src/gromacs/gmxlib/typedefs.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team.
   6  * Copyright (c) 2013,2014, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
  15  *
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  18  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  19  * Lesser General Public License for more details.
  20  *
  21  * You should have received a copy of the GNU Lesser General Public
  22  * License along with GROMACS; if not, see
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  29  * consider code for inclusion in the official distribution, but
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  33  *
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  35  * the research papers on the package. Check out http://www.gromacs.org.
  36  */
  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "typedefs.h"
  39
  40 #ifdef HAVE_CONFIG_H
  41 #include <config.h>
  42 #endif
  43
  44 #include <string.h>
  45
  46 #include "thread_mpi/threads.h"
  47
  48 #include "macros.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"
  53
  54 /* The source code in this file should be thread-safe.
  55       Please keep it that way. */
  56
  57
  58
  59 static gmx_bool            bOverAllocDD     = FALSE;
  60 static tMPI_Thread_mutex_t over_alloc_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
  61
  62
  63 void set_over_alloc_dd(gmx_bool set)
  64 {
  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 */
  68     bOverAllocDD = set;
  69     tMPI_Thread_mutex_unlock(&over_alloc_mutex);
  70 }
  71
  72 int over_alloc_dd(int n)
  73 {
  74     if (bOverAllocDD)
  75     {
  76         return OVER_ALLOC_FAC*n + 100;
  77     }
  78     else
  79     {
  80         return n;
  81     }
  82 }
  83
  84 int gmx_int64_to_int(gmx_int64_t step, const char *warn)
  85 {
  86     int i;
  87
  88     i = (int)step;
  89
  90     if (warn != NULL && (step < INT_MIN || step > INT_MAX))
  91     {
  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);
  96     }
  97
  98     return i;
  99 }
 100
 101 char *gmx_step_str(gmx_int64_t i, char *buf)
 102 {
 103     sprintf(buf, "%"GMX_PRId64, i);
 104
 105     return buf;
 106 }
 107
 108 void init_inputrec(t_inputrec *ir)
 109 {
 110     memset(ir, 0, (size_t)sizeof(*ir));
 111     snew(ir->fepvals, 1);
 112     snew(ir->expandedvals, 1);
 113     snew(ir->simtempvals, 1);
 114 }
 115
 116 static void done_pull_group(t_pull_group *pgrp)
 117 {
 118     if (pgrp->nat > 0)
 119     {
 120         sfree(pgrp->ind);
 121         sfree(pgrp->ind_loc);
 122         sfree(pgrp->weight);
 123         sfree(pgrp->weight_loc);
 124     }
 125 }
 126
 127 static void done_pull(t_pull *pull)
 128 {
 129     int i;
 130
 131     for (i = 0; i < pull->ngroup+1; i++)
 132     {
 133         done_pull_group(pull->group);
 134         done_pull_group(pull->dyna);
 135     }
 136 }
 137
 138 void done_inputrec(t_inputrec *ir)
 139 {
 140     int m;
 141
 142     for (m = 0; (m < DIM); m++)
 143     {
 144         if (ir->ex[m].a)
 145         {
 146             sfree(ir->ex[m].a);
 147         }
 148         if (ir->ex[m].phi)
 149         {
 150             sfree(ir->ex[m].phi);
 151         }
 152         if (ir->et[m].a)
 153         {
 154             sfree(ir->et[m].a);
 155         }
 156         if (ir->et[m].phi)
 157         {
 158             sfree(ir->et[m].phi);
 159         }
 160     }
 161
 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);
 169     sfree(ir->opts.acc);
 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);
 175     sfree(ir->opts.bSH);
 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);
 182     sfree(ir->opts.bTS);
 183
 184     if (ir->pull)
 185     {
 186         done_pull(ir->pull);
 187         sfree(ir->pull);
 188     }
 189 }
 190
 191 static void zero_history(history_t *hist)
 192 {
 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;
 199 }
 200
 201 static void zero_ekinstate(ekinstate_t *eks)
 202 {
 203     eks->ekin_n         = 0;
 204     eks->ekinh          = NULL;
 205     eks->ekinf          = NULL;
 206     eks->ekinh_old      = NULL;
 207     eks->ekinscalef_nhc = NULL;
 208     eks->ekinscaleh_nhc = NULL;
 209     eks->vscale_nhc     = NULL;
 210     eks->dekindl        = 0;
 211     eks->mvcos          = 0;
 212 }
 213
 214 static void init_swapstate(swapstate_t *swapstate)
 215 {
 216     int ii, ic;
 217
 218     swapstate->eSwapCoords = 0;
 219     swapstate->nAverage    = 0;
 220
 221     /* Ion/water position swapping */
 222     for (ic = 0; ic < eCompNR; ic++)
 223     {
 224         for (ii = 0; ii < eIonNR; ii++)
 225         {
 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;
 234         }
 235     }
 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;
 247 }
 248
 249 void init_energyhistory(energyhistory_t * enerhist)
 250 {
 251     enerhist->nener = 0;
 252
 253     enerhist->ener_ave     = NULL;
 254     enerhist->ener_sum     = NULL;
 255     enerhist->ener_sum_sim = NULL;
 256     enerhist->dht          = NULL;
 257
 258     enerhist->nsteps     = 0;
 259     enerhist->nsum       = 0;
 260     enerhist->nsteps_sim = 0;
 261     enerhist->nsum_sim   = 0;
 262
 263     enerhist->dht = NULL;
 264 }
 265
 266 static void done_delta_h_history(delta_h_history_t *dht)
 267 {
 268     int i;
 269
 270     for (i = 0; i < dht->nndh; i++)
 271     {
 272         sfree(dht->dh[i]);
 273     }
 274     sfree(dht->dh);
 275     sfree(dht->ndh);
 276 }
 277
 278 void done_energyhistory(energyhistory_t * enerhist)
 279 {
 280     sfree(enerhist->ener_ave);
 281     sfree(enerhist->ener_sum);
 282     sfree(enerhist->ener_sum_sim);
 283
 284     if (enerhist->dht != NULL)
 285     {
 286         done_delta_h_history(enerhist->dht);
 287         sfree(enerhist->dht);
 288     }
 289 }
 290
 291 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 292 {
 293     int i, j;
 294
 295     state->ngtc          = ngtc;
 296     state->nnhpres       = nnhpres;
 297     state->nhchainlength = nhchainlength;
 298     if (state->ngtc > 0)
 299     {
 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++)
 304         {
 305             for (j = 0; j < state->nhchainlength; j++)
 306             {
 307                 state->nosehoover_xi[i*state->nhchainlength + j]   = 0.0;
 308                 state->nosehoover_vxi[i*state->nhchainlength + j]  = 0.0;
 309             }
 310         }
 311         for (i = 0; i < state->ngtc; i++)
 312         {
 313             state->therm_integral[i]  = 0.0;
 314         }
 315     }
 316     else
 317     {
 318         state->nosehoover_xi  = NULL;
 319         state->nosehoover_vxi = NULL;
 320         state->therm_integral = NULL;
 321     }
 322
 323     if (state->nnhpres > 0)
 324     {
 325         snew(state->nhpres_xi, state->nhchainlength*nnhpres);
 326         snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
 327         for (i = 0; i < nnhpres; i++)
 328         {
 329             for (j = 0; j < state->nhchainlength; j++)
 330             {
 331                 state->nhpres_xi[i*nhchainlength + j]   = 0.0;
 332                 state->nhpres_vxi[i*nhchainlength + j]  = 0.0;
 333             }
 334         }
 335     }
 336     else
 337     {
 338         state->nhpres_xi  = NULL;
 339         state->nhpres_vxi = NULL;
 340     }
 341 }
 342
 343
 344 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
 345 {
 346     int i;
 347
 348     state->natoms = natoms;
 349     state->flags  = 0;
 350     state->lambda = 0;
 351     snew(state->lambda, efptNR);
 352     for (i = 0; i < efptNR; i++)
 353     {
 354         state->lambda[i] = 0;
 355     }
 356     state->veta   = 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)
 366     {
 367         snew(state->x, state->nalloc);
 368         snew(state->v, state->nalloc);
 369     }
 370     else
 371     {
 372         state->x = NULL;
 373         state->v = NULL;
 374     }
 375     state->sd_X = NULL;
 376     state->cg_p = NULL;
 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;
 384     state->cg_gl           = NULL;
 385     state->cg_gl_nalloc    = 0;
 386 }
 387
 388 void done_state(t_state *state)
 389 {
 390     if (state->x)
 391     {
 392         sfree(state->x);
 393     }
 394     if (state->v)
 395     {
 396         sfree(state->v);
 397     }
 398     if (state->sd_X)
 399     {
 400         sfree(state->sd_X);
 401     }
 402     if (state->cg_p)
 403     {
 404         sfree(state->cg_p);
 405     }
 406     state->nalloc = 0;
 407     if (state->cg_gl)
 408     {
 409         sfree(state->cg_gl);
 410     }
 411     state->cg_gl_nalloc = 0;
 412     if (state->lambda)
 413     {
 414         sfree(state->lambda);
 415     }
 416     if (state->ngtc > 0)
 417     {
 418         sfree(state->nosehoover_xi);
 419         sfree(state->nosehoover_vxi);
 420         sfree(state->therm_integral);
 421     }
 422 }
 423
 424 t_state *serial_init_local_state(t_state *state_global)
 425 {
 426     int      i;
 427     t_state *state_local;
 428
 429     snew(state_local, 1);
 430
 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++)
 436     {
 437         state_local->lambda[i] = state_global->lambda[i];
 438     }
 439
 440     return state_local;
 441 }
 442
 443 static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
 444 {
 445     int d, d2;
 446
 447     for (d = YY; d <= ZZ; d++)
 448     {
 449         for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
 450         {
 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.
 454              */
 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)))
 458             {
 459                 if (bInit)
 460                 {
 461                     box_rel[d][d2] = b[d][d2]/b[XX][XX];
 462                 }
 463                 else
 464                 {
 465                     b[d][d2] = b[XX][XX]*box_rel[d][d2];
 466                 }
 467             }
 468         }
 469     }
 470 }
 471
 472 void set_box_rel(t_inputrec *ir, t_state *state)
 473 {
 474     /* Make sure the box obeys the restrictions before we fix the ratios */
 475     correct_box(NULL, 0, state->box, NULL);
 476
 477     clear_mat(state->box_rel);
 478
 479     if (PRESERVE_SHAPE(*ir))
 480     {
 481         do_box_rel(ir, state->box_rel, state->box, TRUE);
 482     }
 483 }
 484
 485 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
 486 {
 487     if (PRESERVE_SHAPE(*ir))
 488     {
 489         do_box_rel(ir, box_rel, b, FALSE);
 490     }
 491 }
 492
 493 real max_cutoff(real cutoff1, real cutoff2)
 494 {
 495     if (cutoff1 == 0 || cutoff2 == 0)
 496     {
 497         return 0;
 498     }
 499     else
 500     {
 501         return max(cutoff1, cutoff2);
 502     }
 503 }
 504
 505 void init_df_history(df_history_t *dfhist, int nlambda)
 506 {
 507     int i;
 508
 509     dfhist->nlambda  = nlambda;
 510     dfhist->bEquil   = 0;
 511     dfhist->wl_delta = 0;
 512
 513     if (nlambda > 0)
 514     {
 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);
 521
 522         /* allocate transition matrices here */
 523         snew(dfhist->Tij, dfhist->nlambda);
 524         snew(dfhist->Tij_empirical, dfhist->nlambda);
 525
 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);
 532
 533         for (i = 0; i < dfhist->nlambda; i++)
 534         {
 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);
 541         }
 542     }
 543 }
 544
 545 extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
 546 {
 547     int i, j;
 548
 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;
 554
 555     for (i = 0; i < df_dest->nlambda; i++)
 556     {
 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];
 563     }
 564
 565     for (i = 0; i < df_dest->nlambda; i++)
 566     {
 567         for (j = 0; j < df_dest->nlambda; j++)
 568         {
 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];
 575         }
 576     }
 577 }
 578
 579 void done_df_history(df_history_t *dfhist)
 580 {
 581     int i;
 582
 583     if (dfhist->nlambda > 0)
 584     {
 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);
 591
 592         for (i = 0; i < dfhist->nlambda; i++)
 593         {
 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]);
 600         }
 601     }
 602     dfhist->bEquil   = 0;
 603     dfhist->nlambda  = 0;
 604     dfhist->wl_delta = 0;
 605 }