int
main()
{
gsl_rng *r = gsl_rng_alloc(gsl_rng_default);
size_t n;
test_poisson(7, 1.0e-1, 0);
test_poisson(7, 1.0e-1, 1);
test_poisson(543, 1.0e-5, 0);
test_poisson(543, 1.0e-5, 1);
test_poisson(1000, 1.0e-6, 0);
test_poisson(1000, 1.0e-6, 1);
test_poisson(5000, 1.0e-7, 0);
test_poisson(5000, 1.0e-7, 1);
test_toeplitz(15, 0.01, 1.0, 0.01);
test_toeplitz(15, 1.0, 1.0, 0.01);
test_toeplitz(50, 1.0, 2.0, 0.01);
test_toeplitz(1000, 0.5, 1.0, 0.01);
for (n = 1; n <= 100; ++n)
{
test_random(n, r, 0);
test_random(n, r, 1);
}
gsl_rng_free(r);
exit (gsl_test_summary());
} /* main() */
int main(int argc,char *argv[])
{
static char *desc[] = {
"testlr tests the PPPM and Ewald method for the",
"long range electrostatics problem."
};
static t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efHAT, "-g", "ghat", ffOPTRD },
{ efOUT, "-o", "rho", ffOPTWR },
{ efOUT, "-op", "lr-pb", ffOPTWR },
{ efOUT, "-of", "lr-four", ffOPTWR },
{ efOUT, "-opt", "tot-pb", ffOPTWR },
{ efOUT, "-oft", "tot-four", ffOPTWR },
{ efOUT, "-fin", "lr-four", ffOPTWR },
{ efEPS, "-es", "sr", ffOPTWR },
{ efEPS, "-elf", "lr-four", ffOPTWR },
{ efEPS, "-etf", "tot-four", ffOPTWR },
{ efEPS, "-qr", "qk-real", ffOPTWR },
{ efEPS, "-qi", "qk-im", ffOPTWR },
{ efEPS, "-elp", "lr-pb", ffOPTWR },
{ efEPS, "-etp", "tot-pb", ffOPTWR },
{ efEPS, "-rho", "rho", ffOPTWR },
{ efEPS, "-qq", "charge", ffOPTWR },
{ efXVG, "-gt", "gk-tab", ffOPTWR },
{ efXVG, "-fcorr","fcorr", ffWRITE },
{ efXVG, "-pcorr","pcorr", ffWRITE },
{ efXVG, "-ftotcorr","ftotcorr", ffWRITE },
{ efXVG, "-ptotcorr","ptotcorr", ffWRITE },
{ efLOG, "-l", "fptest", ffWRITE },
{ efXVG, "-gr", "spread", ffOPTWR },
{ efPDB, "-pf", "pqr-four", ffOPTWR },
{ efPDB, "-phitot", "pppm-phitot", ffOPTWR }
};
#define NFILE asize(fnm)
FILE *log;
t_topology top;
t_tpxheader stath;
t_inputrec ir;
t_block *excl;
t_forcerec *fr;
t_commrec *cr;
t_mdatoms *mdatoms;
t_graph *graph;
int i,step,nre,natoms,nmol;
rvec *x,*f_sr,*f_excl,*f_four,*f_pppm,*f_pois,box_size,hbox;
matrix box;
real t,lambda,vsr,*charge,*phi_f,*phi_pois,*phi_s,*phi_p3m,*rho;
static bool bFour=FALSE,bVerbose=FALSE,bGGhat=FALSE,bPPPM=TRUE,
bPoisson=FALSE,bOld=FALSE,bOldEwald=TRUE;
static int nprocs = 1;
static t_pargs pa[] = {
{ "-np", FALSE, etINT, &nprocs, "Do it in parallel" },
{ "-ewald", FALSE, etBOOL, &bFour, "Do an Ewald solution"},
{ "-pppm", FALSE, etBOOL, &bPPPM, "Do a PPPM solution" },
{ "-poisson",FALSE, etBOOL, &bPoisson,"Do a Poisson solution" },
{ "-v", FALSE, etBOOL, &bVerbose,"Verbose on"},
{ "-ghat", FALSE, etBOOL, &bGGhat, "Generate Ghat function"},
{ "-old", FALSE, etBOOL, &bOld, "Use old function types"},
{ "-oldewald",FALSE,etBOOL, &bOldEwald,"Use old Ewald code"}
};
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (nprocs > 1) {
cr = init_par(&argc,argv);
open_log(ftp2fn(efLOG,NFILE,fnm),cr);
log = stdlog;
}
else {
cr = init_par(&argc,argv);
log = ftp2FILE(efLOG,NFILE,fnm,"w");
stdlog = log; }
/* Read topology and coordinates */
read_tpxheader(ftp2fn(efTPX,NFILE,fnm),&stath,FALSE);
snew(x,stath.natoms);
snew(f_sr,stath.natoms);
snew(f_excl,stath.natoms);
snew(f_four,stath.natoms);
snew(f_pppm,stath.natoms);
snew(f_pois,stath.natoms);
read_tpx(ftp2fn(efTPX,NFILE,fnm),&step,&t,&lambda,&ir,
box,&natoms,x,NULL,NULL,&top);
excl=&(top.atoms.excl);
nmol=top.blocks[ebMOLS].nr;
/* Allocate space for potential, charges and rho (charge density) */
snew(charge,stath.natoms);
snew(phi_f,stath.natoms);
snew(phi_p3m,stath.natoms);
snew(phi_pois,stath.natoms);
snew(phi_s,stath.natoms);
snew(rho,stath.natoms);
/* Set the charges */
for(i=0; (i<natoms); i++)
charge[i]=top.atoms.atom[i].q;
/* Make a simple box vector instead of tensor */
for(i=0; (i<DIM); i++)
box_size[i]=box[i][i];
/* Set some constants */
fr = mk_forcerec();
mdatoms = atoms2md(&(top.atoms),FALSE,FALSE);
set_LRconsts(log,ir.rcoulomb_switch,ir.rcoulomb,box_size,fr);
init_forcerec(log,fr,&ir,&(top.blocks[ebMOLS]),cr,
&(top.blocks[ebCGS]),&(top.idef),mdatoms,box,FALSE);
calc_shifts(box,box_size,fr->shift_vec,FALSE);
/* Periodicity stuff */
graph = mk_graph(&(top.idef),top.atoms.nr,FALSE,FALSE);
shift_self(graph,fr->shift_vec,x);
calc_LRcorrections(log,0,natoms,ir.rcoulomb_switch,
ir.rcoulomb,charge,excl,x,f_excl,bOld);
pr_f("f_excl.dat",natoms,f_excl);
/* Compute the short range potential */
put_atoms_in_box(natoms,box,x);
vsr=phi_sr(log,natoms,x,charge,ir.rcoulomb,
ir.rcoulomb_switch,box_size,phi_s,excl,f_sr,bOld);
pr_f("f_sr.dat",natoms,f_sr);
/* Plot the short range potential in a matrix */
calc_ener(log,"Short Range",TRUE,nmol,natoms,phi_s,charge,excl);
if (bFour)
test_four(log,NFILE,fnm,&(top.atoms),&ir,x,f_four,box_size,charge,phi_f,
phi_s,nmol,cr,bOld,bOldEwald);
if (bPPPM)
test_pppm(log,bVerbose,bGGhat,opt2fn("-g",NFILE,fnm),
&(top.atoms),&ir,x,f_pppm,charge,box_size,phi_p3m,phi_s,nmol,
cr,bOld,&(top.blocks[ebCGS]));
if (bPoisson)
test_poisson(log,bVerbose,
&(top.atoms),&ir,x,f_pois,charge,box_size,phi_pois,
phi_s,nmol,cr,bFour,f_four,phi_f,bOld);
if (bPPPM && bFour)
analyse_diff(log,"PPPM",
top.atoms.nr,f_four,f_pppm,phi_f,phi_p3m,phi_s,
opt2fn("-fcorr",NFILE,fnm),
opt2fn("-pcorr",NFILE,fnm),
opt2fn("-ftotcorr",NFILE,fnm),
opt2fn("-ptotcorr",NFILE,fnm));
if (bPoisson && bFour)
analyse_diff(log,"Poisson",
top.atoms.nr,f_four,f_pois,phi_f,phi_pois,phi_s,
opt2fn("-fcorr",NFILE,fnm),
opt2fn("-pcorr",NFILE,fnm),
opt2fn("-ftotcorr",NFILE,fnm),
opt2fn("-ptotcorr",NFILE,fnm));
gmx_fio_fclose(log);
thanx(stderr);
return 0;
}
