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