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Redefine the default boolean type to gmx_bool.
[gromacs.git] / src / contrib / testlr.c
blobb99d91101f06e6bbe5cd56f5ac0dcf5172ed72b7
1 /*
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35 #include <math.h>
36 #include <string.h>
37 #include "typedefs.h"
38 #include "vec.h"
39 #include "physics.h"
40 #include "macros.h"
41 #include "names.h"
42 #include "smalloc.h"
43 #include "tpxio.h"
44 #include "statutil.h"
45 #include "writeps.h"
46 #include "copyrite.h"
47 #include "xvgr.h"
48 #include "minvert.h"
49 #include "pppm.h"
50 #include "readinp.h"
51 #include "main.h"
52 #include "force.h"
53 #include "nrnb.h"
54 #include "coulomb.h"
55 #include "mshift.h"
56 #include "poisson.h"
57 #include "mdatoms.h"
58
59 static real phi_sr(FILE *log,int nj,rvec x[],real charge[],real rc,real r1,
60 rvec box, real phi[],t_block *excl,rvec f_sr[],gmx_bool bOld)
61 {
62 int i,j,k,m,ni,i1,i2;
63 real pp,r2,R,R_1,R_2,rc2;
64 real qi,qj,vsr,eps,fscal;
65 rvec dx;
66
67 vsr = 0.0;
68 eps = ONE_4PI_EPS0;
69 rc2 = rc*rc;
70 ni=0;
71 for(i=0; (i<nj-1); i++) {
72 qi=charge[i];
73 for(j=i+1; (j<nj); j++) {
74 i1=excl->index[i];
75 i2=excl->index[i+1];
76 for(k=i1; (k<i2); k++)
77 if (excl->a[k] == j)
78 break;
79 if (k == i2) {
80 r2=calc_dx2dx(x[i],x[j],box,dx);
81 if (r2 < rc2) {
82 qj = charge[j];
83 R_1 = invsqrt(r2);
84 R_2 = R_1*R_1;
85 R = invsqrt(R_2);
86 if (bOld) {
87 fscal = old_f(R,rc,r1)*R_2;
88 pp = old_phi(R,rc,r1);
89 }
90 else {
91 fscal = new_f(R,rc)*R_2;
92 pp = new_phi(R,rc);
93 }
94 phi[i] += eps*qj*pp;
95 phi[j] += eps*qi*pp;
96 vsr += eps*qj*qi*pp;
97 for(m=0; (m<DIM); m++) {
98 f_sr[i][m] += dx[m]*fscal;
99 f_sr[j][m] -= dx[m]*fscal;
100 }
101 ni++;
102 }
103 }
104 }
105 }
106 fprintf(log,"There were %d short range interactions, vsr=%g\n",ni,vsr);
107
108 return vsr;
109 }
110
111 void calc_ener(FILE *fp,char *title,gmx_bool bHeader,int nmol,
112 int natoms,real phi[],real charge[],t_block *excl)
113 {
114 int i,i1,i2,j,k;
115 real qq,qi,vv,V,Vex,Vc,Vt;
116
117 qq = 0;
118 V = 0;
119 for(i=0; (i<natoms); i++) {
120 vv = charge[i]*phi[i];
121 V += vv;
122 qq += charge[i]*charge[i];
123 }
124 V = 0.5*V;
125 Vc = 0.5*C*ONE_4PI_EPS0*qq;
126
127 qq = 0;
128 for(i=0; (i<excl->nr); i++) {
129 i1 = excl->index[i];
130 i2 = excl->index[i+1];
131 qi = charge[i];
132 for(j=i1; (j<i2); j++) {
133 k = excl->a[j];
134 if (k != i)
135 qq+=qi*charge[k];
136 }
137 }
138 Vex = qq*0.5*C*ONE_4PI_EPS0;
139
140 Vt = V - Vc - Vex;
141
142 if (bHeader) {
143 fprintf(fp,"%12s %12s %12s %12s %12s %12s\n",
144 "","Vphi","Vself","Vexcl","Vtot","1Mol");
145
146 }
147 fprintf(fp,"%12s %12.5e %12.5e %12.5e %12.5e %12.5e\n",
148 title,V,Vc,Vex,Vt,Vt/nmol);
149 }
150
151 void write_pqr(char *fn,t_atoms *atoms,rvec x[],real phi[],real dx)
152 {
153 FILE *fp;
154 int i,rnr;
155
156 fp=gmx_fio_fopen(fn,"w");
157 for(i=0; (i<atoms->nr); i++) {
158 rnr=atoms->atom[i].resnr;
159 fprintf(fp,"%-6s%5d %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
160 "ATOM",(i+1),*atoms->atomname[i],*atoms->resname[rnr],' ',
161 (rnr+1) % 10000,
162 10*(dx+x[i][XX]),10*x[i][YY],10*(x[i][ZZ]),0.0,phi[i]);
163 }
164 gmx_fio_fclose(fp);
165 }
166
167 void write_grid_pqr(char *fn,int nx,int ny,int nz,real ***phi)
168 {
169 FILE *fp;
170 int i,j,k,rnr=0;
171 real fac=4.0;
172
173 fp=gmx_fio_fopen(fn,"w");
174 for(i=0; (i<nx); i++)
175 for(j=0; (j<ny); j++)
176 for(k=0; (k<nz); k++,rnr++)
177 fprintf(fp,"%-6s%5d %-4.4s%3.3s %c%4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
178 "ATOM",(i+1),"C","C",' ',
179 1+((rnr+1) % 10000),fac*i,fac*j,fac*k,0.0,phi[i][j][k]);
180 gmx_fio_fclose(fp);
181 }
182 void plot_phi(char *fn,rvec box,int natoms,rvec x[],real phi[])
183 {
184 t_psdata eps;
185 real phi_max,rr,gg,bb,fac,dx,x0,y0;
186 real offset;
187 int i;
188
189 phi_max=phi[0];
190 rr=gg=bb=0.0;
191 for(i=0; (i<natoms); i++)
192 phi_max=max(phi_max,fabs(phi[i]));
193
194 if (phi_max==0.0) {
195 fprintf(stderr,"All values zero, see .out file\n");
196 return;
197 }
198 offset=20.0;
199 fac=15.0;
200 #ifdef DEBUG
201 fprintf(stderr,"Scaling box by %g\n",fac);
202 #endif
203 eps=ps_open(fn,0,0,
204 (real)(fac*box[XX]+2*offset),(real)(fac*box[YY]+2*offset));
205 ps_translate(eps,offset,offset);
206 ps_color(eps,0,0,0);
207 ps_box(eps,1,1,(real)(fac*box[XX]-1),(real)(fac*box[YY]-1));
208 dx=0.15*fac;
209 for(i=0; (i<natoms); i++) {
210 rr=gg=bb=1.0;
211 if (phi[i] < 0)
212 gg=bb=(1.0+(phi[i]/phi_max));
213 else
214 rr=gg=(1.0-(phi[i]/phi_max));
215 rr=rgbset(rr);
216 gg=rgbset(gg);
217 bb=rgbset(bb);
218 ps_color(eps,rr,gg,bb);
219 x0=fac*x[i][XX];
220 y0=fac*x[i][YY];
221 ps_fillbox(eps,(real)(x0-dx),(real)(y0-dx),(real)(x0+dx),(real)(y0+dx));
222 }
223 ps_close(eps);
224 }
225
226 void plot_qtab(char *fn,int nx,int ny,int nz,real ***qtab)
227 {
228 rvec box;
229 rvec *xx;
230 real *phi;
231 int i,npt,ix,iy,iz;
232
233 box[XX]=nx;
