src/contrib/pmetest.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.3.99_development_20071104
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2006, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
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  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * Groningen Machine for Chemical Simulation
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40 #include "macros.h"
  41 #include "smalloc.h"
  42 #include "copyrite.h"
  43 #include "main.h"
  44 #include "nrnb.h"
  45 #include "txtdump.h"
  46 #include "tpxio.h"
  47 #include "statutil.h"
  48 #include "futil.h"
  49 #include "gmx_fatal.h"
  50 #include "vec.h"
  51 #include "mdatoms.h"
  52 #include "coulomb.h"
  53 #include "nsb.h"
  54 #include "rmpbc.h"
  55 #include "pme.h"
  56 #include "force.h"
  57 #include "xvgr.h"
  58 #include "pbc.h"
  59
  60 #ifdef GMX_LIB_MPI
  61 #include <mpi.h>
  62 #endif
  63 #ifdef GMX_THREADS
  64 #include "tmpi.h"
  65 #endif
  66
  67 #include "block_tx.h"
  68
  69 rvec *xptr=NULL;
  70
  71 static int comp_xptr(const void *a,const void *b)
  72 {
  73   int  va,vb;
  74   real dx;
  75
  76   va = *(int *)a;
  77   vb = *(int *)b;
  78
  79   if ((dx = (xptr[va][XX] - xptr[vb][XX])) < 0)
  80     return -1;
  81   else if (dx > 0)
  82     return 1;
  83   else
  84     return 0;
  85 }
  86
  87 static void do_my_pme(FILE *fp,real tm,bool bVerbose,t_inputrec *ir,
  88                       rvec x[],rvec xbuf[],rvec f[],
  89                       real charge[],real qbuf[],real qqbuf[],
  90                       matrix box,bool bSort,
  91                       t_commrec *cr,t_nsborder *nsb,t_nrnb *nrnb,
  92                       t_block *excl,real qtot,
  93                       t_forcerec *fr,int index[],FILE *fp_xvg,
  94                       int ngroups,unsigned short cENER[])
  95 {
  96   real   ener,vcorr,q,xx,dvdl=0,vdip,vcharge;
  97   tensor vir,vir_corr,vir_tot;
  98   rvec   mu_tot[2];
  99   int    i,m,ii,ig,jg;
 100   real   **epme,*qptr;
 101
 102   /* Initiate local variables */
 103   fr->f_el_recip = f;
 104   clear_mat(vir);
 105   clear_mat(vir_corr);
 106
 107   if (ngroups > 1) {
 108     fprintf(fp,"There are %d energy groups\n",ngroups);
 109     snew(epme,ngroups);
 110     for(i=0; (i<ngroups); i++)
 111       snew(epme[i],ngroups);
 112   }
 113
 114   /* Put x is in the box, this part needs to be parallellized properly */
 115   /*put_atoms_in_box(box,nsb->natoms,x);*/
 116   /* Here sorting of X (and q) is done.
 117    * Alternatively, one could just put the atoms in one of the
 118    * cr->nnodes slabs. That is much cheaper than sorting.
 119    */
 120   for(i=0; (i<nsb->natoms); i++)
 121     index[i] = i;
 122   if (bSort) {
 123     xptr = x;
 124     qsort(index,nsb->natoms,sizeof(index[0]),comp_xptr);
 125     xptr = NULL; /* To trap unintentional use of the ptr */
 126   }
 127   /* After sorting we only need the part that is to be computed on
 128    * this processor. We also compute the mu_tot here (system dipole)
 129    */
 130   clear_rvec(mu_tot[0]);
 131   for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
 132     ii      = index[i];
 133     q       = charge[ii];
 134     qbuf[i] = q;
 135     for(m=0; (m<DIM); m++) {
 136       xx         = x[ii][m];
 137       xbuf[i][m] = xx;
 138       mu_tot[0][m] += q*xx;
 139     }
 140     clear_rvec(f[ii]);
 141   }
 142   copy_rvec(mu_tot[0],mu_tot[1]);
 143   if (debug) {
 144     pr_rvec(debug,0,"qbuf",qbuf,nsb->natoms,TRUE);
 145     pr_rvecs(debug,0,"xbuf",xbuf,nsb->natoms);
 146     pr_rvecs(debug,0,"box",box,DIM);
 147   }
 148   for(ig=0; (ig<ngroups); ig++) {
 149     for(jg=ig; (jg<ngroups); jg++) {
 150       if (ngroups > 1) {
 151         for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
 152           if ((cENER[i] == ig) || (cENER[i] == jg))
 153             qqbuf[i] = qbuf[i];
 154           else
 155             qqbuf[i] = 0;
 156         }
 157         qptr = qqbuf;
 158       }
 159       else
 160         qptr = qbuf;
 161       ener  = do_pme(fp,bVerbose,ir,xbuf,f,qptr,qptr,box,cr,
 162                      nsb,nrnb,vir,fr->ewaldcoeff,FALSE,0,&dvdl,FALSE);
 163       vcorr = ewald_LRcorrection(fp,nsb,cr,fr,qptr,qptr,excl,xbuf,box,mu_tot,
 164                                  ir->ewald_geometry,ir->epsilon_surface,
 165                                  0,&dvdl,&vdip,&vcharge);
 166       gmx_sum(1,&ener,cr);
 167       gmx_sum(1,&vcorr,cr);
 168       if (ngroups > 1)
 169         epme[ig][jg] = ener+vcorr;
 170     }
 171   }
 172   if (ngroups > 1) {
 173     if (fp_xvg)
 174       fprintf(fp_xvg,"%10.3f",tm);
 175     for(ig=0; (ig<ngroups); ig++) {
 176       for(jg=ig; (jg<ngroups); jg++) {
 177         if (ig != jg)
 178           epme[ig][jg] -= epme[ig][ig]+epme[jg][jg];
 179         if (fp_xvg)
 180           fprintf(fp_xvg,"  %12.5e",epme[ig][jg]);
 181       }
 182     }
 183     if (fp_xvg)
 184       fprintf(fp_xvg,"\n");
 185   }
 186   else {
 187     fprintf(fp,"Time: %10.3f Energy: %12.5e  Correction: %12.5e  Total: %12.5e\n",
 188             tm,ener,vcorr,ener+vcorr);
 189     if (fp_xvg)
 190       fprintf(fp_xvg,"%10.3f %12.5e %12.5e %12.5e\n",tm,ener+vcorr,vdip,vcharge);
 191     if (bVerbose) {
 192       m_add(vir,vir_corr,vir_tot);
 193       gmx_sum(9,vir_tot[0],cr);
 194       pr_rvecs(fp,0,"virial",vir_tot,DIM);
 195     }
 196     fflush(fp);
 197   }
 198 }
 199
 200 int main(int argc,char *argv[])
 201 {
 202   static char *desc[] = {
 203     "The pmetest program tests the scaling of the PME code. When only given",
 204     "a tpr file it will compute PME for one frame. When given a trajectory",
 205     "it will do so for all the frames in the trajectory. Before the PME",
 206     "routine is called the coordinates are sorted along the X-axis.[PAR]",
 207     "As an extra service to the public the program can also compute",
 208     "long-range Coulomb energies for components of the system. When the",
 209     "[TT]-groups[tt] flag is given to the program the energy groups",
 210     "from the tpr file will be read, and half an energy matrix computed."
 211   };
 212   t_commrec    *cr,*mcr;
 213   static t_filenm fnm[] = {
 214     { efTPX, NULL,      NULL,       ffREAD  },
 215     { efTRN, "-o",      NULL,       ffWRITE },
 216     { efLOG, "-g",      "pme",      ffWRITE },
 217     { efTRX, "-f",      NULL,       ffOPTRD },
 218     { efXVG, "-x",      "ener-pme", ffWRITE }
 219   };
 220 #define NFILE asize(fnm)
 221
 222   /* Command line options ! */
 223   static bool bVerbose=FALSE;
 224   static bool bOptFFT=FALSE;
 225   static bool bSort=FALSE;
 226   static int  ewald_geometry=eewg3D;
 227   static int  nnodes=1;
 228   static int  nthreads=1;
 229   static int  pme_order=0;
 230   static rvec grid = { -1, -1, -1 };
 231   static real rc   = 0.0;
 232   static real dtol = 0.0;
 233   static bool bGroups = FALSE;
 234   static t_pargs pa[] = {
 235     { "-np",      FALSE, etINT, {&nnodes},
 236       "Number of nodes, must be the same as used for grompp" },
 237     { "-nt",      FALSE, etINT, {&nthreads},
 238       "Number of threads to start on each node" },
 239     { "-v",       FALSE, etBOOL,{&bVerbose},
 240       "Be loud and noisy" },
 241     { "-sort",    FALSE, etBOOL,{&bSort},
 242       "Sort coordinates. Crucial for domain decomposition." },
 243     { "-grid",    FALSE, etRVEC,{&grid},
 244       "Number of grid cells in X, Y, Z dimension (if -1 use from tpr)" },
 245     { "-order",   FALSE, etINT, {&pme_order},
 246       "Order of the PME spreading algorithm" },
 247     { "-groups",  FALSE, etBOOL, {&bGroups},
 248       "Compute half an energy matrix based on the energy groups in your tpr file" },
 249     { "-rc",      FALSE, etREAL, {&rc},
 250       "Rcoulomb for Ewald summation" },
 251     { "-tol",     FALSE, etREAL, {&dtol},
 252       "Tolerance for Ewald summation" }
 253   };
 254   FILE        *fp;
 255   t_inputrec  *ir;
 256   t_topology  top;
 257   t_tpxheader tpx;
 258   t_nrnb      nrnb;
 259   t_nsborder  *nsb;
 260   t_forcerec  *fr;
 261   t_mdatoms   *mdatoms;
 262   char        title[STRLEN];
 263   int         natoms,step,status,i,ncg,root;
 264   real        t,lambda,ewaldcoeff,qtot;
 265   rvec        *x,*f,*xbuf;
 266   int         *index;
 267   bool        bCont;
 268   real        *charge,*qbuf,*qqbuf;
 269   matrix      box;
 270
 271   /* Start the actual parallel code if necessary */
 272   cr   = init_par(&argc,&argv);
 273   root = 0;
 274
 275   if (MASTER(cr))
 276     CopyRight(stderr,argv[0]);
 277
 278   /* Parse command line on all processors, arguments are passed on in
 279    * init_par (see above)
 280    */
 281   parse_common_args(&argc,argv,
 282                     PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_BE_NICE |
 283                     PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET),
 284                     NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
 285
 286 #ifndef GMX_MPI
 287   if (nnodes > 1)
 288     gmx_fatal(FARGS,"GROMACS compiled without MPI support - can't do parallel runs");
 289 #endif
 290 #ifndef GMX_THREAD_SHM_FDECOMP
 291   if(nthreads > 1)
 292     gmx_fatal(FARGS,"GROMACS compiled without threads support - can only use one thread");
 293 #endif
 294
 295   /* Open log files on all processors */
 296   open_log(ftp2fn(efLOG,NFILE,fnm),cr);
 297   snew(ir,1);
 298
 299   if (MASTER(cr)) {
 300     /* Read tpr file etc. */
 301     read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&tpx,FALSE,NULL,NULL);
 302     snew(x,tpx.natoms);
 303     read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,ir,
 304              box,&natoms,x,NULL,NULL,&top);
 305     /* Charges */
 306     qtot = 0;
 307     snew(charge,natoms);
 308     for(i=0; (i<natoms); i++) {
 309       charge[i] = top.atoms.atom[i].q;
 310       qtot += charge[i];
 311     }
 312
 313     /* Grid stuff */
 314     if (opt2parg_bSet("-grid",asize(pa),pa)) {
 315       ir->nkx = grid[XX];
 316       ir->nky = grid[YY];
 317       ir->nkz = grid[ZZ];
 318     }
 319     /* Check command line parameters for consistency */
 320     if ((ir->nkx <= 0) || (ir->nky <= 0) || (ir->nkz <= 0))
 321       gmx_fatal(FARGS,"PME grid = %d %d %d",ir->nkx,ir->nky,ir->nkz);
 322     if (opt2parg_bSet("-rc",asize(pa),pa))
 323       ir->rcoulomb = rc;
 324     if (ir->rcoulomb <= 0)
 325       gmx_fatal(FARGS,"rcoulomb should be > 0 (not %f)",ir->rcoulomb);
 326     if (opt2parg_bSet("-order",asize(pa),pa))
 327       ir->pme_order = pme_order;
 328     if (ir->pme_order <= 0)
 329       gmx_fatal(FARGS,"pme_order should be > 0 (not %d)",ir->pme_order);
 330     if (opt2parg_bSet("-tol",asize(pa),pa))
 331       ir->ewald_rtol = dtol;
 332     if (ir->ewald_rtol <= 0)
 333       gmx_fatal(FARGS,"ewald_tol should be > 0 (not %f)",ir->ewald_rtol);
 334   }
 335   else {
 336     init_top(&top);
 337   }
 338
 339   /* Add parallellization code here */
 340   snew(nsb,1);
 341   if (MASTER(cr)) {
 342     ncg = top.blocks[ebCGS].multinr[0];
 343     for(i=0; (i<cr->nnodes-1); i++)
 344       top.blocks[ebCGS].multinr[i] = min(ncg,(ncg*(i+1))/cr->nnodes);
 345     for( ; (i<MAXNODES); i++)
 346       top.blocks[ebCGS].multinr[i] = ncg;
 347   }
 348   if (PAR(cr)) {
 349     /* Set some variables to zero to avoid core dumps */
 350     ir->opts.ngtc = ir->opts.ngacc = ir->opts.ngfrz = ir->opts.ngener = 0;
 351 #ifdef GMX_MPI
 352     /* Distribute the data over processors */
 353     MPI_Bcast(&natoms,1,MPI_INT,root,MPI_COMM_WORLD);
 354     MPI_Bcast(ir,sizeof(*ir),MPI_BYTE,root,MPI_COMM_WORLD);
 355     MPI_Bcast(&qtot,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 356 #endif
 357
 358     /* Call some dedicated communication routines, master sends n-1 times */
 359     if (MASTER(cr)) {
 360       for(i=1; (i<cr->nnodes); i++) {
 361         mv_block(i,&(top.blocks[ebCGS]));
 362         mv_block(i,&(top.atoms.excl));
 363       }
 364     }
 365     else {
 366       ld_block(root,&(top.blocks[ebCGS]));
 367       ld_block(root,&(top.atoms.excl));
 368     }
 369     if (!MASTER(cr)) {
 370       snew(charge,natoms);
 371       snew(x,natoms);
 372     }
 373 #ifdef GMX_MPI
 374     MPI_Bcast(charge,natoms,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 375 #endif
 376   }
 377   ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb,ir->ewald_rtol);
 378
 379
 380   if (bVerbose)
 381     pr_inputrec(stdlog,0,"Inputrec",ir);
 382
 383   /* Allocate memory for temp arrays etc. */
 384   snew(xbuf,natoms);
 385   snew(f,natoms);
 386   snew(qbuf,natoms);
 387   snew(qqbuf,natoms);
 388   snew(index,natoms);
 389
 390   /* Initialize the PME code */
 391   init_pme(stdlog,cr,ir->nkx,ir->nky,ir->nkz,ir->pme_order,
 392            natoms,FALSE,bOptFFT,ewald_geometry);
 393
 394   /* MFlops accounting */
 395   init_nrnb(&nrnb);
 396
 397   /* Initialize the work division */
 398   calc_nsb(stdlog,&(top.blocks[ebCGS]),cr->nnodes,nsb,0);
 399   nsb->nodeid = cr->nodeid;
 400   print_nsb(stdlog,"pmetest",nsb);
 401
 402   /* Initiate forcerec */
 403   mdatoms = atoms2md(stdlog,&top.atoms,ir->opts.nFreeze,ir->eI,
 404                      ir->delta_t,0,ir->opts.tau_t,FALSE,FALSE);
 405   snew(fr,1);
 406   init_forcerec(stdlog,fr,ir,&top,cr,mdatoms,nsb,box,FALSE,NULL,NULL,FALSE);
 407
 408   /* First do PME based on coordinates in tpr file, send them to
 409    * other processors if needed.
 410    */
 411   if (MASTER(cr))
 412     fprintf(stdlog,"-----\n"
 413             "Results based on tpr file %s\n",ftp2fn(efTPX,NFILE,fnm));
 414 #ifdef GMX_MPI
 415   if (PAR(cr)) {
 416     MPI_Bcast(x[0],natoms*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 417     MPI_Bcast(box[0],DIM*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 418     MPI_Bcast(&t,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 419   }
 420 #endif
 421   do_my_pme(stdlog,0,bVerbose,ir,x,xbuf,f,charge,qbuf,qqbuf,box,bSort,
 422             cr,nsb,&nrnb,&(top.atoms.excl),qtot,fr,index,NULL,
 423             bGroups ? ir->opts.ngener : 1,mdatoms->cENER);
 424
 425   /* If we have a trajectry file, we will read the frames in it and compute
 426    * the PME energy.
 427    */
 428   if (ftp2bSet(efTRX,NFILE,fnm)) {
 429     fprintf(stdlog,"-----\n"
 430             "Results based on trx file %s\n",ftp2fn(efTRX,NFILE,fnm));
 431     if (MASTER(cr)) {
 432       sfree(x);
 433       natoms = read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
 434       if (natoms != top.atoms.nr)
 435         gmx_fatal(FARGS,"natoms in trx = %d, in tpr = %d",natoms,top.atoms.nr);
 436       fp = xvgropen(ftp2fn(efXVG,NFILE,fnm),"PME Energy","Time (ps)","E (kJ/mol)");
 437     }
 438     else
 439       fp = NULL;
 440     do {
 441       /* Send coordinates, box and time to the other nodes */
 442 #ifdef GMX_MPI
 443       if (PAR(cr)) {
 444         MPI_Bcast(x[0],natoms*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 445         MPI_Bcast(box[0],DIM*DIM,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 446         MPI_Bcast(&t,1,GMX_MPI_REAL,root,MPI_COMM_WORLD);
 447       }
 448 #endif
 449       rm_pbc(&top.idef,nsb->natoms,box,x,x);
 450       /* Call the PME wrapper function */
 451       do_my_pme(stdlog,t,bVerbose,ir,x,xbuf,f,charge,qbuf,qqbuf,box,bSort,cr,
 452                 nsb,&nrnb,&(top.atoms.excl),qtot,fr,index,fp,
 453                 bGroups ? ir->opts.ngener : 1,mdatoms->cENER);
 454       /* Only the master processor reads more data */
 455       if (MASTER(cr))
 456           bCont = read_next_x(status,&t,natoms,x,box);
 457       /* Check whether we need to continue */
 458 #ifdef GMX_MPI
 459       if (PAR(cr))
 460           MPI_Bcast(&bCont,1,MPI_INT,root,MPI_COMM_WORLD);
 461 #endif
 462
 463     } while (bCont);
 464
 465     /* Finish I/O, close files */
 466     if (MASTER(cr)) {
 467       close_trx(status);
 468       ffclose(fp);
 469     }
 470   }
 471
 472   if (bVerbose) {
 473     /* Do some final I/O about performance, might be useful in debugging */
 474     fprintf(stdlog,"-----\n");
 475     print_nrnb(stdlog,&nrnb);
 476   }
 477
 478   /* Finish the parallel stuff */
 479   if (gmx_parallel_env_initialized())
 480     gmx_finalize(cr);
 481
 482   /* Thank the audience, as usual */
 483   if (MASTER(cr))
 484     thanx(stderr);
 485
 486   return 0;
 487 }
 488