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/* Copyright (C) 2005-2015 Massachusetts Institute of Technology
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2, or (at your option)
% any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software Foundation,
% Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*/
/* HDF5 output of fields and arbitrary functions thereof. Works
very similarly to integrate.cpp (using fields::loop_in_chunks). */
#include <stdio.h>
#include <string.h>
#include <math.h>
#include "meep_internals.hpp"
using namespace std;
namespace meep {
/***************************************************************************/
typedef struct {
// information related to the HDF5 dataset (its size, etcetera)
h5file *file;
ivec min_corner, max_corner;
int num_chunks;
realnum *buf;
int bufsz;
int rank;
direction ds[3];
int reim; // whether to output the real or imaginary part
// the function to output and related info (offsets for averaging, etc.)
int num_fields;
const component *components;
component *cS;
complex<double> *ph;
complex<double> *fields;
int *offsets;
int ninveps;
component inveps_cs[3];
direction inveps_ds[3];
int ninvmu;
component invmu_cs[3];
direction invmu_ds[3];
field_function fun;
void *fun_data_;
} h5_output_data;
#define UNUSED(x) (void) x // silence compiler warnings
static void h5_findsize_chunkloop(fields_chunk *fc, int ichnk, component cgrid,
ivec is, ivec ie,
vec s0, vec s1, vec e0, vec e1,
double dV0, double dV1,
ivec shift, complex<double> shift_phase,
const symmetry &S, int sn,
void *data_)
{
UNUSED(ichnk);UNUSED(cgrid);UNUSED(s0);UNUSED(s1);UNUSED(e0);UNUSED(e1);
UNUSED(dV0);UNUSED(dV1);UNUSED(shift_phase);
h5_output_data *data = (h5_output_data *) data_;
ivec isS = S.transform(is, sn) + shift;
ivec ieS = S.transform(ie, sn) + shift;
data->min_corner = min(data->min_corner, min(isS, ieS));
data->max_corner = max(data->max_corner, max(isS, ieS));
data->num_chunks++;
int bufsz = 1;
LOOP_OVER_DIRECTIONS(fc->gv.dim, d)
bufsz *= (ie.in_direction(d) - is.in_direction(d)) / 2 + 1;
data->bufsz = max(data->bufsz, bufsz);
}
static void h5_output_chunkloop(fields_chunk *fc, int ichnk, component cgrid,
ivec is, ivec ie,
vec s0, vec s1, vec e0, vec e1,
double dV0, double dV1,
ivec shift, complex<double> shift_phase,
const symmetry &S, int sn,
void *data_)
{
UNUSED(ichnk);UNUSED(cgrid);UNUSED(s0);UNUSED(s1);UNUSED(e0);UNUSED(e1);
UNUSED(dV0);UNUSED(dV1);
h5_output_data *data = (h5_output_data *) data_;
//-----------------------------------------------------------------------//
// Find output chunk dimensions and strides, etc.
int start[3]={0,0,0}, count[3]={1,1,1};
int offset[3]={0,0,0}, stride[3]={1,1,1};
ivec isS = S.transform(is, sn) + shift;
ivec ieS = S.transform(ie, sn) + shift;
// figure out what yucky_directions (in LOOP_OVER_IVECS)
// correspond to what directions in the transformed vectors (in output).
ivec permute(zero_ivec(fc->gv.dim));
for (int i = 0; i < 3; ++i)
permute.set_direction(fc->gv.yucky_direction(i), i);
permute = S.transform_unshifted(permute, sn);
LOOP_OVER_DIRECTIONS(permute.dim, d)
permute.set_direction(d, abs(permute.in_direction(d)));
// compute the size of the chunk to output, and its strides etc.
