src/gromacs/gmxlib/disre.c

   1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
   2  *
   3  *
   4  *                This source code is part of
   5  *
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   7  *
   8  *          GROningen MAchine for Chemical Simulations
   9  *
  10  *                        VERSION 3.2.0
  11  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  12  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  13  * Copyright (c) 2001-2004, The GROMACS development team,
  14  * check out http://www.gromacs.org for more information.
  15
  16  * This program is free software; you can redistribute it and/or
  17  * modify it under the terms of the GNU General Public License
  18  * as published by the Free Software Foundation; either version 2
  19  * of the License, or (at your option) any later version.
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  36 /* This file is completely threadsafe - keep it that way! */
  37 #ifdef HAVE_CONFIG_H
  38 #include <config.h>
  39 #endif
  40
  41 #include <math.h>
  42 #include "typedefs.h"
  43 #include "sysstuff.h"
  44 #include "smalloc.h"
  45 #include "macros.h"
  46 #include "vec.h"
  47 #include "futil.h"
  48 #include "xvgr.h"
  49 #include "gmx_fatal.h"
  50 #include "bondf.h"
  51 #include "copyrite.h"
  52 #include "disre.h"
  53 #include "main.h"
  54 #include "mtop_util.h"
  55
  56 void init_disres(FILE *fplog,const gmx_mtop_t *mtop,
  57                  t_inputrec *ir,const t_commrec *cr,gmx_bool bPartDecomp,
  58                  t_fcdata *fcd,t_state *state)
  59 {
  60     int          fa,nmol,i,npair,np;
  61     t_iparams    *ip;
  62     t_disresdata *dd;
  63     history_t    *hist;
  64     gmx_mtop_ilistloop_t iloop;
  65     t_ilist      *il;
  66     char         *ptr;
  67
  68     dd = &(fcd->disres);
  69
  70     if (gmx_mtop_ftype_count(mtop,F_DISRES) == 0)
  71     {
  72         dd->nres = 0;
  73
  74         return;
  75     }
  76
  77     if (fplog)
  78     {
  79         fprintf(fplog,"Initializing the distance restraints\n");
  80     }
  81
  82
  83     if (ir->eDisre == edrEnsemble)
  84     {
  85         gmx_fatal(FARGS,"Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
  86     }
  87
  88     dd->dr_weighting = ir->eDisreWeighting;
  89     dd->dr_fc        = ir->dr_fc;
  90     if (EI_DYNAMICS(ir->eI))
  91     {
  92         dd->dr_tau   = ir->dr_tau;
  93     }
  94     else
  95     {
  96         dd->dr_tau   = 0.0;
  97     }
  98     if (dd->dr_tau == 0.0)
  99     {
 100         dd->dr_bMixed = FALSE;
 101         dd->ETerm = 0.0;
 102     }
 103     else
 104     {
 105         dd->dr_bMixed = ir->bDisreMixed;
 106         dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
 107     }
 108     dd->ETerm1        = 1.0 - dd->ETerm;
 109
 110     ip = mtop->ffparams.iparams;
 111
 112     dd->nres  = 0;
 113     dd->npair = 0;
 114     iloop = gmx_mtop_ilistloop_init(mtop);
 115     while (gmx_mtop_ilistloop_next(iloop,&il,&nmol)) {
 116         np = 0;
 117         for(fa=0; fa<il[F_DISRES].nr; fa+=3)
 118         {
 119             np++;
 120             npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
 121             if (np == npair)
 122             {
 123                 dd->nres  += (ir->eDisre==edrEnsemble ? 1 : nmol)*npair;
 124                 dd->npair += nmol*npair;
 125                 np = 0;
 126             }
 127         }
 128     }
 129
 130     if (cr && PAR(cr) && !bPartDecomp)
 131     {
 132         /* Temporary check, will be removed when disre is implemented with DD */
 133         const char *notestr="NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)";
 134
 135         if (MASTER(cr))
 136             fprintf(stderr,"\n%s\n\n",notestr);
 137         if (fplog)
 138             fprintf(fplog,"%s\n",notestr);
 139
 140         if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
 141             dd->nres != dd->npair)
 142         {
 143             gmx_fatal(FARGS,"Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
 144         }
 145         if (ir->nstdisreout != 0)
 146         {
 147             if (fplog)
 148             {
 149                 fprintf(fplog,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
 150             }
 151             if (MASTER(cr))
 152             {
 153                 fprintf(stderr,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
 154             }
 155             ir->nstdisreout = 0;
 156         }
 157     }
 158
 159     snew(dd->rt,dd->npair);
 160
 161     if (dd->dr_tau != 0.0)
 162     {
 163         hist = &state->hist;
 164         /* Set the "history lack" factor to 1 */
 165         state->flags |= (1<<estDISRE_INITF);
 166         hist->disre_initf = 1.0;
 167         /* Allocate space for the r^-3 time averages */
 168         state->flags |= (1<<estDISRE_RM3TAV);
 169         hist->ndisrepairs = dd->npair;
 170         snew(hist->disre_rm3tav,hist->ndisrepairs);
 171     }
 172     /* Allocate space for a copy of rm3tav,
 173      * so we can call do_force without modifying the state.
 174      */
 175     snew(dd->rm3tav,dd->npair);
 176
 177     /* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
 178      * averaged over the processors in one call (in calc_disre_R_6)
 179      */
 180     snew(dd->Rt_6,2*dd->nres);
 181     dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
 182
 183     ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
 184     if (cr && cr->ms != NULL && ptr != NULL)
 185     {
 186 #ifdef GMX_MPI
 187         dd->nsystems = 0;
 188         sscanf(ptr,"%d",&dd->nsystems);
 189         if (fplog)
 190         {
 191             fprintf(fplog,"Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n",dd->nsystems);
 192         }
 193         check_multi_int(fplog,cr->ms,dd->nsystems,
 194                         "the number of systems per ensemble");
 195         if (dd->nsystems <= 0 ||  cr->ms->nsim % dd->nsystems != 0)
 196         {
 197             gmx_fatal(FARGS,"The number of systems %d is not divisible by the number of systems per ensemble %d\n",cr->ms->nsim,dd->nsystems);
 198         }
 199         /* Split the inter-master communicator into different ensembles */
 200         MPI_Comm_split(cr->ms->mpi_comm_masters,
 201                        cr->ms->sim/dd->nsystems,
 202                        cr->ms->sim,
 203                        &dd->mpi_comm_ensemble);
 204         if (fplog)
 205         {
 206             fprintf(fplog,"Our ensemble consists of systems:");
 207             for(i=0; i<dd->nsystems; i++)
 208             {
 209                 fprintf(fplog," %d",
 210                         (cr->ms->sim/dd->nsystems)*dd->nsystems+i);
 211             }
 212             fprintf(fplog,"\n");
 213             }
 214         snew(dd->Rtl_6,dd->nres);
 215 #endif
 216     }
 217     else
 218     {
 219         dd->nsystems = 1;
 220         dd->Rtl_6 = dd->Rt_6;
 221     }
 222
 223     if (dd->npair > 0)
 224     {
 225         if (fplog) {
 226             fprintf(fplog,"There are %d distance restraints involving %d atom pairs\n",dd->nres,dd->npair);
 227         }
 228         if (cr && cr->ms)
 229         {
 230             check_multi_int(fplog,cr->ms,fcd->disres.nres,
 231                             "the number of distance restraints");
 232         }
 233         please_cite(fplog,"Tropp80a");
 234         please_cite(fplog,"Torda89a");
 235     }
 236 }
 237
 238 void calc_disres_R_6(const gmx_multisim_t *ms,
 239                      int nfa,const t_iatom forceatoms[],const t_iparams ip[],
 240                      const rvec x[],const t_pbc *pbc,
 241                      t_fcdata *fcd,history_t *hist)
 242 {
 243     atom_id     ai,aj;
 244     int         fa,res,i,pair,ki,kj,m;
 245     int         type,npair,np;
 246     rvec        dx;
 247     real        *rt,*rm3tav,*Rtl_6,*Rt_6,*Rtav_6;
 248     real        rt_1,rt_3,rt2;
 249     ivec        it,jt,dt;
 250     t_disresdata *dd;
 251     real        ETerm,ETerm1,cf1=0,cf2=0,invn=0;
 252     gmx_bool        bTav;
 253
 254     dd = &(fcd->disres);
 255     bTav         = (dd->dr_tau != 0);
 256     ETerm        = dd->ETerm;
 257     ETerm1       = dd->ETerm1;
 258     rt           = dd->rt;
 259     rm3tav       = dd->rm3tav;
 260     Rtl_6        = dd->Rtl_6;
 261     Rt_6         = dd->Rt_6;
 262     Rtav_6       = dd->Rtav_6;
 263
 264     if (bTav)
 265     {
 266         /* scaling factor to smoothly turn on the restraint forces *
 267          * when using time averaging                               */
 268         dd->exp_min_t_tau = hist->disre_initf*ETerm;
 269
 270         cf1 = dd->exp_min_t_tau;
 271         cf2 = 1.0/(1.0 - dd->exp_min_t_tau);
 272     }
 273
 274     if (dd->nsystems > 1)
 275     {
 276         invn = 1.0/dd->nsystems;
 277     }
 278
 279     /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
 280      * the total number of atoms pairs is nfa/3                          */
 281     res = 0;
 282     fa  = 0;
 283     while (fa < nfa)
 284     {
 285         type  = forceatoms[fa];
 286         npair = ip[type].disres.npair;
 287
 288         Rtav_6[res] = 0.0;
 289         Rt_6[res]   = 0.0;
 290
 291         /* Loop over the atom pairs of 'this' restraint */
 292         np = 0;
 293         while (fa < nfa && np < npair)
 294         {
 295             pair = fa/3;
 296             ai   = forceatoms[fa+1];
 297             aj   = forceatoms[fa+2];
 298
 299             if (pbc)
 300             {
 301                 pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
 302             }
 303             else
 304             {
 305                 rvec_sub(x[ai],x[aj],dx);
 306             }
 307             rt2  = iprod(dx,dx);
 308             rt_1 = gmx_invsqrt(rt2);
 309             rt_3 = rt_1*rt_1*rt_1;
 310
 311             rt[pair]         = sqrt(rt2);
 312             if (bTav)
 313             {
 314                 /* Here we update rm3tav in t_fcdata using the data
 315                  * in history_t.
 316                  * Thus the results stay correct when this routine
 317                  * is called multiple times.
 318                  */
 319                 rm3tav[pair] = cf2*((ETerm - cf1)*hist->disre_rm3tav[pair] +
 320                                     ETerm1*rt_3);
 321             }
 322             else
 323             {
 324                 rm3tav[pair] = rt_3;
 325             }
 326
 327             Rt_6[res]       += rt_3*rt_3;
 328             Rtav_6[res]     += rm3tav[pair]*rm3tav[pair];
 329
 330             fa += 3;
 331             np++;
 332         }
 333         if (dd->nsystems > 1)
 334         {
 335             Rtl_6[res]   = Rt_6[res];
 336             Rt_6[res]   *= invn;
 337             Rtav_6[res] *= invn;
 338         }
 339
 340         res++;
 341     }
 342
 343 #ifdef GMX_MPI
 344     if (dd->nsystems > 1)
 345     {
 346         gmx_sum_comm(2*dd->nres,Rt_6,dd->mpi_comm_ensemble);
 347     }
 348 #endif
 349 }
 350
 351 real ta_disres(int nfa,const t_iatom forceatoms[],const t_iparams ip[],
 352                const rvec x[],rvec f[],rvec fshift[],
 353                const t_pbc *pbc,const t_graph *g,
 354                real lambda,real *dvdlambda,
 355                const t_mdatoms *md,t_fcdata *fcd,
 356                int *global_atom_index)
 357 {
 358     const real sixth=1.0/6.0;
 359     const real seven_three=7.0/3.0;
 360
 361     atom_id     ai,aj;
 362     int         fa,res,npair,p,pair,ki=CENTRAL,m;
 363     int         type;
 364     rvec        dx;
 365     real        weight_rt_1;
 366     real        smooth_fc,Rt,Rtav,rt2,*Rtl_6,*Rt_6,*Rtav_6;
 367     real        k0,f_scal=0,fmax_scal,fk_scal,fij;
 368     real        tav_viol,instant_viol,mixed_viol,violtot,vtot;
 369     real        tav_viol_Rtav7,instant_viol_Rtav7;
 370     real        up1,up2,low;
 371     gmx_bool        bConservative,bMixed,bViolation;
 372     ivec        it,jt,dt;
 373     t_disresdata *dd;
 374     int         dr_weighting;
 375     gmx_bool        dr_bMixed;
 376
 377     dd = &(fcd->disres);
 378     dr_weighting = dd->dr_weighting;
 379     dr_bMixed    = dd->dr_bMixed;
 380     Rtl_6        = dd->Rtl_6;
 381     Rt_6         = dd->Rt_6;
 382     Rtav_6       = dd->Rtav_6;
 383
 384     tav_viol=instant_viol=mixed_viol=tav_viol_Rtav7=instant_viol_Rtav7=0;
 385
 386     smooth_fc = dd->dr_fc;
 387     if (dd->dr_tau != 0)
 388     {
 389         /* scaling factor to smoothly turn on the restraint forces *
 390          * when using time averaging                               */
 391         smooth_fc *= (1.0 - dd->exp_min_t_tau);
 392     }
 393
 394     violtot = 0;
 395     vtot    = 0;
 396
 397     /* 'loop' over all atom pairs (pair_nr=fa/3) involved in restraints, *
 398      * the total number of atoms pairs is nfa/3                          */
 399     res  = 0;
 400     fa   = 0;
 401     while (fa < nfa)
 402     {
 403         type  = forceatoms[fa];
 404         /* Take action depending on restraint, calculate scalar force */
 405         npair = ip[type].disres.npair;
 406         up1   = ip[type].disres.up1;
 407         up2   = ip[type].disres.up2;
 408         low   = ip[type].disres.low;
 409         k0    = smooth_fc*ip[type].disres.kfac;
 410
 411         /* save some flops when there is only one pair */
 412         if (ip[type].disres.type != 2)
 413         {
 414             bConservative = (dr_weighting == edrwConservative) && (npair > 1);
 415             bMixed        = dr_bMixed;
 416             Rt   = pow(Rt_6[res],-sixth);
 417             Rtav = pow(Rtav_6[res],-sixth);
 418         }
 419         else
 420         {
 421             /* When rtype=2 use instantaneous not ensemble avereged distance */
 422             bConservative = (npair > 1);
 423             bMixed        = FALSE;
 424             Rt   = pow(Rtl_6[res],-sixth);
 425             Rtav = Rt;
 426         }
 427
 428         if (Rtav > up1)
 429         {
 430             bViolation = TRUE;
 431             tav_viol = Rtav - up1;
 432         }
 433         else if (Rtav < low)
 434         {
 435             bViolation = TRUE;
 436             tav_viol = Rtav - low;
 437         }
 438         else
 439         {
 440             bViolation = FALSE;
 441         }
 442
 443         if (bViolation)
 444         {
 445             /* NOTE:
 446              * there is no real potential when time averaging is applied
 447              */
 448             vtot += 0.5*k0*sqr(tav_viol);
 449             if (1/vtot == 0)
 450             {
 451                 printf("vtot is inf: %f\n",vtot);
 452             }
 453             if (!bMixed)
 454             {
 455                 f_scal   = -k0*tav_viol;
 456                 violtot += fabs(tav_viol);
 457             }
 458             else
 459             {
 460                 if (Rt > up1)
 461                 {
 462                     if (tav_viol > 0)
 463                     {
 464                         instant_viol = Rt - up1;
 465                     }
 466                     else
 467                     {
 468                         bViolation = FALSE;
 469                     }
 470                 }
 471                 else if (Rt < low)
 472                 {
 473                     if (tav_viol < 0)
 474                     {
 475                         instant_viol = Rt - low;
 476                     }
 477                     else
 478                     {
 479                         bViolation = FALSE;
 480                     }
 481                 }
 482                 else
 483                 {
 484                     bViolation = FALSE;
 485                 }
 486                 if (bViolation)
 487                 {
 488                     mixed_viol = sqrt(tav_viol*instant_viol);
 489                     f_scal     = -k0*mixed_viol;
 490                     violtot   += mixed_viol;
 491                 }
 492             }
 493         }
 494
 495         if (bViolation)
 496         {
 497             fmax_scal = -k0*(up2-up1);
 498             /* Correct the force for the number of restraints */
 499             if (bConservative)
 500             {
 501                 f_scal  = max(f_scal,fmax_scal);
 502                 if (!bMixed)
 503                 {
 504                     f_scal *= Rtav/Rtav_6[res];
 505                 }
 506                 else
 507                 {
 508                     f_scal /= 2*mixed_viol;
 509                     tav_viol_Rtav7     = tav_viol*Rtav/Rtav_6[res];
 510                     instant_viol_Rtav7 = instant_viol*Rt/Rt_6[res];
 511                 }
 512             }
 513             else
 514             {
 515                 f_scal /= (real)npair;
 516                 f_scal  = max(f_scal,fmax_scal);
 517             }
 518
 519             /* Exert the force ... */
 520
 521             /* Loop over the atom pairs of 'this' restraint */
 522             for(p=0; p<npair; p++)
 523             {
 524                 pair = fa/3;
 525                 ai   = forceatoms[fa+1];
 526                 aj   = forceatoms[fa+2];
 527
 528                 if (pbc)
 529                 {
 530                     ki = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
 531                 }
 532                 else
 533                 {
 534                     rvec_sub(x[ai],x[aj],dx);
 535                 }
 536                 rt2 = iprod(dx,dx);
 537
 538                 weight_rt_1 = gmx_invsqrt(rt2);
 539
 540                 if (bConservative)
 541                 {
 542                     if (!dr_bMixed)
 543                     {
 544                         weight_rt_1 *= pow(dd->rm3tav[pair],seven_three);
 545                     }
 546                     else
 547                     {
 548                         weight_rt_1 *= tav_viol_Rtav7*pow(dd->rm3tav[pair],seven_three)+
 549                             instant_viol_Rtav7*pow(dd->rt[pair],-7);
 550                     }
 551                 }
 552
 553                 fk_scal  = f_scal*weight_rt_1;
 554
 555                 if (g)
 556                 {
 557                     ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
 558                     ki=IVEC2IS(dt);
 559                 }
 560
 561                 for(m=0; m<DIM; m++)
 562                 {
 563                     fij            = fk_scal*dx[m];
 564
 565                     f[ai][m]      += fij;
 566                     f[aj][m]      -= fij;
 567                     fshift[ki][m] += fij;
 568                     fshift[CENTRAL][m] -= fij;
 569                 }
 570                 fa += 3;
 571             }
 572         }
 573         else
 574         {
 575             /* No violation so force and potential contributions */
 576             fa += 3*npair;
 577         }
 578         res++;
 579     }
 580
 581     dd->sumviol = violtot;
 582
 583     /* Return energy */
 584     return vtot;
 585 }
 586
 587 void update_disres_history(t_fcdata *fcd,history_t *hist)
 588 {
 589     t_disresdata *dd;
 590     int pair;
 591
 592     dd = &(fcd->disres);
 593     if (dd->dr_tau != 0)
 594     {
 595         /* Copy the new time averages that have been calculated
 596          * in calc_disres_R_6.
 597          */
 598         hist->disre_initf = dd->exp_min_t_tau;
 599         for(pair=0; pair<dd->npair; pair++)
 600         {
 601             hist->disre_rm3tav[pair] = dd->rm3tav[pair];
 602         }
 603     }
 604 }