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(parent: 2f68675) | patch
Add gapsys softcore function.
authorSebastian Kehl <sebastian.kehl@mpcdf.mpg.de>
Mon, 16 Nov 2020 09:27:47 +0000 (10:27 +0100)
committerMagnus Lundborg <magnus.lundborg@scilifelab.se>
Tue, 5 Oct 2021 11:38:46 +0000 (11:38 +0000)
commitbde5e2e28f1b7da1a832e2795789de30f1f014c7
tree458696ea1d1db0461a5e66f6327fd94d08a3db16tree | snapshot
parent2f68675dbc7fa404eac6cbc271056ed7c811ddffcommit | diff
Add gapsys softcore function.

Change nonbonded fep-kernel to allow to use both, standard
beutler function as well as new gapsys function. Add new
input name to choose one of these.
102 files changed:
docs/CMakeLists.txt diff | blob | history
docs/reference-manual/functions/free-energy-interactions.rst diff | blob | history
docs/reference-manual/functions/plots/gapsys-sc.pdf [new file with mode: 0644] blob
docs/reference-manual/functions/plots/gapsys-sc.svg [new file with mode: 0644] blob
docs/reference-manual/references.rst diff | blob | history
src/gromacs/fileio/tpxio.cpp diff | blob | history
src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp diff | blob | history
src/gromacs/gmxlib/nonbonded/nb_softcore.h [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/nb_free_energy.cpp diff | blob | history
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_100.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_101.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_102.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_103.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_104.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_105.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_106.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_107.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_36.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_37.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_38.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_39.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_40.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_41.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_42.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_43.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_44.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_45.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_46.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_47.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_48.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_49.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_50.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_51.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_52.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_53.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_54.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_55.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_56.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_57.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_58.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_59.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_60.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_61.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_62.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_63.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_64.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_65.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_66.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_67.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_68.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_69.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_70.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_71.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_72.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_73.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_74.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_75.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_76.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_77.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_78.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_79.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_80.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_81.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_82.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_83.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_84.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_85.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_86.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_87.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_88.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_89.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_90.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_91.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_92.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_93.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_94.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_95.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_96.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_97.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_98.xml [new file with mode: 0644] blob
src/gromacs/gmxlib/nonbonded/tests/refdata/NBInteraction_NonbondedFepTest_testKernel_99.xml [new file with mode: 0644] blob
src/gromacs/gmxpreprocess/readir.cpp diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricField.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldOscillating.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsElectricFieldPulsed.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsEmptyLines.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsImplicitSolventNo.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsKeyWithoutValue.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_AcceptsMimic.xml diff | blob | history
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml diff | blob | history
src/gromacs/listed_forces/pairs.cpp diff | blob | history
src/gromacs/listed_forces/tests/pairs.cpp diff | blob | history
src/gromacs/listed_forces/tests/refdata/14Interaction_ListedForcesPairsTest_Ifunc_0.xml diff | blob | history
src/gromacs/listed_forces/tests/refdata/14Interaction_ListedForcesPairsTest_Ifunc_1.xml diff | blob | history
src/gromacs/listed_forces/tests/refdata/14Interaction_ListedForcesPairsTest_Ifunc_2.xml diff | blob | history
src/gromacs/mdtypes/inputrec.cpp diff | blob | history
src/gromacs/mdtypes/inputrec.h diff | blob | history
src/gromacs/mdtypes/interaction_const.cpp diff | blob | history
src/gromacs/mdtypes/interaction_const.h diff | blob | history
src/gromacs/mdtypes/md_enums.cpp diff | blob | history
src/gromacs/mdtypes/md_enums.h diff | blob | history
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