for (int i = 0; i < data->rank; ++i) {
direction d = data->ds[i];
int isd = isS.in_direction(d), ied = ieS.in_direction(d);
start[i] = (min(isd, ied) - data->min_corner.in_direction(d)) / 2;
count[i] = abs(ied - isd) / 2 + 1;
if (ied < isd) offset[permute.in_direction(d)] = count[i] - 1;
}
for (int i = 0; i < data->rank; ++i) {
direction d = data->ds[i];
int j = permute.in_direction(d);
for (int k = i + 1; k < data->rank; ++k) stride[j] *= count[k];
offset[j] *= stride[j];
if (offset[j]) stride[j] *= -1;
}
//-----------------------------------------------------------------------//
// Compute the function to output, exactly as in fields::integrate,
// except that here we store its values in a buffer instead of integrating.
int *off = data->offsets;
component *cS = data->cS;
complex<double> *fields = data->fields, *ph = data->ph;
const component *iecs = data->inveps_cs;
const direction *ieds = data->inveps_ds;
int ieos[6];
const component *imcs = data->invmu_cs;
const direction *imds = data->invmu_ds;
int imos[6];
for (int i = 0; i < data->num_fields; ++i) {
cS[i] = S.transform(data->components[i], -sn);
if (cS[i] == Dielectric || cS[i] == Permeability)
ph[i] = 1.0;
else {
fc->gv.yee2cent_offsets(cS[i], off[2*i], off[2*i+1]);
ph[i] = shift_phase * S.phase_shift(cS[i], sn);
}
}
for (int k = 0; k < data->ninveps; ++k)
fc->gv.yee2cent_offsets(iecs[k], ieos[2*k], ieos[2*k+1]);
for (int k = 0; k < data->ninvmu; ++k)
fc->gv.yee2cent_offsets(imcs[k], imos[2*k], imos[2*k+1]);
vec rshift(shift * (0.5*fc->gv.inva));
LOOP_OVER_IVECS(fc->gv, is, ie, idx) {
IVEC_LOOP_LOC(fc->gv, loc);
loc = S.transform(loc, sn) + rshift;
for (int i = 0; i < data->num_fields; ++i) {
if (cS[i] == Dielectric) {
double tr = 0.0;
for (int k = 0; k < data->ninveps; ++k) {
const realnum *ie = fc->s->chi1inv[iecs[k]][ieds[k]];
if (ie) tr += (ie[idx] + ie[idx+ieos[2*k]] + ie[idx+ieos[1+2*k]]
+ ie[idx+ieos[2*k]+ieos[1+2*k]]);
else tr += 4; // default inveps == 1
}
fields[i] = (4 * data->ninveps) / tr;
}
else if (cS[i] == Permeability) {
double tr = 0.0;
for (int k = 0; k < data->ninvmu; ++k) {
const realnum *im = fc->s->chi1inv[imcs[k]][imds[k]];
if (im) tr += (im[idx] + im[idx+imos[2*k]] + im[idx+imos[1+2*k]]
+ im[idx+imos[2*k]+imos[1+2*k]]);
else tr += 4; // default invmu == 1
}
fields[i] = (4 * data->ninvmu) / tr;
}
else {
double f[2];
for (int k = 0; k < 2; ++k)
if (fc->f[cS[i]][k])
f[k] = 0.25 * (fc->f[cS[i]][k][idx]
+ fc->f[cS[i]][k][idx+off[2*i]]
+ fc->f[cS[i]][k][idx+off[2*i+1]]
+ fc->f[cS[i]][k][idx+off[2*i]+off[2*i+1]]);
else
f[k] = 0;
fields[i] = complex<double>(f[0], f[1]) * ph[i];
}
}
complex<double> fun = data->fun(fields, loc, data->fun_data_);
int idx2 = ((((offset[0] + offset[1] + offset[2])
+ loop_i1 * stride[0])
+ loop_i2 * stride[1]) + loop_i3 * stride[2]);
data->buf[idx2] = data->reim ? imag(fun) : real(fun);
}
//-----------------------------------------------------------------------//
data->file->write_chunk(data->rank, start, count, data->buf);
}
void fields::output_hdf5(h5file *file, const char *dataname,
int num_fields, const component *components,
field_function fun, void *fun_data_, int reim,
const volume &where,
bool append_data,
bool single_precision) {
am_now_working_on(FieldOutput);
h5_output_data data;
data.file = file;
data.min_corner = gv.round_vec(where.get_max_corner()) + one_ivec(gv.dim);
data.max_corner = gv.round_vec(where.get_min_corner()) - one_ivec(gv.dim);
data.num_chunks = 0;
data.bufsz = 0;
data.reim = reim;
loop_in_chunks(h5_findsize_chunkloop, (void *) &data,
where, Centered, true, true);
file->prevent_deadlock(); // can't hold a lock since *_to_all is collective
data.max_corner = max_to_all(data.max_corner);
data.min_corner = -max_to_all(-data.min_corner); // i.e., min_to_all
data.num_chunks = sum_to_all(data.num_chunks);
if (data.num_chunks == 0 || !(data.min_corner <= data.max_corner))
return; // no data to write;
int rank = 0, dims[3];
LOOP_OVER_DIRECTIONS(gv.dim, d) {
if (rank >= 3) abort("too many dimensions in output_hdf5");
int n = (data.max_corner.in_direction(d)
- data.min_corner.in_direction(d)) / 2 + 1;
if (n > 1) {
data.ds[rank] = d;
dims[rank++] = n;
}
}
data.rank = rank;
file->create_or_extend_data(dataname, rank, dims,
append_data, single_precision);
data.buf = new realnum[data.bufsz];
data.num_fields = num_fields;
data.components = components;
data.cS = new component[num_fields];
data.ph = new complex<double>[num_fields];
data.fields = new complex<double>[num_fields];
data.fun = fun;
data.fun_data_ = fun_data_;
/* compute inverse-epsilon directions for computing Dielectric fields */
data.ninveps = 0;
bool needs_dielectric = false;
for (int i = 0; i < num_fields; ++i)
if (components[i] == Dielectric) { needs_dielectric = true; break; }
if (needs_dielectric)
FOR_ELECTRIC_COMPONENTS(c) if (gv.has_field(c)) {
if (data.ninveps == 3) abort("more than 3 field components??");
data.inveps_cs[data.ninveps] = c;
data.inveps_ds[data.ninveps] = component_direction(c);
++data.ninveps;
}
/* compute inverse-mu directions for computing Permeability fields */
data.ninvmu = 0;
bool needs_permeability = false;
for (int i = 0; i < num_fields; ++i)
if (components[i] == Permeability) { needs_permeability = true; break; }
if (needs_permeability)
FOR_MAGNETIC_COMPONENTS(c) if (gv.has_field(c)) {
if (data.ninvmu == 3) abort("more than 3 field components??");
data.invmu_cs[data.ninvmu] = c;
data.invmu_ds[data.ninvmu] = component_direction(c);
++data.ninvmu;
}
data.offsets = new int[2 * num_fields];
for (int i = 0; i < 2 * num_fields; ++i)
data.offsets[i] = 0;
loop_in_chunks(h5_output_chunkloop, (void *) &data,
where, Centered, true, true);
delete[] data.offsets;
delete[] data.fields;
delete[] data.ph;
delete[] data.cS;
delete[] data.buf;
file->done_writing_chunks();
finished_working();
}
/***************************************************************************/
void fields::output_hdf5(const char *dataname,
int num_fields, const component *components,
field_function fun, void *fun_data_,
const volume &where,
h5file *file,
bool append_data,
bool single_precision,
const char *prefix,
bool real_part_only)
{
bool delete_file;
if ((delete_file = !file))
file = open_h5file(dataname, h5file::WRITE, prefix, true);
if (real_part_only) {
output_hdf5(file, dataname, num_fields, components, fun, fun_data_,
0, where, append_data, single_precision);
}
else {
int len = strlen(dataname) + 5;
char *dataname2 = new char[len];
snprintf(dataname2, len, "%s%s", dataname, ".r");
output_hdf5(file, dataname2, num_fields, components, fun, fun_data_,
0, where, append_data, single_precision);
snprintf(dataname2, len, "%s%s", dataname, ".i");
output_hdf5(file, dataname2, num_fields, components, fun, fun_data_,
1, where, append_data, single_precision);
delete[] dataname2;
}
if (delete_file) delete file;
}
/***************************************************************************/
typedef struct {
