if (pcrd.params.eGeom == epullgCYL)
{
- apply_forces_cyl_grp(&pull->dyna[coord], pcrd.spatialData.cyl_dev, masses, forces.force01,
- pcrd.scalarForce, -1, f, pull->nthreads);
+ apply_forces_cyl_grp(&pull->dyna[coord],
+ pcrd.spatialData.cyl_dev,
+ masses,
+ forces.force01,
+ pcrd.scalarForce,
+ -1,
+ f,
+ pull->nthreads);
/* Sum the force along the vector and the radial force */
dvec f_tot;
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);
+ apply_forces_grp(
+ &pull->group[pcrd.params.group[0]], masses, forces.force01, -1, f, pull->nthreads);
}
apply_forces_grp(&pull->group[pcrd.params.group[1]], masses, forces.force01, 1, f, pull->nthreads);
if (pcrd.params.ngroup >= 4)
{
- apply_forces_grp(&pull->group[pcrd.params.group[2]], masses, forces.force23, -1, f,
- pull->nthreads);
- apply_forces_grp(&pull->group[pcrd.params.group[3]], masses, forces.force23, 1, f,
- pull->nthreads);
+ apply_forces_grp(
+ &pull->group[pcrd.params.group[2]], masses, forces.force23, -1, f, pull->nthreads);
+ apply_forces_grp(&pull->group[pcrd.params.group[3]], masses, forces.force23, 1, f, pull->nthreads);
}
if (pcrd.params.ngroup >= 6)
{
- apply_forces_grp(&pull->group[pcrd.params.group[4]], masses, forces.force45, -1, f,
- pull->nthreads);
- apply_forces_grp(&pull->group[pcrd.params.group[5]], masses, forces.force45, 1, f,
- pull->nthreads);
+ apply_forces_grp(
+ &pull->group[pcrd.params.group[4]], masses, forces.force45, -1, f, pull->nthreads);
+ apply_forces_grp(&pull->group[pcrd.params.group[5]], masses, forces.force45, 1, f, pull->nthreads);
}
}
}
gmx_fatal(FARGS,
"Distance between pull groups %d and %d (%f nm) is larger than 0.49 times the "
"box size (%f).\n%s",
- pcrd->params.group[groupIndex0], pcrd->params.group[groupIndex1], sqrt(dr2),
- sqrt(0.98 * 0.98 * max_dist2), pcrd->params.eGeom == epullgDIR ? "You might want to consider using \"pull-geometry = direction-periodic\" instead.\n" : "");
+ pcrd->params.group[groupIndex0],
+ pcrd->params.group[groupIndex1],
+ sqrt(dr2),
+ sqrt(0.98 * 0.98 * max_dist2),
+ pcrd->params.eGeom == epullgDIR
+ ? "You might want to consider using \"pull-geometry = "
+ "direction-periodic\" instead.\n"
+ : "");
}
if (pcrd->params.eGeom == epullgDIRPBC)
}
if (debug)
{
- fprintf(debug, "pull coord %d vector: %6.3f %6.3f %6.3f normalized: %6.3f %6.3f %6.3f\n",
- coord_ind, vec[XX], vec[YY], vec[ZZ], spatialData.vec[XX], spatialData.vec[YY],
+ fprintf(debug,
+ "pull coord %d vector: %6.3f %6.3f %6.3f normalized: %6.3f %6.3f %6.3f\n",
+ coord_ind,
+ vec[XX],
+ vec[YY],
+ vec[ZZ],
+ spatialData.vec[XX],
+ spatialData.vec[YY],
spatialData.vec[ZZ]);
}
}
pull_group_work_t* pgrp0 = &pull->group[pcrd->params.group[0]];
pull_group_work_t* pgrp1 = &pull->group[pcrd->params.group[1]];
- low_get_pull_coord_dr(pull, pcrd, pbc, pgrp1->x,
- pcrd->params.eGeom == epullgCYL ? pull->dyna[coord_ind].x : pgrp0->x, 0,
- 1, md2, spatialData.dr01);
+ low_get_pull_coord_dr(pull,
+ pcrd,
+ pbc,
+ pgrp1->x,
+ pcrd->params.eGeom == epullgCYL ? pull->dyna[coord_ind].x : pgrp0->x,
+ 0,
+ 1,
+ md2,
+ spatialData.dr01);
if (pcrd->params.ngroup >= 4)
{
{
gmx_fatal(FARGS,
"Pull reference distance for coordinate %d (%f) needs to be non-negative",
- coord_ind + 1, value_ref);
+ coord_ind + 1,
+ value_ref);
}
}
else if (pcrd->params.eGeom == epullgANGLE || pcrd->params.eGeom == epullgANGLEAXIS)
const PullCoordSpatialData& spatialData = pcrd->spatialData;
if (debug)
{
- fprintf(debug, "Pull coord %zu dr %f %f %f\n", c, spatialData.dr01[XX],
- spatialData.dr01[YY], spatialData.dr01[ZZ]);
+ fprintf(debug,
+ "Pull coord %zu dr %f %f %f\n",
+ c,
+ spatialData.dr01[XX],
+ spatialData.dr01[YY],
+ spatialData.dr01[ZZ]);
}
if (pcrd->params.eGeom == epullgDIR || pcrd->params.eGeom == epullgDIRPBC)
