src/mdlib/mdatom.c

   1 /*
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   9  *                        VERSION 3.2.0
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  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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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40 #include "mdatoms.h"
  41 #include "smalloc.h"
  42 #include "main.h"
  43 #include "qmmm.h"
  44 #include "mtop_util.h"
  45
  46 #define ALMOST_ZERO 1e-30
  47
  48 t_mdatoms *init_mdatoms(FILE *fp,gmx_mtop_t *mtop,bool bFreeEnergy)
  49 {
  50   int    mb,a,g,nmol;
  51   double tmA,tmB;
  52   t_atom *atom;
  53   t_mdatoms *md;
  54   gmx_mtop_atomloop_all_t aloop;
  55   t_ilist *ilist;
  56
  57   snew(md,1);
  58
  59   md->nenergrp = mtop->groups.grps[egcENER].nr;
  60   md->bVCMgrps = FALSE;
  61   tmA = 0.0;
  62   tmB = 0.0;
  63
  64   aloop = gmx_mtop_atomloop_all_init(mtop);
  65   while(gmx_mtop_atomloop_all_next(aloop,&a,&atom)) {
  66     if (ggrpnr(&mtop->groups,egcVCM,a) > 0)
  67       md->bVCMgrps = TRUE;
  68
  69     if (bFreeEnergy && PERTURBED(*atom)) {
  70       md->nPerturbed++;
  71       if (atom->mB != atom->m)
  72         md->nMassPerturbed++;
  73       if (atom->qB != atom->q)
  74         md->nChargePerturbed++;
  75     }
  76
  77     tmA += atom->m;
  78     tmB += atom->mB;
  79   }
  80
  81   md->tmassA = tmA;
  82   md->tmassB = tmB;
  83
  84   if (bFreeEnergy && fp)
  85     fprintf(fp,
  86             "There are %d atoms and %d charges for free energy perturbation\n",
  87             md->nPerturbed,md->nChargePerturbed);
  88
  89   md->bOrires = gmx_mtop_ftype_count(mtop,F_ORIRES);
  90
  91   return md;
  92 }
  93
  94 void atoms2md(gmx_mtop_t *mtop,t_inputrec *ir,
  95               int nindex,int *index,
  96               int start,int homenr,
  97               t_mdatoms *md)
  98 {
  99   t_atoms   *atoms_mol;
 100   int       i,g,ag,as,ae,molb;
 101   real      mA,mB,fac;
 102   t_atom    *atom;
 103   t_grpopts *opts;
 104   gmx_groups_t *groups;
 105   gmx_molblock_t *molblock;
 106
 107   opts = &ir->opts;
 108
 109   groups = &mtop->groups;
 110
 111   molblock = mtop->molblock;
 112
 113   if (index == NULL) {
 114     md->nr = mtop->natoms;
 115   } else {
 116     md->nr = nindex;
 117   }
 118
 119   if (md->nr > md->nalloc) {
 120     md->nalloc = over_alloc_dd(md->nr);
 121
 122     if (md->nMassPerturbed) {
 123       srenew(md->massA,md->nalloc);
 124       srenew(md->massB,md->nalloc);
 125     }
 126     srenew(md->massT,md->nalloc);
 127     srenew(md->invmass,md->nalloc);
 128     srenew(md->chargeA,md->nalloc);
 129     if (md->nPerturbed) {
 130       srenew(md->chargeB,md->nalloc);
 131     }
 132     srenew(md->typeA,md->nalloc);
 133     if (md->nPerturbed) {
 134       srenew(md->typeB,md->nalloc);
 135     }
 136     srenew(md->ptype,md->nalloc);
 137     if (opts->ngtc > 1) {
 138       srenew(md->cTC,md->nalloc);
 139       /* We always copy cTC with domain decomposition */
 140     }
 141     srenew(md->cENER,md->nalloc);
 142     if (opts->ngacc > 1)
 143       srenew(md->cACC,md->nalloc);
 144     if (opts->nFreeze &&
 145         (opts->ngfrz > 1 ||
 146          opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
 147       srenew(md->cFREEZE,md->nalloc);
 148     if (md->bVCMgrps)
 149       srenew(md->cVCM,md->nalloc);
 150     if (md->bOrires)
 151       srenew(md->cORF,md->nalloc);
 152     if (md->nPerturbed)
 153       srenew(md->bPerturbed,md->nalloc);
 154
 155     /* Note that these user t_mdatoms array pointers are NULL
 156      * when there is only one group present.
 157      * Therefore, when adding code, the user should use something like:
 158      * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
 159      */
 160     if (mtop->groups.grpnr[egcUser1] != NULL)
 161       srenew(md->cU1,md->nalloc);
 162     if (mtop->groups.grpnr[egcUser2] != NULL)
 163       srenew(md->cU2,md->nalloc);
 164
 165     if (ir->bQMMM)
 166       srenew(md->bQM,md->nalloc);
 167   }
 168
 169   for(i=0; (i<md->nr); i++) {
 170     if (index == NULL) {
 171       ag = i;
 172       gmx_mtop_atomnr_to_atom(mtop,ag,&atom);
 173     } else {
 174       ag   = index[i];
 175       molb = -1;
 176       ae   = 0;
 177       do {
 178         molb++;
 179         as = ae;
 180         ae = as + molblock[molb].nmol*molblock[molb].natoms_mol;
 181       } while (ag >= ae);
 182       atoms_mol = &mtop->moltype[molblock[molb].type].atoms;
 183       atom = &atoms_mol->atom[(ag - as) % atoms_mol->nr];
 184     }
 185
 186     if (md->cFREEZE) {
 187       md->cFREEZE[i] = ggrpnr(groups,egcFREEZE,ag);
 188     }
 189     if (EI_ENERGY_MINIMIZATION(ir->eI)) {
 190       mA = 1.0;
 191       mB = 1.0;
 192     } else if (ir->eI == eiBD) {
 193       /* Make the mass proportional to the friction coefficient for BD.
 194        * This is necessary for the constraint algorithms.
 195        */
 196       if (ir->bd_fric) {
 197         mA = ir->bd_fric*ir->delta_t;
 198         mB = ir->bd_fric*ir->delta_t;
 199       } else {
 200         fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
 201         mA = atom->m*fac;
 202         mB = atom->mB*fac;
 203       }
 204     } else {
 205       mA = atom->m;
 206       mB = atom->mB;
 207     }
 208     if (md->nMassPerturbed) {
 209       md->massA[i]      = mA;
 210       md->massB[i]      = mB;
 211     }
 212     md->massT[i]        = mA;
 213     if (mA == 0.0) {
 214       md->invmass[i]    = 0;
 215     } else if (md->cFREEZE) {
 216       g = md->cFREEZE[i];
 217       if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 218         /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
 219          * to avoid div by zero in lincs or shake.
 220          * Note that constraints can still move a partially frozen particle.
 221          */
 222         md->invmass[i]  = ALMOST_ZERO;
 223       else
 224         md->invmass[i]  = 1.0/mA;
 225     } else {
 226       md->invmass[i]    = 1.0/mA;
 227     }
 228     md->chargeA[i]      = atom->q;
 229     md->typeA[i]        = atom->type;
 230     if (md->nPerturbed) {
 231       md->chargeB[i]    = atom->qB;
 232       md->typeB[i]      = atom->typeB;
 233       md->bPerturbed[i] = PERTURBED(*atom);
 234     }
 235     md->ptype[i]        = atom->ptype;
 236     if (md->cTC)
 237       md->cTC[i]        = groups->grpnr[egcTC][ag];
 238     md->cENER[i]        =
 239       (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
 240     if (md->cACC)
 241       md->cACC[i]       = groups->grpnr[egcACC][ag];
 242     if (md->cVCM)
 243       md->cVCM[i]       = groups->grpnr[egcVCM][ag];
 244     if (md->cORF)
 245       md->cORF[i]       = groups->grpnr[egcORFIT][ag];
 246
 247     if (md->cU1)
 248       md->cU1[i]        = groups->grpnr[egcUser1][ag];
 249     if (md->cU2)
 250       md->cU2[i]        = groups->grpnr[egcUser2][ag];
 251
 252     if (ir->bQMMM) {
 253       if (groups->grpnr[egcQMMM] == 0 ||
 254           groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1) {
 255         md->bQM[i]      = TRUE;
 256       } else {
 257         md->bQM[i]      = FALSE;
 258       }
 259     }
 260   }
 261
 262   md->start  = start;
 263   md->homenr = homenr;
 264   md->lambda = 0;
 265 }
 266
 267 void update_mdatoms(t_mdatoms *md,real lambda)
 268 {
 269   int    al,end;
 270   real   L1=1.0-lambda;
 271
 272   end=md->nr;
 273
 274   if (md->nMassPerturbed) {
 275     for(al=0; (al<end); al++) {
 276       if (md->bPerturbed[al]) {
 277         md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
 278         if (md->invmass[al] > 1.1*ALMOST_ZERO)
 279           md->invmass[al] = 1.0/md->massT[al];
 280       }
 281     }
 282     md->tmass = L1*md->tmassA + lambda*md->tmassB;
 283   } else {
 284     md->tmass = md->tmassA;
 285   }
 286   md->lambda = lambda;
 287 }