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39 #include "mk_angndx.h"
43 #include "gromacs/commandline/pargs.h"
44 #include "gromacs/fileio/trxio.h"
45 #include "gromacs/topology/ifunc.h"
46 #include "gromacs/topology/topology.h"
47 #include "gromacs/utility/arraysize.h"
48 #include "gromacs/utility/cstringutil.h"
49 #include "gromacs/utility/fatalerror.h"
50 #include "gromacs/utility/futil.h"
51 #include "gromacs/utility/gmxassert.h"
52 #include "gromacs/utility/smalloc.h"
54 static int calc_ntype(int nft, const int *ft, const t_idef *idef)
58 for (i = 0; (i < idef->ntypes); i++)
60 for (f = 0; f < nft; f++)
62 if (idef->functype[i] == ft[f])
72 static void fill_ft_ind(int nft, const int *ft, const t_idef *idef,
73 int ft_ind[], char *grpnames[])
76 int i, f, ftype, ind = 0;
78 /* Loop over all the function types in the topology */
79 for (i = 0; (i < idef->ntypes); i++)
82 /* Check all the selected function types */
83 for (f = 0; f < nft; f++)
86 if (idef->functype[i] == ftype)
92 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
93 idef->iparams[i].harmonic.krA);
96 sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
97 idef->iparams[i].harmonic.krA);
100 sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
101 idef->iparams[i].u_b.kthetaA);
103 case F_QUARTIC_ANGLES:
104 sprintf(buf, "Q_th=%.1f_%.2f_%.2f", idef->iparams[i].qangle.theta,
105 idef->iparams[i].qangle.c[0], idef->iparams[i].qangle.c[1]);
108 sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
109 idef->iparams[i].tab.kA);
112 sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
113 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
116 sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
117 idef->iparams[i].harmonic.krA);
120 sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
123 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
124 idef->iparams[i].harmonic.krA);
127 sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
128 idef->iparams[i].harmonic.krA);
131 sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
135 gmx_fatal(FARGS, "Unsupported function type '%s' selected",
136 interaction_function[ftype].longname);
138 grpnames[ind] = gmx_strdup(buf);
145 static void fill_ang(int nft, const int *ft, int fac,
146 int nr[], int *index[], const int ft_ind[], const t_topology *top,
147 gmx_bool bNoH, real hq)
149 int f, ftype, i, j, indg, nr_fac;
157 atom = top->atoms.atom;
159 for (f = 0; f < nft; f++)
162 ia = idef->il[ftype].iatoms;
163 for (i = 0; (i < idef->il[ftype].nr); )
165 indg = ft_ind[ia[0]];
168 gmx_incons("Routine fill_ang");
173 for (j = 0; j < fac; j++)
175 if (atom[ia[1+j]].m < 1.5)
183 for (j = 0; j < fac; j++)
185 if (atom[ia[1+j]].m < 1.5 && std::abs(atom[ia[1+j]].q) < hq)
193 if (nr[indg] % 1000 == 0)
195 srenew(index[indg], fac*(nr[indg]+1000));
197 nr_fac = fac*nr[indg];
198 for (j = 0; (j < fac); j++)
200 index[indg][nr_fac+j] = ia[j+1];
204 ia += interaction_function[ftype].nratoms+1;
205 i += interaction_function[ftype].nratoms+1;
210 static int *select_ftype(const char *opt, int *nft, int *mult)
212 int *ft = nullptr, ftype;
217 for (ftype = 0; ftype < F_NRE; ftype++)
219 if ((interaction_function[ftype].flags & IF_ATYPE) ||
220 ftype == F_TABANGLES)
252 int gmx_mk_angndx(int argc, char *argv[])
254 static const char *desc[] = {
255 "[THISMODULE] makes an index file for calculation of",
256 "angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
257 "definitions of the angles, dihedrals etc."
259 static const char *opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans", nullptr };
260 static gmx_bool bH = TRUE;
263 { "-type", FALSE, etENUM, {opt},
265 { "-hyd", FALSE, etBOOL, {&bH},
266 "Include angles with atoms with mass < 1.5" },
267 { "-hq", FALSE, etREAL, {&hq},
268 "Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than this value" }
271 gmx_output_env_t *oenv;
275 int nft = 0, *ft, mult = 0;
281 { efTPR, nullptr, nullptr, ffREAD },
282 { efNDX, nullptr, "angle", ffWRITE }
284 #define NFILE asize(fnm)
286 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
287 asize(desc), desc, 0, nullptr, &oenv))
292 GMX_RELEASE_ASSERT(opt[0] != nullptr, "Options inconsistency; opt[0] is NULL");
294 ft = select_ftype(opt[0], &nft, &mult);
296 top = read_top(ftp2fn(efTPR, NFILE, fnm), nullptr);
298 ntype = calc_ntype(nft, ft, &(top->idef));
299 snew(grpnames, ntype);
300 snew(ft_ind, top->idef.ntypes);
301 fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
305 fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
307 out = ftp2FILE(efNDX, NFILE, fnm, "w");
308 for (i = 0; (i < ntype); i++)
312 fprintf(out, "[ %s ]\n", grpnames[i]);
313 for (j = 0; (j < nr[i]*mult); j++)
315 fprintf(out, " %5d", index[i][j]+1);