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   int        m;
  82   rvec       kkk;
  83
  84   /* This was copied from Gromos */
  85   for(m=0; (m<DIM); m++) {
  86     xH1[m]=xAI[m]+matrix1[*l][m];
  87     xH2[m]=xAI[m]+matrix2[*l][m];
  88   }
  89   if (nh > 2)
  90     copy_rvec(xAI,xH3);
  91   if (nh > 3)
  92     copy_rvec(xAI,xH4);
  93
  94   *l=(*l+1) % 6;
  95 }
  96
  97 void calc_h_pos(int nht, rvec xa[], rvec xh[], int *l)
  98 {
  99 #define alfaH   (acos(-1/3.0)) /* 109.47 degrees */
 100 #define alfaHpl (2*M_PI/3)     /* 120 degrees */
 101 #define distH   0.1
 102
 103 #define alfaCOM (DEG2RAD*117)
 104 #define alfaCO  (DEG2RAD*121)
 105 #define alfaCOA (DEG2RAD*115)
 106
 107 #define distO   0.123
 108 #define distOA  0.125
 109 #define distOM  0.136
 110
 111   rvec sa,sb,sij;
 112   real s6,rij,ra,rb,xd;
 113   int  d;
 114
 115   s6=0.5*sqrt(3.e0);
 116
 117   /* common work for constructing one, two or three dihedral hydrogens */
 118   switch (nht) {
 119   case 2:
 120   case 3:
 121   case 4:
 122   case 8:
 123   case 9:
 124     rij = 0.e0;
 125     for(d=0; (d<DIM); d++) {
 126       xd     = xAJ[d];
 127       sij[d] = xAI[d]-xd;
 128       sb[d]  = xd-xAK[d];
 129       rij   += sqr(sij[d]);
 130     }
 131     rij = sqrt(rij);
 132     sa[XX] = sij[YY]*sb[ZZ]-sij[ZZ]*sb[YY];
 133     sa[YY] = sij[ZZ]*sb[XX]-sij[XX]*sb[ZZ];
 134     sa[ZZ] = sij[XX]*sb[YY]-sij[YY]*sb[XX];
 135     ra = 0.e0;
 136     for(d=0; (d<DIM); d++) {
 137       sij[d] = sij[d]/rij;
 138       ra    += sqr(sa[d]);
 139     }
 140     ra = sqrt(ra);
 141     for(d=0; (d<DIM); d++)
 142       sa[d] = sa[d]/ra;
 143
 144     sb[XX] = sa[YY]*sij[ZZ]-sa[ZZ]*sij[YY];
 145     sb[YY] = sa[ZZ]*sij[XX]-sa[XX]*sij[ZZ];
 146     sb[ZZ] = sa[XX]*sij[YY]-sa[YY]*sij[XX];
 147     break;
 148   }/* end switch */
 149
 150   switch (nht) {
 151   case 1: /* construct one planar hydrogen (peptide,rings) */
 152     rij = 0.e0;
 153     rb  = 0.e0;
 154     for(d=0; (d<DIM); d++) {
 155       sij[d] = xAI[d]-xAJ[d];
 156       sb[d]  = xAI[d]-xAK[d];
 157       rij   += sqr(sij[d]);
 158       rb    += sqr(sb[d]);
 159     }
 160     rij = sqrt(rij);
 161     rb  = sqrt(rb);
 162     ra  = 0.e0;
 163     for(d=0; (d<DIM); d++) {
 164       sa[d] = sij[d]/rij+sb[d]/rb;
 165       ra   += sqr(sa[d]);
 166     }
 167     ra = sqrt(ra);
 168     for(d=0; (d<DIM); d++)
 169       xH1[d] = xAI[d]+distH*sa[d]/ra;
 170     break;
 171   case 2: /* one single hydrogen, e.g. hydroxyl */
 172     for(d=0; (d<DIM); d++) {
 173       xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
 174     }
 175     break;
 176   case 3: /* two planar hydrogens, e.g. -NH2 */
 177     for(d=0; (d<DIM); d++) {
 178       xH1[d] = xAI[d]-distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
 179       xH2[d] = xAI[d]+distH*sin(alfaHpl)*sb[d]-distH*cos(alfaHpl)*sij[d];
 180     }
 181     break;
 182   case 4: /* two or three tetrahedral hydrogens, e.g. -CH3 */
 183     for(d=0; (d<DIM); d++) {
 184       xH1[d] = xAI[d]+distH*sin(alfaH)*sb[d]-distH*cos(alfaH)*sij[d];
 185       xH2[d] = ( xAI[d]
 186                    - distH*sin(alfaH)*0.5*sb[d]
 187                    + distH*sin(alfaH)*s6*sa[d]
 188                    - distH*cos(alfaH)*sij[d] );
 189       if ( xH3[XX]!=NOTSET && xH3[YY]!=NOTSET && xH3[ZZ]!=NOTSET )
 190         xH3[d] = ( xAI[d]
 191                      - distH*sin(alfaH)*0.5*sb[d]
 192                      - distH*sin(alfaH)*s6*sa[d]
 193                      - distH*cos(alfaH)*sij[d] );
 194     }
 195     break;
 196   case 5: { /* one tetrahedral hydrogen, e.g. C3CH */
 197     real center;
 198     rvec dxc;
 199
 200     for(d=0; (d<DIM); d++) {
 201       center=(xAJ[d]+xAK[d]+xAL[d])/3.0;
 202       dxc[d]=xAI[d]-center;
 203     }
 204     center=norm(dxc);
 205     for(d=0; (d<DIM); d++)
 206       xH1[d]=xAI[d]+dxc[d]*distH/center;
 207     break;
 208   }
 209   case 6: { /* two tetrahedral hydrogens, e.g. C-CH2-C */
 210     rvec rBB,rCC1,rCC2,rNN;
 211     real bb,nn;
 212
 213     for(d=0; (d<DIM); d++)
 214       rBB[d]=xAI[d]-0.5*(xAJ[d]+xAK[d]);
 215     bb=norm(rBB);
 216
 217     rvec_sub(xAI,xAJ,rCC1);
 218     rvec_sub(xAI,xAK,rCC2);
 219     cprod(rCC1,rCC2,rNN);
 220     nn=norm(rNN);
 221
 222     for(d=0; (d<DIM); d++) {
 223       xH1[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb+
 224                                sin(alfaH/2.0)*rNN[d]/nn);
 225       xH2[d]=xAI[d]+distH*(cos(alfaH/2.0)*rBB[d]/bb-
 226                                sin(alfaH/2.0)*rNN[d]/nn);
 227     }
 228     break;
 229   }
 230   case 7:  /* two water hydrogens */
 231     gen_waterhydrogen(2, xa, xh, l);
 232     break;
 233   case 10: /* three water hydrogens */
 234     gen_waterhydrogen(3, xa, xh, l);
 235     break;
 236   case 11: /* four water hydrogens */
 237     gen_waterhydrogen(4, xa, xh, l);
 238     break;
 239   case 8: /* two carboxyl oxygens, -COO- */
 240     for(d=0; (d<DIM); d++) {
 241       xH1[d] = xAI[d]-distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
 242       xH2[d] = xAI[d]+distOM*sin(alfaCOM)*sb[d]-distOM*cos(alfaCOM)*sij[d];
 243     }
 244     break;
 245   case 9: { /* carboxyl oxygens and hydrogen, -COOH */
 246     rvec xa2[4]; /* i,j,k,l   */
 247
 248     /* first add two oxygens */
 249     for(d=0; (d<DIM); d++) {
 250       xH1[d] = xAI[d]-distO *sin(alfaCO )*sb[d]-distO *cos(alfaCO )*sij[d];
 251       xH2[d] = xAI[d]+distOA*sin(alfaCOA)*sb[d]-distOA*cos(alfaCOA)*sij[d];
 252     }
 253
 254     /* now use rule 2 to add hydrogen to 2nd oxygen */
 255     copy_rvec(xH2, xa2[0]); /* new i = n' */
 256     copy_rvec(xAI, xa2[1]); /* new j = i  */
 257     copy_rvec(xAJ, xa2[2]); /* new k = j  */
 258     copy_rvec(xAK, xa2[3]); /* new l = k, not used */
 259     calc_h_pos(2, xa2, (xh+2), l);
 260
 261     break;
 262   }
 263   default:
 264     gmx_fatal(FARGS,"Invalid argument (%d) for nht in routine genh\n",nht);
 265   } /* end switch */
 266 }