MSD tests for the -mol option.
commit57b3bfe39ec1ceae6dfadd0593d82414b8a12443
authorDavid van der Spoel <spoel@xray.bmc.uu.se>
Sat, 22 Dec 2018 21:33:36 +0000 (22 22:33 +0100)
committerJoe Jordan <e.jjordan12@gmail.com>
Mon, 14 Jan 2019 07:08:54 +0000 (14 08:08 +0100)
treed8aeeadb98d1758492c5f82c0e1b2a56910c92e2
parent7a1945d8759439beb52e9f8572f28e0642fea377
MSD tests for the -mol option.

Had to free some memory as well to make tests pass.
Added basic code for running grompp.

Renamed spc5 files in simulationdatabase that are used
in src/programs/mdrun/tests to tip3p5 since they were
in fact using tip3p and in this manner a conflict with
the gmx_msd tests is avoided.

TODO: re-use the grompp code in moduletest.cpp
from src/programs/mdrun/tests

Part of #2815

Change-Id: I5d5d33f431f1d3089ebaef54b6388348d47ce6e2
18 files changed:
src/gromacs/gmxana/gmx_msd.cpp
src/gromacs/gmxana/tests/gmx_msd.cpp
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolMassWeighted.xml [new file with mode: 0644]
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolNonMassWeighted.xml [new file with mode: 0644]
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolSelected.xml [new file with mode: 0644]
src/programs/mdrun/tests/minimize.cpp
src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.xml
src/programs/mdrun/tests/refdata/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.xml
src/programs/mdrun/tests/rerun.cpp
src/testutils/simulationdatabase.cpp
src/testutils/simulationdatabase.h
src/testutils/simulationdatabase/spc5.ndx
src/testutils/simulationdatabase/spc5.pdb [new file with mode: 0644]
src/testutils/simulationdatabase/spc5.top
src/testutils/simulationdatabase/spc5_3.ndx [new file with mode: 0644]
src/testutils/simulationdatabase/tip3p5.gro [moved from src/testutils/simulationdatabase/spc5.gro with 100% similarity]
src/testutils/simulationdatabase/tip3p5.ndx [copied from src/testutils/simulationdatabase/spc5.ndx with 100% similarity]
src/testutils/simulationdatabase/tip3p5.top [copied from src/testutils/simulationdatabase/spc5.top with 99% similarity]