/dports/science/gromacs/gromacs-2021.4/src/gromacs/topology/ |
H A D | forcefieldparameters.cpp | 89 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 D | topsort.cpp | 145 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 D | topology.cpp | 220 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 D | topology.h | 167 gmx_ffparams_t ffparams; member 231 gmx_localtop_t(const gmx_ffparams_t& ffparams);
|
H A D | mtop_util.cpp | 62 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 D | forcefieldparameters.h | 72 void pr_ffparams(FILE* fp, int indent, const char* title, const gmx_ffparams_t* ffparams, gmx_bool …
|
H A D | idef.cpp | 423 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 D | updategroups.cpp | 155 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() [all …]
|
H A D | settletestdata.cpp | 119 mtop_.ffparams.iparams.push_back(iparams); in SettleTestData() 142 idef_ = std::make_unique<InteractionDefinitions>(mtop_.ffparams); in SettleTestData()
|
H A D | energyoutput.cpp | 292 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 D | constrtestdata.cpp | 142 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 D | convparm.cpp | 445 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() [all …]
|
/dports/science/gromacs/gromacs-2021.4/src/gromacs/listed_forces/ |
H A D | gpubonded_impl.cu | 70 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 D | gpubonded.h | 122 GpuBonded(const gmx_ffparams_t& ffparams,
|
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | forcerec.cpp | 383 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() [all …]
|
H A D | mdatoms.cpp | 441 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 D | calc_verletbuf.cpp | 208 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() [all …]
|
H A D | dispersioncorrection.cpp | 60 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 D | constr.cpp | 211 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 D | wholemoleculetransform.cpp | 48 gmx_localtop_t localTop(mtop.ffparams); in WholeMoleculeTransform()
|
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mimic/ |
H A D | communicator.cpp | 143 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 D | shellfc.cpp | 271 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 D | conversions.hpp | 251 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 D | topologyholder.cpp | 62 localTopology_(std::make_unique<gmx_localtop_t>(globalTopology.ffparams)), in TopologyHolder()
|
/dports/science/gromacs/gromacs-2021.4/src/gromacs/fileio/ |
H A D | tpxio.cpp | 2040 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() [all …]
|