Remove support for implicit solvation
authorMark Abraham <mark.j.abraham@gmail.com>
Mon, 15 Jan 2018 13:01:44 +0000 (14:01 +0100)
committerMark Abraham <mark.j.abraham@gmail.com>
Tue, 23 Jan 2018 17:08:21 +0000 (18:08 +0100)
commit93c6b6d68a85d5c2b0c28819b45461411f249efc
treebc0958e0a2cb3d8896a1a4ec4c7689cc6ee33aaa
parent6a3341067e1f168021d3f96f52fb0ab33dbe76d8
Remove support for implicit solvation

Mdp files with implicit-solvent = no can still be read, and formerly
valid related fields are now ignored, so that default mdp files from
previous versions of GROMACS will work. Anything else for the
implciit-solvent mdp value gives an error in grompp.

grompp can now only write a tpr file that has a false value for
ir->implicit_solvent, but can read older versions. When mdrun is
presented with an older tpr file that did such a simulation, it
refuses to run, presenting a useful error message. Such tpr files are
still useful for other purposes, so can still be read, except that the
fields specific to these methods are ignored.

grompp now ignores the topology directives for related parameters,
which means that force-field folders that are the same as, or
modifications of folders formerly supported by GROMACS still
work. However, the versions currently distributed have none of those
fields.

The group-scheme kernels have been removed, and generation
infrastructure updated so that they do generate the code that's in the
repo. However, now that the python generation scripts no longer
generate GB kernels, the dictionary ordering changes, which changes
the generated output. That output is not sensitive to the order of the
declarations or data-structure elements, so this is only a cosmetic
issue.

Documentation has been removed.

Unit tests on .mdp file handling have had to be updated.

Also removed unused enbcoul enumeration

Refs #1500
Refs #1971
Fixes #1054

Change-Id: Ib241555ff3d8e60012ba0e628ab0f9a3f91eca9e
131 files changed:
docs/manual/algorithms.tex
docs/manual/forcefield.tex
docs/manual/topology.tex
docs/user-guide/cutoff-schemes.rst
docs/user-guide/mdp-options.rst
docs/user-guide/mdrun-performance.rst
docs/user-guide/terminology.rst
src/gromacs/domdec/domdec.cpp
src/gromacs/fileio/tpxio.cpp
src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
src/gromacs/gmxlib/nonbonded/nb_generic.cpp
src/gromacs/gmxlib/nonbonded/nb_kernel.h
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/make_nb_kernel_avx_128_fma_double.py
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_avx_128_fma_double.c
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_template_avx_128_fma_double.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/make_nb_kernel_avx_128_fma_single.py
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_avx_128_fma_single.c
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_template_avx_128_fma_single.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/make_nb_kernel_avx_256_double.py
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_avx_256_double.c
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_template_avx_256_double.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/make_nb_kernel_avx_256_single.py
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_avx_256_single.c
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_template_avx_256_single.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_c/make_nb_kernel_c.py
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwBham_GeomP1P1_c.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_c.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwLJ_GeomP1P1_c.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwNone_GeomP1P1_c.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.cpp [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.h [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_c.c
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_template_c.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/make_nb_kernel_sparc64_hpc_ace_double.py
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sparc64_hpc_ace_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sparc64_hpc_ace_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sparc64_hpc_ace_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_sparc64_hpc_ace_double.c
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/nb_kernel_template_sparc64_hpc_ace_double.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/make_nb_kernel_sse2_double.py
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_sse2_double.c
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_template_sse2_double.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/make_nb_kernel_sse2_single.py
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_sse2_single.c
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_template_sse2_single.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/make_nb_kernel_sse4_1_double.py
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_double.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_sse4_1_double.c
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_template_sse4_1_double.pre
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/make_nb_kernel_sse4_1_single.py
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_single.c [deleted file]
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_sse4_1_single.c
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_template_sse4_1_single.pre
src/gromacs/gmxlib/nonbonded/nonbonded.cpp
src/gromacs/gmxlib/nrnb.cpp
src/gromacs/gmxlib/nrnb.h
src/gromacs/gmxpreprocess/convparm.cpp
src/gromacs/gmxpreprocess/gpp_atomtype.cpp
src/gromacs/gmxpreprocess/gpp_atomtype.h
src/gromacs/gmxpreprocess/grompp.cpp
src/gromacs/gmxpreprocess/nm2type.cpp
src/gromacs/gmxpreprocess/readir.cpp
src/gromacs/gmxpreprocess/resall.cpp
src/gromacs/gmxpreprocess/tests/readir.cpp
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_EmptyInputWorks.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesDifferentKindsOfMdpLines.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_HandlesOnlyCutoffScheme.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_ImplicitSolventNoWorks.xml [new file with mode: 0644]
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_ProducesOutputFromElectricField.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_ProducesOutputFromElectricFieldOscillating.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_ProducesOutputFromElectricFieldPulsed.xml
src/gromacs/gmxpreprocess/tests/refdata/GetIrTest_UserErrorsSilentlyTolerated.xml
src/gromacs/gmxpreprocess/topdirs.cpp
src/gromacs/gmxpreprocess/topio.cpp
src/gromacs/gmxpreprocess/topio.h
src/gromacs/gmxpreprocess/toppush.cpp
src/gromacs/gmxpreprocess/toppush.h
src/gromacs/gmxpreprocess/toputil.cpp
src/gromacs/listed-forces/listed-forces.cpp
src/gromacs/mdlib/broadcaststructs.cpp
src/gromacs/mdlib/force.cpp
src/gromacs/mdlib/force.h
src/gromacs/mdlib/forcerec.cpp
src/gromacs/mdlib/forcerec.h
src/gromacs/mdlib/genborn.cpp [deleted file]
src/gromacs/mdlib/genborn.h [deleted file]
src/gromacs/mdlib/genborn_allvsall.cpp [deleted file]
src/gromacs/mdlib/genborn_allvsall.h [deleted file]
src/gromacs/mdlib/mdebin.cpp
src/gromacs/mdlib/minimize.cpp
src/gromacs/mdlib/shellfc.cpp
src/gromacs/mdlib/shellfc.h
src/gromacs/mdlib/sim_util.cpp
src/gromacs/mdlib/tpi.cpp
src/gromacs/mdtypes/forcerec.h
src/gromacs/mdtypes/inputrec.cpp
src/gromacs/mdtypes/inputrec.h
src/gromacs/mdtypes/md_enums.cpp
src/gromacs/mdtypes/md_enums.h
src/gromacs/tables/forcetable.cpp
src/gromacs/tables/forcetable.h
src/gromacs/timing/wallcycle.cpp
src/gromacs/timing/wallcycle.h
src/gromacs/topology/atoms.cpp
src/gromacs/topology/atoms.h
src/gromacs/topology/idef.cpp
src/gromacs/topology/idef.h
src/gromacs/topology/ifunc.cpp
src/programs/mdrun/md.cpp