int main ( int argc, char **argv ) {
int methodnr;
FLOAT_TYPE alphamin,alphamax,alphastep;
FLOAT_TYPE alpha;
FLOAT_TYPE walltime = 0;
FILE* fout;
system_t *system;
method_t method;
parameters_t parameters, parameters_ewald;
parameters.tuning = parameters_ewald.tuning = 0;
data_t *data = NULL, *data_ewald = NULL;
forces_t *forces, *forces_ewald;
char *pos_file = NULL, *force_file = NULL, *out_file = NULL, *ref_out = NULL, *sys_out = NULL, *rdf_file = NULL, *vtf_file = NULL, *cdf_file = NULL;
error_t error;
FLOAT_TYPE length, prec;
int npart;
FLOAT_TYPE charge;
int form_factor;
FLOAT_TYPE rdf_min, rdf_max;
int rdf_bins;
int inhomo_error_mesh = 64;
int inhomo_error_cao = 5;
int inhomo_mc = 0;
char *inhomo_output = NULL;
FLOAT_TYPE error_k=0.0, ewald_error_k_est, estimate=0.0, error_k_est = 0;
int i,j, calc_k_error, calc_est;
int error_map_mesh=64, error_map_cao=1;
#ifdef _OPENMP
int nthreads;
#endif
cmd_parameters_t params = { NULL, 0, NULL, 0 };
add_param( "rcut", ARG_TYPE_FLOAT, ARG_REQUIRED, &(parameters.rcut), ¶ms );
add_param( "alphamin", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphamin, ¶ms );
add_param( "alphamax", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphamax, ¶ms );
add_param( "alphastep", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphastep, ¶ms );
add_param( "alpha", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alpha, ¶ms );
add_param( "positions", ARG_TYPE_STRING, ARG_OPTIONAL, &pos_file, ¶ms );
add_param( "error_k", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "forces", ARG_TYPE_STRING, ARG_OPTIONAL, &force_file, ¶ms );
add_param( "mesh", ARG_TYPE_INT, ARG_REQUIRED, &(parameters.mesh), ¶ms );
add_param( "cao", ARG_TYPE_INT, ARG_REQUIRED, &(parameters.cao), ¶ms );
add_param( "method", ARG_TYPE_INT, ARG_REQUIRED, &methodnr, ¶ms );
add_param( "mc", ARG_TYPE_INT, ARG_OPTIONAL, &P3M_BRILLOUIN, ¶ms );
add_param( "mc_est", ARG_TYPE_INT, ARG_OPTIONAL, &P3M_BRILLOUIN_TUNING, ¶ms );
add_param( "no_estimate", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "outfile", ARG_TYPE_STRING, ARG_OPTIONAL, &out_file, ¶ms );
add_param( "particles", ARG_TYPE_INT, ARG_OPTIONAL, &npart, ¶ms );
add_param( "box", ARG_TYPE_FLOAT, ARG_OPTIONAL, &length, ¶ms );
add_param( "tune", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "prec", ARG_TYPE_FLOAT, ARG_OPTIONAL, &prec, ¶ms );
add_param( "reference_out", ARG_TYPE_STRING, ARG_OPTIONAL, &ref_out, ¶ms );
add_param( "system_out", ARG_TYPE_STRING, ARG_OPTIONAL, &sys_out, ¶ms );
add_param( "verlet_lists", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "charge", ARG_TYPE_FLOAT, ARG_OPTIONAL, &charge, ¶ms );
add_param( "system_type", ARG_TYPE_INT, ARG_OPTIONAL, &form_factor, ¶ms );
add_param( "rdf", ARG_TYPE_STRING, ARG_OPTIONAL, &rdf_file, ¶ms );
add_param( "rdf_bins", ARG_TYPE_INT, ARG_OPTIONAL, &rdf_bins, ¶ms );
add_param( "rdf_rmin", ARG_TYPE_FLOAT, ARG_OPTIONAL, &rdf_min, ¶ms );
add_param( "rdf_rmax", ARG_TYPE_FLOAT, ARG_OPTIONAL, &rdf_max, ¶ms );
add_param( "cdf", ARG_TYPE_STRING, ARG_OPTIONAL, &cdf_file, ¶ms );
add_param( "no_calculation", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "vtf_file", ARG_TYPE_STRING, ARG_OPTIONAL, &vtf_file, ¶ms );
add_param( "rdf_species", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "no_reference_force", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms);
#ifdef _OPENMP
add_param( "threads", ARG_TYPE_INT, ARG_OPTIONAL, &nthreads, ¶ms );
#endif
add_param( "inhomo_error", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms);
add_param( "inhomo_mesh", ARG_TYPE_INT, ARG_OPTIONAL, &inhomo_error_mesh, ¶ms);
add_param( "inhomo_cao", ARG_TYPE_INT, ARG_OPTIONAL, &inhomo_error_cao, ¶ms);
add_param( "inhomo_mc", ARG_TYPE_INT, ARG_OPTIONAL, &inhomo_mc, ¶ms);
add_param( "inhomo_output", ARG_TYPE_STRING, ARG_OPTIONAL, &inhomo_output, ¶ms);
add_param( "inhomo_uniform", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms);
add_param( "error_map", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms);
add_param( "error_map_mesh", ARG_TYPE_INT, ARG_OPTIONAL, &error_map_mesh, ¶ms);
add_param( "error_map_cao", ARG_TYPE_INT, ARG_OPTIONAL, &error_map_cao, ¶ms);
parse_parameters( argc - 1, argv + 1, params );
calc_k_error = param_isset( "error_k", params );
calc_est = 0;
if(param_isset("no_estimate", params) == 1)
calc_est = 1;
parameters.cao3 = parameters.cao*parameters.cao*parameters.cao;
parameters.ip = parameters.cao - 1;
parameters.alpha = 0.0;
parameters_ewald = parameters;
#ifdef _OPENMP
if(param_isset("threads", params)) {
omp_set_num_threads(nthreads);
}
printf("OpenMP: Using up to %d threads.\n", omp_get_max_threads( ));
#endif
if(!(param_isset("alphamin", params) && param_isset("alphamax", params) && param_isset("alphastep", params)) && !param_isset("alpha", params)) {
puts("Need to provide either alpha-range (alphamin, alphamax, alphastep) or alpha.");
exit(1);
}
if( !param_isset("positions", params) &&
!(param_isset("box", params) && param_isset("particles", params))) {
puts("Need to provide either 'positions' or 'box' and 'particles'.");
exit(1);
}
if( param_isset("positions", params)) {
// Inits the system and reads particle data and parameters from file.
puts("Reading file");
system = Read_system ( ¶meters, pos_file );
puts("Done.");
} else {
puts("Generating system.");
if( !param_isset("charge", params)) {
charge=1.0;
}
if(param_isset("system_type", params)) {
printf("Using system type %d\n", form_factor);
system = generate_system( form_factor, npart, length, charge);
} else {
system = generate_system( SYSTEM_RANDOM, npart, length, charge);
}
puts("Done.");
}
/* inhomo_error(system, NULL, 100); */
if( param_isset("vtf_file", params) == 1)
write_vtf( vtf_file, system );
if( param_isset("rdf", params) == 1) {
puts("Calculating RDF");
if( param_isset("rdf_bins", params) == 0)
rdf_bins = 100;
if( param_isset("rdf_rmin", params) == 0)
rdf_min = 0.0;
if( param_isset("rdf_rmax", params) == 0)
rdf_max = system->length/2;
printf("Using %d bins, %lf <= r <= %lf\n", rdf_bins, rdf_min, rdf_max);
int bins = rdf_bins;
FLOAT_TYPE *rdf = radial_distribution(rdf_min, rdf_max, rdf_bins, system);
/* FLOAT_TYPE *c; */
/* FLOAT_TYPE *rdf_sym = Init_array( 2*bins-1, 2*sizeof(FLOAT_TYPE)); */
/* c = low_pass_forward( bins, rdf, 0.3); */
/* c = low_pass_backward(bins, c, 0.3); */
/* rdf = c; */
/* for(int i = 0; i < 2*bins; i++) { */
/* rdf_sym[i] = c[i]; */
/* } */
/* for(int i = bins; i < 2*bins-1; i++) { */
