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37 /* This file is completely threadsafe - keep it that way! */
43 #include "gromacs/utility/smalloc.h"
44 #include "gromacs/utility/futil.h"
46 #include "gromacs/math/vec.h"
50 #include "gromacs/topology/mtop_util.h"
51 #include "gmx_omp_nthreads.h"
53 static void init_grptcstat(int ngtc, t_grp_tcstat tcstat[])
57 for (i = 0; (i < ngtc); i++)
60 clear_mat(tcstat[i].ekinh);
61 clear_mat(tcstat[i].ekinh_old);
62 clear_mat(tcstat[i].ekinf);
66 static void init_grpstat(gmx_mtop_t *mtop, int ngacc, t_grp_acc gstat[])
69 gmx_mtop_atomloop_all_t aloop;
75 groups = &mtop->groups;
76 aloop = gmx_mtop_atomloop_all_init(mtop);
77 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
79 grp = ggrpnr(groups, egcACC, i);
80 if ((grp < 0) && (grp >= ngacc))
82 gmx_incons("Input for acceleration groups wrong");
85 /* This will not work for integrator BD */
86 gstat[grp].mA += atom->m;
87 gstat[grp].mB += atom->mB;
92 void init_ekindata(FILE gmx_unused *log, gmx_mtop_t *mtop, t_grpopts *opts,
93 gmx_ekindata_t *ekind)
98 fprintf(log, "ngtc: %d, ngacc: %d, ngener: %d\n", opts->ngtc, opts->ngacc,
102 /* bNEMD tells if we should remove remove the COM velocity
103 * from the velocities during velocity scaling in T-coupling.
104 * Turn this on when we have multiple acceleration groups
105 * or one accelerated group.
107 ekind->bNEMD = (opts->ngacc > 1 || norm(opts->acc[0]) > 0);
109 ekind->ngtc = opts->ngtc;
110 snew(ekind->tcstat, opts->ngtc);
111 init_grptcstat(opts->ngtc, ekind->tcstat);
112 /* Set Berendsen tcoupl lambda's to 1,
113 * so runs without Berendsen coupling are not affected.
115 for (i = 0; i < opts->ngtc; i++)
117 ekind->tcstat[i].lambda = 1.0;
118 ekind->tcstat[i].vscale_nhc = 1.0;
119 ekind->tcstat[i].ekinscaleh_nhc = 1.0;
120 ekind->tcstat[i].ekinscalef_nhc = 1.0;
123 nthread = gmx_omp_nthreads_get(emntUpdate);
125 snew(ekind->ekin_work_alloc, nthread);
126 snew(ekind->ekin_work, nthread);
127 snew(ekind->dekindl_work, nthread);
128 #pragma omp parallel for num_threads(nthread) schedule(static)
129 for (thread = 0; thread < nthread; thread++)
131 #define EKIN_WORK_BUFFER_SIZE 2
132 /* Allocate 2 extra elements on both sides, so in single
134 * EKIN_WORK_BUFFER_SIZE*DIM*DIM*sizeof(real) = 72/144 bytes
135 * buffer on both sides to avoid cache pollution.
137 snew(ekind->ekin_work_alloc[thread], ekind->ngtc+2*EKIN_WORK_BUFFER_SIZE);
138 ekind->ekin_work[thread] = ekind->ekin_work_alloc[thread] + EKIN_WORK_BUFFER_SIZE;
139 /* Nasty hack so we can have the per-thread accumulation
140 * variable for dekindl in the same thread-local cache lines
141 * as the per-thread accumulation tensors for ekin[fh],
142 * because they are accumulated in the same loop. */
143 ekind->dekindl_work[thread] = &(ekind->ekin_work[thread][ekind->ngtc][0][0]);
144 #undef EKIN_WORK_BUFFER_SIZE
147 ekind->ngacc = opts->ngacc;
148 snew(ekind->grpstat, opts->ngacc);
149 init_grpstat(mtop, opts->ngacc, ekind->grpstat);
152 void accumulate_u(t_commrec *cr, t_grpopts *opts, gmx_ekindata_t *ekind)
154 /* This routine will only be called when it's necessary */
160 for (g = 0; (g < opts->ngacc); g++)
162 add_binr(rb, DIM, ekind->grpstat[g].u);
166 for (g = 0; (g < opts->ngacc); g++)
168 extract_binr(rb, DIM*g, DIM, ekind->grpstat[g].u);
173 /* I don't think accumulate_ekin is used anymore? */
176 static void accumulate_ekin(t_commrec *cr, t_grpopts *opts,
177 gmx_ekindata_t *ekind)
183 for (g = 0; (g < opts->ngtc); g++)
185 gmx_sum(DIM*DIM, ekind->tcstat[g].ekinf[0], cr);
191 void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
192 t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda)
197 /* calculate mean velocities at whole timestep */
198 for (g = 0; (g < opts->ngtc); g++)
200 ekind->tcstat[g].T = 0;
205 for (g = 0; (g < opts->ngacc); g++)
207 clear_rvec(ekind->grpstat[g].u);
211 for (n = start; (n < start+homenr); n++)
217 for (d = 0; (d < DIM); d++)
219 mv = md->massT[n]*v[n][d];
220 ekind->grpstat[g].u[d] += mv;
224 for (g = 0; (g < opts->ngacc); g++)
226 for (d = 0; (d < DIM); d++)
228 ekind->grpstat[g].u[d] /=
229 (1-lambda)*ekind->grpstat[g].mA + lambda*ekind->grpstat[g].mB;
235 real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
236 gmx_bool bEkinAveVel, gmx_bool bScaleEkin)
240 t_grp_tcstat *tcstat;
249 clear_mat(ekind->ekin);
251 for (i = 0; (i < ngtc); i++)
255 tcstat = &ekind->tcstat[i];
256 /* Sometimes a group does not have degrees of freedom, e.g.
257 * when it consists of shells and virtual sites, then we just
258 * set the temperatue to 0 and also neglect the kinetic
259 * energy, which should be zero anyway.
268 /* in this case, kinetic energy is from the current velocities already */
269 msmul(tcstat->ekinf, tcstat->ekinscalef_nhc, tcstat->ekinf);
274 /* Calculate the full step Ekin as the average of the half steps */
275 for (j = 0; (j < DIM); j++)
277 for (m = 0; (m < DIM); m++)
279 tcstat->ekinf[j][m] =
280 0.5*(tcstat->ekinh[j][m]*tcstat->ekinscaleh_nhc + tcstat->ekinh_old[j][m]);
284 m_add(tcstat->ekinf, ekind->ekin, ekind->ekin);
286 tcstat->Th = calc_temp(trace(tcstat->ekinh), nd);
287 tcstat->T = calc_temp(trace(tcstat->ekinf), nd);
289 /* after the scaling factors have been multiplied in, we can remove them */
292 tcstat->ekinscalef_nhc = 1.0;
296 tcstat->ekinscaleh_nhc = 1.0;
315 *dekindlambda = ekind->dekindl;
319 *dekindlambda = 0.5*(ekind->dekindl + ekind->dekindl_old);