src/gromacs/mdlib/tgroup.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "tgroup.h"
  41
  42 #include <cmath>
  43
  44 #include "gromacs/gmxlib/network.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/mdlib/gmx_omp_nthreads.h"
  47 #include "gromacs/mdlib/rbin.h"
  48 #include "gromacs/mdlib/update.h"
  49 #include "gromacs/mdtypes/group.h"
  50 #include "gromacs/mdtypes/inputrec.h"
  51 #include "gromacs/mdtypes/mdatom.h"
  52 #include "gromacs/topology/mtop_util.h"
  53 #include "gromacs/topology/topology.h"
  54 #include "gromacs/utility/exceptions.h"
  55 #include "gromacs/utility/fatalerror.h"
  56 #include "gromacs/utility/futil.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
  60 {
  61     int i;
  62
  63     for (i = 0; (i < ngtc); i++)
  64     {
  65         tcstat[i].T = 0;
  66         clear_mat(tcstat[i].ekinh);
  67         clear_mat(tcstat[i].ekinh_old);
  68         clear_mat(tcstat[i].ekinf);
  69     }
  70 }
  71
  72 static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
  73 {
  74     gmx_groups_t           *groups;
  75     gmx_mtop_atomloop_all_t aloop;
  76     int                     i, grp;
  77     const t_atom           *atom;
  78
  79     if (ngacc > 0)
  80     {
  81         groups = &mtop->groups;
  82         aloop  = gmx_mtop_atomloop_all_init(mtop);
  83         while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
  84         {
  85             grp = ggrpnr(groups, egcACC, i);
  86             if ((grp < 0) && (grp >= ngacc))
  87             {
  88                 gmx_incons("Input for acceleration groups wrong");
  89             }
  90             gstat[grp].nat++;
  91             /* This will not work for integrator BD */
  92             gstat[grp].mA += atom->m;
  93             gstat[grp].mB += atom->mB;
  94         }
  95     }
  96 }
  97
  98 void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
  99                    gmx_ekindata_t *ekind)
 100 {
 101     int i;
 102     int nthread, thread;
 103 #ifdef DEBUG
 104     fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
 105             opts->ngener);
 106 #endif
 107
 108     /* bNEMD tells if we should remove remove the COM velocity
 109      * from the velocities during velocity scaling in T-coupling.
 110      * Turn this on when we have multiple acceleration groups
 111      * or one accelerated group.
 112      */
 113     ekind->bNEMD = (opts->ngacc > 1 || norm2(opts->acc[0]) > 0);
 114
 115     ekind->ngtc = opts->ngtc;
 116     snew(ekind->tcstat, opts->ngtc);
 117     init_grptcstat(opts->ngtc, ekind->tcstat);
 118     /* Set Berendsen tcoupl lambda's to 1,
 119      * so runs without Berendsen coupling are not affected.
 120      */
 121     for (i = 0; i < opts->ngtc; i++)
 122     {
 123         ekind->tcstat[i].lambda         = 1.0;
 124         ekind->tcstat[i].vscale_nhc     = 1.0;
 125         ekind->tcstat[i].ekinscaleh_nhc = 1.0;
 126         ekind->tcstat[i].ekinscalef_nhc = 1.0;
 127     }
 128
 129     nthread = gmx_omp_nthreads_get(emntUpdate);
 130
 131     snew(ekind->ekin_work_alloc, nthread);
 132     snew(ekind->ekin_work, nthread);
 133     snew(ekind->dekindl_work, nthread);
 134 #pragma omp parallel for num_threads(nthread) schedule(static)
 135     for (thread = 0; thread < nthread; thread++)
 136     {
 137         try
 138         {
 139 #define EKIN_WORK_BUFFER_SIZE 2
 140             /* Allocate 2 extra elements on both sides, so in single
 141              * precision we have
 142              * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
 143              * buffer on both sides to avoid cache pollution.
 144              */
 145             snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
 146             ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
 147             /* Nasty hack so we can have the per-thread accumulation
 148              * variable for dekindl in the same thread-local cache lines
 149              * as the per-thread accumulation tensors for ekin[fh],
 150              * because they are accumulated in the same loop. */
 151             ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
 152 #undef EKIN_WORK_BUFFER_SIZE
 153         }
 154         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 155     }
 156
 157     ekind->ngacc = opts->ngacc;
 158     snew(ekind->grpstat, opts->ngacc);
 159     init_grpstat(mtop, opts->ngacc, ekind->grpstat);
 160 }
 161
 162 void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
 163 {
 164     /* This routine will only be called when it's necessary */
 165     t_bin *rb;
 166     int    g;
 167
 168     rb = mk_bin();
 169
 170     for (g = 0; (g < opts->ngacc); g++)
 171     {
 172         add_binr(rb, DIM, ekind->grpstat[g].u);
 173     }
 174     sum_bin(rb, cr);
 175
 176     for (g = 0; (g < opts->ngacc); g++)
 177     {
 178         extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
 179     }
 180     destroy_bin(rb);
 181 }
 182
 183 /* I don't think accumulate_ekin is used anymore? */
 184
 185 #if 0
 186 static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
 187                             gmx_ekindata_t *ekind)
 188 {
 189     int g;
 190
 191     if (PAR(cr))
 192     {
 193         for (g = 0; (g < opts->ngtc); g++)
 194         {
 195             gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
 196         }
 197     }
 198 }
 199 #endif
 200
 201 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
 202                      t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
 203 {
 204     int  d, g, n;
 205     real mv;
 206
 207     /* calculate mean velocities at whole timestep */
 208     for (g = 0; (g < opts->ngtc); g++)
 209     {
 210         ekind->tcstat[g].T = 0;
 211     }
 212
 213     if (ekind->bNEMD)
 214     {
 215         for (g = 0; (g < opts->ngacc); g++)
 216         {
 217             clear_rvec(ekind->grpstat[g].u);
 218         }
 219
 220         g = 0;
 221         for (n = start; (n < start+homenr); n++)
 222         {
 223             if (md->cACC)
 224             {
 225                 g = md->cACC[n];
 226             }
 227             for (d = 0; (d < DIM); d++)
 228             {
 229                 mv                      = md->massT[n]*v[n][d];
 230                 ekind->grpstat[g].u[d] += mv;
 231             }
 232         }
 233
 234         for (g = 0; (g < opts->ngacc); g++)
 235         {
 236             for (d = 0; (d < DIM); d++)
 237             {
 238                 ekind->grpstat[g].u[d] /=
 239                     (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
 240             }
 241         }
 242     }
 243 }
 244
 245 real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
 246               gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
 247 {
 248     int           i, j, m, ngtc;
 249     real          T;
 250     t_grp_tcstat *tcstat;
 251     real          nrdf, nd, *ndf;
 252
 253     ngtc = opts->ngtc;
 254     ndf  = opts->nrdf;
 255
 256     T    = 0;
 257     nrdf = 0;
 258
 259     clear_mat(ekind->ekin);
 260
 261     for (i = 0; (i < ngtc); i++)
 262     {
 263
 264         nd     = ndf[i];
 265         tcstat = &ekind->tcstat[i];
 266         /* Sometimes a group does not have degrees of freedom, e.g.
 267          * when it consists of shells and virtual sites, then we just
 268          * set the temperatue to 0 and also neglect the kinetic
 269          * energy, which should be  zero anyway.
 270          */
 271
 272         if (nd > 0)
 273         {
 274             if (bEkinAveVel)
 275             {
 276                 if (!bScaleEkin)
 277                 {
 278                     /* in this case, kinetic energy is from the current velocities already */
 279                     msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
 280                 }
 281             }
 282             else
 283             {
 284                 /* Calculate the full step Ekin as the average of the half steps */
 285                 for (j = 0; (j < DIM); j++)
 286                 {
 287                     for (m = 0; (m < DIM); m++)
 288                     {
 289                         tcstat->ekinf[j][m] =
 290                             0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
 291                     }
 292                 }
 293             }
 294             m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
 295
 296             tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
 297             tcstat->T  = calc_temp(trace(tcstat->ekinf), nd);
 298
 299             /* after the scaling factors have been multiplied in, we can remove them */
 300             if (bEkinAveVel)
 301             {
 302                 tcstat->ekinscalef_nhc = 1.0;
 303             }
 304             else
 305             {
 306                 tcstat->ekinscaleh_nhc = 1.0;
 307             }
 308         }
 309         else
 310         {
 311             tcstat->T  = 0;
 312             tcstat->Th = 0;
 313         }
 314         T    += nd*tcstat->T;
 315         nrdf += nd;
 316     }
 317     if (nrdf > 0)
 318     {
 319         T /= nrdf;
 320     }
 321     if (dekindlambda)
 322     {
 323         if (bEkinAveVel)
 324         {
 325             *dekindlambda = ekind->dekindl;
 326         }
 327         else
 328         {
 329             *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
 330         }
 331     }
 332     return T;
 333 }