/* rdf_sym[2*i] = c[2*bins - 2] + (i-bins)*(c[2] - c[0]); */
/* rdf_sym[2*i+1] = c[4*bins - 2*i - 1]; */
/* } */
FILE *rdf_out = fopen(rdf_file, "w");
/* FILE *c_out = fopen("c_fft.dat", "w"); */
/* rshif_array(2*(2*bins-1), c, 2*bins); */
for(int i = 0; i<bins; i++)
fprintf(rdf_out, "%e %e\n", FLOAT_CAST rdf[2*i], FLOAT_CAST rdf[2*i+1]);
/* for(int i = 0; i<2*bins-1; i++) */
/* /\* fprintf(c_out, "%e %e\n", FLOAT_CAST rdf_sym[2*i], FLOAT_CAST rdf_sym[2*i+1] ); *\/ */
/* fprintf(c_out, "%d %e %e\n", i, FLOAT_CAST c[2*i], FLOAT_CAST c[2*i+1] ); */
/* fclose(c_out); */
fclose(rdf_out);
fftw_free(rdf);
/* fftw_free(c); */
puts("Done.");
}
if( param_isset("rdf_species", params) == 1) {
radial_distribution_species(0.0, 3.0, 200, system);
}
forces = Init_forces(system->nparticles);
forces_ewald = Init_forces(system->nparticles);
if(param_isset("reference_out", params))
{
printf("Minimal distance: %.*f\n", DIGITS, FLOAT_CAST Min_distance( system ));
puts("Calculating reference forces.");
printf("Reference precision %e\n.", FLOAT_CAST Calculate_reference_forces( system, ¶meters ));
printf("Reference energy %e\n", system->energy);
puts("Done.");
printf("Writing reference forces to '%s'\n", ref_out);
Write_exact_forces(system, ref_out);
puts("Done.");
}
if(param_isset("system_out", params))
{
printf("Writing system to '%s'\n", sys_out);
Write_system(system, sys_out);
puts("Done.");
}
if(param_isset("forces", params) == 1) {
printf("Reading reference forces from '%s'.\n", force_file);
Read_exact_forces( system, force_file );
puts("Done.");
} else {
if(param_isset("no_reference_force", params) !=1) {
puts("Calculating reference forces.");
printf("Reference precision %e\n.", FLOAT_CAST Calculate_reference_forces( system, ¶meters ));
puts("Done.");
} else {
puts("Skipping reference force calculation.");
}
}
if ( methodnr == method_ewald.method_id )
method = method_ewald;
#ifdef P3M_IK_H
else if ( methodnr == method_p3m_ik.method_id )
method = method_p3m_ik;
#endif
#ifdef P3M_IK_I_H
else if ( methodnr == method_p3m_ik_i.method_id )
method = method_p3m_ik_i;
#endif
#ifdef P3M_AD_H
else if ( methodnr == method_p3m_ad.method_id )
method = method_p3m_ad;
#endif
#ifdef P3M_AD_I_H
else if ( methodnr == method_p3m_ad_i.method_id ) {
method = method_p3m_ad_i;
}
#endif
#ifdef P3M_IK_REAL_H
else if ( methodnr == method_p3m_ik_r.method_id )
method = method_p3m_ik_r;
#endif
#ifdef P3M_AD_R_H
else if ( methodnr == method_p3m_ad_r.method_id )
method = method_p3m_ad_r;
#endif
else {
fprintf ( stderr, "Method %d not know.", methodnr );
exit ( 126 );
}
if ( ( method.Init == NULL ) || ( method.Influence_function == NULL ) || ( method.Kspace_force == NULL ) ) {
fprintf ( stderr,"Internal error: Method '%s' (%d) is not properly defined. Aborting.\n", method.method_name, method.method_id );
exit ( -1 );
}
fprintf ( stderr, "Using %s.\n", method.method_name );
if(param_isset("outfile", params) == 1) {
fout = fopen ( out_file, "w" );
} else {
fout = fopen ( "out.dat","w" );
}
printf ( "Init" );
fflush(stdout);
data = method.Init ( system, ¶meters );
printf ( ".\n" );
if(param_isset("no_reference_force", params) !=1) {
printf ( "Init Ewald" );
data_ewald = method_ewald.Init ( system, ¶meters_ewald );
printf ( ".\n" );
}
/* printf ( "Init neighborlist" ); */
/* Init_neighborlist ( system, ¶meters, data ); */
/* printf ( ".\n" ); */
printf ( "# %8s\t%8s\t%8s\t%8s\t%8s\n", "alpha", "DeltaF", "Estimate", "R-Error-Est", "K-Error-Est Generic-K-Space-err" );
for ( parameters.alpha=alphamin; parameters.alpha<=alphamax; parameters.alpha+=alphastep ) {
parameters_ewald.alpha = parameters.alpha;
method.Influence_function ( system, ¶meters, data ); /* Hockney/Eastwood */
if(!param_isset("no_calculation", params)) {
walltime = wtime();
Calculate_forces ( &method, system, ¶meters, data, forces ); /* Hockney/Eastwood */
walltime = wtime() - walltime;
}
error_k =0.0;
if(calc_k_error == 1) {
for(i=0; i<3; i++) {
memset ( forces_ewald->f_k->fields[i], 0, system->nparticles*sizeof ( FLOAT_TYPE ) );
}
method_ewald.Influence_function ( system, ¶meters_ewald, data_ewald );
method_ewald.Kspace_force( system, ¶meters_ewald, data_ewald, forces_ewald );
error_k =0.0;
for (i=0; i<system->nparticles; i++) {
for (j=0; j<3; j++) {
error_k += SQR( forces->f_k->fields[j][i] - forces_ewald->f_k->fields[j][i] );
}
}
error_k = SQRT(error_k) / SQRT(system->nparticles);
if(param_isset("error_map", params)) {
puts("Writing error map.");
FLOAT_TYPE *error_map;
error_map = Error_map(system, forces, forces_ewald, error_map_mesh, error_map_cao);
FILE *error_out = fopen("error_map.dat", "w");
FILE *error_out_2d = fopen("error_map_2d.dat", "w");
int nx,ny,nz;
int nx_2d_plane = ERROR_MAP_2D_PLANE * error_map_mesh;
int ind;
printf("2d cut plane is nx = %d\n", nx_2d_plane);
for (nx=0; nx<error_map_mesh; nx++) {
for (ny=0; ny<error_map_mesh; ny++) {
for (nz=0; nz<error_map_mesh; nz++) {
ind = 2*((error_map_mesh*error_map_mesh*nx) + error_map_mesh*(ny) + (nz));
fprintf(error_out, "%d %d %d %e\n", nx, ny, nz, FLOAT_CAST error_map[ind]);
if(nx == nx_2d_plane)
fprintf(error_out_2d, "%d %d %e\n", ny, nz, FLOAT_CAST error_map[ind]);
}
}
}
FFTW_FREE(error_map);
}
}
ewald_error_k_est = compute_error_estimate_k( system, ¶meters_ewald, parameters_ewald.alpha);
error = Calculate_errors ( system, forces );
if ( method.Error != NULL ) {
if( calc_est == 0 ) {
estimate = method.Error ( system, ¶meters );
error_k_est = method.Error_k ( system, ¶meters);
}
FLOAT_TYPE err_inhomo = 0.0;
if(param_isset("inhomo_error", params)) {
int uniform = param_isset("inhomo_uniform", params);
err_inhomo = Generic_error_estimate_inhomo(system, ¶meters, uniform, inhomo_error_mesh, inhomo_error_cao, inhomo_mc, inhomo_output, data);
}
FLOAT_TYPE rs_error = Realspace_error( system, ¶meters );
/* printf("Q_uncorr %e, Q_corr %e, Q_nonfluc %e\n", Q_uncorr, Q_corr, Q_nonfluc); */
printf ( "%8lf\t%8e\t%8e\t %8e %8e\t %8e sec\t %8e %8e\n", FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) , FLOAT_CAST estimate,
FLOAT_CAST rs_error , FLOAT_CAST error_k_est, FLOAT_CAST walltime, FLOAT_CAST err_inhomo, FLOAT_CAST error_k );
/* printf ( "%8lf\t%8e\t%8e\t %8e %8e\t %8e sec\n", FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) , FLOAT_CAST estimate, */
/* FLOAT_CAST rs_error , FLOAT_CAST error_k_est, FLOAT_CAST wtime ); */
fprintf ( fout,"% lf\t% e\t% e\t% e\t% e\t% e\t% e\t% e\n",
FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) ,
FLOAT_CAST estimate, FLOAT_CAST Realspace_error( system, ¶meters ),
FLOAT_CAST error_k_est, FLOAT_CAST error_k, FLOAT_CAST ewald_error_k_est, FLOAT_CAST err_inhomo);
} else {
printf ( "%8lf\t%8e\t na\t%8e\t%8e\n", FLOAT_CAST parameters.alpha, FLOAT_CAST error.f / system->nparticles , FLOAT_CAST error.f_r, FLOAT_CAST error.f_k );
fprintf ( fout,"% lf\t% e\t na\n", FLOAT_CAST parameters.alpha, FLOAT_CAST error.f / system->nparticles );
}
#ifdef FORCE_DEBUG
fprintf ( stderr, "%lf rms %e %e %e\n", parameters.alpha, error.f_v[0], error.f_v[1], error.f_v[2] );
#endif
fflush ( stdout );
fflush ( fout );
}
fclose ( fout );
return 0;
}
int main ( int argc, char **argv ) {
int methodnr;
FLOAT_TYPE alphamin,alphamax,alphastep;
FLOAT_TYPE alpha;
FLOAT_TYPE wtime;
FILE* fout;
system_t *system;
method_t method;
parameters_t parameters, parameters_ewald;
data_t *data, *data_ewald;
forces_t *forces, *forces_ewald;
char *pos_file = NULL, *force_file = NULL, *out_file = NULL, *ref_out = NULL, *sys_out = NULL, *rdf_file = NULL, *vtf_file = NULL, *cdf_file = NULL;
error_t error;
FLOAT_TYPE length, prec;
int npart;
FLOAT_TYPE charge;
int form_factor;
FLOAT_TYPE rdf_min, rdf_max;
int rdf_bins;
FLOAT_TYPE error_k=0.0, ewald_error_k_est, estimate=0.0, error_k_est;
int i,j, calc_k_error, calc_est;
#ifdef _OPENMP
int nthreads;
#endif
cmd_parameters_t params = { NULL, 0, NULL, 0 };
add_param( "rcut", ARG_TYPE_FLOAT, ARG_REQUIRED, &(parameters.rcut), ¶ms );
add_param( "alphamin", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphamin, ¶ms );
add_param( "alphamax", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphamax, ¶ms );
add_param( "alphastep", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alphastep, ¶ms );
add_param( "alpha", ARG_TYPE_FLOAT, ARG_OPTIONAL, &alpha, ¶ms );
add_param( "positions", ARG_TYPE_STRING, ARG_OPTIONAL, &pos_file, ¶ms );
add_param( "error_k", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "forces", ARG_TYPE_STRING, ARG_OPTIONAL, &force_file, ¶ms );
add_param( "mesh", ARG_TYPE_INT, ARG_REQUIRED, &(parameters.mesh), ¶ms );
add_param( "cao", ARG_TYPE_INT, ARG_REQUIRED, &(parameters.cao), ¶ms );
add_param( "method", ARG_TYPE_INT, ARG_REQUIRED, &methodnr, ¶ms );
add_param( "mc", ARG_TYPE_INT, ARG_OPTIONAL, &P3M_BRILLOUIN, ¶ms );
add_param( "mc_est", ARG_TYPE_INT, ARG_OPTIONAL, &P3M_BRILLOUIN_TUNING, ¶ms );
add_param( "no_estimate", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "outfile", ARG_TYPE_STRING, ARG_OPTIONAL, &out_file, ¶ms );
add_param( "particles", ARG_TYPE_INT, ARG_OPTIONAL, &npart, ¶ms );
add_param( "box", ARG_TYPE_FLOAT, ARG_OPTIONAL, &length, ¶ms );
add_param( "tune", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "prec", ARG_TYPE_FLOAT, ARG_OPTIONAL, &prec, ¶ms );
add_param( "reference_out", ARG_TYPE_STRING, ARG_OPTIONAL, &ref_out, ¶ms );
add_param( "system_out", ARG_TYPE_STRING, ARG_OPTIONAL, &sys_out, ¶ms );
add_param( "verlet_lists", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "charge", ARG_TYPE_FLOAT, ARG_OPTIONAL, &charge, ¶ms );
add_param( "system_type", ARG_TYPE_INT, ARG_OPTIONAL, &form_factor, ¶ms );
add_param( "rdf", ARG_TYPE_STRING, ARG_OPTIONAL, &rdf_file, ¶ms );
add_param( "rdf_bins", ARG_TYPE_INT, ARG_OPTIONAL, &rdf_bins, ¶ms );
add_param( "rdf_rmin", ARG_TYPE_FLOAT, ARG_OPTIONAL, &rdf_min, ¶ms );
add_param( "rdf_rmax", ARG_TYPE_FLOAT, ARG_OPTIONAL, &rdf_max, ¶ms );
add_param( "cdf", ARG_TYPE_STRING, ARG_OPTIONAL, &cdf_file, ¶ms );
add_param( "no_calculation", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "vtf_file", ARG_TYPE_STRING, ARG_OPTIONAL, &vtf_file, ¶ms );
add_param( "rdf_species", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms );
add_param( "no_reference_force", ARG_TYPE_NONE, ARG_OPTIONAL, NULL, ¶ms);
#ifdef _OPENMP
add_param( "threads", ARG_TYPE_INT, ARG_OPTIONAL, &nthreads, ¶ms );
#endif
parse_parameters( argc - 1, argv + 1, params );
calc_k_error = param_isset( "error_k", params );
calc_est = param_isset( "estimate", params );
parameters.cao3 = parameters.cao*parameters.cao*parameters.cao;
parameters.ip = parameters.cao - 1;
parameters.alpha = 0.0;
parameters_ewald = parameters;
#ifdef _OPENMP
if(param_isset("threads", params)) {
omp_set_num_threads(nthreads);
}
printf("OpenMP: Using up to %d threads.\n", omp_get_max_threads( ));
#endif
if(!(param_isset("alphamin", params) && param_isset("alphamax", params) && param_isset("alphastep", params)) && !param_isset("alpha", params)) {
puts("Need to provide either alpha-range (alphamin, alphamax, alphastep) or alpha.");
exit(1);
}
if( !(param_isset("positions", params) == 1) &&
!((param_isset("box", params) == 1) && (param_isset("particles", params))) ) {
puts("Need to provide either 'positions' or 'box' and 'particles'.");
exit(1);
}
if( param_isset("positions", params) == 1) {
// Inits the system and reads particle data and parameters from file.
puts("Reading file");
system = Read_system ( ¶meters, pos_file );
puts("Done.");
} else {
puts("Generating system.");
if( !(param_isset("charge", params) == 1)) {
charge=1.0;
}
if(param_isset("system_type", params)) {
printf("Using system type %d\n", form_factor);
system = generate_system( form_factor, npart, length, charge);
} else {
system = generate_system( FORM_FACTOR_RANDOM, npart, length, charge);
}
puts("Done.");
}
if( param_isset("vtf_file", params) == 1)
write_vtf( vtf_file, system );
if( param_isset("rdf", params) == 1) {
puts("Calculating RDF");
if( param_isset("rdf_bins", params) == 0)
rdf_bins = 100;
if( param_isset("rdf_rmin", params) == 0)
rdf_min = 0.0;
if( param_isset("rdf_rmax", params) == 0)
rdf_max = system->length/2;
printf("Using %d bins, %lf <= r <= %lf\n", rdf_bins, rdf_min, rdf_max);
int bins = rdf_bins;
FLOAT_TYPE *rdf = radial_distribution(rdf_min, rdf_max, rdf_bins, system);
FLOAT_TYPE *c;
/* FLOAT_TYPE *rdf_sym = Init_array( 2*bins-1, 2*sizeof(FLOAT_TYPE)); */
/* c = low_pass_forward( bins, rdf, 0.3); */
/* c = low_pass_backward(bins, c, 0.3); */
/* rdf = c; */
/* for(int i = 0; i < 2*bins; i++) { */
/* rdf_sym[i] = c[i]; */
/* } */
/* for(int i = bins; i < 2*bins-1; i++) { */
/* rdf_sym[2*i] = c[2*bins - 2] + (i-bins)*(c[2] - c[0]); */
/* rdf_sym[2*i+1] = c[4*bins - 2*i - 1]; */
/* } */
FILE *rdf_out = fopen(rdf_file, "w");
/* FILE *c_out = fopen("c_fft.dat", "w"); */
/* rshif_array(2*(2*bins-1), c, 2*bins); */
for(int i = 0; i<bins; i++)
fprintf(rdf_out, "%e %e\n", FLOAT_CAST rdf[2*i], FLOAT_CAST rdf[2*i+1]);
/* for(int i = 0; i<2*bins-1; i++) */
/* /\* fprintf(c_out, "%e %e\n", FLOAT_CAST rdf_sym[2*i], FLOAT_CAST rdf_sym[2*i+1] ); *\/ */
/* fprintf(c_out, "%d %e %e\n", i, FLOAT_CAST c[2*i], FLOAT_CAST c[2*i+1] ); */
/* fclose(c_out); */
fclose(rdf_out);
fftw_free(rdf);
/* fftw_free(c); */
puts("Done.");
}
if( param_isset("rdf_species", params) == 1) {
radial_distribution_species(0.0, 3.0, 200, system);
}
forces = Init_forces(system->nparticles);
forces_ewald = Init_forces(system->nparticles);
if(param_isset("reference_out", params))
{
printf("Minimal distance: %.*f\n", DIGITS, FLOAT_CAST Min_distance( system ));
puts("Calculating reference forces.");
printf("Reference precision %e\n.", FLOAT_CAST Calculate_reference_forces( system, ¶meters ));
puts("Done.");
printf("Writing reference forces to '%s'\n", ref_out);
Write_exact_forces(system, ref_out);
puts("Done.");
}
if(param_isset("system_out", params))
{
printf("Writing system to '%s'\n", sys_out);
Write_system(system, sys_out);
puts("Done.");
}
if(param_isset("no_calculation", params) == 1)
return 0;
if(param_isset("forces", params) == 1) {
printf("Reading reference forces from '%s'.\n", force_file);
Read_exact_forces( system, force_file );
puts("Done.");
} else {
if(param_isset("no_reference_force", params) !=1) {
puts("Calculating reference forces.");
printf("Reference precision %e\n.", FLOAT_CAST Calculate_reference_forces( system, ¶meters ));
puts("Done.");
} else {
puts("Skipping reference force calculation.");
}
}
if ( methodnr == method_ewald.method_id )
method = method_ewald;
#ifdef P3M_IK_H
else if ( methodnr == method_p3m_ik.method_id )
method = method_p3m_ik;
#endif
#ifdef P3M_IK_I_H
else if ( methodnr == method_p3m_ik_i.method_id )
method = method_p3m_ik_i;
#endif
#ifdef P3M_AD_H
else if ( methodnr == method_p3m_ad.method_id )
method = method_p3m_ad;
#endif
#ifdef P3M_AD_I_H
else if ( methodnr == method_p3m_ad_i.method_id ) {
method = method_p3m_ad_i;
}
#endif
else {
fprintf ( stderr, "Method %d not know.", methodnr );
exit ( 126 );
}
if ( ( method.Init == NULL ) || ( method.Influence_function == NULL ) || ( method.Kspace_force == NULL ) ) {
fprintf ( stderr,"Internal error: Method '%s' (%d) is not properly defined. Aborting.\n", method.method_name, method.method_id );
exit ( -1 );
}
fprintf ( stderr, "Using %s.\n", method.method_name );
if(param_isset("outfile", params) == 1) {
fout = fopen ( out_file, "w" );
} else {
fout = fopen ( "out.dat","w" );
}
printf ( "Init" );
fflush(stdout);
data = method.Init ( system, ¶meters );
printf ( ".\n" );
printf ( "Init Ewald" );
data_ewald = method_ewald.Init ( system, ¶meters_ewald );
printf ( ".\n" );
/* printf ( "Init neighborlist" ); */
/* Init_neighborlist ( system, ¶meters, data ); */
/* printf ( ".\n" ); */
FLOAT_TYPE gen_err_dip, gen_err;
printf ( "# %8s\t%8s\t%8s\t%8s\t%8s\n", "alpha", "DeltaF", "Estimate", "R-Error-Est", "K-Error-Est Generic-K-Space-err" );
for ( parameters.alpha=alphamin; parameters.alpha<=alphamax; parameters.alpha+=alphastep ) {
parameters_ewald.alpha = parameters.alpha;
method.Influence_function ( system, ¶meters, data ); /* Hockney/Eastwood */
wtime = MPI_Wtime();
Calculate_forces ( &method, system, ¶meters, data, forces ); /* Hockney/Eastwood */
