src/kernel/add_par.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 2.0
  11  *
  12  * Copyright (c) 1991-1999
  13  * BIOSON Research Institute, Dept. of Biophysical Chemistry
  14  * University of Groningen, The Netherlands
  15  *
  16  * Please refer to:
  17  * GROMACS: A message-passing parallel molecular dynamics implementation
  18  * H.J.C. Berendsen, D. van der Spoel and R. van Drunen
  19  * Comp. Phys. Comm. 91, 43-56 (1995)
  20  *
  21  * Also check out our WWW page:
  22  * http://md.chem.rug.nl/~gmx
  23  * or e-mail to:
  24  * gromacs@chem.rug.nl
  25  *
  26  * And Hey:
  27  * GRowing Old MAkes el Chrono Sweat
  28  */
  29 static char *SRCID_add_par_c = "$Id$";
  30
  31 #include <string.h>
  32 #include "typedefs.h"
  33 #include "smalloc.h"
  34 #include "grompp.h"
  35 #include "toputil.h"
  36 #include "hackblock.h"
  37
  38 static void clear_atom_list(int i0, atom_id a[])
  39 {
  40   int i;
  41
  42   for (i=i0; i < MAXATOMLIST; i++)
  43     a[i]=-1;
  44 }
  45
  46 static void clear_force_param(int i0, real c[])
  47 {
  48   int i;
  49
  50   for (i=i0; i < MAXFORCEPARAM; i++)
  51     c[i]=NOTSET;
  52 }
  53
  54 void add_param(t_params *ps,int ai,int aj, real *c, char *s)
  55 {
  56   int i;
  57
  58   if ((ai < 0) || (aj < 0))
  59     fatal_error(0,"Trying to add impossible atoms: ai=%d, aj=%d",ai,aj);
  60   pr_alloc(1,ps);
  61   ps->param[ps->nr].AI=ai;
  62   ps->param[ps->nr].AJ=aj;
  63   clear_atom_list(2, ps->param[ps->nr].a);
  64   if (c==NULL)
  65     clear_force_param(0, ps->param[ps->nr].c);
  66   else
  67     for(i=0; (i < MAXFORCEPARAM); i++)
  68       ps->param[ps->nr].c[i]=c[i];
  69   if (s)
  70     ps->param[ps->nr].s = strdup(s);
  71   else
  72     ps->param[ps->nr].s = strdup("");
  73   ps->nr++;
  74 }
  75
  76 void add_imp_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
  77                    char *s)
  78 {
  79   pr_alloc(1,ps);
  80   ps->param[ps->nr].AI=ai;
  81   ps->param[ps->nr].AJ=aj;
  82   ps->param[ps->nr].AK=ak;
  83   ps->param[ps->nr].AL=al;
  84   clear_atom_list  (4, ps->param[ps->nr].a);
  85   ps->param[ps->nr].C0=c0;
  86   ps->param[ps->nr].C1=c1;
  87   clear_force_param(2, ps->param[ps->nr].c);
  88   if (s)
  89     ps->param[ps->nr].s = strdup(s);
  90   else
  91     ps->param[ps->nr].s = strdup("");
  92   ps->nr++;
  93 }
  94
  95 void add_dih_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
  96                    real c2,char *s)
  97 {
  98   pr_alloc(1,ps);
  99   ps->param[ps->nr].AI=ai;
 100   ps->param[ps->nr].AJ=aj;
 101   ps->param[ps->nr].AK=ak;
 102   ps->param[ps->nr].AL=al;
 103   clear_atom_list  (4, ps->param[ps->nr].a);
 104   ps->param[ps->nr].C0=c0;
 105   ps->param[ps->nr].C1=c1;
 106   ps->param[ps->nr].C2=c2;
 107   clear_force_param(3, ps->param[ps->nr].c);
 108   if (s)
 109     ps->param[ps->nr].s = strdup(s);
 110   else
 111     ps->param[ps->nr].s = strdup("");
 112   ps->nr++;
 113 }
 114
 115 void add_dum2_atoms(t_params *ps,int ai,int aj,int ak)
 116 {
 117   pr_alloc(1,ps);
 118   ps->param[ps->nr].AI=ai;
 119   ps->param[ps->nr].AJ=aj;
 120   ps->param[ps->nr].AK=ak;
 121   clear_atom_list  (3, ps->param[ps->nr].a);
 122   clear_force_param(0, ps->param[ps->nr].c);
 123   ps->param[ps->nr].s = strdup("");
 124   ps->nr++;
 125 }
 126
 127 void add_dum3_param(t_params *ps,int ai,int aj,int ak,int al,
 128                     real c0, real c1)
 129 {
 130   pr_alloc(1,ps);
 131   ps->param[ps->nr].AI=ai;
 132   ps->param[ps->nr].AJ=aj;
 133   ps->param[ps->nr].AK=ak;
 134   ps->param[ps->nr].AL=al;
 135   clear_atom_list  (4, ps->param[ps->nr].a);
 136   ps->param[ps->nr].C0=c0;
 137   ps->param[ps->nr].C1=c1;
 138   clear_force_param(2, ps->param[ps->nr].c);
 139   ps->param[ps->nr].s = strdup("");
 140   ps->nr++;
 141 }
 142
 143 void add_dum3_atoms(t_params *ps,int ai,int aj,int ak,int al, bool bSwapParity)
 144 {
 145   pr_alloc(1,ps);
 146   ps->param[ps->nr].AI=ai;
 147   ps->param[ps->nr].AJ=aj;
 148   ps->param[ps->nr].AK=ak;
 149   ps->param[ps->nr].AL=al;
 150   clear_atom_list  (4, ps->param[ps->nr].a);
 151   clear_force_param(0, ps->param[ps->nr].c);
 152   if (bSwapParity)
 153     ps->param[ps->nr].C1=-1;
 154   ps->param[ps->nr].s = strdup("");
 155   ps->nr++;
 156 }
 157
 158 void add_dum4_atoms(t_params *ps,int ai,int aj,int ak,int al,int am)
 159 {
 160   pr_alloc(1,ps);
 161   ps->param[ps->nr].AI=ai;
 162   ps->param[ps->nr].AJ=aj;
 163   ps->param[ps->nr].AK=ak;
 164   ps->param[ps->nr].AL=al;
 165   ps->param[ps->nr].AM=am;
 166   clear_atom_list  (5, ps->param[ps->nr].a);
 167   clear_force_param(0, ps->param[ps->nr].c);
 168   ps->param[ps->nr].s = strdup("");
 169   ps->nr++;
 170 }
 171
 172 int search_jtype(t_restp *rtp,char *name,bool bNterm)
 173 {
 174   int  j,k,kmax,jmax;
 175   char *rtpname,searchname[12];
 176
 177   strcpy(searchname,name);
 178
 179   /* Do a best match comparison */
 180   /* for protein N-terminus, rename H1, H2 and H3 to H */
 181   if ( bNterm && (strlen(searchname)==2) && (searchname[0] == 'H') &&
 182        ( (searchname[1] == '1') || (searchname[1] == '2') ||
 183          (searchname[1] == '3') ) )
 184     searchname[1]='\0';
 185   kmax=0;
 186   jmax=-1;
 187   for(j=0; (j<rtp->natom); j++) {
 188     rtpname=*(rtp->atomname[j]);
 189     if (strcasecmp(searchname,rtpname) == 0) {
 190       jmax=j;
 191       kmax=strlen(searchname);
 192       break;
 193     }
 194     for(k=0; k < min(strlen(searchname), strlen(rtpname)); k++)
 195       if (searchname[k] != rtpname[k])
 196         break;
 197     if (k > kmax) {
 198       kmax=k;
 199       jmax=j;
 200     }
 201   }
 202   if (jmax == -1)
 203     fatal_error(0,"Atom %s not found in database in residue %s",
 204                 searchname,rtp->resname);
 205   if (kmax != strlen(searchname))
 206     fatal_error(0,"Atom %s not found in database in residue %s, "
 207                 "it looks a bit like %s",
 208                 searchname,rtp->resname,*(rtp->atomname[jmax]));
 209   return jmax;
 210 }
 211