field_rfunction fun;
void *fun_data_;
} rintegrand_data;
static complex<double> rintegrand_fun(const complex<double> *fields,
const vec &loc,
void *data_)
{
rintegrand_data *data = (rintegrand_data *) data_;
return data->fun(fields, loc, data->fun_data_);
}
void fields::output_hdf5(const char *dataname,
int num_fields, const component *components,
field_rfunction fun, void *fun_data_,
const volume &where,
h5file *file,
bool append_data,
bool single_precision,
const char *prefix)
{
bool delete_file;
if ((delete_file = !file))
file = open_h5file(dataname, h5file::WRITE, prefix, true);
rintegrand_data data; data.fun = fun; data.fun_data_ = fun_data_;
output_hdf5(file, dataname, num_fields, components, rintegrand_fun,
(void *) &data, 0, where, append_data, single_precision);
if (delete_file) delete file;
}
/***************************************************************************/
static complex<double> component_fun(const complex<double> *fields,
const vec &loc,
void *data_)
{
(void) loc; // unused
(void) data_; // unused
return fields[0];
}
void fields::output_hdf5(component c,
const volume &where,
h5file *file,
bool append_data,
bool single_precision,
const char *prefix) {
if (is_derived(int(c))) {
output_hdf5(derived_component(c),
where, file, append_data, single_precision, prefix);
return;
}
if (coordinate_mismatch(gv.dim, c)) return;
char dataname[256];
bool has_imag = !is_real && c != Dielectric && c != Permeability;
bool delete_file;
if ((delete_file = !file))
file = open_h5file(component_name(c), h5file::WRITE, prefix, true);
snprintf(dataname, 256, "%s%s", component_name(c), has_imag ? ".r" : "");
output_hdf5(file, dataname, 1, &c, component_fun, 0, 0, where,
append_data, single_precision);
if (has_imag) {
snprintf(dataname, 256, "%s.i", component_name(c));
output_hdf5(file, dataname, 1, &c, component_fun, 0, 1, where,
append_data, single_precision);
}
if (delete_file) delete file;
}
/***************************************************************************/
void fields::output_hdf5(derived_component c,
const volume &where,
h5file *file,
bool append_data,
bool single_precision,
const char *prefix) {
if (!is_derived(int(c))) {
output_hdf5(component(c),
where, file, append_data, single_precision, prefix);
return;
}
if (coordinate_mismatch(gv.dim, c)) return;
int nfields;
component cs[12];
field_rfunction fun = derived_component_func(c, gv, nfields, cs);
output_hdf5(component_name(c), nfields, cs, fun, &nfields, where,
file, append_data, single_precision, prefix);
}
/***************************************************************************/
const char *fields::h5file_name(const char *name,
const char *prefix, bool timestamp)
{
const int buflen = 1024;
static char filename[buflen];
char time_step_string[32] = "";
if (timestamp) {
if (dt >= 0.01 && dt < 10)
snprintf(time_step_string, 32, "-%09.2f", time());
else
snprintf(time_step_string, 32, "-%09d", t);
}
snprintf(filename, buflen, "%s/" "%s%s" "%s" "%s" ".h5",
outdir,
prefix ? prefix : "", prefix && prefix[0] ? "-" : "",
name, time_step_string);
return filename;
}
h5file *fields::open_h5file(const char *name, h5file::access_mode mode,
const char *prefix, bool timestamp)
{
const char *filename = h5file_name(name, prefix, timestamp);
if (!quiet && mode == h5file::WRITE)
master_printf("creating output file \"%s\"...\n", filename);
return new h5file(filename, mode, true);
}
} // namespace meep
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