/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdlib/ |
H A D | enerdata_utils.cpp | 147 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 …]
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H A D | stat.cpp | 146 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() [all …]
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H A D | enerdata_utils.h | 51 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,
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H A D | sim_util.cpp | 206 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() [all …]
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H A D | force.cpp | 109 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()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdlib/ |
H A D | force.cpp | 261 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() [all …]
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H A D | force.cpp.preplumed | 255 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]; [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/nbnxm/ |
H A D | kerneldispatch.cpp | 437 … 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() [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdlib/ |
H A D | sim_util.cpp | 212 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() [all …]
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H A D | sim_util.cpp.preplumed | 206 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); [all …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/listed_forces/ |
H A D | listed_forces.cpp | 530 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() [all …]
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H A D | position_restraints.h | 74 gmx_enerdata_t* enerd, 86 gmx_enerdata_t* enerd, 96 gmx_enerdata_t* enerd,
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H A D | gpubonded_impl.cu | 310 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()
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2019.6.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 185 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() [all …]
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H A D | minimize.cpp | 490 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 [all …]
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H A D | md.cpp.preplumed | 174 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); [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdlib/ |
H A D | force.cpp | 118 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() [all …]
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H A D | force.cpp.preplumed | 112 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]); [all …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2020.6.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 647 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 …]
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/dports/science/plumed/plumed2-2.7.2/patches/gromacs-2021.diff/src/gromacs/mdrun/ |
H A D | md.cpp | 664 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 …]
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/mdrun/ |
H A D | md.cpp | 645 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() [all …]
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H A D | isimulator.h | 138 gmx_enerdata_t* enerd, in LegacySimulatorData() 172 enerd(enerd), in LegacySimulatorData() 236 gmx_enerdata_t* enerd; variable
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H A D | tpi.cpp | 758 &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() [all …]
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H A D | mimic.cpp | 301 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()
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/dports/science/gromacs/gromacs-2021.4/src/gromacs/ewald/ |
H A D | pme_gpu.cpp | 311 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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