src/gromacs/mdlib/stat.cpp

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