src/gromacs/gmxana/gmx_mk_angndx.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40
  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"
  51
  52 static int calc_ntype(int nft, int *ft, t_idef *idef)
  53 {
  54     int  i, f, nf = 0;
  55
  56     for (i = 0; (i < idef->ntypes); i++)
  57     {
  58         for (f = 0; f < nft; f++)
  59         {
  60             if (idef->functype[i] == ft[f])
  61             {
  62                 nf++;
  63             }
  64         }
  65     }
  66
  67     return nf;
  68 }
  69
  70 static void fill_ft_ind(int nft, int *ft, t_idef *idef,
  71                         int ft_ind[], char *grpnames[])
  72 {
  73     char buf[125];
  74     int  i, f, ftype, ind = 0;
  75
  76     /* Loop over all the function types in the topology */
  77     for (i = 0; (i < idef->ntypes); i++)
  78     {
  79         ft_ind[i] = -1;
  80         /* Check all the selected function types */
  81         for (f = 0; f < nft; f++)
  82         {
  83             ftype = ft[f];
  84             if (idef->functype[i] == ftype)
  85             {
  86                 ft_ind[i] = ind;
  87                 switch (ftype)
  88                 {
  89                     case F_ANGLES:
  90                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
  91                                 idef->iparams[i].harmonic.krA);
  92                         break;
  93                     case F_G96ANGLES:
  94                         sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
  95                                 idef->iparams[i].harmonic.krA);
  96                         break;
  97                     case F_UREY_BRADLEY:
  98                         sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
  99                                 idef->iparams[i].u_b.kthetaA);
 100                         break;
 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]);
 104                         break;
 105                     case F_TABANGLES:
 106                         sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
 107                                 idef->iparams[i].tab.kA);
 108                         break;
 109                     case F_PDIHS:
 110                         sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
 111                                 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
 112                         break;
 113                     case F_IDIHS:
 114                         sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 115                                 idef->iparams[i].harmonic.krA);
 116                         break;
 117                     case F_RBDIHS:
 118                         sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
 119                         break;
 120                     case  F_RESTRANGLES:
 121                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 122                                 idef->iparams[i].harmonic.krA);
 123                         break;
 124                     case  F_RESTRDIHS:
 125                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 126                                 idef->iparams[i].harmonic.krA);
 127                         break;
 128                     case  F_CBTDIHS:
 129                         sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
 130                         break;
 131
 132                     default:
 133                         gmx_fatal(FARGS, "Unsupported function type '%s' selected",
 134                                   interaction_function[ftype].longname);
 135                 }
 136                 grpnames[ind] = gmx_strdup(buf);
 137                 ind++;
 138             }
 139         }
 140     }
 141 }
 142
 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)
 146 {
 147     int         f, ftype, i, j, indg, nr_fac;
 148     gmx_bool    bUse;
 149     t_idef     *idef;
 150     t_atom     *atom;
 151     t_iatom    *ia;
 152
 153
 154     idef = &top->idef;
 155     atom = top->atoms.atom;
 156
 157     for (f = 0; f < nft; f++)
 158     {
 159         ftype = ft[f];
 160         ia    = idef->il[ftype].iatoms;
 161         for (i = 0; (i < idef->il[ftype].nr); )
 162         {
 163             indg = ft_ind[ia[0]];
 164             if (indg == -1)
 165             {
 166                 gmx_incons("Routine fill_ang");
 167             }
 168             bUse = TRUE;
 169             if (bNoH)
 170             {
 171                 for (j = 0; j < fac; j++)
 172                 {
 173                     if (atom[ia[1+j]].m < 1.5)
 174                     {
 175                         bUse = FALSE;
 176                     }
 177                 }
 178             }
 179             if (hq)
 180             {
 181                 for (j = 0; j < fac; j++)
 182                 {
 183                     if (atom[ia[1+j]].m < 1.5 && std::abs(atom[ia[1+j]].q) < hq)
 184                     {
 185                         bUse = FALSE;
 186                     }
 187                 }
 188             }
 189             if (bUse)
 190             {
 191                 if (nr[indg] % 1000 == 0)
 192                 {
 193                     srenew(index[indg], fac*(nr[indg]+1000));
 194                 }
 195                 nr_fac = fac*nr[indg];
 196                 for (j = 0; (j < fac); j++)
 197                 {
 198                     index[indg][nr_fac+j] = ia[j+1];
 199                 }
 200                 nr[indg]++;
 201             }
 202             ia += interaction_function[ftype].nratoms+1;
 203             i  += interaction_function[ftype].nratoms+1;
 204         }
 205     }
 206 }
 207
 208 static int *select_ftype(const char *opt, int *nft, int *mult)
 209 {
 210     int *ft = NULL, ftype;
 211
 212     if (opt[0] == 'a')
 213     {
 214         *mult = 3;
 215         for (ftype = 0; ftype < F_NRE; ftype++)
 216         {
 217             if ((interaction_function[ftype].flags & IF_ATYPE) ||
 218                 ftype == F_TABANGLES)
 219             {
 220                 (*nft)++;
 221                 srenew(ft, *nft);
 222                 ft[*nft-1] = ftype;
 223             }
 224         }
 225     }
 226     else
 227     {
 228         *mult = 4;
 229         *nft  = 1;
 230         snew(ft, *nft);
 231         switch (opt[0])
 232         {
 233             case 'd':
 234                 ft[0] = F_PDIHS;
 235                 break;
 236             case 'i':
 237                 ft[0] = F_IDIHS;
 238                 break;
 239             case 'r':
 240                 ft[0] = F_RBDIHS;
 241                 break;
 242             default:
 243                 break;
 244         }
 245     }
 246
 247     return ft;
 248 }
 249
 250 int gmx_mk_angndx(int argc, char *argv[])
 251 {
 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."
 256     };
 257     static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
 258     static gmx_bool    bH    = TRUE;
 259     static real        hq    = -1;
 260     t_pargs            pa[]  = {
 261         { "-type", FALSE, etENUM, {opt},
 262           "Type of angle" },
 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" }
 267     };
 268
 269     output_env_t       oenv;
 270     FILE              *out;
 271     t_topology        *top;
 272     int                i, j, ntype;
 273     int                nft = 0, *ft, mult = 0;
 274     int              **index;
 275     int               *ft_ind;
 276     int               *nr;
 277     char             **grpnames;
 278     t_filenm           fnm[] = {
 279         { efTPR, NULL, NULL, ffREAD  },
 280         { efNDX, NULL, "angle", ffWRITE }
 281     };
 282 #define NFILE asize(fnm)
 283
 284     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
 285                            asize(desc), desc, 0, NULL, &oenv))
 286     {
 287         return 0;
 288     }
 289
 290     GMX_RELEASE_ASSERT(opt[0] != 0, "Options inconsistency; opt[0] is NULL");
 291
 292     ft = select_ftype(opt[0], &nft, &mult);
 293
 294     top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
 295
 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);
 300
 301     snew(nr, ntype);
 302     snew(index, ntype);
 303     fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
 304
 305     out = ftp2FILE(efNDX, NFILE, fnm, "w");
 306     for (i = 0; (i < ntype); i++)
 307     {
 308         if (nr[i] > 0)
 309         {
 310             fprintf(out, "[ %s ]\n", grpnames[i]);
 311             for (j = 0; (j < nr[i]*mult); j++)
 312             {
 313                 fprintf(out, " %5d", index[i][j]+1);
 314                 if ((j % 12) == 11)
 315                 {
 316                     fprintf(out, "\n");
 317                 }
 318             }
 319             fprintf(out, "\n");
 320         }
 321     }
 322     gmx_ffclose(out);
 323
 324     return 0;
 325 }