*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief Defines code that writes energy-like quantities.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \author Paul Bauer <paul.bauer.q@gmail.com>
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ *
+ * \ingroup module_mdlib
+ */
#include "gmxpre.h"
#include "energyoutput.h"
#include <cstdlib>
#include <cstring>
+#include <array>
#include <string>
-#include "gromacs/awh/awh.h"
+#include "gromacs/applied_forces/awh/awh.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdlib/mdebin_bar.h"
+#include "gromacs/mdrunutility/handlerestart.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/energyframe.h"
#include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
-static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
-
-static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
-
-static const char *tricl_boxs_nm[] = {
- "Box-XX", "Box-YY", "Box-ZZ",
- "Box-YX", "Box-ZX", "Box-ZY"
-};
+#include "energydrifttracker.h"
-static const char *vol_nm[] = { "Volume" };
+//! Labels for energy file quantities
+//! \{
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
-static const char *dens_nm[] = {"Density" };
+static constexpr std::array<const char*, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
-static const char *pv_nm[] = {"pV" };
+static constexpr std::array<const char*, 6> tricl_boxs_nm = { "Box-XX", "Box-YY", "Box-ZZ",
+ "Box-YX", "Box-ZX", "Box-ZY" };
-static const char *enthalpy_nm[] = {"Enthalpy" };
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* vol_nm[] = { "Volume" };
-static const char *boxvel_nm[] = {
- "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
- "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
-};
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* dens_nm[] = { "Density" };
-#define NBOXS asize(boxs_nm)
-#define NTRICLBOXS asize(tricl_boxs_nm)
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* pv_nm[] = { "pV" };
-const char *egrp_nm[egNR+1] = {
- "Coul-SR", "LJ-SR", "Buck-SR",
- "Coul-14", "LJ-14", nullptr
-};
+// NOLINTNEXTLINE(cppcoreguidelines-avoid-non-const-global-variables)
+static const char* enthalpy_nm[] = { "Enthalpy" };
-/* forward declaration */
-typedef struct t_mde_delta_h_coll t_mde_delta_h_coll;
+static constexpr std::array<const char*, 6> boxvel_nm = { "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
+ "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY" };
-namespace gmx
+const char* enumValueToString(NonBondedEnergyTerms enumValue)
{
+ static constexpr gmx::EnumerationArray<NonBondedEnergyTerms, const char*> nonBondedEnergyTermTypeNames = {
+ "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14"
+ };
+ return nonBondedEnergyTermTypeNames[enumValue];
+}
-namespace detail
-{
+//! \}
-/* This is the collection of energy averages collected during mdrun, and to
- be written out to the .edr file. */
-struct t_mdebin
-{
- double delta_t;
- t_ebin *ebin;
- int ie, iconrmsd, ib, ivol, idens, ipv, ienthalpy;
- int isvir, ifvir, ipres, ivir, isurft, ipc, itemp, itc, itcb, iu, imu;
- int ivcos, ivisc;
- int nE, nEg, nEc, nTC, nTCP, nU, nNHC;
- int *igrp;
- int mde_n, mdeb_n;
- real *tmp_r;
- rvec *tmp_v;
- gmx_bool bConstr;
- gmx_bool bConstrVir;
- gmx_bool bTricl;
- gmx_bool bDynBox;
- gmx_bool bNHC_trotter;
- gmx_bool bPrintNHChains;
- gmx_bool bMTTK;
- gmx_bool bMu; /* true if dipole is calculated */
- gmx_bool bDiagPres;
- gmx_bool bPres;
- int f_nre;
- int epc;
- real ref_p;
- int etc;
- int nCrmsd;
- gmx_bool bEner[F_NRE];
- gmx_bool bEInd[egNR];
- char **print_grpnms;
-
- FILE *fp_dhdl; /* the dhdl.xvg output file */
- double *dE; /* energy components for dhdl.xvg output */
- t_mde_delta_h_coll *dhc; /* the delta U components (raw data + histogram) */
- real *temperatures;
-};
-
-} // namespace detail
-
-using detail::t_mdebin;
-
-namespace
+static bool haveFepLambdaMoves(const t_inputrec& inputrec)
{
+ return (inputrec.bExpanded && inputrec.expandedvals->elmcmove > LambdaMoveCalculation::No)
+ || (inputrec.efep != FreeEnergyPerturbationType::No && inputrec.bDoAwh
+ && awhHasFepLambdaDimension(*inputrec.awhParams));
+}
-//! Legacy init function
-t_mdebin *init_mdebin(ener_file_t fp_ene,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- const pull_t *pull_work,
- FILE *fp_dhdl,
- bool isRerun)
+namespace gmx
{
- 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"
- };
- static const char *mu_nm[] = {
- "Mu-X", "Mu-Y", "Mu-Z"
- };
- static const char *vcos_nm[] = {
- "2CosZ*Vel-X"
- };
- static const char *visc_nm[] = {
- "1/Viscosity"
- };
- static const char *baro_nm[] = {
- "Barostat"
- };
-
- const SimulationGroups *groups;
- char **gnm;
- char buf[256];
- const char *bufi;
- t_mdebin *md;
- int i, j, ni, nj, n, k, kk, ncon, nset;
- gmx_bool bBHAM, b14;
-
- snew(md, 1);
- if (EI_DYNAMICS(ir->eI))
- {
- md->delta_t = ir->delta_t;
+/*! \brief Energy output class
+ *
+ * This is the collection of energy averages collected during mdrun, and to
+ * be written out to the .edr file.
+ *
+ * \todo Use more std containers.
+ * \todo Write free-energy output also to energy file (after adding more tests)
+ */
+EnergyOutput::EnergyOutput(ener_file* fp_ene,
+ const gmx_mtop_t& mtop,
+ const t_inputrec& inputrec,
+ const pull_t* pull_work,
+ FILE* fp_dhdl,
+ bool isRerun,
+ const StartingBehavior startingBehavior,
+ const bool simulationsShareState,
+ const MDModulesNotifiers& mdModulesNotifiers) :
+ haveFepLambdaMoves_(haveFepLambdaMoves(inputrec))
+{
+ 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* 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" };
+ static const char* mu_nm[] = { "Mu-X", "Mu-Y", "Mu-Z" };
+ static const char* vcos_nm[] = { "2CosZ*Vel-X" };
+ static const char* visc_nm[] = { "1/Viscosity" };
+ static const char* baro_nm[] = { "Barostat" };
+
+ const SimulationGroups* groups;
+ char** gnm;
+ char buf[256];
+ const char* bufi;
+ int i, j, ni, nj, n, ncon, nset;
+ bool bBHAM, b14;
+
+ if (EI_DYNAMICS(inputrec.eI))
+ {
+ delta_t_ = inputrec.delta_t;
}
else
{
- md->delta_t = 0;
+ delta_t_ = 0;
}
- groups = &mtop->groups;
+ groups = &mtop.groups;
- bBHAM = (mtop->ffparams.numTypes() > 0) && (mtop->ffparams.functype[0] == F_BHAM);
- b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
- gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
+ bBHAM = (mtop.ffparams.numTypes() > 0) && (mtop.ffparams.functype[0] == F_BHAM);
+ b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
- ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
- nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
- md->bConstr = (ncon > 0 || nset > 0) && !isRerun;
- md->bConstrVir = FALSE;
- if (md->bConstr)
+ ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
+ nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
+ bool bConstr = (ncon > 0 || nset > 0) && !isRerun;
+ nCrmsd_ = 0;
+ if (bConstr)
{
- if (ncon > 0 && ir->eConstrAlg == econtLINCS)
+ if (ncon > 0 && inputrec.eConstrAlg == ConstraintAlgorithm::Lincs)
{
- md->nCrmsd = 1;
+ nCrmsd_ = 1;
}
- md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != nullptr);
}
else
{
- md->nCrmsd = 0;
+ nCrmsd_ = 0;
}
/* Energy monitoring */
- for (i = 0; i < egNR; i++)
+ for (auto& term : bEInd_)
{
- md->bEInd[i] = FALSE;
+ term = false;
}
+ // Setting true only to those energy terms, that have active interactions and
+ // are not vsite terms (not VSITE2, VSITE3, VSITE3FD, VSITE3FAD, VSITE3OUT, VSITE4FD, VSITE4FDN, or VSITEN)
for (i = 0; i < F_NRE; i++)
{
- md->bEner[i] = FALSE;
- if (isRerun &&
- (i == F_EKIN || i == F_ETOT || i == F_ECONSERVED ||
- i == F_TEMP || i == F_PDISPCORR || i == F_PRES))
- {
- continue;
- }
- if (i == F_LJ)
- {
- md->bEner[i] = !bBHAM;
- }
- else if (i == F_BHAM)
- {
- md->bEner[i] = bBHAM;
- }
- else if (i == F_EQM)
- {
- md->bEner[i] = ir->bQMMM;
- }
- else if (i == F_RF_EXCL)
- {
- md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
- }
- else if (i == F_COUL_RECIP)
- {
- md->bEner[i] = EEL_FULL(ir->coulombtype);
- }
- else if (i == F_LJ_RECIP)
- {
- md->bEner[i] = EVDW_PME(ir->vdwtype);
- }
- else if (i == F_LJ14)
- {
- md->bEner[i] = b14;
- }
- else if (i == F_COUL14)
- {
- md->bEner[i] = b14;
- }
- else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
- {
- md->bEner[i] = FALSE;
- }
- else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
- (i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
- (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
- (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
- (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
- (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
- {
- md->bEner[i] = (ir->efep != efepNO);
- }
- else if ((interaction_function[i].flags & IF_VSITE) ||
- (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
- {
- md->bEner[i] = FALSE;
- }
- else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i == F_EQM))
- {
- md->bEner[i] = TRUE;
- }
- else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
- {
- md->bEner[i] = EI_DYNAMICS(ir->eI);
- }
- else if (i == F_DISPCORR || i == F_PDISPCORR)
- {
- md->bEner[i] = (ir->eDispCorr != edispcNO);
- }
- else if (i == F_DISRESVIOL)
- {
- md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
- }
- else if (i == F_ORIRESDEV)
- {
- md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
- }
- else if (i == F_CONNBONDS)
- {
- md->bEner[i] = FALSE;
- }
- else if (i == F_COM_PULL)
- {
- md->bEner[i] = ((ir->bPull && pull_have_potential(pull_work)) ||
- ir->bRot);
- }
- else if (i == F_ECONSERVED)
- {
- md->bEner[i] = (integratorHasConservedEnergyQuantity(ir));
- }
- else
- {
- md->bEner[i] = (gmx_mtop_ftype_count(mtop, i) > 0);
- }
+ bEner_[i] = (gmx_mtop_ftype_count(mtop, i) > 0)
+ && ((interaction_function[i].flags & IF_VSITE) == 0);
}
- md->f_nre = 0;
+ if (!isRerun)
+ {
+ bEner_[F_EKIN] = EI_DYNAMICS(inputrec.eI);
+ bEner_[F_ETOT] = EI_DYNAMICS(inputrec.eI);
+ bEner_[F_TEMP] = EI_DYNAMICS(inputrec.eI);
+
+ bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(&inputrec);
+ bEner_[F_PDISPCORR] = (inputrec.eDispCorr != DispersionCorrectionType::No);
+ bEner_[F_PRES] = true;
+ }
+
+ bEner_[F_LJ] = !bBHAM;
+ bEner_[F_BHAM] = bBHAM;
+ 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);
+ bEner_[F_LJ14] = b14;
+ bEner_[F_COUL14] = b14;
+ bEner_[F_LJC14_Q] = false;
+ bEner_[F_LJC_PAIRS_NB] = false;
+
+
+ bEner_[F_DVDL_COUL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Coul];
+ bEner_[F_DVDL_VDW] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Vdw];
+ bEner_[F_DVDL_BONDED] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Bonded];
+ bEner_[F_DVDL_RESTRAINT] =
+ (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Restraint];
+ bEner_[F_DKDL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Mass];
+ bEner_[F_DVDL] = (inputrec.efep != FreeEnergyPerturbationType::No)
+ && inputrec.fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep];
+
+ bEner_[F_CONSTR] = false;
+ bEner_[F_CONSTRNC] = false;
+ bEner_[F_SETTLE] = false;
+
+ bEner_[F_COUL_SR] = true;
+ bEner_[F_EPOT] = true;
+
+ bEner_[F_DISPCORR] = (inputrec.eDispCorr != DispersionCorrectionType::No);
+ bEner_[F_DISRESVIOL] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
+ 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;
for (i = 0; i < F_NRE; i++)
{
- if (md->bEner[i])
+ if (bEner_[i])
{
- ener_nm[md->f_nre] = interaction_function[i].longname;
- md->f_nre++;
+ ener_nm[f_nre_] = interaction_function[i].longname;
+ f_nre_++;
}
}
- md->epc = isRerun ? epcNO : ir->epc;
- md->bDiagPres = !TRICLINIC(ir->ref_p) && !isRerun;
- md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
- md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
- md->bDynBox = inputrecDynamicBox(ir);
- md->etc = isRerun ? etcNO : ir->etc;
- md->bNHC_trotter = inputrecNvtTrotter(ir) && !isRerun;
- md->bPrintNHChains = ir->bPrintNHChains && !isRerun;
- md->bMTTK = (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)) && !isRerun;
- md->bMu = inputrecNeedMutot(ir);
- md->bPres = !isRerun;
+ epc_ = isRerun ? PressureCoupling::No : inputrec.epc;
+ bDiagPres_ = !TRICLINIC(inputrec.ref_p) && !isRerun;
+ ref_p_ = (inputrec.ref_p[XX][XX] + inputrec.ref_p[YY][YY] + inputrec.ref_p[ZZ][ZZ]) / DIM;
+ bTricl_ = TRICLINIC(inputrec.compress) || TRICLINIC(inputrec.deform);
+ bDynBox_ = inputrecDynamicBox(&inputrec);
+ etc_ = isRerun ? TemperatureCoupling::No : inputrec.etc;
+ bNHC_trotter_ = inputrecNvtTrotter(&inputrec) && !isRerun;
+ bPrintNHChains_ = inputrec.bPrintNHChains && !isRerun;
+ bMTTK_ = (inputrecNptTrotter(&inputrec) || inputrecNphTrotter(&inputrec)) && !isRerun;
+ bMu_ = inputrecNeedMutot(&inputrec);
+ bPres_ = !isRerun;
- md->ebin = mk_ebin();
+ ebin_ = mk_ebin();
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
- md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, nullptr);
- if (md->nCrmsd)
+ ie_ = get_ebin_space(ebin_, f_nre_, ener_nm, nullptr);
+ if (nCrmsd_)
{
- /* This should be called directly after the call for md->ie,
- * such that md->iconrmsd follows directly in the list.
+ /* This should be called directly after the call for ie_,
+ * such that iconrmsd_ follows directly in the list.
*/
- md->iconrmsd = get_ebin_space(md->ebin, md->nCrmsd, conrmsd_nm, "");
+ iconrmsd_ = get_ebin_space(ebin_, nCrmsd_, conrmsd_nm, "");
}
- if (md->bDynBox)
+ if (bDynBox_)
{
- md->ib = get_ebin_space(md->ebin,
- md->bTricl ? NTRICLBOXS : NBOXS,
- md->bTricl ? tricl_boxs_nm : boxs_nm,
- unit_length);
- md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
- md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
- if (md->bDiagPres)
+ ib_ = get_ebin_space(ebin_,
+ bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(),
+ bTricl_ ? tricl_boxs_nm.data() : boxs_nm.data(),
+ unit_length);
+ ivol_ = get_ebin_space(ebin_, 1, vol_nm, unit_volume);
+ idens_ = get_ebin_space(ebin_, 1, dens_nm, unit_density_SI);
+ if (bDiagPres_)
{
- md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
- md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
+ ipv_ = get_ebin_space(ebin_, 1, pv_nm, unit_energy);
+ ienthalpy_ = get_ebin_space(ebin_, 1, enthalpy_nm, unit_energy);
}
}
- if (md->bConstrVir)
- {
- md->isvir = get_ebin_space(md->ebin, asize(sv_nm), sv_nm, unit_energy);
- md->ifvir = get_ebin_space(md->ebin, asize(fv_nm), fv_nm, unit_energy);
- }
- if (md->bPres)
+ if (bPres_)
{
- md->ivir = get_ebin_space(md->ebin, asize(vir_nm), vir_nm, unit_energy);
- md->ipres = get_ebin_space(md->ebin, asize(pres_nm), pres_nm, unit_pres_bar);
- md->isurft = get_ebin_space(md->ebin, asize(surft_nm), surft_nm,
- unit_surft_bar);
+ ivir_ = get_ebin_space(ebin_, asize(vir_nm), vir_nm, unit_energy);
+ ipres_ = get_ebin_space(ebin_, asize(pres_nm), pres_nm, unit_pres_bar);
+ isurft_ = get_ebin_space(ebin_, asize(surft_nm), surft_nm, unit_surft_bar);
}
- if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
+ if (epc_ == PressureCoupling::ParrinelloRahman || epc_ == PressureCoupling::Mttk)
{
- md->ipc = get_ebin_space(md->ebin, md->bTricl ? 6 : 3,
- boxvel_nm, unit_vel);
+ ipc_ = get_ebin_space(ebin_, bTricl_ ? boxvel_nm.size() : DIM, boxvel_nm.data(), unit_vel);
}
- if (md->bMu)
+ if (bMu_)
{
- md->imu = get_ebin_space(md->ebin, asize(mu_nm), mu_nm, unit_dipole_D);
+ imu_ = get_ebin_space(ebin_, asize(mu_nm), mu_nm, unit_dipole_D);
}
- if (ir->cos_accel != 0)
+ if (inputrec.cos_accel != 0)
{
- md->ivcos = get_ebin_space(md->ebin, asize(vcos_nm), vcos_nm, unit_vel);
- md->ivisc = get_ebin_space(md->ebin, asize(visc_nm), visc_nm,
- unit_invvisc_SI);
+ ivcos_ = get_ebin_space(ebin_, asize(vcos_nm), vcos_nm, unit_vel);
+ ivisc_ = get_ebin_space(ebin_, asize(visc_nm), visc_nm, unit_invvisc_SI);
}
/* Energy monitoring */
- for (i = 0; i < egNR; i++)
+ for (auto& term : bEInd_)
{
- md->bEInd[i] = FALSE;
+ term = false;
}
- md->bEInd[egCOULSR] = TRUE;
- md->bEInd[egLJSR ] = TRUE;
+ bEInd_[NonBondedEnergyTerms::CoulombSR] = true;
+ bEInd_[NonBondedEnergyTerms::LJSR] = true;
if (bBHAM)
{
- md->bEInd[egLJSR] = FALSE;
- md->bEInd[egBHAMSR] = TRUE;
+ bEInd_[NonBondedEnergyTerms::LJSR] = false;
+ bEInd_[NonBondedEnergyTerms::BuckinghamSR] = true;
}
if (b14)
{
- md->bEInd[egLJ14] = TRUE;
- md->bEInd[egCOUL14] = TRUE;
+ bEInd_[NonBondedEnergyTerms::LJ14] = true;
+ bEInd_[NonBondedEnergyTerms::Coulomb14] = true;
}
- md->nEc = 0;
- for (i = 0; (i < egNR); i++)
+ nEc_ = 0;
+ for (auto term : bEInd_)
{
- if (md->bEInd[i])
+ if (term)
{
- md->nEc++;
+ nEc_++;
}
}
- n = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
- md->nEg = n;
- md->nE = (n*(n+1))/2;
+ n = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
+ nEg_ = n;
+ nE_ = (n * (n + 1)) / 2;
- snew(md->igrp, md->nE);
- if (md->nE > 1)
+ igrp_.resize(nE_);
+ if (nE_ > 1)
{
n = 0;
- snew(gnm, md->nEc);
- for (k = 0; (k < md->nEc); k++)
+ snew(gnm, nEc_);
+ for (int k = 0; (k < nEc_); k++)
{
snew(gnm[k], STRLEN);
}
ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
for (j = i; (j < gmx::ssize(groups->groups[SimulationAtomGroupType::EnergyOutput])); j++)
