-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 4.6.0
- * Written by Christoph Junghans, Brad Lambeth, and possibly others.
* Copyright (c) 2009 Christoph Junghans, Brad Lambeth.
- * All rights reserved.
-
- * 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) 2012,2014, 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
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* of the License, or (at your option) any later version.
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- * bugs must be traceable. We will be happy to consider code for
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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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*/
+#include "gmxpre.h"
+
+#include <stdlib.h>
+#include <string.h>
-#include "readir.h"
-#include "names.h"
-#include "smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/gmxpreprocess/readir.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#define MAXPTR 254
-static char adress_refs[STRLEN],adress_tf_grp_names[STRLEN], adress_cg_grp_names[STRLEN];
+static char adress_refs[STRLEN], adress_tf_grp_names[STRLEN], adress_cg_grp_names[STRLEN];
-void read_adressparams(int *ninp_p,t_inpfile **inp_p,t_adress *adress, warninp_t wi)
+void read_adressparams(int *ninp_p, t_inpfile **inp_p, t_adress *adress, warninp_t wi)
{
- int nadress_refs,i;
- const char *tmp;
- char *ptr1[MAXPTR];
-
-
- int ninp;
- t_inpfile *inp;
-
- ninp = *ninp_p;
- inp = *inp_p;
-
- EETYPE("adress_type", adress->type, eAdresstype_names);
- RTYPE ("adress_const_wf", adress->const_wf, 1);
- RTYPE ("adress_ex_width", adress->ex_width, 0);
- RTYPE ("adress_hy_width", adress->hy_width, 0);
- RTYPE ("adress_ex_forcecap", adress->ex_forcecap, 0);
- EETYPE("adress_interface_correction",adress->icor, eAdressICtype_names);
- EETYPE("adress_site", adress->site, eAdressSITEtype_names);
- STYPE ("adress_reference_coords", adress_refs, NULL);
- STYPE ("adress_tf_grp_names", adress_tf_grp_names, NULL);
- STYPE ("adress_cg_grp_names", adress_cg_grp_names, NULL);
- EETYPE("adress_do_hybridpairs", adress->do_hybridpairs, yesno_names);
-
- nadress_refs = str_nelem(adress_refs,MAXPTR,ptr1);
-
- for(i=0; (i<nadress_refs); i++) /*read vector components*/
- adress->refs[i]=strtod(ptr1[i],NULL);
- for( ;(i<DIM); i++) /*remaining undefined components of the vector set to zero*/
- adress->refs[i]=0;
-
- *ninp_p = ninp;
- *inp_p = inp;
+ int nadress_refs, i;
+ const char *tmp;
+ char *ptr1[MAXPTR];
+
+
+ int ninp;
+ t_inpfile *inp;
+
+ ninp = *ninp_p;
+ inp = *inp_p;
+
+ EETYPE("adress_type", adress->type, eAdresstype_names);
+ RTYPE ("adress_const_wf", adress->const_wf, 1);
+ RTYPE ("adress_ex_width", adress->ex_width, 0);
+ RTYPE ("adress_hy_width", adress->hy_width, 0);
+ RTYPE ("adress_ex_forcecap", adress->ex_forcecap, 0);
+ EETYPE("adress_interface_correction", adress->icor, eAdressICtype_names);
+ EETYPE("adress_site", adress->site, eAdressSITEtype_names);
+ STYPE ("adress_reference_coords", adress_refs, NULL);
+ STYPE ("adress_tf_grp_names", adress_tf_grp_names, NULL);
+ STYPE ("adress_cg_grp_names", adress_cg_grp_names, NULL);
+ EETYPE("adress_do_hybridpairs", adress->do_hybridpairs, yesno_names);
+
+ nadress_refs = str_nelem(adress_refs, MAXPTR, ptr1);
+
+ for (i = 0; (i < nadress_refs); i++) /*read vector components*/
+ {
+ adress->refs[i] = strtod(ptr1[i], NULL);
+ }
+ for (; (i < DIM); i++) /*remaining undefined components of the vector set to zero*/
+ {
+ adress->refs[i] = 0;
+ }
+
+ *ninp_p = ninp;
+ *inp_p = inp;
}
-void do_adress_index(t_adress *adress, gmx_groups_t *groups,char **gnames,t_grpopts *opts,warninp_t wi){
- int nr,i,j,k;
- char *ptr1[MAXPTR];
- int nadress_cg_grp_names, nadress_tf_grp_names;
-
- /* AdResS coarse grained groups input */
-
- nr = groups->grps[egcENER].nr;
- snew(adress->group_explicit, nr);
- for (i=0; i <nr; i++){
- adress->group_explicit[i] = TRUE;
- }
- adress->n_energy_grps = nr;
-
- nadress_cg_grp_names = str_nelem(adress_cg_grp_names,MAXPTR,ptr1);
-
- if (nadress_cg_grp_names > 0){
- for (i=0; i <nadress_cg_grp_names; i++){
+void do_adress_index(t_adress *adress, gmx_groups_t *groups, char **gnames, t_grpopts *opts, warninp_t wi)
+{
+ int nr, i, j, k;
+ char *ptr1[MAXPTR];
+ int nadress_cg_grp_names, nadress_tf_grp_names;
+
+ /* AdResS coarse grained groups input */
+
+ nr = groups->grps[egcENER].nr;
+ snew(adress->group_explicit, nr);
+ for (i = 0; i < nr; i++)
+ {
+ adress->group_explicit[i] = TRUE;
+ }
+ adress->n_energy_grps = nr;
+
+ nadress_cg_grp_names = str_nelem(adress_cg_grp_names, MAXPTR, ptr1);
+
+ if (nadress_cg_grp_names > 0)
+ {
+ for (i = 0; i < nadress_cg_grp_names; i++)
+ {
/* search for the group name mathching the tf group name */
k = 0;
while ((k < nr) &&
- gmx_strcasecmp(ptr1[i],(char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
- k++;
- if (k==nr) gmx_fatal(FARGS,"Adress cg energy group %s not found\n",ptr1[i]);
+ gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
+ {
+ k++;
+ }
+ if (k == nr)
+ {
+ gmx_fatal(FARGS, "Adress cg energy group %s not found\n", ptr1[i]);
+ }
adress->group_explicit[k] = FALSE;
printf ("AdResS: Energy group %s is treated as coarse-grained \n",
- (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
- }
+ (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
+ }
/* set energy group exclusions between all coarse-grained and explicit groups */
- for (j = 0; j < nr; j++) {
- for (k = 0; k < nr; k++) {
- if (!(adress->group_explicit[k] == adress->group_explicit[j])){
+ for (j = 0; j < nr; j++)
+ {
+ for (k = 0; k < nr; k++)
+ {
+ if (!(adress->group_explicit[k] == adress->group_explicit[j]))
+ {
opts->egp_flags[nr * j + k] |= EGP_EXCL;
- if (debug) fprintf(debug,"AdResS excl %s %s \n",
- (char*)(gnames[groups->grps[egcENER].nm_ind[j]]),
- (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
+ if (debug)
+ {
+ fprintf(debug, "AdResS excl %s %s \n",
+ (char*)(gnames[groups->grps[egcENER].nm_ind[j]]),
+ (char*)(gnames[groups->grps[egcENER].nm_ind[k]]));
+ }
}
}
- }
- }else{
- warning(wi,"For an AdResS simulation at least one coarse-grained energy group has to be specified in adress_cg_grp_names");
- }
+ }
+ }
+ else
+ {
+ warning(wi, "For an AdResS simulation at least one coarse-grained energy group has to be specified in adress_cg_grp_names");
+ }
- /* AdResS multiple tf tables input */
- nadress_tf_grp_names = str_nelem(adress_tf_grp_names,MAXPTR,ptr1);
- adress->n_tf_grps = nadress_tf_grp_names;
- snew(adress->tf_table_index, nadress_tf_grp_names);
+ /* AdResS multiple tf tables input */
+ nadress_tf_grp_names = str_nelem(adress_tf_grp_names, MAXPTR, ptr1);
+ adress->n_tf_grps = nadress_tf_grp_names;
+ snew(adress->tf_table_index, nadress_tf_grp_names);
- nr = groups->grps[egcENER].nr;
+ nr = groups->grps[egcENER].nr;
- if (nadress_tf_grp_names > 0){
- for (i=0; i <nadress_tf_grp_names; i++){
+ if (nadress_tf_grp_names > 0)
+ {
+ for (i = 0; i < nadress_tf_grp_names; i++)
+ {
/* search for the group name mathching the tf group name */
k = 0;
while ((k < nr) &&
- gmx_strcasecmp(ptr1[i],(char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
- k++;
- if (k==nr) gmx_fatal(FARGS,"Adress tf energy group %s not found\n",ptr1[i]);
-
+ gmx_strcasecmp(ptr1[i], (char*)(gnames[groups->grps[egcENER].nm_ind[k]])))
+ {
+ k++;
+ }
+ if (k == nr)
+ {
+ gmx_fatal(FARGS, "Adress tf energy group %s not found\n", ptr1[i]);
+ }
+
adress->tf_table_index[i] = k;
- if (debug) fprintf(debug,"found tf group %s id %d \n",ptr1[i], k);
- if (adress->group_explicit[k]){
- gmx_fatal(FARGS,"Thermodynamic force group %s is not a coarse-grained group in adress_cg_grp_names. The thermodynamic force has to act on the coarse-grained vsite of a molecule.\n",ptr1[i]);
+ if (debug)
+ {
+ fprintf(debug, "found tf group %s id %d \n", ptr1[i], k);
+ }
+ if (adress->group_explicit[k])
+ {
+ gmx_fatal(FARGS, "Thermodynamic force group %s is not a coarse-grained group in adress_cg_grp_names. The thermodynamic force has to act on the coarse-grained vsite of a molecule.\n", ptr1[i]);
}
+ }
}
- }
- /* end AdResS multiple tf tables input */
-
-
+ /* end AdResS multiple tf tables input */
+
+
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff