src/gromacs/mdlib/tgroup.cpp

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