/*
- *
- * 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) 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
+ * 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.
- *
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, 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 http://www.gromacs.org.
+ *
* 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.
- *
- * For more info, check our website at http://www.gromacs.org
- *
- * And Hey:
- * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ * the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <math.h>
-#include "smalloc.h"
-#include "sysstuff.h"
-#include "macros.h"
-#include "string2.h"
-#include "topdirs.h"
#include "toputil.h"
-#include "topdirs.h"
-#include "toputil.h"
-#include "symtab.h"
-#include "gmx_fatal.h"
-#include "gpp_atomtype.h"
+
+#include <assert.h>
+#include <math.h>
+#include <string.h>
+
+#include "gromacs/gmxpreprocess/gpp_atomtype.h"
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* UTILITIES */
-void set_p_string(t_param *p,const char *s)
+void set_p_string(t_param *p, const char *s)
{
- if (s) {
- if (strlen(s) < sizeof(p->s)-1)
- strncpy(p->s,s,sizeof(p->s));
+ if (s)
+ {
+ if (strlen(s) < sizeof(p->s)-1)
+ {
+ strncpy(p->s, s, sizeof(p->s));
+ }
+ else
+ {
+ gmx_fatal(FARGS, "Increase MAXSLEN in include/grompp-impl.h to at least %d,"
+ " or shorten your definition of bonds like %s to at most %d",
+ strlen(s)+1, s, MAXSLEN-1);
+ }
+ }
else
- gmx_fatal(FARGS,"Increase MAXSLEN in include/grompp.h to at least %d,"
- " or shorten your definition of bonds like %s to at most %d",
- strlen(s)+1,s,MAXSLEN-1);
- }
- else
- strcpy(p->s,"");
+ {
+ strcpy(p->s, "");
+ }
}
void pr_alloc (int extra, t_params *pr)
{
- int i,j;
-
- /* get new space for arrays */
- if (extra < 0)
- gmx_fatal(FARGS,"Trying to make array smaller.\n");
- if (extra == 0)
- return;
- if ((pr->nr == 0) && (pr->param != NULL)) {
- fprintf(stderr,"Warning: dangling pointer at %lx\n",
- (unsigned long)pr->param);
- pr->param = NULL;
- }
- if (pr->nr+extra > pr->maxnr) {
- pr->maxnr = max(1.2*pr->maxnr,pr->maxnr + extra);
- srenew(pr->param,pr->maxnr);
- for(i=pr->nr; (i<pr->maxnr); i++) {
- for(j=0; (j<MAXATOMLIST); j++)
- pr->param[i].a[j]=0;
- for(j=0; (j<MAXFORCEPARAM); j++)
- pr->param[i].c[j]=0;
- set_p_string(&(pr->param[i]),"");
+ int i, j;
+
+ /* get new space for arrays */
+ if (extra < 0)
+ {
+ gmx_fatal(FARGS, "Trying to make array smaller.\n");
+ }
+ if (extra == 0)
+ {
+ return;
+ }
+ assert(!((pr->nr == 0) && (pr->param != NULL)));
+ if (pr->nr+extra > pr->maxnr)
+ {
+ pr->maxnr = max(1.2*pr->maxnr, pr->maxnr + extra);
+ srenew(pr->param, pr->maxnr);
+ for (i = pr->nr; (i < pr->maxnr); i++)
+ {
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ pr->param[i].a[j] = 0;
+ }
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ pr->param[i].c[j] = 0;
+ }
+ set_p_string(&(pr->param[i]), "");
+ }
}
- }
}
void init_plist(t_params plist[])
{
- int i;
-
- for(i=0; (i<F_NRE); i++) {
- plist[i].nr = 0;
- plist[i].maxnr = 0;
- plist[i].param = NULL;
-
- /* CMAP */
- plist[i].ncmap=0;
- plist[i].cmap=NULL;
- plist[i].grid_spacing = 0;
- plist[i].nc = 0;
- plist[i].nct = 0;
- plist[i].cmap_types = NULL;
- }
+ int i;
+
+ for (i = 0; (i < F_NRE); i++)
+ {
+ plist[i].nr = 0;
+ plist[i].maxnr = 0;
+ plist[i].param = NULL;
+
+ /* CMAP */
+ plist[i].ncmap = 0;
+ plist[i].cmap = NULL;
+ plist[i].grid_spacing = 0;
+ plist[i].nc = 0;
+ plist[i].nct = 0;
+ plist[i].cmap_types = NULL;
+ }
}
-void cp_param(t_param *dest,t_param *src)
+void cp_param(t_param *dest, t_param *src)
{
- int j;
-
- for(j=0; (j<MAXATOMLIST); j++)
- dest->a[j] = src->a[j];
- for(j=0; (j<MAXFORCEPARAM); j++)
- dest->c[j] = src->c[j];
- strncpy(dest->s,src->s,sizeof(dest->s));
+ int j;
+
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ dest->a[j] = src->a[j];
+ }
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ dest->c[j] = src->c[j];
+ }
+ strncpy(dest->s, src->s, sizeof(dest->s));
}
void add_param_to_list(t_params *list, t_param *b)
{
- int j;
-
- /* allocate one position extra */
- pr_alloc (1,list);
-
- /* fill the arrays */
- for (j=0; (j < MAXFORCEPARAM); j++)
- list->param[list->nr].c[j] = b->c[j];
- for (j=0; (j < MAXATOMLIST); j++)
- list->param[list->nr].a[j] = b->a[j];
- memset(list->param[list->nr].s,0,sizeof(list->param[list->nr].s));
-
- list->nr++;
+ int j;
+
+ /* allocate one position extra */
+ pr_alloc (1, list);
+
+ /* fill the arrays */
+ for (j = 0; (j < MAXFORCEPARAM); j++)
+ {
+ list->param[list->nr].c[j] = b->c[j];
+ }
+ for (j = 0; (j < MAXATOMLIST); j++)
+ {
+ list->param[list->nr].a[j] = b->a[j];
+ }
+ memset(list->param[list->nr].s, 0, sizeof(list->param[list->nr].s));
+
+ list->nr++;
}
void init_molinfo(t_molinfo *mol)
{
- mol->nrexcl = 0;
- mol->excl_set = FALSE;
- mol->bProcessed = FALSE;
- init_plist(mol->plist);
- init_block(&mol->cgs);
- init_block(&mol->mols);
- init_blocka(&mol->excls);
- init_atom(&mol->atoms);
+ mol->nrexcl = 0;
+ mol->excl_set = FALSE;
+ mol->bProcessed = FALSE;
+ init_plist(mol->plist);
+ init_block(&mol->cgs);
+ init_block(&mol->mols);
+ init_blocka(&mol->excls);
+ init_atom(&mol->atoms);
}
/* FREEING MEMORY */
void done_bt (t_params *pl)
{
- sfree(pl->param);
+ sfree(pl->param);
}
void done_mi(t_molinfo *mi)
{
- int i;
-
- done_atom (&(mi->atoms));
- done_block(&(mi->cgs));
- done_block(&(mi->mols));
- for(i=0; (i<F_NRE); i++)
- done_bt(&(mi->plist[i]));
+ int i;
+
+ done_atom (&(mi->atoms));
+ done_block(&(mi->cgs));
+ done_block(&(mi->mols));
+ for (i = 0; (i < F_NRE); i++)
+ {
+ done_bt(&(mi->plist[i]));
+ }
}
/* PRINTING STRUCTURES */
void print_bt(FILE *out, directive d, gpp_atomtype_t at,
- int ftype,int fsubtype,t_params plist[],
- gmx_bool bFullDih)
+ int ftype, int fsubtype, t_params plist[],
+ gmx_bool bFullDih)
{
- /* This dihp is a DIRTY patch because the dih-types do not use
- * all four atoms to determine the type.
- */
- const int dihp[2][2] = { { 1,2 }, { 0,3 } };
- t_params *bt;
- int i,j,f,nral,nrfp;
- gmx_bool bDih=FALSE,bSwapParity;
-
- bt=&(plist[ftype]);
-
- if (!bt->nr)
- return;
-
- f = 0;
- switch(ftype) {
- case F_G96ANGLES:
- f = 1;
- break;
- case F_G96BONDS:
- f = 1;
- break;
- case F_MORSE:
- f = 2;
- break;
- case F_CUBICBONDS:
- f = 3;
- break;
- case F_CONNBONDS:
- f = 4;
- break;
- case F_HARMONIC:
- f = 5;
- break;
- case F_CROSS_BOND_ANGLES:
- f = 2;
- break;
- case F_CROSS_BOND_BONDS:
- f = 3;
- break;
- case F_UREY_BRADLEY:
- f = 4;
- break;
- case F_PDIHS:
- case F_RBDIHS:
- case F_FOURDIHS:
- bDih=TRUE;
- break;
- case F_IDIHS:
- f=1;
- bDih=TRUE;
- break;
- case F_CONSTRNC:
- f=1;
- break;
- case F_VSITE3FD:
- f = 1;
- break;
- case F_VSITE3FAD:
- f = 2;
- break;
- case F_VSITE3OUT:
- f = 3;
- break;
- case F_VSITE4FDN:
- f = 1;
- break;
- case F_CMAP:
- f = 1;
- break;
-
- default:
- bDih=FALSE;
- }
- if (bFullDih)
- bDih=FALSE;
- if (fsubtype)
- f = fsubtype-1;
-
- nral = NRAL(ftype);
- nrfp = NRFP(ftype);
-
- /* header */
- fprintf(out,"[ %s ]\n",dir2str(d));
- fprintf(out,"; ");
- if (!bDih) {
- fprintf (out,"%3s %4s","ai","aj");
- for (j=2; (j<nral); j++)
- fprintf (out," %3c%c",'a','i'+j);
- }
- else
- for (j=0; (j<2); j++)
- fprintf (out,"%3c%c",'a','i'+dihp[f][j]);
-
- fprintf (out," funct");
- for (j=0; (j<nrfp); j++)
- fprintf (out," %12c%1d",'c',j);
- fprintf (out,"\n");
-
- /* print bondtypes */
- for (i=0; (i<bt->nr); i++) {
- bSwapParity = (bt->param[i].C0==NOTSET) && (bt->param[i].C1==-1);
+ /* This dihp is a DIRTY patch because the dih-types do not use
+ * all four atoms to determine the type.
+ */
+ const int dihp[2][2] = { { 1, 2 }, { 0, 3 } };
+ t_params *bt;
+ int i, j, f, nral, nrfp;
+ gmx_bool bDih = FALSE, bSwapParity;
+
+ bt = &(plist[ftype]);
+
+ if (!bt->nr)
+ {
+ return;
+ }
+
+ f = 0;
+ switch (ftype)
+ {
+ case F_G96ANGLES:
+ f = 1;
+ break;
+ case F_G96BONDS:
+ f = 1;
+ break;
+ case F_MORSE:
+ f = 2;
+ break;
+ case F_CUBICBONDS:
+ f = 3;
+ break;
+ case F_CONNBONDS:
+ f = 4;
+ break;
+ case F_HARMONIC:
+ f = 5;
+ break;
+ case F_CROSS_BOND_ANGLES:
+ f = 2;
+ break;
+ case F_CROSS_BOND_BONDS:
+ f = 3;
+ break;
+ case F_UREY_BRADLEY:
+ f = 4;
+ break;
+ case F_PDIHS:
+ case F_RBDIHS:
+ case F_FOURDIHS:
+ bDih = TRUE;
+ break;
+ case F_IDIHS:
+ f = 1;
+ bDih = TRUE;
+ break;
+ case F_CONSTRNC:
+ f = 1;
+ break;
+ case F_VSITE3FD:
+ f = 1;
+ break;
+ case F_VSITE3FAD:
+ f = 2;
+ break;
+ case F_VSITE3OUT:
+ f = 3;
+ break;
+ case F_VSITE4FDN:
+ f = 1;
+ break;
+ case F_CMAP:
+ f = 1;
+ break;
+
+ default:
+ bDih = FALSE;
+ }
+ if (bFullDih)
+ {
+ bDih = FALSE;
+ }
+ if (fsubtype)
+ {
+ f = fsubtype-1;
+ }
+
+ nral = NRAL(ftype);
+ nrfp = NRFP(ftype);
+
+ /* header */
+ fprintf(out, "[ %s ]\n", dir2str(d));
+ fprintf(out, "; ");
if (!bDih)
- for (j=0; (j<nral); j++)
- fprintf (out,"%5s ",get_atomtype_name(bt->param[i].a[j],at));
- else
- for(j=0; (j<2); j++)
- fprintf (out,"%5s ",get_atomtype_name(bt->param[i].a[dihp[f][j]],at));
- fprintf (out,"%5d ", bSwapParity ? -f-1 : f+1);
-
- if (bt->param[i].s[0])
- fprintf(out," %s",bt->param[i].s);
+ {
+ fprintf (out, "%3s %4s", "ai", "aj");
+ for (j = 2; (j < nral); j++)
+ {
+ fprintf (out, " %3c%c", 'a', 'i'+j);
+ }
+ }
else
- for (j=0; (j<nrfp && (bt->param[i].c[j] != NOTSET)); j++)
- fprintf (out,"%13.6e ",bt->param[i].c[j]);
-
- fprintf (out,"\n");
- }
- fprintf (out,"\n");
- fflush (out);
+ {
+ for (j = 0; (j < 2); j++)
+ {
+ fprintf (out, "%3c%c", 'a', 'i'+dihp[f][j]);
+ }
+ }
+
+ fprintf (out, " funct");
+ for (j = 0; (j < nrfp); j++)
+ {
+ fprintf (out, " %12c%1d", 'c', j);
+ }
+ fprintf (out, "\n");
+
+ /* print bondtypes */
+ for (i = 0; (i < bt->nr); i++)
+ {
+ bSwapParity = (bt->param[i].C0 == NOTSET) && (bt->param[i].C1 == -1);
+ if (!bDih)
+ {
+ for (j = 0; (j < nral); j++)
+ {
+ fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[j], at));
+ }
+ }
+ else
+ {
+ for (j = 0; (j < 2); j++)
+ {
+ fprintf (out, "%5s ", get_atomtype_name(bt->param[i].a[dihp[f][j]], at));
+ }
+ }
+ fprintf (out, "%5d ", bSwapParity ? -f-1 : f+1);
+
+ if (bt->param[i].s[0])
+ {
+ fprintf(out, " %s", bt->param[i].s);
+ }
+ else
+ {
+ for (j = 0; (j < nrfp && (bt->param[i].c[j] != NOTSET)); j++)
+ {
+ fprintf (out, "%13.6e ", bt->param[i].c[j]);
+ }
+ }
+
+ fprintf (out, "\n");
+ }
+ fprintf (out, "\n");
+ fflush (out);
}
-void print_blocka(FILE *out, const char *szName,
- const char *szIndex, const char *szA,
- t_blocka *block)
+void print_blocka(FILE *out, const char *szName,
+ const char *szIndex, const char *szA,
+ t_blocka *block)
{
- int i,j;
-
- fprintf (out,"; %s\n",szName);
- fprintf (out,"; %4s %s\n",szIndex,szA);
- for (i=0; (i < block->nr); i++) {
- for (i=0; (i < block->nr); i++) {
- fprintf (out,"%6d",i+1);
- for (j=block->index[i]; (j < ((int)block->index[i+1])); j++)
- fprintf (out,"%5d",block->a[j]+1);
- fprintf (out,"\n");
+ int i, j;
+
+ fprintf (out, "; %s\n", szName);
+ fprintf (out, "; %4s %s\n", szIndex, szA);
+ for (i = 0; (i < block->nr); i++)
+ {
+ for (i = 0; (i < block->nr); i++)
+ {
+ fprintf (out, "%6d", i+1);
+ for (j = block->index[i]; (j < ((int)block->index[i+1])); j++)
+ {
+ fprintf (out, "%5d", block->a[j]+1);
+ }
+ fprintf (out, "\n");
+ }
+ fprintf (out, "\n");
}
- fprintf (out,"\n");
- }
}
void print_excl(FILE *out, int natoms, t_excls excls[])
{
- atom_id i;
- gmx_bool have_excl;
- int j;
-
- have_excl=FALSE;
- for(i=0; i<natoms && !have_excl; i++)
- have_excl = (excls[i].nr > 0);
-
- if (have_excl) {
- fprintf (out,"[ %s ]\n",dir2str(d_exclusions));
- fprintf (out,"; %4s %s\n","i","excluded from i");
- for(i=0; i<natoms; i++)
- if (excls[i].nr > 0) {
- fprintf (out,"%6d ",i+1);
- for(j=0; j<excls[i].nr; j++)
- fprintf (out," %5d",excls[i].e[j]+1);
- fprintf (out,"\n");
- }
- fprintf (out,"\n");
- fflush(out);
- }
+ atom_id i;
+ gmx_bool have_excl;
+ int j;
+
+ have_excl = FALSE;
+ for (i = 0; i < natoms && !have_excl; i++)
+ {
+ have_excl = (excls[i].nr > 0);
+ }
+
+ if (have_excl)
+ {
+ fprintf (out, "[ %s ]\n", dir2str(d_exclusions));
+ fprintf (out, "; %4s %s\n", "i", "excluded from i");
+ for (i = 0; i < natoms; i++)
+ {
+ if (excls[i].nr > 0)
+ {
+ fprintf (out, "%6d ", i+1);
+ for (j = 0; j < excls[i].nr; j++)
+ {
+ fprintf (out, " %5d", excls[i].e[j]+1);
+ }
+ fprintf (out, "\n");
+ }
+ }
+ fprintf (out, "\n");
+ fflush(out);
+ }
}
-static double get_residue_charge(const t_atoms *atoms,int at)
+static double get_residue_charge(const t_atoms *atoms, int at)
{
- int ri;
- double q;
-
- ri = atoms->atom[at].resind;
- q = 0;
- while (at < atoms->nr && atoms->atom[at].resind == ri) {
- q += atoms->atom[at].q;
- at++;
- }
-
- return q;
+ int ri;
+ double q;
+
+ ri = atoms->atom[at].resind;
+ q = 0;
+ while (at < atoms->nr && atoms->atom[at].resind == ri)
+ {
+ q += atoms->atom[at].q;
+ at++;
+ }
+
+ return q;
}
-void print_atoms(FILE *out,gpp_atomtype_t atype,t_atoms *at,int *cgnr,
- gmx_bool bRTPresname)
+void print_atoms(FILE *out, gpp_atomtype_t atype, t_atoms *at, int *cgnr,
+ gmx_bool bRTPresname)
{
- int i,ri;
- int tpA,tpB;
- const char *as;
- char *tpnmA,*tpnmB;
- double qres,qtot;
-
- as=dir2str(d_atoms);
- fprintf(out,"[ %s ]\n",as);
- fprintf(out,"; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
- "nr","type","resnr","residue","atom","cgnr","charge","mass","typeB","chargeB","massB");
-
- qtot = 0;
-
- if (debug)
- fprintf(debug,"This molecule has %d atoms and %d residues\n",
- at->nr,at->nres);
-
- if (at->nres) {
- /* if the information is present... */
- for (i=0; (i < at->nr); i++) {
- ri = at->atom[i].resind;
- if ((i == 0 || ri != at->atom[i-1].resind) &&
- at->resinfo[ri].rtp != NULL) {
- qres = get_residue_charge(at,i);
- fprintf(out,"; residue %3d %-3s rtp %-4s q ",
- at->resinfo[ri].nr,
- *at->resinfo[ri].name,
- *at->resinfo[ri].rtp);
- if (fabs(qres) < 0.001) {
- fprintf(out," %s","0.0");
- } else {
- fprintf(out,"%+3.1f",qres);
- }
- fprintf(out,"\n");
- }
- tpA = at->atom[i].type;
- if ((tpnmA = get_atomtype_name(tpA,atype)) == NULL)
- gmx_fatal(FARGS,"tpA = %d, i= %d in print_atoms",tpA,i);
-
- fprintf(out,"%6d %10s %6d%c %5s %6s %6d %10g %10g",
- i+1,tpnmA,
- at->resinfo[ri].nr,
- at->resinfo[ri].ic,
- bRTPresname ?
- *(at->resinfo[at->atom[i].resind].rtp) :
- *(at->resinfo[at->atom[i].resind].name),
- *(at->atomname[i]),cgnr[i],
- at->atom[i].q,at->atom[i].m);
- if (PERTURBED(at->atom[i])) {
- tpB = at->atom[i].typeB;
- if ((tpnmB = get_atomtype_name(tpB,atype)) == NULL)
- gmx_fatal(FARGS,"tpB = %d, i= %d in print_atoms",tpB,i);
- fprintf(out," %6s %10g %10g",
- tpnmB,at->atom[i].qB,at->atom[i].mB);
- }
- qtot += (double)at->atom[i].q;
- if ( fabs(qtot) < 4*GMX_REAL_EPS )
- qtot=0;
- fprintf(out," ; qtot %.4g\n",qtot);
+ int i, ri;
+ int tpA, tpB;
+ const char *as;
+ char *tpnmA, *tpnmB;
+ double qres, qtot;
+
+ as = dir2str(d_atoms);
+ fprintf(out, "[ %s ]\n", as);
+ fprintf(out, "; %4s %10s %6s %7s%6s %6s %10s %10s %6s %10s %10s\n",
+ "nr", "type", "resnr", "residue", "atom", "cgnr", "charge", "mass", "typeB", "chargeB", "massB");
+
+ qtot = 0;
+
+ if (debug)
+ {
+ fprintf(debug, "This molecule has %d atoms and %d residues\n",
+ at->nr, at->nres);
}
- }
- fprintf(out,"\n");
- fflush(out);
+
+ if (at->nres)
+ {
+ /* if the information is present... */
+ for (i = 0; (i < at->nr); i++)
+ {
+ ri = at->atom[i].resind;
+ if ((i == 0 || ri != at->atom[i-1].resind) &&
+ at->resinfo[ri].rtp != NULL)
+ {
+ qres = get_residue_charge(at, i);
+ fprintf(out, "; residue %3d %-3s rtp %-4s q ",
+ at->resinfo[ri].nr,
+ *at->resinfo[ri].name,
+ *at->resinfo[ri].rtp);
+ if (fabs(qres) < 0.001)
+ {
+ fprintf(out, " %s", "0.0");
+ }
+ else
+ {
+ fprintf(out, "%+3.1f", qres);
+ }
+ fprintf(out, "\n");
+ }
+ tpA = at->atom[i].type;
+ if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
+ {
+ gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
+ }
+
+ fprintf(out, "%6d %10s %6d%c %5s %6s %6d %10g %10g",
+ i+1, tpnmA,
+ at->resinfo[ri].nr,
+ at->resinfo[ri].ic,
+ bRTPresname ?
+ *(at->resinfo[at->atom[i].resind].rtp) :
+ *(at->resinfo[at->atom[i].resind].name),
+ *(at->atomname[i]), cgnr[i],
+ at->atom[i].q, at->atom[i].m);
+ if (PERTURBED(at->atom[i]))
+ {
+ tpB = at->atom[i].typeB;
+ if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
+ {
+ gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
+ }
+ fprintf(out, " %6s %10g %10g",
+ tpnmB, at->atom[i].qB, at->atom[i].mB);
+ }
+ qtot += (double)at->atom[i].q;
+ if (fabs(qtot) < 4*GMX_REAL_EPS)
+ {
+ qtot = 0;
+ }
+ fprintf(out, " ; qtot %.4g\n", qtot);
+ }
+ }
+ fprintf(out, "\n");
+ fflush(out);
}
-void print_bondeds(FILE *out,int natoms,directive d,
- int ftype,int fsubtype,t_params plist[])
+void print_bondeds(FILE *out, int natoms, directive d,
+ int ftype, int fsubtype, t_params plist[])
{
- t_symtab stab;
- gpp_atomtype_t atype;
- t_param *param;
- t_atom *a;
- int i;
-
- atype = init_atomtype();
- snew(a,1);
- snew(param,1);
- open_symtab(&stab);
- for (i=0; (i < natoms); i++) {
- char buf[12];
- sprintf(buf,"%4d",(i+1));
- add_atomtype(atype,&stab,a,buf,param,0,0,0,0,0,0,0);
- }
- print_bt(out,d,atype,ftype,fsubtype,plist,TRUE);
-
- done_symtab(&stab);
- sfree(a);
- sfree(param);
- done_atomtype(atype);
-}
+ t_symtab stab;
+ gpp_atomtype_t atype;
+ t_param *param;
+ t_atom *a;
+ int i;
+ atype = init_atomtype();
+ snew(a, 1);
+ snew(param, 1);
+ open_symtab(&stab);
+ for (i = 0; (i < natoms); i++)
+ {
+ char buf[12];
+ sprintf(buf, "%4d", (i+1));
+ add_atomtype(atype, &stab, a, buf, param, 0, 0, 0, 0, 0, 0, 0);
+ }
+ print_bt(out, d, atype, ftype, fsubtype, plist, TRUE);
+
+ done_symtab(&stab);
+ sfree(a);
+ sfree(param);
+ done_atomtype(atype);
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff