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) 2013,2014,2015, 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  *
  16  * GROMACS is distributed in the hope that it will be useful,
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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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  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
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  29  * consider code for inclusion in the official distribution, but
  30  * derived work must not be called official GROMACS. Details are found
  31  * in the README & COPYING files - if they are missing, get the
  32  * official version at http://www.gromacs.org.
  33  *
  34  * To help us fund GROMACS development, we humbly ask that you cite
  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 "gmxpre.h"
  39
  40 #include "gromacs/legacyheaders/typedefs.h"
  41
  42 #include <string.h>
  43
  44 #include "gromacs/legacyheaders/macros.h"
  45 #include "gromacs/math/vec.h"
  46 #include "gromacs/pbcutil/pbc.h"
  47 #include "gromacs/random/random.h"
  48 #include "gromacs/utility/smalloc.h"
  49
  50 /* The source code in this file should be thread-safe.
  51       Please keep it that way. */
  52
  53 int gmx_int64_to_int(gmx_int64_t step, const char *warn)
  54 {
  55     int i;
  56
  57     i = (int)step;
  58
  59     if (warn != NULL && (step < INT_MIN || step > INT_MAX))
  60     {
  61         fprintf(stderr, "\nWARNING during %s:\n", warn);
  62         fprintf(stderr, "step value ");
  63         fprintf(stderr, "%"GMX_PRId64, step);
  64         fprintf(stderr, " does not fit in int, converted to %d\n\n", i);
  65     }
  66
  67     return i;
  68 }
  69
  70 void init_inputrec(t_inputrec *ir)
  71 {
  72     memset(ir, 0, (size_t)sizeof(*ir));
  73     snew(ir->fepvals, 1);
  74     snew(ir->expandedvals, 1);
  75     snew(ir->simtempvals, 1);
  76 }
  77
  78 static void done_pull_group(t_pull_group *pgrp)
  79 {
  80     if (pgrp->nat > 0)
  81     {
  82         sfree(pgrp->ind);
  83         sfree(pgrp->weight);
  84     }
  85 }
  86
  87 static void done_pull_params(pull_params_t *pull)
  88 {
  89     int i;
  90
  91     for (i = 0; i < pull->ngroup+1; i++)
  92     {
  93         done_pull_group(pull->group);
  94     }
  95
  96     sfree(pull->group);
  97     sfree(pull->coord);
  98 }
  99
 100 void done_inputrec(t_inputrec *ir)
 101 {
 102     int m;
 103
 104     for (m = 0; (m < DIM); m++)
 105     {
 106         if (ir->ex[m].a)
 107         {
 108             sfree(ir->ex[m].a);
 109         }
 110         if (ir->ex[m].phi)
 111         {
 112             sfree(ir->ex[m].phi);
 113         }
 114         if (ir->et[m].a)
 115         {
 116             sfree(ir->et[m].a);
 117         }
 118         if (ir->et[m].phi)
 119         {
 120             sfree(ir->et[m].phi);
 121         }
 122     }
 123
 124     sfree(ir->opts.nrdf);
 125     sfree(ir->opts.ref_t);
 126     sfree(ir->opts.annealing);
 127     sfree(ir->opts.anneal_npoints);
 128     sfree(ir->opts.anneal_time);
 129     sfree(ir->opts.anneal_temp);
 130     sfree(ir->opts.tau_t);
 131     sfree(ir->opts.acc);
 132     sfree(ir->opts.nFreeze);
 133     sfree(ir->opts.QMmethod);
 134     sfree(ir->opts.QMbasis);
 135     sfree(ir->opts.QMcharge);
 136     sfree(ir->opts.QMmult);
 137     sfree(ir->opts.bSH);
 138     sfree(ir->opts.CASorbitals);
 139     sfree(ir->opts.CASelectrons);
 140     sfree(ir->opts.SAon);
 141     sfree(ir->opts.SAoff);
 142     sfree(ir->opts.SAsteps);
 143     sfree(ir->opts.bOPT);
 144     sfree(ir->opts.bTS);
 145
 146     if (ir->pull)
 147     {
 148         done_pull_params(ir->pull);
 149         sfree(ir->pull);
 150     }
 151 }
 152
 153 static void zero_history(history_t *hist)
 154 {
 155     hist->disre_initf  = 0;
 156     hist->ndisrepairs  = 0;
 157     hist->disre_rm3tav = NULL;
 158     hist->orire_initf  = 0;
 159     hist->norire_Dtav  = 0;
 160     hist->orire_Dtav   = NULL;
 161 }
 162
 163 static void zero_ekinstate(ekinstate_t *eks)
 164 {
 165     eks->ekin_n         = 0;
 166     eks->ekinh          = NULL;
 167     eks->ekinf          = NULL;
 168     eks->ekinh_old      = NULL;
 169     eks->ekinscalef_nhc = NULL;
 170     eks->ekinscaleh_nhc = NULL;
 171     eks->vscale_nhc     = NULL;
 172     eks->dekindl        = 0;
 173     eks->mvcos          = 0;
 174 }
 175
 176 static void init_swapstate(swapstate_t *swapstate)
 177 {
 178     int ii, ic;
 179
 180     swapstate->eSwapCoords = 0;
 181     swapstate->nAverage    = 0;
 182
 183     /* Ion/water position swapping */
 184     for (ic = 0; ic < eCompNR; ic++)
 185     {
 186         for (ii = 0; ii < eIonNR; ii++)
 187         {
 188             swapstate->nat_req[ic][ii]        = 0;
 189             swapstate->nat_req_p[ic][ii]      = NULL;
 190             swapstate->inflow_netto[ic][ii]   = 0;
 191             swapstate->inflow_netto_p[ic][ii] = NULL;
 192             swapstate->nat_past[ic][ii]       = NULL;
 193             swapstate->nat_past_p[ic][ii]     = NULL;
 194             swapstate->fluxfromAtoB[ic][ii]   = 0;
 195             swapstate->fluxfromAtoB_p[ic][ii] = NULL;
 196         }
 197     }
 198     swapstate->fluxleak               = NULL;
 199     swapstate->nions                  = 0;
 200     swapstate->comp_from              = NULL;
 201     swapstate->channel_label          = NULL;
 202     swapstate->bFromCpt               = 0;
 203     swapstate->nat[eChan0]            = 0;
 204     swapstate->nat[eChan1]            = 0;
 205     swapstate->xc_old_whole[eChan0]   = NULL;
 206     swapstate->xc_old_whole[eChan1]   = NULL;
 207     swapstate->xc_old_whole_p[eChan0] = NULL;
 208     swapstate->xc_old_whole_p[eChan1] = NULL;
 209 }
 210
 211 void init_energyhistory(energyhistory_t * enerhist)
 212 {
 213     enerhist->nener = 0;
 214
 215     enerhist->ener_ave     = NULL;
 216     enerhist->ener_sum     = NULL;
 217     enerhist->ener_sum_sim = NULL;
 218     enerhist->dht          = NULL;
 219
 220     enerhist->nsteps     = 0;
 221     enerhist->nsum       = 0;
 222     enerhist->nsteps_sim = 0;
 223     enerhist->nsum_sim   = 0;
 224
 225     enerhist->dht = NULL;
 226 }
 227
 228 static void done_delta_h_history(delta_h_history_t *dht)
 229 {
 230     int i;
 231
 232     for (i = 0; i < dht->nndh; i++)
 233     {
 234         sfree(dht->dh[i]);
 235     }
 236     sfree(dht->dh);
 237     sfree(dht->ndh);
 238 }
 239
 240 void done_energyhistory(energyhistory_t * enerhist)
 241 {
 242     sfree(enerhist->ener_ave);
 243     sfree(enerhist->ener_sum);
 244     sfree(enerhist->ener_sum_sim);
 245
 246     if (enerhist->dht != NULL)
 247     {
 248         done_delta_h_history(enerhist->dht);
 249         sfree(enerhist->dht);
 250     }
 251 }
 252
 253 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 254 {
 255     int i, j;
 256
 257     state->ngtc          = ngtc;
 258     state->nnhpres       = nnhpres;
 259     state->nhchainlength = nhchainlength;
 260     if (state->ngtc > 0)
 261     {
 262         snew(state->nosehoover_xi, state->nhchainlength*state->ngtc);
 263         snew(state->nosehoover_vxi, state->nhchainlength*state->ngtc);
 264         snew(state->therm_integral, state->ngtc);
 265         for (i = 0; i < state->ngtc; i++)
 266         {
 267             for (j = 0; j < state->nhchainlength; j++)
 268             {
 269                 state->nosehoover_xi[i*state->nhchainlength + j]   = 0.0;
 270                 state->nosehoover_vxi[i*state->nhchainlength + j]  = 0.0;
 271             }
 272         }
 273         for (i = 0; i < state->ngtc; i++)
 274         {
 275             state->therm_integral[i]  = 0.0;
 276         }
 277     }
 278     else
 279     {
 280         state->nosehoover_xi  = NULL;
 281         state->nosehoover_vxi = NULL;
 282         state->therm_integral = NULL;
 283     }
 284
 285     if (state->nnhpres > 0)
 286     {
 287         snew(state->nhpres_xi, state->nhchainlength*nnhpres);
 288         snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
 289         for (i = 0; i < nnhpres; i++)
 290         {
 291             for (j = 0; j < state->nhchainlength; j++)
 292             {
 293                 state->nhpres_xi[i*nhchainlength + j]   = 0.0;
 294                 state->nhpres_vxi[i*nhchainlength + j]  = 0.0;
 295             }
 296         }
 297     }
 298     else
 299     {
 300         state->nhpres_xi  = NULL;
 301         state->nhpres_vxi = NULL;
 302     }
 303 }
 304
 305
 306 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
 307 {
 308     int i;
 309
 310     state->natoms    = natoms;
 311     state->flags     = 0;
 312     state->fep_state = 0;
 313     state->lambda    = 0;
 314     snew(state->lambda, efptNR);
 315     for (i = 0; i < efptNR; i++)
 316     {
 317         state->lambda[i] = 0;
 318     }
 319     state->veta   = 0;
 320     clear_mat(state->box);
 321     clear_mat(state->box_rel);
 322     clear_mat(state->boxv);
 323     clear_mat(state->pres_prev);
 324     clear_mat(state->svir_prev);
 325     clear_mat(state->fvir_prev);
 326     init_gtc_state(state, ngtc, nnhpres, nhchainlength);
 327     state->nalloc = state->natoms;
 328     if (state->nalloc > 0)
 329     {
 330         snew(state->x, state->nalloc);
 331         snew(state->v, state->nalloc);
 332     }
 333     else
 334     {
 335         state->x = NULL;
 336         state->v = NULL;
 337     }
 338     state->sd_X = NULL;
 339     state->cg_p = NULL;
 340     zero_history(&state->hist);
 341     zero_ekinstate(&state->ekinstate);
 342     init_energyhistory(&state->enerhist);
 343     init_df_history(&state->dfhist, nlambda);
 344     init_swapstate(&state->swapstate);
 345     state->ddp_count       = 0;
 346     state->ddp_count_cg_gl = 0;
 347     state->cg_gl           = NULL;
 348     state->cg_gl_nalloc    = 0;
 349 }
 350
 351 void done_state(t_state *state)
 352 {
 353     if (state->x)
 354     {
 355         sfree(state->x);
 356     }
 357     if (state->v)
 358     {
 359         sfree(state->v);
 360     }
 361     if (state->sd_X)
 362     {
 363         sfree(state->sd_X);
 364     }
 365     if (state->cg_p)
 366     {
 367         sfree(state->cg_p);
 368     }
 369     state->nalloc = 0;
 370     if (state->cg_gl)
 371     {
 372         sfree(state->cg_gl);
 373     }
 374     state->cg_gl_nalloc = 0;
 375     if (state->lambda)
 376     {
 377         sfree(state->lambda);
 378     }
 379     if (state->ngtc > 0)
 380     {
 381         sfree(state->nosehoover_xi);
 382         sfree(state->nosehoover_vxi);
 383         sfree(state->therm_integral);
 384     }
 385 }
 386
 387 t_state *serial_init_local_state(t_state *state_global)
 388 {
 389     int      i;
 390     t_state *state_local;
 391
 392     snew(state_local, 1);
 393
 394     /* Copy all the contents */
 395     *state_local = *state_global;
 396     snew(state_local->lambda, efptNR);
 397     /* local storage for lambda */
 398     for (i = 0; i < efptNR; i++)
 399     {
 400         state_local->lambda[i] = state_global->lambda[i];
 401     }
 402
 403     return state_local;
 404 }
 405
 406 static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
 407 {
 408     int d, d2;
 409
 410     for (d = YY; d <= ZZ; d++)
 411     {
 412         for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
 413         {
 414             /* We need to check if this box component is deformed
 415              * or if deformation of another component might cause
 416              * changes in this component due to box corrections.
 417              */
 418             if (ir->deform[d][d2] == 0 &&
 419                 !(d == ZZ && d2 == XX && ir->deform[d][YY] != 0 &&
 420                   (b[YY][d2] != 0 || ir->deform[YY][d2] != 0)))
 421             {
 422                 if (bInit)
 423                 {
 424                     box_rel[d][d2] = b[d][d2]/b[XX][XX];
 425                 }
 426                 else
 427                 {
 428                     b[d][d2] = b[XX][XX]*box_rel[d][d2];
 429                 }
 430             }
 431         }
 432     }
 433 }
 434
 435 void set_box_rel(t_inputrec *ir, t_state *state)
 436 {
 437     /* Make sure the box obeys the restrictions before we fix the ratios */
 438     correct_box(NULL, 0, state->box, NULL);
 439
 440     clear_mat(state->box_rel);
 441
 442     if (PRESERVE_SHAPE(*ir))
 443     {
 444         do_box_rel(ir, state->box_rel, state->box, TRUE);
 445     }
 446 }
 447
 448 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
 449 {
 450     if (PRESERVE_SHAPE(*ir))
 451     {
 452         do_box_rel(ir, box_rel, b, FALSE);
 453     }
 454 }
 455
 456 real max_cutoff(real cutoff1, real cutoff2)
 457 {
 458     if (cutoff1 == 0 || cutoff2 == 0)
 459     {
 460         return 0;
 461     }
 462     else
 463     {
 464         return max(cutoff1, cutoff2);
 465     }
 466 }
 467
 468 void init_df_history(df_history_t *dfhist, int nlambda)
 469 {
 470     int i;
 471
 472     dfhist->nlambda  = nlambda;
 473     dfhist->bEquil   = 0;
 474     dfhist->wl_delta = 0;
 475
 476     if (nlambda > 0)
 477     {
 478         snew(dfhist->sum_weights, dfhist->nlambda);
 479         snew(dfhist->sum_dg, dfhist->nlambda);
 480         snew(dfhist->sum_minvar, dfhist->nlambda);
 481         snew(dfhist->sum_variance, dfhist->nlambda);
 482         snew(dfhist->n_at_lam, dfhist->nlambda);
 483         snew(dfhist->wl_histo, dfhist->nlambda);
 484
 485         /* allocate transition matrices here */
 486         snew(dfhist->Tij, dfhist->nlambda);
 487         snew(dfhist->Tij_empirical, dfhist->nlambda);
 488
 489         /* allocate accumulators for various transition matrix
 490            free energy methods here */
 491         snew(dfhist->accum_p, dfhist->nlambda);
 492         snew(dfhist->accum_m, dfhist->nlambda);
 493         snew(dfhist->accum_p2, dfhist->nlambda);
 494         snew(dfhist->accum_m2, dfhist->nlambda);
 495
 496         for (i = 0; i < dfhist->nlambda; i++)
 497         {
 498             snew(dfhist->Tij[i], dfhist->nlambda);
 499             snew(dfhist->Tij_empirical[i], dfhist->nlambda);
 500             snew((dfhist->accum_p)[i], dfhist->nlambda);
 501             snew((dfhist->accum_m)[i], dfhist->nlambda);
 502             snew((dfhist->accum_p2)[i], dfhist->nlambda);
 503             snew((dfhist->accum_m2)[i], dfhist->nlambda);
 504         }
 505     }
 506 }
 507
 508 extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
 509 {
 510     int i, j;
 511
 512     /* Currently, there should not be any difference in nlambda between the two,
 513        but this is included for completeness for potential later functionality */
 514     df_dest->nlambda  = df_source->nlambda;
 515     df_dest->bEquil   = df_source->bEquil;
 516     df_dest->wl_delta = df_source->wl_delta;
 517
 518     for (i = 0; i < df_dest->nlambda; i++)
 519     {
 520         df_dest->sum_weights[i]  = df_source->sum_weights[i];
 521         df_dest->sum_dg[i]       = df_source->sum_dg[i];
 522         df_dest->sum_minvar[i]   = df_source->sum_minvar[i];
 523         df_dest->sum_variance[i] = df_source->sum_variance[i];
 524         df_dest->n_at_lam[i]     = df_source->n_at_lam[i];
 525         df_dest->wl_histo[i]     = df_source->wl_histo[i];
 526     }
 527
 528     for (i = 0; i < df_dest->nlambda; i++)
 529     {
 530         for (j = 0; j < df_dest->nlambda; j++)
 531         {
 532             df_dest->accum_p[i][j]        = df_source->accum_p[i][j];
 533             df_dest->accum_m[i][j]        = df_source->accum_m[i][j];
 534             df_dest->accum_p2[i][j]       = df_source->accum_p2[i][j];
 535             df_dest->accum_m2[i][j]       = df_source->accum_m2[i][j];
 536             df_dest->Tij[i][j]            = df_source->Tij[i][j];
 537             df_dest->Tij_empirical[i][j]  = df_source->Tij_empirical[i][j];
 538         }
 539     }
 540 }
 541
 542 void done_df_history(df_history_t *dfhist)
 543 {
 544     int i;
 545
 546     if (dfhist->nlambda > 0)
 547     {
 548         sfree(dfhist->n_at_lam);
 549         sfree(dfhist->wl_histo);
 550         sfree(dfhist->sum_weights);
 551         sfree(dfhist->sum_dg);
 552         sfree(dfhist->sum_minvar);
 553         sfree(dfhist->sum_variance);
 554
 555         for (i = 0; i < dfhist->nlambda; i++)
 556         {
 557             sfree(dfhist->Tij[i]);
 558             sfree(dfhist->Tij_empirical[i]);
 559             sfree(dfhist->accum_p[i]);
 560             sfree(dfhist->accum_m[i]);
 561             sfree(dfhist->accum_p2[i]);
 562             sfree(dfhist->accum_m2[i]);
 563         }
 564     }
 565     dfhist->bEquil   = 0;
 566     dfhist->nlambda  = 0;
 567     dfhist->wl_delta = 0;
 568 }