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37 /* This file is completely threadsafe - keep it that way! */
46 #include "thread_mpi/threads.h"
49 #include "gromacs/math/vec.h"
50 #include "gromacs/pbcutil/pbc.h"
51 #include "gromacs/random/random.h"
52 #include "gromacs/utility/smalloc.h"
54 /* The source code in this file should be thread-safe.
55 Please keep it that way. */
59 static gmx_bool bOverAllocDD = FALSE;
60 static tMPI_Thread_mutex_t over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
63 void set_over_alloc_dd(gmx_bool set)
65 tMPI_Thread_mutex_lock(&over_alloc_mutex);
66 /* we just make sure that we don't set this at the same time.
67 We don't worry too much about reading this rarely-set variable */
69 tMPI_Thread_mutex_unlock(&over_alloc_mutex);
72 int over_alloc_dd(int n)
76 return OVER_ALLOC_FAC*n + 100;
84 int gmx_int64_to_int(gmx_int64_t step, const char *warn)
90 if (warn != NULL && (step < INT_MIN || step > INT_MAX))
92 fprintf(stderr, "\nWARNING during %s:\n", warn);
93 fprintf(stderr, "step value ");
94 fprintf(stderr, "%"GMX_PRId64, step);
95 fprintf(stderr, " does not fit in int, converted to %d\n\n", i);
101 char *gmx_step_str(gmx_int64_t i, char *buf)
103 sprintf(buf, "%"GMX_PRId64, i);
108 void init_inputrec(t_inputrec *ir)
110 memset(ir, 0, (size_t)sizeof(*ir));
111 snew(ir->fepvals, 1);
112 snew(ir->expandedvals, 1);
113 snew(ir->simtempvals, 1);
116 static void done_pull_group(t_pull_group *pgrp)
121 sfree(pgrp->ind_loc);
123 sfree(pgrp->weight_loc);
127 static void done_pull(t_pull *pull)
131 for (i = 0; i < pull->ngroup+1; i++)
133 done_pull_group(pull->group);
134 done_pull_group(pull->dyna);
138 void done_inputrec(t_inputrec *ir)
142 for (m = 0; (m < DIM); m++)
150 sfree(ir->ex[m].phi);
158 sfree(ir->et[m].phi);
162 sfree(ir->opts.nrdf);
163 sfree(ir->opts.ref_t);
164 sfree(ir->opts.annealing);
165 sfree(ir->opts.anneal_npoints);
166 sfree(ir->opts.anneal_time);
167 sfree(ir->opts.anneal_temp);
168 sfree(ir->opts.tau_t);
170 sfree(ir->opts.nFreeze);
171 sfree(ir->opts.QMmethod);
172 sfree(ir->opts.QMbasis);
173 sfree(ir->opts.QMcharge);
174 sfree(ir->opts.QMmult);
176 sfree(ir->opts.CASorbitals);
177 sfree(ir->opts.CASelectrons);
178 sfree(ir->opts.SAon);
179 sfree(ir->opts.SAoff);
180 sfree(ir->opts.SAsteps);
181 sfree(ir->opts.bOPT);
191 static void zero_history(history_t *hist)
193 hist->disre_initf = 0;
194 hist->ndisrepairs = 0;
195 hist->disre_rm3tav = NULL;
196 hist->orire_initf = 0;
197 hist->norire_Dtav = 0;
198 hist->orire_Dtav = NULL;
201 static void zero_ekinstate(ekinstate_t *eks)
206 eks->ekinh_old = NULL;
207 eks->ekinscalef_nhc = NULL;
208 eks->ekinscaleh_nhc = NULL;
209 eks->vscale_nhc = NULL;
214 static void init_swapstate(swapstate_t *swapstate)
218 swapstate->eSwapCoords = 0;
219 swapstate->nAverage = 0;
221 /* Ion/water position swapping */
222 for (ic = 0; ic < eCompNR; ic++)
224 for (ii = 0; ii < eIonNR; ii++)
226 swapstate->nat_req[ic][ii] = 0;
227 swapstate->nat_req_p[ic][ii] = NULL;
228 swapstate->inflow_netto[ic][ii] = 0;
229 swapstate->inflow_netto_p[ic][ii] = NULL;
230 swapstate->nat_past[ic][ii] = NULL;
231 swapstate->nat_past_p[ic][ii] = NULL;
232 swapstate->fluxfromAtoB[ic][ii] = 0;
233 swapstate->fluxfromAtoB_p[ic][ii] = NULL;
236 swapstate->fluxleak = NULL;
237 swapstate->nions = 0;
238 swapstate->comp_from = NULL;
239 swapstate->channel_label = NULL;
240 swapstate->bFromCpt = 0;
241 swapstate->nat[eChan0] = 0;
242 swapstate->nat[eChan1] = 0;
243 swapstate->xc_old_whole[eChan0] = NULL;
244 swapstate->xc_old_whole[eChan1] = NULL;
245 swapstate->xc_old_whole_p[eChan0] = NULL;
246 swapstate->xc_old_whole_p[eChan1] = NULL;
249 void init_energyhistory(energyhistory_t * enerhist)
253 enerhist->ener_ave = NULL;
254 enerhist->ener_sum = NULL;
255 enerhist->ener_sum_sim = NULL;
256 enerhist->dht = NULL;
258 enerhist->nsteps = 0;
260 enerhist->nsteps_sim = 0;
261 enerhist->nsum_sim = 0;
263 enerhist->dht = NULL;
266 static void done_delta_h_history(delta_h_history_t *dht)
270 for (i = 0; i < dht->nndh; i++)
278 void done_energyhistory(energyhistory_t * enerhist)
280 sfree(enerhist->ener_ave);
281 sfree(enerhist->ener_sum);
282 sfree(enerhist->ener_sum_sim);
284 if (enerhist->dht != NULL)
286 done_delta_h_history(enerhist->dht);
287 sfree(enerhist->dht);
291 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
296 state->nnhpres = nnhpres;
297 state->nhchainlength = nhchainlength;
300 snew(state->nosehoover_xi, state->nhchainlength*state->ngtc);
301 snew(state->nosehoover_vxi, state->nhchainlength*state->ngtc);
302 snew(state->therm_integral, state->ngtc);
303 for (i = 0; i < state->ngtc; i++)
305 for (j = 0; j < state->nhchainlength; j++)
307 state->nosehoover_xi[i*state->nhchainlength + j] = 0.0;
308 state->nosehoover_vxi[i*state->nhchainlength + j] = 0.0;
311 for (i = 0; i < state->ngtc; i++)
313 state->therm_integral[i] = 0.0;
318 state->nosehoover_xi = NULL;
319 state->nosehoover_vxi = NULL;
320 state->therm_integral = NULL;
323 if (state->nnhpres > 0)
325 snew(state->nhpres_xi, state->nhchainlength*nnhpres);
326 snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
327 for (i = 0; i < nnhpres; i++)
329 for (j = 0; j < state->nhchainlength; j++)
331 state->nhpres_xi[i*nhchainlength + j] = 0.0;
332 state->nhpres_vxi[i*nhchainlength + j] = 0.0;
338 state->nhpres_xi = NULL;
339 state->nhpres_vxi = NULL;
344 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
348 state->natoms = natoms;
351 snew(state->lambda, efptNR);
352 for (i = 0; i < efptNR; i++)
354 state->lambda[i] = 0;
357 clear_mat(state->box);
358 clear_mat(state->box_rel);
359 clear_mat(state->boxv);
360 clear_mat(state->pres_prev);
361 clear_mat(state->svir_prev);
362 clear_mat(state->fvir_prev);
363 init_gtc_state(state, ngtc, nnhpres, nhchainlength);
364 state->nalloc = state->natoms;
365 if (state->nalloc > 0)
367 snew(state->x, state->nalloc);
368 snew(state->v, state->nalloc);
377 zero_history(&state->hist);
378 zero_ekinstate(&state->ekinstate);
379 init_energyhistory(&state->enerhist);
380 init_df_history(&state->dfhist, nlambda);
381 init_swapstate(&state->swapstate);
382 state->ddp_count = 0;
383 state->ddp_count_cg_gl = 0;
385 state->cg_gl_nalloc = 0;
388 void done_state(t_state *state)
411 state->cg_gl_nalloc = 0;
414 sfree(state->lambda);
418 sfree(state->nosehoover_xi);
419 sfree(state->nosehoover_vxi);
420 sfree(state->therm_integral);
424 t_state *serial_init_local_state(t_state *state_global)
427 t_state *state_local;
429 snew(state_local, 1);
431 /* Copy all the contents */
432 *state_local = *state_global;
433 snew(state_local->lambda, efptNR);
434 /* local storage for lambda */
435 for (i = 0; i < efptNR; i++)
437 state_local->lambda[i] = state_global->lambda[i];
443 static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
447 for (d = YY; d <= ZZ; d++)
449 for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
451 /* We need to check if this box component is deformed
452 * or if deformation of another component might cause
453 * changes in this component due to box corrections.
455 if (ir->deform[d][d2] == 0 &&
456 !(d == ZZ && d2 == XX && ir->deform[d][YY] != 0 &&
457 (b[YY][d2] != 0 || ir->deform[YY][d2] != 0)))
461 box_rel[d][d2] = b[d][d2]/b[XX][XX];
465 b[d][d2] = b[XX][XX]*box_rel[d][d2];
472 void set_box_rel(t_inputrec *ir, t_state *state)
474 /* Make sure the box obeys the restrictions before we fix the ratios */
475 correct_box(NULL, 0, state->box, NULL);
477 clear_mat(state->box_rel);
479 if (PRESERVE_SHAPE(*ir))
481 do_box_rel(ir, state->box_rel, state->box, TRUE);
485 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
487 if (PRESERVE_SHAPE(*ir))
489 do_box_rel(ir, box_rel, b, FALSE);
493 real max_cutoff(real cutoff1, real cutoff2)
495 if (cutoff1 == 0 || cutoff2 == 0)
501 return max(cutoff1, cutoff2);
505 void init_df_history(df_history_t *dfhist, int nlambda)
509 dfhist->nlambda = nlambda;
511 dfhist->wl_delta = 0;
515 snew(dfhist->sum_weights, dfhist->nlambda);
516 snew(dfhist->sum_dg, dfhist->nlambda);
517 snew(dfhist->sum_minvar, dfhist->nlambda);
518 snew(dfhist->sum_variance, dfhist->nlambda);
519 snew(dfhist->n_at_lam, dfhist->nlambda);
520 snew(dfhist->wl_histo, dfhist->nlambda);
522 /* allocate transition matrices here */
523 snew(dfhist->Tij, dfhist->nlambda);
524 snew(dfhist->Tij_empirical, dfhist->nlambda);
526 /* allocate accumulators for various transition matrix
527 free energy methods here */
528 snew(dfhist->accum_p, dfhist->nlambda);
529 snew(dfhist->accum_m, dfhist->nlambda);
530 snew(dfhist->accum_p2, dfhist->nlambda);
531 snew(dfhist->accum_m2, dfhist->nlambda);
533 for (i = 0; i < dfhist->nlambda; i++)
535 snew(dfhist->Tij[i], dfhist->nlambda);
536 snew(dfhist->Tij_empirical[i], dfhist->nlambda);
537 snew((dfhist->accum_p)[i], dfhist->nlambda);
538 snew((dfhist->accum_m)[i], dfhist->nlambda);
539 snew((dfhist->accum_p2)[i], dfhist->nlambda);
540 snew((dfhist->accum_m2)[i], dfhist->nlambda);
545 extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
549 /* Currently, there should not be any difference in nlambda between the two,
550 but this is included for completeness for potential later functionality */
551 df_dest->nlambda = df_source->nlambda;
552 df_dest->bEquil = df_source->bEquil;
553 df_dest->wl_delta = df_source->wl_delta;
555 for (i = 0; i < df_dest->nlambda; i++)
557 df_dest->sum_weights[i] = df_source->sum_weights[i];
558 df_dest->sum_dg[i] = df_source->sum_dg[i];
559 df_dest->sum_minvar[i] = df_source->sum_minvar[i];
560 df_dest->sum_variance[i] = df_source->sum_variance[i];
561 df_dest->n_at_lam[i] = df_source->n_at_lam[i];
562 df_dest->wl_histo[i] = df_source->wl_histo[i];
565 for (i = 0; i < df_dest->nlambda; i++)
567 for (j = 0; j < df_dest->nlambda; j++)
569 df_dest->accum_p[i][j] = df_source->accum_p[i][j];
570 df_dest->accum_m[i][j] = df_source->accum_m[i][j];
571 df_dest->accum_p2[i][j] = df_source->accum_p2[i][j];
572 df_dest->accum_m2[i][j] = df_source->accum_m2[i][j];
573 df_dest->Tij[i][j] = df_source->Tij[i][j];
574 df_dest->Tij_empirical[i][j] = df_source->Tij_empirical[i][j];
579 void done_df_history(df_history_t *dfhist)
583 if (dfhist->nlambda > 0)
585 sfree(dfhist->n_at_lam);
586 sfree(dfhist->wl_histo);
587 sfree(dfhist->sum_weights);
588 sfree(dfhist->sum_dg);
589 sfree(dfhist->sum_minvar);
590 sfree(dfhist->sum_variance);
592 for (i = 0; i < dfhist->nlambda; i++)
594 sfree(dfhist->Tij[i]);
595 sfree(dfhist->Tij_empirical[i]);
596 sfree(dfhist->accum_p[i]);
597 sfree(dfhist->accum_m[i]);
598 sfree(dfhist->accum_p2[i]);
599 sfree(dfhist->accum_m2[i]);
604 dfhist->wl_delta = 0;