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/typedefs.h"
  45 #include "gromacs/legacyheaders/types/ifunc.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"
  52
  53 static int calc_ntype(int nft, int *ft, t_idef *idef)
  54 {
  55     int  i, f, nf = 0;
  56
  57     for (i = 0; (i < idef->ntypes); i++)
  58     {
  59         for (f = 0; f < nft; f++)
  60         {
  61             if (idef->functype[i] == ft[f])
  62             {
  63                 nf++;
  64             }
  65         }
  66     }
  67
  68     return nf;
  69 }
  70
  71 static void fill_ft_ind(int nft, int *ft, t_idef *idef,
  72                         int ft_ind[], char *grpnames[])
  73 {
  74     char buf[125];
  75     int  i, f, ftype, ind = 0;
  76
  77     /* Loop over all the function types in the topology */
  78     for (i = 0; (i < idef->ntypes); i++)
  79     {
  80         ft_ind[i] = -1;
  81         /* Check all the selected function types */
  82         for (f = 0; f < nft; f++)
  83         {
  84             ftype = ft[f];
  85             if (idef->functype[i] == ftype)
  86             {
  87                 ft_ind[i] = ind;
  88                 switch (ftype)
  89                 {
  90                     case F_ANGLES:
  91                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
  92                                 idef->iparams[i].harmonic.krA);
  93                         break;
  94                     case F_G96ANGLES:
  95                         sprintf(buf, "Cos_th=%.1f_%.2f", idef->iparams[i].harmonic.rA,
  96                                 idef->iparams[i].harmonic.krA);
  97                         break;
  98                     case F_UREY_BRADLEY:
  99                         sprintf(buf, "UB_th=%.1f_%.2f2f", idef->iparams[i].u_b.thetaA,
 100                                 idef->iparams[i].u_b.kthetaA);
 101                         break;
 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]);
 105                         break;
 106                     case F_TABANGLES:
 107                         sprintf(buf, "Table=%d_%.2f", idef->iparams[i].tab.table,
 108                                 idef->iparams[i].tab.kA);
 109                         break;
 110                     case F_PDIHS:
 111                         sprintf(buf, "Phi=%.1f_%d_%.2f", idef->iparams[i].pdihs.phiA,
 112                                 idef->iparams[i].pdihs.mult, idef->iparams[i].pdihs.cpA);
 113                         break;
 114                     case F_IDIHS:
 115                         sprintf(buf, "Xi=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 116                                 idef->iparams[i].harmonic.krA);
 117                         break;
 118                     case F_RBDIHS:
 119                         sprintf(buf, "RB-A1=%.2f", idef->iparams[i].rbdihs.rbcA[1]);
 120                         break;
 121                     case  F_RESTRANGLES:
 122                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 123                                 idef->iparams[i].harmonic.krA);
 124                         break;
 125                     case  F_RESTRDIHS:
 126                         sprintf(buf, "Theta=%.1f_%.2f", idef->iparams[i].harmonic.rA,
 127                                 idef->iparams[i].harmonic.krA);
 128                         break;
 129                     case  F_CBTDIHS:
 130                         sprintf(buf, "CBT-A1=%.2f", idef->iparams[i].cbtdihs.cbtcA[1]);
 131                         break;
 132
 133                     default:
 134                         gmx_fatal(FARGS, "Unsupported function type '%s' selected",
 135                                   interaction_function[ftype].longname);
 136                 }
 137                 grpnames[ind] = gmx_strdup(buf);
 138                 ind++;
 139             }
 140         }
 141     }
 142 }
 143
 144 static void fill_ang(int nft, int *ft, int fac,
 145                      int nr[], int *index[], int ft_ind[], t_topology *top,
 146                      gmx_bool bNoH, real hq)
 147 {
 148     int         f, ftype, i, j, indg, nr_fac;
 149     gmx_bool    bUse;
 150     t_idef     *idef;
 151     t_atom     *atom;
 152     t_iatom    *ia;
 153
 154
 155     idef = &top->idef;
 156     atom = top->atoms.atom;
 157
 158     for (f = 0; f < nft; f++)
 159     {
 160         ftype = ft[f];
 161         ia    = idef->il[ftype].iatoms;
 162         for (i = 0; (i < idef->il[ftype].nr); )
 163         {
 164             indg = ft_ind[ia[0]];
 165             if (indg == -1)
 166             {
 167                 gmx_incons("Routine fill_ang");
 168             }
 169             bUse = TRUE;
 170             if (bNoH)
 171             {
 172                 for (j = 0; j < fac; j++)
 173                 {
 174                     if (atom[ia[1+j]].m < 1.5)
 175                     {
 176                         bUse = FALSE;
 177                     }
 178                 }
 179             }
 180             if (hq)
 181             {
 182                 for (j = 0; j < fac; j++)
 183                 {
 184                     if (atom[ia[1+j]].m < 1.5 && std::abs(atom[ia[1+j]].q) < hq)
 185                     {
 186                         bUse = FALSE;
 187                     }
 188                 }
 189             }
 190             if (bUse)
 191             {
 192                 if (nr[indg] % 1000 == 0)
 193                 {
 194                     srenew(index[indg], fac*(nr[indg]+1000));
 195                 }
 196                 nr_fac = fac*nr[indg];
 197                 for (j = 0; (j < fac); j++)
 198                 {
 199                     index[indg][nr_fac+j] = ia[j+1];
 200                 }
 201                 nr[indg]++;
 202             }
 203             ia += interaction_function[ftype].nratoms+1;
 204             i  += interaction_function[ftype].nratoms+1;
 205         }
 206     }
 207 }
 208
 209 static int *select_ftype(const char *opt, int *nft, int *mult)
 210 {
 211     int *ft = NULL, ftype;
 212
 213     if (opt[0] == 'a')
 214     {
 215         *mult = 3;
 216         for (ftype = 0; ftype < F_NRE; ftype++)
 217         {
 218             if ((interaction_function[ftype].flags & IF_ATYPE) ||
 219                 ftype == F_TABANGLES)
 220             {
 221                 (*nft)++;
 222                 srenew(ft, *nft);
 223                 ft[*nft-1] = ftype;
 224             }
 225         }
 226     }
 227     else
 228     {
 229         *mult = 4;
 230         *nft  = 1;
 231         snew(ft, *nft);
 232         switch (opt[0])
 233         {
 234             case 'd':
 235                 ft[0] = F_PDIHS;
 236                 break;
 237             case 'i':
 238                 ft[0] = F_IDIHS;
 239                 break;
 240             case 'r':
 241                 ft[0] = F_RBDIHS;
 242                 break;
 243             default:
 244                 break;
 245         }
 246     }
 247
 248     return ft;
 249 }
 250
 251 int gmx_mk_angndx(int argc, char *argv[])
 252 {
 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."
 257     };
 258     static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
 259     static gmx_bool    bH    = TRUE;
 260     static real        hq    = -1;
 261     t_pargs            pa[]  = {
 262         { "-type", FALSE, etENUM, {opt},
 263           "Type of angle" },
 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" }
 268     };
 269
 270     output_env_t       oenv;
 271     FILE              *out;
 272     t_topology        *top;
 273     int                i, j, ntype;
 274     int                nft = 0, *ft, mult = 0;
 275     int              **index;
 276     int               *ft_ind;
 277     int               *nr;
 278     char             **grpnames;
 279     t_filenm           fnm[] = {
 280         { efTPR, NULL, NULL, ffREAD  },
 281         { efNDX, NULL, "angle", ffWRITE }
 282     };
 283 #define NFILE asize(fnm)
 284
 285     if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
 286                            asize(desc), desc, 0, NULL, &oenv))
 287     {
 288         return 0;
 289     }
 290
 291     GMX_RELEASE_ASSERT(opt[0] != 0, "Options inconsistency; opt[0] is NULL");
 292
 293     ft = select_ftype(opt[0], &nft, &mult);
 294
 295     top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
 296
 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);
 301
 302     snew(nr, ntype);
 303     snew(index, ntype);
 304     fill_ang(nft, ft, mult, nr, index, ft_ind, top, !bH, hq);
 305
 306     out = ftp2FILE(efNDX, NFILE, fnm, "w");
 307     for (i = 0; (i < ntype); i++)
 308     {
 309         if (nr[i] > 0)
 310         {
 311             fprintf(out, "[ %s ]\n", grpnames[i]);
 312             for (j = 0; (j < nr[i]*mult); j++)
 313             {
 314                 fprintf(out, " %5d", index[i][j]+1);
 315                 if ((j % 12) == 11)
 316                 {
 317                     fprintf(out, "\n");
 318                 }
 319             }
 320             fprintf(out, "\n");
 321         }
 322     }
 323     gmx_ffclose(out);
 324
 325     return 0;
 326 }