From 0e40fa198249f471620e495a8947bcbfd08c2b2c Mon Sep 17 00:00:00 2001 From: Mark Abraham Date: Mon, 24 May 2021 05:58:19 +0200 Subject: [PATCH] Remove GMX_CONSTRVIR Simplifies handling of energy output by removing a feature that was likely useful only during debugging yet incurred function-call overhead every MD step even when not used. Resolves previous TODO Updates tests to no longer check such output while not changing the numerical output previously written. --- docs/user-guide/environment-variables.rst | 3 - src/gromacs/mdlib/energyoutput.cpp | 30 - src/gromacs/mdlib/energyoutput.h | 13 - src/gromacs/mdlib/tests/energyoutput.cpp | 31 +- ...ameters_EnergyOutputTest_CheckOutput_0.xml | 160 +--- ...meters_EnergyOutputTest_CheckOutput_10.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_2.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_3.xml | 2 +- ...ameters_EnergyOutputTest_CheckOutput_4.xml | 826 +----------------- ...ameters_EnergyOutputTest_CheckOutput_5.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_6.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_7.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_8.xml | 160 +--- ...ameters_EnergyOutputTest_CheckOutput_9.xml | 160 +--- src/gromacs/mdrun/md.cpp | 2 - src/gromacs/mdrun/mimic.cpp | 2 - src/gromacs/mdrun/minimize.cpp | 10 - src/gromacs/mdrun/rerun.cpp | 2 - src/gromacs/modularsimulator/energydata.cpp | 2 - 19 files changed, 40 insertions(+), 2163 deletions(-) diff --git a/docs/user-guide/environment-variables.rst b/docs/user-guide/environment-variables.rst index ecd06e671e..026654d369 100644 --- a/docs/user-guide/environment-variables.rst +++ b/docs/user-guide/environment-variables.rst @@ -22,9 +22,6 @@ you should consult your local documentation for details. Output Control -------------- -``GMX_CONSTRAINTVIR`` - Print constraint virial and force virial energy terms. - ``GMX_DUMP_NL`` Neighbour list dump level; default 0. diff --git a/src/gromacs/mdlib/energyoutput.cpp b/src/gromacs/mdlib/energyoutput.cpp index cc19e024df..fa5b8dca10 100644 --- a/src/gromacs/mdlib/energyoutput.cpp +++ b/src/gromacs/mdlib/energyoutput.cpp @@ -132,7 +132,6 @@ namespace gmx * be written out to the .edr file. * * \todo Use more std containers. - * \todo Remove GMX_CONSTRAINTVIR * \todo Write free-energy output also to energy file (after adding more tests) */ EnergyOutput::EnergyOutput(ener_file* fp_ene, @@ -148,12 +147,6 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, const char* ener_nm[F_NRE]; static const char* vir_nm[] = { "Vir-XX", "Vir-XY", "Vir-XZ", "Vir-YX", "Vir-YY", "Vir-YZ", "Vir-ZX", "Vir-ZY", "Vir-ZZ" }; - static const char* sv_nm[] = { "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ", - "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ", - "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ" }; - static const char* fv_nm[] = { "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ", - "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ", - "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ" }; static const char* pres_nm[] = { "Pres-XX", "Pres-XY", "Pres-XZ", "Pres-YX", "Pres-YY", "Pres-YZ", "Pres-ZX", "Pres-ZY", "Pres-ZZ" }; static const char* surft_nm[] = { "#Surf*SurfTen" }; @@ -186,7 +179,6 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, ncon = gmx_mtop_ftype_count(mtop, F_CONSTR); nset = gmx_mtop_ftype_count(mtop, F_SETTLE); bool bConstr = (ncon > 0 || nset > 0) && !isRerun; - bConstrVir_ = false; nCrmsd_ = 0; if (bConstr) { @@ -194,7 +186,6 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, { nCrmsd_ = 1; } - bConstrVir_ = (getenv("GMX_CONSTRAINTVIR") != nullptr); } else { @@ -319,11 +310,6 @@ EnergyOutput::EnergyOutput(ener_file* fp_ene, ienthalpy_ = get_ebin_space(ebin_, 1, enthalpy_nm, unit_energy); } } - if (bConstrVir_) - { - isvir_ = get_ebin_space(ebin_, asize(sv_nm), sv_nm, unit_energy); - ifvir_ = get_ebin_space(ebin_, asize(fv_nm), fv_nm, unit_energy); - } if (bPres_) { ivir_ = get_ebin_space(ebin_, asize(vir_nm), vir_nm, unit_energy); @@ -852,8 +838,6 @@ void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL, const matrix box, PTCouplingArrays ptCouplingArrays, int fep_state, - const tensor svir, - const tensor fvir, const tensor vir, const tensor pres, const gmx_ekindata_t* ekind, @@ -916,11 +900,6 @@ void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL, add_ebin(ebin_, ienthalpy_, 1, &enthalpy, bSum); } } - if (bConstrVir_) - { - add_ebin(ebin_, isvir_, 9, svir[0], bSum); - add_ebin(ebin_, ifvir_, 9, fvir[0], bSum); - } if (bPres_) { add_ebin(ebin_, ivir_, 9, vir[0], bSum); @@ -1356,15 +1335,6 @@ void EnergyOutput::printAverages(FILE* log, const SimulationGroups* groups) pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5, eprAVER, true); fprintf(log, "\n"); } - if (bConstrVir_) - { - fprintf(log, " Constraint Virial (%s)\n", unit_energy); - pr_ebin(log, ebin_, isvir_, 9, 3, eprAVER, false); - fprintf(log, "\n"); - fprintf(log, " Force Virial (%s)\n", unit_energy); - pr_ebin(log, ebin_, ifvir_, 9, 3, eprAVER, false); - fprintf(log, "\n"); - } if (bPres_) { fprintf(log, " Total Virial (%s)\n", unit_energy); diff --git a/src/gromacs/mdlib/energyoutput.h b/src/gromacs/mdlib/energyoutput.h index c2d5fd571c..6c5805514e 100644 --- a/src/gromacs/mdlib/energyoutput.h +++ b/src/gromacs/mdlib/energyoutput.h @@ -129,7 +129,6 @@ struct PTCouplingArrays * be written out to the .edr file. * * \todo Use more std containers. - * \todo Remove GMX_CONSTRAINTVIR * \todo Write free-energy output also to energy file (after adding more tests) */ class EnergyOutput @@ -173,8 +172,6 @@ public: * \param[in] lastbox PBC data. * \param[in] ptCouplingArrays Arrays connected to pressure and temperature coupling. * \param[in] fep_state The current alchemical state we are in. - * \param[in] svir Constraint virial. - * \param[in] fvir Force virial. * \param[in] vir Total virial. * \param[in] pres Pressure. * \param[in] ekind Kinetic energy data. @@ -191,8 +188,6 @@ public: const matrix lastbox, PTCouplingArrays ptCouplingArrays, int fep_state, - const tensor svir, - const tensor fvir, const tensor vir, const tensor pres, const gmx_ekindata_t* ekind, @@ -347,14 +342,6 @@ private: //! Index for entalpy (pV + total energy) int ienthalpy_ = 0; - /*! \brief If the constraints virial should be printed. - * Can only be true if "GMX_CONSTRAINTVIR" environmental variable is set */ - bool bConstrVir_ = false; - //! Index for constrains