/*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * This file is part of the GROMACS molecular simulation package.
+ *
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, 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.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
- *
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
- * inclusion in the official distribution, but derived work must not
- * be called official GROMACS. Details are found in the README & COPYING
- * files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
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+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
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+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
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+ *
* To help us fund GROMACS development, we humbly ask that you cite
- * the papers on the package - you can find them in the top README file.
- *
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- *
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- * GROwing Monsters And Cloning Shrimps
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <stdlib.h>
-#include "sysstuff.h"
-#include "princ.h"
-#include "futil.h"
-#include "statutil.h"
-#include "vec.h"
-#include "smalloc.h"
-#include "typedefs.h"
-#include "names.h"
-#include "gmx_fatal.h"
-#include "macros.h"
-#include "rdgroup.h"
-#include "symtab.h"
-#include "readinp.h"
-#include "readir.h"
#include <string.h>
-#include "mdatoms.h"
-#include "pbc.h"
-#include "pull.h"
+
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
static char pulldim[STRLEN];
-static void string2dvec(char buf[], dvec nums)
+static void string2dvec(const char buf[], dvec nums)
+{
+ double dum;
+
+ if (sscanf(buf, "%lf%lf%lf%lf", &nums[0], &nums[1], &nums[2], &dum) != 3)
+ {
+ gmx_fatal(FARGS, "Expected three numbers at input line %s", buf);
+ }
+}
+
+static void init_pull_group(t_pull_group *pg,
+ const char *wbuf)
{
- if (sscanf(buf,"%lf%lf%lf",&nums[0],&nums[1],&nums[2]) != 3)
- gmx_fatal(FARGS,"Expected three numbers at input line %s",buf);
+ double d;
+ int n, m;
+
+ pg->nweight = 0;
+ while (sscanf(wbuf, "%lf %n", &d, &n) == 1)
+ {
+ if (pg->nweight % 100 == 0)
+ {
+ srenew(pg->weight, pg->nweight+100);
+ }
+ pg->weight[pg->nweight++] = d;
+ wbuf += n;
+ }
}
-static void init_pullgrp(t_pullgrp *pg,char *wbuf,
- gmx_bool bRef,int eGeom,char *s_vec)
+static void init_pull_coord(t_pull_coord *pcrd, int eGeom,
+ const char *origin_buf, const char *vec_buf)
{
- double d;
- int n,m;
- dvec vec;
-
- pg->nweight = 0;
- while (sscanf(wbuf,"%lf %n",&d,&n) == 1) {
- if (pg->nweight % 100 == 0) {
- srenew(pg->weight,pg->nweight+100);
+ int m;
+ dvec origin, vec;
+
+ string2dvec(origin_buf, origin);
+ if (pcrd->group[0] != 0 && dnorm(origin) > 0)
+ {
+ gmx_fatal(FARGS, "The pull origin can only be set with an absolute reference");
+ }
+
+ if (eGeom == epullgDIST)
+ {
+ clear_dvec(vec);
+ }
+ else
+ {
+ string2dvec(vec_buf, vec);
+ if (eGeom == epullgDIR || eGeom == epullgCYL)
+ {
+ /* Normalize the direction vector */
+ dsvmul(1/dnorm(vec), vec, vec);
+ }
}
- pg->weight[pg->nweight++] = d;
- wbuf += n;
- }
- if (!bRef) {
- if (eGeom == epullgDIST) {
- clear_dvec(vec);
- } else {
- string2dvec(s_vec,vec);
- if (eGeom == epullgDIR || eGeom == epullgCYL ||
- (eGeom == epullgPOS && dnorm(vec) != 0))
- /* Normalize the direction vector */
- dsvmul(1/dnorm(vec),vec,vec);
+ for (m = 0; m < DIM; m++)
+ {
+ pcrd->origin[m] = origin[m];
+ pcrd->vec[m] = vec[m];
}
- for(m=0; m<DIM; m++)
- pg->vec[m] = vec[m];
- }
}
-char **read_pullparams(int *ninp_p,t_inpfile **inp_p,
- t_pull *pull,gmx_bool *bStart,
- warninp_t wi)
+char **read_pullparams(int *ninp_p, t_inpfile **inp_p,
+ t_pull *pull, gmx_bool *bStart,
+ warninp_t wi)
{
- int ninp,nerror=0,i,nchar,ndim,nscan,m;
- t_inpfile *inp;
- const char *tmp;
- char **grpbuf;
- char dummy[STRLEN],buf[STRLEN],init[STRLEN];
- const char *init_def1="0.0",*init_def3="0.0 0.0 0.0";
- char wbuf[STRLEN],VecTemp[STRLEN];
- dvec vec;
-
- t_pullgrp *pgrp;
-
- ninp = *ninp_p;
- inp = *inp_p;
-
- /* read pull parameters */
- CTYPE("Pull geometry: distance, direction, cylinder or position");
- EETYPE("pull_geometry", pull->eGeom, epullg_names);
- CTYPE("Select components for the pull vector. default: Y Y Y");
- STYPE("pull_dim", pulldim, "Y Y Y");
- CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
- RTYPE("pull_r1", pull->cyl_r1, 1.0);
- CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
- RTYPE("pull_r0", pull->cyl_r0, 1.5);
- RTYPE("pull_constr_tol", pull->constr_tol, 1E-6);
- EETYPE("pull_start", *bStart, yesno_names);
- ITYPE("pull_nstxout", pull->nstxout, 10);
- ITYPE("pull_nstfout", pull->nstfout, 1);
- CTYPE("Number of pull groups");
- ITYPE("pull_ngroups", pull->ngrp,1);
-
- if (pull->cyl_r1 > pull->cyl_r0) {
- warning_error(wi,"pull_r1 > pull_r0");
- }
-
- if (pull->ngrp < 1) {
- gmx_fatal(FARGS,"pull_ngroups should be >= 1");
- }
-
- snew(pull->grp,pull->ngrp+1);
-
- if (pull->eGeom == epullgPOS) {
- ndim = 3;
- } else {
- ndim = 1;
- }
-
- /* pull group options */
- CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
- /* Read the pull groups */
- snew(grpbuf,pull->ngrp+1);
- for(i=0; i<pull->ngrp+1; i++) {
- pgrp = &pull->grp[i];
- snew(grpbuf[i],STRLEN);
- sprintf(buf,"pull_group%d",i);
- STYPE(buf, grpbuf[i], "");
- sprintf(buf,"pull_weights%d",i);
- STYPE(buf, wbuf, "");
- sprintf(buf,"pull_pbcatom%d",i);
- ITYPE(buf, pgrp->pbcatom, 0);
- if (i > 0) {
- sprintf(buf,"pull_vec%d",i);
- STYPE(buf, VecTemp, "0.0 0.0 0.0");
- sprintf(buf,"pull_init%d",i);
- STYPE(buf, init, ndim==1 ? init_def1 : init_def3);
- nscan = sscanf(init,"%lf %lf %lf",&vec[0],&vec[1],&vec[2]);
- if (nscan != ndim) {
- fprintf(stderr,"ERROR: %s should have %d components\n",buf,ndim);
- nerror++;
- }
- for(m=0; m<DIM; m++) {
- pgrp->init[m] = (m<ndim ? vec[m] : 0.0);
- }
- sprintf(buf,"pull_rate%d",i);
- RTYPE(buf, pgrp->rate, 0.0);
- sprintf(buf,"pull_k%d",i);
- RTYPE(buf, pgrp->k, 0.0);
- sprintf(buf,"pull_kB%d",i);
- RTYPE(buf, pgrp->kB, pgrp->k);
+ int ninp, nerror = 0, i, nchar, nscan, m, idum;
+ t_inpfile *inp;
+ const char *tmp;
+ char **grpbuf;
+ char dummy[STRLEN], buf[STRLEN], groups[STRLEN], init[STRLEN];
+ const char *init_def1 = "0.0", *init_def3 = "0.0 0.0 0.0";
+ char wbuf[STRLEN], origin_buf[STRLEN], vec_buf[STRLEN];
+
+ t_pull_group *pgrp;
+ t_pull_coord *pcrd;
+
+ ninp = *ninp_p;
+ inp = *inp_p;
+
+ /* read pull parameters */
+ CTYPE("Pull geometry: distance, direction, direction-periodic or cylinder");
+ EETYPE("pull-geometry", pull->eGeom, epullg_names);
+ CTYPE("Select components for the pull vector. default: Y Y Y");
+ STYPE("pull-dim", pulldim, "Y Y Y");
+ CTYPE("Cylinder radius for dynamic reaction force groups (nm)");
+ RTYPE("pull-r1", pull->cyl_r1, 1.0);
+ CTYPE("Switch from r1 to r0 in case of dynamic reaction force");
+ RTYPE("pull-r0", pull->cyl_r0, 1.5);
+ RTYPE("pull-constr-tol", pull->constr_tol, 1E-6);
+ EETYPE("pull-start", *bStart, yesno_names);
+ EETYPE("pull-print-reference", pull->bPrintRef, yesno_names);
+ ITYPE("pull-nstxout", pull->nstxout, 10);
+ ITYPE("pull-nstfout", pull->nstfout, 1);
+ CTYPE("Number of pull groups");
+ ITYPE("pull-ngroups", pull->ngroup, 1);
+ CTYPE("Number of pull coordinates");
+ ITYPE("pull-ncoords", pull->ncoord, 1);
+
+ if (pull->cyl_r1 > pull->cyl_r0)
+ {
+ warning_error(wi, "pull-r1 > pull_r0");
+ }
+
+ if (pull->ngroup < 1)
+ {
+ gmx_fatal(FARGS, "pull-ngroups should be >= 1");
+ }
+ /* We always add an absolute reference group (index 0), even if not used */
+ pull->ngroup += 1;
+
+ if (pull->ncoord < 1)
+ {
+ gmx_fatal(FARGS, "pull-ncoords should be >= 1");
+ }
+
+ snew(pull->group, pull->ngroup);
+
+ snew(pull->coord, pull->ncoord);
+
+ /* pull group options */
+ CTYPE("Group name, weight (default all 1), vector, init, rate (nm/ps), kJ/(mol*nm^2)");
+
+ /* Read the pull groups */
+ snew(grpbuf, pull->ngroup);
+ /* Group 0 is the absolute reference, we don't read anything for 0 */
+ for (i = 1; i < pull->ngroup; i++)
+ {
+ pgrp = &pull->group[i];
+ snew(grpbuf[i], STRLEN);
+ sprintf(buf, "pull-group%d-name", i);
+ STYPE(buf, grpbuf[i], "");
+ sprintf(buf, "pull-group%d-weights", i);
+ STYPE(buf, wbuf, "");
+ sprintf(buf, "pull-group%d-pbcatom", i);
+ ITYPE(buf, pgrp->pbcatom, 0);
+
+ /* Initialize the pull group */
+ init_pull_group(pgrp, wbuf);
+ }
+
+ /* Read the pull coordinates */
+ for (i = 1; i < pull->ncoord + 1; i++)
+ {
+ pcrd = &pull->coord[i-1];
+ sprintf(buf, "pull-coord%d-groups", i);
+ STYPE(buf, groups, "");
+ nscan = sscanf(groups, "%d %d %d", &pcrd->group[0], &pcrd->group[1], &idum);
+ if (nscan != 2)
+ {
+ fprintf(stderr, "ERROR: %s should have %d components\n", buf, 2);
+ nerror++;
+ }
+ sprintf(buf, "pull-coord%d-origin", i);
+ STYPE(buf, origin_buf, "0.0 0.0 0.0");
+ sprintf(buf, "pull-coord%d-vec", i);
+ STYPE(buf, vec_buf, "0.0 0.0 0.0");
+ sprintf(buf, "pull-coord%d-init", i);
+ RTYPE(buf, pcrd->init, 0.0);
+ sprintf(buf, "pull-coord%d-rate", i);
+ RTYPE(buf, pcrd->rate, 0.0);
+ sprintf(buf, "pull-coord%d-k", i);
+ RTYPE(buf, pcrd->k, 0.0);
+ sprintf(buf, "pull-coord%d-kB", i);
+ RTYPE(buf, pcrd->kB, pcrd->k);
+
+ /* Initialize the pull coordinate */
+ init_pull_coord(pcrd, pull->eGeom, origin_buf, vec_buf);
}
- /* Initialize the pull group */
- init_pullgrp(pgrp,wbuf,i==0,pull->eGeom,VecTemp);
- }
-
- *ninp_p = ninp;
- *inp_p = inp;
+ *ninp_p = ninp;
+ *inp_p = inp;
- return grpbuf;
+ return grpbuf;
}
-void make_pull_groups(t_pull *pull,char **pgnames,t_blocka *grps,char **gnames)
+void make_pull_groups(t_pull *pull,
+ char **pgnames,
+ const t_blocka *grps, char **gnames)
{
- int d,nchar,g,ig=-1,i;
- char *ptr,pulldim1[STRLEN];
- t_pullgrp *pgrp;
-
- ptr = pulldim;
- i = 0;
- for(d=0; d<DIM; d++) {
- if (sscanf(ptr,"%s%n",pulldim1,&nchar) != 1)
- gmx_fatal(FARGS,"Less than 3 pull dimensions given in pull_dim: '%s'",
- pulldim);
-
- if (gmx_strncasecmp(pulldim1,"N",1) == 0) {
- pull->dim[d] = 0;
- } else if (gmx_strncasecmp(pulldim1,"Y",1) == 0) {
- pull->dim[d] = 1;
- i++;
- } else {
- gmx_fatal(FARGS,"Please use Y(ES) or N(O) for pull_dim only (not %s)",
- pulldim1);
+ int g, ig = -1, i;
+ t_pull_group *pgrp;
+
+ /* Absolute reference group (might not be used) is special */
+ pgrp = &pull->group[0];
+ pgrp->nat = 0;
+ pgrp->pbcatom = -1;
+
+ for (g = 1; g < pull->ngroup; g++)
+ {
+ pgrp = &pull->group[g];
+
+ if (strcmp(pgnames[g], "") == 0)
+ {
+ gmx_fatal(FARGS, "Group pull_group%d required by grompp was undefined.", g);
+ }
+
+ ig = search_string(pgnames[g], grps->nr, gnames);
+ pgrp->nat = grps->index[ig+1] - grps->index[ig];
+
+ fprintf(stderr, "Pull group %d '%s' has %d atoms\n",
+ g, pgnames[g], pgrp->nat);
+
+ if (pgrp->nat == 0)
+ {
+ gmx_fatal(FARGS, "Pull group %d '%s' is empty", g, pgnames[g]);
+ }
+
+ snew(pgrp->ind, pgrp->nat);
+ for (i = 0; i < pgrp->nat; i++)
+ {
+ pgrp->ind[i] = grps->a[grps->index[ig]+i];
+ }
+
+ if (pull->eGeom == epullgCYL && g == 1 && pgrp->nweight > 0)
+ {
+ gmx_fatal(FARGS, "Weights are not supported for the reference group with cylinder pulling");
+ }
+ if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
+ {
+ gmx_fatal(FARGS, "Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
+ pgrp->nweight, g, pgnames[g], pgrp->nat);
+ }
+
+ if (pgrp->nat == 1)
+ {
+ /* No pbc is required for this group */
+ pgrp->pbcatom = -1;
+ }
+ else
+ {
+ if (pgrp->pbcatom > 0)
+ {
+ pgrp->pbcatom -= 1;
+ }
+ else if (pgrp->pbcatom == 0)
+ {
+ pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
+ }
+ else
+ {
+ /* Use cosine weighting */
+ pgrp->pbcatom = -1;
+ }
+ }
}
- ptr += nchar;
- }
- if (i == 0)
- gmx_fatal(FARGS,"All entries in pull_dim are N");
-
- for(g=0; g<pull->ngrp+1; g++) {
- pgrp = &pull->grp[g];
- if (g == 0 && strcmp(pgnames[g],"") == 0) {
- pgrp->nat = 0;
- } else {
- ig = search_string(pgnames[g],grps->nr,gnames);
- pgrp->nat = grps->index[ig+1] - grps->index[ig];
+}
+
+void make_pull_coords(t_pull *pull)
+{
+ int ndim, d, nchar, c;
+ char *ptr, pulldim1[STRLEN];
+ t_pull_coord *pcrd;
+
+ ptr = pulldim;
+ ndim = 0;
+ for (d = 0; d < DIM; d++)
+ {
+ if (sscanf(ptr, "%s%n", pulldim1, &nchar) != 1)
+ {
+ gmx_fatal(FARGS, "Less than 3 pull dimensions given in pull_dim: '%s'",
+ pulldim);
+ }
+
+ if (gmx_strncasecmp(pulldim1, "N", 1) == 0)
+ {
+ pull->dim[d] = 0;
+ }
+ else if (gmx_strncasecmp(pulldim1, "Y", 1) == 0)
+ {
+ pull->dim[d] = 1;
+ ndim++;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Please use Y(ES) or N(O) for pull_dim only (not %s)",
+ pulldim1);
+ }
+ ptr += nchar;
}
- if (pgrp->nat > 0) {
- fprintf(stderr,"Pull group %d '%s' has %d atoms\n",
- g,pgnames[g],pgrp->nat);
- snew(pgrp->ind,pgrp->nat);
- for(i=0; i<pgrp->nat; i++)
- pgrp->ind[i] = grps->a[grps->index[ig]+i];
-
- if (pull->eGeom == epullgCYL && g == 0 && pgrp->nweight > 0)
- gmx_fatal(FARGS,"Weights are not supported for the reference group with cylinder pulling");
- if (pgrp->nweight > 0 && pgrp->nweight != pgrp->nat)
- gmx_fatal(FARGS,"Number of weights (%d) for pull group %d '%s' does not match the number of atoms (%d)",
- pgrp->nweight,g,pgnames[g],pgrp->nat);
-
- if (pgrp->nat == 1) {
- /* No pbc is required for this group */
- pgrp->pbcatom = -1;
- } else {
- if (pgrp->pbcatom > 0) {
- pgrp->pbcatom -= 1;
- } else if (pgrp->pbcatom == 0) {
- pgrp->pbcatom = pgrp->ind[(pgrp->nat-1)/2];
- } else {
- /* Use cosine weighting */
- pgrp->pbcatom = -1;
- }
- }
-
- if (g > 0 && pull->eGeom != epullgDIST) {
- for(d=0; d<DIM; d++) {
- if (pgrp->vec[d] != 0 && pull->dim[d] == 0) {
- gmx_fatal(FARGS,"ERROR: pull_vec%d has non-zero %c-component while pull_dim in N\n",g,'x'+d);
- }
- }
- }
-
- if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
- g > 0 && norm2(pgrp->vec) == 0)
- gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s",
- g,EPULLGEOM(pull->eGeom));
- if ((pull->eGeom == epullgPOS) && pgrp->rate != 0 &&
- g > 0 && norm2(pgrp->vec) == 0)
- gmx_fatal(FARGS,"pull_vec%d can not be zero with geometry %s and non-zero rate",
- g,EPULLGEOM(pull->eGeom));
- } else {
- if (g == 0) {
- if (pull->eGeom == epullgCYL)
- gmx_fatal(FARGS,"Absolute reference groups are not supported with geometry %s",EPULLGEOM(pull->eGeom));
- } else {
- gmx_fatal(FARGS,"Pull group %d '%s' is empty",g,pgnames[g]);
- }
- pgrp->pbcatom = -1;
+ if (ndim == 0)
+ {
+ gmx_fatal(FARGS, "All entries in pull_dim are N");
+ }
+
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ if (pcrd->group[0] < 0 || pcrd->group[0] >= pull->ngroup ||
+ pcrd->group[1] < 0 || pcrd->group[1] >= pull->ngroup)
+ {
+ gmx_fatal(FARGS, "Pull group index in pull-coord%d-groups out of range, should be between %d and %d", c+1, 0, pull->ngroup+1);
+ }
+
+ if (pcrd->group[0] == pcrd->group[1])
+ {
+ gmx_fatal(FARGS, "Identical pull group indices in pull-coord%d-groups", c+1);
+ }
+
+ if (pull->eGeom == epullgCYL && pcrd->group[0] != 1)
+ {
+ gmx_fatal(FARGS, "With pull geometry %s, the first pull group should always be 1", EPULLGEOM(pull->eGeom));
+ }
+
+ if (pull->eGeom != epullgDIST)
+ {
+ for (d = 0; d < DIM; d++)
+ {
+ if (pcrd->vec[d] != 0 && pull->dim[d] == 0)
+ {
+ gmx_fatal(FARGS, "ERROR: pull-group%d-vec has non-zero %c-component while pull_dim for the %c-dimension is N\n", c+1, 'x'+d, 'x'+d);
+ }
+ }
+ }
+
+ if ((pull->eGeom == epullgDIR || pull->eGeom == epullgCYL) &&
+ norm2(pcrd->vec) == 0)
+ {
+ gmx_fatal(FARGS, "pull-group%d-vec can not be zero with geometry %s",
+ c+1, EPULLGEOM(pull->eGeom));
+ }
}
- }
}
-void set_pull_init(t_inputrec *ir,gmx_mtop_t *mtop,rvec *x,matrix box,
- const output_env_t oenv,gmx_bool bStart)
+void set_pull_init(t_inputrec *ir, gmx_mtop_t *mtop, rvec *x, matrix box, real lambda,
+ const output_env_t oenv, gmx_bool bStart)
{
- t_mdatoms *md;
- t_pull *pull;
- t_pullgrp *pgrp;
- t_pbc pbc;
- int ndim,g,m;
- double t_start,tinvrate;
- real lambda=0;
- rvec init;
- dvec dr,dev;
-
- /* need to pass in the correct masses if free energy is on*/
- if (ir->efep)
- {
- lambda = ir->fepvals->all_lambda[efptMASS][ir->fepvals->init_fep_state];
- }
- init_pull(NULL,ir,0,NULL,mtop,NULL,oenv,lambda,FALSE,0);
- md = init_mdatoms(NULL,mtop,ir->efep);
- atoms2md(mtop,ir,0,NULL,0,mtop->natoms,md);
- if (ir->efep)
- update_mdatoms(md,ir->fepvals->init_lambda);
-
- pull = ir->pull;
- if (pull->eGeom == epullgPOS)
- ndim = 3;
- else
- ndim = 1;
-
- set_pbc(&pbc,ir->ePBC,box);
-
- t_start = ir->init_t + ir->init_step*ir->delta_t;
-
- pull_calc_coms(NULL,pull,md,&pbc,t_start,x,NULL);
-
- fprintf(stderr,"Pull group natoms pbc atom distance at start reference at t=0\n");
- for(g=0; g<pull->ngrp+1; g++) {
- pgrp = &pull->grp[g];
- fprintf(stderr,"%8d %8d %8d ",g,pgrp->nat,pgrp->pbcatom+1);
- copy_rvec(pgrp->init,init);
- clear_rvec(pgrp->init);
- if (g > 0) {
- if (pgrp->rate == 0)
- tinvrate = 0;
- else
- tinvrate = t_start/pgrp->rate;
- get_pullgrp_distance(pull,&pbc,g,0,dr,dev);
- for(m=0; m<DIM; m++) {
- if (m < ndim)
- fprintf(stderr," %6.3f",dev[m]);
- else
- fprintf(stderr," ");
- }
- fprintf(stderr," ");
- for(m=0; m<DIM; m++) {
- if (bStart)
- pgrp->init[m] = init[m] + dev[m]
- - tinvrate*(pull->eGeom==epullgPOS ? pgrp->vec[m] : 1);
- else
- pgrp->init[m] = init[m];
- if (m < ndim)
- fprintf(stderr," %6.3f",pgrp->init[m]);
- else
- fprintf(stderr," ");
- }
+ t_mdatoms *md;
+ t_pull *pull;
+ t_pull_coord *pcrd;
+ t_pull_group *pgrp0, *pgrp1;
+ t_pbc pbc;
+ int c, m;
+ double t_start, tinvrate;
+ real init;
+ dvec dr;
+ double dev;
+
+ init_pull(NULL, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
+ md = init_mdatoms(NULL, mtop, ir->efep);
+ atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
+ if (ir->efep)
+ {
+ update_mdatoms(md, lambda);
+ }
+ pull = ir->pull;
+
+ set_pbc(&pbc, ir->ePBC, box);
+
+ t_start = ir->init_t + ir->init_step*ir->delta_t;
+
+ pull_calc_coms(NULL, pull, md, &pbc, t_start, x, NULL);
+
+ fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
+ for (c = 0; c < pull->ncoord; c++)
+ {
+ pcrd = &pull->coord[c];
+
+ pgrp0 = &pull->group[pcrd->group[0]];
+ pgrp1 = &pull->group[pcrd->group[1]];
+ fprintf(stderr, "%8d %8d %8d\n",
+ pcrd->group[0], pgrp0->nat, pgrp0->pbcatom+1);
+ fprintf(stderr, "%8d %8d %8d ",
+ pcrd->group[1], pgrp1->nat, pgrp1->pbcatom+1);
+
+ init = pcrd->init;
+ pcrd->init = 0;
+
+ if (pcrd->rate == 0)
+ {
+ tinvrate = 0;
+ }
+ else
+ {
+ tinvrate = t_start/pcrd->rate;
+ }
+ get_pull_coord_distance(pull, c, &pbc, 0, dr, &dev);
+ fprintf(stderr, " %6.3f ", dev);
+
+ if (bStart)
+ {
+ pcrd->init = init + dev - tinvrate;
+ }
+ else
+ {
+ pcrd->init = init;
+ }
+ fprintf(stderr, " %6.3f\n", pcrd->init);
}
- fprintf(stderr,"\n");
- }
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff