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40 #include "gromacs/legacyheaders/typedefs.h"
41 #include "gromacs/utility/smalloc.h"
42 #include "gromacs/commandline/pargs.h"
43 #include "gromacs/legacyheaders/macros.h"
44 #include "gromacs/utility/futil.h"
45 #include "gromacs/utility/fatalerror.h"
46 #include "gromacs/fileio/trxio.h"
48 static int calc_ntype(int nft, int *ft, t_idef *idef)
52 for (i = 0; (i < idef->ntypes); i++)
54 for (f = 0; f < nft; f++)
56 if (idef->functype[i] == ft[f])
66 static void fill_ft_ind(int nft, int *ft, t_idef *idef,
67 int ft_ind[], char *grpnames[])
70 int i, f, ftype, ind = 0;
72 /* Loop over all the function types in the topology */
73 for (i = 0; (i < idef->ntypes); i++)
76 /* Check all the selected function types */
77 for (f = 0; f < nft; f++)
80 if (idef->functype[i] == ftype)
86 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
87 idef->iparams[i].harmonic.krA);
90 sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
91 idef->iparams[i].harmonic.krA);
94 sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
95 idef->iparams[i].u_b.kthetaA);
97 case F_QUARTIC_ANGLES:
98 sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
99 idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
102 sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
103 idef->iparams[i].tab.kA);
106 sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
107 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
110 sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
111 idef->iparams[i].harmonic.krA);
114 sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
117 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
118 idef->iparams[i].harmonic.krA);
121 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
122 idef->iparams[i].harmonic.krA);
125 sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
129 gmx_fatal(FARGS, "Unsupported function type '%s' selected",
130 interaction_function[ftype].longname);
132 grpnames[ind] = gmx_strdup(buf);
139 static void fill_ang(int nft, int *ft, int fac,
140 int nr[], int *index[], int ft_ind[], t_topology *top,
141 gmx_bool bNoH, real hq)
143 int f, ftype, i, j, indg, nr_fac;
151 atom = top->atoms.atom;
153 for (f = 0; f < nft; f++)
156 ia = idef->il[ftype].iatoms;
157 for (i = 0; (i < idef->il[ftype].nr); )
159 indg = ft_ind[ia[0]];
162 gmx_incons("Routine fill_ang");
167 for (j = 0; j < fac; j++)
169 if (atom[ia[1+j]].m < 1.5)
177 for (j = 0; j < fac; j++)
179 if (atom[ia[1+j]].m < 1.5 && fabs(atom[ia[1+j]].q) < hq)
187 if (nr[indg] % 1000 == 0)
189 srenew(index[indg], fac*(nr[indg]+1000));
191 nr_fac = fac*nr[indg];
192 for (j = 0; (j < fac); j++)
194 index[indg][nr_fac+j] = ia[j+1];
198 ia += interaction_function[ftype].nratoms+1;
199 i += interaction_function[ftype].nratoms+1;
204 static int *select_ftype(const char *opt, int *nft, int *mult)
206 int *ft = NULL, ftype;
211 for (ftype = 0; ftype < F_NRE; ftype++)
213 if ((interaction_function[ftype].flags & IF_ATYPE) ||
214 ftype == F_TABANGLES)
246 int gmx_mk_angndx(int argc, char *argv[])
248 static const char *desc[] = {
249 "[THISMODULE] makes an index file for calculation of",
250 "angle distributions etc. It uses a run input file ([TT].tpx[tt]) for the",
251 "definitions of the angles, dihedrals etc."
253 static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
254 static gmx_bool bH = TRUE;
257 { "-type", FALSE, etENUM, {opt},
259 { "-hyd", FALSE, etBOOL, {&bH},
260 "Include angles with atoms with mass < 1.5" },
261 { "-hq", FALSE, etREAL, {&hq},
262 "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
269 int nft = 0, *ft, mult = 0;
275 { efTPX, NULL, NULL, ffREAD },
276 { efNDX, NULL, "angle", ffWRITE }
278 #define NFILE asize(fnm)
280 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
281 asize(desc), desc, 0, NULL, &oenv))
287 ft = select_ftype(opt[0], &nft, &mult);
289 top = read_top(ftp2fn(efTPX, NFILE, fnm), NULL);
291 ntype = calc_ntype(nft, ft, &(top->idef));
292 snew(grpnames, ntype);
293 snew(ft_ind, top->idef.ntypes);
294 fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
298 fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
300 out = ftp2FILE(efNDX, NFILE, fnm, "w");
301 for (i = 0; (i < ntype); i++)
305 fprintf(out, "[ %s ]\n", grpnames[i]);
306 for (j = 0; (j < nr[i]*mult); j++)
308 fprintf(out, " %5d", index[i][j]+1);