virial - int isvir_ = 0; - //! Index for force virial - int ifvir_ = 0; - //! If we have pressure computed bool bPres_ = false; //! Index for total virial diff --git a/src/gromacs/mdlib/tests/energyoutput.cpp b/src/gromacs/mdlib/tests/energyoutput.cpp index 51a06b9f76..f75136b5a1 100644 --- a/src/gromacs/mdlib/tests/energyoutput.cpp +++ b/src/gromacs/mdlib/tests/energyoutput.cpp @@ -162,10 +162,6 @@ public: t_state state_; //! PBC box matrix box_; - //! Virial from constraints - tensor constraintsVirial_; - //! Virial from force computation - tensor forceVirial_; //! Total virial tensor totalVirial_; //! Pressure @@ -237,9 +233,6 @@ public: // Dipole (mu) inputrec_.ewald_geometry = EwaldGeometry::ThreeDC; - // GMX_CONSTRAINTVIR environment variable should also be - // set to print constraints and force virials separately. - gmxSetenv("GMX_CONSTRAINTVIR", "true", 1); // To print constrain RMSD, constraints algorithm should be set to LINCS. inputrec_.eConstrAlg = ConstraintAlgorithm::Lincs; @@ -463,25 +456,9 @@ public: box_[ZZ][YY] = (*testValue += 0.1); box_[ZZ][ZZ] = (*testValue += 0.1); - constraintsVirial_[XX][XX] = (*testValue += 0.1); - constraintsVirial_[XX][YY] = (*testValue += 0.1); - constraintsVirial_[XX][ZZ] = (*testValue += 0.1); - constraintsVirial_[YY][XX] = (*testValue += 0.1); - constraintsVirial_[YY][YY] = (*testValue += 0.1); - constraintsVirial_[YY][ZZ] = (*testValue += 0.1); - constraintsVirial_[ZZ][XX] = (*testValue += 0.1); - constraintsVirial_[ZZ][YY] = (*testValue += 0.1); - constraintsVirial_[ZZ][ZZ] = (*testValue += 0.1); - - forceVirial_[XX][XX] = (*testValue += 0.1); - forceVirial_[XX][YY] = (*testValue += 0.1); - forceVirial_[XX][ZZ] = (*testValue += 0.1); - forceVirial_[YY][XX] = (*testValue += 0.1); - forceVirial_[YY][YY] = (*testValue += 0.1); - forceVirial_[YY][ZZ] = (*testValue += 0.1); - forceVirial_[ZZ][XX] = (*testValue += 0.1); - forceVirial_[ZZ][YY] = (*testValue += 0.1); - forceVirial_[ZZ][ZZ] = (*testValue += 0.1); + // Removing GMX_CONSTRVIR removed a total increment of 1.8 + // To avoid unnecessary changes in reference data, we keep the increment + (*testValue += 1.8); totalVirial_[XX][XX] = (*testValue += 0.1); totalVirial_[XX][YY] = (*testValue += 0.1); @@ -648,8 +625,6 @@ TEST_P(EnergyOutputTest, CheckOutput) state_.nhpres_xi, state_.nhpres_vxi }), state_.fep_state, - constraintsVirial_, - forceVirial_, totalVirial_, pressure_, &ekindata_, 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 f100a6bc7f..2f0e429067 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 @@ - 91 + 73 LJ-14 kJ/mol @@ -92,78 +92,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -377,7 +305,7 @@ 0 0 - 91 + 73 LJ-14 11.499999999999995 @@ -466,78 +394,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -746,7 +602,7 @@ - 91 + 73 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -783,16 +639,6 @@ Current ref_t for group Lipid: 25.8 dVrestraint/dl Constr. rmsd 1.22000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 e7d41dbf15..03e27d25f8 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 @@ - 102 + 84 LJ-14 kJ/mol @@ -124,78 +124,6 @@ Enthalpy kJ/mol - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -421,7 +349,7 @@ 0 0 - 102 + 84 LJ-14 11.499999999999995 @@ -542,78 +470,6 @@ Enthalpy 10.699999999999998 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -834,7 +690,7 @@ - 102 + 84 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -874,16 +730,6 @@ Current ref_t for group Lipid: 25.8 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 f100a6bc7f..2f0e429067 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 @@ - 91 + 73 LJ-14 kJ/mol @@ -92,78 +92,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -377,7 +305,7 @@ 0 0 - 91 + 73 LJ-14 11.499999999999995 @@ -466,78 +394,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -746,7 +602,7 @@ - 91 + 73 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -783,16 +639,6 @@ Current ref_t for group Lipid: 25.8 dVrestraint/dl Constr. rmsd 1.22000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 5376fc9a0a..6f57ceb0a6 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 @@ - 91 + 73 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 efc4d8958b..d01bbf372e 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 @@ - 91 + 73 LJ-14 kJ/mol @@ -92,78 +92,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -377,7 +305,7 @@ 0 0 - 91 + 73 LJ-14 11.499999999999995 @@ -466,78 +394,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -750,7 +606,7 @@ 100 0 - 91 + 73 LJ-14 28.900000000000162 @@ -839,78 +695,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 38.200000000000294 - - - ShakeVir-XY - 38.300000000000296 - - - ShakeVir-XZ - 38.400000000000297 - - - ShakeVir-YX - 38.500000000000298 - - - ShakeVir-YY - 38.6000000000003 - - - ShakeVir-YZ - 38.700000000000301 - - - ShakeVir-ZX - 38.800000000000303 - - - ShakeVir-ZY - 38.900000000000304 - - - ShakeVir-ZZ - 39.000000000000306 - - - ForceVir-XX - 39.100000000000307 - - - ForceVir-XY - 39.200000000000308 - - - ForceVir-XZ - 39.30000000000031 - - - ForceVir-YX - 39.400000000000311 - - - ForceVir-YY - 39.500000000000313 - - - ForceVir-YZ - 39.600000000000314 - - - ForceVir-ZX - 39.700000000000315 - - - ForceVir-ZY - 39.800000000000317 - - - ForceVir-ZZ - 39.900000000000318 - Vir-XX 40.00000000000032 @@ -1123,7 +907,7 @@ 200 0 - 91 + 73 LJ-14 46.300000000000409 @@ -1212,78 +996,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 55.600000000000541 - - - ShakeVir-XY - 55.700000000000543 - - - ShakeVir-XZ - 55.800000000000544 - - - ShakeVir-YX - 55.900000000000546 - - - ShakeVir-YY - 56.000000000000547 - - - ShakeVir-YZ - 56.100000000000549 - - - ShakeVir-ZX - 56.20000000000055 - - - ShakeVir-ZY - 56.300000000000551 - - - ShakeVir-ZZ - 56.400000000000553 - - - ForceVir-XX - 56.500000000000554 - - - ForceVir-XY - 56.600000000000556 - - - ForceVir-XZ - 56.700000000000557 - - - ForceVir-YX - 56.800000000000558 - - - ForceVir-YY - 56.90000000000056 - - - ForceVir-YZ - 57.000000000000561 - - - ForceVir-ZX - 57.100000000000563 - - - ForceVir-ZY - 57.200000000000564 - - - ForceVir-ZZ - 57.300000000000566 - Vir-XX 57.400000000000567 @@ -1496,7 +1208,7 @@ 300 0 - 91 + 73 LJ-14 63.700000000000657 @@ -1585,78 +1297,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 73.000000000000142 - - - ShakeVir-XY - 73.100000000000136 - - - ShakeVir-XZ - 73.200000000000131 - - - ShakeVir-YX - 73.300000000000125 - - - ShakeVir-YY - 73.400000000000119 - - - ShakeVir-YZ - 73.500000000000114 - - - ShakeVir-ZX - 73.600000000000108 - - - ShakeVir-ZY - 73.700000000000102 - - - ShakeVir-ZZ - 73.800000000000097 - - - ForceVir-XX - 73.900000000000091 - - - ForceVir-XY - 74.000000000000085 - - - ForceVir-XZ - 74.10000000000008 - - - ForceVir-YX - 74.200000000000074 - - - ForceVir-YY - 74.300000000000068 - - - ForceVir-YZ - 74.400000000000063 - - - ForceVir-ZX - 74.500000000000057 - - - ForceVir-ZY - 74.600000000000051 - - - ForceVir-ZZ - 74.700000000000045 - Vir-XX 74.80000000000004 @@ -1869,7 +1509,7 @@ 400 0 - 91 + 73 LJ-14 81.099999999999682 @@ -1958,78 +1598,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 90.399999999999153 - - - ShakeVir-XY - 90.499999999999147 - - - ShakeVir-XZ - 90.599999999999142 - - - ShakeVir-YX - 90.699999999999136 - - - ShakeVir-YY - 90.79999999999913 - - - ShakeVir-YZ - 90.899999999999125 - - - ShakeVir-ZX - 90.999999999999119 - - - ShakeVir-ZY - 91.099999999999113 - - - ShakeVir-ZZ - 91.199999999999108 - - - ForceVir-XX - 91.299999999999102 - - - ForceVir-XY - 91.399999999999096 - - - ForceVir-XZ - 91.499999999999091 - - - ForceVir-YX - 91.599999999999085 - - - ForceVir-YY - 91.699999999999079 - - - ForceVir-YZ - 91.799999999999073 - - - ForceVir-ZX - 91.899999999999068 - - - ForceVir-ZY - 91.999999999999062 - - - ForceVir-ZZ - 92.099999999999056 - Vir-XX 92.199999999999051 @@ -2242,7 +1810,7 @@ 500 0 - 91 + 73 LJ-14 98.499999999998693 @@ -2331,78 +1899,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 107.79999999999816 - - - ShakeVir-XY - 107.89999999999816 - - - ShakeVir-XZ - 107.99999999999815 - - - ShakeVir-YX - 108.09999999999815 - - - ShakeVir-YY - 108.19999999999814 - - - ShakeVir-YZ - 108.29999999999814 - - - ShakeVir-ZX - 108.39999999999813 - - - ShakeVir-ZY - 108.49999999999812 - - - ShakeVir-ZZ - 108.59999999999812 - - - ForceVir-XX - 108.69999999999811 - - - ForceVir-XY - 108.79999999999811 - - - ForceVir-XZ - 108.8999999999981 - - - ForceVir-YX - 108.9999999999981 - - - ForceVir-YY - 109.09999999999809 - - - ForceVir-YZ - 109.19999999999808 - - - ForceVir-ZX - 109.29999999999808 - - - ForceVir-ZY - 109.39999999999807 - - - ForceVir-ZZ - 109.49999999999807 - Vir-XX 109.59999999999806 @@ -2615,7 +2111,7 @@ 600 0 - 91 + 73 LJ-14 115.8999999999977 @@ -2704,78 +2200,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 125.19999999999717 - - - ShakeVir-XY - 125.29999999999717 - - - ShakeVir-XZ - 125.39999999999716 - - - ShakeVir-YX - 125.49999999999716 - - - ShakeVir-YY - 125.59999999999715 - - - ShakeVir-YZ - 125.69999999999715 - - - ShakeVir-ZX - 125.79999999999714 - - - ShakeVir-ZY - 125.89999999999714 - - - ShakeVir-ZZ - 125.99999999999713 - - - ForceVir-XX - 126.09999999999712 - - - ForceVir-XY - 126.19999999999712 - - - ForceVir-XZ - 126.29999999999711 - - - ForceVir-YX - 126.39999999999711 - - - ForceVir-YY - 126.4999999999971 - - - ForceVir-YZ - 126.5999999999971 - - - ForceVir-ZX - 126.69999999999709 - - - ForceVir-ZY - 126.79999999999708 - - - ForceVir-ZZ - 126.89999999999708 - Vir-XX 126.99999999999707 @@ -2988,7 +2412,7 @@ 700 0 - 91 + 73 LJ-14 133.29999999999671 @@ -3077,78 +2501,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 142.59999999999619 - - - ShakeVir-XY - 142.69999999999618 - - - ShakeVir-XZ - 142.79999999999617 - - - ShakeVir-YX - 142.89999999999617 - - - ShakeVir-YY - 142.99999999999616 - - - ShakeVir-YZ - 143.09999999999616 - - - ShakeVir-ZX - 143.19999999999615 - - - ShakeVir-ZY - 143.29999999999615 - - - ShakeVir-ZZ - 143.39999999999614 - - - ForceVir-XX - 143.49999999999613 - - - ForceVir-XY - 143.59999999999613 - - - ForceVir-XZ - 143.69999999999612 - - - ForceVir-YX - 143.79999999999612 - - - ForceVir-YY - 143.89999999999611 - - - ForceVir-YZ - 143.99999999999611 - - - ForceVir-ZX - 144.0999999999961 - - - ForceVir-ZY - 144.19999999999609 - - - ForceVir-ZZ - 144.29999999999609 - Vir-XX 144.39999999999608 @@ -3361,7 +2713,7 @@ 800 0 - 91 + 73 LJ-14 150.69999999999573 @@ -3450,78 +2802,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 159.9999999999952 - - - ShakeVir-XY - 160.09999999999519 - - - ShakeVir-XZ - 160.19999999999519 - - - ShakeVir-YX - 160.29999999999518 - - - ShakeVir-YY - 160.39999999999517 - - - ShakeVir-YZ - 160.49999999999517 - - - ShakeVir-ZX - 160.59999999999516 - - - ShakeVir-ZY - 160.69999999999516 - - - ShakeVir-ZZ - 160.79999999999515 - - - ForceVir-XX - 160.89999999999515 - - - ForceVir-XY - 160.99999999999514 - - - ForceVir-XZ - 161.09999999999513 - - - ForceVir-YX - 161.19999999999513 - - - ForceVir-YY - 161.29999999999512 - - - ForceVir-YZ - 161.39999999999512 - - - ForceVir-ZX - 161.49999999999511 - - - ForceVir-ZY - 161.59999999999511 - - - ForceVir-ZZ - 161.6999999999951 - Vir-XX 161.79999999999509 @@ -3734,7 +3014,7 @@ 900 0 - 91 + 73 LJ-14 168.09999999999474 @@ -3823,78 +3103,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 177.39999999999421 - - - ShakeVir-XY - 177.4999999999942 - - - ShakeVir-XZ - 177.5999999999942 - - - ShakeVir-YX - 177.69999999999419 - - - ShakeVir-YY - 177.79999999999418 - - - ShakeVir-YZ - 177.89999999999418 - - - ShakeVir-ZX - 177.99999999999417 - - - ShakeVir-ZY - 178.09999999999417 - - - ShakeVir-ZZ - 178.19999999999416 - - - ForceVir-XX - 178.29999999999416 - - - ForceVir-XY - 178.39999999999415 - - - ForceVir-XZ - 178.49999999999415 - - - ForceVir-YX - 178.59999999999414 - - - ForceVir-YY - 178.69999999999413 - - - ForceVir-YZ - 178.79999999999413 - - - ForceVir-ZX - 178.89999999999412 - - - ForceVir-ZY - 178.99999999999412 - - - ForceVir-ZZ - 179.09999999999411 - Vir-XX 179.19999999999411 @@ -4103,7 +3311,7 @@ - 91 + 73 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -4275,16 +3483,6 @@ Current ref_t for group Lipid: 182.4 dVrestraint/dl Constr. rmsd 9.05000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 9.91000e+01 9.92000e+01 9.93000e+01 - 9.94000e+01 9.95000e+01 9.96000e+01 - 9.97000e+01 9.98000e+01 9.99000e+01 - - Force Virial (kJ/mol) - 1.00000e+02 1.00100e+02 1.00200e+02 - 1.00300e+02 1.00400e+02 1.00500e+02 - 1.00600e+02 1.00700e+02 1.00800e+02 - Total Virial (kJ/mol) 1.00900e+02 1.01000e+02 1.01100e+02 1.01200e+02 1.01300e+02 1.01400e+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 43e5ca6aeb..47a1d4daa6 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 @@ - 95 + 77 LJ-14 kJ/mol @@ -96,78 +96,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -393,7 +321,7 @@ 0 0 - 95 + 77 LJ-14 11.499999999999995 @@ -486,78 +414,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -778,7 +634,7 @@ - 95 + 77 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -815,16 +671,6 @@ Current ref_t for group Lipid: 25.8 dVbonded/dl dVrestraint/dl Constr. rmsd 1.21000e+01 1.22000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 73ca7a122f..e1aaee38df 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 @@ - 98 + 80 LJ-14 kJ/mol @@ -96,78 +96,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -405,7 +333,7 @@ 0 0 - 98 + 80 LJ-14 11.499999999999995 @@ -498,78 +426,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -802,7 +658,7 @@ - 98 + 80 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -839,16 +695,6 @@ Current ref_t for group Lipid: 25.8 dVbonded/dl dVrestraint/dl Constr. rmsd 1.21000e+01 1.22000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 e7d41dbf15..03e27d25f8 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 @@ - 102 + 84 LJ-14 kJ/mol @@ -124,78 +124,6 @@ Enthalpy kJ/mol - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -421,7 +349,7 @@ 0 0 - 102 + 84 LJ-14 11.499999999999995 @@ -542,78 +470,6 @@ Enthalpy 10.699999999999998 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -834,7 +690,7 @@ - 102 + 84 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -874,16 +730,6 @@ Current ref_t for group Lipid: 25.8 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 e7d41dbf15..03e27d25f8 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 @@ - 102 + 84 LJ-14 kJ/mol @@ -124,78 +124,6 @@ Enthalpy kJ/mol - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -421,7 +349,7 @@ 0 0 - 102 + 84 LJ-14 11.499999999999995 @@ -542,78 +470,6 @@ Enthalpy 10.699999999999998 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -834,7 +690,7 @@ - 102 + 84 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -874,16 +730,6 @@ Current ref_t for group Lipid: 25.8 Box-X Box-Y Box-Z 1.99000e+01 2.03000e+01 2.07000e+01 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+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 f100a6bc7f..2f0e429067 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 @@ - 91 + 73 LJ-14 kJ/mol @@ -92,78 +92,6 @@ Constr. rmsd - - ShakeVir-XX - kJ/mol - - - ShakeVir-XY - kJ/mol - - - ShakeVir-XZ - kJ/mol - - - ShakeVir-YX - kJ/mol - - - ShakeVir-YY - kJ/mol - - - ShakeVir-YZ - kJ/mol - - - ShakeVir-ZX - kJ/mol - - - ShakeVir-ZY - kJ/mol - - - ShakeVir-ZZ - kJ/mol - - - ForceVir-XX - kJ/mol - - - ForceVir-XY - kJ/mol - - - ForceVir-XZ - kJ/mol - - - ForceVir-YX - kJ/mol - - - ForceVir-YY - kJ/mol - - - ForceVir-YZ - kJ/mol - - - ForceVir-ZX - kJ/mol - - - ForceVir-ZY - kJ/mol - - - ForceVir-ZZ - kJ/mol - Vir-XX kJ/mol @@ -377,7 +305,7 @@ 0 0 - 91 + 73 LJ-14 11.499999999999995 @@ -466,78 +394,6 @@ Constr. rmsd 0 - - ShakeVir-XX - 20.800000000000047 - - - ShakeVir-XY - 20.900000000000048 - - - ShakeVir-XZ - 21.00000000000005 - - - ShakeVir-YX - 21.100000000000051 - - - ShakeVir-YY - 21.200000000000053 - - - ShakeVir-YZ - 21.300000000000054 - - - ShakeVir-ZX - 21.400000000000055 - - - ShakeVir-ZY - 21.500000000000057 - - - ShakeVir-ZZ - 21.600000000000058 - - - ForceVir-XX - 21.70000000000006 - - - ForceVir-XY - 21.800000000000061 - - - ForceVir-XZ - 21.900000000000063 - - - ForceVir-YX - 22.000000000000064 - - - ForceVir-YY - 22.100000000000065 - - - ForceVir-YZ - 22.200000000000067 - - - ForceVir-ZX - 22.300000000000068 - - - ForceVir-ZY - 22.40000000000007 - - - ForceVir-ZZ - 22.500000000000071 - Vir-XX 22.600000000000072 @@ -746,7 +602,7 @@ - 91 + 73 Current ref_t for group Water: 25.7 Current ref_t for group Lipid: 25.8 @@ -783,16 +639,6 @@ Current ref_t for group Lipid: 25.8 dVrestraint/dl Constr. rmsd 1.22000e+01 0.00000e+00 - Constraint Virial (kJ/mol) - 2.08000e+01 2.09000e+01 2.10000e+01 - 2.11000e+01 2.12000e+01 2.13000e+01 - 2.14000e+01 2.15000e+01 2.16000e+01 - - Force Virial (kJ/mol) - 2.17000e+01 2.18000e+01 2.19000e+01 - 2.20000e+01 2.21000e+01 2.22000e+01 - 2.23000e+01 2.24000e+01 2.25000e+01 - Total Virial (kJ/mol) 2.26000e+01 2.27000e+01 2.28000e+01 2.29000e+01 2.30000e+01 2.31000e+01 diff --git a/src/gromacs/mdrun/md.cpp b/src/gromacs/mdrun/md.cpp index 92c51459b8..810606ed22 100644 --- a/src/gromacs/mdrun/md.cpp +++ b/src/gromacs/mdrun/md.cpp @@ -1863,8 +1863,6 @@ void gmx::LegacySimulator::do_md() state->nhpres_xi, state->nhpres_vxi }, state->fep_state, - shake_vir, - force_vir, total_vir, pres, ekind, diff --git a/src/gromacs/mdrun/mimic.cpp b/src/gromacs/mdrun/mimic.cpp index c014f5ae25..24661da9ac 100644 --- a/src/gromacs/mdrun/mimic.cpp +++ b/src/gromacs/mdrun/mimic.cpp @@ -715,8 +715,6 @@ void gmx::LegacySimulator::do_mimic() state->nhpres_xi, state->nhpres_vxi }), state->fep_state, - shake_vir, - force_vir, total_vir, pres, ekind, diff --git a/src/gromacs/mdrun/minimize.cpp b/src/gromacs/mdrun/minimize.cpp index a1d42aa6c1..6784cfeb0b 100644 --- a/src/gromacs/mdrun/minimize.cpp +++ b/src/gromacs/mdrun/minimize.cpp @@ -1368,8 +1368,6 @@ void LegacySimulator::do_cg() nullBox, PTCouplingArrays(), 0, - nullptr, - nullptr, vir, pres, nullptr, @@ -1819,8 +1817,6 @@ void LegacySimulator::do_cg() nullBox, PTCouplingArrays(), 0, - nullptr, - nullptr, vir, pres, nullptr, @@ -2107,8 +2103,6 @@ void LegacySimulator::do_lbfgs() nullBox, PTCouplingArrays(), 0, - nullptr, - nullptr, vir, pres, nullptr, @@ -2631,8 +2625,6 @@ void LegacySimulator::do_lbfgs() nullBox, PTCouplingArrays(), 0, - nullptr, - nullptr, vir, pres, nullptr, @@ -2909,8 +2901,6 @@ void LegacySimulator::do_steep() nullBox, PTCouplingArrays(), 0, - nullptr, - nullptr, vir, pres, nullptr, diff --git a/src/gromacs/mdrun/rerun.cpp b/src/gromacs/mdrun/rerun.cpp index 78271fae48..fd71258149 100644 --- a/src/gromacs/mdrun/rerun.cpp +++ b/src/gromacs/mdrun/rerun.cpp @@ -797,8 +797,6 @@ void gmx::LegacySimulator::do_rerun() state->nhpres_xi, state->nhpres_vxi }), state->fep_state, - shake_vir, - force_vir, total_vir, pres, ekind, diff --git a/src/gromacs/modularsimulator/energydata.cpp b/src/gromacs/modularsimulator/energydata.cpp index 4396f3f1b1..5553ec2b8d 100644 --- a/src/gromacs/modularsimulator/energydata.cpp +++ b/src/gromacs/modularsimulator/energydata.cpp @@ -266,8 +266,6 @@ void EnergyData::doStep(Step step, Time time, bool isEnergyCalculationStep, bool {}, {} }), freeEnergyPerturbationData_ ? freeEnergyPerturbationData_->currentFEPState() : 0, - shakeVirial_, - forceVirial_, totalVirial_, pressure_, ekind_, -- 2.22.0