std::vector<MoleculeInformation>* mi,
std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
gmx::ArrayRef<InteractionsOfType> interactions,
- int* comb,
+ CombinationRule* comb,
double* reppow,
real* fudgeQQ,
gmx_bool bMorse,
convert_harmonics(*mi, atypes);
}
- if (ir->eDisre == edrNone)
+ if (ir->eDisre == DistanceRestraintRefinement::None)
{
i = rm_interactions(F_DISRES, *mi);
if (i > 0)
gmx::ArrayRef<const MoleculeInformation> molinfo,
gmx_bool bTopB,
const char* fn,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
warninp* wi,
npbcdim = numPbcDimensions(pbcType);
GMX_RELEASE_ASSERT(npbcdim <= DIM, "Invalid npbcdim");
clear_rvec(com);
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
copy_mat(box, invbox);
for (int j = npbcdim; j < DIM; j++)
natoms);
}
hadAtom[ai] = TRUE;
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
fn,
natoms);
}
- if (rc_scaling == erscCOM && !hadAtom[ai])
+ if (rc_scaling == RefCoordScaling::Com && !hadAtom[ai])
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
}
a += nat_molb;
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
if (totmass == 0)
{
com[ZZ]);
}
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
GMX_ASSERT(npbcdim <= DIM, "Only DIM dimensions can have PBC");
{
for (int j = 0; j < npbcdim; j++)
{
- if (rc_scaling == erscALL)
+ if (rc_scaling == RefCoordScaling::All)
{
/* Convert from Cartesian to crystal coordinates */
xp[i][j] *= invbox[j][j];
xp[i][j] += invbox[k][j] * xp[i][k];
}
}
- else if (rc_scaling == erscCOM)
+ else if (rc_scaling == RefCoordScaling::Com)
{
/* Subtract the center of mass */
xp[i][j] -= com[j];
}
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Convert the COM from Cartesian to crystal coordinates */
for (int j = 0; j < npbcdim; j++)
gmx::ArrayRef<const MoleculeInformation> mi,
const char* fnA,
const char* fnB,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
rvec comB,
const int lincsOrderThreshold = 4;
const real shakeToleranceThreshold = 0.005 * ir->delta_t;
- bool lincsWithSufficientTolerance = (ir->eConstrAlg == econtLINCS && ir->nLincsIter >= lincsIterationThreshold
- && ir->nProjOrder >= lincsOrderThreshold);
- bool shakeWithSufficientTolerance =
- (ir->eConstrAlg == econtSHAKE && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
+ bool lincsWithSufficientTolerance =
+ (ir->eConstrAlg == ConstraintAlgorithm::Lincs
+ && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
+ bool shakeWithSufficientTolerance = (ir->eConstrAlg == ConstraintAlgorithm::Shake
+ && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
&& (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
{
return;
"and with masses that differ by more than a factor of %g. This means "
"that there are likely dynamic modes that are only very weakly coupled.",
massFactorThreshold);
- if (ir->cutoff_scheme == ecutsVERLET)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet)
{
message += gmx::formatString(
" To ensure good equipartitioning, you need to either not use "
"hydrogens) or use integrator = %s or decrease one or more tolerances: "
"verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
">= %d or SHAKE tolerance <= %g",
- ei_names[eiSD1],
+ enumValueToString(IntegrationAlgorithm::SD1),
bufferToleranceThreshold,
lincsIterationThreshold,
lincsOrderThreshold,
" To ensure good equipartitioning, we suggest to switch to the %s "
"cutoff-scheme, since that allows for better control over the Verlet "
"buffer size and thus over the energy drift.",
- ecutscheme_names[ecutsVERLET]);
+ enumValueToString(CutoffScheme::Verlet));
}
warning(wi, message);
}
};
std::vector<MoleculeInformation> mi;
std::unique_ptr<MoleculeInformation> intermolecular_interactions;
- int nvsite, comb;
+ int nvsite;
+ CombinationRule comb;
real fudgeQQ;
double reppow;
const char* mdparin;
}
}
- if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == econtSHAKE))
+ if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == ConstraintAlgorithm::Shake))
{
- if (ir->eI == eiCG || ir->eI == eiLBFGS)
+ if (ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
{
- std::string warningMessage = gmx::formatString("Can not do %s with %s, use %s",
- EI(ir->eI),
- econstr_names[econtSHAKE],
- econstr_names[econtLINCS]);
+ std::string warningMessage =
+ gmx::formatString("Can not do %s with %s, use %s",
+ enumValueToString(ir->eI),
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
if (ir->bPeriodicMols)
{
std::string warningMessage =
gmx::formatString("Can not do periodic molecules with %s, use %s",
- econstr_names[econtSHAKE],
- econstr_names[econtLINCS]);
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
}
checkForUnboundAtoms(&sys, bVerbose, wi, logger);
- if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ if (EI_DYNAMICS(ir->eI) && ir->eI != IntegrationAlgorithm::BD)
{
check_bonds_timestep(&sys, ir->delta_t, wi);
}
}
do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifier(), ir, wi);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0)
{
if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
{
pr_symtab(debug, 0, "After close", &sys.symtab);
}
- if (ir->eI == eiMimic)
+ if (ir->eI == IntegrationAlgorithm::Mimic)
{
generate_qmexcl(&sys, ir, logger);
}
/* MRS: eventually figure out better logic for initializing the fep
values that makes declaring the lambda and declaring the state not
potentially conflict if not handled correctly. */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
state.fep_state = ir->fepvals->init_fep_state;
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
}
else
{
- if (ir->fepvals->all_lambda[i] == nullptr)
+ if (ir->fepvals->all_lambda[i].empty())
{
gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
}
if (ir->bPull)
{
- pull = set_pull_init(ir, &sys, state.x.rvec_array(), state.box, state.lambda[efptMASS], wi);
+ pull = set_pull_init(ir,
+ &sys,
+ state.x.rvec_array(),
+ state.box,
+ state.lambda[FreeEnergyPerturbationCouplingType::Mass],
+ wi);
}
/* Modules that supply external potential for pull coordinates
ir->pbcType,
compressibility,
&ir->opts,
- ir->efep != efepNO ? ir->fepvals->all_lambda[efptFEP][ir->fepvals->init_fep_state] : 0,
+ ir->efep != FreeEnergyPerturbationType::No
+ ? ir->fepvals->all_lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Fep)]
+ [ir->fepvals->init_fep_state]
+ : 0,
sys,
wi);
}
* charges. This will double the cost, but the optimal performance will
* then probably be at a slightly larger cut-off and grid spacing.
*/
- if ((ir->efep == efepNO && ratio > 1.0 / 2.0) || (ir->efep != efepNO && ratio > 2.0 / 3.0))
+ if ((ir->efep == FreeEnergyPerturbationType::No && ratio > 1.0 / 2.0)
+ || (ir->efep != FreeEnergyPerturbationType::No && ratio > 2.0 / 3.0))
{
warning_note(
wi,
"The optimal PME mesh load for parallel simulations is below 0.5\n"
"and for highly parallel simulations between 0.25 and 0.33,\n"
"for higher performance, increase the cut-off and the PME grid spacing.\n");
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
warning_note(wi,
"For free energy simulations, the optimal load limit increases from "
std::make_unique<gmx::KeyValueTreeObject>(internalParameterBuilder.build());
}
- if (ir->comm_mode != ecmNO)
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
{
const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
if (ir->nstcomm % nstglobalcomm != 0)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff