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41 #include "gromacs/commandline/pargs.h"
42 #include "gromacs/fileio/trxio.h"
43 #include "gromacs/gmxana/gmx_ana.h"
44 #include "gromacs/legacyheaders/macros.h"
45 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/utility/cstringutil.h"
47 #include "gromacs/utility/fatalerror.h"
48 #include "gromacs/utility/futil.h"
49 #include "gromacs/utility/gmxassert.h"
50 #include "gromacs/utility/smalloc.h"
52 static int calc_ntype(int nft, int *ft, t_idef *idef)
56 for (i = 0; (i < idef->ntypes); i++)
58 for (f = 0; f < nft; f++)
60 if (idef->functype[i] == ft[f])
70 static void fill_ft_ind(int nft, int *ft, t_idef *idef,
71 int ft_ind[], char *grpnames[])
74 int i, f, ftype, ind = 0;
76 /* Loop over all the function types in the topology */
77 for (i = 0; (i < idef->ntypes); i++)
80 /* Check all the selected function types */
81 for (f = 0; f < nft; f++)
84 if (idef->functype[i] == ftype)
90 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
91 idef->iparams[i].harmonic.krA);
94 sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
95 idef->iparams[i].harmonic.krA);
98 sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
99 idef->iparams[i].u_b.kthetaA);
101 case F_QUARTIC_ANGLES:
102 sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
103 idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
106 sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
107 idef->iparams[i].tab.kA);
110 sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
111 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
114 sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
115 idef->iparams[i].harmonic.krA);
118 sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
121 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
122 idef->iparams[i].harmonic.krA);
125 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
126 idef->iparams[i].harmonic.krA);
129 sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
133 gmx_fatal(FARGS, "Unsupported function type '%s' selected",
134 interaction_function[ftype].longname);
136 grpnames[ind] = gmx_strdup(buf);
143 static void fill_ang(int nft, int *ft, int fac,
144 int nr[], int *index[], int ft_ind[], t_topology *top,
145 gmx_bool bNoH, real hq)
147 int f, ftype, i, j, indg, nr_fac;
155 atom = top->atoms.atom;
157 for (f = 0; f < nft; f++)
160 ia = idef->il[ftype].iatoms;
161 for (i = 0; (i < idef->il[ftype].nr); )
163 indg = ft_ind[ia[0]];
166 gmx_incons("Routine fill_ang");
171 for (j = 0; j < fac; j++)
173 if (atom[ia[1+j]].m < 1.5)
181 for (j = 0; j < fac; j++)
183 if (atom[ia[1+j]].m < 1.5 && std::abs(atom[ia[1+j]].q) < hq)
191 if (nr[indg] % 1000 == 0)
193 srenew(index[indg], fac*(nr[indg]+1000));
195 nr_fac = fac*nr[indg];
196 for (j = 0; (j < fac); j++)
198 index[indg][nr_fac+j] = ia[j+1];
202 ia += interaction_function[ftype].nratoms+1;
203 i += interaction_function[ftype].nratoms+1;
208 static int *select_ftype(const char *opt, int *nft, int *mult)
210 int *ft = NULL, ftype;
215 for (ftype = 0; ftype < F_NRE; ftype++)
217 if ((interaction_function[ftype].flags & IF_ATYPE) ||
218 ftype == F_TABANGLES)
250 int gmx_mk_angndx(int argc, char *argv[])
252 static const char *desc[] = {
253 "[THISMODULE] makes an index file for calculation of",
254 "angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
255 "definitions of the angles, dihedrals etc."
257 static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
258 static gmx_bool bH = TRUE;
261 { "-type", FALSE, etENUM, {opt},
263 { "-hyd", FALSE, etBOOL, {&bH},
264 "Include angles with atoms with mass < 1.5" },
265 { "-hq", FALSE, etREAL, {&hq},
266 "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
273 int nft = 0, *ft, mult = 0;
279 { efTPR, NULL, NULL, ffREAD },
280 { efNDX, NULL, "angle", ffWRITE }
282 #define NFILE asize(fnm)
284 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
285 asize(desc), desc, 0, NULL, &oenv))
290 GMX_RELEASE_ASSERT(opt[0] != 0, "Options inconsistency; opt[0] is NULL");
292 ft = select_ftype(opt[0], &nft, &mult);
294 top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
296 ntype = calc_ntype(nft, ft, &(top->idef));
297 snew(grpnames, ntype);
298 snew(ft_ind, top->idef.ntypes);
299 fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
303 fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
305 out = ftp2FILE(efNDX, NFILE, fnm, "w");
306 for (i = 0; (i < ntype); i++)
310 fprintf(out, "[ %s ]\n", grpnames[i]);
311 for (j = 0; (j < nr[i]*mult); j++)
313 fprintf(out, " %5d", index[i][j]+1);