/*
- *
- * 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) 2011,2014, 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,
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+ * 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
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+ * 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.
- *
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- *
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- * 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 "txtdump.h"
#include "gpp_atomtype.h"
+#include <math.h>
+#include <string.h>
+
+#include "gromacs/gmxpreprocess/topdirs.h"
+#include "gromacs/gmxpreprocess/toputil.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
typedef struct gpp_atomtype {
- int nr; /* The number of atomtypes */
- t_atom *atom; /* Array of atoms */
- char ***atomname; /* Names of the atomtypes */
- t_param *nb; /* Nonbonded force default params */
- int *bondatomtype; /* The bond_atomtype for each atomtype */
- real *radius; /* Radius for GBSA stuff */
- real *vol; /* Effective volume for GBSA */
- real *surftens; /* Surface tension with water, for GBSA */
- real *gb_radius; /* Radius for Still model */
- real *S_hct; /* Overlap factor for HCT model */
- int *atomnumber; /* Atomic number, used for QM/MM */
+ int nr; /* The number of atomtypes */
+ t_atom *atom; /* Array of atoms */
+ char ***atomname; /* Names of the atomtypes */
+ t_param *nb; /* Nonbonded force default params */
+ int *bondatomtype; /* The bond_atomtype for each atomtype */
+ real *radius; /* Radius for GBSA stuff */
+ real *vol; /* Effective volume for GBSA */
+ real *surftens; /* Surface tension with water, for GBSA */
+ real *gb_radius; /* Radius for Still model */
+ real *S_hct; /* Overlap factor for HCT model */
+ int *atomnumber; /* Atomic number, used for QM/MM */
} t_gpp_atomtype;
-int get_atomtype_type(const char *str,gpp_atomtype_t ga)
+int get_atomtype_type(const char *str, gpp_atomtype_t ga)
{
- int i;
-
- /* Atom types are always case sensitive */
- for (i=0; (i<ga->nr); i++)
- if (strcmp(str,*(ga->atomname[i])) == 0)
- return i;
-
- return NOTSET;
+ int i;
+
+ /* Atom types are always case sensitive */
+ for (i = 0; (i < ga->nr); i++)
+ {
+ if (strcmp(str, *(ga->atomname[i])) == 0)
+ {
+ return i;
+ }
+ }
+
+ return NOTSET;
}
int get_atomtype_ntypes(gpp_atomtype_t ga)
{
- return ga->nr;
+ return ga->nr;
}
char *get_atomtype_name(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NULL;
-
- return *(ga->atomname[nt]);
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NULL;
+ }
+
+ return *(ga->atomname[nt]);
}
-real get_atomtype_massA(int nt,gpp_atomtype_t ga)
+real get_atomtype_massA(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atom[nt].m;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atom[nt].m;
}
-real get_atomtype_massB(int nt,gpp_atomtype_t ga)
+real get_atomtype_massB(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atom[nt].mB;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atom[nt].mB;
}
-real get_atomtype_qA(int nt,gpp_atomtype_t ga)
-{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atom[nt].q;
+real get_atomtype_qA(int nt, gpp_atomtype_t ga)
+{
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atom[nt].q;
}
-real get_atomtype_qB(int nt,gpp_atomtype_t ga)
+real get_atomtype_qB(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atom[nt].qB;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atom[nt].qB;
}
-int get_atomtype_ptype(int nt,gpp_atomtype_t ga)
+int get_atomtype_ptype(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atom[nt].ptype;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atom[nt].ptype;
}
-int get_atomtype_batype(int nt,gpp_atomtype_t ga)
+int get_atomtype_batype(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->bondatomtype[nt];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->bondatomtype[nt];
}
-int get_atomtype_atomnumber(int nt,gpp_atomtype_t ga)
+int get_atomtype_atomnumber(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->atomnumber[nt];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->atomnumber[nt];
}
-real get_atomtype_radius(int nt,gpp_atomtype_t ga)
+real get_atomtype_radius(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->radius[nt];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->radius[nt];
}
-real get_atomtype_vol(int nt,gpp_atomtype_t ga)
+real get_atomtype_vol(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->vol[nt];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->vol[nt];
}
-real get_atomtype_surftens(int nt,gpp_atomtype_t ga)
+real get_atomtype_surftens(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- return ga->surftens[nt];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ return ga->surftens[nt];
}
-real get_atomtype_gb_radius(int nt,gpp_atomtype_t ga)
+real get_atomtype_gb_radius(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
- return ga->gb_radius[nt];
+ return ga->gb_radius[nt];
}
-real get_atomtype_S_hct(int nt,gpp_atomtype_t ga)
+real get_atomtype_S_hct(int nt, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
- return ga->S_hct[nt];
+ return ga->S_hct[nt];
}
-real get_atomtype_nbparam(int nt,int param,gpp_atomtype_t ga)
+real get_atomtype_nbparam(int nt, int param, gpp_atomtype_t ga)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
- if ((param < 0) || (param >= MAXFORCEPARAM))
- return NOTSET;
- return ga->nb[nt].c[param];
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+ if ((param < 0) || (param >= MAXFORCEPARAM))
+ {
+ return NOTSET;
+ }
+ return ga->nb[nt].c[param];
}
gpp_atomtype_t init_atomtype(void)
{
- gpp_atomtype_t ga;
-
- snew(ga,1);
-
- ga->nr = 0;
- ga->atom = NULL;
- ga->atomname = NULL;
- ga->nb = NULL;
- ga->bondatomtype = NULL;
- ga->radius = NULL;
- ga->vol = NULL;
- ga->surftens = NULL;
- ga->atomnumber = NULL;
- ga->gb_radius = NULL;
- ga->S_hct = NULL;
-
- return ga;
+ gpp_atomtype_t ga;
+
+ snew(ga, 1);
+
+ ga->nr = 0;
+ ga->atom = NULL;
+ ga->atomname = NULL;
+ ga->nb = NULL;
+ ga->bondatomtype = NULL;
+ ga->radius = NULL;
+ ga->vol = NULL;
+ ga->surftens = NULL;
+ ga->atomnumber = NULL;
+ ga->gb_radius = NULL;
+ ga->S_hct = NULL;
+
+ return ga;
}
int
set_atomtype_gbparam(gpp_atomtype_t ga, int i,
- real radius,real vol,real surftens,
+ real radius, real vol, real surftens,
real gb_radius, real S_hct)
{
- if ( (i < 0) || (i>= ga->nr))
- return NOTSET;
+ if ( (i < 0) || (i >= ga->nr))
+ {
+ return NOTSET;
+ }
- ga->radius[i] = radius;
- ga->vol[i] = vol;
- ga->surftens[i] = surftens;
- ga->gb_radius[i] = gb_radius;
- ga->S_hct[i] = S_hct;
+ ga->radius[i] = radius;
+ ga->vol[i] = vol;
+ ga->surftens[i] = surftens;
+ ga->gb_radius[i] = gb_radius;
+ ga->S_hct[i] = S_hct;
- return i;
+ return i;
}
-int set_atomtype(int nt,gpp_atomtype_t ga,t_symtab *tab,
- t_atom *a,const char *name,t_param *nb,
- int bondatomtype,
- real radius,real vol,real surftens,int atomnumber,
+int set_atomtype(int nt, gpp_atomtype_t ga, t_symtab *tab,
+ t_atom *a, const char *name, t_param *nb,
+ int bondatomtype,
+ real radius, real vol, real surftens, int atomnumber,
real gb_radius, real S_hct)
{
- if ((nt < 0) || (nt >= ga->nr))
- return NOTSET;
-
- ga->atom[nt] = *a;
- ga->atomname[nt] = put_symtab(tab,name);
- ga->nb[nt] = *nb;
- ga->bondatomtype[nt] = bondatomtype;
- ga->radius[nt] = radius;
- ga->vol[nt] = vol;
- ga->surftens[nt] = surftens;
- ga->atomnumber[nt] = atomnumber;
- ga->gb_radius[nt] = gb_radius;
- ga->S_hct[nt] = S_hct;
-
- return nt;
+ if ((nt < 0) || (nt >= ga->nr))
+ {
+ return NOTSET;
+ }
+
+ ga->atom[nt] = *a;
+ ga->atomname[nt] = put_symtab(tab, name);
+ ga->nb[nt] = *nb;
+ ga->bondatomtype[nt] = bondatomtype;
+ ga->radius[nt] = radius;
+ ga->vol[nt] = vol;
+ ga->surftens[nt] = surftens;
+ ga->atomnumber[nt] = atomnumber;
+ ga->gb_radius[nt] = gb_radius;
+ ga->S_hct[nt] = S_hct;
+
+ return nt;
}
-int add_atomtype(gpp_atomtype_t ga,t_symtab *tab,
- t_atom *a,const char *name,t_param *nb,
- int bondatomtype,
- real radius,real vol,real surftens,real atomnumber,
- real gb_radius, real S_hct)
+int add_atomtype(gpp_atomtype_t ga, t_symtab *tab,
+ t_atom *a, const char *name, t_param *nb,
+ int bondatomtype,
+ real radius, real vol, real surftens, real atomnumber,
+ real gb_radius, real S_hct)
{
- int i;
-
- for(i=0; (i<ga->nr); i++) {
- if (strcmp(*ga->atomname[i],name) == 0) {
- if (NULL != debug)
- fprintf(debug,"Trying to add atomtype %s again. Skipping it.\n",name);
- break;
- }
- }
- if (i == ga->nr) {
- ga->nr++;
- srenew(ga->atom,ga->nr);
- srenew(ga->atomname,ga->nr);
- srenew(ga->nb,ga->nr);
- srenew(ga->bondatomtype,ga->nr);
- srenew(ga->radius,ga->nr);
- srenew(ga->vol,ga->nr);
- srenew(ga->surftens,ga->nr);
- srenew(ga->atomnumber,ga->nr);
- srenew(ga->gb_radius,ga->nr);
- srenew(ga->S_hct,ga->nr);
-
- return set_atomtype(ga->nr-1,ga,tab,a,name,nb,bondatomtype,radius,
- vol,surftens,atomnumber,gb_radius,S_hct);
- }
- else
- return i;
+ int i;
+
+ for (i = 0; (i < ga->nr); i++)
+ {
+ if (strcmp(*ga->atomname[i], name) == 0)
+ {
+ if (NULL != debug)
+ {
+ fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
+ }
+ break;
+ }
+ }
+ if (i == ga->nr)
+ {
+ ga->nr++;
+ srenew(ga->atom, ga->nr);
+ srenew(ga->atomname, ga->nr);
+ srenew(ga->nb, ga->nr);
+ srenew(ga->bondatomtype, ga->nr);
+ srenew(ga->radius, ga->nr);
+ srenew(ga->vol, ga->nr);
+ srenew(ga->surftens, ga->nr);
+ srenew(ga->atomnumber, ga->nr);
+ srenew(ga->gb_radius, ga->nr);
+ srenew(ga->S_hct, ga->nr);
+
+ return set_atomtype(ga->nr-1, ga, tab, a, name, nb, bondatomtype, radius,
+ vol, surftens, atomnumber, gb_radius, S_hct);
+ }
+ else
+ {
+ return i;
+ }
}
void print_at (FILE * out, gpp_atomtype_t ga)
{
- int i;
- t_atom *atom = ga->atom;
- t_param *nb = ga->nb;
-
- fprintf (out,"[ %s ]\n",dir2str(d_atomtypes));
- fprintf (out,"; %6s %8s %8s %8s %12s %12s\n",
- "type","mass","charge","particle","c6","c12");
- for (i=0; (i<ga->nr); i++)
- fprintf(out,"%8s %8.3f %8.3f %8s %12e %12e\n",
- *(ga->atomname[i]),atom[i].m,atom[i].q,"A",
- nb[i].C0,nb[i].C1);
-
- fprintf (out,"\n");
+ int i;
+ t_atom *atom = ga->atom;
+ t_param *nb = ga->nb;
+
+ fprintf (out, "[ %s ]\n", dir2str(d_atomtypes));
+ fprintf (out, "; %6s %8s %8s %8s %12s %12s\n",
+ "type", "mass", "charge", "particle", "c6", "c12");
+ for (i = 0; (i < ga->nr); i++)
+ {
+ fprintf(out, "%8s %8.3f %8.3f %8s %12e %12e\n",
+ *(ga->atomname[i]), atom[i].m, atom[i].q, "A",
+ nb[i].C0, nb[i].C1);
+ }
+
+ fprintf (out, "\n");
}
void done_atomtype(gpp_atomtype_t ga)
{
- sfree(ga->atom);
- sfree(ga->atomname);
- sfree(ga->nb);
- sfree(ga->bondatomtype);
- sfree(ga->radius);
- sfree(ga->vol);
- sfree(ga->gb_radius);
- sfree(ga->S_hct);
- sfree(ga->surftens);
- sfree(ga->atomnumber);
- ga->nr = 0;
- sfree(ga);
- ga = NULL;
+ sfree(ga->atom);
+ sfree(ga->atomname);
+ sfree(ga->nb);
+ sfree(ga->bondatomtype);
+ sfree(ga->radius);
+ sfree(ga->vol);
+ sfree(ga->gb_radius);
+ sfree(ga->S_hct);
+ sfree(ga->surftens);
+ sfree(ga->atomnumber);
+ ga->nr = 0;
+ sfree(ga);
}
-static int search_atomtypes(gpp_atomtype_t ga,int *n,int typelist[],
- int thistype,
- t_param param[],int ftype)
+static int search_atomtypes(gpp_atomtype_t ga, int *n, int typelist[],
+ int thistype,
+ t_param param[], int ftype)
{
- int i,nn,nrfp,j,k,ntype,tli;
- gmx_bool bFound=FALSE;
-
- nn = *n;
- nrfp = NRFP(ftype);
- ntype = get_atomtype_ntypes(ga);
-
- for(i=0; (i<nn); i++)
- {
- if (typelist[i] == thistype)
- {
- /* This type number has already been added */
- break;
- }
-
- /* Otherwise, check if the parameters are identical to any previously added type */
-
- bFound=TRUE;
- for(j=0;j<ntype && bFound;j++)
- {
- /* Check nonbonded parameters */
- for(k=0;k<nrfp && bFound;k++)
- {
- bFound=(param[ntype*typelist[i]+j].c[k]==param[ntype*thistype+j].c[k]);
- }
-
- /* Check radius, volume, surftens */
- tli = typelist[i];
- bFound = bFound &&
- (get_atomtype_radius(tli,ga) == get_atomtype_radius(thistype,ga)) &&
- (get_atomtype_vol(tli,ga) == get_atomtype_vol(thistype,ga)) &&
- (get_atomtype_surftens(tli,ga) == get_atomtype_surftens(thistype,ga)) &&
- (get_atomtype_atomnumber(tli,ga) == get_atomtype_atomnumber(thistype,ga)) &&
- (get_atomtype_gb_radius(tli,ga) == get_atomtype_gb_radius(thistype,ga)) &&
- (get_atomtype_S_hct(tli,ga) == get_atomtype_S_hct(thistype,ga));
- }
- if (bFound)
- {
- break;
- }
- }
-
- if (i == nn) {
- if (debug)
- fprintf(debug,"Renumbering atomtype %d to %d\n",thistype,nn);
- if (nn == ntype)
- gmx_fatal(FARGS,"Atomtype horror n = %d, %s, %d",nn,__FILE__,__LINE__);
- typelist[nn]=thistype;
- nn++;
- }
- *n = nn;
-
- return i;
+ int i, nn, nrfp, j, k, ntype, tli;
+ gmx_bool bFound = FALSE;
+
+ nn = *n;
+ nrfp = NRFP(ftype);
+ ntype = get_atomtype_ntypes(ga);
+
+ for (i = 0; (i < nn); i++)
+ {
+ if (typelist[i] == thistype)
+ {
+ /* This type number has already been added */
+ break;
+ }
+
+ /* Otherwise, check if the parameters are identical to any previously added type */
+
+ bFound = TRUE;
+ for (j = 0; j < ntype && bFound; j++)
+ {
+ /* Check nonbonded parameters */
+ for (k = 0; k < nrfp && bFound; k++)
+ {
+ bFound = (param[ntype*typelist[i]+j].c[k] == param[ntype*thistype+j].c[k]);
+ }
+
+ /* Check radius, volume, surftens */
+ tli = typelist[i];
+ bFound = bFound &&
+ (get_atomtype_radius(tli, ga) == get_atomtype_radius(thistype, ga)) &&
+ (get_atomtype_vol(tli, ga) == get_atomtype_vol(thistype, ga)) &&
+ (get_atomtype_surftens(tli, ga) == get_atomtype_surftens(thistype, ga)) &&
+ (get_atomtype_atomnumber(tli, ga) == get_atomtype_atomnumber(thistype, ga)) &&
+ (get_atomtype_gb_radius(tli, ga) == get_atomtype_gb_radius(thistype, ga)) &&
+ (get_atomtype_S_hct(tli, ga) == get_atomtype_S_hct(thistype, ga));
+ }
+ if (bFound)
+ {
+ break;
+ }
+ }
+
+ if (i == nn)
+ {
+ if (debug)
+ {
+ fprintf(debug, "Renumbering atomtype %d to %d\n", thistype, nn);
+ }
+ if (nn == ntype)
+ {
+ gmx_fatal(FARGS, "Atomtype horror n = %d, %s, %d", nn, __FILE__, __LINE__);
+ }
+ typelist[nn] = thistype;
+ nn++;
+ }
+ *n = nn;
+
+ return i;
}
-void renum_atype(t_params plist[],gmx_mtop_t *mtop,
- int *wall_atomtype,
- gpp_atomtype_t ga,gmx_bool bVerbose)
+void renum_atype(t_params plist[], gmx_mtop_t *mtop,
+ int *wall_atomtype,
+ gpp_atomtype_t ga, gmx_bool bVerbose)
{
- int i,j,k,l,molt,mi,mj,nat,nrfp,ftype,ntype;
- t_atoms *atoms;
- t_param *nbsnew;
- int *typelist;
- real *new_radius;
- real *new_vol;
- real *new_surftens;
- real *new_gb_radius;
- real *new_S_hct;
- int *new_atomnumber;
- char ***new_atomname;
-
- ntype = get_atomtype_ntypes(ga);
- snew(typelist,ntype);
-
- if (bVerbose)
- fprintf(stderr,"renumbering atomtypes...\n");
-
- /* Since the bonded interactions have been assigned now,
- * we want to reduce the number of atom types by merging
- * ones with identical nonbonded interactions, in addition
- * to removing unused ones.
- *
- * With Generalized-Born electrostatics, or implicit solvent
- * we also check that the atomtype radius, effective_volume
- * and surface tension match.
- *
- * With QM/MM we also check that the atom numbers match
- */
-
- /* Get nonbonded interaction type */
- if (plist[F_LJ].nr > 0)
- ftype=F_LJ;
- else
- ftype=F_BHAM;
-
- /* Renumber atomtypes by first making a list of which ones are actually used.
- * We provide the list of nonbonded parameters so search_atomtypes
- * can determine if two types should be merged.
- */
- nat=0;
- for(molt=0; molt<mtop->nmoltype; molt++) {
- atoms = &mtop->moltype[molt].atoms;
- for(i=0; (i<atoms->nr); i++) {
- atoms->atom[i].type =
- search_atomtypes(ga,&nat,typelist,atoms->atom[i].type,
- plist[ftype].param,ftype);
- atoms->atom[i].typeB=
- search_atomtypes(ga,&nat,typelist,atoms->atom[i].typeB,
- plist[ftype].param,ftype);
- }
- }
-
- for(i=0; i<2; i++) {
- if (wall_atomtype[i] >= 0)
- wall_atomtype[i] = search_atomtypes(ga,&nat,typelist,wall_atomtype[i],
- plist[ftype].param,ftype);
- }
-
- snew(new_radius,nat);
- snew(new_vol,nat);
- snew(new_surftens,nat);
- snew(new_atomnumber,nat);
- snew(new_gb_radius,nat);
- snew(new_S_hct,nat);
- snew(new_atomname,nat);
-
- /* We now have a list of unique atomtypes in typelist */
-
- if (debug)
- pr_ivec(debug,0,"typelist",typelist,nat,TRUE);
-
- /* Renumber nlist */
- nbsnew = NULL;
- snew(nbsnew,plist[ftype].nr);
-
- nrfp = NRFP(ftype);
-
- for(i=k=0; (i<nat); i++)
- {
- mi=typelist[i];
- for(j=0; (j<nat); j++,k++)
- {
- mj=typelist[j];
- for(l=0; (l<nrfp); l++)
- {
- nbsnew[k].c[l]=plist[ftype].param[ntype*mi+mj].c[l];
- }
- }
- new_radius[i] = get_atomtype_radius(mi,ga);
- new_vol[i] = get_atomtype_vol(mi,ga);
- new_surftens[i] = get_atomtype_surftens(mi,ga);
- new_atomnumber[i] = get_atomtype_atomnumber(mi,ga);
- new_gb_radius[i] = get_atomtype_gb_radius(mi,ga);
- new_S_hct[i] = get_atomtype_S_hct(mi,ga);
- new_atomname[i] = ga->atomname[mi];
- }
-
- for(i=0; (i<nat*nat); i++) {
- for(l=0; (l<nrfp); l++)
- plist[ftype].param[i].c[l]=nbsnew[i].c[l];
- }
- plist[ftype].nr=i;
- mtop->ffparams.atnr = nat;
-
- sfree(ga->radius);
- sfree(ga->vol);
- sfree(ga->surftens);
- sfree(ga->atomnumber);
- sfree(ga->gb_radius);
- sfree(ga->S_hct);
- /* Dangling atomname pointers ? */
- sfree(ga->atomname);
-
- ga->radius = new_radius;
- ga->vol = new_vol;
- ga->surftens = new_surftens;
- ga->atomnumber = new_atomnumber;
- ga->gb_radius = new_gb_radius;
- ga->S_hct = new_S_hct;
- ga->atomname = new_atomname;
-
- ga->nr=nat;
-
- sfree(nbsnew);
- sfree(typelist);
+ int i, j, k, l, molt, mi, mj, nat, nrfp, ftype, ntype;
+ t_atoms *atoms;
+ t_param *nbsnew;
+ int *typelist;
+ real *new_radius;
+ real *new_vol;
+ real *new_surftens;
+ real *new_gb_radius;
+ real *new_S_hct;
+ int *new_atomnumber;
+ char ***new_atomname;
+
+ ntype = get_atomtype_ntypes(ga);
+ snew(typelist, ntype);
+
+ if (bVerbose)
+ {
+ fprintf(stderr, "renumbering atomtypes...\n");
+ }
+
+ /* Since the bonded interactions have been assigned now,
+ * we want to reduce the number of atom types by merging
+ * ones with identical nonbonded interactions, in addition
+ * to removing unused ones.
+ *
+ * With Generalized-Born electrostatics, or implicit solvent
+ * we also check that the atomtype radius, effective_volume
+ * and surface tension match.
+ *
+ * With QM/MM we also check that the atom numbers match
+ */
+
+ /* Get nonbonded interaction type */
+ if (plist[F_LJ].nr > 0)
+ {
+ ftype = F_LJ;
+ }
+ else
+ {
+ ftype = F_BHAM;
+ }
+
+ /* Renumber atomtypes by first making a list of which ones are actually used.
+ * We provide the list of nonbonded parameters so search_atomtypes
+ * can determine if two types should be merged.
+ */
+ nat = 0;
+ for (molt = 0; molt < mtop->nmoltype; molt++)
+ {
+ atoms = &mtop->moltype[molt].atoms;
+ for (i = 0; (i < atoms->nr); i++)
+ {
+ atoms->atom[i].type =
+ search_atomtypes(ga, &nat, typelist, atoms->atom[i].type,
+ plist[ftype].param, ftype);
+ atoms->atom[i].typeB =
+ search_atomtypes(ga, &nat, typelist, atoms->atom[i].typeB,
+ plist[ftype].param, ftype);
+ }
+ }
+
+ for (i = 0; i < 2; i++)
+ {
+ if (wall_atomtype[i] >= 0)
+ {
+ wall_atomtype[i] = search_atomtypes(ga, &nat, typelist, wall_atomtype[i],
+ plist[ftype].param, ftype);
+ }
+ }
+
+ snew(new_radius, nat);
+ snew(new_vol, nat);
+ snew(new_surftens, nat);
+ snew(new_atomnumber, nat);
+ snew(new_gb_radius, nat);
+ snew(new_S_hct, nat);
+ snew(new_atomname, nat);
+
+ /* We now have a list of unique atomtypes in typelist */
+
+ if (debug)
+ {
+ pr_ivec(debug, 0, "typelist", typelist, nat, TRUE);
+ }
+
+ /* Renumber nlist */
+ nbsnew = NULL;
+ snew(nbsnew, plist[ftype].nr);
+
+ nrfp = NRFP(ftype);
+
+ for (i = k = 0; (i < nat); i++)
+ {
+ mi = typelist[i];
+ for (j = 0; (j < nat); j++, k++)
+ {
+ mj = typelist[j];
+ for (l = 0; (l < nrfp); l++)
+ {
+ nbsnew[k].c[l] = plist[ftype].param[ntype*mi+mj].c[l];
+ }
+ }
+ new_radius[i] = get_atomtype_radius(mi, ga);
+ new_vol[i] = get_atomtype_vol(mi, ga);
+ new_surftens[i] = get_atomtype_surftens(mi, ga);
+ new_atomnumber[i] = get_atomtype_atomnumber(mi, ga);
+ new_gb_radius[i] = get_atomtype_gb_radius(mi, ga);
+ new_S_hct[i] = get_atomtype_S_hct(mi, ga);
+ new_atomname[i] = ga->atomname[mi];
+ }
+
+ for (i = 0; (i < nat*nat); i++)
+ {
+ for (l = 0; (l < nrfp); l++)
+ {
+ plist[ftype].param[i].c[l] = nbsnew[i].c[l];
+ }
+ }
+ plist[ftype].nr = i;
+ mtop->ffparams.atnr = nat;
+
+ sfree(ga->radius);
+ sfree(ga->vol);
+ sfree(ga->surftens);
+ sfree(ga->atomnumber);
+ sfree(ga->gb_radius);
+ sfree(ga->S_hct);
+ /* Dangling atomname pointers ? */
+ sfree(ga->atomname);
+
+ ga->radius = new_radius;
+ ga->vol = new_vol;
+ ga->surftens = new_surftens;
+ ga->atomnumber = new_atomnumber;
+ ga->gb_radius = new_gb_radius;
+ ga->S_hct = new_S_hct;
+ ga->atomname = new_atomname;
+
+ ga->nr = nat;
+
+ sfree(nbsnew);
+ sfree(typelist);
}
-void copy_atomtype_atomtypes(gpp_atomtype_t ga,t_atomtypes *atomtypes)
+void copy_atomtype_atomtypes(gpp_atomtype_t ga, t_atomtypes *atomtypes)
{
- int i,ntype;
-
- /* Copy the atomtype data to the topology atomtype list */
- ntype = get_atomtype_ntypes(ga);
- atomtypes->nr=ntype;
- snew(atomtypes->radius,ntype);
- snew(atomtypes->vol,ntype);
- snew(atomtypes->surftens,ntype);
- snew(atomtypes->atomnumber,ntype);
- snew(atomtypes->gb_radius,ntype);
- snew(atomtypes->S_hct,ntype);
-
- for(i=0; i<ntype; i++) {
- atomtypes->radius[i] = ga->radius[i];
- atomtypes->vol[i] = ga->vol[i];
- atomtypes->surftens[i] = ga->surftens[i];
- atomtypes->atomnumber[i] = ga->atomnumber[i];
- atomtypes->gb_radius[i] = ga->gb_radius[i];
- atomtypes->S_hct[i] = ga->S_hct[i];
- }
+ int i, ntype;
+
+ /* Copy the atomtype data to the topology atomtype list */
+ ntype = get_atomtype_ntypes(ga);
+ atomtypes->nr = ntype;
+ snew(atomtypes->radius, ntype);
+ snew(atomtypes->vol, ntype);
+ snew(atomtypes->surftens, ntype);
+ snew(atomtypes->atomnumber, ntype);
+ snew(atomtypes->gb_radius, ntype);
+ snew(atomtypes->S_hct, ntype);
+
+ for (i = 0; i < ntype; i++)
+ {
+ atomtypes->radius[i] = ga->radius[i];
+ atomtypes->vol[i] = ga->vol[i];
+ atomtypes->surftens[i] = ga->surftens[i];
+ atomtypes->atomnumber[i] = ga->atomnumber[i];
+ atomtypes->gb_radius[i] = ga->gb_radius[i];
+ atomtypes->S_hct[i] = ga->S_hct[i];
+ }
}
-
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff