//! Labels for energy file quantities
//! \{
-static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
+static const char* conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
-static std::array<const char *, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
+static std::array<const char*, 3> boxs_nm = { "Box-X", "Box-Y", "Box-Z" };
-static std::array<const char *, 6> tricl_boxs_nm = {
- "Box-XX", "Box-YY", "Box-ZZ",
- "Box-YX", "Box-ZX", "Box-ZY"
-};
+static std::array<const char*, 6> tricl_boxs_nm = { "Box-XX", "Box-YY", "Box-ZZ",
+ "Box-YX", "Box-ZX", "Box-ZY" };
-static const char *vol_nm[] = { "Volume" };
+static const char* vol_nm[] = { "Volume" };
-static const char *dens_nm[] = {"Density" };
+static const char* dens_nm[] = { "Density" };
-static const char *pv_nm[] = {"pV" };
+static const char* pv_nm[] = { "pV" };
-static const char *enthalpy_nm[] = {"Enthalpy" };
+static const char* enthalpy_nm[] = { "Enthalpy" };
-static 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"
-};
+static 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" };
-const char *egrp_nm[egNR+1] = {
- "Coul-SR", "LJ-SR", "Buck-SR",
- "Coul-14", "LJ-14", nullptr
-};
+const char* egrp_nm[egNR + 1] = { "Coul-SR", "LJ-SR", "Buck-SR", "Coul-14", "LJ-14", nullptr };
//! \}
namespace gmx
* \todo Remove GMX_CONSTRAINTVIR
* \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 * ir,
- const pull_t * pull_work,
- FILE * fp_dhdl,
+EnergyOutput::EnergyOutput(ener_file* fp_ene,
+ const gmx_mtop_t* mtop,
+ const t_inputrec* ir,
+ const pull_t* pull_work,
+ FILE* fp_dhdl,
bool isRerun,
- const MdModulesNotifier &mdModulesNotifier)
+ const MdModulesNotifier& mdModulesNotifier)
{
- 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;
- int i, j, ni, nj, n, k, kk, ncon, nset;
- bool bBHAM, b14;
+ 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;
+ int i, j, ni, nj, n, k, kk, ncon, nset;
+ bool bBHAM, b14;
if (EI_DYNAMICS(ir->eI))
{
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);
-
- 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;
+ 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);
+ bool bConstr = (ncon > 0 || nset > 0) && !isRerun;
+ bConstrVir_ = false;
+ nCrmsd_ = 0;
if (bConstr)
{
if (ncon > 0 && ir->eConstrAlg == econtLINCS)
// are not vsite terms (not VSITE2, VSITE3, VSITE3FD, VSITE3FAD, VSITE3OUT, VSITE4FD, VSITE4FDN, or VSITEN)
for (i = 0; i < F_NRE; i++)
{
- bEner_[i] = (gmx_mtop_ftype_count(mtop, i) > 0) &&
- ((interaction_function[i].flags & IF_VSITE) == 0);
+ bEner_[i] = (gmx_mtop_ftype_count(mtop, i) > 0)
+ && ((interaction_function[i].flags & IF_VSITE) == 0);
}
if (!isRerun)
{
- bEner_[F_EKIN] = EI_DYNAMICS(ir->eI);
- bEner_[F_ETOT] = EI_DYNAMICS(ir->eI);
- bEner_[F_TEMP] = EI_DYNAMICS(ir->eI);
+ bEner_[F_EKIN] = EI_DYNAMICS(ir->eI);
+ bEner_[F_ETOT] = EI_DYNAMICS(ir->eI);
+ bEner_[F_TEMP] = EI_DYNAMICS(ir->eI);
- bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(ir);
- bEner_[F_PDISPCORR] = (ir->eDispCorr != edispcNO);
- bEner_[F_PRES] = true;
+ bEner_[F_ECONSERVED] = integratorHasConservedEnergyQuantity(ir);
+ bEner_[F_PDISPCORR] = (ir->eDispCorr != edispcNO);
+ bEner_[F_PRES] = true;
}
- bEner_[F_LJ] = !bBHAM;
- bEner_[F_BHAM] = bBHAM;
- bEner_[F_EQM] = ir->bQMMM;
- bEner_[F_RF_EXCL] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
- bEner_[F_COUL_RECIP] = EEL_FULL(ir->coulombtype);
- bEner_[F_LJ_RECIP] = EVDW_PME(ir->vdwtype);
- bEner_[F_LJ14] = b14;
- bEner_[F_COUL14] = b14;
- bEner_[F_LJC14_Q] = false;
- bEner_[F_LJC_PAIRS_NB] = false;
+ bEner_[F_LJ] = !bBHAM;
+ bEner_[F_BHAM] = bBHAM;
+ bEner_[F_EQM] = ir->bQMMM;
+ bEner_[F_RF_EXCL] = (EEL_RF(ir->coulombtype) && ir->cutoff_scheme == ecutsGROUP);
+ bEner_[F_COUL_RECIP] = EEL_FULL(ir->coulombtype);
+ bEner_[F_LJ_RECIP] = EVDW_PME(ir->vdwtype);
+ bEner_[F_LJ14] = b14;
+ bEner_[F_COUL14] = b14;
+ bEner_[F_LJC14_Q] = false;
+ bEner_[F_LJC_PAIRS_NB] = false;
bEner_[F_DVDL_COUL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptCOUL];
bEner_[F_DKDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptMASS];
bEner_[F_DVDL] = (ir->efep != efepNO) && ir->fepvals->separate_dvdl[efptFEP];
- bEner_[F_CONSTR] = false;
- bEner_[F_CONSTRNC] = false;
- bEner_[F_SETTLE] = false;
+ bEner_[F_CONSTR] = false;
+ bEner_[F_CONSTRNC] = false;
+ bEner_[F_SETTLE] = false;
- bEner_[F_COUL_SR] = true;
- bEner_[F_EPOT] = true;
+ bEner_[F_COUL_SR] = true;
+ bEner_[F_EPOT] = true;
- bEner_[F_DISPCORR] = (ir->eDispCorr != edispcNO);
- 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] = ((ir->bPull && pull_have_potential(pull_work)) || ir->bRot);
+ bEner_[F_DISPCORR] = (ir->eDispCorr != edispcNO);
+ 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] = ((ir->bPull && pull_have_potential(pull_work)) || ir->bRot);
MdModulesEnergyOutputToDensityFittingRequestChecker mdModulesAddOutputToDensityFittingFieldRequest;
mdModulesNotifier.notifier_.notify(&mdModulesAddOutputToDensityFittingFieldRequest);
epc_ = isRerun ? epcNO : ir->epc;
bDiagPres_ = !TRICLINIC(ir->ref_p) && !isRerun;
- ref_p_ = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
+ ref_p_ = (ir->ref_p[XX][XX] + ir->ref_p[YY][YY] + ir->ref_p[ZZ][ZZ]) / DIM;
bTricl_ = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
bDynBox_ = inputrecDynamicBox(ir);
etc_ = isRerun ? etcNO : ir->etc;
bMu_ = inputrecNeedMutot(ir);
bPres_ = !isRerun;
- ebin_ = mk_ebin();
+ ebin_ = mk_ebin();
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
- ie_ = get_ebin_space(ebin_, f_nre_, ener_nm, nullptr);
+ ie_ = get_ebin_space(ebin_, f_nre_, ener_nm, nullptr);
if (nCrmsd_)
{
/* This should be called directly after the call for ie_,
}
if (bDynBox_)
{
- 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);
+ 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_)
{
- ipv_ = get_ebin_space(ebin_, 1, pv_nm, unit_energy);
- ienthalpy_ = get_ebin_space(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 (bConstrVir_)
{
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);
+ isurft_ = get_ebin_space(ebin_, asize(surft_nm), surft_nm, unit_surft_bar);
}
if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
{
- ipc_ = get_ebin_space(ebin_, bTricl_ ? boxvel_nm.size() : DIM,
- boxvel_nm.data(), unit_vel);
+ ipc_ = get_ebin_space(ebin_, bTricl_ ? boxvel_nm.size() : DIM, boxvel_nm.data(), unit_vel);
}
if (bMu_)
{
- imu_ = get_ebin_space(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)
{
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);
+ ivisc_ = get_ebin_space(ebin_, asize(visc_nm), visc_nm, unit_invvisc_SI);
}
/* Energy monitoring */
bEInd_[i] = false;
}
bEInd_[egCOULSR] = true;
- bEInd_[egLJSR ] = true;
+ bEInd_[egLJSR] = true;
if (bBHAM)
{
nEc_++;
}
}
- n = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
- nEg_ = n;
- nE_ = (n*(n+1))/2;
+ n = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
+ nEg_ = n;
+ nE_ = (n * (n + 1)) / 2;
snew(igrp_, nE_);
if (nE_ > 1)
{
if (bEInd_[k])
{
- sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
- *(groups->groupNames[ni]), *(groups->groupNames[nj]));
+ sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k], *(groups->groupNames[ni]),
+ *(groups->groupNames[nj]));
kk++;
}
}
- igrp_[n] = get_ebin_space(ebin_, nEc_,
- gnm, unit_energy);
+ igrp_[n] = get_ebin_space(ebin_, nEc_, gnm, unit_energy);
n++;
}
}
nNHC_ = ir->opts.nhchainlength; /* shorthand for number of NH chains */
if (bMTTK_)
{
- 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
{
{
if (bNHC_trotter_)
{
- mde_n_ = 2*nNHC_*nTC_;
+ mde_n_ = 2 * nNHC_ * nTC_;
}
else
{
- mde_n_ = 2*nTC_;
+ mde_n_ = 2 * nTC_;
}
if (epc_ == epcMTTK)
{
- mdeb_n_ = 2*nNHC_*nTCP_;
+ mdeb_n_ = 2 * nNHC_ * nTCP_;
}
}
else
snew(tmp_r_, mde_n_);
// TODO redo the group name memory management to make it more clear
- char **grpnms;
+ char** grpnms;
snew(grpnms, std::max(mde_n_, mdeb_n_)); // Just in case mdeb_n_ > mde_n_
for (i = 0; (i < nTC_); i++)
sprintf(buf, "T-%s", *(groups->groupNames[ni]));
grpnms[i] = gmx_strdup(buf);
}
- itemp_ = get_ebin_space(ebin_, nTC_, grpnms,
- unit_temp_K);
+ itemp_ = get_ebin_space(ebin_, nTC_, grpnms, unit_temp_K);
for (i = 0; i < nTC_; i++)
{
sfree(grpnms[i]);
for (j = 0; (j < nNHC_); j++)
{
sprintf(buf, "Xi-%d-%s", j, bufi);
- grpnms[2*(i*nNHC_+j)] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*nNHC_+j)+1] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
}
}
- itc_ = get_ebin_space(ebin_, mde_n_,
- grpnms, unit_invtime);
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
allocated = mde_n_;
if (bMTTK_)
{
for (i = 0; (i < nTCP_); i++)
{
- bufi = baro_nm[0]; /* All barostat DOF's together for now. */
+ 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*nNHC_+j)] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j)] = gmx_strdup(buf);
sprintf(buf, "vXi-%d-%s", j, bufi);
- grpnms[2*(i*nNHC_+j)+1] = gmx_strdup(buf);
+ grpnms[2 * (i * nNHC_ + j) + 1] = gmx_strdup(buf);
}
}
- itcb_ = get_ebin_space(ebin_, mdeb_n_,
- grpnms, unit_invtime);
+ itcb_ = get_ebin_space(ebin_, mdeb_n_, grpnms, unit_invtime);
allocated = mdeb_n_;
}
}
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);
}
- itc_ = get_ebin_space(ebin_, mde_n_,
- grpnms, unit_invtime);
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, unit_invtime);
allocated = mde_n_;
}
}
}
- else if (etc_ == etcBERENDSEN || etc_ == etcYES ||
- etc_ == etcVRESCALE)
+ else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
{
for (i = 0; (i < nTC_); i++)
{
sprintf(buf, "Lamb-%s", *(groups->groupNames[ni]));
grpnms[i] = gmx_strdup(buf);
}
- itc_ = get_ebin_space(ebin_, mde_n_, grpnms, "");
- allocated = mde_n_;
+ itc_ = get_ebin_space(ebin_, mde_n_, grpnms, "");
+ allocated = mde_n_;
}
for (i = 0; i < allocated; i++)
snew(tmp_v_, nU_);
if (nU_ > 1)
{
- snew(grpnms, 3*nU_);
+ snew(grpnms, 3 * nU_);
for (i = 0; (i < nU_); i++)
{
ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
sprintf(buf, "Ux-%s", *(groups->groupNames[ni]));
- grpnms[3*i+XX] = gmx_strdup(buf);
+ grpnms[3 * i + XX] = gmx_strdup(buf);
sprintf(buf, "Uy-%s", *(groups->groupNames[ni]));
- grpnms[3*i+YY] = gmx_strdup(buf);
+ grpnms[3 * i + YY] = gmx_strdup(buf);
sprintf(buf, "Uz-%s", *(groups->groupNames[ni]));
- grpnms[3*i+ZZ] = gmx_strdup(buf);
+ grpnms[3 * i + ZZ] = gmx_strdup(buf);
}
- iu_ = get_ebin_space(ebin_, 3*nU_, grpnms, unit_vel);
- for (i = 0; i < 3*nU_; i++)
+ iu_ = get_ebin_space(ebin_, 3 * nU_, grpnms, unit_vel);
+ for (i = 0; i < 3 * nU_; i++)
{
sfree(grpnms[i]);
}
{
numTemperatures_ = 0;
}
-
}
EnergyOutput::~EnergyOutput()
* \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)
+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 j, k = 0;
+ int Nsep = 0;
for (j = 0; j < efptNR; j++)
{
str += sprintf(str, "%s", efpt_singular_names[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";
+ *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;
+ 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;
- bool write_pV = false;
+ 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++)
{
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);
}
if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
- 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,
+ 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);
}
}
if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
{
- nsets += 1; /*add fep state for expanded ensemble */
+ nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
- nsets += 1; /* add energy to the dhdl as well */
+ nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
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);
break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
- default:
- energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
+ default: energy = gmx::formatString("%s (%s)", "Total Energy", unit_energy);
}
setname[s++] = energy;
}
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, efpt_singular_names[i], lam);
}
setname[s++] = derivative;
}
if (expand->elmcmove > elmcmoveNO)
{
- nsetsbegin = 1; /* for including the expanded ensemble */
+ nsetsbegin = 1; /* for including the expanded ensemble */
}
else
{
{
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;
}
bool bSum,
double time,
real tmass,
- const gmx_enerdata_t *enerd,
- const t_state *state,
- const t_lambda *fep,
- const t_expanded *expand,
+ const gmx_enerdata_t* enerd,
+ const t_state* state,
+ const t_lambda* fep,
+ const t_expanded* expand,
const matrix box,
const tensor svir,
const tensor fvir,
const tensor vir,
const tensor pres,
- const gmx_ekindata_t *ekind,
+ const gmx_ekindata_t* ekind,
const rvec mu_tot,
- const gmx::Constraints *constr)
+ const gmx::Constraints* constr)
{
int j, k, kk, n, gid;
real crmsd[2], tmp6[6];
bs[2] = box[ZZ][ZZ];
nboxs = boxs_nm.size();
}
- vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
- dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
+ vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
+ dens = (tmass * AMU) / (vol * NANO * NANO * NANO);
add_ebin(ebin_, ib_, nboxs, bs, bSum);
add_ebin(ebin_, ivol_, 1, &vol, bSum);
add_ebin(ebin_, idens_, 1, &dens, bSum);
{
/* This is pV (in kJ/mol). The pressure is the reference pressure,
not the instantaneous pressure */
- pv = vol*ref_p_/PRESFAC;
+ pv = vol * ref_p_ / PRESFAC;
add_ebin(ebin_, ipv_, 1, &pv, bSum);
enthalpy = pv + enerd->term[F_ETOT];
{
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];
+ tmp = (pres[ZZ][ZZ] - (pres[XX][XX] + pres[YY][YY]) * 0.5) * box[ZZ][ZZ];
add_ebin(ebin_, isurft_, 1, &tmp, bSum);
}
if (epc_ == epcPARRINELLORAHMAN || epc_ == epcMTTK)
}
if (ekind && ekind->cosacc.cos_accel != 0)
{
- vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
- dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
+ vol = box[XX][XX] * box[YY][YY] * box[ZZ][ZZ];
+ dens = (tmass * AMU) / (vol * NANO * NANO * 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)));
+ tmp = 1
+ / (ekind->cosacc.cos_accel / (ekind->cosacc.vcos * PICO) * dens
+ * gmx::square(box[ZZ][ZZ] * NANO / (2 * M_PI)));
add_ebin(ebin_, ivisc_, 1, &tmp, bSum);
}
if (nE_ > 1)
{
for (j = 0; j < nNHC_; j++)
{
- k = i*nNHC_+j;
- tmp_r_[2*k] = state->nosehoover_xi[k];
- tmp_r_[2*k+1] = state->nosehoover_vxi[k];
+ k = i * nNHC_ + j;
+ tmp_r_[2 * k] = state->nosehoover_xi[k];
+ tmp_r_[2 * k + 1] = state->nosehoover_vxi[k];
}
}
add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
{
for (j = 0; j < nNHC_; j++)
{
- k = i*nNHC_+j;
- tmp_r_[2*k] = state->nhpres_xi[k];
- tmp_r_[2*k+1] = state->nhpres_vxi[k];
+ k = i * nNHC_ + j;
+ tmp_r_[2 * k] = state->nhpres_xi[k];
+ tmp_r_[2 * k + 1] = state->nhpres_vxi[k];
}
}
add_ebin(ebin_, itcb_, mdeb_n_, tmp_r_, bSum);
{
for (int i = 0; (i < nTC_); i++)
{
- tmp_r_[2*i] = state->nosehoover_xi[i];
- tmp_r_[2*i+1] = state->nosehoover_vxi[i];
+ tmp_r_[2 * i] = state->nosehoover_xi[i];
+ tmp_r_[2 * i + 1] = state->nosehoover_vxi[i];
}
add_ebin(ebin_, itc_, mde_n_, tmp_r_, bSum);
}
}
}
- else if (etc_ == etcBERENDSEN || etc_ == etcYES ||
- etc_ == etcVRESCALE)
+ else if (etc_ == etcBERENDSEN || etc_ == etcYES || etc_ == etcVRESCALE)
{
for (int i = 0; (i < nTC_); i++)
{
{
copy_rvec(ekind->grpstat[i].u, tmp_v_[i]);
}
- add_ebin(ebin_, iu_, 3*nU_, tmp_v_[0], bSum);
+ add_ebin(ebin_, iu_, 3 * nU_, tmp_v_[0], bSum);
}
ebin_increase_count(1, ebin_, bSum);
for (gmx::index i = 0; i < static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1; i++)
{
/* zero for simulated tempering */
- dE_[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
+ dE_[i] = enerd->enerpart_lambda[i + 1] - enerd->enerpart_lambda[0];
if (numTemperatures_ > 0)
{
- GMX_RELEASE_ASSERT(numTemperatures_ > state->fep_state, "Number of lambdas in state is bigger then in input record");
- GMX_RELEASE_ASSERT(numTemperatures_ >= static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1, "Number of lambdas in energy data is bigger then in input record");
+ GMX_RELEASE_ASSERT(numTemperatures_ > state->fep_state,
+ "Number of lambdas in state is bigger then in input record");
+ GMX_RELEASE_ASSERT(
+ numTemperatures_ >= static_cast<gmx::index>(enerd->enerpart_lambda.size()) - 1,
+ "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? */
- dE_[i] += (temperatures_[i]/
- temperatures_[state->fep_state]-1.0)*
- enerd->term[F_EKIN];
+ dE_[i] += (temperatures_[i] / temperatures_[state->fep_state] - 1.0) * enerd->term[F_EKIN];
}
}
{
switch (fep->edHdLPrintEnergy)
{
- case edHdLPrintEnergyPOTENTIAL:
- store_energy = enerd->term[F_EPOT];
- break;
+ case edHdLPrintEnergyPOTENTIAL: store_energy = enerd->term[F_EPOT]; break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
- default:
- store_energy = enerd->term[F_ETOT];
+ default: store_energy = enerd->term[F_ETOT];
}
fprintf(fp_dhdl_, " %#.8g", store_energy);
}
if (fep->separate_dvdl[i])
{
/* assumes F_DVDL is first */
- fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL+i]);
+ fprintf(fp_dhdl_, " %#.8g", enerd->term[F_DVDL + i]);
}
}
}
{
fprintf(fp_dhdl_, " %#.8g", dE_[i]);
}
- if (bDynBox_ &&
- bDiagPres_ &&
- (epc_ != epcNO) &&
- !enerd->enerpart_lambda.empty() &&
- (fep->init_lambda < 0))
+ if (bDynBox_ && bDiagPres_ && (epc_ != epcNO) && !enerd->enerpart_lambda.empty()
+ && (fep->init_lambda < 0))
{
- fprintf(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(fp_dhdl_, "\n");
/* and the binary free energy output */
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 + i];
+ idhdl += 1;
}
}
store_energy = enerd->term[F_ETOT];
/* store_dh is dE */
- mde_delta_h_coll_add_dh(dhc_,
- static_cast<double>(state->fep_state),
- store_energy,
- pv,
- store_dhdl,
- dE_ + fep->lambda_start_n,
- time);
+ mde_delta_h_coll_add_dh(dhc_, static_cast<double>(state->fep_state), store_energy, pv,
+ store_dhdl, dE_ + fep->lambda_start_n, time);
}
}
- ;
}
void EnergyOutput::recordNonEnergyStep()
ebin_increase_count(1, ebin_, false);
}
-void EnergyOutput::printHeader(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);
}
-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)
+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)
{
- t_enxframe fr;
+ 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;
+ 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];
+ int nr[enxNR];
+ int id[enxNR];
+ real* block[enxNR];
/* Optional additional old-style (real-only) blocks. */
for (int i = 0; i < enxNR; i++)
{
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;
+ 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;
+ nr[enxORT] = fcd->orires.nex * 12;
block[enxORT] = fcd->orires.eig;
id[enxORT] = enxORT;
}
fr.block[b].sub[0].type = xdr_datatype_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 = xdr_datatype_double;
+ fr.block[b].sub[0].dval = block[b];
#endif
}
}
/* AWH bias blocks. */
- if (awh != nullptr) // TODO: add boolean flag.
+ if (awh != nullptr) // TODO: add boolean flag.
{
awh->writeToEnergyFrame(step, &fr);
}
}
fprintf(log, " Energies (%s)\n", unit_energy);
- pr_ebin(log, ebin_, ie_, f_nre_+nCrmsd_, 5, eprNORMAL, true);
+ pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprNORMAL, true);
fprintf(log, "\n");
}
}
-void EnergyOutput::printAnnealingTemperatures(FILE *log, SimulationGroups *groups, t_grpopts *opts)
+void EnergyOutput::printAnnealingTemperatures(FILE* log, SimulationGroups* groups, t_grpopts* opts)
{
if (log)
{
}
}
-void EnergyOutput::printAverages(FILE *log, const SimulationGroups *groups)
+void EnergyOutput::printAverages(FILE* log, const SimulationGroups* groups)
{
if (ebin_->nsum_sim <= 0)
{
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));
+ 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, ebin_, ie_, f_nre_+nCrmsd_, 5, eprAVER, true);
+ pr_ebin(log, ebin_, ie_, f_nre_ + nCrmsd_, 5, eprAVER, true);
fprintf(log, "\n");
if (bDynBox_)
{
- pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5,
- eprAVER, true);
+ pr_ebin(log, ebin_, ib_, bTricl_ ? tricl_boxs_nm.size() : boxs_nm.size(), 5, eprAVER, true);
fprintf(log, "\n");
}
if (bConstrVir_)
int ni = groups->groups[SimulationAtomGroupType::EnergyOutput][i];
for (int j = i; (j < nEg_); j++)
{
- 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]),
+ 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);
+ pr_ebin(log, ebin_, igrp_[n], nEc_, nEc_, eprAVER, false);
n++;
}
}
}
if (nU_ > 1)
{
- fprintf(log, "%15s %12s %12s %12s\n",
- "Group", "Ux", "Uy", "Uz");
+ fprintf(log, "%15s %12s %12s %12s\n", "Group", "Ux", "Uy", "Uz");
for (int i = 0; (i < nU_); i++)
{
int ni = groups->groups[SimulationAtomGroupType::Acceleration][i];
fprintf(log, "%15s", *groups->groupNames[ni]);
- pr_ebin(log, ebin_, iu_+3*i, 3, 3, eprAVER, false);
+ pr_ebin(log, ebin_, iu_ + 3 * i, 3, 3, eprAVER, false);
}
fprintf(log, "\n");
}
}
}
-void EnergyOutput::fillEnergyHistory(energyhistory_t *enerhist) const
+void EnergyOutput::fillEnergyHistory(energyhistory_t* enerhist) const
{
- const t_ebin * const ebin = ebin_;
+ const t_ebin* const ebin = ebin_;
enerhist->nsteps = ebin->nsteps;
enerhist->nsum = ebin->nsum;
}
}
-void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t &enerhist)
+void EnergyOutput::restoreFromEnergyHistory(const energyhistory_t& enerhist)
{
unsigned int nener = static_cast<unsigned int>(ebin_->nener);
- 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).",
+ 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());
}
for (int i = 0; i < ebin_->nener; i++)
{
- 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);
+ 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 (dhc_)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff