src/gromacs/mdlib/stat.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cstdio>
  40 #include <cstring>
  41
  42 #include "gromacs/domdec/domdec.h"
  43 #include "gromacs/domdec/domdec_struct.h"
  44 #include "gromacs/fileio/checkpoint.h"
  45 #include "gromacs/fileio/xtcio.h"
  46 #include "gromacs/gmxlib/network.h"
  47 #include "gromacs/math/utilities.h"
  48 #include "gromacs/math/vec.h"
  49 #include "gromacs/mdlib/constr.h"
  50 #include "gromacs/mdlib/md_support.h"
  51 #include "gromacs/mdlib/mdrun.h"
  52 #include "gromacs/mdlib/rbin.h"
  53 #include "gromacs/mdlib/sim_util.h"
  54 #include "gromacs/mdlib/tgroup.h"
  55 #include "gromacs/mdlib/vcm.h"
  56 #include "gromacs/mdtypes/commrec.h"
  57 #include "gromacs/mdtypes/group.h"
  58 #include "gromacs/mdtypes/inputrec.h"
  59 #include "gromacs/mdtypes/md_enums.h"
  60 #include "gromacs/utility/fatalerror.h"
  61 #include "gromacs/utility/futil.h"
  62 #include "gromacs/utility/smalloc.h"
  63
  64 typedef struct gmx_global_stat
  65 {
  66     t_bin *rb;
  67     int   *itc0;
  68     int   *itc1;
  69 } t_gmx_global_stat;
  70
  71 gmx_global_stat_t global_stat_init(const t_inputrec *ir)
  72 {
  73     gmx_global_stat_t gs;
  74
  75     snew(gs, 1);
  76
  77     gs->rb = mk_bin();
  78     snew(gs->itc0, ir->opts.ngtc);
  79     snew(gs->itc1, ir->opts.ngtc);
  80
  81     return gs;
  82 }
  83
  84 void global_stat_destroy(gmx_global_stat_t gs)
  85 {
  86     destroy_bin(gs->rb);
  87     sfree(gs->itc0);
  88     sfree(gs->itc1);
  89     sfree(gs);
  90 }
  91
  92 static int filter_enerdterm(const real *afrom, gmx_bool bToBuffer, real *ato,
  93                             gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner)
  94 {
  95     int i, to, from;
  96
  97     from = 0;
  98     to   = 0;
  99     for (i = 0; i < F_NRE; i++)
 100     {
 101         if (bToBuffer)
 102         {
 103             from = i;
 104         }
 105         else
 106         {
 107             to = i;
 108         }
 109         switch (i)
 110         {
 111             case F_EKIN:
 112             case F_TEMP:
 113             case F_DKDL:
 114                 if (bTemp)
 115                 {
 116                     ato[to++] = afrom[from++];
 117                 }
 118                 break;
 119             case F_PRES:
 120             case F_PDISPCORR:
 121                 if (bPres)
 122                 {
 123                     ato[to++] = afrom[from++];
 124                 }
 125                 break;
 126             default:
 127                 if (bEner)
 128                 {
 129                     ato[to++] = afrom[from++];
 130                 }
 131                 break;
 132         }
 133     }
 134
 135     return to;
 136 }
 137
 138 void global_stat(const gmx_global_stat *gs,
 139                  const t_commrec *cr, gmx_enerdata_t *enerd,
 140                  tensor fvir, tensor svir, rvec mu_tot,
 141                  const t_inputrec *inputrec,
 142                  gmx_ekindata_t *ekind, const gmx::Constraints *constr,
 143                  t_vcm *vcm,
 144                  int nsig, real *sig,
 145                  int *totalNumberOfBondedInteractions,
 146                  gmx_bool bSumEkinhOld, int flags)
 147 /* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
 148 {
 149     t_bin     *rb;
 150     int       *itc0, *itc1;
 151     int        ie    = 0, ifv = 0, isv = 0, irmsd = 0, imu = 0;
 152     int        idedl = 0, idedlo = 0, idvdll = 0, idvdlnl = 0, iepl = 0, icm = 0, imass = 0, ica = 0, inb = 0;
 153     int        isig  = -1;
 154     int        icj   = -1, ici = -1, icx = -1;
 155     int        inn[egNR];
 156     real       copyenerd[F_NRE];
 157     int        nener, j;
 158     double     nb;
 159     gmx_bool   bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bReadEkin;
 160     bool       checkNumberOfBondedInteractions = (flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS) != 0;
 161
 162     bVV           = EI_VV(inputrec->eI);
 163     bTemp         = ((flags & CGLO_TEMPERATURE) != 0);
 164     bEner         = ((flags & CGLO_ENERGY) != 0);
 165     bPres         = ((flags & CGLO_PRESSURE) != 0);
 166     bConstrVir    = ((flags & CGLO_CONSTRAINT) != 0);
 167     bEkinAveVel   = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
 168     bReadEkin     = ((flags & CGLO_READEKIN) != 0);
 169
 170     rb   = gs->rb;
 171     itc0 = gs->itc0;
 172     itc1 = gs->itc1;
 173
 174
 175     reset_bin(rb);
 176     /* This routine copies all the data to be summed to one big buffer
 177      * using the t_bin struct.
 178      */
 179
 180     /* First, we neeed to identify which enerd->term should be
 181        communicated.  Temperature and pressure terms should only be
 182        communicated and summed when they need to be, to avoid repeating
 183        the sums and overcounting. */
 184
 185     nener = filter_enerdterm(enerd->term, TRUE, copyenerd, bTemp, bPres, bEner);
 186
 187     /* First, the data that needs to be communicated with velocity verlet every time
 188        This is just the constraint virial.*/
 189     if (bConstrVir)
 190     {
 191         isv = add_binr(rb, DIM*DIM, svir[0]);
 192     }
 193
 194 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
 195     if (bTemp || !bVV)
 196     {
 197         if (ekind)
 198         {
 199             for (j = 0; (j < inputrec->opts.ngtc); j++)
 200             {
 201                 if (bSumEkinhOld)
 202                 {
 203                     itc0[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
 204                 }
 205                 if (bEkinAveVel && !bReadEkin)
 206                 {
 207                     itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinf[0]);
 208                 }
 209                 else if (!bReadEkin)
 210                 {
 211                     itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh[0]);
 212                 }
 213             }
 214             /* these probably need to be put into one of these categories */
 215             idedl = add_binr(rb, 1, &(ekind->dekindl));
 216             if (bSumEkinhOld)
 217             {
 218                 idedlo = add_binr(rb, 1, &(ekind->dekindl_old));
 219             }
 220             ica   = add_binr(rb, 1, &(ekind->cosacc.mvcos));
 221         }
 222     }
 223
 224     if (bPres)
 225     {
 226         ifv = add_binr(rb, DIM*DIM, fvir[0]);
 227     }
 228
 229     gmx::ArrayRef<real> rmsdData;
 230     if (bEner)
 231     {
 232         ie  = add_binr(rb, nener, copyenerd);
 233         if (constr)
 234         {
 235             rmsdData = constr->rmsdData();
 236             if (!rmsdData.empty())
 237             {
 238                 irmsd = add_binr(rb, 2, rmsdData.data());
 239             }
 240         }
 241         if (!inputrecNeedMutot(inputrec))
 242         {
 243             imu = add_binr(rb, DIM, mu_tot);
 244         }
 245
 246         for (j = 0; (j < egNR); j++)
 247         {
 248             inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
 249         }
 250         if (inputrec->efep != efepNO)
 251         {
 252             idvdll  = add_bind(rb, efptNR, enerd->dvdl_lin);
 253             idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
 254             if (enerd->n_lambda > 0)
 255             {
 256                 iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
 257             }
 258         }
 259     }
 260
 261     if (vcm)
 262     {
 263         icm   = add_binr(rb, DIM*vcm->nr, vcm->group_p[0]);
 264         imass = add_binr(rb, vcm->nr, vcm->group_mass);
 265         if (vcm->mode == ecmANGULAR)
 266         {
 267             icj   = add_binr(rb, DIM*vcm->nr, vcm->group_j[0]);
 268             icx   = add_binr(rb, DIM*vcm->nr, vcm->group_x[0]);
 269             ici   = add_binr(rb, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
 270         }
 271     }
 272
 273     if (checkNumberOfBondedInteractions)
 274     {
 275         nb  = cr->dd->nbonded_local;
 276         inb = add_bind(rb, 1, &nb);
 277     }
 278     if (nsig > 0)
 279     {
 280         isig = add_binr(rb, nsig, sig);
 281     }
 282
 283     /* Global sum it all */
 284     if (debug)
 285     {
 286         fprintf(debug, "Summing %d energies\n", rb->maxreal);
 287     }
 288     sum_bin(rb, cr);
 289
 290     /* Extract all the data locally */
 291
 292     if (bConstrVir)
 293     {
 294         extract_binr(rb, isv, DIM*DIM, svir[0]);
 295     }
 296
 297     /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
 298     if (bTemp || !bVV)
 299     {
 300         if (ekind)
 301         {
 302             for (j = 0; (j < inputrec->opts.ngtc); j++)
 303             {
 304                 if (bSumEkinhOld)
 305                 {
 306                     extract_binr(rb, itc0[j], DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
 307                 }
 308                 if (bEkinAveVel && !bReadEkin)
 309                 {
 310                     extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinf[0]);
 311                 }
 312                 else if (!bReadEkin)
 313                 {
 314                     extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinh[0]);
 315                 }
 316             }
 317             extract_binr(rb, idedl, 1, &(ekind->dekindl));
 318             if (bSumEkinhOld)
 319             {
 320                 extract_binr(rb, idedlo, 1, &(ekind->dekindl_old));
 321             }
 322             extract_binr(rb, ica, 1, &(ekind->cosacc.mvcos));
 323         }
 324     }
 325     if (bPres)
 326     {
 327         extract_binr(rb, ifv, DIM*DIM, fvir[0]);
 328     }
 329
 330     if (bEner)
 331     {
 332         extract_binr(rb, ie, nener, copyenerd);
 333         if (!rmsdData.empty())
 334         {
 335             extract_binr(rb, irmsd, rmsdData);
 336         }
 337         if (!inputrecNeedMutot(inputrec))
 338         {
 339             extract_binr(rb, imu, DIM, mu_tot);
 340         }
 341
 342         for (j = 0; (j < egNR); j++)
 343         {
 344             extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
 345         }
 346         if (inputrec->efep != efepNO)
 347         {
 348             extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
 349             extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
 350             if (enerd->n_lambda > 0)
 351             {
 352                 extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
 353             }
 354         }
 355
 356         filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
 357     }
 358
 359     if (vcm)
 360     {
 361         extract_binr(rb, icm, DIM*vcm->nr, vcm->group_p[0]);
 362         extract_binr(rb, imass, vcm->nr, vcm->group_mass);
 363         if (vcm->mode == ecmANGULAR)
 364         {
 365             extract_binr(rb, icj, DIM*vcm->nr, vcm->group_j[0]);
 366             extract_binr(rb, icx, DIM*vcm->nr, vcm->group_x[0]);
 367             extract_binr(rb, ici, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
 368         }
 369     }
 370
 371     if (checkNumberOfBondedInteractions)
 372     {
 373         extract_bind(rb, inb, 1, &nb);
 374         *totalNumberOfBondedInteractions = gmx::roundToInt(nb);
 375     }
 376
 377     if (nsig > 0)
 378     {
 379         extract_binr(rb, isig, nsig, sig);
 380     }
 381 }
 382
 383 bool do_per_step(int64_t step, int64_t nstep)
 384 {
 385     if (nstep != 0)
 386     {
 387         return (step % nstep) == 0;
 388     }
 389     else
 390     {
 391         return false;
 392     }
 393 }