234 box[YY]=ny;
235 box[ZZ]=nz;
236
237 npt=(box[XX]*box[YY]*box[ZZ]);
238 snew(xx,npt);
239 snew(phi,npt);
240 nx/=2;
241 ny/=2;
242 nz/=2;
243 i=0;
244 for(ix=-nx; (ix<nx); ix++)
245 for(iy=-ny; (iy<ny); iy++)
246 for(iz=-nz; (iz<nz); iz++,i++) {
247 xx[i][XX]=ix+nx+0.5;
248 xx[i][YY]=iy+ny+0.5;
249 xx[i][ZZ]=iz+nz+0.5; /* onzin */
250 phi[i]=qtab[ix+nx][iy+ny][iz+nz];
251 }
252
253 plot_phi(fn,box,npt,xx,phi);
254
255 sfree(xx);
256 sfree(phi);
257 }
258
259 void print_phi(char *fn,int natoms,rvec x[],real phi[])
260 {
261 FILE *fp;
262 int i;
263
264 fp=gmx_fio_fopen(fn,"w");
265 for(i=0; (i<natoms); i++)
266 fprintf(fp,"%10d %12.5e\n",i,phi[i]);
267 gmx_fio_fclose(fp);
268 }
269
270 void pr_f(char *fn,int natoms,rvec f[])
271 {
272 FILE *fp;
273 int i;
274
275 fp=gmx_fio_fopen(fn,"w");
276 for(i=0; (i<natoms); i++)
277 fprintf(fp," %12.5e\n %12.5e\n %12.5e\n",f[i][XX],f[i][YY],f[i][ZZ]);
278 gmx_fio_fclose(fp);
279 }
280
281 void test_pppm(FILE *log, gmx_bool bVerbose,
282 gmx_bool bGenerGhat, char *ghatfn,
283 t_atoms *atoms, t_inputrec *ir,
284 rvec x[], rvec f[],
285 real charge[], rvec box,
286 real phi[], real phi_s[],
287 int nmol, t_commrec *cr,
288 gmx_bool bOld, t_block *cgs)
289 {
290 char buf[256];
291 real ener;
292 int i;
293 t_nrnb nrnb;
294 t_nsborder nsb;
295
296 init_nrnb(&nrnb);
297 calc_nsb(cgs,1,&nsb,0);
298
299 /* First time only setup is done! */
300 init_pppm(log,cr,&nsb,bVerbose,bOld,box,ghatfn,ir);
301
302 ener = do_pppm(log,bVerbose,x,f,charge,box,phi,cr,&nsb,&nrnb);
303 fprintf(log,"Vpppm = %g\n",ener);
304
305 sprintf(buf,"PPPM-%d.pdb",ir->nkx);
306 write_pqr(buf,atoms,x,phi,0);
307
308 pr_f("pppm-force",atoms->nr,f);
309
310 calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
311
312 for(i=0; (i<atoms->nr); i++)
313 phi[i]+=phi_s[i];
314 sprintf(buf,"PPPM-%d+SR",ir->nkx);
315 calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
316 strcat(buf,".pdb");
317 write_pqr(buf,atoms,x,phi,0);
318 }
319
320 void test_poisson(FILE *log, gmx_bool bVerbose,
321 t_atoms *atoms, t_inputrec *ir,
322 rvec x[], rvec f[],
323 real charge[], rvec box,
324 real phi[], real phi_s[],
325 int nmol, t_commrec *cr,
326 gmx_bool bFour, rvec f_four[],
327 real phi_f[], gmx_bool bOld)
328 {
329 char buf[256];
330 real ener;
331 rvec beta;
332 int i,nit;
333 t_nrnb nrnb;
334
335 init_nrnb(&nrnb);
336
337 /* First time only setup is done! */
338 if (bFour) {
339 for(i=0; (i<atoms->nr); i++)
340 phi_f[i] -= phi_s[i];
