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37 /* This file is completely threadsafe - keep it that way! */
40 #include "gromacs/legacyheaders/typedefs.h"
46 #include "gromacs/legacyheaders/macros.h"
47 #include "gromacs/math/vec.h"
48 #include "gromacs/pbcutil/pbc.h"
49 #include "gromacs/random/random.h"
50 #include "gromacs/utility/smalloc.h"
52 /* The source code in this file should be thread-safe.
53 Please keep it that way. */
55 int gmx_int64_to_int(gmx_int64_t step, const char *warn)
61 if (warn != NULL && (step < INT_MIN || step > INT_MAX))
63 fprintf(stderr, "\nWARNING during %s:\n", warn);
64 fprintf(stderr, "step value ");
65 fprintf(stderr, "%"GMX_PRId64, step);
66 fprintf(stderr, " does not fit in int, converted to %d\n\n", i);
72 void init_inputrec(t_inputrec *ir)
74 memset(ir, 0, (size_t)sizeof(*ir));
76 snew(ir->expandedvals, 1);
77 snew(ir->simtempvals, 1);
80 static void done_pull_group(t_pull_group *pgrp)
87 sfree(pgrp->weight_loc);
91 static void done_pull(t_pull *pull)
95 for (i = 0; i < pull->ngroup+1; i++)
97 done_pull_group(pull->group);
98 done_pull_group(pull->dyna);
102 void done_inputrec(t_inputrec *ir)
106 for (m = 0; (m < DIM); m++)
114 sfree(ir->ex[m].phi);
122 sfree(ir->et[m].phi);
126 sfree(ir->opts.nrdf);
127 sfree(ir->opts.ref_t);
128 sfree(ir->opts.annealing);
129 sfree(ir->opts.anneal_npoints);
130 sfree(ir->opts.anneal_time);
131 sfree(ir->opts.anneal_temp);
132 sfree(ir->opts.tau_t);
134 sfree(ir->opts.nFreeze);
135 sfree(ir->opts.QMmethod);
136 sfree(ir->opts.QMbasis);
137 sfree(ir->opts.QMcharge);
138 sfree(ir->opts.QMmult);
140 sfree(ir->opts.CASorbitals);
141 sfree(ir->opts.CASelectrons);
142 sfree(ir->opts.SAon);
143 sfree(ir->opts.SAoff);
144 sfree(ir->opts.SAsteps);
145 sfree(ir->opts.bOPT);
155 static void zero_history(history_t *hist)
157 hist->disre_initf = 0;
158 hist->ndisrepairs = 0;
159 hist->disre_rm3tav = NULL;
160 hist->orire_initf = 0;
161 hist->norire_Dtav = 0;
162 hist->orire_Dtav = NULL;
165 static void zero_ekinstate(ekinstate_t *eks)
170 eks->ekinh_old = NULL;
171 eks->ekinscalef_nhc = NULL;
172 eks->ekinscaleh_nhc = NULL;
173 eks->vscale_nhc = NULL;
178 static void init_swapstate(swapstate_t *swapstate)
182 swapstate->eSwapCoords = 0;
183 swapstate->nAverage = 0;
185 /* Ion/water position swapping */
186 for (ic = 0; ic < eCompNR; ic++)
188 for (ii = 0; ii < eIonNR; ii++)
190 swapstate->nat_req[ic][ii] = 0;
191 swapstate->nat_req_p[ic][ii] = NULL;
192 swapstate->inflow_netto[ic][ii] = 0;
193 swapstate->inflow_netto_p[ic][ii] = NULL;
194 swapstate->nat_past[ic][ii] = NULL;
195 swapstate->nat_past_p[ic][ii] = NULL;
196 swapstate->fluxfromAtoB[ic][ii] = 0;
197 swapstate->fluxfromAtoB_p[ic][ii] = NULL;
200 swapstate->fluxleak = NULL;
201 swapstate->nions = 0;
202 swapstate->comp_from = NULL;
203 swapstate->channel_label = NULL;
204 swapstate->bFromCpt = 0;
205 swapstate->nat[eChan0] = 0;
206 swapstate->nat[eChan1] = 0;
207 swapstate->xc_old_whole[eChan0] = NULL;
208 swapstate->xc_old_whole[eChan1] = NULL;
209 swapstate->xc_old_whole_p[eChan0] = NULL;
210 swapstate->xc_old_whole_p[eChan1] = NULL;
213 void init_energyhistory(energyhistory_t * enerhist)
217 enerhist->ener_ave = NULL;
218 enerhist->ener_sum = NULL;
219 enerhist->ener_sum_sim = NULL;
220 enerhist->dht = NULL;
222 enerhist->nsteps = 0;
224 enerhist->nsteps_sim = 0;
225 enerhist->nsum_sim = 0;
227 enerhist->dht = NULL;
230 static void done_delta_h_history(delta_h_history_t *dht)
234 for (i = 0; i < dht->nndh; i++)
242 void done_energyhistory(energyhistory_t * enerhist)
244 sfree(enerhist->ener_ave);
245 sfree(enerhist->ener_sum);
246 sfree(enerhist->ener_sum_sim);
248 if (enerhist->dht != NULL)
250 done_delta_h_history(enerhist->dht);
251 sfree(enerhist->dht);
255 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
260 state->nnhpres = nnhpres;
261 state->nhchainlength = nhchainlength;
264 snew(state->nosehoover_xi, state->nhchainlength*state->ngtc);
265 snew(state->nosehoover_vxi, state->nhchainlength*state->ngtc);
266 snew(state->therm_integral, state->ngtc);
267 for (i = 0; i < state->ngtc; i++)
269 for (j = 0; j < state->nhchainlength; j++)
271 state->nosehoover_xi[i*state->nhchainlength + j] = 0.0;
272 state->nosehoover_vxi[i*state->nhchainlength + j] = 0.0;
275 for (i = 0; i < state->ngtc; i++)
277 state->therm_integral[i] = 0.0;
282 state->nosehoover_xi = NULL;
283 state->nosehoover_vxi = NULL;
284 state->therm_integral = NULL;
287 if (state->nnhpres > 0)
289 snew(state->nhpres_xi, state->nhchainlength*nnhpres);
290 snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
291 for (i = 0; i < nnhpres; i++)
293 for (j = 0; j < state->nhchainlength; j++)
295 state->nhpres_xi[i*nhchainlength + j] = 0.0;
296 state->nhpres_vxi[i*nhchainlength + j] = 0.0;
302 state->nhpres_xi = NULL;
303 state->nhpres_vxi = NULL;
308 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
312 state->natoms = natoms;
315 snew(state->lambda, efptNR);
316 for (i = 0; i < efptNR; i++)
318 state->lambda[i] = 0;
321 clear_mat(state->box);
322 clear_mat(state->box_rel);
323 clear_mat(state->boxv);
324 clear_mat(state->pres_prev);
325 clear_mat(state->svir_prev);
326 clear_mat(state->fvir_prev);
327 init_gtc_state(state, ngtc, nnhpres, nhchainlength);
328 state->nalloc = state->natoms;
329 if (state->nalloc > 0)
331 snew(state->x, state->nalloc);
332 snew(state->v, state->nalloc);
341 zero_history(&state->hist);
342 zero_ekinstate(&state->ekinstate);
343 init_energyhistory(&state->enerhist);
344 init_df_history(&state->dfhist, nlambda);
345 init_swapstate(&state->swapstate);
346 state->ddp_count = 0;
347 state->ddp_count_cg_gl = 0;
349 state->cg_gl_nalloc = 0;
352 void done_state(t_state *state)
375 state->cg_gl_nalloc = 0;
378 sfree(state->lambda);
382 sfree(state->nosehoover_xi);
383 sfree(state->nosehoover_vxi);
384 sfree(state->therm_integral);
388 t_state *serial_init_local_state(t_state *state_global)
391 t_state *state_local;
393 snew(state_local, 1);
395 /* Copy all the contents */
396 *state_local = *state_global;
397 snew(state_local->lambda, efptNR);
398 /* local storage for lambda */
399 for (i = 0; i < efptNR; i++)
401 state_local->lambda[i] = state_global->lambda[i];
407 static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
411 for (d = YY; d <= ZZ; d++)
413 for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
415 /* We need to check if this box component is deformed
416 * or if deformation of another component might cause
417 * changes in this component due to box corrections.
419 if (ir->deform[d][d2] == 0 &&
420 !(d == ZZ && d2 == XX && ir->deform[d][YY] != 0 &&
421 (b[YY][d2] != 0 || ir->deform[YY][d2] != 0)))
425 box_rel[d][d2] = b[d][d2]/b[XX][XX];
429 b[d][d2] = b[XX][XX]*box_rel[d][d2];
436 void set_box_rel(t_inputrec *ir, t_state *state)
438 /* Make sure the box obeys the restrictions before we fix the ratios */
439 correct_box(NULL, 0, state->box, NULL);
441 clear_mat(state->box_rel);
443 if (PRESERVE_SHAPE(*ir))
445 do_box_rel(ir, state->box_rel, state->box, TRUE);
449 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
451 if (PRESERVE_SHAPE(*ir))
453 do_box_rel(ir, box_rel, b, FALSE);
457 real max_cutoff(real cutoff1, real cutoff2)
459 if (cutoff1 == 0 || cutoff2 == 0)
465 return max(cutoff1, cutoff2);
469 void init_df_history(df_history_t *dfhist, int nlambda)
473 dfhist->nlambda = nlambda;
475 dfhist->wl_delta = 0;
479 snew(dfhist->sum_weights, dfhist->nlambda);
480 snew(dfhist->sum_dg, dfhist->nlambda);
481 snew(dfhist->sum_minvar, dfhist->nlambda);
482 snew(dfhist->sum_variance, dfhist->nlambda);
483 snew(dfhist->n_at_lam, dfhist->nlambda);
484 snew(dfhist->wl_histo, dfhist->nlambda);
486 /* allocate transition matrices here */
487 snew(dfhist->Tij, dfhist->nlambda);
488 snew(dfhist->Tij_empirical, dfhist->nlambda);
490 /* allocate accumulators for various transition matrix
491 free energy methods here */
492 snew(dfhist->accum_p, dfhist->nlambda);
493 snew(dfhist->accum_m, dfhist->nlambda);
494 snew(dfhist->accum_p2, dfhist->nlambda);
495 snew(dfhist->accum_m2, dfhist->nlambda);
497 for (i = 0; i < dfhist->nlambda; i++)
499 snew(dfhist->Tij[i], dfhist->nlambda);
500 snew(dfhist->Tij_empirical[i], dfhist->nlambda);
501 snew((dfhist->accum_p)[i], dfhist->nlambda);
502 snew((dfhist->accum_m)[i], dfhist->nlambda);
503 snew((dfhist->accum_p2)[i], dfhist->nlambda);
504 snew((dfhist->accum_m2)[i], dfhist->nlambda);
509 extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
513 /* Currently, there should not be any difference in nlambda between the two,
514 but this is included for completeness for potential later functionality */
515 df_dest->nlambda = df_source->nlambda;
516 df_dest->bEquil = df_source->bEquil;
517 df_dest->wl_delta = df_source->wl_delta;
519 for (i = 0; i < df_dest->nlambda; i++)
521 df_dest->sum_weights[i] = df_source->sum_weights[i];
522 df_dest->sum_dg[i] = df_source->sum_dg[i];
523 df_dest->sum_minvar[i] = df_source->sum_minvar[i];
524 df_dest->sum_variance[i] = df_source->sum_variance[i];
525 df_dest->n_at_lam[i] = df_source->n_at_lam[i];
526 df_dest->wl_histo[i] = df_source->wl_histo[i];
529 for (i = 0; i < df_dest->nlambda; i++)
531 for (j = 0; j < df_dest->nlambda; j++)
533 df_dest->accum_p[i][j] = df_source->accum_p[i][j];
534 df_dest->accum_m[i][j] = df_source->accum_m[i][j];
535 df_dest->accum_p2[i][j] = df_source->accum_p2[i][j];
536 df_dest->accum_m2[i][j] = df_source->accum_m2[i][j];
537 df_dest->Tij[i][j] = df_source->Tij[i][j];
538 df_dest->Tij_empirical[i][j] = df_source->Tij_empirical[i][j];
543 void done_df_history(df_history_t *dfhist)
547 if (dfhist->nlambda > 0)
549 sfree(dfhist->n_at_lam);
550 sfree(dfhist->wl_histo);
551 sfree(dfhist->sum_weights);
552 sfree(dfhist->sum_dg);
553 sfree(dfhist->sum_minvar);
554 sfree(dfhist->sum_variance);
556 for (i = 0; i < dfhist->nlambda; i++)
558 sfree(dfhist->Tij[i]);
559 sfree(dfhist->Tij_empirical[i]);
560 sfree(dfhist->accum_p[i]);
561 sfree(dfhist->accum_m[i]);
562 sfree(dfhist->accum_p2[i]);
563 sfree(dfhist->accum_m2[i]);
568 dfhist->wl_delta = 0;