From ce303af479db202478503bbc9340f7afaedc917c Mon Sep 17 00:00:00 2001 From: Dmitry Morozov Date: Mon, 7 Jun 2021 11:00:13 +0000 Subject: [PATCH] Added EnergyOutputRequestChecker notification for MDModules --- src/gromacs/mdlib/energyoutput.cpp | 10 +- src/gromacs/mdlib/tests/energyoutput.cpp | 2 - ...ameters_EnergyOutputTest_CheckOutput_0.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_1.xml | 35 +-- ...meters_EnergyOutputTest_CheckOutput_10.xml | 47 ++-- ...meters_EnergyOutputTest_CheckOutput_11.xml | 48 ++-- ...ameters_EnergyOutputTest_CheckOutput_2.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_3.xml | 2 +- ...ameters_EnergyOutputTest_CheckOutput_4.xml | 244 +++++++----------- ...ameters_EnergyOutputTest_CheckOutput_5.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_6.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_7.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_8.xml | 46 ++-- ...ameters_EnergyOutputTest_CheckOutput_9.xml | 46 ++-- src/gromacs/utility/mdmodulesnotifiers.h | 14 + 15 files changed, 308 insertions(+), 416 deletions(-) diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp index a0b0abb1d5..469fac5336 100644 --- a/src/gromacs/mdlib/energyoutput.cpp +++ b/src/gromacs/mdlib/energyoutput.cpp @@ -219,7 +219,6 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, bEner_[F_LJ] = !bBHAM; bEner_[F_BHAM] = bBHAM; - bEner_[F_EQM] = inputrec.bQMMM; bEner_[F_RF_EXCL] = (EEL_RF(inputrec.coulombtype) && inputrec.cutoff_scheme == CutoffScheme::Group); bEner_[F_COUL_RECIP] = EEL_FULL(inputrec.coulombtype); bEner_[F_LJ_RECIP] = EVDW_PME(inputrec.vdwtype); @@ -255,11 +254,16 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, bEner_[F_ORIRESDEV] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0); bEner_[F_COM_PULL] = ((inputrec.bPull && pull_have_potential(*pull_work)) || inputrec.bRot); + // Check MDModules for any energy output MDModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest; mdModulesNotifiers.simulationSetupNotifier_.notify(&mdModulesAddOutputToDensityFittingFieldRequest); bEner_[F_DENSITYFITTING] = mdModulesAddOutputToDensityFittingFieldRequest.energyOutputToDensityFitting_; + MDModulesEnergyOutputToQMMMRequestChecker mdModulesAddOutputToQMMMFieldRequest; + mdModulesNotifiers.simulationSetupNotifier_.notify(&mdModulesAddOutputToQMMMFieldRequest); + + bEner_[F_EQM] = mdModulesAddOutputToQMMMFieldRequest.energyOutputToQMMM_; // Counting the energy terms that will be printed and saving their names f_nre_ = 0; @@ -1209,8 +1213,8 @@ void EnergyOutput::printStepToEnergyFile(ener_file* fp_ene, fr.block[b].sub[0].type = XdrDataType::Float; fr.block[b].sub[0].fval = block[b]; #else - fr.block[b].sub[0].type = XdrDataType::Double; - fr.block[b].sub[0].dval = block[b]; + fr.block[b].sub[0].type = XdrDataType::Double; + fr.block[b].sub[0].dval = block[b]; #endif } diff --git a/src/gromacs/mdlib/tests/energyoutput.cpp b/src/gromacs/mdlib/tests/energyoutput.cpp index f75136b5a1..f8e974acc4 100644 --- a/src/gromacs/mdlib/tests/energyoutput.cpp +++ b/src/gromacs/mdlib/tests/energyoutput.cpp @@ -202,8 +202,6 @@ public: // Input record inputrec_.delta_t = 0.001; - // F_EQM - inputrec_.bQMMM = true; // F_RF_EXCL will not be tested - group scheme is not supported any more inputrec_.cutoff_scheme = CutoffScheme::Verlet; // F_COUL_RECIP diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml index 2f0e429067..1a0e2ae77f 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_0.xml @@ -3,7 +3,7 @@ - 73 + 72 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -305,7 +301,7 @@ 0 0 - 73 + 72 LJ-14 11.499999999999995 @@ -338,10 +334,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -602,21 +594,21 @@ - 73 + 72 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -630,14 +622,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_1.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_1.xml index ac633a4567..6244d10719 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_1.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_1.xml @@ -3,7 +3,7 @@ - 45 + 44 LJ-14 kJ/mol @@ -36,10 +36,7 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - + Potential kJ/mol @@ -193,7 +190,7 @@ 0 0 - 45 + 44 LJ-14 11.499999999999995 @@ -226,10 +223,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -378,19 +371,17 @@ - 45 + 44 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl - 1.22000e+01 + Coul. recip. LJ recip. COM Pull En. Potential dVremain/dl + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -404,12 +395,10 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl - 1.22000e+01 + Coul. recip. LJ recip. COM Pull En. Potential dVremain/dl + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 Total Dipole (D) 2.44000e+01 2.45000e+01 2.46000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml index 03e27d25f8..dca4f6a59a 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_10.xml @@ -3,7 +3,7 @@ - 84 + 83 LJ-14 kJ/mol @@ -36,10 +36,7 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - + Potential kJ/mol @@ -349,7 +346,7 @@ 0 0 - 84 + 83 LJ-14 11.499999999999995 @@ -382,10 +379,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -690,21 +683,21 @@ - 84 + 83 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -718,14 +711,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_11.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_11.xml index e6bfeeccd9..2d64c6a245 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_11.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_11.xml @@ -3,7 +3,7 @@ - 114 + 113 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -469,7 +465,7 @@ 0 0 - 114 + 113 LJ-14 11.499999999999995 @@ -502,10 +498,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -930,23 +922,25 @@ - 114 + 113 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 + Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 + <====== ############### ==> <==== A V E R A G E S ====> <== ############### ======> @@ -956,14 +950,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml index 2f0e429067..1a0e2ae77f 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_2.xml @@ -3,7 +3,7 @@ - 73 + 72 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -305,7 +301,7 @@ 0 0 - 73 + 72 LJ-14 11.499999999999995 @@ -338,10 +334,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -602,21 +594,21 @@ - 73 + 72 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -630,14 +622,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml index 6f57ceb0a6..14aa65bdab 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_3.xml @@ -1,7 +1,7 @@ - 73 + 72 Current ref_t for group Water: 0.0 Current ref_t for group Lipid: 0.0 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml index d01bbf372e..8ce251b703 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_4.xml @@ -3,7 +3,7 @@ - 73 + 72 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -305,7 +301,7 @@ 0 0 - 73 + 72 LJ-14 11.499999999999995 @@ -338,10 +334,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -606,7 +598,7 @@ 100 0 - 73 + 72 LJ-14 28.900000000000162 @@ -639,10 +631,6 @@ COM Pull En. 30.300000000000182 - - Quantum En. - 28.500000000000156 - Potential 27.900000000000148 @@ -907,7 +895,7 @@ 200 0 - 73 + 72 LJ-14 46.300000000000409 @@ -940,10 +928,6 @@ COM Pull En. 47.700000000000429 - - Quantum En. - 45.900000000000404 - Potential 45.300000000000395 @@ -1208,7 +1192,7 @@ 300 0 - 73 + 72 LJ-14 63.700000000000657 @@ -1241,10 +1225,6 @@ COM Pull En. 65.100000000000591 - - Quantum En. - 63.300000000000651 - Potential 62.700000000000642 @@ -1509,7 +1489,7 @@ 400 0 - 73 + 72 LJ-14 81.099999999999682 @@ -1542,10 +1522,6 @@ COM Pull En. 82.499999999999602 - - Quantum En. - 80.699999999999704 - Potential 80.099999999999739 @@ -1810,7 +1786,7 @@ 500 0 - 73 + 72 LJ-14 98.499999999998693 @@ -1843,10 +1819,6 @@ COM Pull En. 99.899999999998613 - - Quantum En. - 98.099999999998715 - Potential 97.499999999998749 @@ -2111,7 +2083,7 @@ 600 0 - 73 + 72 LJ-14 115.8999999999977 @@ -2144,10 +2116,6 @@ COM Pull En. 117.29999999999762 - - Quantum En. - 115.49999999999773 - Potential 114.89999999999776 @@ -2412,7 +2380,7 @@ 700 0 - 73 + 72 LJ-14 133.29999999999671 @@ -2445,10 +2413,6 @@ COM Pull En. 134.69999999999663 - - Quantum En. - 132.89999999999674 - Potential 132.29999999999677 @@ -2713,7 +2677,7 @@ 800 0 - 73 + 72 LJ-14 150.69999999999573 @@ -2746,10 +2710,6 @@ COM Pull En. 152.09999999999565 - - Quantum En. - 150.29999999999575 - Potential 149.69999999999578 @@ -3014,7 +2974,7 @@ 900 0 - 73 + 72 LJ-14 168.09999999999474 @@ -3047,10 +3007,6 @@ COM Pull En. 169.49999999999466 - - Quantum En. - 167.69999999999476 - Potential 167.09999999999479 @@ -3311,21 +3267,21 @@ - 73 + 72 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 43.1 Current ref_t for group Lipid: 43.2 @@ -3333,14 +3289,14 @@ Current ref_t for group Lipid: 43.2 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 2.89000e+01 2.90000e+01 2.77000e+01 2.99000e+01 2.78000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 2.87000e+01 2.88000e+01 3.03000e+01 2.85000e+01 2.79000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 2.80000e+01 2.81000e+01 2.82000e+01 3.00000e+01 2.83000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 2.98000e+01 2.97000e+01 2.93000e+01 2.94000e+01 2.95000e+01 - dVrestraint/dl Constr. rmsd - 2.96000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 2.87000e+01 2.88000e+01 3.03000e+01 2.79000e+01 2.80000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 2.81000e+01 2.82000e+01 3.00000e+01 2.83000e+01 2.98000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 2.97000e+01 2.93000e+01 2.94000e+01 2.95000e+01 2.96000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 60.5 Current ref_t for group Lipid: 60.6 @@ -3348,14 +3304,14 @@ Current ref_t for group Lipid: 60.6 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 4.63000e+01 4.64000e+01 4.51000e+01 4.73000e+01 4.52000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 4.61000e+01 4.62000e+01 4.77000e+01 4.59000e+01 4.53000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 4.54000e+01 4.55000e+01 4.56000e+01 4.74000e+01 4.57000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 4.72000e+01 4.71000e+01 4.67000e+01 4.68000e+01 4.69000e+01 - dVrestraint/dl Constr. rmsd - 4.70000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 4.61000e+01 4.62000e+01 4.77000e+01 4.53000e+01 4.54000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 4.55000e+01 4.56000e+01 4.74000e+01 4.57000e+01 4.72000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 4.71000e+01 4.67000e+01 4.68000e+01 4.69000e+01 4.70000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 77.9 Current ref_t for group Lipid: 78.0 @@ -3363,14 +3319,14 @@ Current ref_t for group Lipid: 78.0 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 6.37000e+01 6.38000e+01 6.25000e+01 6.47000e+01 6.26000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 6.35000e+01 6.36000e+01 6.51000e+01 6.33000e+01 6.27000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 6.28000e+01 6.29000e+01 6.30000e+01 6.48000e+01 6.31000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 6.46000e+01 6.45000e+01 6.41000e+01 6.42000e+01 6.43000e+01 - dVrestraint/dl Constr. rmsd - 6.44000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 6.35000e+01 6.36000e+01 6.51000e+01 6.27000e+01 6.28000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 6.29000e+01 6.30000e+01 6.48000e+01 6.31000e+01 6.46000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 6.45000e+01 6.41000e+01 6.42000e+01 6.43000e+01 6.44000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 95.3 Current ref_t for group Lipid: 95.4 @@ -3378,14 +3334,14 @@ Current ref_t for group Lipid: 95.4 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 8.11000e+01 8.12000e+01 7.99000e+01 8.21000e+01 8.00000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 8.09000e+01 8.10000e+01 8.25000e+01 8.07000e+01 8.01000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 8.02000e+01 8.03000e+01 8.04000e+01 8.22000e+01 8.05000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 8.20000e+01 8.19000e+01 8.15000e+01 8.16000e+01 8.17000e+01 - dVrestraint/dl Constr. rmsd - 8.18000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 8.09000e+01 8.10000e+01 8.25000e+01 8.01000e+01 8.02000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 8.03000e+01 8.04000e+01 8.22000e+01 8.05000e+01 8.20000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 8.19000e+01 8.15000e+01 8.16000e+01 8.17000e+01 8.18000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 112.7 Current ref_t for group Lipid: 112.8 @@ -3393,14 +3349,14 @@ Current ref_t for group Lipid: 112.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 9.85000e+01 9.86000e+01 9.73000e+01 9.95000e+01 9.74000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 9.83000e+01 9.84000e+01 9.99000e+01 9.81000e+01 9.75000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 9.76000e+01 9.77000e+01 9.78000e+01 9.96000e+01 9.79000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 9.94000e+01 9.93000e+01 9.89000e+01 9.90000e+01 9.91000e+01 - dVrestraint/dl Constr. rmsd - 9.92000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 9.83000e+01 9.84000e+01 9.99000e+01 9.75000e+01 9.76000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 9.77000e+01 9.78000e+01 9.96000e+01 9.79000e+01 9.94000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 9.93000e+01 9.89000e+01 9.90000e+01 9.91000e+01 9.92000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 130.1 Current ref_t for group Lipid: 130.2 @@ -3408,14 +3364,14 @@ Current ref_t for group Lipid: 130.2 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15900e+02 1.16000e+02 1.14700e+02 1.16900e+02 1.14800e+02 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.15700e+02 1.15800e+02 1.17300e+02 1.15500e+02 1.14900e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.15000e+02 1.15100e+02 1.15200e+02 1.17000e+02 1.15300e+02 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.16800e+02 1.16700e+02 1.16300e+02 1.16400e+02 1.16500e+02 - dVrestraint/dl Constr. rmsd - 1.16600e+02 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.15700e+02 1.15800e+02 1.17300e+02 1.14900e+02 1.15000e+02 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.15100e+02 1.15200e+02 1.17000e+02 1.15300e+02 1.16800e+02 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.16700e+02 1.16300e+02 1.16400e+02 1.16500e+02 1.16600e+02 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 147.5 Current ref_t for group Lipid: 147.6 @@ -3423,14 +3379,14 @@ Current ref_t for group Lipid: 147.6 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.33300e+02 1.33400e+02 1.32100e+02 1.34300e+02 1.32200e+02 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.33100e+02 1.33200e+02 1.34700e+02 1.32900e+02 1.32300e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.32400e+02 1.32500e+02 1.32600e+02 1.34400e+02 1.32700e+02 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.34200e+02 1.34100e+02 1.33700e+02 1.33800e+02 1.33900e+02 - dVrestraint/dl Constr. rmsd - 1.34000e+02 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.33100e+02 1.33200e+02 1.34700e+02 1.32300e+02 1.32400e+02 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.32500e+02 1.32600e+02 1.34400e+02 1.32700e+02 1.34200e+02 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.34100e+02 1.33700e+02 1.33800e+02 1.33900e+02 1.34000e+02 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 164.9 Current ref_t for group Lipid: 165.0 @@ -3438,14 +3394,14 @@ Current ref_t for group Lipid: 165.0 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.50700e+02 1.50800e+02 1.49500e+02 1.51700e+02 1.49600e+02 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.50500e+02 1.50600e+02 1.52100e+02 1.50300e+02 1.49700e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.49800e+02 1.49900e+02 1.50000e+02 1.51800e+02 1.50100e+02 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.51600e+02 1.51500e+02 1.51100e+02 1.51200e+02 1.51300e+02 - dVrestraint/dl Constr. rmsd - 1.51400e+02 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.50500e+02 1.50600e+02 1.52100e+02 1.49700e+02 1.49800e+02 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.49900e+02 1.50000e+02 1.51800e+02 1.50100e+02 1.51600e+02 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.51500e+02 1.51100e+02 1.51200e+02 1.51300e+02 1.51400e+02 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 182.3 Current ref_t for group Lipid: 182.4 @@ -3453,14 +3409,14 @@ Current ref_t for group Lipid: 182.4 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.68100e+02 1.68200e+02 1.66900e+02 1.69100e+02 1.67000e+02 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.67900e+02 1.68000e+02 1.69500e+02 1.67700e+02 1.67100e+02 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.67200e+02 1.67300e+02 1.67400e+02 1.69200e+02 1.67500e+02 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.69000e+02 1.68900e+02 1.68500e+02 1.68600e+02 1.68700e+02 - dVrestraint/dl Constr. rmsd - 1.68800e+02 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.67900e+02 1.68000e+02 1.69500e+02 1.67100e+02 1.67200e+02 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.67300e+02 1.67400e+02 1.69200e+02 1.67500e+02 1.69000e+02 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.68900e+02 1.68500e+02 1.68600e+02 1.68700e+02 1.68800e+02 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 182.3 Current ref_t for group Lipid: 182.4 @@ -3474,14 +3430,14 @@ Current ref_t for group Lipid: 182.4 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 8.98000e+01 8.99000e+01 8.86000e+01 9.08000e+01 8.87000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 8.96000e+01 8.97000e+01 9.12000e+01 8.94000e+01 8.88000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 8.89000e+01 8.90000e+01 8.91000e+01 9.09000e+01 8.92000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 9.07000e+01 9.06000e+01 9.02000e+01 9.03000e+01 9.04000e+01 - dVrestraint/dl Constr. rmsd - 9.05000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 8.96000e+01 8.97000e+01 9.12000e+01 8.88000e+01 8.89000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 8.90000e+01 8.91000e+01 9.09000e+01 8.92000e+01 9.07000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 9.06000e+01 9.02000e+01 9.03000e+01 9.04000e+01 9.05000e+01 + Constr. rmsd + 0.00000e+00 Total Virial (kJ/mol) 1.00900e+02 1.01000e+02 1.01100e+02 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml index 47a1d4daa6..dfabe87c24 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_5.xml @@ -3,7 +3,7 @@ - 77 + 76 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -321,7 +317,7 @@ 0 0 - 77 + 76 LJ-14 11.499999999999995 @@ -354,10 +350,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -634,21 +626,21 @@ - 77 + 76 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -662,14 +654,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml index e1aaee38df..66aa3b56aa 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_6.xml @@ -3,7 +3,7 @@ - 80 + 79 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -333,7 +329,7 @@ 0 0 - 80 + 79 LJ-14 11.499999999999995 @@ -366,10 +362,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -658,21 +650,21 @@ - 80 + 79 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -686,14 +678,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml index 03e27d25f8..cbed94e643 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_7.xml @@ -3,7 +3,7 @@ - 84 + 83 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -349,7 +345,7 @@ 0 0 - 84 + 83 LJ-14 11.499999999999995 @@ -382,10 +378,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -690,21 +682,21 @@ - 84 + 83 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -718,14 +710,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml index 03e27d25f8..cbed94e643 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_8.xml @@ -3,7 +3,7 @@ - 84 + 83 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -349,7 +345,7 @@ 0 0 - 84 + 83 LJ-14 11.499999999999995 @@ -382,10 +378,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -690,21 +682,21 @@ - 84 + 83 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -718,14 +710,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Conserved En. Temperature Pres. DC (bar) - 1.06000e+01 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 - Pressure (bar) dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl - 1.09000e+01 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 - dVbonded/dl dVrestraint/dl Constr. rmsd - 1.21000e+01 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Conserved En. Temperature Pres. DC (bar) Pressure (bar) + 1.07000e+01 1.30000e+01 1.08000e+01 1.26000e+01 1.09000e+01 + dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl + 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 + dVrestraint/dl Constr. rmsd + 1.22000e+01 0.00000e+00 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 diff --git a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml index 2f0e429067..1a0e2ae77f 100644 --- a/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml +++ b/src/gromacs/mdlib/tests/refdata/WithParameters_EnergyOutputTest_CheckOutput_9.xml @@ -3,7 +3,7 @@ - 73 + 72 LJ-14 kJ/mol @@ -36,10 +36,6 @@ COM Pull En. kJ/mol - - Quantum En. - kJ/mol - Potential kJ/mol @@ -305,7 +301,7 @@ 0 0 - 73 + 72 LJ-14 11.499999999999995 @@ -338,10 +334,6 @@ COM Pull En. 12.89999999999999 - - Quantum En. - 11.099999999999996 - Potential 10.499999999999998 @@ -602,21 +594,21 @@ - 73 + 72 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -630,14 +622,14 @@ Current ref_t for group Lipid: 25.8 Energies (kJ/mol) LJ-14 Coulomb-14 LJ (SR) Disper. corr. Coulomb (SR) 1.15000e+01 1.16000e+01 1.03000e+01 1.25000e+01 1.04000e+01 - Coul. recip. LJ recip. COM Pull En. Quantum En. Potential - 1.13000e+01 1.14000e+01 1.29000e+01 1.11000e+01 1.05000e+01 - Kinetic En. Total Energy Temperature Pres. DC (bar) Pressure (bar) - 1.06000e+01 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 - dVremain/dl dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl - 1.24000e+01 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 - dVrestraint/dl Constr. rmsd - 1.22000e+01 0.00000e+00 + Coul. recip. LJ recip. COM Pull En. Potential Kinetic En. + 1.13000e+01 1.14000e+01 1.29000e+01 1.05000e+01 1.06000e+01 + Total Energy Temperature Pres. DC (bar) Pressure (bar) dVremain/dl + 1.07000e+01 1.08000e+01 1.26000e+01 1.09000e+01 1.24000e+01 + dEkin/dl dVcoul/dl dVvdw/dl dVbonded/dl dVrestraint/dl + 1.23000e+01 1.19000e+01 1.20000e+01 1.21000e+01 1.22000e+01 + Constr. rmsd + 0.00000e+00 Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 diff --git a/src/gromacs/utility/mdmodulesnotifiers.h b/src/gromacs/utility/mdmodulesnotifiers.h index 101cb09d0f..020091515f 100644 --- a/src/gromacs/utility/mdmodulesnotifiers.h +++ b/src/gromacs/utility/mdmodulesnotifiers.h @@ -78,6 +78,16 @@ struct MDModulesEnergyOutputToDensityFittingRequestChecker bool energyOutputToDensityFitting_ = false; }; +/*! \libinternal \brief Check if QMMM module outputs energy to a specific field. + * + * Ensures that energy is output for QMMM module. + */ +struct MDModulesEnergyOutputToQMMMRequestChecker +{ + //! Trigger output to density fitting energy field + bool energyOutputToQMMM_ = false; +}; + /*! \libinternal * \brief Collect errors for the energy calculation frequency. * @@ -289,6 +299,9 @@ struct MDModulesNotifiers * MDModulesEnergyOutputToDensityFittingRequestChecker* enables modules to * report if they want to write their energy output * to the density fitting field in the energy files + * MDModulesEnergyOutputToQMMMRequestChecker* enables QMMM module to + * report if it want to write their energy output + * to the "Quantum En." field in the energy files * SeparatePmeRanksPermitted* enables modules to report if they want * to disable dedicated PME ranks * const PbcType& provides modules with the periodic boundary condition type @@ -305,6 +318,7 @@ struct MDModulesNotifiers const MDLogger&, const gmx_mtop_t&, MDModulesEnergyOutputToDensityFittingRequestChecker*, + MDModulesEnergyOutputToQMMMRequestChecker*, SeparatePmeRanksPermitted*, const PbcType&, const SimulationTimeStep&, -- 2.22.0