341 ener = do_optimize_poisson(log,bVerbose,ir,atoms->nr,x,f,charge,
342 box,phi,cr,&nrnb,f_four,phi_f,beta,bOld);
343 for(i=0; (i<atoms->nr); i++)
344 phi_f[i] += phi_s[i];
345 nit = 0;
346 }
347 else {
348 ener = do_poisson(log,bVerbose,ir,atoms->nr,x,f,charge,box,phi,
349 cr,&nrnb,&nit,bOld);
350 }
351
352 fprintf(log,"Vpoisson = %g, nit = %d\n",ener,nit);
353
354 sprintf(buf,"POISSON-%d.pdb",ir->nkx);
355 write_pqr(buf,atoms,x,phi,0);
356
357 pr_f("poisson-force",atoms->nr,f);
358
359 calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
360
361 for(i=0; (i<atoms->nr); i++)
362 phi[i]+=phi_s[i];
363 sprintf(buf,"POISSON-%d+SR",ir->nkx);
364 calc_ener(log,buf,FALSE,nmol,atoms->nr,phi,charge,&atoms->excl);
365 strcat(buf,".pdb");
366 write_pqr(buf,atoms,x,phi,0);
367 }
368
369 void test_four(FILE *log,int NFILE,t_filenm fnm[],t_atoms *atoms,
370 t_inputrec *ir,rvec x[],rvec f[],rvec box,real charge[],
371 real phi_f[],real phi_s[],int nmol,t_commrec *cr,
372 gmx_bool bOld,gmx_bool bOldEwald)
373 {
374 int i;
375 real energy;
376 ewald_tab_t et;
377
378 init_ewald_tab(&et, NULL, ir, log);
379
380 if (bOldEwald)
381 energy = do_ewald(log,ir,atoms->nr,x,f,charge,box,phi_f,cr,bOld,et);
382 else
383 energy = do_ewald_new(log,ir,atoms->nr,x,f,charge,box,phi_f,cr,bOld,et);
384
385 /*symmetrize_phi(log,atoms->nr,phi_f,bVerbose);*/
386
387 /* Plot the long range fourier solution in a matrix */
388 plot_phi(opt2fn("-elf",NFILE,fnm),box,atoms->nr,x,phi_f);
389 print_phi(opt2fn("-of",NFILE,fnm),atoms->nr,x,phi_f);
390 calc_ener(log,"Fourier",FALSE,nmol,atoms->nr,phi_f,charge,&atoms->excl);
391 write_pqr(opt2fn("-pf",NFILE,fnm),atoms,x,phi_f,0.0/*1.5*box[XX]*/);
392 pr_f("four-force",atoms->nr,f);
393
394 /* Calc and plot the total potential */
395 for(i=0; (i<atoms->nr); i++) {
396 phi_f[i]+=phi_s[i];
397 /*clear_rvec(f[i]);*/
398 }
399 calc_ener(log,"Fourier+SR",FALSE,nmol,atoms->nr,phi_f,charge,&atoms->excl);
400 }
401
402 static void print_opts(FILE *fp,t_inputrec *ir,gmx_bool bFour)
403 {
404 fprintf(fp,"Ewald solution: %s\n",gmx_bool_names[bFour]);
405 fprintf(fp,"r1: %10.3e\n",ir->rcoulomb_switch);
406 fprintf(fp,"rc: %10.3e\n",ir->rcoulomb);
407 if (bFour)
408 fprintf(fp,"KVectors: %10d %10d %10d\n",ir->nkx,ir->nky,ir->nkz);
409 fprintf(fp,"\n");
410 }
411
412 int main(int argc,char *argv[])
413 {
414 static char *desc[] = {
415 "testlr tests the PPPM and Ewald method for the",
416 "long range electrostatics problem."
417 };
418 static t_filenm fnm[] = {
419 { efTPX, NULL, NULL, ffREAD },
420 { efHAT, "-g", "ghat", ffOPTRD },
421 { efOUT, "-o", "rho", ffOPTWR },
422 { efOUT, "-op", "lr-pb", ffOPTWR },
423 { efOUT, "-of", "lr-four", ffOPTWR },
424 { efOUT, "-opt", "tot-pb", ffOPTWR },
425 { efOUT, "-oft", "tot-four", ffOPTWR },
426 { efOUT, "-fin", "lr-four", ffOPTWR },
427 { efEPS, "-es", "sr", ffOPTWR },
428 { efEPS, "-elf", "lr-four", ffOPTWR },
429 { efEPS, "-etf", "tot-four", ffOPTWR },
430 { efEPS, "-qr", "qk-real", ffOPTWR },
431 { efEPS, "-qi", "qk-im", ffOPTWR },
432 { efEPS, "-elp", "lr-pb", ffOPTWR },
433 { efEPS, "-etp", "tot-pb", ffOPTWR },
434 { efEPS, "-rho", "rho", ffOPTWR },
435 { efEPS, "-qq", "charge", ffOPTWR },
436 { efXVG, "-gt", "gk-tab", ffOPTWR },
437 { efXVG, "-fcorr","fcorr", ffWRITE },
438 { efXVG, "-pcorr","pcorr", ffWRITE },
439 { efXVG, "-ftotcorr","ftotcorr", ffWRITE },
440 { efXVG, "-ptotcorr","ptotcorr", ffWRITE },
441 { efLOG, "-l", "fptest", ffWRITE },
442 { efXVG, "-gr", "spread", ffOPTWR },
443 { efPDB, "-pf", "pqr-four", ffOPTWR },
444 { efPDB, "-phitot", "pppm-phitot", ffOPTWR }
445 };
446 #define NFILE asize(fnm)
447 FILE *log;
448 t_topology top;
449 t_tpxheader stath;
450 t_inputrec ir;
451 t_block *excl;
452 t_forcerec *fr;
453 t_commrec *cr;
454 t_mdatoms *mdatoms;
455 t_graph *graph;
456 int i,step,nre,natoms,nmol;
457 rvec *x,*f_sr,*f_excl,*f_four,*f_pppm,*f_pois,box_size,hbox;
458 matrix box;
459 real t,lambda,vsr,*charge,*phi_f,*phi_pois,*phi_s,*phi_p3m,*rho;
460 output_env_t oenv;
461
462 static gmx_bool bFour=FALSE,bVerbose=FALSE,bGGhat=FALSE,bPPPM=TRUE,
463 bPoisson=FALSE,bOld=FALSE,bOldEwald=TRUE;
464 static int nprocs = 1;
465 static t_pargs pa[] = {
466 { "-np", FALSE, etINT, &nprocs, "Do it in parallel" },
467 { "-ewald", FALSE, etBOOL, &bFour, "Do an Ewald solution"},
468 { "-pppm", FALSE, etBOOL, &bPPPM, "Do a PPPM solution" },
469 { "-poisson",FALSE, etBOOL, &bPoisson,"Do a Poisson solution" },
470 { "-v", FALSE, etBOOL, &bVerbose,"Verbose on"},
471 { "-ghat", FALSE, etBOOL, &bGGhat, "Generate Ghat function"},
472 { "-old", FALSE, etBOOL, &bOld, "Use old function types"},
473 { "-oldewald",FALSE,etBOOL, &bOldEwald,"Use old Ewald code"}
474 };
475
476 CopyRight(stderr,argv[0]);
477 parse_common_args_r(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
478 NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
479
480 if (nprocs > 1) {
481 cr = init_par(&argc,argv);
482 open_log(ftp2fn(efLOG,NFILE,fnm),cr);
483 log = stdlog;
484 }
485 else {
486 cr = init_par(&argc,argv);
487 log = ftp2FILE(efLOG,NFILE,fnm,"w");
488 stdlog = log; }
489
490
491 /* Read topology and coordinates */
492 read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&stath,FALSE);
493 snew(x,stath.natoms);
494 snew(f_sr,stath.natoms);
495 snew(f_excl,stath.natoms);
496 snew(f_four,stath.natoms);
497 snew(f_pppm,stath.natoms);
498 snew(f_pois,stath.natoms);
499 read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,&ir,
500 box,&natoms,x,NULL,NULL,&top);
501 excl=&(top.atoms.excl);
502 nmol=top.blocks[ebMOLS].nr;
503
504 /* Allocate space for potential, charges and rho (charge density) */
505 snew(charge,stath.natoms);
506 snew(phi_f,stath.natoms);
507 snew(phi_p3m,stath.natoms);
508 snew(phi_pois,stath.natoms);
509 snew(phi_s,stath.natoms);
510 snew(rho,stath.natoms);
511
512 /* Set the charges */
513 for(i=0; (i<natoms); i++)
514 charge[i]=top.atoms.atom[i].q;
515
516 /* Make a simple box vector instead of tensor */
517 for(i=0; (i<DIM); i++)
518 box_size[i]=box[i][i];
519
520 /* Set some constants */
521 fr = mk_forcerec();
522 mdatoms = atoms2md(&(top.atoms),FALSE,FALSE);
523
524 set_LRconsts(log,ir.rcoulomb_switch,ir.rcoulomb,box_size,fr);
525 init_forcerec(log,fr,&ir,&(top.blocks[ebMOLS]),cr,
526 &(top.blocks[ebCGS]),&(top.idef),mdatoms,box,FALSE);
527 calc_shifts(box,box_size,fr->shift_vec,FALSE);
528
529 /* Periodicity stuff */
530 graph = mk_graph(&(top.idef),top.atoms.nr,FALSE,FALSE);
531 shift_self(graph,fr->shift_vec,x);
532
533 calc_LRcorrections(log,0,natoms,ir.rcoulomb_switch,
534 ir.rcoulomb,charge,excl,x,f_excl,bOld);
535 pr_f("f_excl.dat",natoms,f_excl);
536
537 /* Compute the short range potential */
538 put_atoms_in_box(natoms,box,x);
539 vsr=phi_sr(log,natoms,x,charge,ir.rcoulomb,
540 ir.rcoulomb_switch,box_size,phi_s,excl,f_sr,bOld);
541 pr_f("f_sr.dat",natoms,f_sr);
542
543 /* Plot the short range potential in a matrix */
544 calc_ener(log,"Short Range",TRUE,nmol,natoms,phi_s,charge,excl);
545
546
547 if (bFour)
548 test_four(log,NFILE,fnm,&(top.atoms),&ir,x,f_four,box_size,charge,phi_f,
549 phi_s,nmol,cr,bOld,bOldEwald);
550
551 if (bPPPM)
552 test_pppm(log,bVerbose,bGGhat,opt2fn("-g",NFILE,fnm),
553 &(top.atoms),&ir,x,f_pppm,charge,box_size,phi_p3m,phi_s,nmol,
554 cr,bOld,&(top.blocks[ebCGS]));
555
556 if (bPoisson)
557 test_poisson(log,bVerbose,
558 &(top.atoms),&ir,x,f_pois,charge,box_size,phi_pois,
559 phi_s,nmol,cr,bFour,f_four,phi_f,bOld);
560
561 if (bPPPM && bFour)
562 analyse_diff(log,"PPPM",oenv,
563 top.atoms.nr,f_four,f_pppm,phi_f,phi_p3m,phi_s,
564 opt2fn("-fcorr",NFILE,fnm),
565 opt2fn("-pcorr",NFILE,fnm),
566 opt2fn("-ftotcorr",NFILE,fnm),
567 opt2fn("-ptotcorr",NFILE,fnm));
568
569 if (bPoisson && bFour)
570 analyse_diff(log,"Poisson",oenv,
571 top.atoms.nr,f_four,f_pois,phi_f,phi_pois,phi_s,
572 opt2fn("-fcorr",NFILE,fnm),
573 opt2fn("-pcorr",NFILE,fnm),
574 opt2fn("-ftotcorr",NFILE,fnm),
575 opt2fn("-ptotcorr",NFILE,fnm));
576
577 gmx_fio_fclose(log);
578
579 thanx(stderr);
580
581 return 0;
582 }
583
The ultimate molecular dynamics simulation package