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37 /* This file is completely threadsafe - keep it that way! */
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/fileio/futil.h"
53 #include "mtop_util.h"
54 #include "gmx_omp_nthreads.h"
56 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
60 for (i = 0; (i < ngtc); i++)
63 clear_mat(tcstat[i].ekinh);
64 clear_mat(tcstat[i].ekinh_old);
65 clear_mat(tcstat[i].ekinf);
69 static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
72 gmx_mtop_atomloop_all_t aloop;
78 groups = &mtop->groups;
79 aloop = gmx_mtop_atomloop_all_init(mtop);
80 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
82 grp = ggrpnr(groups, egcACC, i);
83 if ((grp < 0) && (grp >= ngacc))
85 gmx_incons("Input for acceleration groups wrong");
88 /* This will not work for integrator BD */
89 gstat[grp].mA += atom->m;
90 gstat[grp].mB += atom->mB;
95 void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
96 gmx_ekindata_t *ekind)
101 fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
105 /* bNEMD tells if we should remove remove the COM velocity
106 * from the velocities during velocity scaling in T-coupling.
107 * Turn this on when we have multiple acceleration groups
108 * or one accelerated group.
110 ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
112 ekind->ngtc = opts->ngtc;
113 snew(ekind->tcstat, opts->ngtc);
114 init_grptcstat(opts->ngtc, ekind->tcstat);
115 /* Set Berendsen tcoupl lambda's to 1,
116 * so runs without Berendsen coupling are not affected.
118 for (i = 0; i < opts->ngtc; i++)
120 ekind->tcstat[i].lambda = 1.0;
121 ekind->tcstat[i].vscale_nhc = 1.0;
122 ekind->tcstat[i].ekinscaleh_nhc = 1.0;
123 ekind->tcstat[i].ekinscalef_nhc = 1.0;
126 nthread = gmx_omp_nthreads_get(emntUpdate);
128 snew(ekind->ekin_work_alloc, nthread);
129 snew(ekind->ekin_work, nthread);
130 snew(ekind->dekindl_work, nthread);
131 #pragma omp parallel for num_threads(nthread) schedule(static)
132 for (thread = 0; thread < nthread; thread++)
134 #define EKIN_WORK_BUFFER_SIZE 2
135 /* Allocate 2 extra elements on both sides, so in single
137 * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
138 * buffer on both sides to avoid cache pollution.
140 snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
141 ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
142 /* Nasty hack so we can have the per-thread accumulation
143 * variable for dekindl in the same thread-local cache lines
144 * as the per-thread accumulation tensors for ekin[fh],
145 * because they are accumulated in the same loop. */
146 ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
147 #undef EKIN_WORK_BUFFER_SIZE
150 ekind->ngacc = opts->ngacc;
151 snew(ekind->grpstat, opts->ngacc);
152 init_grpstat(mtop, opts->ngacc, ekind->grpstat);
155 void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
157 /* This routine will only be called when it's necessary */
163 for (g = 0; (g < opts->ngacc); g++)
165 add_binr(rb, DIM, ekind->grpstat[g].u);
169 for (g = 0; (g < opts->ngacc); g++)
171 extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
176 /* I don't think accumulate_ekin is used anymore? */
179 static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
180 gmx_ekindata_t *ekind)
186 for (g = 0; (g < opts->ngtc); g++)
188 gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
194 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
195 t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
200 /* calculate mean velocities at whole timestep */
201 for (g = 0; (g < opts->ngtc); g++)
203 ekind->tcstat[g].T = 0;
208 for (g = 0; (g < opts->ngacc); g++)
210 clear_rvec(ekind->grpstat[g].u);
214 for (n = start; (n < start+homenr); n++)
220 for (d = 0; (d < DIM); d++)
222 mv = md->massT[n]*v[n][d];
223 ekind->grpstat[g].u[d] += mv;
227 for (g = 0; (g < opts->ngacc); g++)
229 for (d = 0; (d < DIM); d++)
231 ekind->grpstat[g].u[d] /=
232 (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
238 real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
239 gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
243 t_grp_tcstat *tcstat;
252 clear_mat(ekind->ekin);
254 for (i = 0; (i < ngtc); i++)
258 tcstat = &ekind->tcstat[i];
259 /* Sometimes a group does not have degrees of freedom, e.g.
260 * when it consists of shells and virtual sites, then we just
261 * set the temperatue to 0 and also neglect the kinetic
262 * energy, which should be zero anyway.
271 /* in this case, kinetic energy is from the current velocities already */
272 msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
277 /* Calculate the full step Ekin as the average of the half steps */
278 for (j = 0; (j < DIM); j++)
280 for (m = 0; (m < DIM); m++)
282 tcstat->ekinf[j][m] =
283 0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
287 m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
289 tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
290 tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
292 /* after the scaling factors have been multiplied in, we can remove them */
295 tcstat->ekinscalef_nhc = 1.0;
299 tcstat->ekinscaleh_nhc = 1.0;
318 *dekindlambda = ekind->dekindl;
322 *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);