pgrp1 = &pull->group[pcrd->params.group[1]];
/* Get the current difference vector */
- low_get_pull_coord_dr(pull, pcrd, pbc, rnew[pcrd->params.group[1]],
- rnew[pcrd->params.group[0]], 0, 1, -1, unc_ij);
+ low_get_pull_coord_dr(
+ pull, pcrd, pbc, rnew[pcrd->params.group[1]], rnew[pcrd->params.group[0]], 0, 1, -1, unc_ij);
if (debug)
{
gmx_fatal(
FARGS,
"The pull constraint reference distance for group %zu is <= 0 (%f)",
- c, pcrd->value_ref);
+ c,
+ pcrd->value_ref);
}
{
if (debug)
{
- fprintf(debug, "Pull ax^2+bx+c=0: a=%e b=%e c=%e lambda=%e\n", c_a, c_b,
- c_c, lambda);
+ fprintf(debug, "Pull ax^2+bx+c=0: a=%e b=%e c=%e lambda=%e\n", c_a, c_b, c_c, lambda);
}
}
g1 = pcrd->params.group[1];
low_get_pull_coord_dr(pull, pcrd, pbc, rnew[g1], rnew[g0], 0, 1, -1, tmp);
low_get_pull_coord_dr(pull, pcrd, pbc, dr1, dr0, 0, 1, -1, tmp3);
- fprintf(debug, "Pull cur %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n", rnew[g0][0],
- rnew[g0][1], rnew[g0][2], rnew[g1][0], rnew[g1][1], rnew[g1][2], dnorm(tmp));
- fprintf(debug, "Pull ref %8s %8s %8s %8s %8s %8s d: %8.5f\n", "", "", "", "", "",
- "", pcrd->value_ref);
- fprintf(debug, "Pull cor %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n", dr0[0],
- dr0[1], dr0[2], dr1[0], dr1[1], dr1[2], dnorm(tmp3));
+ fprintf(debug,
+ "Pull cur %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ rnew[g0][0],
+ rnew[g0][1],
+ rnew[g0][2],
+ rnew[g1][0],
+ rnew[g1][1],
+ rnew[g1][2],
+ dnorm(tmp));
+ fprintf(debug,
+ "Pull ref %8s %8s %8s %8s %8s %8s d: %8.5f\n",
+ "",
+ "",
+ "",
+ "",
+ "",
+ "",
+ pcrd->value_ref);
+ fprintf(debug,
+ "Pull cor %8.5f %8.5f %8.5f j:%8.5f %8.5f %8.5f d: %8.5f\n",
+ dr0[0],
+ dr0[1],
+ dr0[2],
+ dr1[0],
+ dr1[1],
+ dr1[2],
+ dnorm(tmp3));
} /* END DEBUG */
/* Update the COMs with dr */
continue;
}
- low_get_pull_coord_dr(pull, &coord, pbc, rnew[coord.params.group[1]],
- rnew[coord.params.group[0]], 0, 1, -1, unc_ij);
+ low_get_pull_coord_dr(
+ pull, &coord, pbc, rnew[coord.params.group[1]], rnew[coord.params.group[0]], 0, 1, -1, unc_ij);
switch (coord.params.eGeom)
{
"Pull constraint not converged: "
"groups %d %d,"
"d_ref = %f, current d = %f\n",
- coord.params.group[0], coord.params.group[1], coord.value_ref, dnorm(unc_ij));
+ coord.params.group[0],
+ coord.params.group[1],
+ coord.value_ref,
+ dnorm(unc_ij));
}
bConverged_all = FALSE;
dist_32 = sqrdist_32 * inv_dist_32;
/* Forces on groups 0, 1 */
- a_01 = pcrd.scalarForce * dist_32 / m2; /* scalarForce is -dV/dphi */
- dsvmul(-a_01, spatialData.planevec_m,
- forces.force01); /* added sign to get force on group 1, not 0 */
+ a_01 = pcrd.scalarForce * dist_32 / m2; /* scalarForce is -dV/dphi */
+ dsvmul(-a_01, spatialData.planevec_m, forces.force01); /* added sign to get force on group 1, not 0 */
/* Forces on groups 4, 5 */
a_45 = -pcrd.scalarForce * dist_32 / n2;
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which is out of the pull coordinate range %d - %zu\n",
- provider, coord_index + 1, 1, pull->coord.size());
+ provider,
+ coord_index + 1,
+ 1,
+ pull->coord.size());
}
pull_coord_work_t* pcrd = &pull->coord[coord_index];
FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"which of type '%s', whereas external potentials are only supported with type '%s'",
- provider, coord_index + 1, epull_names[pcrd->params.eType], epull_names[epullEXTERNAL]);
+ provider,
+ coord_index + 1,
+ epull_names[pcrd->params.eType],
+ epull_names[epullEXTERNAL]);
}
GMX_RELEASE_ASSERT(!pcrd->params.externalPotentialProvider.empty(),
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.c_str());
+ provider,
+ coord_index + 1,
+ pcrd->params.externalPotentialProvider.c_str());
}
/* Lock to avoid (extremely unlikely) simultaneous reading and writing of
gmx_fatal(FARGS,
"Module '%s' attempted to register an external potential for pull coordinate %d "
"more than once",
- provider, coord_index + 1);
+ provider,
+ coord_index + 1);
}
pcrd->bExternalPotentialProviderHasBeenRegistered = true;
"No external provider for external pull potentials have been provided for %d "
"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->numUnregisteredExternalPotentials,
+ c + 1,
pull->coord[c].params.externalPotentialProvider.c_str());
}
}
forceWithVirial->addVirialContribution(virial);
}
- apply_forces_coord(pull, coord_index, pullCoordForces, masses,
- as_rvec_array(forceWithVirial->force_.data()));
+ apply_forces_coord(
+ pull, coord_index, pullCoordForces, masses, as_rvec_array(forceWithVirial->force_.data()));
}
pull->numExternalPotentialsStillToBeAppliedThisStep--;
if (debug && dd != nullptr)
{
- fprintf(debug, "Our DD rank (%3d) pull #atoms>0 or master: %s, will be part %s\n", dd->rank,
- gmx::boolToString(bMustParticipate), gmx::boolToString(bWillParticipate));
+ fprintf(debug,
+ "Our DD rank (%3d) pull #atoms>0 or master: %s, will be part %s\n",
+ dd->rank,
+ gmx::boolToString(bMustParticipate),
+ gmx::boolToString(bWillParticipate));
}
if (bWillParticipate)
}
else
{
- gmx_fatal(FARGS, "The total%s mass of pull group %d is zero",
- !pg->params.weight.empty() ? " weighted" : "", g);
+ gmx_fatal(FARGS,
+ "The total%s mass of pull group %d is zero",
+ !pg->params.weight.empty() ? " weighted" : "",
+ g);
}
}
if (fplog)
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->group.emplace_back(pull_params->group[i],
+ atomSets->add(pull_params->group[i].ind),
pull_params->bSetPbcRefToPrevStepCOM);
}
"%d in the input is larger than that supported by the code (up to %d). "
"You are probably reading a tpr file generated with a newer version of "
"Gromacs with an binary from an older version of Gromacs.",
- c + 1, pcrd->params.eGeom, epullgNR - 1);
+ c + 1,
+ pcrd->params.eGeom,
+ epullgNR - 1);
}
if (pcrd->params.eType == epullCONSTRAINT)
gmx_fatal(FARGS,
"Pulling of type %s can not be combined with geometry %s. Consider using "
"pull type %s.",
- epull_names[pcrd->params.eType], epullg_names[pcrd->params.eGeom],
+ epull_names[pcrd->params.eType],
+ epullg_names[pcrd->params.eGeom],
epull_names[epullUMBRELLA]);
}
if (pcrd->params.eType != epullEXTERNAL)
{
low_set_pull_coord_reference_value(
- pcrd, c,
- pcrd->params.init * pull_conversion_factor_userinput2internal(&pcrd->params));
+ pcrd, c, pcrd->params.init * pull_conversion_factor_userinput2internal(&pcrd->params));
}
else
{
int numRealGroups = pull->group.size() - 1;
GMX_RELEASE_ASSERT(numRealGroups > 0,
"The reference absolute position pull group should always be present");
- fprintf(fplog, "with %zu pull coordinate%s and %d group%s\n", pull->coord.size(),
- pull->coord.size() == 1 ? "" : "s", numRealGroups, numRealGroups == 1 ? "" : "s");
+ fprintf(fplog,
+ "with %zu pull coordinate%s and %d group%s\n",
+ pull->coord.size(),
+ pull->coord.size() == 1 ? "" : "s",
+ numRealGroups,
+ numRealGroups == 1 ? "" : "s");
if (bAbs)
{
fprintf(fplog, "with an absolute reference\n");
}
}
const auto& referenceGroup = pull->group[coord.params.group[0]];
- pull->dyna.emplace_back(referenceGroup.params, referenceGroup.atomSet,
- pull->params.bSetPbcRefToPrevStepCOM);
+ pull->dyna.emplace_back(
+ referenceGroup.params, referenceGroup.atomSet, pull->params.bSetPbcRefToPrevStepCOM);
}
}
{
/* Only the master rank has the checkpointed COM from the previous step */
gmx_bcast(sizeof(double) * state->pull_com_prev_step.size(),
- &state->pull_com_prev_step[0], cr->mpi_comm_mygroup);
+ &state->pull_com_prev_step[0],
+ cr->mpi_comm_mygroup);
}
setPrevStepPullComFromState(pull_work, state);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff