src/gromacs/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  *
  21  * If you want to redistribute modifications, please consider that
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  24  * inclusion in the official distribution, but derived work must not
  25  * be called official GROMACS. Details are found in the README & COPYING
  26  * files - if they are missing, get the official version at www.gromacs.org.
  27  *
  28  * To help us fund GROMACS development, we humbly ask that you cite
  29  * the papers on the package - you can find them in the top README file.
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  34  * GROwing Monsters And Cloning Shrimps
  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 "sim_util.h"
  67 #include "update.h"
  68 #include "physics.h"
  69 #include "main.h"
  70 #include "mdatoms.h"
  71 #include "force.h"
  72 #include "bondf.h"
  73 #include "pme.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 #include "pull_rotation.h"
  84 #include "gmx_random.h"
  85 #include "domdec.h"
  86 #include "partdec.h"
  87 #include "gmx_wallcycle.h"
  88 #include "genborn.h"
  89 #include "nbnxn_atomdata.h"
  90 #include "nbnxn_search.h"
  91 #include "nbnxn_kernels/nbnxn_kernel_ref.h"
  92 #include "nbnxn_kernels/nbnxn_kernel_simd_4xn.h"
  93 #include "nbnxn_kernels/nbnxn_kernel_simd_2xnn.h"
  94 #include "nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
  95
  96 #ifdef GMX_LIB_MPI
  97 #include <mpi.h>
  98 #endif
  99 #ifdef GMX_THREAD_MPI
 100 #include "tmpi.h"
 101 #endif
 102
 103 #include "adress.h"
 104 #include "qmmm.h"
 105
 106 #include "nbnxn_cuda_data_mgmt.h"
 107 #include "nbnxn_cuda/nbnxn_cuda.h"
 108
 109 #if 0
 110 typedef struct gmx_timeprint {
 111
 112 } t_gmx_timeprint;
 113 #endif
 114
 115 /* Portable version of ctime_r implemented in src/gmxlib/string2.c, but we do not want it declared in public installed headers */
 116 char *
 117 gmx_ctime_r(const time_t *clock,char *buf, int n);
 118
 119
 120 double
 121 gmx_gettime()
 122 {
 123 #ifdef HAVE_GETTIMEOFDAY
 124         struct timeval t;
 125         double seconds;
 126
 127         gettimeofday(&t,NULL);
 128
 129         seconds = (double) t.tv_sec + 1e-6*(double)t.tv_usec;
 130
 131         return seconds;
 132 #else
 133         double  seconds;
 134
 135         seconds = time(NULL);
 136
 137         return seconds;
 138 #endif
 139 }
 140
 141
 142 #define difftime(end,start) ((double)(end)-(double)(start))
 143
 144 void print_time(FILE *out,gmx_runtime_t *runtime,gmx_large_int_t step,
 145                 t_inputrec *ir, t_commrec *cr)
 146 {
 147     time_t finish;
 148     char   timebuf[STRLEN];
 149     double dt;
 150     char buf[48];
 151
 152 #ifndef GMX_THREAD_MPI
 153     if (!PAR(cr))
 154 #endif
 155     {
 156         fprintf(out,"\r");
 157     }
 158     fprintf(out,"step %s",gmx_step_str(step,buf));
 159     if ((step >= ir->nstlist))
 160     {
 161         runtime->last = gmx_gettime();
 162         dt = difftime(runtime->last,runtime->real);
 163         runtime->time_per_step = dt/(step - ir->init_step + 1);
 164
 165         dt = (ir->nsteps + ir->init_step - step)*runtime->time_per_step;
 166
 167         if (ir->nsteps >= 0)
 168         {
 169             if (dt >= 300)
 170             {
 171                 finish = (time_t) (runtime->last + dt);
 172                 gmx_ctime_r(&finish,timebuf,STRLEN);
 173                 sprintf(buf,"%s",timebuf);
 174                 buf[strlen(buf)-1]='\0';
 175                 fprintf(out,", will finish %s",buf);
 176             }
 177             else
 178                 fprintf(out,", remaining runtime: %5d s          ",(int)dt);
 179         }
 180         else
 181         {
 182             fprintf(out," performance: %.1f ns/day    ",
 183                     ir->delta_t/1000*24*60*60/runtime->time_per_step);
 184         }
 185     }
 186 #ifndef GMX_THREAD_MPI
 187     if (PAR(cr))
 188     {
 189         fprintf(out,"\n");
 190     }
 191 #endif
 192
 193     fflush(out);
 194 }
 195
 196 #ifdef NO_CLOCK
 197 #define clock() -1
 198 #endif
 199
 200 static double set_proctime(gmx_runtime_t *runtime)
 201 {
 202     double diff;
 203 #ifdef GMX_CRAY_XT3
 204     double prev;
 205
 206     prev = runtime->proc;
 207     runtime->proc = dclock();
 208
 209     diff = runtime->proc - prev;
 210 #else
 211     clock_t prev;
 212
 213     prev = runtime->proc;
 214     runtime->proc = clock();
 215
 216     diff = (double)(runtime->proc - prev)/(double)CLOCKS_PER_SEC;
 217 #endif
 218     if (diff < 0)
 219     {
 220         /* The counter has probably looped, ignore this data */
 221         diff = 0;
 222     }
 223
 224     return diff;
 225 }
 226
 227 void runtime_start(gmx_runtime_t *runtime)
 228 {
 229     runtime->real = gmx_gettime();
 230     runtime->proc          = 0;
 231     set_proctime(runtime);
 232     runtime->realtime      = 0;
 233     runtime->proctime      = 0;
 234     runtime->last          = 0;
 235     runtime->time_per_step = 0;
 236 }
 237
 238 void runtime_end(gmx_runtime_t *runtime)
 239 {
 240     double now;
 241
 242     now = gmx_gettime();
 243
 244     runtime->proctime += set_proctime(runtime);
 245     runtime->realtime  = now - runtime->real;
 246     runtime->real      = now;
 247 }
 248
 249 void runtime_upd_proc(gmx_runtime_t *runtime)
 250 {
 251     runtime->proctime += set_proctime(runtime);
 252 }
 253
 254 void print_date_and_time(FILE *fplog,int nodeid,const char *title,
 255                          const gmx_runtime_t *runtime)
 256 {
 257     int i;
 258     char timebuf[STRLEN];
 259     char time_string[STRLEN];
 260     time_t tmptime;
 261
 262     if (fplog)
 263     {
 264         if (runtime != NULL)
 265         {
 266             tmptime = (time_t) runtime->real;
 267             gmx_ctime_r(&tmptime,timebuf,STRLEN);
 268         }
 269         else
 270         {
 271             tmptime = (time_t) gmx_gettime();
 272             gmx_ctime_r(&tmptime,timebuf,STRLEN);
 273         }
 274         for(i=0; timebuf[i]>=' '; i++)
 275         {
 276             time_string[i]=timebuf[i];
 277         }
 278         time_string[i]='\0';
 279
 280         fprintf(fplog,"%s on node %d %s\n",title,nodeid,time_string);
 281     }
 282 }
 283
 284 static void sum_forces(int start,int end,rvec f[],rvec flr[])
 285 {
 286   int i;
 287
 288   if (gmx_debug_at) {
 289     pr_rvecs(debug,0,"fsr",f+start,end-start);
 290     pr_rvecs(debug,0,"flr",flr+start,end-start);
 291   }
 292   for(i=start; (i<end); i++)
 293     rvec_inc(f[i],flr[i]);
 294 }
 295
 296 /*
 297  * calc_f_el calculates forces due to an electric field.
 298  *
 299  * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
 300  *
 301  * Et[] contains the parameters for the time dependent
 302  * part of the field (not yet used).
 303  * Ex[] contains the parameters for
 304  * the spatial dependent part of the field. You can have cool periodic
 305  * fields in principle, but only a constant field is supported
 306  * now.
 307  * The function should return the energy due to the electric field
 308  * (if any) but for now returns 0.
 309  *
 310  * WARNING:
 311  * There can be problems with the virial.
 312  * Since the field is not self-consistent this is unavoidable.
 313  * For neutral molecules the virial is correct within this approximation.
 314  * For neutral systems with many charged molecules the error is small.
 315  * But for systems with a net charge or a few charged molecules
 316  * the error can be significant when the field is high.
 317  * Solution: implement a self-consitent electric field into PME.
 318  */
 319 static void calc_f_el(FILE *fp,int  start,int homenr,
 320                       real charge[],rvec x[],rvec f[],
 321                       t_cosines Ex[],t_cosines Et[],double t)
 322 {
 323     rvec Ext;
 324     real t0;
 325     int  i,m;
 326
 327     for(m=0; (m<DIM); m++)
 328     {
 329         if (Et[m].n > 0)
 330         {
 331             if (Et[m].n == 3)
 332             {
 333                 t0 = Et[m].a[1];
 334                 Ext[m] = cos(Et[m].a[0]*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(Et[m].a[2])));
 335             }
 336             else
 337             {
 338                 Ext[m] = cos(Et[m].a[0]*t);
 339             }
 340         }
 341         else
 342         {
 343             Ext[m] = 1.0;
 344         }
 345         if (Ex[m].n > 0)
 346         {
 347             /* Convert the field strength from V/nm to MD-units */
 348             Ext[m] *= Ex[m].a[0]*FIELDFAC;
 349             for(i=start; (i<start+homenr); i++)
 350                 f[i][m] += charge[i]*Ext[m];
 351         }
 352         else
 353         {
 354             Ext[m] = 0;
 355         }
 356     }
 357     if (fp != NULL)
 358     {
 359         fprintf(fp,"%10g  %10g  %10g  %10g #FIELD\n",t,
 360                 Ext[XX]/FIELDFAC,Ext[YY]/FIELDFAC,Ext[ZZ]/FIELDFAC);
 361     }
 362 }
 363
 364 static void calc_virial(FILE *fplog,int start,int homenr,rvec x[],rvec f[],
 365                         tensor vir_part,t_graph *graph,matrix box,
 366                         t_nrnb *nrnb,const t_forcerec *fr,int ePBC)
 367 {
 368   int i,j;
 369   tensor virtest;
 370
 371   /* The short-range virial from surrounding boxes */
 372   clear_mat(vir_part);
 373   calc_vir(fplog,SHIFTS,fr->shift_vec,fr->fshift,vir_part,ePBC==epbcSCREW,box);
 374   inc_nrnb(nrnb,eNR_VIRIAL,SHIFTS);
 375
 376   /* Calculate partial virial, for local atoms only, based on short range.
 377    * Total virial is computed in global_stat, called from do_md
 378    */
 379   f_calc_vir(fplog,start,start+homenr,x,f,vir_part,graph,box);
 380   inc_nrnb(nrnb,eNR_VIRIAL,homenr);
 381
 382   /* Add position restraint contribution */
 383   for(i=0; i<DIM; i++) {
 384     vir_part[i][i] += fr->vir_diag_posres[i];
 385   }
 386
 387   /* Add wall contribution */
 388   for(i=0; i<DIM; i++) {
 389     vir_part[i][ZZ] += fr->vir_wall_z[i];
 390   }
 391
 392   if (debug)
 393     pr_rvecs(debug,0,"vir_part",vir_part,DIM);
 394 }
 395
 396 static void posres_wrapper(FILE *fplog,
 397                            int flags,
 398                            gmx_bool bSepDVDL,
 399                            t_inputrec *ir,
 400                            t_nrnb *nrnb,
 401                            gmx_localtop_t *top,
 402                            matrix box,rvec x[],
 403                            rvec f[],
 404                            gmx_enerdata_t *enerd,
 405                            real *lambda,
 406                            t_forcerec *fr)
 407 {
 408     t_pbc pbc;
 409     real  v,dvdl;
 410     int   i;
 411
 412     /* Position restraints always require full pbc */
 413     set_pbc(&pbc,ir->ePBC,box);
 414     dvdl = 0;
 415     v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
 416                top->idef.iparams_posres,
 417                (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
 418                ir->ePBC==epbcNONE ? NULL : &pbc,
 419                lambda[efptRESTRAINT],&dvdl,
 420                fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
 421     if (bSepDVDL)
 422     {
 423         fprintf(fplog,sepdvdlformat,
 424                 interaction_function[F_POSRES].longname,v,dvdl);
 425     }
 426     enerd->term[F_POSRES] += v;
 427     /* If just the force constant changes, the FEP term is linear,
 428      * but if k changes, it is not.
 429      */
 430     enerd->dvdl_nonlin[efptRESTRAINT] += dvdl;
 431     inc_nrnb(nrnb,eNR_POSRES,top->idef.il[F_POSRES].nr/2);
 432
 433     if ((ir->fepvals->n_lambda > 0) && (flags & GMX_FORCE_DHDL))
 434     {
 435         for(i=0; i<enerd->n_lambda; i++)
 436         {
 437             real dvdl_dum,lambda_dum;
 438
 439             lambda_dum = (i==0 ? lambda[efptRESTRAINT] : ir->fepvals->all_lambda[efptRESTRAINT][i-1]);
 440             v = posres(top->idef.il[F_POSRES].nr,top->idef.il[F_POSRES].iatoms,
 441                        top->idef.iparams_posres,
 442                        (const rvec*)x,NULL,NULL,
 443                        ir->ePBC==epbcNONE ? NULL : &pbc,lambda_dum,&dvdl,
 444                        fr->rc_scaling,fr->ePBC,fr->posres_com,fr->posres_comB);
 445             enerd->enerpart_lambda[i] += v;
 446         }
 447     }
 448 }
 449
 450 static void pull_potential_wrapper(FILE *fplog,
 451                                    gmx_bool bSepDVDL,
 452                                    t_commrec *cr,
 453                                    t_inputrec *ir,
 454                                    matrix box,rvec x[],
 455                                    rvec f[],
 456                                    tensor vir_force,
 457                                    t_mdatoms *mdatoms,
 458                                    gmx_enerdata_t *enerd,
 459                                    real *lambda,
 460                                    double t)
 461 {
 462     t_pbc  pbc;
 463     real   dvdl;
 464
 465     /* Calculate the center of mass forces, this requires communication,
 466      * which is why pull_potential is called close to other communication.
 467      * The virial contribution is calculated directly,
 468      * which is why we call pull_potential after calc_virial.
 469      */
 470     set_pbc(&pbc,ir->ePBC,box);
 471     dvdl = 0;
 472     enerd->term[F_COM_PULL] +=
 473         pull_potential(ir->ePull,ir->pull,mdatoms,&pbc,
 474                        cr,t,lambda[efptRESTRAINT],x,f,vir_force,&dvdl);
 475     if (bSepDVDL)
 476     {
 477         fprintf(fplog,sepdvdlformat,"Com pull",enerd->term[F_COM_PULL],dvdl);
 478     }
 479     enerd->dvdl_lin[efptRESTRAINT] += dvdl;
 480 }
 481
 482 static void pme_receive_force_ener(FILE *fplog,
 483                                    gmx_bool bSepDVDL,
 484                                    t_commrec *cr,
 485                                    gmx_wallcycle_t wcycle,
 486                                    gmx_enerdata_t *enerd,
 487                                    t_forcerec *fr)
 488 {
 489     real   e,v,dvdl;
 490     float  cycles_ppdpme,cycles_seppme;
 491
 492     cycles_ppdpme = wallcycle_stop(wcycle,ewcPPDURINGPME);
 493     dd_cycles_add(cr->dd,cycles_ppdpme,ddCyclPPduringPME);
 494
 495     /* In case of node-splitting, the PP nodes receive the long-range
 496      * forces, virial and energy from the PME nodes here.
 497      */
 498     wallcycle_start(wcycle,ewcPP_PMEWAITRECVF);
 499     dvdl = 0;
 500     gmx_pme_receive_f(cr,fr->f_novirsum,fr->vir_el_recip,&e,&dvdl,
 501                       &cycles_seppme);
 502     if (bSepDVDL)
 503     {
 504         fprintf(fplog,sepdvdlformat,"PME mesh",e,dvdl);
 505     }
 506     enerd->term[F_COUL_RECIP] += e;
 507     enerd->dvdl_lin[efptCOUL] += dvdl;
 508     if (wcycle)
 509     {
 510         dd_cycles_add(cr->dd,cycles_seppme,ddCyclPME);
 511     }
 512     wallcycle_stop(wcycle,ewcPP_PMEWAITRECVF);
 513 }
 514
 515 static void print_large_forces(FILE *fp,t_mdatoms *md,t_commrec *cr,
 516                                gmx_large_int_t step,real pforce,rvec *x,rvec *f)
 517 {
 518   int  i;
 519   real pf2,fn2;
 520   char buf[STEPSTRSIZE];
 521
 522   pf2 = sqr(pforce);
 523   for(i=md->start; i<md->start+md->homenr; i++) {
 524     fn2 = norm2(f[i]);
 525     /* We also catch NAN, if the compiler does not optimize this away. */
 526     if (fn2 >= pf2 || fn2 != fn2) {
 527       fprintf(fp,"step %s  atom %6d  x %8.3f %8.3f %8.3f  force %12.5e\n",
 528               gmx_step_str(step,buf),
 529               ddglatnr(cr->dd,i),x[i][XX],x[i][YY],x[i][ZZ],sqrt(fn2));
 530     }
 531   }
 532 }
 533
 534 static void post_process_forces(FILE *fplog,
 535                                 t_commrec *cr,
 536                                 gmx_large_int_t step,
 537                                 t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 538                                 gmx_localtop_t *top,
 539                                 matrix box,rvec x[],
 540                                 rvec f[],
 541                                 tensor vir_force,
 542                                 t_mdatoms *mdatoms,
 543                                 t_graph *graph,
 544                                 t_forcerec *fr,gmx_vsite_t *vsite,
 545                                 int flags)
 546 {
 547     if (fr->bF_NoVirSum)
 548     {
 549         if (vsite)
 550         {
 551             /* Spread the mesh force on virtual sites to the other particles...
 552              * This is parallellized. MPI communication is performed
 553              * if the constructing atoms aren't local.
 554              */
 555             wallcycle_start(wcycle,ewcVSITESPREAD);
 556             spread_vsite_f(fplog,vsite,x,fr->f_novirsum,NULL,
 557                            (flags & GMX_FORCE_VIRIAL),fr->vir_el_recip,
 558                            nrnb,
 559                            &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
 560             wallcycle_stop(wcycle,ewcVSITESPREAD);
 561         }
 562         if (flags & GMX_FORCE_VIRIAL)
 563         {
 564             /* Now add the forces, this is local */
 565             if (fr->bDomDec)
 566             {
 567                 sum_forces(0,fr->f_novirsum_n,f,fr->f_novirsum);
 568             }
 569             else
 570             {
 571                 sum_forces(mdatoms->start,mdatoms->start+mdatoms->homenr,
 572                            f,fr->f_novirsum);
 573             }
 574             if (EEL_FULL(fr->eeltype))
 575             {
 576                 /* Add the mesh contribution to the virial */
 577                 m_add(vir_force,fr->vir_el_recip,vir_force);
 578             }
 579             if (debug)
 580             {
 581                 pr_rvecs(debug,0,"vir_force",vir_force,DIM);
 582             }
 583         }
 584     }
 585
 586     if (fr->print_force >= 0)
 587     {
 588         print_large_forces(stderr,mdatoms,cr,step,fr->print_force,x,f);
 589     }
 590 }
 591
 592 static void do_nb_verlet(t_forcerec *fr,
 593                          interaction_const_t *ic,
 594                          gmx_enerdata_t *enerd,
 595                          int flags, int ilocality,
 596                          int clearF,
 597                          t_nrnb *nrnb,
 598                          gmx_wallcycle_t wcycle)
 599 {
 600     int     nnbl, kernel_type, enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
 601     char    *env;
 602     nonbonded_verlet_group_t  *nbvg;
 603
 604     if (!(flags & GMX_FORCE_NONBONDED))
 605     {
 606         /* skip non-bonded calculation */
 607         return;
 608     }
 609
 610     nbvg = &fr->nbv->grp[ilocality];
 611
 612     /* CUDA kernel launch overhead is already timed separately */
 613     if (fr->cutoff_scheme != ecutsVERLET)
 614     {
 615         gmx_incons("Invalid cut-off scheme passed!");
 616     }
 617
 618     if (nbvg->kernel_type != nbnxnk8x8x8_CUDA)
 619     {
 620         wallcycle_sub_start(wcycle, ewcsNONBONDED);
 621     }
 622     switch (nbvg->kernel_type)
 623     {
 624         case nbnxnk4x4_PlainC:
 625             nbnxn_kernel_ref(&nbvg->nbl_lists,
 626                              nbvg->nbat, ic,
 627                              fr->shift_vec,
 628                              flags,
 629                              clearF,
 630                              fr->fshift[0],
 631                              enerd->grpp.ener[egCOULSR],
 632                              fr->bBHAM ?
 633                              enerd->grpp.ener[egBHAMSR] :
 634                              enerd->grpp.ener[egLJSR]);
 635             break;
 636
 637         case nbnxnk4xN_SIMD_4xN:
 638             nbnxn_kernel_simd_4xn(&nbvg->nbl_lists,
 639                                   nbvg->nbat, ic,
 640                                   nbvg->ewald_excl,
 641                                   fr->shift_vec,
 642                                   flags,
 643                                   clearF,
 644                                   fr->fshift[0],
 645                                   enerd->grpp.ener[egCOULSR],
 646                                   fr->bBHAM ?
 647                                   enerd->grpp.ener[egBHAMSR] :
 648                                   enerd->grpp.ener[egLJSR]);
 649             break;
 650         case nbnxnk4xN_SIMD_2xNN:
 651             nbnxn_kernel_simd_2xnn(&nbvg->nbl_lists,
 652                                    nbvg->nbat, ic,
 653                                    nbvg->ewald_excl,
 654                                    fr->shift_vec,
 655                                    flags,
 656                                    clearF,
 657                                    fr->fshift[0],
 658                                    enerd->grpp.ener[egCOULSR],
 659                                    fr->bBHAM ?
 660                                    enerd->grpp.ener[egBHAMSR] :
 661                                    enerd->grpp.ener[egLJSR]);
 662             break;
 663
 664         case nbnxnk8x8x8_CUDA:
 665             nbnxn_cuda_launch_kernel(fr->nbv->cu_nbv, nbvg->nbat, flags, ilocality);
 666             break;
 667
 668         case nbnxnk8x8x8_PlainC:
 669             nbnxn_kernel_gpu_ref(nbvg->nbl_lists.nbl[0],
 670                                  nbvg->nbat, ic,
 671                                  fr->shift_vec,
 672                                  flags,
 673                                  clearF,
 674                                  nbvg->nbat->out[0].f,
 675                                  fr->fshift[0],
 676                                  enerd->grpp.ener[egCOULSR],
 677                                  fr->bBHAM ?
 678                                  enerd->grpp.ener[egBHAMSR] :
 679                                  enerd->grpp.ener[egLJSR]);
 680             break;
 681
 682         default:
 683             gmx_incons("Invalid nonbonded kernel type passed!");
 684
 685     }
 686     if (nbvg->kernel_type != nbnxnk8x8x8_CUDA)
 687     {
 688         wallcycle_sub_stop(wcycle, ewcsNONBONDED);
 689     }
 690
 691     if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
 692     {
 693         enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
 694     }
 695     else if (nbvg->ewald_excl == ewaldexclTable)
 696     {
 697         enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_TAB;
 698     }
 699     else
 700     {
 701         enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
 702     }
 703     enr_nbnxn_kernel_lj = eNR_NBNXN_LJ;
 704     if (flags & GMX_FORCE_ENERGY)
 705     {
 706         /* In eNR_??? the nbnxn F+E kernels are always the F kernel + 1 */
 707         enr_nbnxn_kernel_ljc += 1;
 708         enr_nbnxn_kernel_lj  += 1;
 709     }
 710
 711     inc_nrnb(nrnb,enr_nbnxn_kernel_ljc,
 712              nbvg->nbl_lists.natpair_ljq);
 713     inc_nrnb(nrnb,enr_nbnxn_kernel_lj,
 714              nbvg->nbl_lists.natpair_lj);
 715     inc_nrnb(nrnb,enr_nbnxn_kernel_ljc-eNR_NBNXN_LJ_RF+eNR_NBNXN_RF,
 716              nbvg->nbl_lists.natpair_q);
 717 }
 718
 719 void do_force_cutsVERLET(FILE *fplog,t_commrec *cr,
 720               t_inputrec *inputrec,
 721               gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
 722               gmx_localtop_t *top,
 723               gmx_mtop_t *mtop,
 724               gmx_groups_t *groups,
 725               matrix box,rvec x[],history_t *hist,
 726               rvec f[],
 727               tensor vir_force,
 728               t_mdatoms *mdatoms,
 729               gmx_enerdata_t *enerd,t_fcdata *fcd,
 730               real *lambda,t_graph *graph,
 731               t_forcerec *fr, interaction_const_t *ic,
 732               gmx_vsite_t *vsite,rvec mu_tot,
 733               double t,FILE *field,gmx_edsam_t ed,
 734               gmx_bool bBornRadii,
 735               int flags)
 736 {
 737     int     cg0,cg1,i,j;
 738     int     start,homenr;
 739     int     nb_kernel_type;
 740     double  mu[2*DIM];
 741     gmx_bool   bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
 742     gmx_bool   bDoLongRange,bDoForces,bSepLRF,bUseGPU,bUseOrEmulGPU;
 743     gmx_bool   bDiffKernels=FALSE;
 744     matrix  boxs;
 745     rvec    vzero,box_diag;
 746     real    e,v,dvdl;
 747     float  cycles_pme,cycles_force;
 748     nonbonded_verlet_t *nbv;
 749
 750     cycles_force = 0;
 751     nbv = fr->nbv;
 752     nb_kernel_type = fr->nbv->grp[0].kernel_type;
 753
 754     start  = mdatoms->start;
 755     homenr = mdatoms->homenr;
 756
 757     bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));
 758
 759     clear_mat(vir_force);
 760
 761     cg0 = 0;
 762     if (DOMAINDECOMP(cr))
 763     {
 764         cg1 = cr->dd->ncg_tot;
 765     }
 766     else
 767     {
 768         cg1 = top->cgs.nr;
 769     }
 770     if (fr->n_tpi > 0)
 771     {
 772         cg1--;
 773     }
 774
 775     bStateChanged = (flags & GMX_FORCE_STATECHANGED);
 776     bNS           = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
 777     bFillGrid     = (bNS && bStateChanged);
 778     bCalcCGCM     = (bFillGrid && !DOMAINDECOMP(cr));
 779     bDoLongRange  = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DO_LR));
 780     bDoForces     = (flags & GMX_FORCE_FORCES);
 781     bSepLRF       = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
 782     bUseGPU       = fr->nbv->bUseGPU;
 783     bUseOrEmulGPU = bUseGPU || (nbv->grp[0].kernel_type == nbnxnk8x8x8_PlainC);
 784
 785     if (bStateChanged)
 786     {
 787         update_forcerec(fplog,fr,box);
 788
 789         if (NEED_MUTOT(*inputrec))
 790         {
 791             /* Calculate total (local) dipole moment in a temporary common array.
 792              * This makes it possible to sum them over nodes faster.
 793              */
 794             calc_mu(start,homenr,
 795                     x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
 796                     mu,mu+DIM);
 797         }
 798     }
 799
 800     if (fr->ePBC != epbcNONE) {
 801         /* Compute shift vectors every step,
 802          * because of pressure coupling or box deformation!
 803          */
 804         if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
 805             calc_shifts(box,fr->shift_vec);
 806
 807         if (bCalcCGCM) {
 808             put_atoms_in_box_omp(fr->ePBC,box,homenr,x);
 809             inc_nrnb(nrnb,eNR_SHIFTX,homenr);
 810         }
 811         else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
 812             unshift_self(graph,box,x);
 813         }
 814     }
 815
 816     nbnxn_atomdata_copy_shiftvec(flags & GMX_FORCE_DYNAMICBOX,
 817                                   fr->shift_vec,nbv->grp[0].nbat);
 818
 819 #ifdef GMX_MPI
 820     if (!(cr->duty & DUTY_PME)) {
 821         /* Send particle coordinates to the pme nodes.
 822          * Since this is only implemented for domain decomposition
 823          * and domain decomposition does not use the graph,
 824          * we do not need to worry about shifting.
 825          */
 826
 827         wallcycle_start(wcycle,ewcPP_PMESENDX);
 828
 829         bBS = (inputrec->nwall == 2);
 830         if (bBS) {
 831             copy_mat(box,boxs);
 832             svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
 833         }
 834
 835         gmx_pme_send_x(cr,bBS ? boxs : box,x,
 836                        mdatoms->nChargePerturbed,lambda[efptCOUL],
 837                        (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),step);
 838
 839         wallcycle_stop(wcycle,ewcPP_PMESENDX);
 840     }
 841 #endif /* GMX_MPI */
 842
 843     /* do gridding for pair search */
 844     if (bNS)
 845     {
 846         if (graph && bStateChanged)
 847         {
 848             /* Calculate intramolecular shift vectors to make molecules whole */
 849             mk_mshift(fplog,graph,fr->ePBC,box,x);
 850         }
 851
 852         clear_rvec(vzero);
 853         box_diag[XX] = box[XX][XX];
 854         box_diag[YY] = box[YY][YY];
 855         box_diag[ZZ] = box[ZZ][ZZ];
 856
 857         wallcycle_start(wcycle,ewcNS);
 858         if (!fr->bDomDec)
 859         {
 860             wallcycle_sub_start(wcycle,ewcsNBS_GRID_LOCAL);
 861             nbnxn_put_on_grid(nbv->nbs,fr->ePBC,box,
 862                               0,vzero,box_diag,
 863                               0,mdatoms->homenr,-1,fr->cginfo,x,
 864                               0,NULL,
 865                               nbv->grp[eintLocal].kernel_type,
 866                               nbv->grp[eintLocal].nbat);
 867             wallcycle_sub_stop(wcycle,ewcsNBS_GRID_LOCAL);
 868         }
 869         else
 870         {
 871             wallcycle_sub_start(wcycle,ewcsNBS_GRID_NONLOCAL);
 872             nbnxn_put_on_grid_nonlocal(nbv->nbs,domdec_zones(cr->dd),
 873                                        fr->cginfo,x,
 874                                        nbv->grp[eintNonlocal].kernel_type,
 875                                        nbv->grp[eintNonlocal].nbat);
 876             wallcycle_sub_stop(wcycle,ewcsNBS_GRID_NONLOCAL);
 877         }
 878
 879         if (nbv->ngrp == 1 ||
 880             nbv->grp[eintNonlocal].nbat == nbv->grp[eintLocal].nbat)
 881         {
 882             nbnxn_atomdata_set(nbv->grp[eintLocal].nbat,eatAll,
 883                                 nbv->nbs,mdatoms,fr->cginfo);
 884         }
 885         else
 886         {
 887             nbnxn_atomdata_set(nbv->grp[eintLocal].nbat,eatLocal,
 888                                 nbv->nbs,mdatoms,fr->cginfo);
 889             nbnxn_atomdata_set(nbv->grp[eintNonlocal].nbat,eatAll,
 890                                 nbv->nbs,mdatoms,fr->cginfo);
 891         }
 892         wallcycle_stop(wcycle, ewcNS);
 893     }
 894
 895     /* initialize the GPU atom data and copy shift vector */
 896     if (bUseGPU)
 897     {
 898         if (bNS)
 899         {
 900             wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
 901             nbnxn_cuda_init_atomdata(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
 902             wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
 903         }
 904
 905         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
 906         nbnxn_cuda_upload_shiftvec(nbv->cu_nbv, nbv->grp[eintLocal].nbat);
 907         wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
 908     }
 909
 910     /* do local pair search */
 911     if (bNS)
 912     {
 913         wallcycle_start_nocount(wcycle,ewcNS);
 914         wallcycle_sub_start(wcycle,ewcsNBS_SEARCH_LOCAL);
 915         nbnxn_make_pairlist(nbv->nbs,nbv->grp[eintLocal].nbat,
 916                             &top->excls,
 917                             ic->rlist,
 918                             nbv->min_ci_balanced,
 919                             &nbv->grp[eintLocal].nbl_lists,
 920                             eintLocal,
 921                             nbv->grp[eintLocal].kernel_type,
 922                             nrnb);
 923         wallcycle_sub_stop(wcycle,ewcsNBS_SEARCH_LOCAL);
 924
 925         if (bUseGPU)
 926         {
 927             /* initialize local pair-list on the GPU */
 928             nbnxn_cuda_init_pairlist(nbv->cu_nbv,
 929                                      nbv->grp[eintLocal].nbl_lists.nbl[0],
 930                                      eintLocal);
 931         }
 932         wallcycle_stop(wcycle, ewcNS);
 933     }
 934     else
 935     {
 936         wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
 937         wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
 938         nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatLocal,FALSE,x,
 939                                         nbv->grp[eintLocal].nbat);
 940         wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
 941         wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
 942     }
 943
 944     if (bUseGPU)
 945     {
 946         wallcycle_start(wcycle,ewcLAUNCH_GPU_NB);
 947         /* launch local nonbonded F on GPU */
 948         do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFNo,
 949                      nrnb, wcycle);
 950         wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
 951     }
 952
 953     /* Communicate coordinates and sum dipole if necessary +
 954        do non-local pair search */
 955     if (DOMAINDECOMP(cr))
 956     {
 957         bDiffKernels = (nbv->grp[eintNonlocal].kernel_type !=
 958                         nbv->grp[eintLocal].kernel_type);
 959
 960         if (bDiffKernels)
 961         {
 962             /* With GPU+CPU non-bonded calculations we need to copy
 963              * the local coordinates to the non-local nbat struct
 964              * (in CPU format) as the non-local kernel call also
 965              * calculates the local - non-local interactions.
 966              */
 967             wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
 968             wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
 969             nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatLocal,TRUE,x,
 970                                              nbv->grp[eintNonlocal].nbat);
 971             wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
 972             wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
 973         }
 974
 975         if (bNS)
 976         {
 977             wallcycle_start_nocount(wcycle,ewcNS);
 978             wallcycle_sub_start(wcycle,ewcsNBS_SEARCH_NONLOCAL);
 979
 980             if (bDiffKernels)
 981             {
 982                 nbnxn_grid_add_simple(nbv->nbs,nbv->grp[eintNonlocal].nbat);
 983             }
 984
 985             nbnxn_make_pairlist(nbv->nbs,nbv->grp[eintNonlocal].nbat,
 986                                 &top->excls,
 987                                 ic->rlist,
 988                                 nbv->min_ci_balanced,
 989                                 &nbv->grp[eintNonlocal].nbl_lists,
 990                                 eintNonlocal,
 991                                 nbv->grp[eintNonlocal].kernel_type,
 992                                 nrnb);
 993
 994             wallcycle_sub_stop(wcycle,ewcsNBS_SEARCH_NONLOCAL);
 995
 996             if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_CUDA)
 997             {
 998                 /* initialize non-local pair-list on the GPU */
 999                 nbnxn_cuda_init_pairlist(nbv->cu_nbv,
1000                                          nbv->grp[eintNonlocal].nbl_lists.nbl[0],
1001                                          eintNonlocal);
1002             }
1003             wallcycle_stop(wcycle,ewcNS);
1004         }
1005         else
1006         {
1007             wallcycle_start(wcycle,ewcMOVEX);
1008             dd_move_x(cr->dd,box,x);
1009
1010             /* When we don't need the total dipole we sum it in global_stat */
1011             if (bStateChanged && NEED_MUTOT(*inputrec))
1012             {
1013                 gmx_sumd(2*DIM,mu,cr);
1014             }
1015             wallcycle_stop(wcycle,ewcMOVEX);
1016
1017             wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1018             wallcycle_sub_start(wcycle, ewcsNB_X_BUF_OPS);
1019             nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs,eatNonlocal,FALSE,x,
1020                                             nbv->grp[eintNonlocal].nbat);
1021             wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
1022             cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1023         }
1024
1025         if (bUseGPU && !bDiffKernels)
1026         {
1027             wallcycle_start(wcycle,ewcLAUNCH_GPU_NB);
1028             /* launch non-local nonbonded F on GPU */
1029             do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFNo,
1030                          nrnb, wcycle);
1031             cycles_force += wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
1032         }
1033     }
1034
1035     if (bUseGPU)
1036     {
1037         /* launch D2H copy-back F */
1038         wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
1039         if (DOMAINDECOMP(cr) && !bDiffKernels)
1040         {
1041             nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintNonlocal].nbat,
1042                                       flags, eatNonlocal);
1043         }
1044         nbnxn_cuda_launch_cpyback(nbv->cu_nbv, nbv->grp[eintLocal].nbat,
1045                                   flags, eatLocal);
1046         cycles_force += wallcycle_stop(wcycle,ewcLAUNCH_GPU_NB);
1047     }
1048
1049     if (bStateChanged && NEED_MUTOT(*inputrec))
1050     {
1051         if (PAR(cr))
1052         {
1053             gmx_sumd(2*DIM,mu,cr);
1054         }
1055
1056         for(i=0; i<2; i++)
1057         {
1058             for(j=0;j<DIM;j++)
1059             {
1060                 fr->mu_tot[i][j] = mu[i*DIM + j];
1061             }
1062         }
1063     }
1064     if (fr->efep == efepNO)
1065     {
1066         copy_rvec(fr->mu_tot[0],mu_tot);
1067     }
1068     else
1069     {
1070         for(j=0; j<DIM; j++)
1071         {
1072             mu_tot[j] =
1073                 (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] +
1074                 lambda[efptCOUL]*fr->mu_tot[1][j];
1075         }
1076     }
1077
1078     /* Reset energies */
1079     reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
1080     clear_rvecs(SHIFTS,fr->fshift);
1081
1082     if (DOMAINDECOMP(cr))
1083     {
1084         if (!(cr->duty & DUTY_PME))
1085         {
1086             wallcycle_start(wcycle,ewcPPDURINGPME);
1087             dd_force_flop_start(cr->dd,nrnb);
1088         }
1089     }
1090
1091     /* Start the force cycle counter.
1092      * This counter is stopped in do_forcelow_level.
1093      * No parallel communication should occur while this counter is running,
1094      * since that will interfere with the dynamic load balancing.
1095      */
1096     wallcycle_start(wcycle,ewcFORCE);
1097     if (bDoForces)
1098     {
1099         /* Reset forces for which the virial is calculated separately:
1100          * PME/Ewald forces if necessary */
1101         if (fr->bF_NoVirSum)
1102         {
1103             if (flags & GMX_FORCE_VIRIAL)
1104             {
1105                 fr->f_novirsum = fr->f_novirsum_alloc;
1106                 if (fr->bDomDec)
1107                 {
1108                     clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
1109                 }
1110                 else
1111                 {
1112                     clear_rvecs(homenr,fr->f_novirsum+start);
1113                 }
1114             }
1115             else
1116             {
1117                 /* We are not calculating the pressure so we do not need
1118                  * a separate array for forces that do not contribute
1119                  * to the pressure.
1120                  */
1121                 fr->f_novirsum = f;
1122             }
1123         }
1124
1125         /* Clear the short- and long-range forces */
1126         clear_rvecs(fr->natoms_force_constr,f);
1127         if(bSepLRF && do_per_step(step,inputrec->nstcalclr))
1128         {
1129             clear_rvecs(fr->natoms_force_constr,fr->f_twin);
1130         }
1131
1132         clear_rvec(fr->vir_diag_posres);
1133     }
1134     if (inputrec->ePull == epullCONSTRAINT)
1135     {
1136         clear_pull_forces(inputrec->pull);
1137     }
1138
1139     /* update QMMMrec, if necessary */
1140     if(fr->bQMMM)
1141     {
1142         update_QMMMrec(cr,fr,x,mdatoms,box,top);
1143     }
1144
1145     if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1146     {
1147         posres_wrapper(fplog,flags,bSepDVDL,inputrec,nrnb,top,box,x,
1148                        f,enerd,lambda,fr);
1149     }
1150
1151     /* Compute the bonded and non-bonded energies and optionally forces */
1152     do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
1153                       cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
1154                       x,hist,f, bSepLRF ? fr->f_twin : f,enerd,fcd,mtop,top,fr->born,
1155                       &(top->atomtypes),bBornRadii,box,
1156                       inputrec->fepvals,lambda,graph,&(top->excls),fr->mu_tot,
1157                       flags, &cycles_pme);
1158
1159     if(bSepLRF)
1160     {
1161         if (do_per_step(step,inputrec->nstcalclr))
1162         {
1163             /* Add the long range forces to the short range forces */
1164             for(i=0; i<fr->natoms_force_constr; i++)
1165             {
1166                 rvec_add(fr->f_twin[i],f[i],f[i]);
1167             }
1168         }
1169     }
1170
1171     if (!bUseOrEmulGPU)
1172     {
1173         /* Maybe we should move this into do_force_lowlevel */
1174         do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFYes,
1175                      nrnb, wcycle);
1176     }
1177
1178
1179     if (!bUseOrEmulGPU || bDiffKernels)
1180     {
1181         int aloc;
1182
1183         if (DOMAINDECOMP(cr))
1184         {
1185             do_nb_verlet(fr, ic, enerd, flags, eintNonlocal,
1186                          bDiffKernels ? enbvClearFYes : enbvClearFNo,
1187                          nrnb, wcycle);
1188         }
1189
1190         if (!bUseOrEmulGPU)
1191         {
1192             aloc = eintLocal;
1193         }
1194         else
1195         {
1196             aloc = eintNonlocal;
1197         }
1198
1199         /* Add all the non-bonded force to the normal force array.
1200          * This can be split into a local a non-local part when overlapping
1201          * communication with calculation with domain decomposition.
1202          */
1203         cycles_force += wallcycle_stop(wcycle,ewcFORCE);
1204         wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1205         wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1206         nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatAll,nbv->grp[aloc].nbat,f);
1207         wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1208         cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1209         wallcycle_start_nocount(wcycle,ewcFORCE);
1210
1211         /* if there are multiple fshift output buffers reduce them */
1212         if ((flags & GMX_FORCE_VIRIAL) &&
1213             nbv->grp[aloc].nbl_lists.nnbl > 1)
1214         {
1215             nbnxn_atomdata_add_nbat_fshift_to_fshift(nbv->grp[aloc].nbat,
1216                                                       fr->fshift);
1217         }
1218     }
1219
1220     cycles_force += wallcycle_stop(wcycle,ewcFORCE);
1221
1222     if (ed)
1223     {
1224         do_flood(fplog,cr,x,f,ed,box,step,bNS);
1225     }
1226
1227     if (bUseOrEmulGPU && !bDiffKernels)
1228     {
1229         /* wait for non-local forces (or calculate in emulation mode) */
1230         if (DOMAINDECOMP(cr))
1231         {
1232             if (bUseGPU)
1233             {
1234                 wallcycle_start(wcycle,ewcWAIT_GPU_NB_NL);
1235                 nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1236                                     nbv->grp[eintNonlocal].nbat,
1237                                     flags, eatNonlocal,
1238                                     enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1239                                     fr->fshift);
1240                 cycles_force += wallcycle_stop(wcycle,ewcWAIT_GPU_NB_NL);
1241             }
1242             else
1243             {
1244                 wallcycle_start_nocount(wcycle,ewcFORCE);
1245                 do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFYes,
1246                              nrnb, wcycle);
1247                 cycles_force += wallcycle_stop(wcycle,ewcFORCE);
1248             }
1249             wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1250             wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1251             /* skip the reduction if there was no non-local work to do */
1252             if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1253             {
1254                 nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatNonlocal,
1255                                                nbv->grp[eintNonlocal].nbat,f);
1256             }
1257             wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1258             cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1259         }
1260     }
1261
1262     if (bDoForces)
1263     {
1264         /* Communicate the forces */
1265         if (PAR(cr))
1266         {
1267             wallcycle_start(wcycle,ewcMOVEF);
1268             if (DOMAINDECOMP(cr))
1269             {
1270                 dd_move_f(cr->dd,f,fr->fshift);
1271                 /* Do we need to communicate the separate force array
1272                  * for terms that do not contribute to the single sum virial?
1273                  * Position restraints and electric fields do not introduce
1274                  * inter-cg forces, only full electrostatics methods do.
1275                  * When we do not calculate the virial, fr->f_novirsum = f,
1276                  * so we have already communicated these forces.
1277                  */
1278                 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1279                     (flags & GMX_FORCE_VIRIAL))
1280                 {
1281                     dd_move_f(cr->dd,fr->f_novirsum,NULL);
1282                 }
1283                 if (bSepLRF)
1284                 {
1285                     /* We should not update the shift forces here,
1286                      * since f_twin is already included in f.
1287                      */
1288                     dd_move_f(cr->dd,fr->f_twin,NULL);
1289                 }
1290             }
1291             wallcycle_stop(wcycle,ewcMOVEF);
1292         }
1293     }
1294
1295     if (bUseOrEmulGPU)
1296     {
1297         /* wait for local forces (or calculate in emulation mode) */
1298         if (bUseGPU)
1299         {
1300             wallcycle_start(wcycle,ewcWAIT_GPU_NB_L);
1301             nbnxn_cuda_wait_gpu(nbv->cu_nbv,
1302                                 nbv->grp[eintLocal].nbat,
1303                                 flags, eatLocal,
1304                                 enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
1305                                 fr->fshift);
1306             wallcycle_stop(wcycle,ewcWAIT_GPU_NB_L);
1307
1308             /* now clear the GPU outputs while we finish the step on the CPU */
1309             nbnxn_cuda_clear_outputs(nbv->cu_nbv, flags);
1310         }
1311         else
1312         {
1313             wallcycle_start_nocount(wcycle,ewcFORCE);
1314             do_nb_verlet(fr, ic, enerd, flags, eintLocal,
1315                          DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
1316                          nrnb, wcycle);
1317             wallcycle_stop(wcycle,ewcFORCE);
1318         }
1319         wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
1320         wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
1321         if (nbv->grp[eintLocal].nbl_lists.nbl[0]->nsci > 0)
1322         {
1323             /* skip the reduction if there was no non-local work to do */
1324             nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs,eatLocal,
1325                                            nbv->grp[eintLocal].nbat,f);
1326         }
1327         wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
1328         wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
1329     }
1330
1331     if (DOMAINDECOMP(cr))
1332     {
1333         dd_force_flop_stop(cr->dd,nrnb);
1334         if (wcycle)
1335         {
1336             dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
1337         }
1338     }
1339
1340     if (bDoForces)
1341     {
1342         if (IR_ELEC_FIELD(*inputrec))
1343         {
1344             /* Compute forces due to electric field */
1345             calc_f_el(MASTER(cr) ? field : NULL,
1346                       start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
1347                       inputrec->ex,inputrec->et,t);
1348         }
1349
1350         /* If we have NoVirSum forces, but we do not calculate the virial,
1351          * we sum fr->f_novirum=f later.
1352          */
1353         if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1354         {
1355             wallcycle_start(wcycle,ewcVSITESPREAD);
1356             spread_vsite_f(fplog,vsite,x,f,fr->fshift,FALSE,NULL,nrnb,
1357                            &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
1358             wallcycle_stop(wcycle,ewcVSITESPREAD);
1359
1360             if (bSepLRF)
1361             {
1362                 wallcycle_start(wcycle,ewcVSITESPREAD);
1363                 spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,FALSE,NULL,
1364                                nrnb,
1365                                &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
1366                 wallcycle_stop(wcycle,ewcVSITESPREAD);
1367             }
1368         }
1369
1370         if (flags & GMX_FORCE_VIRIAL)
1371         {
1372             /* Calculation of the virial must be done after vsites! */
1373             calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
1374                         vir_force,graph,box,nrnb,fr,inputrec->ePBC);
1375         }
1376     }
1377
1378     if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
1379     {
1380         pull_potential_wrapper(fplog,bSepDVDL,cr,inputrec,box,x,
1381                                f,vir_force,mdatoms,enerd,lambda,t);
1382     }
1383
1384     if (PAR(cr) && !(cr->duty & DUTY_PME))
1385     {
1386         /* In case of node-splitting, the PP nodes receive the long-range
1387          * forces, virial and energy from the PME nodes here.
1388          */
1389         pme_receive_force_ener(fplog,bSepDVDL,cr,wcycle,enerd,fr);
1390     }
1391
1392     if (bDoForces)
1393     {
1394         post_process_forces(fplog,cr,step,nrnb,wcycle,
1395                             top,box,x,f,vir_force,mdatoms,graph,fr,vsite,
1396                             flags);
1397     }
1398
1399     /* Sum the potential energy terms from group contributions */
1400     sum_epot(&(inputrec->opts),&(enerd->grpp),enerd->term);
1401 }
1402
1403 void do_force_cutsGROUP(FILE *fplog,t_commrec *cr,
1404               t_inputrec *inputrec,
1405               gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
1406               gmx_localtop_t *top,
1407               gmx_mtop_t *mtop,
1408               gmx_groups_t *groups,
1409               matrix box,rvec x[],history_t *hist,
1410               rvec f[],
1411               tensor vir_force,
1412               t_mdatoms *mdatoms,
1413               gmx_enerdata_t *enerd,t_fcdata *fcd,
1414               real *lambda,t_graph *graph,
1415               t_forcerec *fr,gmx_vsite_t *vsite,rvec mu_tot,
1416               double t,FILE *field,gmx_edsam_t ed,
1417               gmx_bool bBornRadii,
1418               int flags)
1419 {
1420     int    cg0,cg1,i,j;
1421     int    start,homenr;
1422     double mu[2*DIM];
1423     gmx_bool   bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
1424     gmx_bool   bDoLongRangeNS,bDoForces,bDoPotential,bSepLRF;
1425     gmx_bool   bDoAdressWF;
1426     matrix boxs;
1427     rvec   vzero,box_diag;
1428     real   e,v,dvdlambda[efptNR];
1429     t_pbc  pbc;
1430     float  cycles_pme,cycles_force;
1431
1432     start  = mdatoms->start;
1433     homenr = mdatoms->homenr;
1434
1435     bSepDVDL = (fr->bSepDVDL && do_per_step(step,inputrec->nstlog));
1436
1437     clear_mat(vir_force);
1438
1439     if (PARTDECOMP(cr))
1440     {
1441         pd_cg_range(cr,&cg0,&cg1);
1442     }
1443     else
1444     {
1445         cg0 = 0;
1446         if (DOMAINDECOMP(cr))
1447         {
1448             cg1 = cr->dd->ncg_tot;
1449         }
1450         else
1451         {
1452             cg1 = top->cgs.nr;
1453         }
1454         if (fr->n_tpi > 0)
1455         {
1456             cg1--;
1457         }
1458     }
1459
1460     bStateChanged  = (flags & GMX_FORCE_STATECHANGED);
1461     bNS            = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
1462     /* Should we update the long-range neighborlists at this step? */
1463     bDoLongRangeNS = fr->bTwinRange && bNS;
1464     /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
1465     bFillGrid      = (bNS && bStateChanged);
1466     bCalcCGCM      = (bFillGrid && !DOMAINDECOMP(cr));
1467     bDoForces      = (flags & GMX_FORCE_FORCES);
1468     bDoPotential   = (flags & GMX_FORCE_ENERGY);
1469     bSepLRF        = ((inputrec->nstcalclr>1) && bDoForces &&
1470                       (flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
1471
1472     /* should probably move this to the forcerec since it doesn't change */
1473     bDoAdressWF   = ((fr->adress_type!=eAdressOff));
1474
1475     if (bStateChanged)
1476     {
1477         update_forcerec(fplog,fr,box);
1478
1479         if (NEED_MUTOT(*inputrec))
1480         {
1481             /* Calculate total (local) dipole moment in a temporary common array.
1482              * This makes it possible to sum them over nodes faster.
1483              */
1484             calc_mu(start,homenr,
1485                     x,mdatoms->chargeA,mdatoms->chargeB,mdatoms->nChargePerturbed,
1486                     mu,mu+DIM);
1487         }
1488     }
1489
1490     if (fr->ePBC != epbcNONE) {
1491         /* Compute shift vectors every step,
1492          * because of pressure coupling or box deformation!
1493          */
1494         if ((flags & GMX_FORCE_DYNAMICBOX) && bStateChanged)
1495             calc_shifts(box,fr->shift_vec);
1496
1497         if (bCalcCGCM) {
1498             put_charge_groups_in_box(fplog,cg0,cg1,fr->ePBC,box,
1499                     &(top->cgs),x,fr->cg_cm);
1500             inc_nrnb(nrnb,eNR_CGCM,homenr);
1501             inc_nrnb(nrnb,eNR_RESETX,cg1-cg0);
1502         }
1503         else if (EI_ENERGY_MINIMIZATION(inputrec->eI) && graph) {
1504             unshift_self(graph,box,x);
1505         }
1506     }
1507     else if (bCalcCGCM) {
1508         calc_cgcm(fplog,cg0,cg1,&(top->cgs),x,fr->cg_cm);
1509         inc_nrnb(nrnb,eNR_CGCM,homenr);
1510     }
1511
1512     if (bCalcCGCM) {
1513         if (PAR(cr)) {
1514             move_cgcm(fplog,cr,fr->cg_cm);
1515         }
1516         if (gmx_debug_at)
1517             pr_rvecs(debug,0,"cgcm",fr->cg_cm,top->cgs.nr);
1518     }
1519
1520 #ifdef GMX_MPI
1521     if (!(cr->duty & DUTY_PME)) {
1522         /* Send particle coordinates to the pme nodes.
1523          * Since this is only implemented for domain decomposition
1524          * and domain decomposition does not use the graph,
1525          * we do not need to worry about shifting.
1526          */
1527
1528         wallcycle_start(wcycle,ewcPP_PMESENDX);
1529
1530         bBS = (inputrec->nwall == 2);
1531         if (bBS) {
1532             copy_mat(box,boxs);
1533             svmul(inputrec->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
1534         }
1535
1536         gmx_pme_send_x(cr,bBS ? boxs : box,x,
1537                        mdatoms->nChargePerturbed,lambda[efptCOUL],
1538                        (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),step);
1539
1540         wallcycle_stop(wcycle,ewcPP_PMESENDX);
1541     }
1542 #endif /* GMX_MPI */
1543
1544     /* Communicate coordinates and sum dipole if necessary */
1545     if (PAR(cr))
1546     {
1547         wallcycle_start(wcycle,ewcMOVEX);
1548         if (DOMAINDECOMP(cr))
1549         {
1550             dd_move_x(cr->dd,box,x);
1551         }
1552         else
1553         {
1554             move_x(fplog,cr,GMX_LEFT,GMX_RIGHT,x,nrnb);
1555         }
1556         wallcycle_stop(wcycle,ewcMOVEX);
1557     }
1558
1559     /* update adress weight beforehand */
1560     if(bStateChanged && bDoAdressWF)
1561     {
1562         /* need pbc for adress weight calculation with pbc_dx */
1563         set_pbc(&pbc,inputrec->ePBC,box);
1564         if(fr->adress_site == eAdressSITEcog)
1565         {
1566             update_adress_weights_cog(top->idef.iparams,top->idef.il,x,fr,mdatoms,
1567                                       inputrec->ePBC==epbcNONE ? NULL : &pbc);
1568         }
1569         else if (fr->adress_site == eAdressSITEcom)
1570         {
1571             update_adress_weights_com(fplog,cg0,cg1,&(top->cgs),x,fr,mdatoms,
1572                                       inputrec->ePBC==epbcNONE ? NULL : &pbc);
1573         }
1574         else if (fr->adress_site == eAdressSITEatomatom){
1575             update_adress_weights_atom_per_atom(cg0,cg1,&(top->cgs),x,fr,mdatoms,
1576                                                 inputrec->ePBC==epbcNONE ? NULL : &pbc);
1577         }
1578         else
1579         {
1580             update_adress_weights_atom(cg0,cg1,&(top->cgs),x,fr,mdatoms,
1581                                        inputrec->ePBC==epbcNONE ? NULL : &pbc);
1582         }
1583     }
1584
1585     if (NEED_MUTOT(*inputrec))
1586     {
1587
1588         if (bStateChanged)
1589         {
1590             if (PAR(cr))
1591             {
1592                 gmx_sumd(2*DIM,mu,cr);
1593             }
1594             for(i=0; i<2; i++)
1595             {
1596                 for(j=0;j<DIM;j++)
1597                 {
1598                     fr->mu_tot[i][j] = mu[i*DIM + j];
1599                 }
1600             }
1601         }
1602         if (fr->efep == efepNO)
1603         {
1604             copy_rvec(fr->mu_tot[0],mu_tot);
1605         }
1606         else
1607         {
1608             for(j=0; j<DIM; j++)
1609             {
1610                 mu_tot[j] =
1611                     (1.0 - lambda[efptCOUL])*fr->mu_tot[0][j] + lambda[efptCOUL]*fr->mu_tot[1][j];
1612             }
1613         }
1614     }
1615
1616     /* Reset energies */
1617     reset_enerdata(&(inputrec->opts),fr,bNS,enerd,MASTER(cr));
1618     clear_rvecs(SHIFTS,fr->fshift);
1619
1620     if (bNS)
1621     {
1622         wallcycle_start(wcycle,ewcNS);
1623
1624         if (graph && bStateChanged)
1625         {
1626             /* Calculate intramolecular shift vectors to make molecules whole */
1627             mk_mshift(fplog,graph,fr->ePBC,box,x);
1628         }
1629
1630         /* Do the actual neighbour searching and if twin range electrostatics
1631          * also do the calculation of long range forces and energies.
1632          */
1633         for (i=0;i<efptNR;i++) {dvdlambda[i] = 0;}
1634         ns(fplog,fr,x,box,
1635            groups,&(inputrec->opts),top,mdatoms,
1636            cr,nrnb,lambda,dvdlambda,&enerd->grpp,bFillGrid,
1637            bDoLongRangeNS);
1638         if (bSepDVDL)
1639         {
1640             fprintf(fplog,sepdvdlformat,"LR non-bonded",0.0,dvdlambda);
1641         }
1642         enerd->dvdl_lin[efptVDW] += dvdlambda[efptVDW];
1643         enerd->dvdl_lin[efptCOUL] += dvdlambda[efptCOUL];
1644
1645         wallcycle_stop(wcycle,ewcNS);
1646     }
1647
1648     if (inputrec->implicit_solvent && bNS)
1649     {
1650         make_gb_nblist(cr,inputrec->gb_algorithm,inputrec->rlist,
1651                        x,box,fr,&top->idef,graph,fr->born);
1652     }
1653
1654     if (DOMAINDECOMP(cr))
1655     {
1656         if (!(cr->duty & DUTY_PME))
1657         {
1658             wallcycle_start(wcycle,ewcPPDURINGPME);
1659             dd_force_flop_start(cr->dd,nrnb);
1660         }
1661     }
1662
1663     if (inputrec->bRot)
1664     {
1665         /* Enforced rotation has its own cycle counter that starts after the collective
1666          * coordinates have been communicated. It is added to ddCyclF to allow
1667          * for proper load-balancing */
1668         wallcycle_start(wcycle,ewcROT);
1669         do_rotation(cr,inputrec,box,x,t,step,wcycle,bNS);
1670         wallcycle_stop(wcycle,ewcROT);
1671     }
1672
1673     /* Start the force cycle counter.
1674      * This counter is stopped in do_forcelow_level.
1675      * No parallel communication should occur while this counter is running,
1676      * since that will interfere with the dynamic load balancing.
1677      */
1678     wallcycle_start(wcycle,ewcFORCE);
1679
1680     if (bDoForces)
1681     {
1682         /* Reset forces for which the virial is calculated separately:
1683          * PME/Ewald forces if necessary */
1684         if (fr->bF_NoVirSum)
1685         {
1686             if (flags & GMX_FORCE_VIRIAL)
1687             {
1688                 fr->f_novirsum = fr->f_novirsum_alloc;
1689                 if (fr->bDomDec)
1690                 {
1691                     clear_rvecs(fr->f_novirsum_n,fr->f_novirsum);
1692                 }
1693                 else
1694                 {
1695                     clear_rvecs(homenr,fr->f_novirsum+start);
1696                 }
1697             }
1698             else
1699             {
1700                 /* We are not calculating the pressure so we do not need
1701                  * a separate array for forces that do not contribute
1702                  * to the pressure.
1703                  */
1704                 fr->f_novirsum = f;
1705             }
1706         }
1707
1708         /* Clear the short- and long-range forces */
1709         clear_rvecs(fr->natoms_force_constr,f);
1710         if(bSepLRF && do_per_step(step,inputrec->nstcalclr))
1711         {
1712             clear_rvecs(fr->natoms_force_constr,fr->f_twin);
1713         }
1714
1715         clear_rvec(fr->vir_diag_posres);
1716     }
1717     if (inputrec->ePull == epullCONSTRAINT)
1718     {
1719         clear_pull_forces(inputrec->pull);
1720     }
1721
1722     /* update QMMMrec, if necessary */
1723     if(fr->bQMMM)
1724     {
1725         update_QMMMrec(cr,fr,x,mdatoms,box,top);
1726     }
1727
1728     if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_POSRES].nr > 0)
1729     {
1730         posres_wrapper(fplog,flags,bSepDVDL,inputrec,nrnb,top,box,x,
1731                        f,enerd,lambda,fr);
1732     }
1733
1734     if ((flags & GMX_FORCE_BONDED) && top->idef.il[F_FBPOSRES].nr > 0)
1735     {
1736         /* Flat-bottomed position restraints always require full pbc */
1737         if(!(bStateChanged && bDoAdressWF))
1738         {
1739             set_pbc(&pbc,inputrec->ePBC,box);
1740         }
1741         v = fbposres(top->idef.il[F_FBPOSRES].nr,top->idef.il[F_FBPOSRES].iatoms,
1742                      top->idef.iparams_fbposres,
1743                      (const rvec*)x,fr->f_novirsum,fr->vir_diag_posres,
1744                      inputrec->ePBC==epbcNONE ? NULL : &pbc,
1745                      fr->rc_scaling,fr->ePBC,fr->posres_com);
1746         enerd->term[F_FBPOSRES] += v;
1747         inc_nrnb(nrnb,eNR_FBPOSRES,top->idef.il[F_FBPOSRES].nr/2);
1748     }
1749
1750     /* Compute the bonded and non-bonded energies and optionally forces */
1751     do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
1752                       cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
1753                       x,hist,f, bSepLRF ? fr->f_twin : f,enerd,fcd,mtop,top,fr->born,
1754                       &(top->atomtypes),bBornRadii,box,
1755                       inputrec->fepvals,lambda,
1756                       graph,&(top->excls),fr->mu_tot,
1757                       flags,
1758                       &cycles_pme);
1759
1760     if(bSepLRF)
1761     {
1762         if (do_per_step(step,inputrec->nstcalclr))
1763         {
1764             /* Add the long range forces to the short range forces */
1765             for(i=0; i<fr->natoms_force_constr; i++)
1766             {
1767                 rvec_add(fr->f_twin[i],f[i],f[i]);
1768             }
1769         }
1770     }
1771
1772     cycles_force = wallcycle_stop(wcycle,ewcFORCE);
1773
1774     if (ed)
1775     {
1776         do_flood(fplog,cr,x,f,ed,box,step,bNS);
1777     }
1778
1779     if (DOMAINDECOMP(cr))
1780     {
1781         dd_force_flop_stop(cr->dd,nrnb);
1782         if (wcycle)
1783         {
1784             dd_cycles_add(cr->dd,cycles_force-cycles_pme,ddCyclF);
1785         }
1786     }
1787
1788     if (bDoForces)
1789     {
1790         if (IR_ELEC_FIELD(*inputrec))
1791         {
1792             /* Compute forces due to electric field */
1793             calc_f_el(MASTER(cr) ? field : NULL,
1794                       start,homenr,mdatoms->chargeA,x,fr->f_novirsum,
1795                       inputrec->ex,inputrec->et,t);
1796         }
1797
1798         if (bDoAdressWF && fr->adress_icor == eAdressICThermoForce)
1799         {
1800             /* Compute thermodynamic force in hybrid AdResS region */
1801             adress_thermo_force(start,homenr,&(top->cgs),x,fr->f_novirsum,fr,mdatoms,
1802                                 inputrec->ePBC==epbcNONE ? NULL : &pbc);
1803         }
1804
1805         /* Communicate the forces */
1806         if (PAR(cr))
1807         {
1808             wallcycle_start(wcycle,ewcMOVEF);
1809             if (DOMAINDECOMP(cr))
1810             {
1811                 dd_move_f(cr->dd,f,fr->fshift);
1812                 /* Do we need to communicate the separate force array
1813                  * for terms that do not contribute to the single sum virial?
1814                  * Position restraints and electric fields do not introduce
1815                  * inter-cg forces, only full electrostatics methods do.
1816                  * When we do not calculate the virial, fr->f_novirsum = f,
1817                  * so we have already communicated these forces.
1818                  */
1819                 if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
1820                     (flags & GMX_FORCE_VIRIAL))
1821                 {
1822                     dd_move_f(cr->dd,fr->f_novirsum,NULL);
1823                 }
1824                 if (bSepLRF)
1825                 {
1826                     /* We should not update the shift forces here,
1827                      * since f_twin is already included in f.
1828                      */
1829                     dd_move_f(cr->dd,fr->f_twin,NULL);
1830                 }
1831             }
1832             else
1833             {
1834                 pd_move_f(cr,f,nrnb);
1835                 if (bSepLRF)
1836                 {
1837                     pd_move_f(cr,fr->f_twin,nrnb);
1838                 }
1839             }
1840             wallcycle_stop(wcycle,ewcMOVEF);
1841         }
1842
1843         /* If we have NoVirSum forces, but we do not calculate the virial,
1844          * we sum fr->f_novirum=f later.
1845          */
1846         if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
1847         {
1848             wallcycle_start(wcycle,ewcVSITESPREAD);
1849             spread_vsite_f(fplog,vsite,x,f,fr->fshift,FALSE,NULL,nrnb,
1850                            &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
1851             wallcycle_stop(wcycle,ewcVSITESPREAD);
1852
1853             if (bSepLRF)
1854             {
1855                 wallcycle_start(wcycle,ewcVSITESPREAD);
1856                 spread_vsite_f(fplog,vsite,x,fr->f_twin,NULL,FALSE,NULL,
1857                                nrnb,
1858                                &top->idef,fr->ePBC,fr->bMolPBC,graph,box,cr);
1859                 wallcycle_stop(wcycle,ewcVSITESPREAD);
1860             }
1861         }
1862
1863         if (flags & GMX_FORCE_VIRIAL)
1864         {
1865             /* Calculation of the virial must be done after vsites! */
1866             calc_virial(fplog,mdatoms->start,mdatoms->homenr,x,f,
1867                         vir_force,graph,box,nrnb,fr,inputrec->ePBC);
1868         }
1869     }
1870
1871     if (inputrec->ePull == epullUMBRELLA || inputrec->ePull == epullCONST_F)
1872     {
1873         pull_potential_wrapper(fplog,bSepDVDL,cr,inputrec,box,x,
1874                                f,vir_force,mdatoms,enerd,lambda,t);
1875     }
1876
1877     /* Add the forces from enforced rotation potentials (if any) */
1878     if (inputrec->bRot)
1879     {
1880         wallcycle_start(wcycle,ewcROTadd);
1881         enerd->term[F_COM_PULL] += add_rot_forces(inputrec->rot, f, cr,step,t);
1882         wallcycle_stop(wcycle,ewcROTadd);
1883     }
1884
1885     if (PAR(cr) && !(cr->duty & DUTY_PME))
1886     {
1887         /* In case of node-splitting, the PP nodes receive the long-range
1888          * forces, virial and energy from the PME nodes here.
1889          */
1890         pme_receive_force_ener(fplog,bSepDVDL,cr,wcycle,enerd,fr);
1891     }
1892
1893     if (bDoForces)
1894     {
1895         post_process_forces(fplog,cr,step,nrnb,wcycle,
1896                             top,box,x,f,vir_force,mdatoms,graph,fr,vsite,
1897                             flags);
1898     }
1899
1900     /* Sum the potential energy terms from group contributions */
1901     sum_epot(&(inputrec->opts),&(enerd->grpp),enerd->term);
1902 }
1903
1904 void do_force(FILE *fplog,t_commrec *cr,
1905               t_inputrec *inputrec,
1906               gmx_large_int_t step,t_nrnb *nrnb,gmx_wallcycle_t wcycle,
1907               gmx_localtop_t *top,
1908               gmx_mtop_t *mtop,
1909               gmx_groups_t *groups,
1910               matrix box,rvec x[],history_t *hist,
1911               rvec f[],
1912               tensor vir_force,
1913               t_mdatoms *mdatoms,
1914               gmx_enerdata_t *enerd,t_fcdata *fcd,
1915               real *lambda,t_graph *graph,
1916               t_forcerec *fr,
1917               gmx_vsite_t *vsite,rvec mu_tot,
1918               double t,FILE *field,gmx_edsam_t ed,
1919               gmx_bool bBornRadii,
1920               int flags)
1921 {
1922     /* modify force flag if not doing nonbonded */
1923     if (!fr->bNonbonded)
1924     {
1925         flags &= ~GMX_FORCE_NONBONDED;
1926     }
1927
1928     switch (inputrec->cutoff_scheme)
1929     {
1930         case ecutsVERLET:
1931             do_force_cutsVERLET(fplog, cr, inputrec,
1932                                 step, nrnb, wcycle,
1933                                 top, mtop,
1934                                 groups,
1935                                 box, x, hist,
1936                                 f, vir_force,
1937                                 mdatoms,
1938                                 enerd, fcd,
1939                                 lambda, graph,
1940                                 fr, fr->ic,
1941                                 vsite, mu_tot,
1942                                 t, field, ed,
1943                                 bBornRadii,
1944                                 flags);
1945             break;
1946         case ecutsGROUP:
1947              do_force_cutsGROUP(fplog, cr, inputrec,
1948                                 step, nrnb, wcycle,
1949                                 top, mtop,
1950                                 groups,
1951                                 box, x, hist,
1952                                 f, vir_force,
1953                                 mdatoms,
1954                                 enerd, fcd,
1955                                 lambda, graph,
1956                                 fr, vsite, mu_tot,
1957                                 t, field, ed,
1958                                 bBornRadii,
1959                                 flags);
1960             break;
1961         default:
1962             gmx_incons("Invalid cut-off scheme passed!");
1963     }
1964 }
1965
1966
1967 void do_constrain_first(FILE *fplog,gmx_constr_t constr,
1968                         t_inputrec *ir,t_mdatoms *md,
1969                         t_state *state,rvec *f,
1970                         t_graph *graph,t_commrec *cr,t_nrnb *nrnb,
1971                         t_forcerec *fr, gmx_localtop_t *top, tensor shake_vir)
1972 {
1973     int    i,m,start,end;
1974     gmx_large_int_t step;
1975     real   dt=ir->delta_t;
1976     real   dvdl_dum;
1977     rvec   *savex;
1978
1979     snew(savex,state->natoms);
1980
1981     start = md->start;
1982     end   = md->homenr + start;
1983
1984     if (debug)
1985         fprintf(debug,"vcm: start=%d, homenr=%d, end=%d\n",
1986                 start,md->homenr,end);
1987     /* Do a first constrain to reset particles... */
1988     step = ir->init_step;
1989     if (fplog)
1990     {
1991         char buf[STEPSTRSIZE];
1992         fprintf(fplog,"\nConstraining the starting coordinates (step %s)\n",
1993                 gmx_step_str(step,buf));
1994     }
1995     dvdl_dum = 0;
1996
1997     /* constrain the current position */
1998     constrain(NULL,TRUE,FALSE,constr,&(top->idef),
1999               ir,NULL,cr,step,0,md,
2000               state->x,state->x,NULL,
2001               fr->bMolPBC,state->box,
2002               state->lambda[efptBONDED],&dvdl_dum,
2003               NULL,NULL,nrnb,econqCoord,
2004               ir->epc==epcMTTK,state->veta,state->veta);
2005     if (EI_VV(ir->eI))
2006     {
2007         /* constrain the inital velocity, and save it */
2008         /* also may be useful if we need the ekin from the halfstep for velocity verlet */
2009         /* might not yet treat veta correctly */
2010         constrain(NULL,TRUE,FALSE,constr,&(top->idef),
2011                   ir,NULL,cr,step,0,md,
2012                   state->x,state->v,state->v,
2013                   fr->bMolPBC,state->box,
2014                   state->lambda[efptBONDED],&dvdl_dum,
2015                   NULL,NULL,nrnb,econqVeloc,
2016                   ir->epc==epcMTTK,state->veta,state->veta);
2017     }
2018     /* constrain the inital velocities at t-dt/2 */
2019     if (EI_STATE_VELOCITY(ir->eI) && ir->eI!=eiVV)
2020     {
2021         for(i=start; (i<end); i++)
2022         {
2023             for(m=0; (m<DIM); m++)
2024             {
2025                 /* Reverse the velocity */
2026                 state->v[i][m] = -state->v[i][m];
2027                 /* Store the position at t-dt in buf */
2028                 savex[i][m] = state->x[i][m] + dt*state->v[i][m];
2029             }
2030         }
2031     /* Shake the positions at t=-dt with the positions at t=0
2032      * as reference coordinates.
