalysis/modules/freevolume.h [new file with mode: 0644]
src/gromacs/trajectoryanalysis/tests/CMakeLists.txt
src/gromacs/trajectoryanalysis/tests/freevolume.cpp [new file with mode: 0644]
src/gromacs/trajectoryanalysis/tests/freevolume.tpr [new file with mode: 0644]
src/gromacs/trajectoryanalysis/tests/freevolume.xtc [new file with mode: 0644]
src/gromacs/trajectoryanalysis/tests/refdata/FreeVolumeModuleTest_ComputesFreeVolume.xml [new file with mode: 0644]
src/gromacs/trajectoryanalysis/tests/refdata/FreeVolumeModuleTest_ComputesFreeVolumeSelection.xml [new file with mode: 0644]