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37 /* This file is completely threadsafe - keep it that way! */
47 #include "gromacs/fileio/futil.h"
54 #include "mtop_util.h"
55 #include "gmx_omp_nthreads.h"
57 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
61 for (i = 0; (i < ngtc); i++)
64 clear_mat(tcstat[i].ekinh);
65 clear_mat(tcstat[i].ekinh_old);
66 clear_mat(tcstat[i].ekinf);
70 static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
73 gmx_mtop_atomloop_all_t aloop;
79 groups = &mtop->groups;
80 aloop = gmx_mtop_atomloop_all_init(mtop);
81 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
83 grp = ggrpnr(groups, egcACC, i);
84 if ((grp < 0) && (grp >= ngacc))
86 gmx_incons("Input for acceleration groups wrong");
89 /* This will not work for integrator BD */
90 gstat[grp].mA += atom->m;
91 gstat[grp].mB += atom->mB;
96 void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
97 gmx_ekindata_t *ekind)
102 fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
106 /* bNEMD tells if we should remove remove the COM velocity
107 * from the velocities during velocity scaling in T-coupling.
108 * Turn this on when we have multiple acceleration groups
109 * or one accelerated group.
111 ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
113 ekind->ngtc = opts->ngtc;
114 snew(ekind->tcstat, opts->ngtc);
115 init_grptcstat(opts->ngtc, ekind->tcstat);
116 /* Set Berendsen tcoupl lambda's to 1,
117 * so runs without Berendsen coupling are not affected.
119 for (i = 0; i < opts->ngtc; i++)
121 ekind->tcstat[i].lambda = 1.0;
122 ekind->tcstat[i].vscale_nhc = 1.0;
123 ekind->tcstat[i].ekinscaleh_nhc = 1.0;
124 ekind->tcstat[i].ekinscalef_nhc = 1.0;
127 nthread = gmx_omp_nthreads_get(emntUpdate);
129 snew(ekind->ekin_work_alloc, nthread);
130 snew(ekind->ekin_work, nthread);
131 snew(ekind->dekindl_work, nthread);
132 #pragma omp parallel for num_threads(nthread) schedule(static)
133 for (thread = 0; thread < nthread; thread++)
135 #define EKIN_WORK_BUFFER_SIZE 2
136 /* Allocate 2 extra elements on both sides, so in single
138 * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
139 * buffer on both sides to avoid cache pollution.
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
151 ekind->ngacc = opts->ngacc;
152 snew(ekind->grpstat, opts->ngacc);
153 init_grpstat(mtop, opts->ngacc, ekind->grpstat);
156 void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
158 /* This routine will only be called when it's necessary */
164 for (g = 0; (g < opts->ngacc); g++)
166 add_binr(rb, DIM, ekind->grpstat[g].u);
170 for (g = 0; (g < opts->ngacc); g++)
172 extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
177 /* I don't think accumulate_ekin is used anymore? */
180 static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
181 gmx_ekindata_t *ekind)
187 for (g = 0; (g < opts->ngtc); g++)
189 gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
195 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
196 t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
201 /* calculate mean velocities at whole timestep */
202 for (g = 0; (g < opts->ngtc); g++)
204 ekind->tcstat[g].T = 0;
209 for (g = 0; (g < opts->ngacc); g++)
211 clear_rvec(ekind->grpstat[g].u);
215 for (n = start; (n < start+homenr); n++)
221 for (d = 0; (d < DIM); d++)
223 mv = md->massT[n]*v[n][d];
224 ekind->grpstat[g].u[d] += mv;
228 for (g = 0; (g < opts->ngacc); g++)
230 for (d = 0; (d < DIM); d++)
232 ekind->grpstat[g].u[d] /=
233 (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
239 real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
240 gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
244 t_grp_tcstat *tcstat;
253 clear_mat(ekind->ekin);
255 for (i = 0; (i < ngtc); i++)
259 tcstat = &ekind->tcstat[i];
260 /* Sometimes a group does not have degrees of freedom, e.g.
261 * when it consists of shells and virtual sites, then we just
262 * set the temperatue to 0 and also neglect the kinetic
263 * energy, which should be zero anyway.
272 /* in this case, kinetic energy is from the current velocities already */
273 msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
278 /* Calculate the full step Ekin as the average of the half steps */
279 for (j = 0; (j < DIM); j++)
281 for (m = 0; (m < DIM); m++)
283 tcstat->ekinf[j][m] =
284 0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
288 m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
290 tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
291 tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
293 /* after the scaling factors have been multiplied in, we can remove them */
296 tcstat->ekinscalef_nhc = 1.0;
300 tcstat->ekinscaleh_nhc = 1.0;
319 *dekindlambda = ekind->dekindl;
323 *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);