/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Obtain the maximum and minimum coordinates of the group to be embedded */
static int init_ins_at(t_block *ins_at, t_block *rest_at, t_state *state, pos_ins_t *pos_ins,
- gmx_groups_t *groups, int ins_grp_id, real xy_max)
+ SimulationGroups *groups, int ins_grp_id, real xy_max)
{
int i, gid, c = 0;
real xmin, xmax, ymin, ymax, zmin, zmax;
for (i = 0; i < state->natoms; i++)
{
- gid = groups->grpnr[egcFREEZE][i];
- if (groups->grps[egcFREEZE].nm_ind[gid] == ins_grp_id)
+ gid = groups->groupNumbers[SimulationAtomGroupType::Freeze][i];
+ if (groups->groups[SimulationAtomGroupType::Freeze].nm_ind[gid] == ins_grp_id)
{
xmin = std::min(xmin, x[i][XX]);
xmax = std::max(xmax, x[i][XX]);
}
/*remove all lipids and waters overlapping and update all important structures (e.g. state and mtop)*/
-static void rm_group(gmx_groups_t *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state,
+static void rm_group(SimulationGroups *groups, gmx_mtop_t *mtop, rm_t *rm_p, t_state *state,
t_block *ins_at, pos_ins_t *pos_ins)
{
int j, k, n, rm, mol_id, at, block;
rvec *x_tmp, *v_tmp;
int *list;
- unsigned char *new_egrp[egcNR];
+ gmx::EnumerationArray < SimulationAtomGroupType, std::vector < unsigned char>> new_egrp;
gmx_bool bRM;
int RMmolblock;
snew(x_tmp, state->natoms);
snew(v_tmp, state->natoms);
- for (int i = 0; i < egcNR; i++)
+ for (auto group : keysOf(groups->groupNumbers))
{
- if (groups->grpnr[i] != nullptr)
+ if (!groups->groupNumbers[group].empty())
{
- groups->ngrpnr[i] = state->natoms;
- snew(new_egrp[i], state->natoms);
+ groups->groupNumbers[group].resize(state->natoms);
+ new_egrp[group].resize(state->natoms);
}
}
if (!bRM)
{
- for (j = 0; j < egcNR; j++)
+ for (auto group : keysOf(groups->groupNumbers))
{
- if (groups->grpnr[j] != nullptr)
+ if (!groups->groupNumbers[group].empty())
{
- new_egrp[j][i-rm] = groups->grpnr[j][i];
+ new_egrp[group][i-rm] = groups->groupNumbers[group][i];
}
}
copy_rvec(x[i], x_tmp[i-rm]);
}
sfree(v_tmp);
- for (int i = 0; i < egcNR; i++)
+ for (auto group : keysOf(groups->groupNumbers))
{
- if (groups->grpnr[i] != nullptr)
+ if (!groups->groupNumbers[group].empty())
{
- sfree(groups->grpnr[i]);
- groups->grpnr[i] = new_egrp[i];
+ groups->groupNumbers[group] = new_egrp[group];
}
}
resize(membed->r_ins, x, membed->pos_ins, membed->fac);
}
-/* We would like gn to be const as well, but C doesn't allow this */
-/* TODO this is utility functionality (search for the index of a
- string in a collection), so should be refactored and located more
- centrally. Also, it nearly duplicates the same string in readir.c */
-static int search_string(const char *s, int ng, char *gn[])
-{
- int i;
-
- for (i = 0; (i < ng); i++)
- {
- if (gmx_strcasecmp(s, gn[i]) == 0)
- {
- return i;
- }
- }
-
- gmx_fatal(FARGS,
- "Group %s selected for embedding was not found in the index file.\n"
- "Group names must match either [moleculetype] names or custom index group\n"
- "names, in which case you must supply an index file to the '-n' option\n"
- "of grompp.",
- s);
-}
-
gmx_membed_t *init_membed(FILE *fplog, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop,
t_inputrec *inputrec, t_state *state, t_commrec *cr, real *cpt)
{
- char *ins, **gnames;
- int i, rm_bonded_at, fr_id, fr_i = 0, tmp_id, warn = 0;
- int ng, j, max_lip_rm, ins_grp_id, ntype, lip_rm;
- real prot_area;
- rvec *r_ins = nullptr;
- t_block *ins_at, *rest_at;
- pos_ins_t *pos_ins;
- mem_t *mem_p;
- rm_t *rm_p;
- gmx_groups_t *groups;
- gmx_bool bExcl = FALSE;
- t_atoms atoms;
- t_pbc *pbc;
- char **piecename = nullptr;
- gmx_membed_t *membed = nullptr;
+ char *ins;
+ int i, rm_bonded_at, fr_id, fr_i = 0, tmp_id, warn = 0;
+ int ng, j, max_lip_rm, ins_grp_id, ntype, lip_rm;
+ real prot_area;
+ rvec *r_ins = nullptr;
+ t_block *ins_at, *rest_at;
+ pos_ins_t *pos_ins;
+ mem_t *mem_p;
+ rm_t *rm_p;
+ SimulationGroups *groups;
+ gmx_bool bExcl = FALSE;
+ t_atoms atoms;
+ t_pbc *pbc;
+ char **piecename = nullptr;
+ gmx_membed_t *membed = nullptr;
/* input variables */
real xy_fac = 0.5;
*cpt = -1;
}
groups = &(mtop->groups);
- snew(gnames, groups->ngrpname);
- for (i = 0; i < groups->ngrpname; i++)
+ std::vector<std::string> gnames;
+ for (const auto &groupName : groups->groupNames)
{
- gnames[i] = *(groups->grpname[i]);
+ gnames.emplace_back(*groupName);
}
atoms = gmx_mtop_global_atoms(mtop);
snew(mem_p, 1);
fprintf(stderr, "\nSelect a group to embed in the membrane:\n");
get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(ins_at->nr), &(ins_at->index), &ins);
- ins_grp_id = search_string(ins, groups->ngrpname, gnames);
+
+ auto found = std::find_if(gnames.begin(), gnames.end(),
+ [&ins](const auto &name)
+ { return gmx::equalCaseInsensitive(ins, name); });
+
+ if (found == gnames.end())
+ {
+ gmx_fatal(FARGS,
+ "Group %s selected for embedding was not found in the index file.\n"
+ "Group names must match either [moleculetype] names or custom index group\n"
+ "names, in which case you must supply an index file to the '-n' option\n"
+ "of grompp.", ins);
+ }
+ else
+ {
+ ins_grp_id = std::distance(gnames.begin(), found);
+ }
fprintf(stderr, "\nSelect a group to embed %s into (e.g. the membrane):\n", ins);
get_index(&atoms, opt2fn_null("-mn", nfile, fnm), 1, &(mem_p->mem_at.nr), &(mem_p->mem_at.index), &(mem_p->name));
for (i = 0; i < inputrec->opts.ngfrz; i++)
{
- tmp_id = mtop->groups.grps[egcFREEZE].nm_ind[i];
+ tmp_id = mtop->groups.groups[SimulationAtomGroupType::Freeze].nm_ind[i];
if (ins_grp_id == tmp_id)
{
fr_id = tmp_id;
}
}
- ng = groups->grps[egcENER].nr;
+ ng = groups->groups[SimulationAtomGroupType::EnergyOutput].nr;
if (ng == 1)
{
gmx_input("No energy groups defined. This is necessary for energy exclusion in the freeze group");
if (inputrec->opts.egp_flags[ng*i+j] == EGP_EXCL)
{
bExcl = TRUE;
- if ( (groups->grps[egcENER].nm_ind[i] != ins_grp_id) ||
- (groups->grps[egcENER].nm_ind[j] != ins_grp_id) )
+ if ( (groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[i] != ins_grp_id) ||
+ (groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[j] != ins_grp_id) )
{
gmx_fatal(FARGS, "Energy exclusions \"%s\" and \"%s\" do not match the group "
- "to embed \"%s\"", *groups->grpname[groups->grps[egcENER].nm_ind[i]],
- *groups->grpname[groups->grps[egcENER].nm_ind[j]], ins);
+ "to embed \"%s\"", *groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[i]],
+ *groups->groupNames[groups->groups[SimulationAtomGroupType::EnergyOutput].nm_ind[j]], ins);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff