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,gmx_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     if (ir->adress_type!=eAdressOff)
 168       srenew(md->wf,md->nalloc);
 169       srenew(md->tf_table_index,md->nalloc);
 170
 171       md->purecg = FALSE;
 172       md->pureex = FALSE;
 173   }
 174
 175   for(i=0; (i<md->nr); i++) {
 176     if (index == NULL) {
 177       ag = i;
 178       gmx_mtop_atomnr_to_atom(mtop,ag,&atom);
 179     } else {
 180       ag   = index[i];
 181       molb = -1;
 182       ae   = 0;
 183       do {
 184         molb++;
 185         as = ae;
 186         ae = as + molblock[molb].nmol*molblock[molb].natoms_mol;
 187       } while (ag >= ae);
 188       atoms_mol = &mtop->moltype[molblock[molb].type].atoms;
 189       atom = &atoms_mol->atom[(ag - as) % atoms_mol->nr];
 190     }
 191
 192     if (md->cFREEZE) {
 193       md->cFREEZE[i] = ggrpnr(groups,egcFREEZE,ag);
 194     }
 195     if (EI_ENERGY_MINIMIZATION(ir->eI)) {
 196       mA = 1.0;
 197       mB = 1.0;
 198     } else if (ir->eI == eiBD) {
 199       /* Make the mass proportional to the friction coefficient for BD.
 200        * This is necessary for the constraint algorithms.
 201        */
 202       if (ir->bd_fric) {
 203         mA = ir->bd_fric*ir->delta_t;
 204         mB = ir->bd_fric*ir->delta_t;
 205       } else {
 206         fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
 207         mA = atom->m*fac;
 208         mB = atom->mB*fac;
 209       }
 210     } else {
 211       mA = atom->m;
 212       mB = atom->mB;
 213     }
 214     if (md->nMassPerturbed) {
 215       md->massA[i]      = mA;
 216       md->massB[i]      = mB;
 217     }
 218     md->massT[i]        = mA;
 219     if (mA == 0.0) {
 220       md->invmass[i]    = 0;
 221     } else if (md->cFREEZE) {
 222       g = md->cFREEZE[i];
 223       if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 224         /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
 225          * to avoid div by zero in lincs or shake.
 226          * Note that constraints can still move a partially frozen particle.
 227          */
 228         md->invmass[i]  = ALMOST_ZERO;
 229       else
 230         md->invmass[i]  = 1.0/mA;
 231     } else {
 232       md->invmass[i]    = 1.0/mA;
 233     }
 234     md->chargeA[i]      = atom->q;
 235     md->typeA[i]        = atom->type;
 236     if (md->nPerturbed) {
 237       md->chargeB[i]    = atom->qB;
 238       md->typeB[i]      = atom->typeB;
 239       md->bPerturbed[i] = PERTURBED(*atom);
 240     }
 241     md->ptype[i]        = atom->ptype;
 242     if (md->cTC)
 243       md->cTC[i]        = groups->grpnr[egcTC][ag];
 244     md->cENER[i]        =
 245       (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
 246     if (md->cACC)
 247       md->cACC[i]       = groups->grpnr[egcACC][ag];
 248     if (md->cVCM)
 249       md->cVCM[i]       = groups->grpnr[egcVCM][ag];
 250     if (md->cORF)
 251       md->cORF[i]       = groups->grpnr[egcORFIT][ag];
 252
 253     if (md->cU1)
 254       md->cU1[i]        = groups->grpnr[egcUser1][ag];
 255     if (md->cU2)
 256       md->cU2[i]        = groups->grpnr[egcUser2][ag];
 257
 258     if (ir->bQMMM) {
 259       if (groups->grpnr[egcQMMM] == 0 ||
 260           groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1) {
 261         md->bQM[i]      = TRUE;
 262       } else {
 263         md->bQM[i]      = FALSE;
 264       }
 265     }
 266     /* Initialize AdResS weighting functions to adressw */
 267     if (ir->adress_type!=eAdressOff){
 268        md->wf[i]           = 1.0;
 269         /* if no tf table groups specified, use default table */
 270        md->tf_table_index[i] = DEFAULT_TF_TABLE;
 271        if (ir->n_adress_tf_grps > 0){
 272             /* if tf table groups specified, tf is only applied to thoose energy groups*/
 273             md->tf_table_index[i] = NO_TF_TABLE;
 274             /* check wether atom is in one of the relevant energy groups and assign a table index */
 275             for (g=0; g<ir->n_adress_tf_grps; g++){
 276                 if (md->cENER[i] == ir->adress_tf_table_index[g]){
 277                    md->tf_table_index[i] = g;
 278                 }
 279             }
 280         }
 281     }
 282   }
 283
 284   md->start  = start;
 285   md->homenr = homenr;
 286   md->lambda = 0;
 287 }
 288
 289 void update_mdatoms(t_mdatoms *md,real lambda)
 290 {
 291   int    al,end;
 292   real   L1=1.0-lambda;
 293
 294   end=md->nr;
 295
 296   if (md->nMassPerturbed) {
 297     for(al=0; (al<end); al++) {
 298       if (md->bPerturbed[al]) {
 299         md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
 300         if (md->invmass[al] > 1.1*ALMOST_ZERO)
 301           md->invmass[al] = 1.0/md->massT[al];
 302       }
 303     }
 304     md->tmass = L1*md->tmassA + lambda*md->tmassB;
 305   } else {
 306     md->tmass = md->tmassA;
 307   }
 308   md->lambda = lambda;
 309 }