src/gromacs/mdlib/stat.c

   1 /*
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   3  *
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   5  * Copyright (c) 2001-2004, The GROMACS development team.
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   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <string.h>
  42 #include <stdio.h>
  43 #include "typedefs.h"
  44 #include "types/commrec.h"
  45 #include "gromacs/utility/fatalerror.h"
  46 #include "network.h"
  47 #include "txtdump.h"
  48 #include "names.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/math/utilities.h"
  51 #include "force.h"
  52 #include "vcm.h"
  53 #include "gromacs/utility/smalloc.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "network.h"
  56 #include "rbin.h"
  57 #include "tgroup.h"
  58 #include "gromacs/fileio/xtcio.h"
  59 #include "gromacs/fileio/gmxfio.h"
  60 #include "gromacs/fileio/trnio.h"
  61 #include "domdec.h"
  62 #include "constr.h"
  63 #include "checkpoint.h"
  64 #include "md_support.h"
  65 #include "mdrun.h"
  66 #include "sim_util.h"
  67
  68 typedef struct gmx_global_stat
  69 {
  70     t_bin *rb;
  71     int   *itc0;
  72     int   *itc1;
  73 } t_gmx_global_stat;
  74
  75 gmx_global_stat_t global_stat_init(t_inputrec *ir)
  76 {
  77     gmx_global_stat_t gs;
  78
  79     snew(gs, 1);
  80
  81     gs->rb = mk_bin();
  82     snew(gs->itc0, ir->opts.ngtc);
  83     snew(gs->itc1, ir->opts.ngtc);
  84
  85     return gs;
  86 }
  87
  88 void global_stat_destroy(gmx_global_stat_t gs)
  89 {
  90     destroy_bin(gs->rb);
  91     sfree(gs->itc0);
  92     sfree(gs->itc1);
  93     sfree(gs);
  94 }
  95
  96 static int filter_enerdterm(real *afrom, gmx_bool bToBuffer, real *ato,
  97                             gmx_bool bTemp, gmx_bool bPres, gmx_bool bEner)
  98 {
  99     int i, to, from;
 100
 101     from = 0;
 102     to   = 0;
 103     for (i = 0; i < F_NRE; i++)
 104     {
 105         if (bToBuffer)
 106         {
 107             from = i;
 108         }
 109         else
 110         {
 111             to = i;
 112         }
 113         switch (i)
 114         {
 115             case F_EKIN:
 116             case F_TEMP:
 117             case F_DKDL:
 118                 if (bTemp)
 119                 {
 120                     ato[to++] = afrom[from++];
 121                 }
 122                 break;
 123             case F_PRES:
 124             case F_PDISPCORR:
 125                 if (bPres)
 126                 {
 127                     ato[to++] = afrom[from++];
 128                 }
 129                 break;
 130             default:
 131                 if (bEner)
 132                 {
 133                     ato[to++] = afrom[from++];
 134                 }
 135                 break;
 136         }
 137     }
 138
 139     return to;
 140 }
 141
 142 void global_stat(FILE *fplog, gmx_global_stat_t gs,
 143                  t_commrec *cr, gmx_enerdata_t *enerd,
 144                  tensor fvir, tensor svir, rvec mu_tot,
 145                  t_inputrec *inputrec,
 146                  gmx_ekindata_t *ekind, gmx_constr_t constr,
 147                  t_vcm *vcm,
 148                  int nsig, real *sig,
 149                  gmx_mtop_t *top_global, t_state *state_local,
 150                  gmx_bool bSumEkinhOld, int flags)
 151 /* instead of current system, gmx_booleans for summing virial, kinetic energy, and other terms */
 152 {
 153     t_bin     *rb;
 154     int       *itc0, *itc1;
 155     int        ie    = 0, ifv = 0, isv = 0, irmsd = 0, imu = 0;
 156     int        idedl = 0, idvdll = 0, idvdlnl = 0, iepl = 0, icm = 0, imass = 0, ica = 0, inb = 0;
 157     int        isig  = -1;
 158     int        icj   = -1, ici = -1, icx = -1;
 159     int        inn[egNR];
 160     real       copyenerd[F_NRE];
 161     int        nener, j;
 162     real      *rmsd_data = NULL;
 163     double     nb;
 164     gmx_bool   bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bFirstIterate, bReadEkin;
 165
 166     bVV           = EI_VV(inputrec->eI);
 167     bTemp         = flags & CGLO_TEMPERATURE;
 168     bEner         = flags & CGLO_ENERGY;
 169     bPres         = (flags & CGLO_PRESSURE);
 170     bConstrVir    = (flags & CGLO_CONSTRAINT);
 171     bFirstIterate = (flags & CGLO_FIRSTITERATE);
 172     bEkinAveVel   = (inputrec->eI == eiVV || (inputrec->eI == eiVVAK && bPres));
 173     bReadEkin     = (flags & CGLO_READEKIN);
 174
 175     rb   = gs->rb;
 176     itc0 = gs->itc0;
 177     itc1 = gs->itc1;
 178
 179
 180     reset_bin(rb);
 181     /* This routine copies all the data to be summed to one big buffer
 182      * using the t_bin struct.
 183      */
 184
 185     /* First, we neeed to identify which enerd->term should be
 186        communicated.  Temperature and pressure terms should only be
 187        communicated and summed when they need to be, to avoid repeating
 188        the sums and overcounting. */
 189
 190     nener = filter_enerdterm(enerd->term, TRUE, copyenerd, bTemp, bPres, bEner);
 191
 192     /* First, the data that needs to be communicated with velocity verlet every time
 193        This is just the constraint virial.*/
 194     if (bConstrVir)
 195     {
 196         isv = add_binr(rb, DIM*DIM, svir[0]);
 197         where();
 198     }
 199
 200 /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
 201     if (bTemp || !bVV)
 202     {
 203         if (ekind)
 204         {
 205             for (j = 0; (j < inputrec->opts.ngtc); j++)
 206             {
 207                 if (bSumEkinhOld)
 208                 {
 209                     itc0[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
 210                 }
 211                 if (bEkinAveVel && !bReadEkin)
 212                 {
 213                     itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinf[0]);
 214                 }
 215                 else if (!bReadEkin)
 216                 {
 217                     itc1[j] = add_binr(rb, DIM*DIM, ekind->tcstat[j].ekinh[0]);
 218                 }
 219             }
 220             /* these probably need to be put into one of these categories */
 221             where();
 222             idedl = add_binr(rb, 1, &(ekind->dekindl));
 223             where();
 224             ica   = add_binr(rb, 1, &(ekind->cosacc.mvcos));
 225             where();
 226         }
 227     }
 228     where();
 229
 230     if ((bPres || !bVV) && bFirstIterate)
 231     {
 232         ifv = add_binr(rb, DIM*DIM, fvir[0]);
 233     }
 234
 235
 236     if (bEner)
 237     {
 238         where();
 239         if (bFirstIterate)
 240         {
 241             ie  = add_binr(rb, nener, copyenerd);
 242         }
 243         where();
 244         if (constr)
 245         {
 246             rmsd_data = constr_rmsd_data(constr);
 247             if (rmsd_data)
 248             {
 249                 irmsd = add_binr(rb, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
 250             }
 251         }
 252         if (!NEED_MUTOT(*inputrec))
 253         {
 254             imu = add_binr(rb, DIM, mu_tot);
 255             where();
 256         }
 257
 258         if (bFirstIterate)
 259         {
 260             for (j = 0; (j < egNR); j++)
 261             {
 262                 inn[j] = add_binr(rb, enerd->grpp.nener, enerd->grpp.ener[j]);
 263             }
 264             where();
 265             if (inputrec->efep != efepNO)
 266             {
 267                 idvdll  = add_bind(rb, efptNR, enerd->dvdl_lin);
 268                 idvdlnl = add_bind(rb, efptNR, enerd->dvdl_nonlin);
 269                 if (enerd->n_lambda > 0)
 270                 {
 271                     iepl = add_bind(rb, enerd->n_lambda, enerd->enerpart_lambda);
 272                 }
 273             }
 274         }
 275     }
 276
 277     if (vcm)
 278     {
 279         icm   = add_binr(rb, DIM*vcm->nr, vcm->group_p[0]);
 280         where();
 281         imass = add_binr(rb, vcm->nr, vcm->group_mass);
 282         where();
 283         if (vcm->mode == ecmANGULAR)
 284         {
 285             icj   = add_binr(rb, DIM*vcm->nr, vcm->group_j[0]);
 286             where();
 287             icx   = add_binr(rb, DIM*vcm->nr, vcm->group_x[0]);
 288             where();
 289             ici   = add_binr(rb, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
 290             where();
 291         }
 292     }
 293
 294     if (DOMAINDECOMP(cr))
 295     {
 296         nb  = cr->dd->nbonded_local;
 297         inb = add_bind(rb, 1, &nb);
 298     }
 299     where();
 300     if (nsig > 0)
 301     {
 302         isig = add_binr(rb, nsig, sig);
 303     }
 304
 305     /* Global sum it all */
 306     if (debug)
 307     {
 308         fprintf(debug, "Summing %d energies\n", rb->maxreal);
 309     }
 310     sum_bin(rb, cr);
 311     where();
 312
 313     /* Extract all the data locally */
 314
 315     if (bConstrVir)
 316     {
 317         extract_binr(rb, isv, DIM*DIM, svir[0]);
 318     }
 319
 320     /* We need the force virial and the kinetic energy for the first time through with velocity verlet */
 321     if (bTemp || !bVV)
 322     {
 323         if (ekind)
 324         {
 325             for (j = 0; (j < inputrec->opts.ngtc); j++)
 326             {
 327                 if (bSumEkinhOld)
 328                 {
 329                     extract_binr(rb, itc0[j], DIM*DIM, ekind->tcstat[j].ekinh_old[0]);
 330                 }
 331                 if (bEkinAveVel && !bReadEkin)
 332                 {
 333                     extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinf[0]);
 334                 }
 335                 else if (!bReadEkin)
 336                 {
 337                     extract_binr(rb, itc1[j], DIM*DIM, ekind->tcstat[j].ekinh[0]);
 338                 }
 339             }
 340             extract_binr(rb, idedl, 1, &(ekind->dekindl));
 341             extract_binr(rb, ica, 1, &(ekind->cosacc.mvcos));
 342             where();
 343         }
 344     }
 345     if ((bPres || !bVV) && bFirstIterate)
 346     {
 347         extract_binr(rb, ifv, DIM*DIM, fvir[0]);
 348     }
 349
 350     if (bEner)
 351     {
 352         if (bFirstIterate)
 353         {
 354             extract_binr(rb, ie, nener, copyenerd);
 355             if (rmsd_data)
 356             {
 357                 extract_binr(rb, irmsd, inputrec->eI == eiSD2 ? 3 : 2, rmsd_data);
 358             }
 359             if (!NEED_MUTOT(*inputrec))
 360             {
 361                 extract_binr(rb, imu, DIM, mu_tot);
 362             }
 363
 364             for (j = 0; (j < egNR); j++)
 365             {
 366                 extract_binr(rb, inn[j], enerd->grpp.nener, enerd->grpp.ener[j]);
 367             }
 368             if (inputrec->efep != efepNO)
 369             {
 370                 extract_bind(rb, idvdll, efptNR, enerd->dvdl_lin);
 371                 extract_bind(rb, idvdlnl, efptNR, enerd->dvdl_nonlin);
 372                 if (enerd->n_lambda > 0)
 373                 {
 374                     extract_bind(rb, iepl, enerd->n_lambda, enerd->enerpart_lambda);
 375                 }
 376             }
 377             if (DOMAINDECOMP(cr))
 378             {
 379                 extract_bind(rb, inb, 1, &nb);
 380                 if ((int)(nb + 0.5) != cr->dd->nbonded_global)
 381                 {
 382                     dd_print_missing_interactions(fplog, cr, (int)(nb + 0.5), top_global, state_local);
 383                 }
 384             }
 385             where();
 386
 387             filter_enerdterm(copyenerd, FALSE, enerd->term, bTemp, bPres, bEner);
 388         }
 389     }
 390
 391     if (vcm)
 392     {
 393         extract_binr(rb, icm, DIM*vcm->nr, vcm->group_p[0]);
 394         where();
 395         extract_binr(rb, imass, vcm->nr, vcm->group_mass);
 396         where();
 397         if (vcm->mode == ecmANGULAR)
 398         {
 399             extract_binr(rb, icj, DIM*vcm->nr, vcm->group_j[0]);
 400             where();
 401             extract_binr(rb, icx, DIM*vcm->nr, vcm->group_x[0]);
 402             where();
 403             extract_binr(rb, ici, DIM*DIM*vcm->nr, vcm->group_i[0][0]);
 404             where();
 405         }
 406     }
 407
 408     if (nsig > 0)
 409     {
 410         extract_binr(rb, isig, nsig, sig);
 411     }
 412     where();
 413 }
 414
 415 int do_per_step(gmx_int64_t step, gmx_int64_t nstep)
 416 {
 417     if (nstep != 0)
 418     {
 419         return ((step % nstep) == 0);
 420     }
 421     else
 422     {
 423         return 0;
 424     }
 425 }