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  *
  16  * GROMACS is distributed in the hope that it will be useful,
  17  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  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
  23  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  24  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  25  *
  26  * If you want to redistribute modifications to GROMACS, please
  27  * consider that scientific software is very special. Version
  28  * control is crucial - bugs must be traceable. We will be happy to
  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 "config.h"
  43
  44 #include <string.h>
  45
  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"
  51
  52 /* The source code in this file should be thread-safe.
  53       Please keep it that way. */
  54
  55 int gmx_int64_to_int(gmx_int64_t step, const char *warn)
  56 {
  57     int i;
  58
  59     i = (int)step;
  60
  61     if (warn != NULL && (step < INT_MIN || step > INT_MAX))
  62     {
  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);
  67     }
  68
  69     return i;
  70 }
  71
  72 void init_inputrec(t_inputrec *ir)
  73 {
  74     memset(ir, 0, (size_t)sizeof(*ir));
  75     snew(ir->fepvals, 1);
  76     snew(ir->expandedvals, 1);
  77     snew(ir->simtempvals, 1);
  78 }
  79
  80 static void done_pull_group(t_pull_group *pgrp)
  81 {
  82     if (pgrp->nat > 0)
  83     {
  84         sfree(pgrp->ind);
  85         sfree(pgrp->ind_loc);
  86         sfree(pgrp->weight);
  87         sfree(pgrp->weight_loc);
  88     }
  89 }
  90
  91 static void done_pull(t_pull *pull)
  92 {
  93     int i;
  94
  95     for (i = 0; i < pull->ngroup+1; i++)
  96     {
  97         done_pull_group(pull->group);
  98         done_pull_group(pull->dyna);
  99     }
 100 }
 101
 102 void done_inputrec(t_inputrec *ir)
 103 {
 104     int m;
 105
 106     for (m = 0; (m < DIM); m++)
 107     {
 108         if (ir->ex[m].a)
 109         {
 110             sfree(ir->ex[m].a);
 111         }
 112         if (ir->ex[m].phi)
 113         {
 114             sfree(ir->ex[m].phi);
 115         }
 116         if (ir->et[m].a)
 117         {
 118             sfree(ir->et[m].a);
 119         }
 120         if (ir->et[m].phi)
 121         {
 122             sfree(ir->et[m].phi);
 123         }
 124     }
 125
 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);
 133     sfree(ir->opts.acc);
 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);
 139     sfree(ir->opts.bSH);
 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);
 146     sfree(ir->opts.bTS);
 147
 148     if (ir->pull)
 149     {
 150         done_pull(ir->pull);
 151         sfree(ir->pull);
 152     }
 153 }
 154
 155 static void zero_history(history_t *hist)
 156 {
 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;
 163 }
 164
 165 static void zero_ekinstate(ekinstate_t *eks)
 166 {
 167     eks->ekin_n         = 0;
 168     eks->ekinh          = NULL;
 169     eks->ekinf          = NULL;
 170     eks->ekinh_old      = NULL;
 171     eks->ekinscalef_nhc = NULL;
 172     eks->ekinscaleh_nhc = NULL;
 173     eks->vscale_nhc     = NULL;
 174     eks->dekindl        = 0;
 175     eks->mvcos          = 0;
 176 }
 177
 178 static void init_swapstate(swapstate_t *swapstate)
 179 {
 180     int ii, ic;
 181
 182     swapstate->eSwapCoords = 0;
 183     swapstate->nAverage    = 0;
 184
 185     /* Ion/water position swapping */
 186     for (ic = 0; ic < eCompNR; ic++)
 187     {
 188         for (ii = 0; ii < eIonNR; ii++)
 189         {
 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;
 198         }
 199     }
 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;
 211 }
 212
 213 void init_energyhistory(energyhistory_t * enerhist)
 214 {
 215     enerhist->nener = 0;
 216
 217     enerhist->ener_ave     = NULL;
 218     enerhist->ener_sum     = NULL;
 219     enerhist->ener_sum_sim = NULL;
 220     enerhist->dht          = NULL;
 221
 222     enerhist->nsteps     = 0;
 223     enerhist->nsum       = 0;
 224     enerhist->nsteps_sim = 0;
 225     enerhist->nsum_sim   = 0;
 226
 227     enerhist->dht = NULL;
 228 }
 229
 230 static void done_delta_h_history(delta_h_history_t *dht)
 231 {
 232     int i;
 233
 234     for (i = 0; i < dht->nndh; i++)
 235     {
 236         sfree(dht->dh[i]);
 237     }
 238     sfree(dht->dh);
 239     sfree(dht->ndh);
 240 }
 241
 242 void done_energyhistory(energyhistory_t * enerhist)
 243 {
 244     sfree(enerhist->ener_ave);
 245     sfree(enerhist->ener_sum);
 246     sfree(enerhist->ener_sum_sim);
 247
 248     if (enerhist->dht != NULL)
 249     {
 250         done_delta_h_history(enerhist->dht);
 251         sfree(enerhist->dht);
 252     }
 253 }
 254
 255 void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
 256 {
 257     int i, j;
 258
 259     state->ngtc          = ngtc;
 260     state->nnhpres       = nnhpres;
 261     state->nhchainlength = nhchainlength;
 262     if (state->ngtc > 0)
 263     {
 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++)
 268         {
 269             for (j = 0; j < state->nhchainlength; j++)
 270             {
 271                 state->nosehoover_xi[i*state->nhchainlength + j]   = 0.0;
 272                 state->nosehoover_vxi[i*state->nhchainlength + j]  = 0.0;
 273             }
 274         }
 275         for (i = 0; i < state->ngtc; i++)
 276         {
 277             state->therm_integral[i]  = 0.0;
 278         }
 279     }
 280     else
 281     {
 282         state->nosehoover_xi  = NULL;
 283         state->nosehoover_vxi = NULL;
 284         state->therm_integral = NULL;
 285     }
 286
 287     if (state->nnhpres > 0)
 288     {
 289         snew(state->nhpres_xi, state->nhchainlength*nnhpres);
 290         snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
 291         for (i = 0; i < nnhpres; i++)
 292         {
 293             for (j = 0; j < state->nhchainlength; j++)
 294             {
 295                 state->nhpres_xi[i*nhchainlength + j]   = 0.0;
 296                 state->nhpres_vxi[i*nhchainlength + j]  = 0.0;
 297             }
 298         }
 299     }
 300     else
 301     {
 302         state->nhpres_xi  = NULL;
 303         state->nhpres_vxi = NULL;
 304     }
 305 }
 306
 307
 308 void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
 309 {
 310     int i;
 311
 312     state->natoms = natoms;
 313     state->flags  = 0;
 314     state->lambda = 0;
 315     snew(state->lambda, efptNR);
 316     for (i = 0; i < efptNR; i++)
 317     {
 318         state->lambda[i] = 0;
 319     }
 320     state->veta   = 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)
 330     {
 331         snew(state->x, state->nalloc);
 332         snew(state->v, state->nalloc);
 333     }
 334     else
 335     {
 336         state->x = NULL;
 337         state->v = NULL;
 338     }
 339     state->sd_X = NULL;
 340     state->cg_p = NULL;
 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;
 348     state->cg_gl           = NULL;
 349     state->cg_gl_nalloc    = 0;
 350 }
 351
 352 void done_state(t_state *state)
 353 {
 354     if (state->x)
 355     {
 356         sfree(state->x);
 357     }
 358     if (state->v)
 359     {
 360         sfree(state->v);
 361     }
 362     if (state->sd_X)
 363     {
 364         sfree(state->sd_X);
 365     }
 366     if (state->cg_p)
 367     {
 368         sfree(state->cg_p);
 369     }
 370     state->nalloc = 0;
 371     if (state->cg_gl)
 372     {
 373         sfree(state->cg_gl);
 374     }
 375     state->cg_gl_nalloc = 0;
 376     if (state->lambda)
 377     {
 378         sfree(state->lambda);
 379     }
 380     if (state->ngtc > 0)
 381     {
 382         sfree(state->nosehoover_xi);
 383         sfree(state->nosehoover_vxi);
 384         sfree(state->therm_integral);
 385     }
 386 }
 387
 388 t_state *serial_init_local_state(t_state *state_global)
 389 {
 390     int      i;
 391     t_state *state_local;
 392
 393     snew(state_local, 1);
 394
 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++)
 400     {
 401         state_local->lambda[i] = state_global->lambda[i];
 402     }
 403
 404     return state_local;
 405 }
 406
 407 static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
 408 {
 409     int d, d2;
 410
 411     for (d = YY; d <= ZZ; d++)
 412     {
 413         for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
 414         {
 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.
 418              */
 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)))
 422             {
 423                 if (bInit)
 424                 {
 425                     box_rel[d][d2] = b[d][d2]/b[XX][XX];
 426                 }
 427                 else
 428                 {
 429                     b[d][d2] = b[XX][XX]*box_rel[d][d2];
 430                 }
 431             }
 432         }
 433     }
 434 }
 435
 436 void set_box_rel(t_inputrec *ir, t_state *state)
 437 {
 438     /* Make sure the box obeys the restrictions before we fix the ratios */
 439     correct_box(NULL, 0, state->box, NULL);
 440
 441     clear_mat(state->box_rel);
 442
 443     if (PRESERVE_SHAPE(*ir))
 444     {
 445         do_box_rel(ir, state->box_rel, state->box, TRUE);
 446     }
 447 }
 448
 449 void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
 450 {
 451     if (PRESERVE_SHAPE(*ir))
 452     {
 453         do_box_rel(ir, box_rel, b, FALSE);
 454     }
 455 }
 456
 457 real max_cutoff(real cutoff1, real cutoff2)
 458 {
 459     if (cutoff1 == 0 || cutoff2 == 0)
 460     {
 461         return 0;
 462     }
 463     else
 464     {
 465         return max(cutoff1, cutoff2);
 466     }
 467 }
 468
 469 void init_df_history(df_history_t *dfhist, int nlambda)
 470 {
 471     int i;
 472
 473     dfhist->nlambda  = nlambda;
 474     dfhist->bEquil   = 0;
 475     dfhist->wl_delta = 0;
 476
 477     if (nlambda > 0)
 478     {
 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);
 485
 486         /* allocate transition matrices here */
 487         snew(dfhist->Tij, dfhist->nlambda);
 488         snew(dfhist->Tij_empirical, dfhist->nlambda);
 489
 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);
 496
 497         for (i = 0; i < dfhist->nlambda; i++)
 498         {
 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);
 505         }
 506     }
 507 }
 508
 509 extern void copy_df_history(df_history_t *df_dest, df_history_t *df_source)
 510 {
 511     int i, j;
 512
 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;
 518
 519     for (i = 0; i < df_dest->nlambda; i++)
 520     {
 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];
 527     }
 528
 529     for (i = 0; i < df_dest->nlambda; i++)
 530     {
 531         for (j = 0; j < df_dest->nlambda; j++)
 532         {
 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];
 539         }
 540     }
 541 }
 542
 543 void done_df_history(df_history_t *dfhist)
 544 {
 545     int i;
 546
 547     if (dfhist->nlambda > 0)
 548     {
 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);
 555
 556         for (i = 0; i < dfhist->nlambda; i++)
 557         {
 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]);
 564         }
 565     }
 566     dfhist->bEquil   = 0;
 567     dfhist->nlambda  = 0;
 568     dfhist->wl_delta = 0;
 569 }