src/gromacs/mdlib/mdatoms.cpp

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  37 #include "gmxpre.h"
  38
  39 #include "mdatoms.h"
  40
  41 #include <math.h>
  42
  43 #include "gromacs/gmxlib/gmx_omp_nthreads.h"
  44 #include "gromacs/mdlib/qmmm.h"
  45 #include "gromacs/topology/mtop_util.h"
  46 #include "gromacs/topology/topology.h"
  47 #include "gromacs/utility/exceptions.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 #define ALMOST_ZERO 1e-30
  51
  52 t_mdatoms *init_mdatoms(FILE *fp, const gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
  53 {
  54     int                     a;
  55     double                  tmA, tmB;
  56     t_atom                 *atom;
  57     t_mdatoms              *md;
  58     gmx_mtop_atomloop_all_t aloop;
  59
  60     snew(md, 1);
  61
  62     md->nenergrp = mtop->groups.grps[egcENER].nr;
  63     md->bVCMgrps = FALSE;
  64     tmA          = 0.0;
  65     tmB          = 0.0;
  66
  67     aloop = gmx_mtop_atomloop_all_init(mtop);
  68     while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
  69     {
  70         if (ggrpnr(&mtop->groups, egcVCM, a) > 0)
  71         {
  72             md->bVCMgrps = TRUE;
  73         }
  74
  75         if (bFreeEnergy && PERTURBED(*atom))
  76         {
  77             md->nPerturbed++;
  78             if (atom->mB != atom->m)
  79             {
  80                 md->nMassPerturbed++;
  81             }
  82             if (atom->qB != atom->q)
  83             {
  84                 md->nChargePerturbed++;
  85             }
  86             if (atom->typeB != atom->type)
  87             {
  88                 md->nTypePerturbed++;
  89             }
  90         }
  91
  92         tmA += atom->m;
  93         tmB += atom->mB;
  94     }
  95
  96     md->tmassA = tmA;
  97     md->tmassB = tmB;
  98
  99     if (bFreeEnergy && fp)
 100     {
 101         fprintf(fp,
 102                 "There are %d atoms and %d charges for free energy perturbation\n",
 103                 md->nPerturbed, md->nChargePerturbed);
 104     }
 105
 106     md->bOrires = gmx_mtop_ftype_count(mtop, F_ORIRES);
 107
 108     return md;
 109 }
 110
 111 void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
 112               int nindex, const int *index,
 113               int homenr,
 114               t_mdatoms *md)
 115 {
 116     gmx_bool              bLJPME;
 117     gmx_mtop_atomlookup_t alook;
 118     int                   i;
 119     const t_grpopts      *opts;
 120     const gmx_groups_t   *groups;
 121     int                   nthreads gmx_unused;
 122     const real            oneOverSix = 1.0 / 6.0;
 123
 124     bLJPME = EVDW_PME(ir->vdwtype);
 125
 126     opts = &ir->opts;
 127
 128     groups = &mtop->groups;
 129
 130     /* Index==NULL indicates no DD (unless we have a DD node with no
 131      * atoms), so also check for homenr. This should be
 132      * signaled properly with an extra parameter or nindex==-1.
 133      */
 134     if (index == NULL && (homenr > 0))
 135     {
 136         md->nr = mtop->natoms;
 137     }
 138     else
 139     {
 140         md->nr = nindex;
 141     }
 142
 143     if (md->nr > md->nalloc)
 144     {
 145         md->nalloc = over_alloc_dd(md->nr);
 146
 147         if (md->nMassPerturbed)
 148         {
 149             srenew(md->massA, md->nalloc);
 150             srenew(md->massB, md->nalloc);
 151         }
 152         srenew(md->massT, md->nalloc);
 153         srenew(md->invmass, md->nalloc);
 154         srenew(md->chargeA, md->nalloc);
 155         srenew(md->typeA, md->nalloc);
 156         if (md->nPerturbed)
 157         {
 158             srenew(md->chargeB, md->nalloc);
 159             srenew(md->typeB, md->nalloc);
 160         }
 161         if (bLJPME)
 162         {
 163             srenew(md->sqrt_c6A, md->nalloc);
 164             srenew(md->sigmaA, md->nalloc);
 165             srenew(md->sigma3A, md->nalloc);
 166             if (md->nPerturbed)
 167             {
 168                 srenew(md->sqrt_c6B, md->nalloc);
 169                 srenew(md->sigmaB, md->nalloc);
 170                 srenew(md->sigma3B, md->nalloc);
 171             }
 172         }
 173         srenew(md->ptype, md->nalloc);
 174         if (opts->ngtc > 1)
 175         {
 176             srenew(md->cTC, md->nalloc);
 177             /* We always copy cTC with domain decomposition */
 178         }
 179         srenew(md->cENER, md->nalloc);
 180         if (opts->ngacc > 1)
 181         {
 182             srenew(md->cACC, md->nalloc);
 183         }
 184         if (opts->nFreeze &&
 185             (opts->ngfrz > 1 ||
 186              opts->nFreeze[0][XX] || opts->nFreeze[0][YY] || opts->nFreeze[0][ZZ]))
 187         {
 188             srenew(md->cFREEZE, md->nalloc);
 189         }
 190         if (md->bVCMgrps)
 191         {
 192             srenew(md->cVCM, md->nalloc);
 193         }
 194         if (md->bOrires)
 195         {
 196             srenew(md->cORF, md->nalloc);
 197         }
 198         if (md->nPerturbed)
 199         {
 200             srenew(md->bPerturbed, md->nalloc);
 201         }
 202
 203         /* Note that these user t_mdatoms array pointers are NULL
 204          * when there is only one group present.
 205          * Therefore, when adding code, the user should use something like:
 206          * gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
 207          */
 208         if (mtop->groups.grpnr[egcUser1] != NULL)
 209         {
 210             srenew(md->cU1, md->nalloc);
 211         }
 212         if (mtop->groups.grpnr[egcUser2] != NULL)
 213         {
 214             srenew(md->cU2, md->nalloc);
 215         }
 216
 217         if (ir->bQMMM)
 218         {
 219             srenew(md->bQM, md->nalloc);
 220         }
 221     }
 222
 223     alook = gmx_mtop_atomlookup_init(mtop);
 224
 225     // cppcheck-suppress unreadVariable
 226     nthreads = gmx_omp_nthreads_get(emntDefault);
 227 #pragma omp parallel for num_threads(nthreads) schedule(static)
 228     for (i = 0; i < md->nr; i++)
 229     {
 230         try
 231         {
 232             int      g, ag;
 233             real     mA, mB, fac;
 234             real     c6, c12;
 235             t_atom  *atom;
 236
 237             if (index == NULL)
 238             {
 239                 ag = i;
 240             }
 241             else
 242             {
 243                 ag   = index[i];
 244             }
 245             gmx_mtop_atomnr_to_atom(alook, ag, &atom);
 246
 247             if (md->cFREEZE)
 248             {
 249                 md->cFREEZE[i] = ggrpnr(groups, egcFREEZE, ag);
 250             }
 251             if (EI_ENERGY_MINIMIZATION(ir->eI))
 252             {
 253                 /* Displacement is proportional to F, masses used for constraints */
 254                 mA = 1.0;
 255                 mB = 1.0;
 256             }
 257             else if (ir->eI == eiBD)
 258             {
 259                 /* With BD the physical masses are irrelevant.
 260                  * To keep the code simple we use most of the normal MD code path
 261                  * for BD. Thus for constraining the masses should be proportional
 262                  * to the friction coefficient. We set the absolute value such that
 263                  * m/2<(dx/dt)^2> = m/2*2kT/fric*dt = kT/2 => m=fric*dt/2
 264                  * Then if we set the (meaningless) velocity to v=dx/dt, we get the
 265                  * correct kinetic energy and temperature using the usual code path.
 266                  * Thus with BD v*dt will give the displacement and the reported
 267                  * temperature can signal bad integration (too large time step).
 268                  */
 269                 if (ir->bd_fric > 0)
 270                 {
 271                     mA = 0.5*ir->bd_fric*ir->delta_t;
 272                     mB = 0.5*ir->bd_fric*ir->delta_t;
 273                 }
 274                 else
 275                 {
 276                     /* The friction coefficient is mass/tau_t */
 277                     fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
 278                     mA  = 0.5*atom->m*fac;
 279                     mB  = 0.5*atom->mB*fac;
 280                 }
 281             }
 282             else
 283             {
 284                 mA = atom->m;
 285                 mB = atom->mB;
 286             }
 287             if (md->nMassPerturbed)
 288             {
 289                 md->massA[i]  = mA;
 290                 md->massB[i]  = mB;
 291             }
 292             md->massT[i]    = mA;
 293             if (mA == 0.0)
 294             {
 295                 md->invmass[i]    = 0;
 296             }
 297             else if (md->cFREEZE)
 298             {
 299                 g = md->cFREEZE[i];
 300                 if (opts->nFreeze[g][XX] && opts->nFreeze[g][YY] && opts->nFreeze[g][ZZ])
 301                 {
 302                     /* Set the mass of completely frozen particles to ALMOST_ZERO iso 0
 303                      * to avoid div by zero in lincs or shake.
 304                      * Note that constraints can still move a partially frozen particle.
 305                      */
 306                     md->invmass[i]  = ALMOST_ZERO;
 307                 }
 308                 else
 309                 {
 310                     md->invmass[i]  = 1.0/mA;
 311                 }
 312             }
 313             else
 314             {
 315                 md->invmass[i]    = 1.0/mA;
 316             }
 317             md->chargeA[i]      = atom->q;
 318             md->typeA[i]        = atom->type;
 319             if (bLJPME)
 320             {
 321                 c6                = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
 322                 c12               = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
 323                 md->sqrt_c6A[i]   = sqrt(c6);
 324                 if (c6 == 0.0 || c12 == 0)
 325                 {
 326                     md->sigmaA[i] = 1.0;
 327                 }
 328                 else
 329                 {
 330                     md->sigmaA[i] = pow(c12/c6, oneOverSix);
 331                 }
 332                 md->sigma3A[i]    = 1/(md->sigmaA[i]*md->sigmaA[i]*md->sigmaA[i]);
 333             }
 334             if (md->nPerturbed)
 335             {
 336                 md->bPerturbed[i] = PERTURBED(*atom);
 337                 md->chargeB[i]    = atom->qB;
 338                 md->typeB[i]      = atom->typeB;
 339                 if (bLJPME)
 340                 {
 341                     c6                = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
 342                     c12               = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
 343                     md->sqrt_c6B[i]   = sqrt(c6);
 344                     if (c6 == 0.0 || c12 == 0)
 345                     {
 346                         md->sigmaB[i] = 1.0;
 347                     }
 348                     else
 349                     {
 350                         md->sigmaB[i] = pow(c12/c6, oneOverSix);
 351                     }
 352                     md->sigma3B[i]    = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
 353                 }
 354             }
 355             md->ptype[i]    = atom->ptype;
 356             if (md->cTC)
 357             {
 358                 md->cTC[i]    = groups->grpnr[egcTC][ag];
 359             }
 360             md->cENER[i]    =
 361                 (groups->grpnr[egcENER] ? groups->grpnr[egcENER][ag] : 0);
 362             if (md->cACC)
 363             {
 364                 md->cACC[i]   = groups->grpnr[egcACC][ag];
 365             }
 366             if (md->cVCM)
 367             {
 368                 md->cVCM[i]       = groups->grpnr[egcVCM][ag];
 369             }
 370             if (md->cORF)
 371             {
 372                 md->cORF[i]       = groups->grpnr[egcORFIT][ag];
 373             }
 374
 375             if (md->cU1)
 376             {
 377                 md->cU1[i]        = groups->grpnr[egcUser1][ag];
 378             }
 379             if (md->cU2)
 380             {
 381                 md->cU2[i]        = groups->grpnr[egcUser2][ag];
 382             }
 383
 384             if (ir->bQMMM)
 385             {
 386                 if (groups->grpnr[egcQMMM] == 0 ||
 387                     groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
 388                 {
 389                     md->bQM[i]      = TRUE;
 390                 }
 391                 else
 392                 {
 393                     md->bQM[i]      = FALSE;
 394                 }
 395             }
 396         }
 397         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 398     }
 399
 400     gmx_mtop_atomlookup_destroy(alook);
 401
 402     md->homenr = homenr;
 403     md->lambda = 0;
 404 }
 405
 406 void update_mdatoms(t_mdatoms *md, real lambda)
 407 {
 408     int    al, end;
 409     real   L1 = 1.0-lambda;
 410
 411     end = md->nr;
 412
 413     if (md->nMassPerturbed)
 414     {
 415         for (al = 0; (al < end); al++)
 416         {
 417             if (md->bPerturbed[al])
 418             {
 419                 md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
 420                 if (md->invmass[al] > 1.1*ALMOST_ZERO)
 421                 {
 422                     md->invmass[al] = 1.0/md->massT[al];
 423                 }
 424             }
 425         }
 426         md->tmass = L1*md->tmassA + lambda*md->tmassB;
 427     }
 428     else
 429     {
 430         md->tmass = md->tmassA;
 431     }
 432     md->lambda = lambda;
 433 }