int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_pme_error[tt] estimates the error of the electrostatic forces",
"if using the sPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"The part of the error that stems from self interaction of the particles "
"is computationally demanding. However, a good a approximation is to",
"just use a fraction of the particles for this term which can be",
"indicated by the flag [TT]-self[tt].[PAR]",
};
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=1.0;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
gmx_bool bVerbose=FALSE;
int seed=0;
static t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
"If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles" },
{ "-seed", FALSE, etINT, {&seed},
"Random number seed used for Monte Carlo algorithm when [TT]-self[tt] is set to a value between 0.0 and 1.0" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
#ifdef GMX_LIB_MPI
MPI_Barrier(MPI_COMM_WORLD);
#endif
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file and do some tuning if requested */
estimate_PME_error(&info, &state, &mtop, fp, bVerbose, seed, cr);
if (MASTER(cr))
{
/* Write out optimized tpr file if requested */
if ( opt2bSet("-so",NFILE,fnm) || bTUNE )
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
}
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
/* Estimate the error of the SPME Ewald sum. This estimate is based upon
* a) a homogeneous distribution of the charges
* b) a total charge of zero.
*/
static void estimate_PME_error(t_inputinfo *info, t_state *state,
gmx_mtop_t *mtop, FILE *fp_out, gmx_bool bVerbose, unsigned int seed,
t_commrec *cr)
{
rvec *x=NULL; /* The coordinates */
real *q=NULL; /* The charges */
real edir=0.0; /* real space error */
real erec=0.0; /* reciprocal space error */
real derr=0.0; /* difference of real and reciprocal space error */
real derr0=0.0; /* difference of real and reciprocal space error */
real beta=0.0; /* splitting parameter beta */
real beta0=0.0; /* splitting parameter beta */
int ncharges; /* The number of atoms with charges */
int nsamples; /* The number of samples used for the calculation of the
* self-energy error term */
int i=0;
if (MASTER(cr))
fprintf(fp_out, "\n--- PME ERROR ESTIMATE ---\n");
/* Prepare an x and q array with only the charged atoms */
ncharges = prepare_x_q(&q, &x, mtop, state->x, cr);
if (MASTER(cr))
{
calc_q2all(mtop, &(info->q2all), &(info->q2allnr));
info->ewald_rtol[0]=gmx_erfc(info->rcoulomb[0]*info->ewald_beta[0]);
/* Write some info to log file */
fprintf(fp_out, "Box volume : %g nm^3\n", info->volume);
fprintf(fp_out, "Number of charged atoms : %d (total atoms %d)\n",ncharges, info->natoms);
fprintf(fp_out, "Coulomb radius : %g nm\n", info->rcoulomb[0]);
fprintf(fp_out, "Ewald_rtol : %g\n", info->ewald_rtol[0]);
fprintf(fp_out, "Ewald parameter beta : %g\n", info->ewald_beta[0]);
fprintf(fp_out, "Interpolation order : %d\n", info->pme_order[0]);
fprintf(fp_out, "Fourier grid (nx,ny,nz) : %d x %d x %d\n",
info->nkx[0],info->nky[0],info->nkz[0]);
fflush(fp_out);
}
if (PAR(cr))
bcast_info(info, cr);
/* Calculate direct space error */
info->e_dir[0] = estimate_direct(info);
/* Calculate reciprocal space error */
info->e_rec[0] = estimate_reciprocal(info, x, q, ncharges, fp_out, bVerbose,
seed, &nsamples, cr);
if (PAR(cr))
bcast_info(info, cr);
if (MASTER(cr))
{
fprintf(fp_out, "Direct space error est. : %10.3e kJ/(mol*nm)\n", info->e_dir[0]);
fprintf(fp_out, "Reciprocal sp. err. est.: %10.3e kJ/(mol*nm)\n", info->e_rec[0]);
fprintf(fp_out, "Self-energy error term was estimated using %d samples\n", nsamples);
fflush(fp_out);
fprintf(stderr, "Direct space error est. : %10.3e kJ/(mol*nm)\n", info->e_dir[0]);
fprintf(stderr, "Reciprocal sp. err. est.: %10.3e kJ/(mol*nm)\n", info->e_rec[0]);
}
i=0;
if (info->bTUNE)
{
if(MASTER(cr))
fprintf(stderr,"Starting tuning ...\n");
edir=info->e_dir[0];
erec=info->e_rec[0];
derr0=edir-erec;
beta0=info->ewald_beta[0];
if (derr>0.0)
info->ewald_beta[0]+=0.1;
else
info->ewald_beta[0]-=0.1;
info->e_dir[0] = estimate_direct(info);
info->e_rec[0] = estimate_reciprocal(info, x, q, ncharges, fp_out, bVerbose,
seed, &nsamples, cr);
if (PAR(cr))
bcast_info(info, cr);
edir=info->e_dir[0];
erec=info->e_rec[0];
derr=edir-erec;
while ( fabs(derr/min(erec,edir)) > 1e-4)
{
beta=info->ewald_beta[0];
beta-=derr*(info->ewald_beta[0]-beta0)/(derr-derr0);
beta0=info->ewald_beta[0];
info->ewald_beta[0]=beta;
derr0=derr;
info->e_dir[0] = estimate_direct(info);
info->e_rec[0] = estimate_reciprocal(info, x, q, ncharges, fp_out, bVerbose,
seed, &nsamples, cr);
if (PAR(cr))
bcast_info(info, cr);
edir=info->e_dir[0];
erec=info->e_rec[0];
derr=edir-erec;
if (MASTER(cr))
{
i++;
fprintf(stderr,"difference between real and rec. space error (step %d): %g\n",i,fabs(derr));
fprintf(stderr,"old beta: %f\n",beta0);
fprintf(stderr,"new beta: %f\n",beta);
}
}
info->ewald_rtol[0]=gmx_erfc(info->rcoulomb[0]*info->ewald_beta[0]);
if (MASTER(cr))
{
/* Write some info to log file */
fflush(fp_out);
fprintf(fp_out, "========= After tuning ========\n");
fprintf(fp_out, "Direct space error est. : %10.3e kJ/(mol*nm)\n", info->e_dir[0]);
fprintf(fp_out, "Reciprocal sp. err. est.: %10.3e kJ/(mol*nm)\n", info->e_rec[0]);
fprintf(stderr, "Direct space error est. : %10.3e kJ/(mol*nm)\n", info->e_dir[0]);
fprintf(stderr, "Reciprocal sp. err. est.: %10.3e kJ/(mol*nm)\n", info->e_rec[0]);
fprintf(fp_out, "Ewald_rtol : %g\n", info->ewald_rtol[0]);
fprintf(fp_out, "Ewald parameter beta : %g\n", info->ewald_beta[0]);
fflush(fp_out);
}
}
}
int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"g_pme_error estimates the error of the electrostatic forces",
"if using the SPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"As a part of the error stems from self interaction of the particles "
"and is computationally very demanding a good a approximation is possible",
"if just a fraction of the particles is used to calculate the average",
"of this error by using the flag [TT]-self[tt].[PAR]",
};
int repeats=2;
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=-1.0;
t_perf **perfdata;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
static t_filenm fnm[] = {
/* g_tune_pme */
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
/***********************/
/* g_tune_pme options: */
/***********************/
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from tpr file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"If flag is set the splitting parameter will be tuned to distribute the error equally in real and rec. space" },
{ "-self", FALSE, etREAL, {&fracself},
"If positive, determine selfinteraction error just over this fraction (default=1.0)" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file */
estimate_PME_error(&info, &state, &mtop, fp, cr);
if (MASTER(cr))
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
