src/mdlib/sim_util.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  *
   6  *                 G   R   O   M   A   C   S
   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.
  20  *
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  26  * files - if they are missing, get the official version at www.gromacs.org.
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  35  */
  36 #ifdef HAVE_CONFIG_H
  37 #include <config.h>
  38 #endif
  39
  40 #ifdef GMX_CRAY_XT3
  41 #include<catamount/dclock.h>
  42 #endif
  43
  44
  45 #include <stdio.h>
  46 #include <time.h>
  47 #ifdef HAVE_SYS_TIME_H
  48 #include <sys/time.h>
  49 #endif
  50 #include <math.h>
  51 #include "typedefs.h"
  52 #include "string2.h"
  53 #include "gmxfio.h"
  54 #include "smalloc.h"
  55 #include "names.h"
  56 #include "confio.h"
  57 #include "mvdata.h"
  58 #include "txtdump.h"
  59 #include "pbc.h"
  60 #include "chargegroup.h"
  61 #include "vec.h"
  62 #include "time.h"
  63 #include "nrnb.h"
  64 #include "mshift.h"
  65 #include "mdrun.h"
  66 #include "update.h"
  67 #include "physics.h"
  68 #include "main.h"
  69 #include "mdatoms.h"
  70 #include "force.h"
  71 #include "bondf.h"
  72 #include "pme.h"
  73 #include "pppm.h"
  74 #include "disre.h"
  75 #include "orires.h"
  76 #include "network.h"
  77 #include "calcmu.h"
  78 #include "constr.h"
  79 #include "xvgr.h"
  80 #include "trnio.h"
  81 #include "xtcio.h"
  82 #include "copyrite.h"
  83
  84 #include "mpelogging.h"
  85 #include "domdec.h"
  86 #include "partdec.h"
  87 #include "gmx_wallcycle.h"
  88 #include "genborn.h"
  89
  90 #ifdef GMX_LIB_MPI
  91 #include <mpi.h>
  92 #endif
  93 #ifdef GMX_THREADS
  94 #include "tmpi.h"
  95 #endif
  96
  97 #include "qmmm.h"
  98
  99 #if 0
 100 typedef struct gmx_timeprint {
 101
 102 } t_gmx_timeprint;
 103 #endif
 104
 105 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
 106 char *
 107 gmx_ctime_r(const time_t *clock,char *buf, int n);
 108
 109
 110 double
 111 gmx_gettime()
 112 {
 113 #ifdef HAVE_GETTIMEOFDAY
 114         struct timeval t;
 115         struct timezone tz = { 0,0 };
 116         double seconds;
 117
 118         gettimeofday(&t,&tz);
 119
 120         seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;
 121
 122         return seconds;
 123 #else
 124         double  seconds;
 125
 126         seconds = time(NULL);
 127
 128         return seconds;
 129 #endif
 130 }
 131
 132
 133 #define difftime(end,start) ((double)(end)-(double)(start))
 134
 135 void print_time(FILE *out,gmx_runtime_t *runtime,gmx_large_int_t step,
 136                 t_inputrec *ir, t_commrec *cr)
 137 {
 138     time_t finish;
 139     char   timebuf[STRLEN];
 140     double dt;
 141     char buf[48];
 142
 143 #ifndef GMX_THREADS
 144     if (!PAR(cr))
 145 #endif
 146     {
 147         fprintf(out,"\r");
 148     }
 149     fprintf(out,"step %s",gmx_step_str(step,buf));
 150     if ((step >= ir->nstlist))
 151     {
 152         if ((ir->nstlist == 0) || ((step % ir->nstlist) == 0))
 153         {
 154             /* We have done a full cycle let's update time_per_step */
 155             runtime->last = gmx_gettime();
 156             dt = difftime(runtime->last,runtime->real);
 157             runtime->time_per_step = dt/(step - ir->init_step + 1);
 158         }
 159         dt = (ir->nsteps + ir->init_step - step)*runtime->time_per_step;
 160
 161         if (ir->nsteps >= 0)
 162         {
 163             if (dt >= 300)
 164             {
 165                 finish = (time_t) (runtime->last + dt);
 166                 gmx_ctime_r(&finish,timebuf,STRLEN);
 167                 sprintf(buf,"%s",timebuf);
 168                 buf[strlen(buf)-1]='\0';
 169                 fprintf(out,", will finish %s",buf);
 170             }
 171             else
 172                 fprintf(out,", remaining runtime: %5d s          ",(int)dt);
 173         }
 174         else
 175         {
 176             fprintf(out," performance: %.1f ns/day    ",
 177                     ir->delta_t/1000*24*60*60/runtime->time_per_step);
 178         }
 179     }
 180 #ifndef GMX_THREADS
 181     if (PAR(cr))
 182     {
 183         fprintf(out,"\n");
 184     }
 185 #endif
 186
 187     fflush(out);
 188 }
 189
 190 #ifdef NO_CLOCK
 191 #define clock() -1
 192 #endif
 193
 194 static double set_proctime(gmx_runtime_t *runtime)
 195 {
 196     double diff;
 197 #ifdef GMX_CRAY_XT3
 198     double prev;
 199
 200     prev = runtime->proc;
 201     runtime->proc = dclock();
 202
 203     diff = runtime->proc - prev;
 204 #else
 205     clock_t prev;
 206
 207     prev = runtime->proc;
 208     runtime->proc = clock();
 209
 210     diff = (double)(runtime->proc - prev)/(double)CLOCKS_PER_SEC;
 211 #endif
 212     if (diff < 0)
 213     {
 214         /* The counter has probably looped, ignore this data */
 215         diff = 0;
 216     }
 217
 218     return diff;
 219 }
 220
 221 void runtime_start(gmx_runtime_t *runtime)
 222 {
 223     runtime->real = gmx_gettime();
 224     runtime->proc          = 0;
 225     set_proctime(runtime);
 226     runtime->realtime      = 0;
 227     runtime->proctime      = 0;
 228     runtime->last          = 0;
 229     runtime->time_per_step = 0;
 230 }
 231
 232 void runtime_end(gmx_runtime_t *runtime)
 233 {
 234     double now;
 235
 236     now = gmx_gettime();
 237
 238     runtime->proctime += set_proctime(runtime);
 239     runtime->realtime  = now - runtime->real;
 240     runtime->real      = now;
 241 }
 242
 243 void runtime_upd_proc(gmx_runtime_t *runtime)
 244 {
 245     runtime->proctime += set_proctime(runtime);
 246 }
 247
 248 void print_date_and_time(FILE *fplog,int nodeid,const char *title,
 249                          const gmx_runtime_t *runtime)
 250 {
 251     int i;
 252     char timebuf[STRLEN];
 253     char time_string[STRLEN];
 254     time_t tmptime;
 255
 256     if (fplog)
 257     {
 258         if (runtime != NULL)
 259         {
 260             tmptime = (time_t) runtime->real;
 261             gmx_ctime_r(&tmptime,timebuf,STRLEN);
 262         }
 263         else
 264         {
 265             tmptime = (time_t) gmx_gettime();
 266             gmx_ctime_r(&tmptime,timebuf,STRLEN);
 267         }
 268         for(i=0; timebuf[i]>=' '; i++)
 269         {
 270             time_string[i]=timebuf[i];
 271         }
 272         time_string[i]='\0';
 273
 274         fprintf(fplog,"%s on node %d %s\n",title,nodeid,time_string);
 275     }
 276 }
 277
 278 static void sum_forces(int start,int end,rvec f[],rvec flr[])
 279 {
 280   int i;
 281
 282   if (gmx_debug_at) {
 283     pr_rvecs(debug,0,"fsr",f+start,end-start);
 284     pr_rvecs(debug,0,"flr",flr+start,end-start);
 285   }
 286   for(i=start; (i<end); i++)
 287     rvec_inc(f[i],flr[i]);
 288 }
 289
 290 /*
 291  * calc_f_el calculates forces due to an electric field.
 292  *
 293  * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
 294  *
 295  * Et[] contains the parameters for the time dependent
 296  * part of the field (not yet used).
 297  * Ex[] contains the parameters for
 298  * the spatial dependent part of the field. You can have cool periodic
 299  * fields in principle, but only a constant field is supported
 300  * now.
 301  * The function should return the energy due to the electric field
 302  * (if any) but for now returns 0.
 303  *
 304  * WARNING:
 305  * There can be problems with the virial.
 306  * Since the field is not self-consistent this is unavoidable.
 307  * For neutral molecules the virial is correct within this approximation.
 308  * For neutral systems with many charged molecules the error is small.
 309  * But for systems with a net charge or a few charged molecules
 310  * the error can be significant when the field is high.
 311  * Solution: implement a self-consitent electric field into PME.
 312  */
 313 static void calc_f_el(FILE *fp,int  start,int homenr,
 314                       real charge[],rvec x[],rvec f[],
 315                       t_cosines Ex[],t_cosines Et[],double t)
 316 {
 317     rvec Ext;
 318     real t0;
 319     int  i,m;
 320
 321     for(m=0; (m<DIM); m++)
 322     {
 323         if (Et[m].n > 0)
 324         {
 325             if (Et[m].n == 3)
 326             {
 327                 t0 = Et[m].a[1];
 328                 Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
 329             }
 330             else
 331             {
 332                 Ext[m] = cos(Et[m].a[0]*t);
 333             }
 334         }
 335         else
 336         {
 337             Ext[m] = 1.0;
 338         }
 339         if (Ex[m].n > 0)
 340         {
 341             /* Convert the field strength from V/nm to MD-units */
 342             Ext[m] *= Ex[m].a[0]*FIELDFAC;
 343             for(i=start; (i<start+homenr); i++)
 344                 f[i][m] += charge[i]*Ext[m];
 345         }
 346         else
 347         {
 348             Ext[m] = 0;
 349         }
 350     }
 351     if (fp != NULL)
 352     {
 353         fprintf(fp,"%10g  %10g  %10g  %10g #FIELD\n",t,
 354                 Ext[XX]/FIELDFAC,Ext[YY]/FIELDFAC,Ext[ZZ]/FIELDFAC);
 355     }
 356 }
 357
 358 static void calc_virial(FILE *fplog,int start,int homenr,rvec x[],rvec f[],
 359                         tensor vir_part,t_graph *graph,matrix box,
 360                         t_nrnb *nrnb,const t_forcerec *fr,int ePBC)
 361 {
 362   int i,j;
 363   tensor virtest;
 364
 365   /* The short-range virial from surrounding boxes */
 366   clear_mat(vir_part);
 367   calc_vir(fplog,SHIFTS,fr->shift_vec,fr->fshift,vir_part,ePBC==epbcSCREW,box);
 368   inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS);
 369
 370   /* Calculate partial virial, for local atoms only, based on short range.
 371    * Total virial is computed in global_stat, called from do_md
 372    */
 373   f_calc_vir(fplog,start,start+homenr,x,f,vir_part,graph,box);
 374   inc_nrnb(nrnb,eNR_VIRIAL,homenr);
 375
 376   /* Add position restraint contribution */
 377   for(i=0; i<DIM; i++) {
 378     vir_part[i][i] += fr->vir_diag_posres[i];
 379   }
 380
 381   /* Add wall contribution */
 382   for(i=0; i<DIM; i++) {
 383     vir_part[i][ZZ] += fr->vir_wall_z[i];
 384   }
 385
 386   if (debug)
 387     pr_rvecs(debug,0,"vir_part",vir_part,DIM);
 388 }
 389
 390 static void print_large_forces(FILE *fp,t_mdatoms *md,t_commrec *cr,
 391                                gmx_large_int_t step,real pforce,rvec *x,rvec *f)
 392 {
 393   int  i;
 394   real pf2,fn2;
 395   char buf[STEPSTRSIZE];
 396
 397   pf2 = sqr(pforce);
 398   for(i=md->start; i<md->start+md->homenr; i++) {
 399     fn2 = norm2(f[i]);
 400     /* We also catch NAN, if the compiler does not optimize this away. */
 401     if (fn2 >= pf2 || fn2 != fn2) {
 402       fprintf(fp,"step %s  atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
 403               gmx_step_str(step,buf),
 404               ddglatnr(cr->dd,i),x[i][XX],x[i][YY],x[i][ZZ],sqrt(fn2));
 405     }
 406   }
 407 }
 408
 409 void do_force(FILE *fplog,t_commrec *cr,
 410               t_inputrec *inputrec,
 411               gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 412               gmx_localtop_t *top,
 413               gmx_mtop_t *mtop,
 414               gmx_groups_t *groups,
 415               matrix box,rvec x[],history_t *hist,
 416               rvec f[],
 417               tensor vir_force,
 418               t_mdatoms *mdatoms,
 419               gmx_enerdata_t *enerd,t_fcdata *fcd,
 420               real lambda,t_graph *graph,
 421               t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
 422               double t,FILE *field,gmx_edsam_t ed,
 423               gmx_bool bBornRadii,
 424               int flags)
 425 {
 426     int    cg0,cg1,i,j;
 427     int    start,homenr;
 428     double mu[2*DIM];
 429     gmx_bool   bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
 430     gmx_bool   bDoLongRange,bDoForces,bSepLRF;
 431     matrix boxs;
 432     real   e,v,dvdl;
 433     t_pbc  pbc;
 434     float  cycles_ppdpme,cycles_pme,cycles_seppme,cycles_force;
 435
 436     start  = mdatoms->start;
 437     homenr = mdatoms->homenr;
 438
 439     bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));
 440
 441     clear_mat(vir_force);
 442
 443     if (PARTDECOMP(cr))
 444     {
 445         pd_cg_range(cr,&cg0,&cg1);
 446     }
 447     else
 448     {
 449         cg0 = 0;
 450         if (DOMAINDECOMP(cr))
 451         {
 452             cg1 = cr->dd->ncg_tot;
 453         }
 454         else
 455         {
 456             cg1 = top->cgs.nr;
 457         }
 458         if (fr->n_tpi > 0)
 459         {
 460             cg1--;
 461         }
 462     }
 463
 464     bStateChanged = (flags & GMX_FORCE_STATECHANGED);
 465     bNS           = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
 466     bFillGrid     = (bNS && bStateChanged);
 467     bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
 468     bDoLongRange  = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
 469     bDoForces     = (flags & GMX_FORCE_FORCES);
 470     bSepLRF       = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
 471
 472     if (bStateChanged)
 473     {
 474         update_forcerec(fplog,fr,box);
 475
 476         /* Calculate total (local) dipole moment in a temporary common array.
