3 * This source code is part of
7 * GROningen MAchine for Chemical Simulations
10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * GROningen Mixture of Alchemy and Childrens' Stories
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
)
63 real pp
,r2
,R
,R_1
,R_2
,rc2
;
64 real qi
,qj
,vsr
,eps
,fscal
;
71 for(i
=0; (i
<nj
-1); i
++) {
73 for(j
=i
+1; (j
<nj
); j
++) {
76 for(k
=i1
; (k
<i2
); k
++)
80 r2
=calc_dx2dx(x
[i
],x
[j
],box
,dx
);
87 fscal
= old_f(R
,rc
,r1
)*R_2
;
88 pp
= old_phi(R
,rc
,r1
);
91 fscal
= new_f(R
,rc
)*R_2
;
97 for(m
=0; (m
<DIM
); m
++) {
98 f_sr
[i
][m
] += dx
[m
]*fscal
;
99 f_sr
[j
][m
] -= dx
[m
]*fscal
;
106 fprintf(log
,"There were %d short range interactions, vsr=%g\n",ni
,vsr
);
111 void calc_ener(FILE *fp
,char *title
,gmx_bool bHeader
,int nmol
,
112 int natoms
,real phi
[],real charge
[],t_block
*excl
)
115 real qq
,qi
,vv
,V
,Vex
,Vc
,Vt
;
119 for(i
=0; (i
<natoms
); i
++) {
120 vv
= charge
[i
]*phi
[i
];
122 qq
+= charge
[i
]*charge
[i
];
125 Vc
= 0.5*C
*ONE_4PI_EPS0
*qq
;
128 for(i
=0; (i
<excl
->nr
); i
++) {
130 i2
= excl
->index
[i
+1];
132 for(j
=i1
; (j
<i2
); j
++) {
138 Vex
= qq
*0.5*C
*ONE_4PI_EPS0
;
143 fprintf(fp
,"%12s %12s %12s %12s %12s %12s\n",
144 "","Vphi","Vself","Vexcl","Vtot","1Mol");
147 fprintf(fp
,"%12s %12.5e %12.5e %12.5e %12.5e %12.5e\n",
148 title
,V
,Vc
,Vex
,Vt
,Vt
/nmol
);
151 void write_pqr(char *fn
,t_atoms
*atoms
,rvec x
[],real phi
[],real dx
)
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
],' ',
162 10*(dx
+x
[i
][XX
]),10*x
[i
][YY
],10*(x
[i
][ZZ
]),0.0,phi
[i
]);
167 void write_grid_pqr(char *fn
,int nx
,int ny
,int nz
,real
***phi
)
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
]);
182 void plot_phi(char *fn
,rvec box
,int natoms
,rvec x
[],real phi
[])
185 real phi_max
,rr
,gg
,bb
,fac
,dx
,x0
,y0
;
191 for(i
=0; (i
<natoms
); i
++)
192 phi_max
=max(phi_max
,fabs(phi
[i
]));
195 fprintf(stderr
,"All values zero, see .out file\n");
201 fprintf(stderr
,"Scaling box by %g\n",fac
);
204 (real
)(fac
*box
[XX
]+2*offset
),(real
)(fac
*box
[YY
]+2*offset
));
205 ps_translate(eps
,offset
,offset
);
207 ps_box(eps
,1,1,(real
)(fac
*box
[XX
]-1),(real
)(fac
*box
[YY
]-1));
209 for(i
=0; (i
<natoms
); i
++) {
212 gg
=bb
=(1.0+(phi
[i
]/phi_max
));
214 rr
=gg
=(1.0-(phi
[i
]/phi_max
));
218 ps_color(eps
,rr
,gg
,bb
);
221 ps_fillbox(eps
,(real
)(x0
-dx
),(real
)(y0
-dx
),(real
)(x0
+dx
),(real
)(y0
+dx
));
226 void plot_qtab(char *fn
,int nx
,int ny
,int nz
,real
***qtab
)
237 npt
=(box
[XX
]*box
[YY
]*box
[ZZ
]);
244 for(ix
=-nx
; (ix
<nx
); ix
++)
245 for(iy
=-ny
; (iy
<ny
); iy
++)
246 for(iz
=-nz
; (iz
<nz
); iz
++,i
++) {
249 xx
[i
][ZZ
]=iz
+nz
+0.5; /* onzin */
250 phi
[i
]=qtab
[ix
+nx
][iy
+ny
][iz
+nz
];
253 plot_phi(fn
,box
,npt
,xx
,phi
);
259 void print_phi(char *fn
,int natoms
,rvec x
[],real phi
[])
264 fp
=gmx_fio_fopen(fn
,"w");
265 for(i
=0; (i
<natoms
); i
++)
266 fprintf(fp
,"%10d %12.5e\n",i
,phi
[i
]);
270 void pr_f(char *fn
,int natoms
,rvec f
[])
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
]);
281 void test_pppm(FILE *log
, gmx_bool bVerbose
,
282 gmx_bool bGenerGhat
, char *ghatfn
,
283 t_atoms
*atoms
, t_inputrec
*ir
,
285 real charge
[], rvec box
,
286 real phi
[], real phi_s
[],
287 int nmol
, t_commrec
*cr
,
288 gmx_bool bOld
, t_block
*cgs
)
297 calc_nsb(cgs
,1,&nsb
,0);
299 /* First time only setup is done! */
300 init_pppm(log
,cr
,&nsb
,bVerbose
,bOld
,box
,ghatfn
,ir
);
302 ener
= do_pppm(log
,bVerbose
,x
,f
,charge
,box
,phi
,cr
,&nsb
,&nrnb
);
303 fprintf(log
,"Vpppm = %g\n",ener
);
305 sprintf(buf
,"PPPM-%d.pdb",ir
->nkx
);
306 write_pqr(buf
,atoms
,x
,phi
,0);
308 pr_f("pppm-force",atoms
->nr
,f
);
310 calc_ener(log
,buf
,FALSE
,nmol
,atoms
->nr
,phi
,charge
,&atoms
->excl
);
312 for(i
=0; (i
<atoms
->nr
); i
++)
314 sprintf(buf
,"PPPM-%d+SR",ir
->nkx
);
315 calc_ener(log
,buf
,FALSE
,nmol
,atoms
->nr
,phi
,charge
,&atoms
->excl
);
317 write_pqr(buf
,atoms
,x
,phi
,0);
320 void test_poisson(FILE *log
, gmx_bool bVerbose
,
321 t_atoms
*atoms
, t_inputrec
*ir
,
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
)
337 /* First time only setup is done! */
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
];
348 ener
= do_poisson(log
,bVerbose
,ir
,atoms
->nr
,x
,f
,charge
,box
,phi
,
352 fprintf(log
,"Vpoisson = %g, nit = %d\n",ener
,nit
);
354 sprintf(buf
,"POISSON-%d.pdb",ir
->nkx
);
355 write_pqr(buf
,atoms
,x
,phi
,0);
357 pr_f("poisson-force",atoms
->nr
,f
);
359 calc_ener(log
,buf
,FALSE
,nmol
,atoms
->nr
,phi
,charge
,&atoms
->excl
);
361 for(i
=0; (i
<atoms
->nr
); i
++)
363 sprintf(buf
,"POISSON-%d+SR",ir
->nkx
);
364 calc_ener(log
,buf
,FALSE
,nmol
,atoms
->nr
,phi
,charge
,&atoms
->excl
);
366 write_pqr(buf
,atoms
,x
,phi
,0);
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
)
378 init_ewald_tab(&et
, NULL
, ir
, log
);
381 energy
= do_ewald(log
,ir
,atoms
->nr
,x
,f
,charge
,box
,phi_f
,cr
,bOld
,et
);
383 energy
= do_ewald_new(log
,ir
,atoms
->nr
,x
,f
,charge
,box
,phi_f
,cr
,bOld
,et
);
385 /*symmetrize_phi(log,atoms->nr,phi_f,bVerbose);*/
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
);
394 /* Calc and plot the total potential */
395 for(i
=0; (i
<atoms
->nr
); i
++) {
397 /*clear_rvec(f[i]);*/
399 calc_ener(log
,"Fourier+SR",FALSE
,nmol
,atoms
->nr
,phi_f
,charge
,&atoms
->excl
);
402 static void print_opts(FILE *fp
,t_inputrec
*ir
,gmx_bool bFour
)
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
);
408 fprintf(fp
,"KVectors: %10d %10d %10d\n",ir
->nkx
,ir
->nky
,ir
->nkz
);
412 int main(int argc
,char *argv
[])
414 static char *desc
[] = {
415 "testlr tests the PPPM and Ewald method for the",
416 "long range electrostatics problem."
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
}
446 #define NFILE asize(fnm)
456 int i
,step
,nre
,natoms
,nmol
;
457 rvec
*x
,*f_sr
,*f_excl
,*f_four
,*f_pppm
,*f_pois
,box_size
,hbox
;
459 real t
,lambda
,vsr
,*charge
,*phi_f
,*phi_pois
,*phi_s
,*phi_p3m
,*rho
;
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"}
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
);
481 cr
= init_par(&argc
,argv
);
482 open_log(ftp2fn(efLOG
,NFILE
,fnm
),cr
);
486 cr
= init_par(&argc
,argv
);
487 log
= ftp2FILE(efLOG
,NFILE
,fnm
,"w");
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
;
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
);
512 /* Set the charges */
513 for(i
=0; (i
<natoms
); i
++)
514 charge
[i
]=top
.atoms
.atom
[i
].q
;
516 /* Make a simple box vector instead of tensor */
517 for(i
=0; (i
<DIM
); i
++)
518 box_size
[i
]=box
[i
][i
];
520 /* Set some constants */
522 mdatoms
= atoms2md(&(top
.atoms
),FALSE
,FALSE
);
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
);
529 /* Periodicity stuff */
530 graph
= mk_graph(&(top
.idef
),top
.atoms
.nr
,FALSE
,FALSE
);
531 shift_self(graph
,fr
->shift_vec
,x
);
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
);
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
);
543 /* Plot the short range potential in a matrix */
544 calc_ener(log
,"Short Range",TRUE
,nmol
,natoms
,phi_s
,charge
,excl
);
548 test_four(log
,NFILE
,fnm
,&(top
.atoms
),&ir
,x
,f_four
,box_size
,charge
,phi_f
,
549 phi_s
,nmol
,cr
,bOld
,bOldEwald
);
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
]));
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
);
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
));
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
));