src/gromacs/gmxpreprocess/tomorse.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "tomorse.h"
  41
  42 #include <ctype.h>
  43 #include <stdlib.h>
  44 #include <string.h>
  45
  46 #include <cmath>
  47
  48 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  49 #include "gromacs/gmxpreprocess/grompp-impl.h"
  50 #include "gromacs/gmxpreprocess/toputil.h"
  51 #include "gromacs/legacyheaders/typedefs.h"
  52 #include "gromacs/legacyheaders/types/ifunc.h"
  53 #include "gromacs/utility/cstringutil.h"
  54 #include "gromacs/utility/fatalerror.h"
  55 #include "gromacs/utility/futil.h"
  56 #include "gromacs/utility/smalloc.h"
  57
  58 typedef struct {
  59     char *ai, *aj;
  60     real  e_diss;
  61 } t_2morse;
  62
  63 static t_2morse *read_dissociation_energies(int *n2morse)
  64 {
  65     FILE       *fp;
  66     char        ai[32], aj[32];
  67     double      e_diss;
  68     const char *fn     = "edissoc.dat";
  69     t_2morse   *t2m    = NULL;
  70     int         maxn2m = 0, n2m = 0;
  71     int         nread;
  72
  73     /* Open the file with dissociation energies */
  74     fp = libopen(fn);
  75     do
  76     {
  77         /* Try and read two atom names and an energy term from it */
  78         nread = fscanf(fp, "%s%s%lf", ai, aj, &e_diss);
  79         if (nread == 3)
  80         {
  81             /* If we got three terms, it probably was OK, no further checking */
  82             if (n2m >= maxn2m)
  83             {
  84                 /* Increase memory for 16 at once, some mallocs are stupid */
  85                 maxn2m += 16;
  86                 srenew(t2m, maxn2m);
  87             }
  88             /* Copy the values */
  89             t2m[n2m].ai     = gmx_strdup(ai);
  90             t2m[n2m].aj     = gmx_strdup(aj);
  91             t2m[n2m].e_diss = e_diss;
  92             /* Increment counter */
  93             n2m++;
  94         }
  95         /* If we did not read three items, quit reading */
  96     }
  97     while (nread == 3);
  98     gmx_ffclose(fp);
  99
 100     /* Set the return values */
 101     *n2morse = n2m;
 102
 103     return t2m;
 104 }
 105
 106 static int nequal(char *a1, char *a2)
 107 {
 108     int i;
 109
 110     /* Count the number of (case insensitive) characters that are equal in
 111      * two strings. If they are equally long their respective null characters are
 112      * counted also.
 113      */
 114     for (i = 0; (a1[i] != '\0') && (a2[i] != '\0'); i++)
 115     {
 116         if (toupper(a1[i]) != toupper(a2[i]))
 117         {
 118             break;
 119         }
 120     }
 121     if ((a1[i] == '\0') && (a2[i] == '\0'))
 122     {
 123         i++;
 124     }
 125
 126     return i;
 127 }
 128
 129 static real search_e_diss(int n2m, t_2morse t2m[], char *ai, char *aj)
 130 {
 131     int  i;
 132     int  ibest = -1;
 133     int  nii, njj, nbstii = 0, nbstjj = 0;
 134     real ediss = 400;
 135
 136     /* Do a best match search for dissociation energies */
 137     for (i = 0; (i < n2m); i++)
 138     {
 139         /* Check for a perfect match */
 140         if (((gmx_strcasecmp(t2m[i].ai, ai) == 0) && (gmx_strcasecmp(t2m[i].aj, aj) == 0)) ||
 141             ((gmx_strcasecmp(t2m[i].aj, ai) == 0) && (gmx_strcasecmp(t2m[i].ai, aj) == 0)))
 142         {
 143             ibest = i;
 144             break;
 145         }
 146         else
 147         {
 148             /* Otherwise count the number of equal characters in the strings ai and aj
 149              * and the ones from the file
 150              */
 151             nii = nequal(t2m[i].ai, ai);
 152             njj = nequal(t2m[i].aj, aj);
 153             if (((nii >  nbstii) && (njj >= nbstjj)) ||
 154                 ((nii >= nbstii) && (njj >  nbstjj)))
 155             {
 156                 if ((nii > 0) && (njj > 0))
 157                 {
 158                     ibest  = i;
 159                     nbstii = nii;
 160                     nbstjj = njj;
 161                 }
 162             }
 163             else
 164             {
 165                 /* Swap ai and aj (at least in counting the number of equal chars) */
 166                 nii = nequal(t2m[i].ai, aj);
 167                 njj = nequal(t2m[i].aj, ai);
 168                 if (((nii >  nbstii) && (njj >= nbstjj)) ||
 169                     ((nii >= nbstii) && (njj >  nbstjj)))
 170                 {
 171                     if ((nii > 0) && (njj > 0))
 172                     {
 173                         ibest  = i;
 174                         nbstii = nii;
 175                         nbstjj = njj;
 176                     }
 177                 }
 178             }
 179         }
 180     }
 181     /* Return the dissocation energy corresponding to the best match, if we have
 182      * found one. Do some debug output anyway.
 183      */
 184     if (ibest == -1)
 185     {
 186         if (debug)
 187         {
 188             fprintf(debug, "MORSE: Couldn't find E_diss for bond %s - %s, using default %g\n", ai, aj, ediss);
 189         }
 190         return ediss;
 191     }
 192     else
 193     {
 194         if (debug)
 195         {
 196             fprintf(debug, "MORSE: Dissoc. E (%10.3f) for bond %4s-%4s taken from bond %4s-%4s\n",
 197                     t2m[ibest].e_diss, ai, aj, t2m[ibest].ai, t2m[ibest].aj);
 198         }
 199         return t2m[ibest].e_diss;
 200     }
 201 }
 202
 203 void convert_harmonics(int nrmols, t_molinfo mols[], gpp_atomtype_t atype)
 204 {
 205     int       n2m;
 206     t_2morse *t2m;
 207
 208     int       i, j, k, last, ni, nj;
 209     int       nrharm, nrmorse, bb;
 210     real      edis, kb, b0, beta;
 211     gmx_bool *bRemoveHarm;
 212
 213     /* First get the data */
 214     t2m = read_dissociation_energies(&n2m);
 215     if (debug)
 216     {
 217         fprintf(debug, "MORSE: read %d dissoc energies\n", n2m);
 218     }
 219     if (n2m <= 0)
 220     {
 221         fprintf(stderr, "No dissocation energies read\n");
 222         return;
 223     }
 224
 225     /* For all the molecule types */
 226     for (i = 0; (i < nrmols); i++)
 227     {
 228         /* Check how many morse and harmonic BONDSs there are, increase size of
 229          * morse with the number of harmonics
 230          */
 231         nrmorse = mols[i].plist[F_MORSE].nr;
 232
 233         for (bb = 0; (bb < F_NRE); bb++)
 234         {
 235             if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE))
 236             {
 237                 nrharm  = mols[i].plist[bb].nr;
 238                 pr_alloc(nrharm, &(mols[i].plist[F_MORSE]));
 239                 snew(bRemoveHarm, nrharm);
 240
 241                 /* Now loop over the harmonics, trying to convert them */
 242                 for (j = 0; (j < nrharm); j++)
 243                 {
 244                     ni   = mols[i].plist[bb].param[j].ai();
 245                     nj   = mols[i].plist[bb].param[j].aj();
 246                     edis =
 247                         search_e_diss(n2m, t2m,
 248                                       get_atomtype_name(mols[i].atoms.atom[ni].type, atype),
 249                                       get_atomtype_name(mols[i].atoms.atom[nj].type, atype));
 250                     if (edis != 0)
 251                     {
 252                         bRemoveHarm[j] = TRUE;
 253                         b0             = mols[i].plist[bb].param[j].c[0];
 254                         kb             = mols[i].plist[bb].param[j].c[1];
 255                         beta           = std::sqrt(kb/(2*edis));
 256                         mols[i].plist[F_MORSE].param[nrmorse].a[0] = ni;
 257                         mols[i].plist[F_MORSE].param[nrmorse].a[1] = nj;
 258                         mols[i].plist[F_MORSE].param[nrmorse].c[0] = b0;
 259                         mols[i].plist[F_MORSE].param[nrmorse].c[1] = edis;
 260                         mols[i].plist[F_MORSE].param[nrmorse].c[2] = beta;
 261                         nrmorse++;
 262                     }
 263                 }
 264                 mols[i].plist[F_MORSE].nr = nrmorse;
 265
 266                 /* Now remove the harmonics */
 267                 for (j = last = 0; (j < nrharm); j++)
 268                 {
 269                     if (!bRemoveHarm[j])
 270                     {
 271                         /* Copy it to the last position */
 272                         for (k = 0; (k < MAXATOMLIST); k++)
 273                         {
 274                             mols[i].plist[bb].param[last].a[k] =
 275                                 mols[i].plist[bb].param[j].a[k];
 276                         }
 277                         for (k = 0; (k < MAXFORCEPARAM); k++)
 278                         {
 279                             mols[i].plist[bb].param[last].c[k] =
 280                                 mols[i].plist[bb].param[j].c[k];
 281                         }
 282                         last++;
 283                     }
 284                 }
 285                 sfree(bRemoveHarm);
 286                 fprintf(stderr, "Converted %d out of %d %s to morse bonds for mol %d\n",
 287                         nrharm-last, nrharm, interaction_function[bb].name, i);
 288                 mols[i].plist[bb].nr = last;
 289             }
 290         }
 291     }
 292     sfree(t2m);
 293 }