#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull_internal.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
/* Accumulate the forces, in case we have multiple constraint steps */
pcrd->f_scal += dr_tot[c]/((pull->group[pcrd->params.group[0]].invtm + pull->group[pcrd->params.group[1]].invtm)*dt*dt);
- if (vir != NULL && pcrd->params.eGeom != epullgDIRPBC && bMaster)
+ if (vir != nullptr && pcrd->params.eGeom != epullgDIRPBC && bMaster)
{
double f_invr;
/* Adds the pull contribution to the virial */
static void add_virial_coord(tensor vir, const pull_coord_work_t *pcrd)
{
- if (vir != NULL && pcrd->params.eGeom != epullgDIRPBC)
+ if (vir != nullptr && pcrd->params.eGeom != epullgDIRPBC)
{
/* Add the pull contribution for each distance vector to the virial. */
add_virial_coord_dr(vir, pcrd->dr01, pcrd->f01);
int coord_index,
const char *provider)
{
- GMX_RELEASE_ASSERT(pull != NULL, "register_external_pull_potential called before init_pull");
- GMX_RELEASE_ASSERT(provider != NULL, "register_external_pull_potential called with NULL as provider name");
+ GMX_RELEASE_ASSERT(pull != nullptr, "register_external_pull_potential called before init_pull");
+ GMX_RELEASE_ASSERT(provider != nullptr, "register_external_pull_potential called with NULL as provider name");
if (coord_index < 0 || coord_index > pull->ncoord - 1)
{
provider, coord_index + 1, epull_names[pcrd->params.eType], epull_names[epullEXTERNAL]);
}
- GMX_RELEASE_ASSERT(pcrd->params.externalPotentialProvider != NULL, "The external potential provider string for a pull coordinate is NULL");
+ GMX_RELEASE_ASSERT(pcrd->params.externalPotentialProvider != nullptr, "The external potential provider string for a pull coordinate is NULL");
if (gmx_strcasecmp(provider, pcrd->params.externalPotentialProvider) != 0)
{
{
real dVdl = 0;
- pull_calc_coms(cr, pull, md, pbc, t, x, NULL);
+ pull_calc_coms(cr, pull, md, pbc, t, x, nullptr);
for (int c = 0; c < pull->ncoord; c++)
{
}
do_pull_pot_coord(pull, c, pbc, t, lambda,
- &V, MASTER(cr) ? vir : NULL, &dVdl);
+ &V, MASTER(cr) ? vir : nullptr, &dVdl);
/* Distribute the force over the atoms in the pulled groups */
apply_forces_coord(pull, c, md, f);
{
pg->nalloc_loc = over_alloc_dd(pg->nat_loc+1);
srenew(pg->ind_loc, pg->nalloc_loc);
- if (pg->epgrppbc == epgrppbcCOS || pg->params.weight != NULL)
+ if (pg->epgrppbc == epgrppbcCOS || pg->params.weight != nullptr)
{
srenew(pg->weight_loc, pg->nalloc_loc);
}
}
pg->ind_loc[pg->nat_loc] = ii;
- if (pg->params.weight != NULL)
+ if (pg->params.weight != nullptr)
{
pg->weight_loc[pg->nat_loc] = pg->params.weight[i];
}
}
else
{
- ga2la = NULL;
+ ga2la = nullptr;
}
/* We always make the master node participate, such that it can do i/o
* and to simplify MC type extensions people might have.
*/
- bMustParticipate = (comm->bParticipateAll || dd == NULL || DDMASTER(dd));
+ bMustParticipate = (comm->bParticipateAll || dd == nullptr || DDMASTER(dd));
for (g = 0; g < pull->ngroup; g++)
{
(comm->bParticipate &&
comm->must_count >= comm->setup_count - history_count);
- if (debug && dd != NULL)
+ if (debug && dd != nullptr)
{
fprintf(debug, "Our DD rank (%3d) pull #atoms>0 or master: %d, will be part %d\n",
dd->rank, bMustParticipate, bWillParticipate);
const gmx_mtop_t *mtop,
const t_inputrec *ir, real lambda)
{
- int i, ii, d, nfrozen, ndim;
- real m, w, mbd;
- double tmass, wmass, wwmass;
- const gmx_groups_t *groups;
- gmx_mtop_atomlookup_t alook;
- t_atom *atom;
-
if (EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
{
/* There are no masses in the integrator.
{
pg->nat_loc = 0;
pg->nalloc_loc = 0;
- pg->ind_loc = NULL;
- pg->weight_loc = NULL;
+ pg->ind_loc = nullptr;
+ pg->weight_loc = nullptr;
}
else
{
}
}
- groups = &mtop->groups;
-
- alook = gmx_mtop_atomlookup_init(mtop);
+ const gmx_groups_t *groups = &mtop->groups;
- nfrozen = 0;
- tmass = 0;
- wmass = 0;
- wwmass = 0;
- for (i = 0; i < pg->params.nat; i++)
+ /* Count frozen dimensions and (weighted) mass */
+ int nfrozen = 0;
+ double tmass = 0;
+ double wmass = 0;
+ double wwmass = 0;
+ int molb = 0;
+ for (int i = 0; i < pg->params.nat; i++)
{
- ii = pg->params.ind[i];
- gmx_mtop_atomnr_to_atom(alook, ii, &atom);
+ int ii = pg->params.ind[i];
if (bConstraint && ir->opts.nFreeze)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
if (pulldim_con[d] == 1 &&
ir->opts.nFreeze[ggrpnr(groups, egcFREEZE, ii)][d])
}
}
}
+ const t_atom &atom = mtopGetAtomParameters(mtop, ii, &molb);
+ real m;
if (ir->efep == efepNO)
{
- m = atom->m;
+ m = atom.m;
}
else
{
- m = (1 - lambda)*atom->m + lambda*atom->mB;
+ m = (1 - lambda)*atom.m + lambda*atom.mB;
}
+ real w;
if (pg->params.nweight > 0)
{
w = pg->params.weight[i];
}
else if (ir->eI == eiBD)
{
+ real mbd;
if (ir->bd_fric)
{
mbd = ir->bd_fric*ir->delta_t;
}
else
{
- if (groups->grpnr[egcTC] == NULL)
+ if (groups->grpnr[egcTC] == nullptr)
{
mbd = ir->delta_t/ir->opts.tau_t[0];
}
wwmass += m*w*w;
}
- gmx_mtop_atomlookup_destroy(alook);
-
if (wmass == 0)
{
/* We can have single atom groups with zero mass with potential pulling
}
else
{
- ndim = 0;
- for (d = 0; d < DIM; d++)
+ int ndim = 0;
+ for (int d = 0; d < DIM; d++)
{
ndim += pulldim_con[d]*pg->params.nat;
}
/* Copy the pull parameters */
pull->params = *pull_params;
/* Avoid pointer copies */
- pull->params.group = NULL;
- pull->params.coord = NULL;
+ pull->params.group = nullptr;
+ pull->params.coord = nullptr;
pull->ncoord = pull_params->ncoord;
pull->ngroup = pull_params->ngroup;
}
else
{
- if (pgrp->params.weight != NULL)
+ if (pgrp->params.weight != nullptr)
{
gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
}
#if GMX_MPI
/* Use a sub-communicator when we have more than 32 ranks */
- comm->bParticipateAll = (cr == NULL || !DOMAINDECOMP(cr) ||
+ comm->bParticipateAll = (cr == nullptr || !DOMAINDECOMP(cr) ||
cr->dd->nnodes <= 32 ||
- getenv("GMX_PULL_PARTICIPATE_ALL") != NULL);
+ getenv("GMX_PULL_PARTICIPATE_ALL") != nullptr);
/* This sub-commicator is not used with comm->bParticipateAll,
* so we can always initialize it to NULL.
*/
comm->setup_count = 0;
comm->must_count = 0;
- if (!comm->bParticipateAll && fplog != NULL)
+ if (!comm->bParticipateAll && fplog != nullptr)
{
fprintf(fplog, "Will use a sub-communicator for pull communication\n");
}
- comm->rbuf = NULL;
- comm->dbuf = NULL;
- comm->dbuf_cyl = NULL;
+ comm->rbuf = nullptr;
+ comm->dbuf = nullptr;
+ comm->dbuf_cyl = nullptr;
/* We still need to initialize the PBC reference coordinates */
pull->bSetPBCatoms = TRUE;
/* Only do I/O when we are doing dynamics and if we are the MASTER */
- pull->out_x = NULL;
- pull->out_f = NULL;
+ pull->out_x = nullptr;
+ pull->out_f = nullptr;
if (bOutFile)
{
/* Check for px and pf filename collision, if we are writing
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff