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(const gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
  73 {
  74     const 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 = getGroupType(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, const gmx_mtop_t *mtop, const t_grpopts *opts,
  99                    gmx_ekindata_t *ekind)
 100 {
 101     int i;
 102     int nthread, thread;
 103
 104     /* bNEMD tells if we should remove remove the COM velocity
 105      * from the velocities during velocity scaling in T-coupling.
 106      * Turn this on when we have multiple acceleration groups
 107      * or one accelerated group.
 108      */
 109     ekind->bNEMD = (opts->ngacc > 1 || norm2(opts->acc[0]) > 0);
 110
 111     ekind->ngtc = opts->ngtc;
 112     snew(ekind->tcstat, opts->ngtc);
 113     init_grptcstat(opts->ngtc, ekind->tcstat);
 114     /* Set Berendsen tcoupl lambda's to 1,
 115      * so runs without Berendsen coupling are not affected.
 116      */
 117     for (i = 0; i < opts->ngtc; i++)
 118     {
 119         ekind->tcstat[i].lambda         = 1.0;
 120         ekind->tcstat[i].vscale_nhc     = 1.0;
 121         ekind->tcstat[i].ekinscaleh_nhc = 1.0;
 122         ekind->tcstat[i].ekinscalef_nhc = 1.0;
 123     }
 124
 125     nthread = gmx_omp_nthreads_get(emntUpdate);
 126
 127     snew(ekind->ekin_work_alloc, nthread);
 128     snew(ekind->ekin_work, nthread);
 129     snew(ekind->dekindl_work, nthread);
 130 #pragma omp parallel for num_threads(nthread) schedule(static)
 131     for (thread = 0; thread < nthread; thread++)
 132     {
 133         try
 134         {
 135 #define EKIN_WORK_BUFFER_SIZE 2
 136             /* Allocate 2 extra elements on both sides, so in single
 137              * precision we have
 138              * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
 139              * buffer on both sides to avoid cache pollution.
 140              */
 141             snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
 142             ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
 143             /* Nasty hack so we can have the per-thread accumulation
 144              * variable for dekindl in the same thread-local cache lines
 145              * as the per-thread accumulation tensors for ekin[fh],
 146              * because they are accumulated in the same loop. */
 147             ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
 148 #undef EKIN_WORK_BUFFER_SIZE
 149         }
 150         GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
 151     }
 152
 153     ekind->ngacc = opts->ngacc;
 154     snew(ekind->grpstat, opts->ngacc);
 155     init_grpstat(mtop, opts->ngacc, ekind->grpstat);
 156 }
 157
 158 void accumulate_u(const t_commrec *cr, const t_grpopts *opts, gmx_ekindata_t *ekind)
 159 {
 160     /* This routine will only be called when it's necessary */
 161     t_bin *rb;
 162     int    g;
 163
 164     rb = mk_bin();
 165
 166     for (g = 0; (g < opts->ngacc); g++)
 167     {
 168         add_binr(rb, DIM, ekind->grpstat[g].u);
 169     }
 170     sum_bin(rb, cr);
 171
 172     for (g = 0; (g < opts->ngacc); g++)
 173     {
 174         extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
 175     }
 176     destroy_bin(rb);
 177 }
 178
 179 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
 180                      const t_grpopts *opts, const rvec v[], const t_mdatoms *md, real lambda)
 181 {
 182     int  d, g, n;
 183     real mv;
 184
 185     /* calculate mean velocities at whole timestep */
 186     for (g = 0; (g < opts->ngtc); g++)
 187     {
 188         ekind->tcstat[g].T = 0;
 189     }
 190
 191     if (ekind->bNEMD)
 192     {
 193         for (g = 0; (g < opts->ngacc); g++)
 194         {
 195             clear_rvec(ekind->grpstat[g].u);
 196         }
 197
 198         g = 0;
 199         for (n = start; (n < start+homenr); n++)
 200         {
 201             if (md->cACC)
 202             {
 203                 g = md->cACC[n];
 204             }
 205             for (d = 0; (d < DIM); d++)
 206             {
 207                 mv                      = md->massT[n]*v[n][d];
 208                 ekind->grpstat[g].u[d] += mv;
 209             }
 210         }
 211
 212         for (g = 0; (g < opts->ngacc); g++)
 213         {
 214             for (d = 0; (d < DIM); d++)
 215             {
 216                 ekind->grpstat[g].u[d] /=
 217                     (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
 218             }
 219         }
 220     }
 221 }
 222
 223 real sum_ekin(const t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
 224               gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
 225 {
 226     int           i, j, m, ngtc;
 227     real          T;
 228     t_grp_tcstat *tcstat;
 229     real          nrdf, nd, *ndf;
 230
 231     ngtc = opts->ngtc;
 232     ndf  = opts->nrdf;
 233
 234     T    = 0;
 235     nrdf = 0;
 236
 237     clear_mat(ekind->ekin);
 238
 239     for (i = 0; (i < ngtc); i++)
 240     {
 241
 242         nd     = ndf[i];
 243         tcstat = &ekind->tcstat[i];
 244         /* Sometimes a group does not have degrees of freedom, e.g.
 245          * when it consists of shells and virtual sites, then we just
 246          * set the temperatue to 0 and also neglect the kinetic
 247          * energy, which should be  zero anyway.
 248          */
 249
 250         if (nd > 0)
 251         {
 252             if (bEkinAveVel)
 253             {
 254                 if (!bScaleEkin)
 255                 {
 256                     /* in this case, kinetic energy is from the current velocities already */
 257                     msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
 258                 }
 259             }
 260             else
 261             {
 262                 /* Calculate the full step Ekin as the average of the half steps */
 263                 for (j = 0; (j < DIM); j++)
 264                 {
 265                     for (m = 0; (m < DIM); m++)
 266                     {
 267                         tcstat->ekinf[j][m] =
 268                             0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
 269                     }
 270                 }
 271             }
 272             m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
 273
 274             tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
 275             tcstat->T  = calc_temp(trace(tcstat->ekinf), nd);
 276
 277             /* after the scaling factors have been multiplied in, we can remove them */
 278             if (bEkinAveVel)
 279             {
 280                 tcstat->ekinscalef_nhc = 1.0;
 281             }
 282             else
 283             {
 284                 tcstat->ekinscaleh_nhc = 1.0;
 285             }
 286         }
 287         else
 288         {
 289             tcstat->T  = 0;
 290             tcstat->Th = 0;
 291         }
 292         T    += nd*tcstat->T;
 293         nrdf += nd;
 294     }
 295     if (nrdf > 0)
 296     {
 297         T /= nrdf;
 298     }
 299     if (dekindlambda)
 300     {
 301         if (bEkinAveVel)
 302         {
 303             *dekindlambda = ekind->dekindl;
 304         }
 305         else
 306         {
 307             *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);
 308         }
 309     }
 310     return T;
 311 }