{
- nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
- for (k = kk = 0; (k < egNR); k++)
+ nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
+ int k = 0;
+ for (auto key : keysOf(bEInd_))
{
- if (md->bEInd[k])
+ if (bEInd_[key])
{
- sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
- *(groups->groupNames[ni]), *(groups->groupNames[nj]));
- kk++;
+ sprintf(gnm[k],
+ "%s:%s-%s",
+ enumValueToString(key),
+ *(groups->groupNames[ni]),
+ *(groups->groupNames[nj]));
+ k++;
}
}
- md->igrp[n] = get_ebin_space(md->ebin, md->nEc,
- gnm, unit_energy);
+ igrp_[n] = get_ebin_space(ebin_, nEc_, gnm, unit_energy);
n++;
}
}
- for (k = 0; (k < md->nEc); k++)
+ for (int k = 0; (k < nEc_); k++)
{
sfree(gnm[k]);
}
sfree(gnm);
- if (n != md->nE)
+ if (n != nE_)
{
gmx_incons("Number of energy terms wrong");
}
}
- md->nTC = isRerun ? 0 : groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
- md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
- if (md->bMTTK)
+ nTC_ = isRerun ? 0 : groups->groups[SimulationAtomGroupType::TemperatureCoupling].size();
+ nNHC_ = inputrec.opts.nhchainlength; /* shorthand for number of NH chains */
+ if (bMTTK_)
{
- md->nTCP = 1; /* assume only one possible coupling system for barostat
- for now */
+ nTCP_ = 1; /* assume only one possible coupling system for barostat
+ for now */
}
else
{
- md->nTCP = 0;
+ nTCP_ = 0;
}
- if (md->etc == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
- if (md->bNHC_trotter)
+ if (bNHC_trotter_)
{
- md->mde_n = 2*md->nNHC*md->nTC;
+ mde_n_ = 2 * nNHC_ * nTC_;
}
else
{
- md->mde_n = 2*md->nTC;
+ mde_n_ = 2 * nTC_;
}
- if (md->epc == epcMTTK)
+ if (epc_ == PressureCoupling::Mttk)
{
- md->mdeb_n = 2*md->nNHC*md->nTCP;
+ mdeb_n_ = 2 * nNHC_ * nTCP_;
}
}
else
{
- md->mde_n = md->nTC;
- md->mdeb_n = 0;
+ mde_n_ = nTC_;
+ mdeb_n_ = 0;
}
- snew(md->tmp_r, md->mde_n);
-
+ tmp_r_.resize(mde_n_);
// TODO redo the group name memory management to make it more clear
- char **grpnms;
- snew(grpnms, std::max(md->mde_n, md->mdeb_n)); // Just in case md->mdeb_n > md->mde_n
+ char** grpnms;
+ snew(grpnms, std::max(mde_n_, mdeb_n_)); // Just in case mdeb_n_ > mde_n_
- for (i = 0; (i < md->nTC); i++)
+ for (i = 0; (i < nTC_); i++)
{
ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
sprintf(buf, "T-%s", *(groups->groupNames[ni]));
grpnms[i] = gmx_strdup(buf);
}
- md->itemp = get_ebin_space(md->ebin, md->nTC, grpnms,
- unit_temp_K);
- for (i = 0; i < md->nTC; i++)
+ itemp_ = get_ebin_space(ebin_, nTC_, grpnms, unit_temp_K);
+ for (i = 0; i < nTC_; i++)
{
sfree(grpnms[i]);
}
int allocated = 0;
- if (md->etc == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
- if (md->bPrintNHChains)
+ if (bPrintNHChains_)
{
- if (md->bNHC_trotter)
+ if (bNHC_trotter_)
{
- for (i = 0; (i < md->nTC); i++)
+ for (i = 0; (i < nTC_); i++)
{
ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
bufi = *(groups->groupNames[ni]);
- for (j = 0; (j < md->nNHC); j++)
+ for (j = 0; (j < nNHC_); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
}
}
- md->itc = get_ebin_space(md->ebin, md->mde_n,
- grpnms, unit_invtime);
- allocated = md->mde_n;
- if (md->bMTTK)
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
+ allocated = mde_n_;
+ if (bMTTK_)
{
- for (i = 0; (i < md->nTCP); i++)
+ for (i = 0; (i < nTCP_); i++)
{
- bufi = baro_nm[0]; /* All barostat DOF's together for now. */
- for (j = 0; (j < md->nNHC); j++)
+ bufi = baro_nm[0]; /* All barostat DOF's together for now. */
+ for (j = 0; (j < nNHC_); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*md->nNHC+j)+1] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
}
}
- md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
- grpnms, unit_invtime);
- allocated = md->mdeb_n;
+ itcb_ = get_ebin_space(ebin_, mdeb_n_, grpnms, unit_invtime);
+ allocated = mdeb_n_;
}
}
else
{
- for (i = 0; (i < md->nTC); i++)
+ for (i = 0; (i < nTC_); i++)
{
ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
bufi = *(groups->groupNames[ni]);
sprintf(buf, "Xi-%s", bufi);
- grpnms[2*i] = gmx_strdup(buf);
+ grpnms[2 * i] = gmx_strdup(buf);
sprintf(buf, "vXi-%s", bufi);
- grpnms[2*i+1] = gmx_strdup(buf);
+ grpnms[2 * i + 1] = gmx_strdup(buf);
}
- md->itc = get_ebin_space(md->ebin, md->mde_n,
- grpnms, unit_invtime);
- allocated = md->mde_n;
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
+ allocated = mde_n_;
}
}
}
- else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
- md->etc == etcVRESCALE)
+ else if (etc_ == TemperatureCoupling::Berendsen || etc_ == TemperatureCoupling::Yes
+ || etc_ == TemperatureCoupling::VRescale)
{
- for (i = 0; (i < md->nTC); i++)
+ for (i = 0; (i < nTC_); i++)
{
ni = groups->groups[SimulationAtomGroupType::TemperatureCoupling][i];
sprintf(buf, "Lamb-%s", *(groups->groupNames[ni]));
grpnms[i] = gmx_strdup(buf);
}
- md->itc = get_ebin_space(md->ebin, md->mde_n, grpnms, "");
- allocated = md->mde_n;
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, "");
+ allocated = mde_n_;
}
for (i = 0; i < allocated; i++)
}
sfree(grpnms);
- md->nU = groups->groups[SimulationAtomGroupType::Acceleration].size();
- snew(md->tmp_v, md->nU);
- if (md->nU > 1)
+ /* Note that fp_ene should be valid on the master rank and null otherwise */
+ if (fp_ene != nullptr && startingBehavior != StartingBehavior::RestartWithAppending)
{
- snew(grpnms, 3*md->nU);
- for (i = 0; (i < md->nU); i++)
- {
- ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
- sprintf(buf, "Ux-%s", *(groups->groupNames[ni]));
- grpnms[3*i+XX] = gmx_strdup(buf);
- sprintf(buf, "Uy-%s", *(groups->groupNames[ni]));
- grpnms[3*i+YY] = gmx_strdup(buf);
- sprintf(buf, "Uz-%s", *(groups->groupNames[ni]));
- grpnms[3*i+ZZ] = gmx_strdup(buf);
- }
- md->iu = get_ebin_space(md->ebin, 3*md->nU, grpnms, unit_vel);
- for (i = 0; i < 3*md->nU; i++)
- {
- sfree(grpnms[i]);
- }
- sfree(grpnms);
+ do_enxnms(fp_ene, &ebin_->nener, &ebin_->enm);
}
- if (fp_ene)
- {
- do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
- }
-
- md->print_grpnms = nullptr;
-
/* check whether we're going to write dh histograms */
- md->dhc = nullptr;
- if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
+ dhc_ = nullptr;
+ if (inputrec.fepvals->separate_dhdl_file == SeparateDhdlFile::No)
{
/* Currently dh histograms are only written with dynamics */
- if (EI_DYNAMICS(ir->eI))
+ if (EI_DYNAMICS(inputrec.eI))
{
- snew(md->dhc, 1);
-
- mde_delta_h_coll_init(md->dhc, ir);
+ dhc_ = std::make_unique<t_mde_delta_h_coll>(inputrec);
}
- md->fp_dhdl = nullptr;
- snew(md->dE, ir->fepvals->n_lambda);
+ fp_dhdl_ = nullptr;
+ dE_.resize(inputrec.fepvals->n_lambda);
}
else
{
- md->fp_dhdl = fp_dhdl;
- snew(md->dE, ir->fepvals->n_lambda);
+ fp_dhdl_ = fp_dhdl;
+ dE_.resize(inputrec.fepvals->n_lambda);
}
- if (ir->bSimTemp)
+ if (inputrec.bSimTemp)
{
- int i;
- snew(md->temperatures, ir->fepvals->n_lambda);
- for (i = 0; i < ir->fepvals->n_lambda; i++)
- {
- md->temperatures[i] = ir->simtempvals->temperatures[i];
- }
+ temperatures_ = inputrec.simtempvals->temperatures;
+ }
+
+ if (EI_MD(inputrec.eI) && !simulationsShareState)
+ {
+ conservedEnergyTracker_ = std::make_unique<EnergyDriftTracker>(mtop.natoms);
}
- return md;
}
-//! Legacy cleanup function
-void done_mdebin(t_mdebin *mdebin)
+EnergyOutput::~EnergyOutput()
{
- sfree(mdebin->igrp);
- sfree(mdebin->tmp_r);
- sfree(mdebin->tmp_v);
- done_ebin(mdebin->ebin);
- done_mde_delta_h_coll(mdebin->dhc);
- sfree(mdebin->dE);
- sfree(mdebin->temperatures);
- if (mdebin->nE > 1 && mdebin->print_grpnms != nullptr)
- {
- for (int n = 0; n < mdebin->nE; n++)
- {
- sfree(mdebin->print_grpnms[n]);
- }
- sfree(mdebin->print_grpnms);
- }
- sfree(mdebin);
+ done_ebin(ebin_);
}
-} // namespace
} // namespace gmx
-/* print a lambda vector to a string
- fep = the inputrec's FEP input data
- i = the index of the lambda vector
- get_native_lambda = whether to print the native lambda
- get_names = whether to print the names rather than the values
- str = the pre-allocated string buffer to print to. */
-static void print_lambda_vector(t_lambda *fep, int i,
- gmx_bool get_native_lambda, gmx_bool get_names,
- char *str)
+/*! \brief Print a lambda vector to a string
+ *
+ * \param[in] fep The inputrec's FEP input data
+ * \param[in] i The index of the lambda vector
+ * \param[in] get_native_lambda Whether to print the native lambda
+ * \param[in] get_names Whether to print the names rather than the values
+ * \param[in,out] str The pre-allocated string buffer to print to.
+ */
+static void print_lambda_vector(t_lambda* fep, int i, bool get_native_lambda, bool get_names, char* str)
{
- int j, k = 0;
- int Nsep = 0;
+ int k = 0;
+ int Nsep = 0;
- for (j = 0; j < efptNR; j++)
+ for (auto j : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[j])
{
{
str += sprintf(str, "("); /* set the opening parenthesis*/
}
- for (j = 0; j < efptNR; j++)
+ for (auto j : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[j])
{
}
else
{
- str += sprintf(str, "%s", efpt_singular_names[j]);
+ str += sprintf(str, "%s", enumValueToStringSingular(j));
}
/* print comma for the next item */
- if (k < Nsep-1)
+ if (k < Nsep - 1)
{
str += sprintf(str, ", ");
}
}
}
-FILE *open_dhdl(const char *filename, const t_inputrec *ir,
- const gmx_output_env_t *oenv)
+FILE* open_dhdl(const char* filename, const t_inputrec* ir, const gmx_output_env_t* oenv)
{
- FILE *fp;
+ FILE* fp;
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
- *lambdastate = "\\lambda state";
- int i, nsets, nsets_de, nsetsbegin;
- int n_lambda_terms = 0;
- t_lambda *fep = ir->fepvals; /* for simplicity */
- t_expanded *expand = ir->expandedvals;
- char lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
-
- int nsets_dhdl = 0;
- int s = 0;
- int nsetsextend;
- gmx_bool write_pV = FALSE;
+ *lambdastate = "\\lambda state";
+ int i, nsets, nsets_de, nsetsbegin;
+ int n_lambda_terms = 0;
+ t_lambda* fep = ir->fepvals.get(); /* for simplicity */
+ char lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
+
+ int nsets_dhdl = 0;
+ int s = 0;
+ int nsetsextend;
+ bool write_pV = false;
/* count the number of different lambda terms */
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
{
title = gmx::formatString("%s", dhdl);
label_x = gmx::formatString("Time (ps)");
- label_y = gmx::formatString("%s (%s %s)",
- dhdl, unit_energy, "[\\lambda]\\S-1\\N");
+ label_y = gmx::formatString("%s (%s %s)", dhdl, unit_energy, "[\\lambda]\\S-1\\N");
}
else
{
title = gmx::formatString("%s and %s", dhdl, deltag);
label_x = gmx::formatString("Time (ps)");
- label_y = gmx::formatString("%s and %s (%s %s)",
- dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
+ label_y = gmx::formatString(
+ "%s and %s (%s %s)", dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename, "w+");
xvgr_header(fp, title.c_str(), label_x, label_y, exvggtXNY, oenv);
{
buf = gmx::formatString("T = %g (K) ", ir->opts.ref_t[0]);
}
- if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
+ if ((ir->efep != FreeEnergyPerturbationType::SlowGrowth)
+ && (ir->efep != FreeEnergyPerturbationType::Expanded)
+ && !(ir->bDoAwh && awhHasFepLambdaDimension(*ir->awhParams)))
{
- if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
+ if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
{
/* compatibility output */
buf += gmx::formatString("%s = %.4f", lambda, fep->init_lambda);
}
else
{
- print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
- lambda_vec_str);
- print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
- lambda_name_str);
- buf += gmx::formatString("%s %d: %s = %s",
- lambdastate, fep->init_fep_state,
- lambda_name_str, lambda_vec_str);
+ print_lambda_vector(fep, fep->init_fep_state, true, false, lambda_vec_str);
+ print_lambda_vector(fep, fep->init_fep_state, true, true, lambda_name_str);
+ buf += gmx::formatString(
+ "%s %d: %s = %s", lambdastate, fep->init_fep_state, lambda_name_str, lambda_vec_str);
}
}
xvgr_subtitle(fp, buf.c_str(), oenv);
nsets_dhdl = 0;
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
nsets_dhdl = n_lambda_terms;
}
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
- if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
+ if (haveFepLambdaMoves(*ir))
{
- nsets += 1; /*add fep state for expanded ensemble */
+ nsets += 1; /*add fep state for expanded ensemble */
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
- nsets += 1; /* add energy to the dhdl as well */
+ nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
- if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
+ if ((ir->epc != PressureCoupling::No) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for
the reduced potential (only needed with foreign
lambda, and only output when init_lambda is not
set in order to maintain compatibility of the
dhdl.xvg file) */
- write_pV = TRUE;
+ write_pV = true;
}
std::vector<std::string> setname(nsetsextend);
- if (expand->elmcmove > elmcmoveNO)
+ if (haveFepLambdaMoves(*ir))
{
/* state for the fep_vals, if we have alchemical sampling */
setname[s++] = "Thermodynamic state";
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
std::string energy;
switch (fep->edHdLPrintEnergy)
{
- case edHdLPrintEnergyPOTENTIAL:
+ case FreeEnergyPrintEnergy::Potential:
energy = gmx::formatString("%s (%s)", "Potential Energy", unit_energy);
break;
- case edHdLPrintEnergyTOTAL:
- case edHdLPrintEnergyYES:
- default:
- energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
+ case FreeEnergyPrintEnergy::Total:
+ case FreeEnergyPrintEnergy::Yes:
+ default: energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
}
setname[s++] = energy;
}
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- for (i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
std::string derivative;
- if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
+ if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
{
/* compatibility output */
derivative = gmx::formatString("%s %s %.4f", dhdl, lambda, fep->init_lambda);
{
lam = fep->all_lambda[i][fep->init_fep_state];
}
- derivative = gmx::formatString("%s %s = %.4f", dhdl, efpt_singular_names[i],
- lam);
+ derivative = gmx::formatString("%s %s = %.4f", dhdl, enumValueToStringSingular(i), lam);
}
setname[s++] = derivative;
}
* from this xvg legend.
*/
- if (expand->elmcmove > elmcmoveNO)
+ if (haveFepLambdaMoves(*ir))
{
- nsetsbegin = 1; /* for including the expanded ensemble */
+ nsetsbegin = 1; /* for including the expanded ensemble */
}
else
{
nsetsbegin = 0;
}
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
nsetsbegin += 1;
}
for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
- print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
+ print_lambda_vector(fep, i, false, false, lambda_vec_str);
std::string buf;
- if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
+ if ((fep->init_lambda >= 0) && (n_lambda_terms == 1))
{
/* for compatible dhdl.xvg files */
buf = gmx::formatString("%s %s %s", deltag, lambda, lambda_vec_str);
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
- buf += gmx::formatString("T = %g (%s)",
- ir->simtempvals->temperatures[s-(nsetsbegin)],
- unit_temp_K);
+ buf += gmx::formatString(
+ "T = %g (%s)", ir->simtempvals->temperatures[s - (nsetsbegin)], unit_temp_K);
}
setname[s++] = buf;
}
namespace gmx
{
-namespace
-{
-//! Legacy update function
-void upd_mdebin(t_mdebin *md,
- gmx_bool bDoDHDL,
- gmx_bool bSum,
- double time,
- real tmass,
- gmx_enerdata_t *enerd,
- t_state *state,
- t_lambda *fep,
- t_expanded *expand,
- matrix box,
- tensor svir,
- tensor fvir,
- tensor vir,
- tensor pres,
- gmx_ekindata_t *ekind,
- rvec mu_tot,
- const gmx::Constraints *constr)
+void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL,
+ bool bSum,
+ double time,
+ real tmass,
+ const gmx_enerdata_t* enerd,
+ const t_lambda* fep,
+ const matrix box,
+ PTCouplingArrays ptCouplingArrays,
+ int fep_state,
+ const tensor vir,
+ const tensor pres,
+ const gmx_ekindata_t* ekind,
+ const rvec mu_tot,
+ const gmx::Constraints* constr)
{
- int j, k, kk, n, gid;
- real crmsd[2], tmp6[6];
- real bs[NTRICLBOXS], vol, dens, pv, enthalpy;
- real eee[egNR];
- double store_dhdl[efptNR];
- real store_energy = 0;
- real tmp;
+ int j, k, kk, n, gid;
+ real crmsd[2], tmp6[6];
+ real bs[tricl_boxs_nm.size()], vol, dens, enthalpy;
+ real eee[static_cast<int>(NonBondedEnergyTerms::Count)];
+ gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, double> store_dhdl;
+ real store_energy = 0;
+ real tmp;
+ real pv = 0.0; // static analyzer warns about uninitialized variable warnings here.
/* Do NOT use the box in the state variable, but the separate box provided
* as an argument. This is because we sometimes need to write the box from
* the last timestep to match the trajectory frames.
*/
- add_ebin_indexed(md->ebin, md->ie, gmx::ArrayRef<gmx_bool>(md->bEner), enerd->term, bSum);
- if (md->nCrmsd)
+ add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
+ if (nCrmsd_)
{
crmsd[0] = constr->rmsd();
- add_ebin(md->ebin, md->iconrmsd, md->nCrmsd, crmsd, FALSE);
+ add_ebin(ebin_, iconrmsd_, nCrmsd_, crmsd, false);
}
- if (md->bDynBox)
+ if (bDynBox_)
{
int nboxs;
- if (md->bTricl)
+ if (bTricl_)
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[3] = box[YY][XX];
bs[4] = box[ZZ][XX];
bs[5] = box[ZZ][YY];
- nboxs = NTRICLBOXS;
+ nboxs = tricl_boxs_nm.size();
}
else
{
bs[0] = box[XX][XX];
bs[1] = box[YY][YY];
bs[2] = box[ZZ][ZZ];
- nboxs = NBOXS;
+ nboxs = boxs_nm.size();
}
- vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
- dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
- add_ebin(md->ebin, md->ib, nboxs, bs, bSum);
- add_ebin(md->ebin, md->ivol, 1, &vol, bSum);
- add_ebin(md->ebin, md->idens, 1, &dens, bSum);
+ vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
+ dens = (tmass * gmx::c_amu) / (vol * gmx::c_nano * gmx::c_nano * gmx::c_nano);
+ add_ebin(ebin_, ib_, nboxs, bs, bSum);
+ add_ebin(ebin_, ivol_, 1, &vol, bSum);
+ add_ebin(ebin_, idens_, 1, &dens, bSum);
- if (md->bDiagPres)
+ if (bDiagPres_)
{
/* This is pV (in kJ/mol). The pressure is the reference pressure,
not the instantaneous pressure */
- pv = vol*md->ref_p/PRESFAC;
+ pv = vol * ref_p_ / gmx::c_presfac;
- add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
+ add_ebin(ebin_, ipv_, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];
- add_ebin(md->ebin, md->ienthalpy, 1, &enthalpy, bSum);
+ add_ebin(ebin_, ienthalpy_, 1, &enthalpy, bSum);
}
}
- if (md->bConstrVir)
- {
- add_ebin(md->ebin, md->isvir, 9, svir[0], bSum);
- add_ebin(md->ebin, md->ifvir, 9, fvir[0], bSum);
- }
- if (md->bPres)
+ if (bPres_)
{
- add_ebin(md->ebin, md->ivir, 9, vir[0], bSum);
- add_ebin(md->ebin, md->ipres, 9, pres[0], bSum);
- tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
- add_ebin(md->ebin, md->isurft, 1, &tmp, bSum);
+ add_ebin(ebin_, ivir_, 9, vir[0], bSum);
+ add_ebin(ebin_, ipres_, 9, pres[0], bSum);
+ tmp = (pres[ZZ][ZZ] - (pres[XX][XX] + pres[YY][YY]) * 0.5) * box[ZZ][ZZ];
+ add_ebin(ebin_, isurft_, 1, &tmp, bSum);
}
- if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
+ if (epc_ == PressureCoupling::ParrinelloRahman || epc_ == PressureCoupling::Mttk)
{
- tmp6[0] = state->boxv[XX][XX];
- tmp6[1] = state->boxv[YY][YY];
- tmp6[2] = state->boxv[ZZ][ZZ];
- tmp6[3] = state->boxv[YY][XX];
- tmp6[4] = state->boxv[ZZ][XX];
- tmp6[5] = state->boxv[ZZ][YY];
- add_ebin(md->ebin, md->ipc, md->bTricl ? 6 : 3, tmp6, bSum);
+ tmp6[0] = ptCouplingArrays.boxv[XX][XX];
+ tmp6[1] = ptCouplingArrays.boxv[YY][YY];
+ tmp6[2] = ptCouplingArrays.boxv[ZZ][ZZ];
+ tmp6[3] = ptCouplingArrays.boxv[YY][XX];
+ tmp6[4] = ptCouplingArrays.boxv[ZZ][XX];
+ tmp6[5] = ptCouplingArrays.boxv[ZZ][YY];
+ add_ebin(ebin_, ipc_, bTricl_ ? 6 : 3, tmp6, bSum);
}
- if (md->bMu)
+ if (bMu_)
{
- add_ebin(md->ebin, md->imu, 3, mu_tot, bSum);
+ add_ebin(ebin_, imu_, 3, mu_tot, bSum);
}
if (ekind && ekind->cosacc.cos_accel != 0)
{
- vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
- dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
- add_ebin(md->ebin, md->ivcos, 1, &(ekind->cosacc.vcos), bSum);
+ vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
+ dens = (tmass * gmx::c_amu) / (vol * gmx::c_nano * gmx::c_nano * gmx::c_nano);
+ add_ebin(ebin_, ivcos_, 1, &(ekind->cosacc.vcos), bSum);
/* 1/viscosity, unit 1/(kg m^-1 s^-1) */
- tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
- *dens*gmx::square(box[ZZ][ZZ]*NANO/(2*M_PI)));
- add_ebin(md->ebin, md->ivisc, 1, &tmp, bSum);
+ tmp = 1
+ / (ekind->cosacc.cos_accel / (ekind->cosacc.vcos * gmx::c_pico) * dens
+ * gmx::square(box[ZZ][ZZ] * gmx::c_nano / (2 * M_PI)));
+ add_ebin(ebin_, ivisc_, 1, &tmp, bSum);
}
- if (md->nE > 1)
+ if (nE_ > 1)
{
n = 0;
- for (int i = 0; (i < md->nEg); i++)
+ for (int i = 0; (i < nEg_); i++)
{
- for (j = i; (j < md->nEg); j++)
+ for (j = i; (j < nEg_); j++)
{
- gid = GID(i, j, md->nEg);
- for (k = kk = 0; (k < egNR); k++)
+ gid = GID(i, j, nEg_);
+ for (k = kk = 0; (k < static_cast<int>(NonBondedEnergyTerms::Count)); k++)
{
- if (md->bEInd[k])
+ if (bEInd_[k])
{
- eee[kk++] = enerd->grpp.ener[k][gid];
+ eee[kk++] = enerd->grpp.energyGroupPairTerms[k][gid];
}
}
- add_ebin(md->ebin, md->igrp[n], md->nEc, eee, bSum);
+ add_ebin(ebin_, igrp_[n], nEc_, eee, bSum);
n++;
}
}
if (ekind)
{
- for (int i = 0; (i < md->nTC); i++)
+ for (int i = 0; (i < nTC_); i++)
{
- md->tmp_r[i] = ekind->tcstat[i].T;
+ tmp_r_[i] = ekind->tcstat[i].T;
}
- add_ebin(md->ebin, md->itemp, md->nTC, md->tmp_r, bSum);
+ add_ebin(ebin_, itemp_, nTC_, tmp_r_.data(), bSum);
- if (md->etc == etcNOSEHOOVER)
+ if (etc_ == TemperatureCoupling::NoseHoover)
{
/* whether to print Nose-Hoover chains: */
- if (md->bPrintNHChains)
+ if (bPrintNHChains_)
{
- if (md->bNHC_trotter)
+ if (bNHC_trotter_)
{
- for (int i = 0; (i < md->nTC); i++)
+ for (int i = 0; (i < nTC_); i++)
{
- for (j = 0; j < md->nNHC; j++)
+ for (j = 0; j < nNHC_; j++)
{
- k = i*md->nNHC+j;
- md->tmp_r[2*k] = state->nosehoover_xi[k];
- md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
+ k = i * nNHC_ + j;
+ tmp_r_[2 * k] = ptCouplingArrays.nosehoover_xi[k];
+ tmp_r_[2 * k + 1] = ptCouplingArrays.nosehoover_vxi[k];
}
}
- add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
+ add_ebin(ebin_, itc_, mde_n_, tmp_r_.data(), bSum);
- if (md->bMTTK)
+ if (bMTTK_)
{
- for (int i = 0; (i < md->nTCP); i++)
+ for (int i = 0; (i < nTCP_); i++)
{
- for (j = 0; j < md->nNHC; j++)
+ for (j = 0; j < nNHC_; j++)
{
- k = i*md->nNHC+j;
- md->tmp_r[2*k] = state->nhpres_xi[k];
- md->tmp_r[2*k+1] = state->nhpres_vxi[k];
+ k = i * nNHC_ + j;
+ tmp_r_[2 * k] = ptCouplingArrays.nhpres_xi[k];
+ tmp_r_[2 * k + 1] = ptCouplingArrays.nhpres_vxi[k];
}
}
- add_ebin(md->ebin, md->itcb, md->mdeb_n, md->tmp_r, bSum);
+ add_ebin(ebin_, itcb_, mdeb_n_, tmp_r_.data(), bSum);
}
}
else
{
- for (int i = 0; (i < md->nTC); i++)
+ for (int i = 0; (i < nTC_); i++)
{
- md->tmp_r[2*i] = state->nosehoover_xi[i];
- md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
+ tmp_r_[2 * i] = ptCouplingArrays.nosehoover_xi[i];
+ tmp_r_[2 * i + 1] = ptCouplingArrays.nosehoover_vxi[i];
}
- add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
+ add_ebin(ebin_, itc_, mde_n_, tmp_r_.data(), bSum);
}
}
}
- else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
- md->etc == etcVRESCALE)
+ else if (etc_ == TemperatureCoupling::Berendsen || etc_ == TemperatureCoupling::Yes
+ || etc_ == TemperatureCoupling::VRescale)
{
- for (int i = 0; (i < md->nTC); i++)
+ for (int i = 0; (i < nTC_); i++)
{
- md->tmp_r[i] = ekind->tcstat[i].lambda;
+ tmp_r_[i] = ekind->tcstat[i].lambda;
}
- add_ebin(md->ebin, md->itc, md->nTC, md->tmp_r, bSum);
- }
- }
-
- if (ekind && md->nU > 1)
- {
- for (int i = 0; (i < md->nU); i++)
- {
- copy_rvec(ekind->grpstat[i].u, md->tmp_v[i]);
+ add_ebin(ebin_, itc_, nTC_, tmp_r_.data(), bSum);
}
- add_ebin(md->ebin, md->iu, 3*md->nU, md->tmp_v[0], bSum);
}
- ebin_increase_count(md->ebin, bSum);
+ ebin_increase_count(1, ebin_, bSum);
- /* BAR + thermodynamic integration values */
- if ((md->fp_dhdl || md->dhc) && bDoDHDL)
+ // BAR + thermodynamic integration values
+ if ((fp_dhdl_ || dhc_) && bDoDHDL)
{
- for (gmx::index i = 0; i < static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1; i++)
+ const auto& foreignTerms = enerd->foreignLambdaTerms;
+ for (int i = 0; i < foreignTerms.numLambdas(); i++)
{
/* zero for simulated tempering */
- md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
- if (md->temperatures != nullptr)
+ dE_[i] = foreignTerms.deltaH(i);
+ if (!temperatures_.empty())
{
+ GMX_RELEASE_ASSERT(gmx::ssize(temperatures_) > fep_state,
+ "Number of lambdas in state is bigger then in input record");
+ GMX_RELEASE_ASSERT(
+ gmx::ssize(temperatures_) >= foreignTerms.numLambdas(),
+ "Number of lambdas in energy data is bigger then in input record");
/* MRS: is this right, given the way we have defined the exchange probabilities? */
/* is this even useful to have at all? */
- md->dE[i] += (md->temperatures[i]/
- md->temperatures[state->fep_state]-1.0)*
- enerd->term[F_EKIN];
+ dE_[i] += (temperatures_[i] / temperatures_[fep_state] - 1.0) * enerd->term[F_EKIN];
}
}
- if (md->fp_dhdl)
+ if (fp_dhdl_)
{
- fprintf(md->fp_dhdl, "%.4f", time);
+ fprintf(fp_dhdl_, "%.4f", time);
/* the current free energy state */
/* print the current state if we are doing expanded ensemble */
- if (expand->elmcmove > elmcmoveNO)
+ if (haveFepLambdaMoves_)
{
- fprintf(md->fp_dhdl, " %4d", state->fep_state);
+ fprintf(fp_dhdl_, " %4d", fep_state);
}
/* total energy (for if the temperature changes */
- if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
+ if (fep->edHdLPrintEnergy != FreeEnergyPrintEnergy::No)
{
switch (fep->edHdLPrintEnergy)
{
- case edHdLPrintEnergyPOTENTIAL:
+ case FreeEnergyPrintEnergy::Potential:
store_energy = enerd->term[F_EPOT];
break;
- case edHdLPrintEnergyTOTAL:
- case edHdLPrintEnergyYES:
- default:
- store_energy = enerd->term[F_ETOT];
+ case FreeEnergyPrintEnergy::Total:
+ case FreeEnergyPrintEnergy::Yes:
+ default: store_energy = enerd->term[F_ETOT];
}
- fprintf(md->fp_dhdl, " %#.8g", store_energy);
+ fprintf(fp_dhdl_, " %#.8g", store_energy);
}
- if (fep->dhdl_derivatives == edhdlderivativesYES)
+ if (fep->dhdl_derivatives == DhDlDerivativeCalculation::Yes)
{
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
- fprintf(md->fp_dhdl, " %#.8g", enerd->term[F_DVDL+i]);
+ fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL + static_cast<int>(i)]);
}
}
}
for (int i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
- fprintf(md->fp_dhdl, " %#.8g", md->dE[i]);
+ fprintf(fp_dhdl_, " %#.8g", dE_[i]);
}
- if (md->bDynBox &&
- md->bDiagPres &&
- (md->epc != epcNO) &&
- !enerd->enerpart_lambda.empty() &&
- (fep->init_lambda < 0))
+ if (bDynBox_ && bDiagPres_ && (epc_ != PressureCoupling::No)
+ && foreignTerms.numLambdas() > 0 && (fep->init_lambda < 0))
{
- fprintf(md->fp_dhdl, " %#.8g", pv); /* PV term only needed when
- there are alternate state
- lambda and we're not in
- compatibility mode */
+ fprintf(fp_dhdl_, " %#.8g", pv); /* PV term only needed when
+ there are alternate state
+ lambda and we're not in
+ compatibility mode */
}
- fprintf(md->fp_dhdl, "\n");
+ fprintf(fp_dhdl_, "\n");
/* and the binary free energy output */
}
- if (md->dhc && bDoDHDL)
+ if (dhc_ && bDoDHDL)
{
int idhdl = 0;
- for (int i = 0; i < efptNR; i++)
+ for (auto i : keysOf(fep->separate_dvdl))
{
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
- store_dhdl[idhdl] = enerd->term[F_DVDL+i];
- idhdl += 1;
+ store_dhdl[idhdl] = enerd->term[F_DVDL + static_cast<int>(i)];
+ idhdl += 1;
}
}
store_energy = enerd->term[F_ETOT];
/* store_dh is dE */
- mde_delta_h_coll_add_dh(md->dhc,
- static_cast<double>(state->fep_state),
+ mde_delta_h_coll_add_dh(dhc_.get(),
+ static_cast<double>(fep_state),
store_energy,
pv,
store_dhdl,
- md->dE + fep->lambda_start_n,
+ dE_.data() + fep->lambda_start_n,
time);
}
}
-}
-
-} // namespace
-void EnergyOutput::recordNonEnergyStep()
-{
- ebin_increase_count(mdebin->ebin, false);
-}
-
-namespace
-{
-
-//! Legacy output function
-void npr(FILE *log, int n, char c)
-{
- for (; (n > 0); n--)
+ if (conservedEnergyTracker_)
{
- fprintf(log, "%c", c);
+ conservedEnergyTracker_->addPoint(
+ time, bEner_[F_ECONSERVED] ? enerd->term[F_ECONSERVED] : enerd->term[F_ETOT]);
}
}
-//! Legacy output function
-void pprint(FILE *log, const char *s, t_mdebin *md)
+void EnergyOutput::recordNonEnergyStep()
{
- char CHAR = '#';
- int slen;
- char buf1[22], buf2[22];
-
- slen = strlen(s);
- fprintf(log, "\t<====== ");
- npr(log, slen, CHAR);
- fprintf(log, " ==>\n");
- fprintf(log, "\t<==== %s ====>\n", s);
- fprintf(log, "\t<== ");
- npr(log, slen, CHAR);
- fprintf(log, " ======>\n\n");
-
- fprintf(log, "\tStatistics over %s steps using %s frames\n",
- gmx_step_str(md->ebin->nsteps_sim, buf1),
- gmx_step_str(md->ebin->nsum_sim, buf2));
- fprintf(log, "\n");
+ ebin_increase_count(1, ebin_, false);
}
-} // namespace
-
-void print_ebin_header(FILE *log, int64_t steps, double time)
+void EnergyOutput::printHeader(FILE* log, int64_t steps, double time)
{
char buf[22];
- fprintf(log, " %12s %12s\n"
+ fprintf(log,
+ " %12s %12s\n"
" %12s %12.5f\n\n",
- "Step", "Time", gmx_step_str(steps, buf), time);
+ "Step",
+ "Time",
+ gmx_step_str(steps, buf),
+ time);
}
-namespace
-{
-
-// TODO It is too many responsibilities for this function to handle
-// both .edr and .log output for both per-time and time-average data.
-//! Legacy ebin output function
-void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
- FILE *log,
- int64_t step, double time,
- int mode,
- t_mdebin *md, t_fcdata *fcd,
- SimulationGroups *groups, t_grpopts *opts,
- gmx::Awh *awh)
+void EnergyOutput::printStepToEnergyFile(ener_file* fp_ene,
+ bool bEne,
+ bool bDR,
+ bool bOR,
+ FILE* log,
+ int64_t step,
+ double time,
+ t_fcdata* fcd,
+ gmx::Awh* awh)
{
- /*static char **grpnms=NULL;*/
- char buf[246];
- int i, j, n, ni, nj, b;
- int ndisre = 0;
-
+ t_enxframe fr;
+ init_enxframe(&fr);
+ fr.t = time;
+ fr.step = step;
+ fr.nsteps = ebin_->nsteps;
+ fr.dt = delta_t_;
+ fr.nsum = ebin_->nsum;
+ fr.nre = (bEne) ? ebin_->nener : 0;
+ fr.ener = ebin_->e;
+ int ndisre = bDR ? fcd->disres->npair : 0;
/* these are for the old-style blocks (1 subblock, only reals), because
there can be only one per ID for these */
- int nr[enxNR];
- int id[enxNR];
- real *block[enxNR];
-
- t_enxframe fr;
+ int nr[enxNR];
+ int id[enxNR];
+ real* block[enxNR];
+ /* Optional additional old-style (real-only) blocks. */
+ for (int i = 0; i < enxNR; i++)
+ {
+ nr[i] = 0;
+ }
- if (mode == eprAVER && md->ebin->nsum_sim <= 0)
+ if (bOR && fcd->orires)
{
- if (log)
- {
- fprintf(log, "Not enough data recorded to report energy averages\n");
- }
- return;
+ t_oriresdata& orires = *fcd->orires;
+ diagonalize_orires_tensors(&orires);
+ nr[enxOR] = orires.numRestraints;
+ block[enxOR] = orires.orientationsTimeAndEnsembleAv.data();
+ id[enxOR] = enxOR;
+ nr[enxORI] = (orires.orientations.data() != orires.orientationsTimeAndEnsembleAv.data())
+ ? orires.numRestraints
+ : 0;
+ block[enxORI] = orires.orientations.data();
+ id[enxORI] = enxORI;
+ nr[enxORT] = ssize(orires.eigenOutput);
+ block[enxORT] = orires.eigenOutput.data();
+ id[enxORT] = enxORT;
}
- switch (mode)
- {
- case eprNORMAL:
- init_enxframe(&fr);
- fr.t = time;
- fr.step = step;
- fr.nsteps = md->ebin->nsteps;
- fr.dt = md->delta_t;
- fr.nsum = md->ebin->nsum;
- fr.nre = (bEne) ? md->ebin->nener : 0;
- fr.ener = md->ebin->e;
- ndisre = bDR ? fcd->disres.npair : 0;
- /* Optional additional old-style (real-only) blocks. */
- for (i = 0; i < enxNR; i++)
- {
- nr[i] = 0;
- }
- if (bOR && fcd->orires.nr > 0)
+ /* whether we are going to write anything out: */
+ if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
+ {
+ /* the old-style blocks go first */
+ fr.nblock = 0;
+ for (int i = 0; i < enxNR; i++)
+ {
+ if (nr[i] > 0)
{
- diagonalize_orires_tensors(&(fcd->orires));
- nr[enxOR] = fcd->orires.nr;
- block[enxOR] = fcd->orires.otav;
- id[enxOR] = enxOR;
- nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
- fcd->orires.nr : 0;
- block[enxORI] = fcd->orires.oinsl;
- id[enxORI] = enxORI;
- nr[enxORT] = fcd->orires.nex*12;
- block[enxORT] = fcd->orires.eig;
- id[enxORT] = enxORT;
+ fr.nblock = i + 1;
}
-
- /* whether we are going to wrte anything out: */
- if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
- {
-
- /* the old-style blocks go first */
- fr.nblock = 0;
- for (i = 0; i < enxNR; i++)
- {
- if (nr[i] > 0)
- {
- fr.nblock = i + 1;
- }
- }
- add_blocks_enxframe(&fr, fr.nblock);
- for (b = 0; b < fr.nblock; b++)
- {
- add_subblocks_enxblock(&(fr.block[b]), 1);
- fr.block[b].id = id[b];
- fr.block[b].sub[0].nr = nr[b];
+ }
+ add_blocks_enxframe(&fr, fr.nblock);
+ for (int b = 0; b < fr.nblock; b++)
+ {
+ add_subblocks_enxblock(&(fr.block[b]), 1);
+ fr.block[b].id = id[b];
+ fr.block[b].sub[0].nr = nr[b];
#if !GMX_DOUBLE
- fr.block[b].sub[0].type = xdr_datatype_float;
- fr.block[b].sub[0].fval = block[b];
+ fr.block[b].sub[0].type = XdrDataType::Float;
+ fr.block[b].sub[0].fval = block[b];
#else
- fr.block[b].sub[0].type = xdr_datatype_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
- }
+ }
- /* check for disre block & fill it. */
- if (ndisre > 0)
- {
- int db = fr.nblock;
- fr.nblock += 1;
- add_blocks_enxframe(&fr, fr.nblock);
-
- add_subblocks_enxblock(&(fr.block[db]), 2);
- fr.block[db].id = enxDISRE;
- fr.block[db].sub[0].nr = ndisre;
- fr.block[db].sub[1].nr = ndisre;
+ /* check for disre block & fill it. */
+ if (ndisre > 0)
+ {
+ int db = fr.nblock;
+ fr.nblock += 1;
+ add_blocks_enxframe(&fr, fr.nblock);
+
+ add_subblocks_enxblock(&(fr.block[db]), 2);
+ const t_disresdata& disres = *fcd->disres;
+ fr.block[db].id = enxDISRE;
+ fr.block[db].sub[0].nr = ndisre;
+ fr.block[db].sub[1].nr = ndisre;
#if !GMX_DOUBLE
- fr.block[db].sub[0].type = xdr_datatype_float;
- fr.block[db].sub[1].type = xdr_datatype_float;
- fr.block[db].sub[0].fval = fcd->disres.rt;
- fr.block[db].sub[1].fval = fcd->disres.rm3tav;
+ fr.block[db].sub[0].type = XdrDataType::Float;
+ fr.block[db].sub[1].type = XdrDataType::Float;
+ fr.block[db].sub[0].fval = disres.rt;
+ fr.block[db].sub[1].fval = disres.rm3tav;
#else
- fr.block[db].sub[0].type = xdr_datatype_double;
- fr.block[db].sub[1].type = xdr_datatype_double;
- fr.block[db].sub[0].dval = fcd->disres.rt;
- fr.block[db].sub[1].dval = fcd->disres.rm3tav;
+ fr.block[db].sub[0].type = XdrDataType::Double;
+ fr.block[db].sub[1].type = XdrDataType::Double;
+ fr.block[db].sub[0].dval = disres.rt;
+ fr.block[db].sub[1].dval = disres.rm3tav;
#endif
- }
- /* here we can put new-style blocks */
+ }
+ /* here we can put new-style blocks */
- /* Free energy perturbation blocks */
- if (md->dhc)
- {
- mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
- }
+ /* Free energy perturbation blocks */
+ if (dhc_)
+ {
+ mde_delta_h_coll_handle_block(dhc_.get(), &fr, fr.nblock);
+ }
- /* we can now free & reset the data in the blocks */
- if (md->dhc)
- {
- mde_delta_h_coll_reset(md->dhc);
- }
+ /* we can now free & reset the data in the blocks */
+ if (dhc_)
+ {
+ mde_delta_h_coll_reset(dhc_.get());
+ }
- /* AWH bias blocks. */
- if (awh != nullptr) // TODO: add boolean in t_mdebin. See in mdebin.h.
- {
- awh->writeToEnergyFrame(step, &fr);
- }
+ /* AWH bias blocks. */
+ if (awh != nullptr) // TODO: add boolean flag.
+ {
+ awh->writeToEnergyFrame(step, &fr);
+ }
- /* do the actual I/O */
- do_enx(fp_ene, &fr);
- if (fr.nre)
- {
- /* We have stored the sums, so reset the sum history */
- reset_ebin_sums(md->ebin);
- }
- }
- free_enxframe(&fr);
- break;
- case eprAVER:
- if (log)
- {
- pprint(log, "A V E R A G E S", md);
- }
- break;
- case eprRMS:
- if (log)
- {
- pprint(log, "R M S - F L U C T U A T I O N S", md);
- }
- break;
- default:
- gmx_fatal(FARGS, "Invalid print mode (%d)", mode);
+ /* do the actual I/O */
+ do_enx(fp_ene, &fr);
+ if (fr.nre)
+ {
+ /* We have stored the sums, so reset the sum history */
+ reset_ebin_sums(ebin_);
+ }
+ }
+ free_enxframe(&fr);
+ if (log)
+ {
+ if (bOR && fcd->orires)
+ {
+ print_orires_log(log, fcd->orires.get());
+ }
+
+ fprintf(log, " Energies (%s)\n", unit_energy);
+ pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprNORMAL, true);
+ fprintf(log, "\n");
}
+}
+void EnergyOutput::printAnnealingTemperatures(FILE* log, const SimulationGroups* groups, const t_grpopts* opts)
+{
if (log)
{
if (opts)
{
- for (i = 0; i < opts->ngtc; i++)
+ for (int i = 0; i < opts->ngtc; i++)
{
- if (opts->annealing[i] != eannNO)
+ if (opts->annealing[i] != SimulatedAnnealing::No)
{
- fprintf(log, "Current ref_t for group %s: %8.1f\n",
+ fprintf(log,
+ "Current ref_t for group %s: %8.1f\n",
*(groups->groupNames[groups->groups[SimulationAtomGroupType::TemperatureCoupling][i]]),
opts->ref_t[i]);
}
}
+ fprintf(log, "\n");
}
- if (mode == eprNORMAL && bOR && fcd->orires.nr > 0)
+ }
+}
+
+void EnergyOutput::printAverages(FILE* log, const SimulationGroups* groups)
+{
+ if (ebin_->nsum_sim <= 0)
+ {
+ if (log)
{
- print_orires_log(log, &(fcd->orires));
+ fprintf(log, "Not enough data recorded to report energy averages\n");
}
+ return;
+ }
+ if (log)
+ {
+
+ char buf1[22], buf2[22];
+
+ fprintf(log, "\t<====== ############### ==>\n");
+ fprintf(log, "\t<==== A V E R A G E S ====>\n");
+ fprintf(log, "\t<== ############### ======>\n\n");
+
+ fprintf(log,
+ "\tStatistics over %s steps using %s frames\n",
+ gmx_step_str(ebin_->nsteps_sim, buf1),
+ gmx_step_str(ebin_->nsum_sim, buf2));
+ fprintf(log, "\n");
+
fprintf(log, " Energies (%s)\n", unit_energy);
- pr_ebin(log, md->ebin, md->ie, md->f_nre+md->nCrmsd, 5, mode, TRUE);
+ pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprAVER, true);
fprintf(log, "\n");
- if (mode == eprAVER)
+ if (bDynBox_)
{
- if (md->bDynBox)
- {
- pr_ebin(log, md->ebin, md->ib, md->bTricl ? NTRICLBOXS : NBOXS, 5,
- mode, TRUE);
- fprintf(log, "\n");
- }
- if (md->bConstrVir)
- {
- fprintf(log, " Constraint Virial (%s)\n", unit_energy);
- pr_ebin(log, md->ebin, md->isvir, 9, 3, mode, FALSE);
- fprintf(log, "\n");
- fprintf(log, " Force Virial (%s)\n", unit_energy);
- pr_ebin(log, md->ebin, md->ifvir, 9, 3, mode, FALSE);
- fprintf(log, "\n");
- }
- if (md->bPres)
- {
- fprintf(log, " Total Virial (%s)\n", unit_energy);
- pr_ebin(log, md->ebin, md->ivir, 9, 3, mode, FALSE);
- fprintf(log, "\n");
- fprintf(log, " Pressure (%s)\n", unit_pres_bar);
- pr_ebin(log, md->ebin, md->ipres, 9, 3, mode, FALSE);
- fprintf(log, "\n");
- }
- if (md->bMu)
- {
- fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
- pr_ebin(log, md->ebin, md->imu, 3, 3, mode, FALSE);
- fprintf(log, "\n");
- }
+ pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5, eprAVER, true);
+ fprintf(log, "\n");
+ }
+ if (bPres_)
+ {
+ fprintf(log, " Total Virial (%s)\n", unit_energy);
+ pr_ebin(log, ebin_, ivir_, 9, 3, eprAVER, false);
+ fprintf(log, "\n");
+ fprintf(log, " Pressure (%s)\n", unit_pres_bar);
+ pr_ebin(log, ebin_, ipres_, 9, 3, eprAVER, false);
+ fprintf(log, "\n");
+ }
+ if (bMu_)
+ {
+ fprintf(log, " Total Dipole (%s)\n", unit_dipole_D);
+ pr_ebin(log, ebin_, imu_, 3, 3, eprAVER, false);
+ fprintf(log, "\n");
+ }
- if (md->nE > 1)
+ if (nE_ > 1)
+ {
+ int padding = 8 - strlen(unit_energy);
+ fprintf(log, "%*sEpot (%s) ", padding, "", unit_energy);
+ for (auto key : keysOf(bEInd_))
{
- if (md->print_grpnms == nullptr)
+ if (bEInd_[key])
{
- snew(md->print_grpnms, md->nE);
- n = 0;
- for (i = 0; (i < md->nEg); i++)
- {
- ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
- for (j = i; (j < md->nEg); j++)
- {
- nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
- sprintf(buf, "%s-%s", *(groups->groupNames[ni]),
- *(groups->groupNames[nj]));
- md->print_grpnms[n++] = gmx_strdup(buf);
- }
- }
- }
- sprintf(buf, "Epot (%s)", unit_energy);
- fprintf(log, "%15s ", buf);
- for (i = 0; (i < egNR); i++)
- {
- if (md->bEInd[i])
- {
- fprintf(log, "%12s ", egrp_nm[i]);
- }
+ fprintf(log, "%12s ", enumValueToString(key));
}
- fprintf(log, "\n");
- for (i = 0; (i < md->nE); i++)
- {
- fprintf(log, "%15s", md->print_grpnms[i]);
- pr_ebin(log, md->ebin, md->igrp[i], md->nEc, md->nEc, mode,
- FALSE);
- }
- fprintf(log, "\n");
- }
- if (md->nTC > 1)
- {
- pr_ebin(log, md->ebin, md->itemp, md->nTC, 4, mode, TRUE);
- fprintf(log, "\n");
}
- if (md->nU > 1)
+ fprintf(log, "\n");
+
+ int n = 0;
+ for (int i = 0; (i < nEg_); i++)
{
- fprintf(log, "%15s %12s %12s %12s\n",
- "Group", "Ux", "Uy", "Uz");
- for (i = 0; (i < md->nU); i++)
+ int ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
+ for (int j = i; (j < nEg_); j++)
{
- ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
- fprintf(log, "%15s", *groups->groupNames[ni]);
- pr_ebin(log, md->ebin, md->iu+3*i, 3, 3, mode, FALSE);
+ int nj = groups->groups[SimulationAtomGroupType::EnergyOutput][j];
+ int padding =
+ 14 - (strlen(*(groups->groupNames[ni])) + strlen(*(groups->groupNames[nj])));
+ fprintf(log, "%*s%s-%s", padding, "", *(groups->groupNames[ni]), *(groups->groupNames[nj]));
+ pr_ebin(log, ebin_, igrp_[n], nEc_, nEc_, eprAVER, false);
+ n++;
}
- fprintf(log, "\n");
}
+ fprintf(log, "\n");
+ }
+ if (nTC_ > 1)
+ {
+ pr_ebin(log, ebin_, itemp_, nTC_, 4, eprAVER, true);
+ fprintf(log, "\n");
}
}
-
}
-//! Legacy update function
-void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin)
+void EnergyOutput::fillEnergyHistory(energyhistory_t* enerhist) const
{
- const t_ebin * const ebin = mdebin->ebin;
+ const t_ebin* const ebin = ebin_;
enerhist->nsteps = ebin->nsteps;
enerhist->nsum = ebin->nsum;
enerhist->ener_sum_sim[i] = ebin->e_sim[i].esum;
}
}
- if (mdebin->dhc)
+ if (dhc_)
{
- mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
+ mde_delta_h_coll_update_energyhistory(dhc_.get(), enerhist);
}
}
-//! Legacy restore function
-void restore_energyhistory_from_state(t_mdebin * mdebin,
- const energyhistory_t * enerhist)
+void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t& enerhist)
{
- unsigned int nener = static_cast<unsigned int>(mdebin->ebin->nener);
+ unsigned int nener = static_cast<unsigned int>(ebin_->nener);
- GMX_RELEASE_ASSERT(enerhist, "Need valid history to restore");
-
- if ((enerhist->nsum > 0 && nener != enerhist->ener_sum.size()) ||
- (enerhist->nsum_sim > 0 && nener != enerhist->ener_sum_sim.size()))
+ if ((enerhist.nsum > 0 && nener != enerhist.ener_sum.size())
+ || (enerhist.nsum_sim > 0 && nener != enerhist.ener_sum_sim.size()))
{
- gmx_fatal(FARGS, "Mismatch between number of energies in run input (%u) and checkpoint file (%zu or %zu).",
- nener, enerhist->ener_sum.size(), enerhist->ener_sum_sim.size());
+ gmx_fatal(FARGS,
+ "Mismatch between number of energies in run input (%u) and checkpoint file (%zu "
+ "or %zu).",
+ nener,
+ enerhist.ener_sum.size(),
+ enerhist.ener_sum_sim.size());
}
- mdebin->ebin->nsteps = enerhist->nsteps;
- mdebin->ebin->nsum = enerhist->nsum;
- mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
- mdebin->ebin->nsum_sim = enerhist->nsum_sim;
+ ebin_->nsteps = enerhist.nsteps;
+ ebin_->nsum = enerhist.nsum;
+ ebin_->nsteps_sim = enerhist.nsteps_sim;
+ ebin_->nsum_sim = enerhist.nsum_sim;
- for (int i = 0; i < mdebin->ebin->nener; i++)
+ for (int i = 0; i < ebin_->nener; i++)
{
- mdebin->ebin->e[i].eav =
- (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
- mdebin->ebin->e[i].esum =
- (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
- mdebin->ebin->e_sim[i].esum =
- (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
+ ebin_->e[i].eav = (enerhist.nsum > 0 ? enerhist.ener_ave[i] : 0);
+ ebin_->e[i].esum = (enerhist.nsum > 0 ? enerhist.ener_sum[i] : 0);
+ ebin_->e_sim[i].esum = (enerhist.nsum_sim > 0 ? enerhist.ener_sum_sim[i] : 0);
}
- if (mdebin->dhc)
+ if (dhc_)
{
- mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist->deltaHForeignLambdas.get());
+ mde_delta_h_coll_restore_energyhistory(dhc_.get(), enerhist.deltaHForeignLambdas.get());
}
}
-} // namespace
-
-EnergyOutput::EnergyOutput()
- : mdebin(nullptr)
-{
-}
-
-void EnergyOutput::prepare(ener_file *fp_ene,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- const pull_t *pull_work,
- FILE *fp_dhdl,
- bool isRerun)
-{
- mdebin = init_mdebin(fp_ene, mtop, ir, pull_work, fp_dhdl, isRerun);
-}
-
-EnergyOutput::~EnergyOutput()
-{
- done_mdebin(mdebin);
-}
-
-t_ebin *EnergyOutput::getEbin()
-{
- return mdebin->ebin;
-}
-
-void EnergyOutput::addDataAtEnergyStep(bool bDoDHDL,
- bool bSum,
- double time,
- real tmass,
- gmx_enerdata_t *enerd,
- t_state *state,
- t_lambda *fep,
- t_expanded *expand,
- matrix box,
- tensor svir,
- tensor fvir,
- tensor vir,
- tensor pres,
- gmx_ekindata_t *ekind,
- rvec mu_tot,
- const gmx::Constraints *constr)
-{
- upd_mdebin(mdebin, bDoDHDL, bSum, time, tmass, enerd, state, fep,
- expand, box, svir, fvir, vir, pres, ekind, mu_tot, constr);
-}
-
-void EnergyOutput::printStepToEnergyFile(ener_file *fp_ene, bool bEne, bool bDR, bool bOR,
- FILE *log,
- int64_t step, double time,
- int mode,
- t_fcdata *fcd,
- SimulationGroups *groups, t_grpopts *opts,
- gmx::Awh *awh)
-{
- print_ebin(fp_ene, bEne, bDR, bOR, log, step, time, mode,
- mdebin, fcd, groups, opts, awh);
-}
-
int EnergyOutput::numEnergyTerms() const
{
- return mdebin->ebin->nener;
+ return ebin_->nener;
}
-void EnergyOutput::fillEnergyHistory(energyhistory_t *enerhist) const
+void EnergyOutput::printEnergyConservation(FILE* fplog, int simulationPart, bool usingMdIntegrator) const
{
- update_energyhistory(enerhist, mdebin);
-}
+ if (fplog == nullptr)
+ {
+ return;
+ }
-void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t &enerhist)
-{
- restore_energyhistory_from_state(mdebin, &enerhist);
+ if (conservedEnergyTracker_)
+ {
+ std::string partName = formatString("simulation part #%d", simulationPart);
+ fprintf(fplog, "\n%s\n", conservedEnergyTracker_->energyDriftString(partName).c_str());
+ }
+ else if (usingMdIntegrator)
+ {
+ fprintf(fplog,
+ "\nCannot report drift of the conserved energy quantity because simulations share "
+ "state\n\n");
+ }
}
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff