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/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/
H A Dforcefieldparameters.cpp89 void pr_ffparams(FILE* fp, int indent, const char* title, const gmx_ffparams_t* ffparams, gmx_bool … in pr_ffparams() argument
95 fprintf(fp, "atnr=%d\n", ffparams->atnr); in pr_ffparams()
97 fprintf(fp, "ntypes=%d\n", ffparams->numTypes()); in pr_ffparams()
98 for (i = 0; i < ffparams->numTypes(); i++) in pr_ffparams()
102 interaction_function[ffparams->functype[i]].name); in pr_ffparams()
103 pr_iparams(fp, ffparams->functype[i], ffparams->iparams[i]); in pr_ffparams()
105 pr_double(fp, indent, "reppow", ffparams->reppow); in pr_ffparams()
106 pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ); in pr_ffparams()
107 pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers); in pr_ffparams()
H A Dtopsort.cpp145 const gmx_ffparams_t* ffparams = &mtop->ffparams; in gmx_mtop_bondeds_free_energy() local
149 for (int i = 0; i < ffparams->numTypes(); i++) in gmx_mtop_bondeds_free_energy()
151 int ftype = ffparams->functype[i]; in gmx_mtop_bondeds_free_energy()
154 if (ip_pert(ftype, &ffparams->iparams[i])) in gmx_mtop_bondeds_free_energy()
H A Dtopology.cpp220 gmx_localtop_t::gmx_localtop_t(const gmx_ffparams_t& ffparams) : idef(ffparams) {} in gmx_localtop_t() argument
348 const gmx_ffparams_t* ffparams, in pr_moltype() argument
361 pr_ilist(fp, indent, interaction_function[j].longname, ffparams->functype.data(), in pr_moltype()
362 molt->ilist[j], bShowNumbers, bShowParameters, ffparams->iparams.data()); in pr_moltype()
409 mtop->ffparams.functype.data(), (*mtop->intermolecular_ilist)[j], in pr_mtop()
410 bShowNumbers, bShowParameters, mtop->ffparams.iparams.data()); in pr_mtop()
413 pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers); in pr_mtop()
417 pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt, &mtop->ffparams, bShowNumbers, in pr_mtop()
689 compareFfparams(fp, mtop1.ffparams, mtop2.ffparams, relativeTolerance, absoluteTolerance); in compareMtop()
703 compareFfparamAB(fp, mtop1.ffparams, relativeTolerance, absoluteTolerance); in compareMtopAB()
H A Dtopology.h167 gmx_ffparams_t ffparams; member
231 gmx_localtop_t(const gmx_ffparams_t& ffparams);
H A Dmtop_util.cpp62 for (int i = 0; i < mtop->ffparams.atnr; ++i) in gmx_mtop_count_atomtypes()
654 const gmx_ffparams_t* ffp = &mtop.ffparams; in copyFFParametersFromMtop()
1109 const auto& ffparams = mtop.ffparams; in havePerturbedConstraints() local
1111 for (gmx::index i = 0; i < gmx::ssize(ffparams.functype); i++) in havePerturbedConstraints()
1113 if (ffparams.functype[i] == F_CONSTR || ffparams.functype[i] == F_CONSTRNC) in havePerturbedConstraints()
1115 const auto& iparams = ffparams.iparams[i]; in havePerturbedConstraints()
H A Dforcefieldparameters.h72 void pr_ffparams(FILE* fp, int indent, const char* title, const gmx_ffparams_t* ffparams, gmx_bool …
H A Didef.cpp423 InteractionDefinitions::InteractionDefinitions(const gmx_ffparams_t& ffparams) : in InteractionDefinitions() argument
424 iparams(ffparams.iparams), in InteractionDefinitions()
425 functype(ffparams.functype), in InteractionDefinitions()
426 cmap_grid(ffparams.cmap_grid) in InteractionDefinitions()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/tests/
H A Dupdategroups.cpp155 mtop.ffparams.iparams.push_back(iparams); in TEST()
174 mtop.ffparams.iparams.push_back(iparams); in TEST()
192 mtop.ffparams.iparams.push_back(iparams); in TEST()
194 mtop.ffparams.iparams.push_back(iparams); in TEST()
221 mtop.ffparams.iparams.push_back(iparams); in TEST()
235 mtop.ffparams.iparams.push_back(iparams); in TEST()
256 mtop.ffparams.iparams.push_back(iparams[0]); in TEST()
257 mtop.ffparams.iparams.push_back(iparams[1]); in TEST()
286 mtop.ffparams.iparams.push_back(iparams); in TEST()
288 mtop.ffparams.iparams.push_back(iparams); in TEST()
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H A Dsettletestdata.cpp119 mtop_.ffparams.iparams.push_back(iparams); in SettleTestData()
142 idef_ = std::make_unique<InteractionDefinitions>(mtop_.ffparams); in SettleTestData()
H A Denergyoutput.cpp292 mtop_.ffparams.iparams.resize(F_NRE); in EnergyOutputTest()
293 mtop_.ffparams.functype.resize(F_NRE); in EnergyOutputTest()
294 mtop_.ffparams.iparams.at(F_CONSTR).constr.dA = 1.0; in EnergyOutputTest()
295 mtop_.ffparams.iparams.at(F_CONSTR).constr.dB = 1.0; in EnergyOutputTest()
296 mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dA = 1.0; in EnergyOutputTest()
297 mtop_.ffparams.iparams.at(F_CONSTRNC).constr.dB = 1.0; in EnergyOutputTest()
H A Dconstrtestdata.cpp142 auto& iparams = mtop_.ffparams.iparams; in ConstraintsTestData()
149 idef_ = std::make_unique<InteractionDefinitions>(mtop_.ffparams); in ConstraintsTestData()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/gmxpreprocess/
H A Dconvparm.cpp445 static int enter_params(gmx_ffparams_t* ffparams, in enter_params() argument
469 if (ffparams->functype[type] == ftype in enter_params()
481 const int type = ffparams->numTypes() - 1; in enter_params()
482 if (type >= 0 && ffparams->functype[type] == ftype in enter_params()
490 const int type = ffparams->numTypes(); in enter_params()
492 ffparams->iparams.push_back(newparam); in enter_params()
493 ffparams->functype.push_back(ftype); in enter_params()
495 GMX_ASSERT(ffparams->iparams.size() == ffparams->functype.size(), "sizes should match"); in enter_params()
513 gmx_ffparams_t* ffparams, in enter_function() argument
518 int start = ffparams->numTypes(); in enter_function()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/listed_forces/
H A Dgpubonded_impl.cu70 GpuBonded::Impl::Impl(const gmx_ffparams_t& ffparams, in Impl() argument
87 allocateDeviceBuffer(&d_forceParams_, ffparams.numTypes(), deviceContext_); in Impl()
91 copyToDeviceBuffer(&d_forceParams_, ffparams.iparams.data(), 0, ffparams.numTypes(), in Impl()
347 GpuBonded::GpuBonded(const gmx_ffparams_t& ffparams, in GpuBonded() argument
352 impl_(new Impl(ffparams, electrostaticsScaleFactor, deviceContext, deviceStream, wcycle)) in GpuBonded()
H A Dgpubonded.h122 GpuBonded(const gmx_ffparams_t& ffparams,
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Dforcerec.cpp383 c6 = mtop->ffparams.iparams[atoms->atom[i].type * (mtop->ffparams.atnr + 1)].lj.c6; in set_chargesum()
405 c6 = mtop->ffparams.iparams[atoms->atom[i].typeB * (mtop->ffparams.atnr + 1)].lj.c6; in set_chargesum()
445 ntypes = mtop->ffparams.atnr; in calcBuckinghamBMax()
470 b = mtop->ffparams.iparams[tpi * ntypes + tpj].bham.b; in calcBuckinghamBMax()
839 ic->reppow = mtop->ffparams.reppow; in init_interaction_const()
843 ic->useBuckingham = (mtop->ffparams.functype[0] == F_BHAM); in init_interaction_const()
1024 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM); in init_forcerec()
1160 fr->fudgeQQ = mtop->ffparams.fudgeQQ; in init_forcerec()
1190 fr->ntype = mtop->ffparams.atnr; in init_forcerec()
1191 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM); in init_forcerec()
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H A Dmdatoms.cpp441 c6 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c6; in atoms2md()
442 c12 = mtop->ffparams.iparams[atom.type * (mtop->ffparams.atnr + 1)].lj.c12; in atoms2md()
461 c6 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c6; in atoms2md()
462 c12 = mtop->ffparams.iparams[atom.typeB * (mtop->ffparams.atnr + 1)].lj.c12; in atoms2md()
H A Dcalc_verletbuf.cpp208 const gmx_ffparams_t& ffparams, in get_vsite_masses() argument
219 const t_iparams& ip = ffparams.iparams[ilist.iatoms[i]]; in get_vsite_masses()
292 real coeff = ffparams.iparams[ilist.iatoms[i + j]].vsiten.a; in get_vsite_masses()
352 ip = &mtop.ffparams.iparams[il.iatoms[i]]; in getVerletBufferAtomtypes()
374 ip = &mtop.ffparams.iparams[il.iatoms[i]]; in getVerletBufferAtomtypes()
393 get_vsite_masses(moltype, mtop.ffparams, setMassesToOne, vsite_m); in getVerletBufferAtomtypes()
920 real repPow = mtop.ffparams.reppow; in calcVerletBufferSize()
1185 real length = ffparams.iparams[type].constr.dA; in getAtomConstraintProps()
1196 const gmx_ffparams_t& ffparams, in chanceOfUpdateGroupCrossingCell() argument
1207 const auto atomConstraintProps = getAtomConstraintProps(moltype, ffparams); in chanceOfUpdateGroupCrossingCell()
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H A Ddispersioncorrection.cpp60 static std::vector<real> mk_nbfp_combination_rule(const gmx_ffparams_t& ffparams, const int comb_ru… in mk_nbfp_combination_rule() argument
62 const int atnr = ffparams.atnr; in mk_nbfp_combination_rule()
70 const real c6i = ffparams.iparams[i * (atnr + 1)].lj.c6; in mk_nbfp_combination_rule()
71 const real c12i = ffparams.iparams[i * (atnr + 1)].lj.c12; in mk_nbfp_combination_rule()
72 const real c6j = ffparams.iparams[j * (atnr + 1)].lj.c6; in mk_nbfp_combination_rule()
73 const real c12j = ffparams.iparams[j * (atnr + 1)].lj.c12; in mk_nbfp_combination_rule()
125 mtop.ffparams, in TopologyParams()
H A Dconstr.cpp211 const gmx_ffparams_t& ffparams = impl_->mtop.ffparams; in havePerturbedConstraints() local
213 for (size_t i = 0; i < ffparams.functype.size(); i++) in havePerturbedConstraints()
215 if ((ffparams.functype[i] == F_CONSTR || ffparams.functype[i] == F_CONSTRNC) in havePerturbedConstraints()
216 && ffparams.iparams[i].constr.dA != ffparams.iparams[i].constr.dB) in havePerturbedConstraints()
987 mapping.push_back(make_at2con(moltype, mtop.ffparams.iparams, flexibleConstraintTreatment)); in makeAtomToConstraintMappings()
1041 … int count = countFlexibleConstraints(mtop.moltype[molblock.type].ilist, mtop.ffparams.iparams); in Impl()
H A Dwholemoleculetransform.cpp48 gmx_localtop_t localTop(mtop.ffparams); in WholeMoleculeTransform()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mimic/
H A Dcommunicator.cpp143 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) in sendInitData()
167 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) in sendInitData()
169 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) in sendInitData()
171 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dB) in sendInitData()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/
H A Dshellfc.cpp271 const gmx_ffparams_t* ffparams; in init_shell_flexcon() local
339 ffparams = &mtop->ffparams; in init_shell_flexcon()
360 ftype = ffparams->functype[type]; in init_shell_flexcon()
441 shell[nsi].k += ffparams->iparams[type].harmonic.krA; in init_shell_flexcon()
444 shell[nsi].k += ffparams->iparams[type].cubic.kb; in init_shell_flexcon()
456 / ffparams->iparams[type].polarize.alpha; in init_shell_flexcon()
466 alpha = (ffparams->iparams[type].wpol.al_x in init_shell_flexcon()
467 + ffparams->iparams[type].wpol.al_y in init_shell_flexcon()
468 + ffparams->iparams[type].wpol.al_z) in init_shell_flexcon()
/dports/science/gromacs/gromacs-2021.4/api/nblib/listed_forces/
H A Dconversions.hpp251 gmx_ffparams_t& ffparams = *ffparamsHolder; in createFFparams() local
254 auto copyParamsOneType = [&ffparams](const auto& interactionElement) in createFFparams()
256 detail::transferParameters(interactionElement, ffparams); in createFFparams()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/modularsimulator/
H A Dtopologyholder.cpp62 localTopology_(std::make_unique<gmx_localtop_t>(globalTopology.ffparams)), in TopologyHolder()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/
H A Dtpxio.cpp2040 serializer->doInt(&ffparams->atnr); in do_ffparams()
2041 int numTypes = ffparams->numTypes(); in do_ffparams()
2045 ffparams->functype.resize(numTypes); in do_ffparams()
2046 ffparams->iparams.resize(numTypes); in do_ffparams()
2049 serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size()); in do_ffparams()
2053 serializer->doDouble(&ffparams->reppow); in do_ffparams()
2057 ffparams->reppow = 12.0; in do_ffparams()
2060 serializer->doReal(&ffparams->fudgeQQ); in do_ffparams()
2066 for (int i = 0; i < ffparams->numTypes(); i++) in do_ffparams()
2076 ffparams->functype[i] += 1; in do_ffparams()
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