3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
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.
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33 * Groningen Machine for Chemical Simulation
49 #include "gmx_fatal.h"
71 static int comp_xptr(const void *a,const void *b)
79 if ((dx = (xptr[va][XX] - xptr[vb][XX])) < 0)
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[])
96 real ener,vcorr,q,xx,dvdl=0,vdip,vcharge;
97 tensor vir,vir_corr,vir_tot;
102 /* Initiate local variables */
108 fprintf(fp,"There are %d energy groups\n",ngroups);
110 for(i=0; (i<ngroups); i++)
111 snew(epme[i],ngroups);
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.
120 for(i=0; (i<nsb->natoms); i++)
124 qsort(index,nsb->natoms,sizeof(index[0]),comp_xptr);
125 xptr = NULL; /* To trap unintentional use of the ptr */
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)
130 clear_rvec(mu_tot[0]);
131 for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
135 for(m=0; (m<DIM); m++) {
138 mu_tot[0][m] += q*xx;
142 copy_rvec(mu_tot[0],mu_tot[1]);
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);
148 for(ig=0; (ig<ngroups); ig++) {
149 for(jg=ig; (jg<ngroups); jg++) {
151 for(i=START(nsb); (i<START(nsb)+HOMENR(nsb)); i++) {
152 if ((cENER[i] == ig) || (cENER[i] == jg))
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);
167 gmx_sum(1,&vcorr,cr);
169 epme[ig][jg] = ener+vcorr;
174 fprintf(fp_xvg,"%10.3f",tm);
175 for(ig=0; (ig<ngroups); ig++) {
176 for(jg=ig; (jg<ngroups); jg++) {
178 epme[ig][jg] -= epme[ig][ig]+epme[jg][jg];
180 fprintf(fp_xvg," %12.5e",epme[ig][jg]);
184 fprintf(fp_xvg,"\n");
187 fprintf(fp,"Time: %10.3f Energy: %12.5e Correction: %12.5e Total: %12.5e\n",
188 tm,ener,vcorr,ener+vcorr);
190 fprintf(fp_xvg,"%10.3f %12.5e %12.5e %12.5e\n",tm,ener+vcorr,vdip,vcharge);
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);
200 int main(int argc,char *argv[])
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."
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 }
220 #define NFILE asize(fnm)
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;
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" }
263 int natoms,step,status,i,ncg,root;
264 real t,lambda,ewaldcoeff,qtot;
268 real *charge,*qbuf,*qqbuf;
271 /* Start the actual parallel code if necessary */
272 cr = init_par(&argc,&argv);
276 CopyRight(stderr,argv[0]);
278 /* Parse command line on all processors, arguments are passed on in
279 * init_par (see above)
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);
288 gmx_fatal(FARGS,"GROMACS compiled without MPI support - can't do parallel runs");
290 #ifndef GMX_THREAD_SHM_FDECOMP
292 gmx_fatal(FARGS,"GROMACS compiled without threads support - can only use one thread");
295 /* Open log files on all processors */
296 open_log(ftp2fn(efLOG,NFILE,fnm),cr);
300 /* Read tpr file etc. */
301 read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&tpx,FALSE,NULL,NULL);
303 read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,ir,
304 box,&natoms,x,NULL,NULL,&top);
308 for(i=0; (i<natoms); i++) {
309 charge[i] = top.atoms.atom[i].q;
314 if (opt2parg_bSet("-grid",asize(pa),pa)) {
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))
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);
339 /* Add parallellization code here */
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;
349 /* Set some variables to zero to avoid core dumps */
350 ir->opts.ngtc = ir->opts.ngacc = ir->opts.ngfrz = ir->opts.ngener = 0;
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);
358 /* Call some dedicated communication routines, master sends n-1 times */
360 for(i=1; (i<cr->nnodes); i++) {
361 mv_block(i,&(top.blocks[ebCGS]));
362 mv_block(i,&(top.atoms.excl));
366 ld_block(root,&(top.blocks[ebCGS]));
367 ld_block(root,&(top.atoms.excl));
374 MPI_Bcast(charge,natoms,GMX_MPI_REAL,root,MPI_COMM_WORLD);
377 ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb,ir->ewald_rtol);
381 pr_inputrec(stdlog,0,"Inputrec",ir);
383 /* Allocate memory for temp arrays etc. */
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);
394 /* MFlops accounting */
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);
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);
406 init_forcerec(stdlog,fr,ir,&top,cr,mdatoms,nsb,box,FALSE,NULL,NULL,FALSE);
408 /* First do PME based on coordinates in tpr file, send them to
409 * other processors if needed.
412 fprintf(stdlog,"-----\n"
413 "Results based on tpr file %s\n",ftp2fn(efTPX,NFILE,fnm));
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);
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);
425 /* If we have a trajectry file, we will read the frames in it and compute
428 if (ftp2bSet(efTRX,NFILE,fnm)) {
429 fprintf(stdlog,"-----\n"
430 "Results based on trx file %s\n",ftp2fn(efTRX,NFILE,fnm));
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)");
441 /* Send coordinates, box and time to the other nodes */
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);
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 */
456 bCont = read_next_x(status,&t,natoms,x,box);
457 /* Check whether we need to continue */
460 MPI_Bcast(&bCont,1,MPI_INT,root,MPI_COMM_WORLD);
465 /* Finish I/O, close files */
473 /* Do some final I/O about performance, might be useful in debugging */
474 fprintf(stdlog,"-----\n");
475 print_nrnb(stdlog,&nrnb);
478 /* Finish the parallel stuff */
479 if (gmx_parallel_env_initialized())
482 /* Thank the audience, as usual */