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