src/gromacs/tools/mk_angndx.cpp

   1 /*
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   7  * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  38 #include "gmxpre.h"
  39
  40 #include "mk_angndx.h"
  41
  42 #include <cmath>
  43
  44 #include "gromacs/commandline/pargs.h"
  45 #include "gromacs/fileio/trxio.h"
  46 #include "gromacs/topology/ifunc.h"
  47 #include "gromacs/topology/topology.h"
  48 #include "gromacs/utility/arraysize.h"
  49 #include "gromacs/utility/cstringutil.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/futil.h"
  52 #include "gromacs/utility/gmxassert.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 static int calc_ntype(int nft, const int* ft, const t_idef* idef)
  56 {
  57     int i, f, nf = 0;
  58
  59     for (i = 0; (i < idef->ntypes); i++)
  60     {
  61         for (f = 0; f < nft; f++)
  62         {
  63             if (idef->functype[i] == ft[f])
  64             {
  65                 nf++;
  66             }
  67         }
  68     }
  69
  70     return nf;
  71 }
  72
  73 static void fill_ft_ind(int nft, const int* ft, const t_idef* idef, int ft_ind[], char* grpnames[])
  74 {
  75     char buf[125];
  76     int  i, f, ftype, ind = 0;
  77
  78     /* Loop over all the function types in the topology */
  79     for (i = 0; (i < idef->ntypes); i++)
  80     {
  81         ft_ind[i] = -1;
  82         /* Check all the selected function types */
  83         for (f = 0; f < nft; f++)
  84         {
  85             ftype = ft[f];
  86             if (idef->functype[i] == ftype)
  87             {
  88                 ft_ind[i] = ind;
  89                 switch (ftype)
  90                 {
  91                     case F_ANGLES:
  92                         sprintf(buf,
  93                                 "Theta=%.1f_%.2f",
  94                                 idef->iparams[i].harmonic.rA,
  95                                 idef->iparams[i].harmonic.krA);
  96                         break;
  97                     case F_G96ANGLES:
  98                         sprintf(buf,
  99                                 "Cos_th=%.1f_%.2f",
 100                                 idef->iparams[i].harmonic.rA,
 101                                 idef->iparams[i].harmonic.krA);
 102                         break;
 103                     case F_UREY_BRADLEY:
 104                         sprintf(buf,
 105                                 "UB_th=%.1f_%.2f2f",
 106                                 idef->iparams[i].u_b.thetaA,
 107                                 idef->iparams[i].u_b.kthetaA);
 108                         break;
 109                     case F_QUARTIC_ANGLES:
 110                         sprintf(buf,
 111                                 "Q_th=%.1f_%.2f_%.2f",
 112                                 idef->iparams[i].qangle.theta,
 113                                 idef->iparams[i].qangle.c[0],
 114                                 idef->iparams[i].qangle.c[1]);
 115                         break;
 116                     case F_TABANGLES:
 117                         sprintf(buf,
 118                                 "Table=%d_%.2f",
 119                                 idef->iparams[i].tab.table,
 120                                 idef->iparams[i].tab.kA);
 121                         break;
 122                     case F_PDIHS:
 123                         sprintf(buf,
 124                                 "Phi=%.1f_%d_%.2f",
 125                                 idef->iparams[i].pdihs.phiA,
 126                                 idef->iparams[i].pdihs.mult,
 127                                 idef->iparams[i].pdihs.cpA);
 128                         break;
 129                     case F_IDIHS:
 130                         sprintf(buf,
 131                                 "Xi=%.1f_%.2f",
 132                                 idef->iparams[i].harmonic.rA,
 133                                 idef->iparams[i].harmonic.krA);
 134                         break;
 135                     case F_RBDIHS:
 136                         sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
 137                         break;
 138                     case F_RESTRANGLES:
 139                         // Fall through intended
 140                     case F_RESTRDIHS:
 141                         sprintf(buf,
 142                                 "Theta=%.1f_%.2f",
 143                                 idef->iparams[i].harmonic.rA,
 144                                 idef->iparams[i].harmonic.krA);
 145                         break;
 146                     case F_CBTDIHS:
 147                         sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
 148                         break;
 149
 150                     default:
 151                         gmx_fatal(FARGS,
 152                                   "Unsupported function type '%s' selected",
 153                                   interaction_function[ftype].longname);
 154                 }
 155                 grpnames[ind] = gmx_strdup(buf);
 156                 ind++;
 157             }
 158         }
 159     }
 160 }
 161
 162 static void fill_ang(int               nft,
 163                      const int*        ft,
 164                      int               fac,
 165                      int               nr[],
 166                      int*              index[],
 167                      const int         ft_ind[],
 168                      const t_topology* top,
 169                      gmx_bool          bNoH,
 170                      real              hq)
 171 {
 172     int           f, ftype, i, j, indg, nr_fac;
 173     gmx_bool      bUse;
 174     const t_idef* idef;
 175     t_atom*       atom;
 176     t_iatom*      ia;
 177
 178
 179     idef = &top->idef;
 180     atom = top->atoms.atom;
 181
 182     for (f = 0; f < nft; f++)
 183     {
 184         ftype = ft[f];
 185         ia    = idef->il[ftype].iatoms;
 186         for (i = 0; (i < idef->il[ftype].nr);)
 187         {
 188             indg = ft_ind[ia[0]];
 189             if (indg == -1)
 190             {
 191                 gmx_incons("Routine fill_ang");
 192             }
 193             bUse = TRUE;
 194             if (bNoH)
 195             {
 196                 for (j = 0; j < fac; j++)
 197                 {
 198                     if (atom[ia[1 + j]].m < 1.5)
 199                     {
 200                         bUse = FALSE;
 201                     }
 202                 }
 203             }
 204             if (hq != 0.0F)
 205             {
 206                 for (j = 0; j < fac; j++)
 207                 {
 208                     if (atom[ia[1 + j]].m < 1.5 && std::abs(atom[ia[1 + j]].q) < hq)
 209                     {
 210                         bUse = FALSE;
 211                     }
 212                 }
 213             }
 214             if (bUse)
 215             {
 216                 if (nr[indg] % 1000 == 0)
 217                 {
 218                     srenew(index[indg], fac * (nr[indg] + 1000));
 219                 }
 220                 nr_fac = fac * nr[indg];
 221                 for (j = 0; (j < fac); j++)
 222                 {
 223                     index[indg][nr_fac + j] = ia[j + 1];
 224                 }
 225                 nr[indg]++;
 226             }
 227             ia += interaction_function[ftype].nratoms + 1;
 228             i += interaction_function[ftype].nratoms + 1;
 229         }
 230     }
 231 }
 232
 233 static int* select_ftype(const char* opt, int* nft, int* mult)
 234 {
 235     int *ft = nullptr, ftype;
 236
 237     if (opt[0] == 'a')
 238     {
 239         *mult = 3;
 240         for (ftype = 0; ftype < F_NRE; ftype++)
 241         {
 242             if ((interaction_function[ftype].flags & IF_ATYPE) || ftype == F_TABANGLES)
 243             {
 244                 (*nft)++;
 245                 srenew(ft, *nft);
 246                 ft[*nft - 1] = ftype;
 247             }
 248         }
 249     }
 250     else
 251     {
 252         *mult = 4;
 253         *nft  = 1;
 254         snew(ft, *nft);
 255         switch (opt[0])
 256         {
 257             case 'd': ft[0] = F_PDIHS; break;
 258             case 'i': ft[0] = F_IDIHS; break;
 259             case 'r': ft[0] = F_RBDIHS; break;
 260             default: break;
 261         }
 262     }
 263
 264     return ft;
 265 }
 266
 267 int gmx_mk_angndx(int argc, char* argv[])
 268 {
 269     static const char* desc[] = {
 270         "[THISMODULE] makes an index file for calculation of",
 271         "angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
 272         "definitions of the angles, dihedrals etc."
 273     };
 274     static const char* opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans",
 275                                  nullptr };
 276     static gmx_bool    bH    = TRUE;
 277     static real        hq    = -1;
 278     t_pargs            pa[]  = { { "-type", FALSE, etENUM, { opt }, "Type of angle" },
 279                      { "-hyd", FALSE, etBOOL, { &bH }, "Include angles with atoms with mass < 1.5" },
 280                      { "-hq",
 281                        FALSE,
 282                        etREAL,
 283                        { &hq },
 284                        "Ignore angles with atoms with mass < 1.5 and magnitude of their charge "
 285                        "less than this value" } };
 286
 287     gmx_output_env_t* oenv;
 288     FILE*             out;
 289     t_topology*       top;
 290     int               i, j, ntype;
 291     int               nft = 0, *ft, mult = 0;
 292     int**             index;
 293     int*              ft_ind;
 294     int*              nr;
 295     char**            grpnames;
 296     t_filenm fnm[] = { { efTPR, nullptr, nullptr, ffREAD }, { efNDX, nullptr, "angle", ffWRITE } };
 297 #define NFILE asize(fnm)
 298
 299     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 300     {
 301         return 0;
 302     }
 303
 304     GMX_RELEASE_ASSERT(opt[0] != nullptr, "Options inconsistency; opt[0] is NULL");
 305
 306     ft = select_ftype(opt[0], &nft, &mult);
 307
 308     top = read_top(ftp2fn(efTPR, NFILE, fnm), nullptr);
 309
 310     ntype = calc_ntype(nft, ft, &(top->idef));
 311     snew(grpnames, ntype);
 312     snew(ft_ind, top->idef.ntypes);
 313     fill_ft_ind(nft, ft, &top->idef, ft_ind, grpnames);
 314
 315     snew(nr, ntype);
 316     snew(index, ntype);
 317     fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
 318
 319     out = ftp2FILE(efNDX, NFILE, fnm, "w");
 320     for (i = 0; (i < ntype); i++)
 321     {
 322         if (nr[i] > 0)
 323         {
 324             fprintf(out, "[ %s ]\n", grpnames[i]);
 325             for (j = 0; (j < nr[i] * mult); j++)
 326             {
 327                 fprintf(out, " %5d", index[i][j] + 1);
 328                 if ((j % 12) == 11)
 329                 {
 330                     fprintf(out, "\n");
 331                 }
 332             }
 333             fprintf(out, "\n");
 334         }
 335     }
 336     gmx_ffclose(out);
 337
 338     return 0;
 339 }