src/kernel/tomorse.c

   1 /*
   2  * $Id$
   3  *
   4  *                This source code is part of
   5  *
   6  *                 G   R   O   M   A   C   S
   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.1
  11  * Copyright (c) 1991-2001, University of Groningen, The Netherlands
  12  * This program is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU General Public License
  14  * as published by the Free Software Foundation; either version 2
  15  * of the License, or (at your option) any later version.
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  32
  33 /* This file is completely threadsafe - keep it that way! */
  34 #include <stdlib.h>
  35 #include <math.h>
  36 #include <ctype.h>
  37 #include "typedefs.h"
  38 #include "string2.h"
  39 #include "grompp.h"
  40 #include "futil.h"
  41 #include "smalloc.h"
  42 #include "fatal.h"
  43
  44 typedef struct {
  45   char *ai,*aj;
  46   real e_diss;
  47 } t_2morse;
  48
  49 static t_2morse *read_dissociation_energies(int *n2morse)
  50 {
  51   FILE     *fp;
  52   char     ai[32],aj[32];
  53   double   e_diss;
  54   char     *fn="edissoc.dat";
  55   t_2morse *t2m=NULL;
  56   int      maxn2m=0,n2m=0;
  57   int      nread;
  58
  59   /* Open the file with dissociation energies */
  60   fp = libopen(fn);
  61   do {
  62     /* Try and read two atom names and an energy term from it */
  63     nread = fscanf(fp,"%s%s%lf",ai,aj,&e_diss);
  64     if (nread == 3) {
  65       /* If we got three terms, it probably was OK, no further checking */
  66       if (n2m >= maxn2m) {
  67         /* Increase memory for 16 at once, some mallocs are stupid */
  68         maxn2m += 16;
  69         srenew(t2m,maxn2m);
  70       }
  71       /* Copy the values */
  72       t2m[n2m].ai = strdup(ai);
  73       t2m[n2m].aj = strdup(aj);
  74       t2m[n2m].e_diss = e_diss;
  75       /* Increment counter */
  76       n2m++;
  77     }
  78     /* If we did not read three items, quit reading */
  79   } while (nread == 3);
  80   ffclose(fp);
  81
  82   /* Set the return values */
  83   *n2morse = n2m;
  84
  85   return t2m;
  86 }
  87
  88 static int nequal(char *a1,char *a2)
  89 {
  90   int i;
  91
  92   /* Count the number of (case insensitive) characters that are equal in
  93    * two strings. If they are equally long their respective null characters are
  94    * counted also.
  95    */
  96   for(i=0; (a1[i] != '\0') && (a2[i] != '\0'); i++)
  97     if (toupper(a1[i]) != toupper(a2[i]))
  98       break;
  99   if ((a1[i] == '\0') && (a2[i] == '\0'))
 100     i++;
 101
 102   return i;
 103 }
 104
 105 static real search_e_diss(int n2m,t_2morse t2m[],char *ai,char *aj)
 106 {
 107   int i;
 108   int ibest=-1;
 109   int nii,njj,nbstii=0,nbstjj=0;
 110   real ediss = 400;
 111
 112   /* Do a best match search for dissociation energies */
 113   for(i=0; (i<n2m); i++) {
 114     /* Check for a perfect match */
 115     if (((strcasecmp(t2m[i].ai,ai) == 0) && (strcasecmp(t2m[i].aj,aj) == 0)) ||
 116         ((strcasecmp(t2m[i].aj,ai) == 0) && (strcasecmp(t2m[i].ai,aj) == 0))) {
 117       ibest = i;
 118       break;
 119     }
 120     else {
 121       /* Otherwise count the number of equal characters in the strings ai and aj
 122        * and the ones from the file
 123        */
 124       nii = nequal(t2m[i].ai,ai);
 125       njj = nequal(t2m[i].aj,aj);
 126       if (((nii >  nbstii) && (njj >= nbstjj)) ||
 127           ((nii >= nbstii) && (njj >  nbstjj))) {
 128         if ((nii > 0) && (njj > 0)) {
 129           ibest  = i;
 130           nbstii = nii;
 131           nbstjj = njj;
 132         }
 133       }
 134       else {
 135         /* Swap ai and aj (at least in counting the number of equal chars) */
 136         nii = nequal(t2m[i].ai,aj);
 137         njj = nequal(t2m[i].aj,ai);
 138         if (((nii >  nbstii) && (njj >= nbstjj)) ||
 139             ((nii >= nbstii) && (njj >  nbstjj))) {
 140           if ((nii > 0) && (njj > 0)) {
 141             ibest  = i;
 142             nbstii = nii;
 143             nbstjj = njj;
 144           }
 145         }
 146       }
 147     }
 148   }
 149   /* Return the dissocation energy corresponding to the best match, if we have
 150    * found one. Do some debug output anyway.
 151    */
 152   if (ibest == -1) {
 153     if (debug)
 154       fprintf(debug,"MORSE: Couldn't find E_diss for bond %s - %s, using default %g\n",ai,aj,ediss);
 155     return ediss;
 156   }
 157   else {
 158     if (debug)
 159       fprintf(debug,"MORSE: Dissoc. E (%10.3f) for bond %4s-%4s taken from bond %4s-%4s\n",
 160               t2m[ibest].e_diss,ai,aj,t2m[ibest].ai,t2m[ibest].aj);
 161     return t2m[ibest].e_diss;
 162   }
 163 }
 164
 165 void convert_harmonics(int nrmols,t_molinfo mols[],t_atomtype *atype)
 166 {
 167   int      n2m;
 168   t_2morse *t2m;
 169
 170   int  i,j,k,last,ni,nj;
 171   int  nrharm,nrmorse,bb;
 172   real edis,kb,b0,beta;
 173   bool *bRemoveHarm;
 174
 175   /* First get the data */
 176   t2m = read_dissociation_energies(&n2m);
 177   if (debug)
 178     fprintf(debug,"MORSE: read %d dissoc energies\n",n2m);
 179   if (n2m <= 0) {
 180     fprintf(stderr,"No dissocation energies read\n");
 181     return;
 182   }
 183
 184   /* For all the molecule types */
 185   for(i=0; (i<nrmols); i++) {
 186     /* Check how many morse and harmonic BONDSs there are, increase size of
 187      * morse with the number of harmonics
 188      */
 189     nrmorse = mols[i].plist[F_MORSE].nr;
 190
 191     for(bb=0; (bb < F_NRE); bb++) {
 192       if ((interaction_function[bb].flags & IF_BTYPE) && (bb != F_MORSE)) {
 193         nrharm  = mols[i].plist[bb].nr;
 194         srenew(mols[i].plist[F_MORSE].param,nrmorse+nrharm);
 195         snew(bRemoveHarm,nrharm);
 196
 197         /* Now loop over the harmonics, trying to convert them */
 198         for(j=0; (j<nrharm); j++) {
 199           ni   = mols[i].plist[bb].param[j].AI;
 200           nj   = mols[i].plist[bb].param[j].AJ;
 201           edis = search_e_diss(n2m,t2m,
 202                                *atype->atomname[mols[i].atoms.atom[ni].type],
 203                                *atype->atomname[mols[i].atoms.atom[nj].type]);
 204           if (edis != 0) {
 205             bRemoveHarm[j] = TRUE;
 206             b0   = mols[i].plist[bb].param[j].c[0];
 207             kb   = mols[i].plist[bb].param[j].c[1];
 208             beta = sqrt(kb/(2*edis));
 209             mols[i].plist[F_MORSE].param[nrmorse].a[0] = ni;
 210             mols[i].plist[F_MORSE].param[nrmorse].a[1] = nj;
 211             mols[i].plist[F_MORSE].param[nrmorse].c[0] = b0;
 212             mols[i].plist[F_MORSE].param[nrmorse].c[1] = edis;
 213             mols[i].plist[F_MORSE].param[nrmorse].c[2] = beta;
 214             nrmorse++;
 215           }
 216         }
 217         mols[i].plist[F_MORSE].nr = nrmorse;
 218
 219         /* Now remove the harmonics */
 220         for(j=last=0; (j<nrharm); j++) {
 221           if (!bRemoveHarm[j]) {
 222             /* Copy it to the last position */
 223             for(k=0; (k<MAXATOMLIST); k++)
 224               mols[i].plist[bb].param[last].a[k] =
 225                 mols[i].plist[bb].param[j].a[k];
 226             for(k=0; (k<MAXFORCEPARAM); k++)
 227               mols[i].plist[bb].param[last].c[k] =
 228                 mols[i].plist[bb].param[j].c[k];
 229             last++;
 230           }
 231         }
 232         sfree(bRemoveHarm);
 233         fprintf(stderr,"Converted %d out of %d %s to morse bonds for mol %d\n",
 234                 nrharm-last,nrharm,interaction_function[bb].name,i);
 235         mols[i].plist[bb].nr = last;
 236       }
 237     }
 238   }
 239   sfree(t2m);
 240 }