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Searched refs:enerd (Results 1 – 25 of 90) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/
H A Denerdata_utils.cpp147 enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i]; in set_dhdl_output()
151 enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]); in set_dhdl_output()
156 enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i]; in set_dhdl_output()
160 enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]); in set_dhdl_output()
221 sum_epot(enerd->grpp, enerd->term); in accumulatePotentialEnergies()
225 enerd->term[F_DVDL] = 0.0; in accumulatePotentialEnergies()
286 enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR]; in accumulateKineticLambdaComponents()
290 enerd->term[F_DVDL] += enerd->term[F_DVDL_CONSTR]; in accumulateKineticLambdaComponents()
296 enerd->foreignLambdaTerms.finalizeKineticContributions(enerd->term, enerd->dvdl_lin[efptMASS], in accumulateKineticLambdaComponents()
349 enerd->term[i] = 0.0_real; in reset_enerdata()
[all …]
H A Dstat.cpp146 gmx_enerdata_t* enerd, in global_stat() argument
258 inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j].data()); in global_stat()
262 idvdll = add_bind(rb, efptNR, enerd->dvdl_lin); in global_stat()
263 idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin); in global_stat()
264 if (enerd->foreignLambdaTerms.numLambdas() > 0) in global_stat()
267 enerd->foreignLambdaTerms.energies().data()); in global_stat()
354 extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j].data()); in global_stat()
358 extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin); in global_stat()
359 extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin); in global_stat()
360 if (enerd->foreignLambdaTerms.numLambdas() > 0) in global_stat()
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H A Denerdata_utils.h51 void reset_foreign_enerdata(gmx_enerdata_t* enerd);
54 void reset_dvdl_enerdata(gmx_enerdata_t* enerd);
57 void reset_enerdata(gmx_enerdata_t* enerd);
73 void accumulatePotentialEnergies(gmx_enerdata_t* enerd,
78 void accumulateKineticLambdaComponents(gmx_enerdata_t* enerd,
H A Dsim_util.cpp206 enerd->term[F_COM_PULL] += in pull_potential_wrapper()
209 enerd->dvdl_lin[efptRESTRAINT] += dvdl; in pull_potential_wrapper()
235 enerd->term[F_COUL_RECIP] += e_q; in pme_receive_force_ener()
236 enerd->term[F_LJ_RECIP] += e_lj; in pme_receive_force_ener()
237 enerd->dvdl_lin[efptCOUL] += dvdl_q; in pme_receive_force_ener()
238 enerd->dvdl_lin[efptVDW] += dvdl_lj; in pme_receive_force_ener()
534 enerd.term[F_LJ], enerd.term[F_COUL_SR], in checkPotentialEnergyValidity()
645 enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, in computeSpecialForces()
1595 reset_enerdata(enerd); in do_force()
1735 enerd->dvdl_lin[efptVDW] += dvdl_walls; in do_force()
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H A Dforce.cpp109 gmx_enerdata_t* enerd, in calculateLongRangeNonbondeds() argument
247 enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL]; in calculateLongRangeNonbondeds()
248 enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW]; in calculateLongRangeNonbondeds()
249 enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q; in calculateLongRangeNonbondeds()
250 enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj; in calculateLongRangeNonbondeds()
255 ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]); in calculateLongRangeNonbondeds()
258 ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]); in calculateLongRangeNonbondeds()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdlib/
H A Dforce.cpp261 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term); in do_force_lowlevel()
262 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT]; in do_force_lowlevel()
644 snew(enerd->enerpart_lambda, enerd->n_lambda); in init_enerdata()
648 enerd->n_lambda = 0; in init_enerdata()
666 if (enerd->n_lambda) in destroy_enerdata()
743 enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i]; in sum_dhdl()
747 … efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]); in sum_dhdl()
752 enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i]; in sum_dhdl()
756 … efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]); in sum_dhdl()
763 enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR]; in sum_dhdl()
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H A Dforce.cpp.preplumed255 sum_epot(&(enerd->foreign_grpp), enerd->foreign_term);
256 enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
631 snew(enerd->enerpart_lambda, enerd->n_lambda);
635 enerd->n_lambda = 0;
653 if (enerd->n_lambda)
730 enerd->term[index] = enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
734 … efpt_names[i], i, enerd->term[index], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
739 enerd->term[F_DVDL] += enerd->dvdl_lin[i] + enerd->dvdl_nonlin[i];
743 … efpt_names[0], i, enerd->term[F_DVDL], enerd->dvdl_nonlin[i], enerd->dvdl_lin[i]);
750 enerd->term[F_DVDL_BONDED] += enerd->term[F_DVDL_CONSTR];
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/nbnxm/
H A Dkerneldispatch.cpp437 … fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data(), in dispatchNonbondedKernel()
449 fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data()); in dispatchNonbondedKernel()
500 kernel_data.energygrp_elec = enerd->grpp.ener[egCOULSR].data(); in dispatchFreeEnergyKernel()
501 kernel_data.energygrp_vdw = enerd->grpp.ener[egLJSR].data(); in dispatchFreeEnergyKernel()
520 enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW]; in dispatchFreeEnergyKernel()
521 enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL]; in dispatchFreeEnergyKernel()
525 enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW]; in dispatchFreeEnergyKernel()
526 enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL]; in dispatchFreeEnergyKernel()
549 reset_foreign_enerdata(enerd); in dispatchFreeEnergyKernel()
561 sum_epot(enerd->foreign_grpp, enerd->foreign_term); in dispatchFreeEnergyKernel()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdlib/
H A Dsim_util.cpp212 enerd->term[F_COM_PULL] += in pull_potential_wrapper()
215 enerd->dvdl_lin[efptRESTRAINT] += dvdl; in pull_potential_wrapper()
241 enerd->term[F_COUL_RECIP] += e_q; in pme_receive_force_ener()
242 enerd->term[F_LJ_RECIP] += e_lj; in pme_receive_force_ener()
243 enerd->dvdl_lin[efptCOUL] += dvdl_q; in pme_receive_force_ener()
244 enerd->dvdl_lin[efptVDW] += dvdl_lj; in pme_receive_force_ener()
540 enerd.term[F_LJ], enerd.term[F_COUL_SR], in checkPotentialEnergyValidity()
651 enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda, in computeSpecialForces()
1594 reset_enerdata(enerd); in do_force()
1734 enerd->dvdl_lin[efptVDW] += dvdl_walls; in do_force()
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H A Dsim_util.cpp.preplumed206 enerd->term[F_COM_PULL] +=
209 enerd->dvdl_lin[efptRESTRAINT] += dvdl;
235 enerd->term[F_COUL_RECIP] += e_q;
236 enerd->term[F_LJ_RECIP] += e_lj;
237 enerd->dvdl_lin[efptCOUL] += dvdl_q;
238 enerd->dvdl_lin[efptVDW] += dvdl_lj;
534 enerd.term[F_LJ], enerd.term[F_COUL_SR],
585 * \param[in,out] enerd Energy buffer
645 enerd->foreignLambdaTerms.finalizePotentialContributions(enerd->dvdl_lin, lambda,
1588 reset_enerdata(enerd);
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/listed_forces/
H A Dlisted_forces.cpp530 epot = enerd->term; in calcBondedForces()
531 grpp = &enerd->grpp; in calcBondedForces()
588 gmx_enerdata_t* enerd, in calc_listed() argument
610 reduce_thread_output(&forceWithShiftForces, enerd->term, &enerd->grpp, dvdl, bt, stepWork); in calc_listed()
616 enerd->dvdl_nonlin[i] += dvdl[i]; in calc_listed()
625 enerd->term[F_DISRESVIOL] = fcd->disres->sumviol; in calc_listed()
760 enerd->term[F_ORIRESDEV] = calc_orires_dev( in calculate()
797 reset_foreign_enerdata(enerd); in calculate()
803 … shiftForceBufferLambda_, &(enerd->foreign_grpp), enerd->foreign_term, in calculate()
