/*
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+ *
* 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.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* 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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+ *
* 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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* For more info, check our website at http://www.gromacs.org
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* And Hey:
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*/
#include "futil.h"
#include "gmx_fatal.h"
-static int calc_ntype(int nft,int *ft,t_idef *idef)
+static int calc_ntype(int nft, int *ft, t_idef *idef)
{
- int i,f,nf=0;
+ int i, f, nf = 0;
- for(i=0; (i<idef->ntypes); i++) {
- for(f=0; f<nft; f++) {
- if (idef->functype[i] == ft[f])
- nf++;
+ for (i = 0; (i < idef->ntypes); i++)
+ {
+ for (f = 0; f < nft; f++)
+ {
+ if (idef->functype[i] == ft[f])
+ {
+ nf++;
+ }
+ }
}
- }
- return nf;
+ return nf;
}
-static void fill_ft_ind(int nft,int *ft,t_idef *idef,
- int ft_ind[],char *grpnames[])
+static void fill_ft_ind(int nft, int *ft, t_idef *idef,
+ int ft_ind[], char *grpnames[])
{
- char buf[125];
- int i,f,ftype,ind=0;
+ char buf[125];
+ int i, f, ftype, ind = 0;
- /* Loop over all the function types in the topology */
- for(i=0; (i<idef->ntypes); i++) {
- ft_ind[i] = -1;
- /* Check all the selected function types */
- for(f=0; f<nft; f++) {
- ftype = ft[f];
- if (idef->functype[i] == ftype) {
- ft_ind[i] = ind;
- switch (ftype) {
- case F_ANGLES:
- sprintf(buf,"Theta=%.1f_%.2f",idef->iparams[i].harmonic.rA,
- idef->iparams[i].harmonic.krA);
- break;
- case F_G96ANGLES:
- sprintf(buf,"Cos_th=%.1f_%.2f",idef->iparams[i].harmonic.rA,
- idef->iparams[i].harmonic.krA);
- break;
- case F_UREY_BRADLEY:
- sprintf(buf,"UB_th=%.1f_%.2f2f",idef->iparams[i].u_b.thetaA,
- idef->iparams[i].u_b.kthetaA);
- break;
- case F_QUARTIC_ANGLES:
- sprintf(buf,"Q_th=%.1f_%.2f_%.2f",idef->iparams[i].qangle.theta,
- idef->iparams[i].qangle.c[0],idef->iparams[i].qangle.c[1]);
- break;
- case F_TABANGLES:
- sprintf(buf,"Table=%d_%.2f",idef->iparams[i].tab.table,
- idef->iparams[i].tab.kA);
- break;
- case F_PDIHS:
- sprintf(buf,"Phi=%.1f_%d_%.2f",idef->iparams[i].pdihs.phiA,
- idef->iparams[i].pdihs.mult,idef->iparams[i].pdihs.cpA);
- break;
- case F_IDIHS:
- sprintf(buf,"Xi=%.1f_%.2f",idef->iparams[i].harmonic.rA,
- idef->iparams[i].harmonic.krA);
- break;
- case F_RBDIHS:
- sprintf(buf,"RB-A1=%.2f",idef->iparams[i].rbdihs.rbcA[1]);
- break;
- default:
- gmx_fatal(FARGS,"Unsupported function type '%s' selected",
- interaction_function[ftype].longname);
- }
- grpnames[ind]=strdup(buf);
- ind++;
- }
+ /* Loop over all the function types in the topology */
+ for (i = 0; (i < idef->ntypes); i++)
+ {
+ ft_ind[i] = -1;
+ /* Check all the selected function types */
+ for (f = 0; f < nft; f++)
+ {
+ ftype = ft[f];
+ if (idef->functype[i] == ftype)
+ {
+ ft_ind[i] = ind;
+ switch (ftype)
+ {
+ case F_ANGLES:
+ sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ idef->iparams[i].harmonic.krA);
+ break;
+ case F_G96ANGLES:
+ sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ idef->iparams[i].harmonic.krA);
+ break;
+ case F_UREY_BRADLEY:
+ sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
+ idef->iparams[i].u_b.kthetaA);
+ break;
+ case F_QUARTIC_ANGLES:
+ sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
+ idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
+ break;
+ case F_TABANGLES:
+ sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
+ idef->iparams[i].tab.kA);
+ break;
+ case F_PDIHS:
+ sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
+ idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
+ break;
+ case F_IDIHS:
+ sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
+ idef->iparams[i].harmonic.krA);
+ break;
+ case F_RBDIHS:
+ sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
+ break;
+ default:
+ gmx_fatal(FARGS, "Unsupported function type '%s' selected",
+ interaction_function[ftype].longname);
+ }
+ grpnames[ind] = strdup(buf);
+ ind++;
+ }
+ }
}
- }
}
-static void fill_ang(int nft,int *ft,int fac,
- int nr[],int *index[],int ft_ind[],t_topology *top,
- gmx_bool bNoH,real hq)
+static void fill_ang(int nft, int *ft, int fac,
+ int nr[], int *index[], int ft_ind[], t_topology *top,
+ gmx_bool bNoH, real hq)
{
- int f,ftype,i,j,indg,nr_fac;
- gmx_bool bUse;
- t_idef *idef;
- t_atom *atom;
- t_iatom *ia;
+ int f, ftype, i, j, indg, nr_fac;
+ gmx_bool bUse;
+ t_idef *idef;
+ t_atom *atom;
+ t_iatom *ia;
- idef = &top->idef;
- atom = top->atoms.atom;
+ idef = &top->idef;
+ atom = top->atoms.atom;
- for(f=0; f<nft; f++) {
- ftype = ft[f];
- ia = idef->il[ftype].iatoms;
- for(i=0; (i<idef->il[ftype].nr); ) {
- indg = ft_ind[ia[0]];
- if (indg == -1)
- gmx_incons("Routine fill_ang");
- bUse = TRUE;
- if (bNoH) {
- for(j=0; j<fac; j++) {
- if (atom[ia[1+j]].m < 1.5)
- bUse = FALSE;
- }
- }
- if (hq) {
- for(j=0; j<fac; j++) {
- if (atom[ia[1+j]].m < 1.5 && fabs(atom[ia[1+j]].q) < hq)
- bUse = FALSE;
- }
- }
- if (bUse) {
- if (nr[indg] % 1000 == 0) {
- srenew(index[indg],fac*(nr[indg]+1000));
- }
- nr_fac = fac*nr[indg];
- for(j=0; (j<fac); j++)
- index[indg][nr_fac+j] = ia[j+1];
- nr[indg]++;
- }
- ia += interaction_function[ftype].nratoms+1;
- i += interaction_function[ftype].nratoms+1;
+ for (f = 0; f < nft; f++)
+ {
+ ftype = ft[f];
+ ia = idef->il[ftype].iatoms;
+ for (i = 0; (i < idef->il[ftype].nr); )
+ {
+ indg = ft_ind[ia[0]];
+ if (indg == -1)
+ {
+ gmx_incons("Routine fill_ang");
+ }
+ bUse = TRUE;
+ if (bNoH)
+ {
+ for (j = 0; j < fac; j++)
+ {
+ if (atom[ia[1+j]].m < 1.5)
+ {
+ bUse = FALSE;
+ }
+ }
+ }
+ if (hq)
+ {
+ for (j = 0; j < fac; j++)
+ {
+ if (atom[ia[1+j]].m < 1.5 && fabs(atom[ia[1+j]].q) < hq)
+ {
+ bUse = FALSE;
+ }
+ }
+ }
+ if (bUse)
+ {
+ if (nr[indg] % 1000 == 0)
+ {
+ srenew(index[indg], fac*(nr[indg]+1000));
+ }
+ nr_fac = fac*nr[indg];
+ for (j = 0; (j < fac); j++)
+ {
+ index[indg][nr_fac+j] = ia[j+1];
+ }
+ nr[indg]++;
+ }
+ ia += interaction_function[ftype].nratoms+1;
+ i += interaction_function[ftype].nratoms+1;
+ }
}
- }
}
-static int *select_ftype(const char *opt,int *nft,int *mult)
+static int *select_ftype(const char *opt, int *nft, int *mult)
{
- int *ft=NULL,ftype;
+ int *ft = NULL, ftype;
- if (opt[0] == 'a') {
- *mult = 3;
- for(ftype=0; ftype<F_NRE; ftype++) {
- if ((interaction_function[ftype].flags & IF_ATYPE) ||
- ftype == F_TABANGLES) {
- (*nft)++;
- srenew(ft,*nft);
- ft[*nft-1] = ftype;
- }
+ if (opt[0] == 'a')
+ {
+ *mult = 3;
+ for (ftype = 0; ftype < F_NRE; ftype++)
+ {
+ if ((interaction_function[ftype].flags & IF_ATYPE) ||
+ ftype == F_TABANGLES)
+ {
+ (*nft)++;
+ srenew(ft, *nft);
+ ft[*nft-1] = ftype;
+ }
+ }
}
- } else {
- *mult = 4;
- *nft = 1;
- snew(ft,*nft);
- switch(opt[0]) {
- case 'd':
- ft[0] = F_PDIHS;
- break;
- case 'i':
- ft[0] = F_IDIHS;
- break;
- case 'r':
- ft[0] = F_RBDIHS;
- break;
- default:
- break;
+ else
+ {
+ *mult = 4;
+ *nft = 1;
+ snew(ft, *nft);
+ switch (opt[0])
+ {
+ case 'd':
+ ft[0] = F_PDIHS;
+ break;
+ case 'i':
+ ft[0] = F_IDIHS;
+ break;
+ case 'r':
+ ft[0] = F_RBDIHS;
+ break;
+ default:
+ break;
+ }
}
- }
- return ft;
+ return ft;
}
-int gmx_mk_angndx(int argc,char *argv[])
+int gmx_mk_angndx(int argc, char *argv[])
{
- static const char *desc[] = {
- "[TT]mk_angndx[tt] makes an index file for calculation of",
- "angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
- "definitions of the angles, dihedrals etc."
- };
- static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
- static gmx_bool bH=TRUE;
- static real hq=-1;
- t_pargs pa[] = {
- { "-type", FALSE, etENUM, {opt},
- "Type of angle" },
- { "-hyd", FALSE, etBOOL, {&bH},
- "Include angles with atoms with mass < 1.5" },
- { "-hq", FALSE, etREAL, {&hq},
- "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
- };
-
- output_env_t oenv;
- FILE *out;
- t_topology *top;
- int i,j,ntype;
- int nft=0,*ft,mult=0;
- int **index;
- int *ft_ind;
- int *nr;
- char **grpnames;
- t_filenm fnm[] = {
- { efTPX, NULL, NULL, ffREAD },
- { efNDX, NULL, "angle", ffWRITE }
- };
+ static const char *desc[] = {
+ "[TT]mk_angndx[tt] makes an index file for calculation of",
+ "angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
+ "definitions of the angles, dihedrals etc."
+ };
+ static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
+ static gmx_bool bH = TRUE;
+ static real hq = -1;
+ t_pargs pa[] = {
+ { "-type", FALSE, etENUM, {opt},
+ "Type of angle" },
+ { "-hyd", FALSE, etBOOL, {&bH},
+ "Include angles with atoms with mass < 1.5" },
+ { "-hq", FALSE, etREAL, {&hq},
+ "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
+ };
+
+ output_env_t oenv;
+ FILE *out;
+ t_topology *top;
+ int i, j, ntype;
+ int nft = 0, *ft, mult = 0;
+ int **index;
+ int *ft_ind;
+ int *nr;
+ char **grpnames;
+ t_filenm fnm[] = {
+ { efTPX, NULL, NULL, ffREAD },
+ { efNDX, NULL, "angle", ffWRITE }
+ };
#define NFILE asize(fnm)
- parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
- asize(desc),desc,0,NULL,&oenv);
+ parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, NULL, &oenv);
+
+
+ ft = select_ftype(opt[0], &nft, &mult);
+ top = read_top(ftp2fn(efTPX, NFILE, fnm), NULL);
- ft = select_ftype(opt[0],&nft,&mult);
+ ntype = calc_ntype(nft, ft, &(top->idef));
+ snew(grpnames, ntype);
+ snew(ft_ind, top->idef.ntypes);
+ fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
- top = read_top(ftp2fn(efTPX,NFILE,fnm),NULL);
+ snew(nr, ntype);
+ snew(index, ntype);
+ fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
- ntype = calc_ntype(nft,ft,&(top->idef));
- snew(grpnames,ntype);
- snew(ft_ind,top->idef.ntypes);
- fill_ft_ind(nft,ft,&top->idef,ft_ind,grpnames);
-
- snew(nr,ntype);
- snew(index,ntype);
- fill_ang(nft,ft,mult,nr,index,ft_ind,top,!bH,hq);
-
- out=ftp2FILE(efNDX,NFILE,fnm,"w");
- for(i=0; (i<ntype); i++) {
- if (nr[i] > 0) {
- fprintf(out,"[ %s ]\n",grpnames[i]);
- for(j=0; (j<nr[i]*mult); j++) {
- fprintf(out," %5d",index[i][j]+1);
- if ((j % 12) == 11)
- fprintf(out,"\n");
- }
- fprintf(out,"\n");
+ out = ftp2FILE(efNDX, NFILE, fnm, "w");
+ for (i = 0; (i < ntype); i++)
+ {
+ if (nr[i] > 0)
+ {
+ fprintf(out, "[ %s ]\n", grpnames[i]);
+ for (j = 0; (j < nr[i]*mult); j++)
+ {
+ fprintf(out, " %5d", index[i][j]+1);
+ if ((j % 12) == 11)
+ {
+ fprintf(out, "\n");
+ }
+ }
+ fprintf(out, "\n");
+ }
}
- }
- ffclose(out);
-
- thanx(stderr);
-
- return 0;
+ ffclose(out);
+
+ thanx(stderr);
+
+ return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff