static int groupPbcFromParams(const t_pull_group& params, bool setPbcRefToPrevStepCOM)
{
- if (params.nat <= 1)
+ if (params.ind.size() <= 1)
{
/* no PBC required */
return epgrppbcNONE;
{
auto localAtomIndices = pgrp->atomSet.localIndex();
- if (pgrp->params.nat == 1 && pgrp->atomSet.numAtomsLocal() == 1)
+ if (pgrp->params.ind.size() == 1 && pgrp->atomSet.numAtomsLocal() == 1)
{
/* Only one atom and our rank has this atom: we can skip
* the mass weighting, which means that this code also works
apply_forces_vec_torque(pull, &pcrd, masses, f);
}
- if (pull->group[pcrd.params.group[0]].params.nat > 0)
+ if (!pull->group[pcrd.params.group[0]].params.ind.empty())
{
apply_forces_grp(&pull->group[pcrd.params.group[0]], masses, forces.force01, -1, f,
pull->nthreads);
const pull_group_work_t* pgrp0 = &pull->group[pcrd->params.group[0]];
/* Only the first group can be an absolute reference, in that case nat=0 */
- if (pgrp0->params.nat == 0)
+ if (pgrp0->params.ind.empty())
{
for (int m = 0; m < DIM; m++)
{
provider, coord_index + 1, epull_names[pcrd->params.eType], epull_names[epullEXTERNAL]);
}
- GMX_RELEASE_ASSERT(pcrd->params.externalPotentialProvider != nullptr,
+ GMX_RELEASE_ASSERT(!pcrd->params.externalPotentialProvider.empty(),
"The external potential provider string for a pull coordinate is NULL");
- if (gmx_strcasecmp(provider, pcrd->params.externalPotentialProvider) != 0)
+ if (gmx_strcasecmp(provider, pcrd->params.externalPotentialProvider.c_str()) != 0)
{
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which expects the external potential to be provided by a module named '%s'",
- provider, coord_index + 1, pcrd->params.externalPotentialProvider);
+ provider, coord_index + 1, pcrd->params.externalPotentialProvider.c_str());
}
/* Lock to avoid (extremely unlikely) simultaneous reading and writing of
"pull coordinates. The first coordinate without provider is number %zu, which "
"expects a module named '%s' to provide the external potential.",
pull->numUnregisteredExternalPotentials, c + 1,
- pull->coord[c].params.externalPotentialProvider);
+ pull->coord[c].params.externalPotentialProvider.c_str());
}
}
* But we still want to have the correct mass-weighted COMs.
* So we store the real masses in the weights.
*/
- const bool setWeights = (pg->params.nweight > 0 || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD);
+ const bool setWeights =
+ (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD);
/* In parallel, store we need to extract localWeights from weights at DD time */
std::vector<real>& weights = ((cr && PAR(cr)) ? pg->globalWeights : pg->localWeights);
double wmass = 0;
double wwmass = 0;
int molb = 0;
- for (int i = 0; i < pg->params.nat; i++)
+ for (int i = 0; i < int(pg->params.ind.size()); i++)
{
int ii = pg->params.ind[i];
if (bConstraint && ir->opts.nFreeze)
m = (1 - lambda) * atom.m + lambda * atom.mB;
}
real w;
- if (pg->params.nweight > 0)
+ if (!pg->params.weight.empty())
{
w = pg->params.weight[i];
}
/* We can have single atom groups with zero mass with potential pulling
* without cosine weighting.
*/
- if (pg->params.nat == 1 && !bConstraint && pg->epgrppbc != epgrppbcCOS)
+ if (pg->params.ind.size() == 1 && !bConstraint && pg->epgrppbc != epgrppbcCOS)
{
/* With one atom the mass doesn't matter */
wwmass = 1;
else
{
gmx_fatal(FARGS, "The total%s mass of pull group %d is zero",
- pg->params.weight ? " weighted" : "", g);
+ !pg->params.weight.empty() ? " weighted" : "", g);
}
}
if (fplog)
{
- fprintf(fplog, "Pull group %d: %5d atoms, mass %9.3f", g, pg->params.nat, tmass);
- if (pg->params.weight || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
+ fprintf(fplog, "Pull group %d: %5zu atoms, mass %9.3f", g, pg->params.ind.size(), tmass);
+ if (!pg->params.weight.empty() || EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
{
fprintf(fplog, ", weighted mass %9.3f", wmass * wmass / wwmass);
}
int ndim = 0;
for (int d = 0; d < DIM; d++)
{
- ndim += pulldim_con[d] * pg->params.nat;
+ ndim += pulldim_con[d] * pg->params.ind.size();
}
if (fplog && nfrozen > 0 && nfrozen < ndim)
{
/* Copy the pull parameters */
pull->params = *pull_params;
- /* Avoid pointer copies */
- pull->params.group = nullptr;
- pull->params.coord = nullptr;
for (int i = 0; i < pull_params->ngroup; ++i)
{
- pull->group.emplace_back(pull_params->group[i],
- atomSets->add({ pull_params->group[i].ind,
- pull_params->group[i].ind + pull_params->group[i].nat }),
+ pull->group.emplace_back(pull_params->group[i], atomSets->add(pull_params->group[i].ind),
pull_params->bSetPbcRefToPrevStepCOM);
}
pull->bXOutAverage = pull_params->bXOutAverage;
pull->bFOutAverage = pull_params->bFOutAverage;
- GMX_RELEASE_ASSERT(pull->group[0].params.nat == 0,
+ GMX_RELEASE_ASSERT(pull->group[0].params.ind.empty(),
"pull group 0 is an absolute reference group and should not contain atoms");
pull->numCoordinatesWithExternalPotential = 0;
bAbs = FALSE;
for (const pull_coord_work_t& coord : pull->coord)
{
- if (pull->group[coord.params.group[0]].params.nat == 0
- || pull->group[coord.params.group[1]].params.nat == 0)
+ if (pull->group[coord.params.group[0]].params.ind.empty()
+ || pull->group[coord.params.group[1]].params.ind.empty())
{
bAbs = TRUE;
}
// Don't include the reference group 0 in loop
for (size_t g = 1; g < pull->group.size(); g++)
{
- if (pull->group[g].params.nat > 1 && pull->group[g].params.pbcatom < 0)
+ if (pull->group[g].params.ind.size() > 1 && pull->group[g].params.pbcatom < 0)
{
/* We are using cosine weighting */
fprintf(fplog, "Cosine weighting is used for group %zu\n", g);
pull_group_work_t* pgrp;
pgrp = &pull->group[g];
- if (pgrp->params.nat > 0)
+ if (!pgrp->params.ind.empty())
{
/* There is an issue when a group is used in multiple coordinates
* and constraints are applied in different dimensions with atoms
{
case epgrppbcREFAT: pull->bRefAt = TRUE; break;
case epgrppbcCOS:
- if (pgrp->params.weight != nullptr)
+ if (!pgrp->params.weight.empty())
{
gmx_fatal(FARGS,
"Pull groups can not have relative weights and cosine weighting "
{
if (coord.params.eGeom == epullgCYL)
{
- if (pull->group[coord.params.group[0]].params.nat == 0)
+ if (pull->group[coord.params.group[0]].params.ind.empty())
{
gmx_fatal(FARGS,
"A cylinder pull group is not supported when using absolute "
destroy_pull(pull);
}
-gmx_bool pull_have_potential(const struct pull_t* pull)
+bool pull_have_potential(const pull_t& pull)
{
- return pull->bPotential;
+ return pull.bPotential;
}
-gmx_bool pull_have_constraint(const struct pull_t* pull)
+bool pull_have_constraint(const pull_t& pull)
{
- return pull->bConstraint;
+ return pull.bConstraint;
}
-bool pull_have_constraint(const pull_params_t* pullParameters)
+bool pull_have_constraint(const pull_params_t& pullParameters)
{
- if (pullParameters == nullptr)
+ for (int c = 0; c < pullParameters.ncoord; c++)
{
- return false;
- }
- for (int c = 0; c < pullParameters->ncoord; c++)
- {
- if (pullParameters->coord[c].eType == epullCONSTRAINT)
+ if (pullParameters.coord[c].eType == epullCONSTRAINT)
{
return true;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff