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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/topology/ifunc.h"
45 #include "gromacs/topology/topology.h"
46 #include "gromacs/utility/arraysize.h"
47 #include "gromacs/utility/cstringutil.h"
48 #include "gromacs/utility/fatalerror.h"
49 #include "gromacs/utility/futil.h"
50 #include "gromacs/utility/gmxassert.h"
51 #include "gromacs/utility/smalloc.h"
53 static int calc_ntype(int nft, const int *ft, const t_idef *idef)
57 for (i = 0; (i < idef->ntypes); i++)
59 for (f = 0; f < nft; f++)
61 if (idef->functype[i] == ft[f])
71 static void fill_ft_ind(int nft, const int *ft, const t_idef *idef,
72 int ft_ind[], char *grpnames[])
75 int i, f, ftype, ind = 0;
77 /* Loop over all the function types in the topology */
78 for (i = 0; (i < idef->ntypes); i++)
81 /* Check all the selected function types */
82 for (f = 0; f < nft; f++)
85 if (idef->functype[i] == ftype)
91 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
92 idef->iparams[i].harmonic.krA);
95 sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
96 idef->iparams[i].harmonic.krA);
99 sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
100 idef->iparams[i].u_b.kthetaA);
102 case F_QUARTIC_ANGLES:
103 sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
104 idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
107 sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
108 idef->iparams[i].tab.kA);
111 sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
112 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
115 sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
116 idef->iparams[i].harmonic.krA);
119 sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
122 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
123 idef->iparams[i].harmonic.krA);
126 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
127 idef->iparams[i].harmonic.krA);
130 sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
134 gmx_fatal(FARGS, "Unsupported function type '%s' selected",
135 interaction_function[ftype].longname);
137 grpnames[ind] = gmx_strdup(buf);
144 static void fill_ang(int nft, const int *ft, int fac,
145 int nr[], int *index[], const int ft_ind[], const t_topology *top,
146 gmx_bool bNoH, real hq)
148 int f, ftype, i, j, indg, nr_fac;
156 atom = top->atoms.atom;
158 for (f = 0; f < nft; f++)
161 ia = idef->il[ftype].iatoms;
162 for (i = 0; (i < idef->il[ftype].nr); )
164 indg = ft_ind[ia[0]];
167 gmx_incons("Routine fill_ang");
172 for (j = 0; j < fac; j++)
174 if (atom[ia[1+j]].m < 1.5)
182 for (j = 0; j < fac; j++)
184 if (atom[ia[1+j]].m < 1.5 && std::abs(atom[ia[1+j]].q) < hq)
192 if (nr[indg] % 1000 == 0)
194 srenew(index[indg], fac*(nr[indg]+1000));
196 nr_fac = fac*nr[indg];
197 for (j = 0; (j < fac); j++)
199 index[indg][nr_fac+j] = ia[j+1];
203 ia += interaction_function[ftype].nratoms+1;
204 i += interaction_function[ftype].nratoms+1;
209 static int *select_ftype(const char *opt, int *nft, int *mult)
211 int *ft = nullptr, ftype;
216 for (ftype = 0; ftype < F_NRE; ftype++)
218 if ((interaction_function[ftype].flags & IF_ATYPE) ||
219 ftype == F_TABANGLES)
251 int gmx_mk_angndx(int argc, char *argv[])
253 static const char *desc[] = {
254 "[THISMODULE] makes an index file for calculation of",
255 "angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
256 "definitions of the angles, dihedrals etc."
258 static const char *opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans", nullptr };
259 static gmx_bool bH = TRUE;
262 { "-type", FALSE, etENUM, {opt},
264 { "-hyd", FALSE, etBOOL, {&bH},
265 "Include angles with atoms with mass < 1.5" },
266 { "-hq", FALSE, etREAL, {&hq},
267 "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
270 gmx_output_env_t *oenv;
274 int nft = 0, *ft, mult = 0;
280 { efTPR, nullptr, nullptr, ffREAD },
281 { efNDX, nullptr, "angle", ffWRITE }
283 #define NFILE asize(fnm)
285 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
286 asize(desc), desc, 0, nullptr, &oenv))
291 GMX_RELEASE_ASSERT(opt[0] != nullptr, "Options inconsistency; opt[0] is NULL");
293 ft = select_ftype(opt[0], &nft, &mult);
295 top = read_top(ftp2fn(efTPR, NFILE, fnm), nullptr);
297 ntype = calc_ntype(nft, ft, &(top->idef));
298 snew(grpnames, ntype);
299 snew(ft_ind, top->idef.ntypes);
300 fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
304 fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
306 out = ftp2FILE(efNDX, NFILE, fnm, "w");
307 for (i = 0; (i < ntype); i++)
311 fprintf(out, "[ %s ]\n", grpnames[i]);
312 for (j = 0; (j < nr[i]*mult); j++)
314 fprintf(out, " %5d", index[i][j]+1);