 477          * This makes it possible to sum them over nodes faster.
 478          */
 479         calc_mu(start,homenr,
 480                 x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
 481                 mu,mu+DIM);
 482     }
 483
 484   if (fr->ePBC != epbcNONE) {
 485     /* Compute shift vectors every step,
 486      * because of pressure coupling or box deformation!
 487      */
 488     if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
 489       calc_shifts(box,fr->shift_vec);
 490
 491     if (bCalcCGCM) {
 492       put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box,
 493                                &(top->cgs),x,fr->cg_cm);
 494       inc_nrnb(nrnb,eNR_CGCM,homenr);
 495       inc_nrnb(nrnb,eNR_RESETX,cg1-cg0);
 496     }
 497     else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
 498       unshift_self(graph,box,x);
 499     }
 500   }
 501   else if (bCalcCGCM) {
 502     calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm);
 503     inc_nrnb(nrnb,eNR_CGCM,homenr);
 504   }
 505
 506   if (bCalcCGCM) {
 507     if (PAR(cr)) {
 508       move_cgcm(fplog,cr,fr->cg_cm);
 509     }
 510     if (gmx_debug_at)
 511       pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr);
 512   }
 513
 514 #ifdef GMX_MPI
 515   if (!(cr->duty & DUTY_PME)) {
 516     /* Send particle coordinates to the pme nodes.
 517      * Since this is only implemented for domain decomposition
 518      * and domain decomposition does not use the graph,
 519      * we do not need to worry about shifting.
 520      */
 521
 522     wallcycle_start(wcycle,ewcPP_PMESENDX);
 523     GMX_MPE_LOG(ev_send_coordinates_start);
 524
 525     bBS = (inputrec->nwall == 2);
 526     if (bBS) {
 527       copy_mat(box,boxs);
 528       svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
 529     }
 530
 531     gmx_pme_send_x(cr,bBS ? boxs : box,x,
 532                    mdatoms->nChargePerturbed,lambda,
 533                    ( flags & GMX_FORCE_VIRIAL),step);
 534
 535     GMX_MPE_LOG(ev_send_coordinates_finish);
 536     wallcycle_stop(wcycle,ewcPP_PMESENDX);
 537   }
 538 #endif /* GMX_MPI */
 539
 540     /* Communicate coordinates and sum dipole if necessary */
 541     if (PAR(cr))
 542     {
 543         wallcycle_start(wcycle,ewcMOVEX);
 544         if (DOMAINDECOMP(cr))
 545         {
 546             dd_move_x(cr->dd,box,x);
 547         }
 548         else
 549         {
 550             move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb);
 551         }
 552         /* When we don't need the total dipole we sum it in global_stat */
 553         if (bStateChanged && NEED_MUTOT(*inputrec))
 554         {
 555             gmx_sumd(2*DIM,mu,cr);
 556         }
 557         wallcycle_stop(wcycle,ewcMOVEX);
 558     }
 559     if (bStateChanged)
 560     {
 561         for(i=0; i<2; i++)
 562         {
 563             for(j=0;j<DIM;j++)
 564             {
 565                 fr->mu_tot[i][j] = mu[i*DIM + j];
 566             }
 567         }
 568     }
 569     if (fr->efep == efepNO)
 570     {
 571         copy_rvec(fr->mu_tot[0],mu_tot);
 572     }
 573     else
 574     {
 575         for(j=0; j<DIM; j++)
 576         {
 577             mu_tot[j] =
 578                 (1.0 - lambda)*fr->mu_tot[0][j] + lambda*fr->mu_tot[1][j];
 579         }
 580     }
 581
 582     /* Reset energies */
 583     reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
 584     clear_rvecs(SHIFTS,fr->fshift);
 585
 586     if (bNS)
 587     {
 588         wallcycle_start(wcycle,ewcNS);
 589
 590         if (graph && bStateChanged)
 591         {
 592             /* Calculate intramolecular shift vectors to make molecules whole */
 593             mk_mshift(fplog,graph,fr->ePBC,box,x);
 594         }
 595
 596         /* Reset long range forces if necessary */
 597         if (fr->bTwinRange)
 598         {
 599             /* Reset the (long-range) forces if necessary */
 600             clear_rvecs(fr->natoms_force_constr,bSepLRF ? fr->f_twin : f);
 601         }
 602
 603         /* Do the actual neighbour searching and if twin range electrostatics
 604          * also do the calculation of long range forces and energies.
 605          */
 606         dvdl = 0;
 607         ns(fplog,fr,x,box,
 608            groups,&(inputrec->opts),top,mdatoms,
 609            cr,nrnb,lambda,&dvdl,&enerd->grpp,bFillGrid,
 610            bDoLongRange,bDoForces,bSepLRF ? fr->f_twin : f);
 611         if (bSepDVDL)
 612         {
 613             fprintf(fplog,sepdvdlformat,"LR non-bonded",0.0,dvdl);
 614         }
 615         enerd->dvdl_lin += dvdl;
 616
 617         wallcycle_stop(wcycle,ewcNS);
 618     }
 619
 620     if (inputrec->implicit_solvent && bNS)
 621     {
 622         make_gb_nblist(cr,inputrec->gb_algorithm,inputrec->rlist,
 623                        x,box,fr,&top->idef,graph,fr->born);
 624     }
 625
 626     if (DOMAINDECOMP(cr))
 627     {
 628         if (!(cr->duty & DUTY_PME))
 629         {
 630             wallcycle_start(wcycle,ewcPPDURINGPME);
 631             dd_force_flop_start(cr->dd,nrnb);
 632         }
 633     }
 634
 635     /* Start the force cycle counter.
 636      * This counter is stopped in do_forcelow_level.
 637      * No parallel communication should occur while this counter is running,
 638      * since that will interfere with the dynamic load balancing.
 639      */
 640     wallcycle_start(wcycle,ewcFORCE);
 641
 642     if (bDoForces)
 643     {
 644         /* Reset forces for which the virial is calculated separately:
 645          * PME/Ewald forces if necessary */
 646         if (fr->bF_NoVirSum)
 647         {
 648             if (flags & GMX_FORCE_VIRIAL)
 649             {
 650                 fr->f_novirsum = fr->f_novirsum_alloc;
 651                 GMX_BARRIER(cr->mpi_comm_mygroup);
 652                 if (fr->bDomDec)
 653                 {
 654                     clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
 655                 }
 656                 else
 657                 {
 658                     clear_rvecs(homenr,fr->f_novirsum+start);
 659                 }
 660                 GMX_BARRIER(cr->mpi_comm_mygroup);
 661             }
 662             else
 663             {
 664                 /* We are not calculating the pressure so we do not need
 665                  * a separate array for forces that do not contribute
 666                  * to the pressure.
 667                  */
 668                 fr->f_novirsum = f;
 669             }
 670         }
 671
 672         if (bSepLRF)
 673         {
 674             /* Add the long range forces to the short range forces */
 675             for(i=0; i<fr->natoms_force_constr; i++)
 676             {
 677                 copy_rvec(fr->f_twin[i],f[i]);
 678             }
 679         }
 680         else if (!(fr->bTwinRange && bNS))
 681         {
 682             /* Clear the short-range forces */
 683             clear_rvecs(fr->natoms_force_constr,f);
 684         }
 685
 686         clear_rvec(fr->vir_diag_posres);
 687
 688         GMX_BARRIER(cr->mpi_comm_mygroup);
 689     }
 690     if (inputrec->ePull == epullCONSTRAINT)
 691     {
 692         clear_pull_forces(inputrec->pull);
 693     }
 694
 695     /* update QMMMrec, if necessary */
 696     if(fr->bQMMM)
 697     {
 698         update_QMMMrec(cr,fr,x,mdatoms,box,top);
 699     }
 700
 701     if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
 702     {
 703         /* Position restraints always require full pbc */
 704         set_pbc(&pbc,inputrec->ePBC,box);
 705         v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
 706                    top->idef.iparams_posres,
 707                    (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
 708                    inputrec->ePBC==epbcNONE ? NULL : &pbc,lambda,&dvdl,
 709                    fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
 710         if (bSepDVDL)
 711         {
 712             fprintf(fplog,sepdvdlformat,
 713                     interaction_function[F_POSRES].longname,v,dvdl);
 714         }
 715         enerd->term[F_POSRES] += v;
 716         /* This linear lambda dependence assumption is only correct
 717          * when only k depends on lambda,
 718          * not when the reference position depends on lambda.
 719          * grompp checks for this.
 720          */
 721         enerd->dvdl_lin += dvdl;
 722         inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2);
 723     }
 724
 725     /* Compute the bonded and non-bonded energies and optionally forces */
 726     do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
 727                       cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
 728                       x,hist,f,enerd,fcd,mtop,top,fr->born,
 729                       &(top->atomtypes),bBornRadii,box,
 730                       lambda,graph,&(top->excls),fr->mu_tot,
 731                       flags,&cycles_pme);
 732
 733     cycles_force = wallcycle_stop(wcycle,ewcFORCE);
 734     GMX_BARRIER(cr->mpi_comm_mygroup);
 735
 736     if (ed)
 737     {
 738         do_flood(fplog,cr,x,f,ed,box,step);
 739     }
 740
 741     if (DOMAINDECOMP(cr))
 742     {
 743         dd_force_flop_stop(cr->dd,nrnb);
 744         if (wcycle)
 745         {
 746             dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
 747         }
 748     }
 749
 750     if (bDoForces)
 751     {
 752         if (IR_ELEC_FIELD(*inputrec))
 753         {
 754             /* Compute forces due to electric field */
 755             calc_f_el(MASTER(cr) ? field : NULL,
 756                       start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
 757                       inputrec->ex,inputrec->et,t);
 758         }
 759
 760         /* Communicate the forces */
 761         if (PAR(cr))
 762         {
 763             wallcycle_start(wcycle,ewcMOVEF);
 764             if (DOMAINDECOMP(cr))
 765             {
 766                 dd_move_f(cr->dd,f,fr->fshift);
 767                 /* Do we need to communicate the separate force array
 768                  * for terms that do not contribute to the single sum virial?
 769                  * Position restraints and electric fields do not introduce
 770                  * inter-cg forces, only full electrostatics methods do.
 771                  * When we do not calculate the virial, fr->f_novirsum = f,
 772                  * so we have already communicated these forces.
 773                  */
 774                 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
 775                     (flags & GMX_FORCE_VIRIAL))
 776                 {
 777                     dd_move_f(cr->dd,fr->f_novirsum,NULL);
 778                 }
 779                 if (bSepLRF)
 780                 {
 781                     /* We should not update the shift forces here,
 782                      * since f_twin is already included in f.
 783                      */
 784                     dd_move_f(cr->dd,fr->f_twin,NULL);
 785                 }
 786             }
 787             else
 788             {
 789                 pd_move_f(cr,f,nrnb);
 790                 if (bSepLRF)
 791                 {
 792                     pd_move_f(cr,fr->f_twin,nrnb);
 793                 }
 794             }
 795             wallcycle_stop(wcycle,ewcMOVEF);
 796         }
 797
 798         /* If we have NoVirSum forces, but we do not calculate the virial,
 799          * we sum fr->f_novirum=f later.
 800          */
 801         if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
 802         {
 803             wallcycle_start(wcycle,ewcVSITESPREAD);
 804             spread_vsite_f(fplog,vsite,x,f,fr->fshift,nrnb,
 805                            &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
 806             wallcycle_stop(wcycle,ewcVSITESPREAD);
 807
 808             if (bSepLRF)
 809             {
 810                 wallcycle_start(wcycle,ewcVSITESPREAD);
 811                 spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,
 812                                nrnb,
 813                                &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
 814                 wallcycle_stop(wcycle,ewcVSITESPREAD);
 815             }
 816         }
 817
 818         if (flags & GMX_FORCE_VIRIAL)
 819         {
 820             /* Calculation of the virial must be done after vsites! */
 821             calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
 822                         vir_force,graph,box,nrnb,fr,inputrec->ePBC);
 823         }
 824     }
 825
 826     if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
 827     {
 828         /* Calculate the center of mass forces, this requires communication,
 829          * which is why pull_potential is called close to other communication.
 830          * The virial contribution is calculated directly,
 831          * which is why we call pull_potential after calc_virial.
 832          */
 833         set_pbc(&pbc,inputrec->ePBC,box);
 834         dvdl = 0;
 835         enerd->term[F_COM_PULL] =
 836             pull_potential(inputrec->ePull,inputrec->pull,mdatoms,&pbc,
 837                            cr,t,lambda,x,f,vir_force,&dvdl);
 838         if (bSepDVDL)
 839         {
 840             fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl);
 841         }
 842         enerd->dvdl_lin += dvdl;
 843     }
 844
 845     if (PAR(cr) && !(cr->duty & DUTY_PME))
 846     {
 847         cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME);
 848         dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME);
 849
 850         /* In case of node-splitting, the PP nodes receive the long-range
 851          * forces, virial and energy from the PME nodes here.
 852          */
 853         wallcycle_start(wcycle,ewcPP_PMEWAITRECVF);
 854         dvdl = 0;
 855         gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl,
 856                           &cycles_seppme);
 857         if (bSepDVDL)
 858         {
 859             fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl);
 860         }
 861         enerd->term[F_COUL_RECIP] += e;
 862         enerd->dvdl_lin += dvdl;
 863         if (wcycle)
 864         {
 865             dd_cycles_add(cr->dd,cycles_seppme,ddCyclPME);
 866         }
 867         wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF);
 868     }
 869
 870     if (bDoForces && fr->bF_NoVirSum)
 871     {
 872         if (vsite)
 873         {
 874             /* Spread the mesh force on virtual sites to the other particles...
 875              * This is parallellized. MPI communication is performed
 876              * if the constructing atoms aren't local.
 877              */
 878             wallcycle_start(wcycle,ewcVSITESPREAD);
 879             spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,nrnb,
 880                            &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
 881             wallcycle_stop(wcycle,ewcVSITESPREAD);
 882         }
 883         if (flags & GMX_FORCE_VIRIAL)
 884         {
 885             /* Now add the forces, this is local */
 886             if (fr->bDomDec)
 887             {
 888                 sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum);
 889             }
 890             else
 891             {
 892                 sum_forces(start,start+homenr,f,fr->f_novirsum);
 893             }
 894             if (EEL_FULL(fr->eeltype))
 895             {
 896                 /* Add the mesh contribution to the virial */
 897                 m_add(vir_force,fr->vir_el_recip,vir_force);
 898             }
 899             if (debug)
 900             {
 901                 pr_rvecs(debug,0,"vir_force",vir_force,DIM);
 902             }
 903         }
 904     }
 905
 906     /* Sum the potential energy terms from group contributions */
 907     sum_epot(&(inputrec->opts),enerd);
 908
 909     if (fr->print_force >= 0 && bDoForces)
 910     {
 911         print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f);
 912     }
 913 }
 914
 915 void do_constrain_first(FILE *fplog,gmx_constr_t constr,
 916                         t_inputrec *ir,t_mdatoms *md,
 917                         t_state *state,rvec *f,
 918                         t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
 919                         t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir)
 920 {
 921     int    i,m,start,end;
 922     gmx_large_int_t step;
 923     double mass,tmass,vcm[4];
 924     real   dt=ir->delta_t;
 925     real   dvdlambda;
 926     rvec   *savex;
 927
 928     snew(savex,state->natoms);
 929
 930     start = md->start;
 931     end   = md->homenr + start;
 932
 933     if (debug)
 934         fprintf(debug,"vcm: start=%d, homenr=%d, end=%d\n",
 935                 start,md->homenr,end);
 936     /* Do a first constrain to reset particles... */
 937     step = ir->init_step;
 938     if (fplog)
 939     {
 940         char buf[STEPSTRSIZE];
 941         fprintf(fplog,"\nConstraining the starting coordinates (step %s)\n",
 942                 gmx_step_str(step,buf));
 943     }
 944     dvdlambda = 0;
 945
 946     /* constrain the current position */
 947     constrain(NULL,TRUE,FALSE,constr,&(top->idef),
 948               ir,NULL,cr,step,0,md,
 949               state->x,state->x,NULL,
 950               state->box,state->lambda,&dvdlambda,
 951               NULL,NULL,nrnb,econqCoord,ir->epc==epcMTTK,state->veta,state->veta);
 952     if (EI_VV(ir->eI))
 953     {
 954         /* constrain the inital velocity, and save it */
 955         /* also may be useful if we need the ekin from the halfstep for velocity verlet */
 956         /* might not yet treat veta correctly */
 957         constrain(NULL,TRUE,FALSE,constr,&(top->idef),
 958                   ir,NULL,cr,step,0,md,
 959                   state->x,state->v,state->v,
 960                   state->box,state->lambda,&dvdlambda,
 961                   NULL,NULL,nrnb,econqVeloc,ir->epc==epcMTTK,state->veta,state->veta);
 962     }
 963     /* constrain the inital velocities at t-dt/2 */
 964     if (EI_STATE_VELOCITY(ir->eI) && ir->eI!=eiVV)
 965     {
 966         for(i=start; (i<end); i++)
 967         {
 968             for(m=0; (m<DIM); m++)
 969             {
 970                 /* Reverse the velocity */
 971                 state->v[i][m] = -state->v[i][m];
 972                 /* Store the position at t-dt in buf */
 973                 savex[i][m] = state->x[i][m] + dt*state->v[i][m];
 974             }
 975         }
 976     /* Shake the positions at t=-dt with the positions at t=0
 977      * as reference coordinates.
 978          */
 979         if (fplog)
 980         {
 981             char buf[STEPSTRSIZE];
 982             fprintf(fplog,"\nConstraining the coordinates at t0-dt (step %s)\n",
 983                     gmx_step_str(step,buf));
 984         }
 985         dvdlambda = 0;
 986         constrain(NULL,TRUE,FALSE,constr,&(top->idef),
 987                   ir,NULL,cr,step,-1,md,
 988                   state->x,savex,NULL,
 989                   state->box,state->lambda,&dvdlambda,
 990                   state->v,NULL,nrnb,econqCoord,ir->epc==epcMTTK,state->veta,state->veta);
 991
 992         for(i=start; i<end; i++) {
 993             for(m=0; m<DIM; m++) {
 994                 /* Re-reverse the velocities */
 995                 state->v[i][m] = -state->v[i][m];
 996             }
 997         }
 998     }
 999
1000     for(m=0; (m<4); m++)
1001         vcm[m] = 0;
1002     for(i=start; i<end; i++) {
1003         mass = md->massT[i];
1004         for(m=0; m<DIM; m++) {
1005             vcm[m] += state->v[i][m]*mass;
1006         }
1007         vcm[3] += mass;
1008     }
1009
1010     if (ir->nstcomm != 0 || debug) {
1011         /* Compute the global sum of vcm */
1012         if (debug)
1013             fprintf(debug,"vcm: %8.3f  %8.3f  %8.3f,"
1014                     " total mass = %12.5e\n",vcm[XX],vcm[YY],vcm[ZZ],vcm[3]);
1015         if (PAR(cr))
1016             gmx_sumd(4,vcm,cr);
1017         tmass = vcm[3];
1018         for(m=0; (m<DIM); m++)
1019             vcm[m] /= tmass;
1020         if (debug)
1021             fprintf(debug,"vcm: %8.3f  %8.3f  %8.3f,"
1022                     " total mass = %12.5e\n",vcm[XX],vcm[YY],vcm[ZZ],tmass);
1023         if (ir->nstcomm != 0) {
1024             /* Now we have the velocity of center of mass, let's remove it */
1025             for(i=start; (i<end); i++) {
1026                 for(m=0; (m<DIM); m++)
1027                     state->v[i][m] -= vcm[m];
1028             }
1029
1030         }
1031     }
1032     sfree(savex);
1033 }
1034
1035 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr)
1036 {
1037   double eners[2],virs[2],enersum,virsum,y0,f,g,h;
1038   double r0,r1,r,rc3,rc9,ea,eb,ec,pa,pb,pc,pd;
1039   double invscale,invscale2,invscale3;
1040   int    ri0,ri1,ri,i,offstart,offset;
1041   real   scale,*vdwtab;
1042
1043   fr->enershiftsix = 0;
1044   fr->enershifttwelve = 0;
1045   fr->enerdiffsix = 0;
1046   fr->enerdifftwelve = 0;
1047   fr->virdiffsix = 0;
1048   fr->virdifftwelve = 0;
1049
1050   if (eDispCorr != edispcNO) {
1051     for(i=0; i<2; i++) {
1052       eners[i] = 0;
1053       virs[i]  = 0;
1054     }
1055     if ((fr->vdwtype == evdwSWITCH) || (fr->vdwtype == evdwSHIFT)) {
1056       if (fr->rvdw_switch == 0)
1057         gmx_fatal(FARGS,
1058                   "With dispersion correction rvdw-switch can not be zero "
1059                   "for vdw-type = %s",evdw_names[fr->vdwtype]);
1060
1061       scale  = fr->nblists[0].tab.scale;
1062       vdwtab = fr->nblists[0].vdwtab;
1063
1064       /* Round the cut-offs to exact table values for precision */
1065       ri0 = floor(fr->rvdw_switch*scale);
1066       ri1 = ceil(fr->rvdw*scale);
1067       r0  = ri0/scale;
1068       r1  = ri1/scale;
1069       rc3 = r0*r0*r0;
1070       rc9  = rc3*rc3*rc3;
1071
1072       if (fr->vdwtype == evdwSHIFT) {
1073         /* Determine the constant energy shift below rvdw_switch */
1074         fr->enershiftsix    = (real)(-1.0/(rc3*rc3)) - vdwtab[8*ri0];
1075         fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - vdwtab[8*ri0 + 4];
1076       }
1077       /* Add the constant part from 0 to rvdw_switch.
1078        * This integration from 0 to rvdw_switch overcounts the number
1079        * of interactions by 1, as it also counts the self interaction.
1080        * We will correct for this later.
1081        */
1082       eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
1083       eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;
1084
1085       invscale = 1.0/(scale);
1086       invscale2 = invscale*invscale;
1087       invscale3 = invscale*invscale2;
1088
1089       /* following summation derived from cubic spline definition,
1090         Numerical Recipies in C, second edition, p. 113-116.  Exact
1091         for the cubic spline.  We first calculate the negative of
1092         the energy from rvdw to rvdw_switch, assuming that g(r)=1,
1093         and then add the more standard, abrupt cutoff correction to
1094         that result, yielding the long-range correction for a
1095         switched function.  We perform both the pressure and energy
1096         loops at the same time for simplicity, as the computational
1097         cost is low. */
1098
1099       for (i=0;i<2;i++) {
1100         enersum = 0.0; virsum = 0.0;
1101         if (i==0)
1102           offstart = 0;
1103         else
1104           offstart = 4;
1105         for (ri=ri0; ri<ri1; ri++) {
1106           r = ri*invscale;
1107           ea = invscale3;
1108           eb = 2.0*invscale2*r;
1109           ec = invscale*r*r;
1110
1111           pa = invscale3;
1112           pb = 3.0*invscale2*r;
1113           pc = 3.0*invscale*r*r;
1114           pd = r*r*r;
1115
1116           /* this "8" is from the packing in the vdwtab array - perhaps
1117             should be #define'ed? */
1118           offset = 8*ri + offstart;
1119           y0 = vdwtab[offset];
1120           f = vdwtab[offset+1];
1121           g = vdwtab[offset+2];
1122           h = vdwtab[offset+3];
1123
1124           enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2)+
1125             g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
1126           virsum  +=  f*(pa/4 + pb/3 + pc/2 + pd) +
1127             2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
1128
1129         }
1130         enersum *= 4.0*M_PI;
1131         virsum  *= 4.0*M_PI;
1132         eners[i] -= enersum;
1133         virs[i]  -= virsum;
1134       }
1135
1136       /* now add the correction for rvdw_switch to infinity */
1137       eners[0] += -4.0*M_PI/(3.0*rc3);
1138       eners[1] +=  4.0*M_PI/(9.0*rc9);
1139       virs[0]  +=  8.0*M_PI/rc3;
1140       virs[1]  += -16.0*M_PI/(3.0*rc9);
1141     }
1142     else if ((fr->vdwtype == evdwCUT) || (fr->vdwtype == evdwUSER)) {
1143       if (fr->vdwtype == evdwUSER && fplog)
1144         fprintf(fplog,
1145                 "WARNING: using dispersion correction with user tables\n");
1146       rc3  = fr->rvdw*fr->rvdw*fr->rvdw;
1147       rc9  = rc3*rc3*rc3;
1148       eners[0] += -4.0*M_PI/(3.0*rc3);
1149       eners[1] +=  4.0*M_PI/(9.0*rc9);
1150       virs[0]  +=  8.0*M_PI/rc3;
1151       virs[1]  += -16.0*M_PI/(3.0*rc9);
1152     } else {
1153       gmx_fatal(FARGS,
1154                 "Dispersion correction is not implemented for vdw-type = %s",
1155                 evdw_names[fr->vdwtype]);
1156     }
1157     fr->enerdiffsix    = eners[0];
1158     fr->enerdifftwelve = eners[1];
1159     /* The 0.5 is due to the Gromacs definition of the virial */
1160     fr->virdiffsix     = 0.5*virs[0];
1161     fr->virdifftwelve  = 0.5*virs[1];
1162   }
1163 }
1164
1165 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
1166                    gmx_large_int_t step,int natoms,
1167                    matrix box,real lambda,tensor pres,tensor virial,
1168                    real *prescorr, real *enercorr, real *dvdlcorr)
1169 {
1170     gmx_bool bCorrAll,bCorrPres;
1171     real dvdlambda,invvol,dens,ninter,avcsix,avctwelve,enerdiff,svir=0,spres=0;
1172     int  m;
1173
1174     *prescorr = 0;
1175     *enercorr = 0;
1176     *dvdlcorr = 0;
1177
1178     clear_mat(virial);
1179     clear_mat(pres);
1180
1181     if (ir->eDispCorr != edispcNO) {
1182         bCorrAll  = (ir->eDispCorr == edispcAllEner ||
1183                      ir->eDispCorr == edispcAllEnerPres);
1184         bCorrPres = (ir->eDispCorr == edispcEnerPres ||
1185                      ir->eDispCorr == edispcAllEnerPres);
1186
1187         invvol = 1/det(box);
1188         if (fr->n_tpi)
1189         {
1190             /* Only correct for the interactions with the inserted molecule */
1191             dens = (natoms - fr->n_tpi)*invvol;
1192             ninter = fr->n_tpi;
1193         }
1194         else
1195         {
1196             dens = natoms*invvol;
1197             ninter = 0.5*natoms;
1198         }
1199
1200         if (ir->efep == efepNO)
1201         {
1202             avcsix    = fr->avcsix[0];
1203             avctwelve = fr->avctwelve[0];
1204         }
1205         else
1206         {
1207             avcsix    = (1 - lambda)*fr->avcsix[0]    + lambda*fr->avcsix[1];
1208             avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
1209         }
1210
1211         enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
1212         *enercorr += avcsix*enerdiff;
1213         dvdlambda = 0.0;
1214         if (ir->efep != efepNO)
1215         {
1216             dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
1217         }
1218         if (bCorrAll)
1219         {
1220             enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
1221             *enercorr += avctwelve*enerdiff;
1222             if (fr->efep != efepNO)
1223             {
1224                 dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
1225             }
1226         }
1227
1228         if (bCorrPres)
1229         {
1230             svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
1231             if (ir->eDispCorr == edispcAllEnerPres)
1232             {
1233                 svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
1234             }
1235             /* The factor 2 is because of the Gromacs virial definition */
1236             spres = -2.0*invvol*svir*PRESFAC;
1237
1238             for(m=0; m<DIM; m++) {
1239                 virial[m][m] += svir;
1240                 pres[m][m] += spres;
1241             }
1242             *prescorr += spres;
1243         }
1244
1245         /* Can't currently control when it prints, for now, just print when degugging */
1246         if (debug)
1247         {
1248             if (bCorrAll) {
1249                 fprintf(debug,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1250                         avcsix,avctwelve);
1251             }
1252             if (bCorrPres)
1253             {
1254                 fprintf(debug,
1255                         "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
1256                         *enercorr,spres,svir);
1257             }
1258             else
1259             {
1260                 fprintf(debug,"Long Range LJ corr.: Epot %10g\n",*enercorr);
1261             }
1262         }
1263
1264         if (fr->bSepDVDL && do_per_step(step,ir->nstlog))
1265         {
1266             fprintf(fplog,sepdvdlformat,"Dispersion correction",
1267                     *enercorr,dvdlambda);
1268         }
1269         if (fr->efep != efepNO)
1270         {
1271             *dvdlcorr += dvdlambda;
1272         }
1273     }
1274 }
1275
1276 void do_pbc_first(FILE *fplog,matrix box,t_forcerec *fr,
1277                   t_graph *graph,rvec x[])
1278 {
1279   if (fplog)
1280     fprintf(fplog,"Removing pbc first time\n");
1281   calc_shifts(box,fr->shift_vec);
1282   if (graph) {
1283     mk_mshift(fplog,graph,fr->ePBC,box,x);
1284     if (gmx_debug_at)
1285       p_graph(debug,"do_pbc_first 1",graph);
1286     shift_self(graph,box,x);
1287     /* By doing an extra mk_mshift the molecules that are broken
1288      * because they were e.g. imported from another software
1289      * will be made whole again. Such are the healing powers
1290      * of GROMACS.
1291      */
1292     mk_mshift(fplog,graph,fr->ePBC,box,x);
1293     if (gmx_debug_at)
1294       p_graph(debug,"do_pbc_first 2",graph);
1295   }
1296   if (fplog)
1297     fprintf(fplog,"Done rmpbc\n");
1298 }
1299
1300 static void low_do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
1301                             gmx_mtop_t *mtop,rvec x[],
1302                             gmx_bool bFirst)
1303 {
1304   t_graph *graph;
1305   int mb,as,mol;
1306   gmx_molblock_t *molb;
1307
1308   if (bFirst && fplog)
1309     fprintf(fplog,"Removing pbc first time\n");
1310
1311   snew(graph,1);
1312   as = 0;
1313   for(mb=0; mb<mtop->nmolblock; mb++) {
1314     molb = &mtop->molblock[mb];
1315     if (molb->natoms_mol == 1 ||
1316         (!bFirst && mtop->moltype[molb->type].cgs.nr == 1)) {
1317       /* Just one atom or charge group in the molecule, no PBC required */
1318       as += molb->nmol*molb->natoms_mol;
1319     } else {
1320       /* Pass NULL iso fplog to avoid graph prints for each molecule type */
1321       mk_graph_ilist(NULL,mtop->moltype[molb->type].ilist,
1322                      0,molb->natoms_mol,FALSE,FALSE,graph);
1323
1324       for(mol=0; mol<molb->nmol; mol++) {
1325         mk_mshift(fplog,graph,ePBC,box,x+as);
1326
1327         shift_self(graph,box,x+as);
1328         /* The molecule is whole now.
1329          * We don't need the second mk_mshift call as in do_pbc_first,
1330          * since we no longer need this graph.
1331          */
1332
1333         as += molb->natoms_mol;
1334       }
1335       done_graph(graph);
1336     }
1337   }
1338   sfree(graph);
1339 }
1340
1341 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
1342                        gmx_mtop_t *mtop,rvec x[])
1343 {
1344   low_do_pbc_mtop(fplog,ePBC,box,mtop,x,TRUE);
1345 }
1346
1347 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
1348                  gmx_mtop_t *mtop,rvec x[])
1349 {
1350   low_do_pbc_mtop(fplog,ePBC,box,mtop,x,FALSE);
1351 }
1352
1353 void finish_run(FILE *fplog,t_commrec *cr,const char *confout,
1354                 t_inputrec *inputrec,
1355                 t_nrnb nrnb[],gmx_wallcycle_t wcycle,
1356                 gmx_runtime_t *runtime,
1357                 gmx_bool bWriteStat)
1358 {
1359   int    i,j;
1360   t_nrnb *nrnb_tot=NULL;
1361   real   delta_t;
1362   double nbfs,mflop;
1363   double cycles[ewcNR];
1364
1365   wallcycle_sum(cr,wcycle,cycles);
1366
1367   if (cr->nnodes > 1) {
1368     if (SIMMASTER(cr))
1369       snew(nrnb_tot,1);
1370 #ifdef GMX_MPI
1371     MPI_Reduce(nrnb->n,nrnb_tot->n,eNRNB,MPI_DOUBLE,MPI_SUM,
1372                MASTERRANK(cr),cr->mpi_comm_mysim);
1373 #endif
1374   } else {
1375     nrnb_tot = nrnb;
1376   }
1377
1378   if (SIMMASTER(cr)) {
1379     print_flop(fplog,nrnb_tot,&nbfs,&mflop);
1380     if (cr->nnodes > 1) {
1381       sfree(nrnb_tot);
1382     }
1383   }
1384
1385   if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr)) {
1386     print_dd_statistics(cr,inputrec,fplog);
1387   }
1388
1389 #ifdef GMX_MPI
1390     if (PARTDECOMP(cr))
1391     {
1392         if (MASTER(cr))
1393         {
1394             t_nrnb     *nrnb_all;
1395             int        s;
1396             MPI_Status stat;
1397
1398             snew(nrnb_all,cr->nnodes);
1399             nrnb_all[0] = *nrnb;
1400             for(s=1; s<cr->nnodes; s++)
1401             {
1402                 MPI_Recv(nrnb_all[s].n,eNRNB,MPI_DOUBLE,s,0,
1403                          cr->mpi_comm_mysim,&stat);
1404             }
1405             pr_load(fplog,cr,nrnb_all);
1406             sfree(nrnb_all);
1407         }
1408         else
1409         {
1410             MPI_Send(nrnb->n,eNRNB,MPI_DOUBLE,MASTERRANK(cr),0,
1411                      cr->mpi_comm_mysim);
1412         }
1413     }
1414 #endif
1415
1416   if (SIMMASTER(cr)) {
1417     wallcycle_print(fplog,cr->nnodes,cr->npmenodes,runtime->realtime,
1418                     wcycle,cycles);
1419
1420     if (EI_DYNAMICS(inputrec->eI)) {
1421       delta_t = inputrec->delta_t;
1422     } else {
1423       delta_t = 0;
1424     }
1425
1426     if (fplog) {
1427         print_perf(fplog,runtime->proctime,runtime->realtime,
1428                    cr->nnodes-cr->npmenodes,
1429                    runtime->nsteps_done,delta_t,nbfs,mflop);
1430     }
1431     if (bWriteStat) {
1432         print_perf(stderr,runtime->proctime,runtime->realtime,
1433                    cr->nnodes-cr->npmenodes,
1434                    runtime->nsteps_done,delta_t,nbfs,mflop);
1435     }
1436
1437     /*
1438     runtime=inputrec->nsteps*inputrec->delta_t;
1439     if (bWriteStat) {
1440       if (cr->nnodes == 1)
1441         fprintf(stderr,"\n\n");
1442       print_perf(stderr,nodetime,realtime,runtime,&ntot,
1443                  cr->nnodes-cr->npmenodes,FALSE);
1444     }
1445     wallcycle_print(fplog,cr->nnodes,cr->npmenodes,realtime,wcycle,cycles);
1446     print_perf(fplog,nodetime,realtime,runtime,&ntot,cr->nnodes-cr->npmenodes,
1447                TRUE);
1448     if (PARTDECOMP(cr))
1449       pr_load(fplog,cr,nrnb_all);
1450     if (cr->nnodes > 1)
1451       sfree(nrnb_all);
1452     */
1453   }
1454 }
1455
1456 void init_md(FILE *fplog,
1457              t_commrec *cr,t_inputrec *ir,const output_env_t oenv,
1458              double *t,double *t0,
1459              real *lambda,double *lam0,
1460              t_nrnb *nrnb,gmx_mtop_t *mtop,
1461              gmx_update_t *upd,
1462              int nfile,const t_filenm fnm[],
1463              gmx_mdoutf_t **outf,t_mdebin **mdebin,
1464              tensor force_vir,tensor shake_vir,rvec mu_tot,
1465              gmx_bool *bSimAnn,t_vcm **vcm, t_state *state, unsigned long Flags)
1466 {
1467     int  i,j,n;
1468     real tmpt,mod;
1469
1470     /* Initial values */
1471     *t = *t0       = ir->init_t;
1472     if (ir->efep != efepNO)
1473     {
1474         *lam0 = ir->init_lambda;
1475         *lambda = *lam0 + ir->init_step*ir->delta_lambda;
1476     }
1477     else
1478     {
1479         *lambda = *lam0   = 0.0;
1480     }
1481
1482     *bSimAnn=FALSE;
1483     for(i=0;i<ir->opts.ngtc;i++)
1484     {
1485         /* set bSimAnn if any group is being annealed */
1486         if(ir->opts.annealing[i]!=eannNO)
1487         {
1488             *bSimAnn = TRUE;
1489         }
1490     }
1491     if (*bSimAnn)
1492     {
1493         update_annealing_target_temp(&(ir->opts),ir->init_t);
1494     }
1495
1496     if (upd)
1497     {
1498         *upd = init_update(fplog,ir);
1499     }
1500
1501     if (vcm != NULL)
1502     {
1503         *vcm = init_vcm(fplog,&mtop->groups,ir);
1504     }
1505
1506     if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
1507     {
1508         if (ir->etc == etcBERENDSEN)
1509         {
1510             please_cite(fplog,"Berendsen84a");
1511         }
1512         if (ir->etc == etcVRESCALE)
1513         {
1514             please_cite(fplog,"Bussi2007a");
1515         }
1516     }
1517
1518     init_nrnb(nrnb);
1519
1520     if (nfile != -1)
1521     {
1522         *outf = init_mdoutf(nfile,fnm,Flags,cr,ir,oenv);
1523
1524         *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : (*outf)->fp_ene,
1525                               mtop,ir, (*outf)->fp_dhdl);
1526     }
1527
1528     /* Initiate variables */
1529     clear_mat(force_vir);
1530     clear_mat(shake_vir);
1531     clear_rvec(mu_tot);
1532
1533     debug_gmx();
1534 }
1535