src/gromacs/mdlib/stat.cpp

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