src/gmxlib/calch.c

   1 /*
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   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
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   7  *          GROningen MAchine for Chemical Simulations
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   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
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  15  * This program is free software; you can redistribute it and/or
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  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "macros.h"
  40 #include "calch.h"
  41 #include "maths.h"
  42 #include "vec.h"
  43 #include "physics.h"
  44
  45 #define xAI xa[0]
  46 #define xAJ xa[1]
  47 #define xAK xa[2]
  48 #define xAL xa[3]
  49 #define xH1 xh[0]
  50 #define xH2 xh[1]
  51 #define xH3 xh[2]
  52 #define xH4 xh[3]
  53
  54 /* The source code in this file should be thread-safe.
  55       Please keep it that way. */
  56
  57 static void gen_waterhydrogen(int nh,rvec xa[], rvec xh[],int *l)
  58 {
  59 #define AA 0.081649
  60 #define BB 0.0
  61 #define CC 0.0577350
  62   const  rvec   matrix1[6] = {
  63     { AA,     BB,     CC },
  64     { AA,     BB,     CC },
  65     { AA,     BB,     CC },
  66     { -AA,    BB,     CC },
  67     { -AA,    BB,     CC },
  68     { BB,     AA,    -CC }
  69   };
  70   const  rvec   matrix2[6] = {
  71     { -AA,   BB,   CC },
  72     { BB,    AA,  -CC },
  73     { BB,   -AA,  -CC },
  74     { BB,    AA,  -CC },
  75     { BB,   -AA,  -CC },
  76     { BB,   -AA,  -CC }
  77   };
  78 #undef AA
  79 #undef BB
  80 #undef CC
  81   /*static int l=0; removed due to thread-safety issues*/
  82   int        m;
  83   rvec       kkk;
  84
  85   /* This was copied from Gromos */
  86   for(m=0; (m<DIM); m++) {
  87     xH1[m]=xAI[m]+matrix1[*l][m];
  88     xH2[m]=xAI[m]+matrix2[*l][m];
  89   }
  90   if (nh > 2)
  91     copy_rvec(xAI,xH3);
  92   if (nh > 3)
  93     copy_rvec(xAI,xH4);
  94
  95   *l=(*l+1) % 6;
  96 }
  97
  98 void calc_h_pos(int nht, rvec xa[], rvec xh[], int *l)
  99 {
 100 #define alfaH   (acos(-1/3.0)) /* 109.47 degrees */
 101 #define alfaHpl (2*M_PI/3)     /* 120 degrees */
 102 #define distH   0.1
 103
 104 #define alfaCOM (DEG2RAD*117)
 105 #define alfaCO  (DEG2RAD*121)
 106 #define alfaCOA (DEG2RAD*115)
 107
 108 #define distO   0.123
 109 #define distOA  0.125
 110 #define distOM  0.136
 111
 112   rvec sa,sb,sij;
 113   real s6,rij,ra,rb,xd;
 114   int  d;
 115
 116   s6=0.5*sqrt(3.e0);
 117
 118   /* common work for constructing one, two or three dihedral hydrogens */
 119   switch (nht) {
 120   case 2:
 121   case 3:
 122   case 4:
 123   case 8:
 124   case 9:
 125     rij = 0.e0;
 126     for(d=0; (d<DIM); d++) {
 127       xd     = xAJ[d];
 128       sij[d] = xAI[d]-xd;
 129       sb[d]  = xd-xAK[d];
 130       rij   += sqr(sij[d]);
 131     }
 132     rij = sqrt(rij);
 133     sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
 134     sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
 135     sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
 136     ra = 0.e0;
 137     for(d=0; (d<DIM); d++) {
 138       sij[d] = sij[d]/rij;
 139       ra    += sqr(sa[d]);
 140     }
 141     ra = sqrt(ra);
 142     for(d=0; (d<DIM); d++)
 143       sa[d] = sa[d]/ra;
 144
 145     sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
 146     sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
 147     sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
 148     break;
 149   }/* end switch */
 150
 151   switch (nht) {
 152   case 1: /* construct one planar hydrogen (peptide,rings) */
 153     rij = 0.e0;
 154     rb  = 0.e0;
 155     for(d=0; (d<DIM); d++) {
 156       sij[d] = xAI[d]-xAJ[d];
 157       sb[d]  = xAI[d]-xAK[d];
 158       rij   += sqr(sij[d]);
 159       rb    += sqr(sb[d]);
 160     }
 161     rij = sqrt(rij);
 162     rb  = sqrt(rb);
 163     ra  = 0.e0;
 164     for(d=0; (d<DIM); d++) {
 165       sa[d] = sij[d]/rij+sb[d]/rb;
 166       ra   += sqr(sa[d]);
 167     }
 168     ra = sqrt(ra);
 169     for(d=0; (d<DIM); d++)
 170       xH1[d] = xAI[d]+distH*sa[d]/ra;
 171     break;
 172   case 2: /* one single hydrogen, e.g. hydroxyl */
 173     for(d=0; (d<DIM); d++) {
 174       xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
 175     }
 176     break;
 177   case 3: /* two planar hydrogens, e.g. -NH2 */
 178     for(d=0; (d<DIM); d++) {
 179       xH1[d] = xAI[d]-distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
 180       xH2[d] = xAI[d]+distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
 181     }
 182     break;
 183   case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
 184     for(d=0; (d<DIM); d++) {
 185       xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
 186       xH2[d] = ( xAI[d]
 187                    - distH*sin(alfaH)*0.5*sb[d]
 188                    + distH*sin(alfaH)*s6*sa[d]
 189                    - distH*cos(alfaH)*sij[d] );
 190       if ( xH3[XX]!=NOTSET && xH3[YY]!=NOTSET && xH3[ZZ]!=NOTSET )
 191         xH3[d] = ( xAI[d]
 192                      - distH*sin(alfaH)*0.5*sb[d]
 193                      - distH*sin(alfaH)*s6*sa[d]
 194                      - distH*cos(alfaH)*sij[d] );
 195     }
 196     break;
 197   case 5: { /* one tetrahedral hydrogen, e.g. C3CH */
 198     real center;
 199     rvec dxc;
 200
 201     for(d=0; (d<DIM); d++) {
 202       center=(xAJ[d]+xAK[d]+xAL[d])/3.0;
 203       dxc[d]=xAI[d]-center;
 204     }
 205     center=norm(dxc);
 206     for(d=0; (d<DIM); d++)
 207       xH1[d]=xAI[d]+dxc[d]*distH/center;
 208     break;
 209   }
 210   case 6: { /* two tetrahedral hydrogens, e.g. C-CH2-C */
 211     rvec rBB,rCC1,rCC2,rNN;
 212     real bb,nn;
 213
 214     for(d=0; (d<DIM); d++)
 215       rBB[d]=xAI[d]-0.5*(xAJ[d]+xAK[d]);
 216     bb=norm(rBB);
 217
 218     rvec_sub(xAI,xAJ,rCC1);
 219     rvec_sub(xAI,xAK,rCC2);
 220     cprod(rCC1,rCC2,rNN);
 221     nn=norm(rNN);
 222
 223     for(d=0; (d<DIM); d++) {
 224       xH1[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
 225                                sin(alfaH/2.0)*rNN[d]/nn);
 226       xH2[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
 227                                sin(alfaH/2.0)*rNN[d]/nn);
 228     }
 229     break;
 230   }
 231   case 7:  /* two water hydrogens */
 232     gen_waterhydrogen(2, xa, xh, l);
 233     break;
 234   case 10: /* three water hydrogens */
 235     gen_waterhydrogen(3, xa, xh, l);
 236     break;
 237   case 11: /* four water hydrogens */
 238     gen_waterhydrogen(4, xa, xh, l);
 239     break;
 240   case 8: /* two carboxyl oxygens, -COO- */
 241     for(d=0; (d<DIM); d++) {
 242       xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
 243       xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
 244     }
 245     break;
 246   case 9: { /* carboxyl oxygens and hydrogen, -COOH */
 247     rvec xa2[4]; /* i,j,k,l   */
 248
 249     /* first add two oxygens */
 250     for(d=0; (d<DIM); d++) {
 251       xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
 252       xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
 253     }
 254
 255     /* now use rule 2 to add hydrogen to 2nd oxygen */
 256     copy_rvec(xH2, xa2[0]); /* new i = n' */
 257     copy_rvec(xAI, xa2[1]); /* new j = i  */
 258     copy_rvec(xAJ, xa2[2]); /* new k = j  */
 259     copy_rvec(xAK, xa2[3]); /* new l = k, not used */
 260     calc_h_pos(2, xa2, (xh+2), l);
 261
 262     break;
 263   }
 264   default:
 265     gmx_fatal(FARGS,"Invalid argument (%d) for nht in routine genh\n",nht);
 266   } /* end switch */
 267 }