wtime = MPI_Wtime() - wtime;
error_k =0.0;
if(calc_k_error == 1) {
puts("kerror");
for(i=0;i<3;i++) {
memset ( forces_ewald->f_k->fields[i], 0, system->nparticles*sizeof ( FLOAT_TYPE ) );
}
method_ewald.Influence_function ( system, ¶meters_ewald, data_ewald );
method_ewald.Kspace_force( system, ¶meters_ewald, data_ewald, forces_ewald );
error_k =0.0;
for (i=0; i<system->nparticles; i++) {
for (j=0;j<3;j++) {
/* printf("f_k_p3m [%lf, %lf, %lf] f_k_ewald [%lf, %lf %lf]\n", */
/* forces->f_k->fields[0][i],forces->f_k->fields[1][i],forces->f_k->fields[2][i], */
/* forces_ewald->f_k->fields[0][i],forces_ewald->f_k->fields[1][i],forces_ewald->f_k->fields[2][i]); */
error_k += SQR( forces->f_k->fields[j][i] - forces_ewald->f_k->fields[j][i] );
}
}
error_k = SQRT(error_k) / SQRT(system->nparticles);
}
ewald_error_k_est = compute_error_estimate_k( system, ¶meters_ewald, parameters_ewald.alpha);
error = Calculate_errors ( system, forces );
if ( method.Error != NULL ) {
if( calc_est == 0 )
estimate = method.Error ( system, ¶meters );
error_k_est = method.Error_k ( system, ¶meters);
FLOAT_TYPE Q_uncorr, Q_corr, Q_nonfluc;
/* Q_uncorr = Generic_error_estimate( A_ad, B_ad, C_ewald, system, ¶meters, data); */
/* Q_corr = Generic_error_estimate( A_ad_water, B_ad_water, C_ewald_water, system, ¶meters, data); */
FLOAT_TYPE corrected_est, corrected_total, rs_error;
corrected_est = system->q2 / (system->length * SQR(system->length)) * SQRT( ( Q_uncorr - Q_corr ) / system->nparticles );
gen_err = system->q2 / (system->length * SQR(system->length)) * SQRT( ( Q_uncorr ) / system->nparticles );
gen_err_dip = ((Q_corr > 0) - (Q_corr < 0)) * system->q2 / (system->length * SQR(system->length)) * SQRT( ( FLOAT_ABS(Q_corr) ) / system->nparticles );
rs_error =Realspace_error( system, ¶meters );
corrected_total = SQRT( SQR(rs_error) + SQR(corrected_est));
/* printf("Q_uncorr %e, Q_corr %e, Q_nonfluc %e\n", Q_uncorr, Q_corr, Q_nonfluc); */
printf ( "%8lf\t%8e\t%8e\t %8e %8e\t %8e sec\t %8e\t %e\t %e\n", FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) , FLOAT_CAST estimate,
FLOAT_CAST rs_error , FLOAT_CAST error_k_est, FLOAT_CAST wtime, FLOAT_CAST gen_err, FLOAT_CAST gen_err_dip, FLOAT_CAST corrected_total );
/* printf ( "%8lf\t%8e\t%8e\t %8e %8e\t %8e sec\n", FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) , FLOAT_CAST estimate, */
/* FLOAT_CAST rs_error , FLOAT_CAST error_k_est, FLOAT_CAST wtime ); */
fprintf ( fout,"% lf\t% e\t% e\t% e\t% e\t% e\t% e\t% e\n",
FLOAT_CAST parameters.alpha, FLOAT_CAST (error.f / SQRT(system->nparticles)) ,
FLOAT_CAST estimate, FLOAT_CAST Realspace_error( system, ¶meters ),
FLOAT_CAST error_k_est, FLOAT_CAST error_k, FLOAT_CAST ewald_error_k_est, FLOAT_CAST corrected_total);
} else {
printf ( "%8lf\t%8e\t na\t%8e\t%8e\n", FLOAT_CAST parameters.alpha, FLOAT_CAST error.f / system->nparticles , FLOAT_CAST error.f_r, FLOAT_CAST error.f_k );
fprintf ( fout,"% lf\t% e\t na\n", FLOAT_CAST parameters.alpha, FLOAT_CAST error.f / system->nparticles );
}
#ifdef FORCE_DEBUG
fprintf ( stderr, "%lf rms %e %e %e\n", parameters.alpha, error.f_v[0], error.f_v[1], error.f_v[2] );
#endif
fflush ( stdout );
fflush ( fout );
}
fclose ( fout );
return 0;
}