void
toi_init(int argc, char **argv)
{
gv_tbl = st_init_numtable();
Init_thread();
THREAD(cur_thr)->recv = main_thread();
if (THREAD(main_thread())->env_tbl)
st_free_table(THREAD(main_thread())->env_tbl);
THREAD(main_thread())->env_tbl = gv_tbl;
Init_symbol();
Init_class();
/* have to call Init_thread() again */
Init_thread();
Init_kernel();
cself = cKernel;
Init_numeric();
Init_float();
Init_integer();
Init_array();
Init_hash();
Init_string();
Init_iostream();
Init_exception();
toi_set_argv(argc, argv);
Init_gc();
signal(SIGINT, handle_sigint);
}
void rshif_array( int N, FLOAT_TYPE *data, int shift ) {
FLOAT_TYPE *buf = Init_array( N, sizeof(FLOAT_TYPE));
for(int i=0; i<N; i++)
buf[(shift+i) % N] = data[i];
for(int i=0; i<N; i++)
data[i] = buf[i];
fftw_free(buf);
}
FLOAT_TYPE *low_pass_forward( int N, FLOAT_TYPE *data, FLOAT_TYPE alpha) {
FLOAT_TYPE *ret = Init_array( N, 2*sizeof(FLOAT_TYPE));
ret[0] = data[0];
ret[1] = data[1];
for(int i = 1; i<N; i++) {
ret[2*i ] = data[2*i];
ret[2*i+1] = ret[2*i-1] + alpha * ( data[2*i+1] - ret[2*i-1]);
}
return ret;
}
FLOAT_TYPE *low_pass_backward( int N, FLOAT_TYPE *data, FLOAT_TYPE alpha) {
FLOAT_TYPE *ret = Init_array( N, 2*sizeof(FLOAT_TYPE));
ret[2*N-1] = data[2*N-1];
ret[2*N-2] = data[2*N-2];
for(int i = N - 2; i>=0; i--) {
ret[2*i ] = data[2*i];
ret[2*i+1] = ret[2*i+3] + alpha * ( data[2*i+1] - ret[2*i+3]);
}
return ret;
}
FLOAT_TYPE *radial_charge_distribution(FLOAT_TYPE r_min, FLOAT_TYPE r_max, int bins, system_t *s) {
FLOAT_TYPE *rdf = Init_array( bins, 2*sizeof(FLOAT_TYPE));
FLOAT_TYPE dr = (r_max - r_min) / bins, dx, dy, dz, r2, r, r_min2, r_max2;
FLOAT_TYPE lengthi = 1.0/s->length;
int n=0, bin;
FLOAT_TYPE r_in, r_out;
FLOAT_TYPE bin_volume;
memset(rdf, 0, 2*bins*sizeof(FLOAT_TYPE));
r_min2 = SQR(r_min);
r_max2 = SQR(r_max);
for(int i=0; i<s->nparticles; i++) {
for(int j=0; j<s->nparticles; j++) {
if(i==j)
continue;
dx = s->p->x[i] - s->p->x[j];
dx -= ROUND(dx*lengthi)*s->length;
dy = s->p->y[i] - s->p->y[j];
dy -= ROUND(dy*lengthi)*s->length;
dz = s->p->z[i] - s->p->z[j];
dz -= ROUND(dz*lengthi)*s->length;
r2 = SQR(dx) + SQR(dy) + SQR(dz);
if((r2 < r_min2) || (r2 > r_max2))
continue;
r = SQRT(r2);
bin = (int)((r - r_min)/dr);
rdf[2*bin+1]+= s->q[i] * s->q[j];
n++;
}
}
printf("#rdf[0] %lf\n", rdf[0]);
printf("#rdf[1] %lf\n", rdf[1]);
printf("#rdf[2] %lf\n", rdf[2]);
for(int i=0; i<bins; i++) {
r_in = i*dr + r_min;
r_out = r_in + dr;
bin_volume = 4.0/3.0 * PI * (r_out *r_out*r_out - r_in * r_in * r_in );
rdf[2*i] = 0.5 * (r_in + r_out);
rdf[2*i+1] /= n * bin_volume / (s->length *SQR(s->length));
}
return rdf;
}
FLOAT_TYPE *rdf_fft( int N, FLOAT_TYPE *rdf) {
fftw_plan p;
FLOAT_TYPE *data = Init_array( N, 2*sizeof(FLOAT_TYPE));
p = fftw_plan_dft_1d( N, (fftw_complex *)data, (fftw_complex *)data, FFTW_FORWARD, FFTW_PATIENT);
memset(data, 0, 2*N*sizeof(FLOAT_TYPE));
for(int i=0; i<N; i++)
data[2*i] = rdf[2*i+1];
FFTW_EXECUTE(p);
return data;
}
parameters_t *Tune( const method_t *m, system_t *s, FLOAT_TYPE precision, FLOAT_TYPE rcut ) {
parameters_t *p = Init_array( 1, sizeof( parameters_t ) );
//Parameter iteraters, best parameter set
parameters_t it, p_best;
// Array to store forces
forces_t *f = Init_forces(s->nparticles);
data_t *d = NULL;
FLOAT_TYPE rcut_max = 0.5 * s->length;
FLOAT_TYPE rcut_step = 0.25 * s->length;
FLOAT_TYPE last_success = -1.0;
FLOAT_TYPE best_time=1e250, time=1e240;
FLOAT_TYPE rs_error, error = -1.0;
int success = 0;
int direction=1;
int failed_once=0;
TUNE_TRACE(printf("Starting tuning for '%s' with prec '%e'\n", m->method_name, precision);)
for(it.mesh = MESH_MIN; it.mesh <= MESH_MAX; it.mesh+=MESH_STEP ) {
void radial_distribution_species(FLOAT_TYPE r_min, FLOAT_TYPE r_max, int bins, system_t *s) {
FLOAT_TYPE *rdf = Init_array( 4*bins, sizeof(FLOAT_TYPE));
FLOAT_TYPE dr = (r_max - r_min) / bins, dx, dy, dz, r2, r, r_min2, r_max2;
FLOAT_TYPE lengthi = 1.0/s->length;
int n[4], bin;
FLOAT_TYPE r_in, r_out;
FLOAT_TYPE bin_volume;
memset(rdf, 0, 4*bins*sizeof(FLOAT_TYPE));
memset( n, 0, 4*sizeof(int));
r_min2 = SQR(r_min);
r_max2 = SQR(r_max);
for(int i=0; i<s->nparticles; i++) {
for(int j=0; j<s->nparticles; j++) {
if(i==j)
continue;
dx = s->p->x[i] - s->p->x[j];
dx -= ROUND(dx*lengthi)*s->length;
dy = s->p->y[i] - s->p->y[j];
dy -= ROUND(dy*lengthi)*s->length;
dz = s->p->z[i] - s->p->z[j];
dz -= ROUND(dz*lengthi)*s->length;
r2 = SQR(dx) + SQR(dy) + SQR(dz);
if((r2 < r_min2) || (r2 > r_max2))
continue;
r = SQRT(r2);
bin = (int)((r - r_min)/dr);
if( (s->q[i] > 0.0) && (s->q[j] > 0.0)) {
/* printf("(%d, %d): ++ (%e, %e), at %lf\n", i, j, s->q[i], s->q[j], r); */
rdf[bin]++;
n[0]++;
}
if( (s->q[i] > 0.0) && (s->q[j] < 0.0)) {
/* printf("(%d, %d): +- (%e, %e), at %lf\n", i, j, s->q[i], s->q[j], r); */
rdf[bins+bin]++;
n[1]++;
}
if( (s->q[i] < 0.0) && (s->q[j] < 0.0)) {
rdf[2*bins+bin]++;
n[2]++;
}
if( (s->q[i] < 0.0) && (s->q[j] > 0.0)) {
rdf[3*bins+bin]++;
n[3]++;
}
}
}
FILE *f = fopen("rdf_+-.dat", "w");
for(int i=0; i<bins; i++) {
r_in = i*dr + r_min;
r_out = r_in + dr;
bin_volume = 4.0/3.0 * PI * (r_out *r_out*r_out - r_in * r_in * r_in );
fprintf( f, "%e ", 0.5 * (r_in + r_out));
fprintf( f, "%e ", rdf[i] / (n[0] * bin_volume) );
fprintf( f, "%e ", rdf[bins+i] / (n[1] * bin_volume) );
fprintf( f, "%e ", rdf[2*bins+i] / (n[2] * bin_volume) );
fprintf( f, "%e ", rdf[3*bins+i] / (n[3] * bin_volume) );
fprintf( f, "\n");
}
fclose(f);
fftw_free(rdf);
}
data_t *Init_data(const method_t *m, system_t *s, parameters_t *p) {
int mesh3 = p->mesh*p->mesh*p->mesh;
data_t *d = (data_t *)Init_array(1, sizeof(data_t));
d->mesh = p->mesh;
if ( m->flags & METHOD_FLAG_Qmesh)
d->Qmesh = (FLOAT_TYPE *)Init_array(2*mesh3, sizeof(FLOAT_TYPE));
else
d->Qmesh = NULL;
if ( m->flags & METHOD_FLAG_ik ) {
d->Fmesh = Init_vector_array(2*mesh3);
d->Dn = (FLOAT_TYPE *)Init_array(d->mesh, sizeof(FLOAT_TYPE));
Init_differential_operator(d);
}
else {
d->Fmesh = NULL;
d->Dn = NULL;
}
d->nshift = NULL;
if ( m->flags & METHOD_FLAG_nshift ) {
d->nshift = (FLOAT_TYPE *)Init_array(d->mesh, sizeof(FLOAT_TYPE));
Init_nshift(d);
}
d->dQ[0] = NULL;
d->dQ[1] = NULL;
if( m->flags & METHOD_FLAG_self_force_correction)
d->self_force_corrections = (FLOAT_TYPE *)Init_array(my_power(1+2*P3M_SELF_BRILLOUIN, 3), 3*sizeof(FLOAT_TYPE));
if ( m->flags & METHOD_FLAG_ad ) {
int i;
int max = ( m->flags & METHOD_FLAG_interlaced) ? 2 : 1;
for (i = 0; i < max; i++) {
d->dQ[i] = (FLOAT_TYPE *)Init_array( 3*s->nparticles*p->cao3, sizeof(FLOAT_TYPE) );
}
}
if ( m->flags & METHOD_FLAG_ca ) {
int i;
int max = ( m->flags & METHOD_FLAG_interlaced ) ? 2 : 1;
d->cf[1] = NULL;
d->ca_ind[1] = NULL;
for (i = 0; i < max; i++) {
d->cf[i] = (FLOAT_TYPE *)Init_array( p->cao3 * s->nparticles, sizeof(FLOAT_TYPE));
d->ca_ind[i] = (int *)Init_array( 3*s->nparticles, sizeof(int));
}
if( !p->tuning )
d->inter = Init_interpolation( p->ip, m->flags & METHOD_FLAG_ad );
else {
if(dummy_inter == NULL)
dummy_inter = Init_interpolation( 6, 1 );
d->inter = dummy_inter;
}
}
else {
d->cf[0] = NULL;
d->ca_ind[0] = NULL;
d->cf[1] = NULL;
d->ca_ind[1] = NULL;
d->inter = NULL;
}
if ( m->flags & METHOD_FLAG_G_hat) {
if( !p->tuning) {
d->G_hat = (FLOAT_TYPE *)Init_array(mesh3, sizeof(FLOAT_TYPE));
m->Influence_function( s, p, d );
} else {
dummy_g_realloc(d->mesh);
d->G_hat = dummy_g;
}
}
else
d->G_hat = NULL;
d->forward_plans = 0;
d->backward_plans = 0;
return d;
}