2033          */
2034         if (fplog)
2035         {
2036             char buf[STEPSTRSIZE];
2037             fprintf(fplog,"\nConstraining the coordinates at t0-dt (step %s)\n",
2038                     gmx_step_str(step,buf));
2039         }
2040         dvdl_dum = 0;
2041         constrain(NULL,TRUE,FALSE,constr,&(top->idef),
2042                   ir,NULL,cr,step,-1,md,
2043                   state->x,savex,NULL,
2044                   fr->bMolPBC,state->box,
2045                   state->lambda[efptBONDED],&dvdl_dum,
2046                   state->v,NULL,nrnb,econqCoord,
2047                   ir->epc==epcMTTK,state->veta,state->veta);
2048
2049         for(i=start; i<end; i++) {
2050             for(m=0; m<DIM; m++) {
2051                 /* Re-reverse the velocities */
2052                 state->v[i][m] = -state->v[i][m];
2053             }
2054         }
2055     }
2056     sfree(savex);
2057 }
2058
2059 void calc_enervirdiff(FILE *fplog,int eDispCorr,t_forcerec *fr)
2060 {
2061   double eners[2],virs[2],enersum,virsum,y0,f,g,h;
2062   double r0,r1,r,rc3,rc9,ea,eb,ec,pa,pb,pc,pd;
2063   double invscale,invscale2,invscale3;
2064   int    ri0,ri1,ri,i,offstart,offset;
2065   real   scale,*vdwtab,tabfactor,tmp;
2066
2067   fr->enershiftsix = 0;
2068   fr->enershifttwelve = 0;
2069   fr->enerdiffsix = 0;
2070   fr->enerdifftwelve = 0;
2071   fr->virdiffsix = 0;
2072   fr->virdifftwelve = 0;
2073
2074   if (eDispCorr != edispcNO) {
2075     for(i=0; i<2; i++) {
2076       eners[i] = 0;
2077       virs[i]  = 0;
2078     }
2079     if ((fr->vdwtype == evdwSWITCH) || (fr->vdwtype == evdwSHIFT)) {
2080       if (fr->rvdw_switch == 0)
2081         gmx_fatal(FARGS,
2082                   "With dispersion correction rvdw-switch can not be zero "
2083                   "for vdw-type = %s",evdw_names[fr->vdwtype]);
2084
2085       scale  = fr->nblists[0].table_elec_vdw.scale;
2086       vdwtab = fr->nblists[0].table_vdw.data;
2087
2088       /* Round the cut-offs to exact table values for precision */
2089       ri0 = floor(fr->rvdw_switch*scale);
2090       ri1 = ceil(fr->rvdw*scale);
2091       r0  = ri0/scale;
2092       r1  = ri1/scale;
2093       rc3 = r0*r0*r0;
2094       rc9  = rc3*rc3*rc3;
2095
2096       if (fr->vdwtype == evdwSHIFT)
2097       {
2098           /* Determine the constant energy shift below rvdw_switch.
2099            * Table has a scale factor since we have scaled it down to compensate
2100            * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
2101            */
2102           fr->enershiftsix    = (real)(-1.0/(rc3*rc3)) - 6.0*vdwtab[8*ri0];
2103           fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - 12.0*vdwtab[8*ri0 + 4];
2104       }
2105       /* Add the constant part from 0 to rvdw_switch.
2106        * This integration from 0 to rvdw_switch overcounts the number
2107        * of interactions by 1, as it also counts the self interaction.
2108        * We will correct for this later.
2109        */
2110       eners[0] += 4.0*M_PI*fr->enershiftsix*rc3/3.0;
2111       eners[1] += 4.0*M_PI*fr->enershifttwelve*rc3/3.0;
2112
2113       invscale = 1.0/(scale);
2114       invscale2 = invscale*invscale;
2115       invscale3 = invscale*invscale2;
2116
2117       /* following summation derived from cubic spline definition,
2118         Numerical Recipies in C, second edition, p. 113-116.  Exact
2119         for the cubic spline.  We first calculate the negative of
2120         the energy from rvdw to rvdw_switch, assuming that g(r)=1,
2121         and then add the more standard, abrupt cutoff correction to
2122         that result, yielding the long-range correction for a
2123         switched function.  We perform both the pressure and energy
2124         loops at the same time for simplicity, as the computational
2125         cost is low. */
2126
2127       for (i=0;i<2;i++) {
2128         enersum = 0.0; virsum = 0.0;
2129         if (i==0)
2130         {
2131             offstart = 0;
2132             /* Since the dispersion table has been scaled down a factor 6.0 and the repulsion
2133              * a factor 12.0 to compensate for the c6/c12 parameters inside nbfp[] being scaled
2134              * up (to save flops in kernels), we need to correct for this.
2135              */
2136             tabfactor = 6.0;
2137         }
2138         else
2139         {
2140             offstart = 4;
2141             tabfactor = 12.0;
2142         }
2143         for (ri=ri0; ri<ri1; ri++) {
2144           r = ri*invscale;
2145           ea = invscale3;
2146           eb = 2.0*invscale2*r;
2147           ec = invscale*r*r;
2148
2149           pa = invscale3;
2150           pb = 3.0*invscale2*r;
2151           pc = 3.0*invscale*r*r;
2152           pd = r*r*r;
2153
2154           /* this "8" is from the packing in the vdwtab array - perhaps should be #define'ed? */
2155           offset = 8*ri + offstart;
2156           y0 = vdwtab[offset];
2157           f  = vdwtab[offset+1];
2158           g  = vdwtab[offset+2];
2159           h  = vdwtab[offset+3];
2160
2161           enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2) + g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
2162           virsum  += f*(pa/4 + pb/3 + pc/2 + pd) + 2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
2163         }
2164
2165         enersum *= 4.0*M_PI*tabfactor;
2166         virsum  *= 4.0*M_PI*tabfactor;
2167         eners[i] -= enersum;
2168         virs[i]  -= virsum;
2169       }
2170
2171       /* now add the correction for rvdw_switch to infinity */
2172       eners[0] += -4.0*M_PI/(3.0*rc3);
2173       eners[1] +=  4.0*M_PI/(9.0*rc9);
2174       virs[0]  +=  8.0*M_PI/rc3;
2175       virs[1]  += -16.0*M_PI/(3.0*rc9);
2176     }
2177     else if ((fr->vdwtype == evdwCUT) || (fr->vdwtype == evdwUSER)) {
2178       if (fr->vdwtype == evdwUSER && fplog)
2179         fprintf(fplog,
2180                 "WARNING: using dispersion correction with user tables\n");
2181       rc3  = fr->rvdw*fr->rvdw*fr->rvdw;
2182       rc9  = rc3*rc3*rc3;
2183       /* Contribution beyond the cut-off */
2184       eners[0] += -4.0*M_PI/(3.0*rc3);
2185       eners[1] +=  4.0*M_PI/(9.0*rc9);
2186       if (fr->vdw_modifier==eintmodPOTSHIFT) {
2187           /* Contribution within the cut-off */
2188           eners[0] += -4.0*M_PI/(3.0*rc3);
2189           eners[1] +=  4.0*M_PI/(3.0*rc9);
2190       }
2191       /* Contribution beyond the cut-off */
2192       virs[0]  +=  8.0*M_PI/rc3;
2193       virs[1]  += -16.0*M_PI/(3.0*rc9);
2194     } else {
2195       gmx_fatal(FARGS,
2196                 "Dispersion correction is not implemented for vdw-type = %s",
2197                 evdw_names[fr->vdwtype]);
2198     }
2199     fr->enerdiffsix    = eners[0];
2200     fr->enerdifftwelve = eners[1];
2201     /* The 0.5 is due to the Gromacs definition of the virial */
2202     fr->virdiffsix     = 0.5*virs[0];
2203     fr->virdifftwelve  = 0.5*virs[1];
2204   }
2205 }
2206
2207 void calc_dispcorr(FILE *fplog,t_inputrec *ir,t_forcerec *fr,
2208                    gmx_large_int_t step,int natoms,
2209                    matrix box,real lambda,tensor pres,tensor virial,
2210                    real *prescorr, real *enercorr, real *dvdlcorr)
2211 {
2212     gmx_bool bCorrAll,bCorrPres;
2213     real dvdlambda,invvol,dens,ninter,avcsix,avctwelve,enerdiff,svir=0,spres=0;
2214     int  m;
2215
2216     *prescorr = 0;
2217     *enercorr = 0;
2218     *dvdlcorr = 0;
2219
2220     clear_mat(virial);
2221     clear_mat(pres);
2222
2223     if (ir->eDispCorr != edispcNO) {
2224         bCorrAll  = (ir->eDispCorr == edispcAllEner ||
2225                      ir->eDispCorr == edispcAllEnerPres);
2226         bCorrPres = (ir->eDispCorr == edispcEnerPres ||
2227                      ir->eDispCorr == edispcAllEnerPres);
2228
2229         invvol = 1/det(box);
2230         if (fr->n_tpi)
2231         {
2232             /* Only correct for the interactions with the inserted molecule */
2233             dens = (natoms - fr->n_tpi)*invvol;
2234             ninter = fr->n_tpi;
2235         }
2236         else
2237         {
2238             dens = natoms*invvol;
2239             ninter = 0.5*natoms;
2240         }
2241
2242         if (ir->efep == efepNO)
2243         {
2244             avcsix    = fr->avcsix[0];
2245             avctwelve = fr->avctwelve[0];
2246         }
2247         else
2248         {
2249             avcsix    = (1 - lambda)*fr->avcsix[0]    + lambda*fr->avcsix[1];
2250             avctwelve = (1 - lambda)*fr->avctwelve[0] + lambda*fr->avctwelve[1];
2251         }
2252
2253         enerdiff = ninter*(dens*fr->enerdiffsix - fr->enershiftsix);
2254         *enercorr += avcsix*enerdiff;
2255         dvdlambda = 0.0;
2256         if (ir->efep != efepNO)
2257         {
2258             dvdlambda += (fr->avcsix[1] - fr->avcsix[0])*enerdiff;
2259         }
2260         if (bCorrAll)
2261         {
2262             enerdiff = ninter*(dens*fr->enerdifftwelve - fr->enershifttwelve);
2263             *enercorr += avctwelve*enerdiff;
2264             if (fr->efep != efepNO)
2265             {
2266                 dvdlambda += (fr->avctwelve[1] - fr->avctwelve[0])*enerdiff;
2267             }
2268         }
2269
2270         if (bCorrPres)
2271         {
2272             svir = ninter*dens*avcsix*fr->virdiffsix/3.0;
2273             if (ir->eDispCorr == edispcAllEnerPres)
2274             {
2275                 svir += ninter*dens*avctwelve*fr->virdifftwelve/3.0;
2276             }
2277             /* The factor 2 is because of the Gromacs virial definition */
2278             spres = -2.0*invvol*svir*PRESFAC;
2279
2280             for(m=0; m<DIM; m++) {
2281                 virial[m][m] += svir;
2282                 pres[m][m] += spres;
2283             }
2284             *prescorr += spres;
2285         }
2286
2287         /* Can't currently control when it prints, for now, just print when degugging */
2288         if (debug)
2289         {
2290             if (bCorrAll) {
2291                 fprintf(debug,"Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
2292                         avcsix,avctwelve);
2293             }
2294             if (bCorrPres)
2295             {
2296                 fprintf(debug,
2297                         "Long Range LJ corr.: Epot %10g, Pres: %10g, Vir: %10g\n",
2298                         *enercorr,spres,svir);
2299             }
2300             else
2301             {
2302                 fprintf(debug,"Long Range LJ corr.: Epot %10g\n",*enercorr);
2303             }
2304         }
2305
2306         if (fr->bSepDVDL && do_per_step(step,ir->nstlog))
2307         {
2308             fprintf(fplog,sepdvdlformat,"Dispersion correction",
2309                     *enercorr,dvdlambda);
2310         }
2311         if (fr->efep != efepNO)
2312         {
2313             *dvdlcorr += dvdlambda;
2314         }
2315     }
2316 }
2317
2318 void do_pbc_first(FILE *fplog,matrix box,t_forcerec *fr,
2319                   t_graph *graph,rvec x[])
2320 {
2321   if (fplog)
2322     fprintf(fplog,"Removing pbc first time\n");
2323   calc_shifts(box,fr->shift_vec);
2324   if (graph) {
2325     mk_mshift(fplog,graph,fr->ePBC,box,x);
2326     if (gmx_debug_at)
2327       p_graph(debug,"do_pbc_first 1",graph);
2328     shift_self(graph,box,x);
2329     /* By doing an extra mk_mshift the molecules that are broken
2330      * because they were e.g. imported from another software
2331      * will be made whole again. Such are the healing powers
2332      * of GROMACS.
2333      */
2334     mk_mshift(fplog,graph,fr->ePBC,box,x);
2335     if (gmx_debug_at)
2336       p_graph(debug,"do_pbc_first 2",graph);
2337   }
2338   if (fplog)
2339     fprintf(fplog,"Done rmpbc\n");
2340 }
2341
2342 static void low_do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
2343                             gmx_mtop_t *mtop,rvec x[],
2344                             gmx_bool bFirst)
2345 {
2346   t_graph *graph;
2347   int mb,as,mol;
2348   gmx_molblock_t *molb;
2349
2350   if (bFirst && fplog)
2351     fprintf(fplog,"Removing pbc first time\n");
2352
2353   snew(graph,1);
2354   as = 0;
2355   for(mb=0; mb<mtop->nmolblock; mb++) {
2356     molb = &mtop->molblock[mb];
2357     if (molb->natoms_mol == 1 ||
2358         (!bFirst && mtop->moltype[molb->type].cgs.nr == 1)) {
2359       /* Just one atom or charge group in the molecule, no PBC required */
2360       as += molb->nmol*molb->natoms_mol;
2361     } else {
2362       /* Pass NULL iso fplog to avoid graph prints for each molecule type */
2363       mk_graph_ilist(NULL,mtop->moltype[molb->type].ilist,
2364                      0,molb->natoms_mol,FALSE,FALSE,graph);
2365
2366       for(mol=0; mol<molb->nmol; mol++) {
2367         mk_mshift(fplog,graph,ePBC,box,x+as);
2368
2369         shift_self(graph,box,x+as);
2370         /* The molecule is whole now.
2371          * We don't need the second mk_mshift call as in do_pbc_first,
2372          * since we no longer need this graph.
2373          */
2374
2375         as += molb->natoms_mol;
2376       }
2377       done_graph(graph);
2378     }
2379   }
2380   sfree(graph);
2381 }
2382
2383 void do_pbc_first_mtop(FILE *fplog,int ePBC,matrix box,
2384                        gmx_mtop_t *mtop,rvec x[])
2385 {
2386   low_do_pbc_mtop(fplog,ePBC,box,mtop,x,TRUE);
2387 }
2388
2389 void do_pbc_mtop(FILE *fplog,int ePBC,matrix box,
2390                  gmx_mtop_t *mtop,rvec x[])
2391 {
2392   low_do_pbc_mtop(fplog,ePBC,box,mtop,x,FALSE);
2393 }
2394
2395 void finish_run(FILE *fplog,t_commrec *cr,const char *confout,
2396                 t_inputrec *inputrec,
2397                 t_nrnb nrnb[],gmx_wallcycle_t wcycle,
2398                 gmx_runtime_t *runtime,
2399                 wallclock_gpu_t *gputimes,
2400                 int omp_nth_pp,
2401                 gmx_bool bWriteStat)
2402 {
2403     int    i,j;
2404     t_nrnb *nrnb_tot=NULL;
2405     real   delta_t;
2406     double nbfs,mflop;
2407
2408     wallcycle_sum(cr,wcycle);
2409
2410     if (cr->nnodes > 1)
2411     {
2412         snew(nrnb_tot,1);
2413 #ifdef GMX_MPI
2414         MPI_Allreduce(nrnb->n,nrnb_tot->n,eNRNB,MPI_DOUBLE,MPI_SUM,
2415                       cr->mpi_comm_mysim);
2416 #endif
2417     }
2418     else
2419     {
2420         nrnb_tot = nrnb;
2421     }
2422
2423 #if defined(GMX_MPI) && !defined(GMX_THREAD_MPI)
2424     if (cr->nnodes > 1)
2425     {
2426         /* reduce nodetime over all MPI processes in the current simulation */
2427         double sum;
2428         MPI_Allreduce(&runtime->proctime,&sum,1,MPI_DOUBLE,MPI_SUM,
2429                       cr->mpi_comm_mysim);
2430         runtime->proctime = sum;
2431     }
2432 #endif
2433
2434     if (SIMMASTER(cr))
2435     {
2436         print_flop(fplog,nrnb_tot,&nbfs,&mflop);
2437     }
2438     if (cr->nnodes > 1)
2439     {
2440         sfree(nrnb_tot);
2441     }
2442
2443     if ((cr->duty & DUTY_PP) && DOMAINDECOMP(cr))
2444     {
2445         print_dd_statistics(cr,inputrec,fplog);
2446     }
2447
2448 #ifdef GMX_MPI
2449     if (PARTDECOMP(cr))
2450     {
2451         if (MASTER(cr))
2452         {
2453             t_nrnb     *nrnb_all;
2454             int        s;
2455             MPI_Status stat;
2456
2457             snew(nrnb_all,cr->nnodes);
2458             nrnb_all[0] = *nrnb;
2459             for(s=1; s<cr->nnodes; s++)
2460             {
2461                 MPI_Recv(nrnb_all[s].n,eNRNB,MPI_DOUBLE,s,0,
2462                          cr->mpi_comm_mysim,&stat);
2463             }
2464             pr_load(fplog,cr,nrnb_all);
2465             sfree(nrnb_all);
2466         }
2467         else
2468         {
2469             MPI_Send(nrnb->n,eNRNB,MPI_DOUBLE,MASTERRANK(cr),0,
2470                      cr->mpi_comm_mysim);
2471         }
2472     }
2473 #endif
2474
2475     if (SIMMASTER(cr))
2476     {
2477         wallcycle_print(fplog,cr->nnodes,cr->npmenodes,runtime->realtime,
2478                         wcycle,gputimes);
2479
2480         if (EI_DYNAMICS(inputrec->eI))
2481         {
2482             delta_t = inputrec->delta_t;
2483         }
2484         else
2485         {
2486             delta_t = 0;
2487         }
2488
2489         if (fplog)
2490         {
2491             print_perf(fplog,runtime->proctime,runtime->realtime,
2492                        cr->nnodes-cr->npmenodes,
2493                        runtime->nsteps_done,delta_t,nbfs,mflop,
2494                        omp_nth_pp);
2495         }
2496         if (bWriteStat)
2497         {
2498             print_perf(stderr,runtime->proctime,runtime->realtime,
2499                        cr->nnodes-cr->npmenodes,
2500                        runtime->nsteps_done,delta_t,nbfs,mflop,
2501                        omp_nth_pp);
2502         }
2503     }
2504 }
2505
2506 extern void initialize_lambdas(FILE *fplog,t_inputrec *ir,int *fep_state,real *lambda,double *lam0)
2507 {
2508     /* this function works, but could probably use a logic rewrite to keep all the different
2509        types of efep straight. */
2510
2511     int i;
2512     t_lambda *fep = ir->fepvals;
2513
2514     if ((ir->efep==efepNO) && (ir->bSimTemp == FALSE)) {
2515         for (i=0;i<efptNR;i++)  {
2516             lambda[i] = 0.0;
2517             if (lam0)
2518             {
2519                 lam0[i] = 0.0;
2520             }
2521         }
2522         return;
2523     } else {
2524         *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
2525                                              if checkpoint is set -- a kludge is in for now
2526                                              to prevent this.*/
2527         for (i=0;i<efptNR;i++)
2528         {
2529             /* overwrite lambda state with init_lambda for now for backwards compatibility */
2530             if (fep->init_lambda>=0) /* if it's -1, it was never initializd */
2531             {
2532                 lambda[i] = fep->init_lambda;
2533                 if (lam0) {
2534                     lam0[i] = lambda[i];
2535                 }
2536             }
2537             else
2538             {
2539                 lambda[i] = fep->all_lambda[i][*fep_state];
2540                 if (lam0) {
2541                     lam0[i] = lambda[i];
2542                 }
2543             }
2544         }
2545         if (ir->bSimTemp) {
2546             /* need to rescale control temperatures to match current state */
2547             for (i=0;i<ir->opts.ngtc;i++) {
2548                 if (ir->opts.ref_t[i] > 0) {
2549                     ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
2550                 }
2551             }
2552         }
2553     }
2554
2555     /* Send to the log the information on the current lambdas */
2556     if (fplog != NULL)
2557     {
2558         fprintf(fplog,"Initial vector of lambda components:[ ");
2559         for (i=0;i<efptNR;i++)
2560         {
2561             fprintf(fplog,"%10.4f ",lambda[i]);
2562         }
2563         fprintf(fplog,"]\n");
2564     }
2565     return;
2566 }
2567
2568
2569 void init_md(FILE *fplog,
2570              t_commrec *cr,t_inputrec *ir,const output_env_t oenv,
2571              double *t,double *t0,
2572              real *lambda, int *fep_state, double *lam0,
2573              t_nrnb *nrnb,gmx_mtop_t *mtop,
2574              gmx_update_t *upd,
2575              int nfile,const t_filenm fnm[],
2576              gmx_mdoutf_t **outf,t_mdebin **mdebin,
2577              tensor force_vir,tensor shake_vir,rvec mu_tot,
2578              gmx_bool *bSimAnn,t_vcm **vcm, t_state *state, unsigned long Flags)
2579 {
2580     int  i,j,n;
2581     real tmpt,mod;
2582
2583     /* Initial values */
2584     *t = *t0       = ir->init_t;
2585
2586     *bSimAnn=FALSE;
2587     for(i=0;i<ir->opts.ngtc;i++)
2588     {
2589         /* set bSimAnn if any group is being annealed */
2590         if(ir->opts.annealing[i]!=eannNO)
2591         {
2592             *bSimAnn = TRUE;
2593         }
2594     }
2595     if (*bSimAnn)
2596     {
2597         update_annealing_target_temp(&(ir->opts),ir->init_t);
2598     }
2599
2600     /* Initialize lambda variables */
2601     initialize_lambdas(fplog,ir,fep_state,lambda,lam0);
2602
2603     if (upd)
2604     {
2605         *upd = init_update(fplog,ir);
2606     }
2607
2608
2609     if (vcm != NULL)
2610     {
2611         *vcm = init_vcm(fplog,&mtop->groups,ir);
2612     }
2613
2614     if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
2615     {
2616         if (ir->etc == etcBERENDSEN)
2617         {
2618             please_cite(fplog,"Berendsen84a");
2619         }
2620         if (ir->etc == etcVRESCALE)
2621         {
2622             please_cite(fplog,"Bussi2007a");
2623         }
2624     }
2625
2626     init_nrnb(nrnb);
2627
2628     if (nfile != -1)
2629     {
2630         *outf = init_mdoutf(nfile,fnm,Flags,cr,ir,oenv);
2631
2632         *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : (*outf)->fp_ene,
2633                               mtop,ir, (*outf)->fp_dhdl);
2634     }
2635
2636     if (ir->bAdress)
2637     {
2638       please_cite(fplog,"Fritsch12");
2639       please_cite(fplog,"Junghans10");
2640     }
2641     /* Initiate variables */
2642     clear_mat(force_vir);
2643     clear_mat(shake_vir);
2644     clear_rvec(mu_tot);
2645
2646     debug_gmx();
2647 }
2648