*/
#include "gmxpre.h"
-#include <assert.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cassert>
+#include <cstdlib>
+#include <cstring>
+#include "gromacs/domdec/localatomsetmanager.h"
#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxpreprocess/readir.h"
}
}
-char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
- pull_params_t *pull,
- warninp_t wi)
+char **read_pullparams(std::vector<t_inpfile> *inp,
+ pull_params_t *pull,
+ warninp_t wi)
{
- int ninp, nscan, idum;
- t_inpfile *inp;
- const char *tmp;
- char **grpbuf;
- char buf[STRLEN];
- char provider[STRLEN], groups[STRLEN], dim_buf[STRLEN];
- char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
+ int nscan, idum;
+ char **grpbuf;
+ char buf[STRLEN];
+ char provider[STRLEN], groups[STRLEN], dim_buf[STRLEN];
+ char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
- t_pull_group *pgrp;
- t_pull_coord *pcrd;
-
- ninp = *ninp_p;
- inp = *inp_p;
+ t_pull_group *pgrp;
+ t_pull_coord *pcrd;
/* read pull parameters */
- CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
- RTYPE("pull-cylinder-r", pull->cylinder_r, 1.5);
- RTYPE("pull-constr-tol", pull->constr_tol, 1E-6);
- EETYPE("pull-print-com", pull->bPrintCOM, yesno_names);
- EETYPE("pull-print-ref-value", pull->bPrintRefValue, yesno_names);
- EETYPE("pull-print-components", pull->bPrintComp, yesno_names);
- ITYPE("pull-nstxout", pull->nstxout, 50);
- ITYPE("pull-nstfout", pull->nstfout, 50);
- CTYPE("Number of pull groups");
- ITYPE("pull-ngroups", pull->ngroup, 1);
- CTYPE("Number of pull coordinates");
- ITYPE("pull-ncoords", pull->ncoord, 1);
+ printStringNoNewline(inp, "Cylinder radius for dynamic reaction force groups (nm)");
+ pull->cylinder_r = get_ereal(inp, "pull-cylinder-r", 1.5, wi);
+ pull->constr_tol = get_ereal(inp, "pull-constr-tol", 1E-6, wi);
+ pull->bPrintCOM = (get_eeenum(inp, "pull-print-com", yesno_names, wi) != 0);
+ pull->bPrintRefValue = (get_eeenum(inp, "pull-print-ref-value", yesno_names, wi) != 0);
+ pull->bPrintComp = (get_eeenum(inp, "pull-print-components", yesno_names, wi) != 0);
+ pull->nstxout = get_eint(inp, "pull-nstxout", 50, wi);
+ pull->nstfout = get_eint(inp, "pull-nstfout", 50, wi);
+ printStringNoNewline(inp, "Number of pull groups");
+ pull->ngroup = get_eint(inp, "pull-ngroups", 1, wi);
+ printStringNoNewline(inp, "Number of pull coordinates");
+ pull->ncoord = get_eint(inp, "pull-ncoords", 1, wi);
if (pull->ngroup < 1)
{
snew(pull->coord, pull->ncoord);
/* pull group options */
- CTYPE("Group and coordinate parameters");
+ printStringNoNewline(inp, "Group and coordinate parameters");
/* Read the pull groups */
snew(grpbuf, pull->ngroup);
pgrp = &pull->group[groupNum];
snew(grpbuf[groupNum], STRLEN);
sprintf(buf, "pull-group%d-name", groupNum);
- STYPE(buf, grpbuf[groupNum], "");
+ setStringEntry(inp, buf, grpbuf[groupNum], "");
sprintf(buf, "pull-group%d-weights", groupNum);
- STYPE(buf, wbuf, "");
+ setStringEntry(inp, buf, wbuf, "");
sprintf(buf, "pull-group%d-pbcatom", groupNum);
- ITYPE(buf, pgrp->pbcatom, 0);
+ pgrp->pbcatom = get_eint(inp, buf, 0, wi);
/* Initialize the pull group */
init_pull_group(pgrp, wbuf);
{
pcrd = &pull->coord[coordNum - 1];
sprintf(buf, "pull-coord%d-type", coordNum);
- EETYPE(buf, pcrd->eType, epull_names);
+ pcrd->eType = get_eeenum(inp, buf, epull_names, wi);
sprintf(buf, "pull-coord%d-potential-provider", coordNum);
- STYPE(buf, provider, "");
+ setStringEntry(inp, buf, provider, "");
pcrd->externalPotentialProvider = gmx_strdup(provider);
sprintf(buf, "pull-coord%d-geometry", coordNum);
- EETYPE(buf, pcrd->eGeom, epullg_names);
+ pcrd->eGeom = get_eeenum(inp, buf, epullg_names, wi);
sprintf(buf, "pull-coord%d-groups", coordNum);
- STYPE(buf, groups, "");
+ setStringEntry(inp, buf, groups, "");
switch (pcrd->eGeom)
{
}
sprintf(buf, "pull-coord%d-dim", coordNum);
- STYPE(buf, dim_buf, "Y Y Y");
+ setStringEntry(inp, buf, dim_buf, "Y Y Y");
sprintf(buf, "pull-coord%d-origin", coordNum);
- STYPE(buf, origin_buf, "0.0 0.0 0.0");
+ setStringEntry(inp, buf, origin_buf, "0.0 0.0 0.0");
sprintf(buf, "pull-coord%d-vec", coordNum);
- STYPE(buf, vec_buf, "0.0 0.0 0.0");
+ setStringEntry(inp, buf, vec_buf, "0.0 0.0 0.0");
sprintf(buf, "pull-coord%d-start", coordNum);
- EETYPE(buf, pcrd->bStart, yesno_names);
+ pcrd->bStart = (get_eeenum(inp, buf, yesno_names, wi) != 0);
sprintf(buf, "pull-coord%d-init", coordNum);
- RTYPE(buf, pcrd->init, 0.0);
+ pcrd->init = get_ereal(inp, buf, 0.0, wi);
sprintf(buf, "pull-coord%d-rate", coordNum);
- RTYPE(buf, pcrd->rate, 0.0);
+ pcrd->rate = get_ereal(inp, buf, 0.0, wi);
sprintf(buf, "pull-coord%d-k", coordNum);
- RTYPE(buf, pcrd->k, 0.0);
+ pcrd->k = get_ereal(inp, buf, 0.0, wi);
sprintf(buf, "pull-coord%d-kB", coordNum);
- RTYPE(buf, pcrd->kB, pcrd->k);
+ pcrd->kB = get_ereal(inp, buf, pcrd->k, wi);
/* Initialize the pull coordinate */
init_pull_coord(pcrd, coordNum, dim_buf, origin_buf, vec_buf, wi);
}
- *ninp_p = ninp;
- *inp_p = inp;
-
return grpbuf;
}
pull_t *set_pull_init(t_inputrec *ir, const gmx_mtop_t *mtop,
rvec *x, matrix box, real lambda,
- const gmx_output_env_t *oenv,
warninp_t wi)
{
pull_params_t *pull;
double t_start;
pull = ir->pull;
- pull_work = init_pull(nullptr, pull, ir, 0, nullptr, mtop, nullptr, oenv, lambda, FALSE, ContinuationOptions());
- auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
- auto md = mdAtoms->mdatoms();
+ gmx::LocalAtomSetManager atomSets;
+ pull_work = init_pull(nullptr, pull, ir, mtop, nullptr, &atomSets, lambda);
+ auto mdAtoms = gmx::makeMDAtoms(nullptr, *mtop, *ir, false);
+ auto md = mdAtoms->mdatoms();
atoms2md(mtop, ir, -1, nullptr, mtop->natoms, mdAtoms.get());
if (ir->efep)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff