src/gromacs/gmxana/gmx_mk_angndx.c

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