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(parent: a641639) | patch
Migrate gmx msd to the trajectoryanalysis framework
authorKevin Boyd <kevin44boyd@gmail.com>
Tue, 16 Mar 2021 17:28:24 +0000 (17:28 +0000)
committerPaul Bauer <paul.bauer.q@gmail.com>
Tue, 16 Mar 2021 17:28:24 +0000 (17:28 +0000)
commitcbd70146be5958cbb7ba2e56a349552fbfa60778
treee04bab299052abca588515c449270396c74db1c3tree | snapshot
parenta6416394629f5349172082f18d4183ea5b73996ccommit | diff
Migrate gmx msd to the trajectoryanalysis framework

Features to still be added
-tensor, for the MSD tensor
-pdb, for per molecule B-factors
-rmcomm, for system COM removal
-mw, for tuning mass-weighting options
-maxtau, for limiting resource usage and unneccessary computation (refs #3870)
-improvements to documentation and maybe some flag behavior changes (refs #3869)

Refs #2368
29 files changed:
docs/release-notes/2022/major/tools.rst diff | blob | history
src/gromacs/gmxana/gmx_ana.h diff | blob | history
src/gromacs/gmxana/gmx_msd.cpp [deleted file] blob | history
src/gromacs/gmxana/tests/CMakeLists.txt diff | blob | history
src/gromacs/gmxana/tests/gmx_msd.cpp [deleted file] blob | history
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolMassWeighted.xml [deleted file] blob | history
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolNonMassWeighted.xml [deleted file] blob | history
src/gromacs/gmxana/tests/refdata/MsdMolTest_diffMolSelected.xml [deleted file] blob | history
src/gromacs/trajectoryanalysis/modules.cpp diff | blob | history
src/gromacs/trajectoryanalysis/modules/msd.cpp [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/modules/msd.h [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/CMakeLists.txt diff | blob | history
src/gromacs/trajectoryanalysis/tests/msd.cpp [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_beginFit.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_endFit.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_molTest.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_multipleGroupsWork.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_notEnoughPointsForFitErrorEstimate.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_oneDimensionalDiffusion.xml [moved from src/gromacs/gmxana/tests/refdata/MsdTest_oneDimensionalDiffusion.xml with 67% similarity] diff | blob | history
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_threeDimensionalDiffusion.xml [moved from src/gromacs/gmxana/tests/refdata/MsdTest_threeDimensionalDiffusion.xml with 67% similarity] diff | blob | history
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_trestartGreaterThanDt.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_trestartLessThanDt.xml [new file with mode: 0644] blob
src/gromacs/trajectoryanalysis/tests/refdata/MsdModuleTest_twoDimensionalDiffusion.xml [moved from src/gromacs/gmxana/tests/refdata/MsdTest_twoDimensionalDiffusion.xml with 67% similarity] diff | blob | history
src/programs/legacymodules.cpp diff | blob | history
src/testutils/simulationdatabase/alanine_vsite_solvated.ndx diff | blob | history
src/testutils/simulationdatabase/alanine_vsite_solvated.xtc [new file with mode: 0644] blob
src/testutils/simulationdatabase/msd.ndx [new file with mode: 0644] blob
src/testutils/simulationdatabase/msd_coords.gro [new file with mode: 0644] blob
src/testutils/simulationdatabase/msd_traj.xtc [new file with mode: 0644] blob
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