805 sum_epot(enerd->foreign_grpp, enerd->foreign_term); in calculate()
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H A Dposition_restraints.h74 gmx_enerdata_t* enerd,
86 gmx_enerdata_t* enerd,
96 gmx_enerdata_t* enerd,
H A Dgpubonded_impl.cu310 void GpuBonded::Impl::waitAccumulateEnergyTerms(gmx_enerdata_t* enerd) in waitAccumulateEnergyTerms() argument
325 enerd->term[fType] += vTot_[fType]; in waitAccumulateEnergyTerms()
330 gmx_grppairener_t* grppener = &enerd->grpp; in waitAccumulateEnergyTerms()
391 void GpuBonded::waitAccumulateEnergyTerms(gmx_enerdata_t* enerd) in waitAccumulateEnergyTerms() argument
393 impl_->waitAccumulateEnergyTerms(enerd); in waitAccumulateEnergyTerms()
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/
H A Dmd.cpp185 gmx_enerdata_t *enerd; in do_md() local
280 snew(enerd, 1); in do_md()
282 enerd); in do_md()
569 real temp = enerd->term[F_TEMP]; in do_md()
1220 last_ekin = enerd->term[F_EKIN]; in do_md()
1529 enerd->term[F_EKIN] = last_ekin; in do_md()
1531 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN]; in do_md()
1537 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity; in do_md()
1541 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ); in do_md()
1738 destroy_enerdata(enerd); in do_md()
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H A Dminimize.cpp490 snew(*enerd, 1); in init_em()
492 *enerd); in init_em()
866 gmx_enerdata_t *enerd; member in __anonf1e4b5e50211::EnergyEvaluator
984 enerd->term[F_DISPCORR] = enercorr; in run()
985 enerd->term[F_EPOT] += enercorr; in run()
989 ems->epot = enerd->term[F_EPOT]; in run()
1011 enerd->term[F_PRES] = in run()
1162 gmx_enerdata_t *enerd; in do_cg() local
1790 gmx_enerdata_t *enerd; in do_lbfgs() local
2516 gmx_enerdata_t *enerd; in do_steep() local
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H A Dmd.cpp.preplumed174 gmx_enerdata_t *enerd;
263 snew(enerd, 1);
265 enerd);
552 real temp = enerd->term[F_TEMP];
1022 last_ekin = enerd->term[F_EKIN];
1331 enerd->term[F_EKIN] = last_ekin;
1333 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
1339 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
1343 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
1540 destroy_enerdata(enerd);
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdlib/
H A Dforce.cpp118 gmx_enerdata_t* enerd, in do_force_lowlevel() argument
135 enerd->term[F_EQM] = calculate_QMMM(cr, &forceOutputs->forceWithShiftForces(), fr); in do_force_lowlevel()
144 enerd->grpp.ener[egLJSR].data(), nrnb); in do_force_lowlevel()
145 enerd->dvdl_lin[efptVDW] += dvdl_walls; in do_force_lowlevel()
190 graph, enerd, nrnb, lambda, md, fcd, in do_force_lowlevel()
352 enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL]; in do_force_lowlevel()
353 enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW]; in do_force_lowlevel()
354 enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q; in do_force_lowlevel()
355 enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj; in do_force_lowlevel()
360 ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]); in do_force_lowlevel()
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H A Dforce.cpp.preplumed112 gmx_enerdata_t* enerd,
129 enerd->term[F_EQM] = calculate_QMMM(cr, &forceOutputs->forceWithShiftForces(), fr);
138 enerd->grpp.ener[egLJSR].data(), nrnb);
139 enerd->dvdl_lin[efptVDW] += dvdl_walls;
184 graph, enerd, nrnb, lambda, md, fcd,
346 enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
347 enerd->dvdl_lin[efptVDW] += ewaldOutput.dvdl[efptVDW];
348 enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
349 enerd->term[F_LJ_RECIP] = Vlr_lj + ewaldOutput.Vcorr_lj;
354 ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/
H A Dmd.cpp647 real temp = enerd->term[F_TEMP]; in do_md()
961 int nlambda = enerd->enerpart_lambda.end() - enerd->enerpart_lambda.begin(); in do_md()
1259 enerd->term[F_TEMP] = in do_md()
1293 last_ekin = enerd->term[F_EKIN]; in do_md()
1556 enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr; in do_md()
1560 enerd->term[F_DVDL_CONSTR] += dvdl_constr; in do_md()
1657 sum_dhdl(enerd, state->lambda, *ir->fepvals); in do_md()
1692 enerd->term[F_EKIN] = last_ekin; in do_md()
1694 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN]; in do_md()
1700 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity; in do_md()
[all …]
/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/
H A Dmd.cpp664 real temp = enerd->term[F_TEMP]; in do_md()
957 int nlambda = enerd->foreignLambdaTerms.numLambdas(); in do_md()
1259 enerd->term[F_TEMP] = in do_md()
1261 enerd->term[F_EKIN] = trace(ekind->ekin); in do_md()
1292 last_ekin = enerd->term[F_EKIN]; in do_md()
1583 enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr; in do_md()
1587 enerd->term[F_DVDL_CONSTR] += dvdl_constr; in do_md()
1715 enerd->term[F_EKIN] = last_ekin; in do_md()
1717 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN]; in do_md()
1723 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity; in do_md()
[all …]
/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/
H A Dmd.cpp645 real temp = enerd->term[F_TEMP]; in do_md()
1057 enerd->term[F_TEMP] = in do_md()
1059 enerd->term[F_EKIN] = trace(ekind->ekin); in do_md()
1090 last_ekin = enerd->term[F_EKIN]; in do_md()
1094 saved_conserved_quantity -= enerd->term[F_DISPCORR]; in do_md()
1381 enerd->term[F_DVDL_CONSTR] += 2 * dvdl_constr; in do_md()
1385 enerd->term[F_DVDL_CONSTR] += dvdl_constr; in do_md()
1513 enerd->term[F_EKIN] = last_ekin; in do_md()
1515 enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN]; in do_md()
1521 enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity; in do_md()
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H A Disimulator.h138 gmx_enerdata_t* enerd, in LegacySimulatorData()
172 enerd(enerd), in LegacySimulatorData()
236 gmx_enerdata_t* enerd; variable
H A Dtpi.cpp758 &state_global->hist, &f.view(), force_vir, mdatoms, enerd, in do_tpi()
774 enerd->term[F_DISPCORR] = correction.energy; in do_tpi()
775 enerd->term[F_EPOT] += correction.energy; in do_tpi()
776 enerd->term[F_PRES] += correction.pressure; in do_tpi()
777 enerd->term[F_DVDL] += correction.dvdl; in do_tpi()
781 enerd->term[F_DISPCORR] = 0; in do_tpi()
785 enerd->term[F_EPOT] += rfExclusionEnergy; in do_tpi()
788 epot = enerd->term[F_EPOT]; in do_tpi()
838 sum_UgembU[e++] += enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] * embU; in do_tpi()
843 sum_UgembU[e++] += enerd->term[F_DISPCORR] * embU; in do_tpi()
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H A Dmimic.cpp301 makeConstArrayRef(state->v), state->box, mdatoms, nrnb, vcm, nullptr, enerd, in do_mimic()
425 imdSession, pull_work, bNS, force_flags, &top, constr, enerd, in do_mimic()
442 &f.view(), force_vir, mdatoms, enerd, state->lambda, fr, runScheduleWork, in do_mimic()
470 enerd, nullptr, nullptr, nullptr, nullptr, constr, &signaller, in do_mimic()
497 MimicCommunicator::sendEnergies(enerd->term[F_EPOT]); in do_mimic()
512 accumulateKineticLambdaComponents(enerd, state->lambda, *ir->fepvals); in do_mimic()
520 doFreeEnergyPerturbation, bCalcEnerStep, t, mdatoms->tmass, enerd, ir->fepvals, in do_mimic()
/dports/science/gromacs/gromacs-2021.4/src/gromacs/ewald/
H A Dpme_gpu.cpp311 gmx_enerdata_t* enerd) in pme_gpu_reduce_outputs() argument
318 GMX_ASSERT(enerd, "Invalid energy output manager"); in pme_gpu_reduce_outputs()
320 enerd->term[F_COUL_RECIP] += output.coulombEnergy_; in pme_gpu_reduce_outputs()
321 enerd->dvdl_lin[efptCOUL] += output.coulombDvdl_; in pme_gpu_reduce_outputs()
334 gmx_enerdata_t* enerd, in pme_gpu_try_finish_task() argument
382 pme_gpu_reduce_outputs(computeEnergyAndVirial, output, wcycle, forceWithVirial, enerd); in pme_gpu_try_finish_task()
416 gmx_enerdata_t* enerd, in pme_gpu_wait_and_reduce() argument
425 pme_gpu_reduce_outputs(computeEnergyAndVirial, output, wcycle, forceWithVirial, enerd); in pme_gpu_wait_and_reduce()

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