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Commit 14aa69d8 authored by Cristian Lalescu's avatar Cristian Lalescu
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add ksample code 

HDF5 is complaining that I'm closing an invalid dtype, no idea what
that's about...
parent 2e0e8758
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with 72 additions and 11 deletions
bfps/NavierStokes.py
+ 72
− 11
View file @ 14aa69d8
...@@ -90,17 +90,31 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -90,17 +90,31 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
def write_fluid_stats(self): def write_fluid_stats(self):
self.fluid_includes += '#include <cmath>\n' self.fluid_includes += '#include <cmath>\n'
self.fluid_includes += '#include "fftw_tools.hpp"\n' self.fluid_includes += '#include "fftw_tools.hpp"\n'
if self.dtype == np.float32: ## ksamples
field_H5T = 'H5T_NATIVE_FLOAT' #self.stat_src += '{0} *ksamples = new {0}[nksamples];\n'.format(self.C_dtype)
elif self.dtype == np.float64: self.stat_src += """
field_H5T = 'H5T_NATIVE_DOUBLE' //begincpp
//endcpp
"""
self.stat_src += """ self.stat_src += """
//begincpp //begincpp
double *velocity_moments = fftw_alloc_real(10*4); double *velocity_moments = fftw_alloc_real(10*4);
double *vorticity_moments = fftw_alloc_real(10*4); double *vorticity_moments = fftw_alloc_real(10*4);
ptrdiff_t *hist_velocity = new ptrdiff_t[histogram_bins*4]; ptrdiff_t *hist_velocity = new ptrdiff_t[histogram_bins*4];
ptrdiff_t *hist_vorticity = new ptrdiff_t[histogram_bins*4]; ptrdiff_t *hist_vorticity = new ptrdiff_t[histogram_bins*4];
{0} *ksample_values;
fs->compute_velocity(fs->cvorticity); fs->compute_velocity(fs->cvorticity);
if (fs->cd->myrank == 0)
{{
ksample_values = new {0}[nksamples*6];
for (int i=0; i<nksamples; i++)
{{
ptrdiff_t cindex = (ptrdiff_t(kindices[2*i+1])*fs->cd->subsizes[2] + ptrdiff_t(kindices[2*i]))*3;
std::copy(({0}*)(fs->cvelocity + cindex),
({0}*)(fs->cvelocity + cindex + 3),
ksample_values + i*6);
}}
}}
double *spec_velocity = fftw_alloc_real(fs->nshells*9); double *spec_velocity = fftw_alloc_real(fs->nshells*9);
double *spec_vorticity = fftw_alloc_real(fs->nshells*9); double *spec_vorticity = fftw_alloc_real(fs->nshells*9);
fs->cospectrum(fs->cvelocity, fs->cvelocity, spec_velocity); fs->cospectrum(fs->cvelocity, fs->cvelocity, spec_velocity);
...@@ -117,8 +131,8 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -117,8 +131,8 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
hist_vorticity, hist_vorticity,
max_vorticity_estimate, max_vorticity_estimate,
histogram_bins); histogram_bins);
if (myrank == 0) if (fs->cd->myrank == 0)
{ {{
hid_t Cdset, wspace, mspace; hid_t Cdset, wspace, mspace;
int ndims; int ndims;
hsize_t count[4], offset[4], dims[4]; hsize_t count[4], offset[4], dims[4];
...@@ -127,7 +141,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -127,7 +141,7 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
offset[2] = 0; offset[2] = 0;
offset[3] = 0; offset[3] = 0;
//endcpp //endcpp
""" """.format(self.C_dtype)
size_setups = [""" size_setups = ["""
count[0] = 1; count[0] = 1;
count[1] = nx; count[1] = nx;
...@@ -148,7 +162,11 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -148,7 +162,11 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
count[1] = fs->nshells; count[1] = fs->nshells;
count[2] = 3; count[2] = 3;
count[3] = 3; count[3] = 3;
"""] """,]
if self.dtype == np.float32:
field_H5T = 'H5T_NATIVE_FLOAT'
elif self.dtype == np.float64:
field_H5T = 'H5T_NATIVE_DOUBLE'
stat_template = """ stat_template = """
//begincpp //begincpp
Cdset = H5Dopen(stat_file, "{0}", H5P_DEFAULT); Cdset = H5Dopen(stat_file, "{0}", H5P_DEFAULT);
...@@ -189,6 +207,17 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -189,6 +207,17 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
self.stat_src += size_setups[i] + stat_outputs[i] self.stat_src += size_setups[i] + stat_outputs[i]
self.stat_src += """ self.stat_src += """
//begincpp //begincpp
count[0] = 1;
count[1] = nksamples;
count[2] = 3;
Cdset = H5Dopen(stat_file, "/statistics/ksamples/velocity", H5P_DEFAULT);
wspace = H5Dget_space(Cdset);
ndims = H5Sget_simple_extent_dims(wspace, dims, NULL);
mspace = H5Screate_simple(ndims, count, NULL);
H5Sselect_hyperslab(wspace, H5S_SELECT_SET, offset, NULL, count, NULL);
H5Dwrite(Cdset, H5T_field_complex, mspace, wspace, H5P_DEFAULT, ksample_values);
H5Dclose(Cdset);
delete[] ksample_values;
} }
fftw_free(spec_velocity); fftw_free(spec_velocity);
fftw_free(spec_vorticity); fftw_free(spec_vorticity);
...@@ -201,8 +230,15 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -201,8 +230,15 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
return None return None
def fill_up_fluid_code(self): def fill_up_fluid_code(self):
self.fluid_includes += '#include <cstring>\n' self.fluid_includes += '#include <cstring>\n'
self.fluid_variables += 'fluid_solver<{0}> *fs;\n'.format(self.C_dtype) self.fluid_variables += ('fluid_solver<{0}> *fs;\n'.format(self.C_dtype) +
'int *kindices;\n' +
'int nksamples;\n' +
'hid_t H5T_field_complex;\n')
self.write_fluid_stats() self.write_fluid_stats()
if self.dtype == np.float32:
field_H5T = 'H5T_NATIVE_FLOAT'
elif self.dtype == np.float64:
field_H5T = 'H5T_NATIVE_DOUBLE'
self.fluid_start += """ self.fluid_start += """
//begincpp //begincpp
char fname[512]; char fname[512];
...@@ -220,8 +256,28 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -220,8 +256,28 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
strncpy(fs->forcing_type, forcing_type, 128); strncpy(fs->forcing_type, forcing_type, 128);
fs->iteration = iteration; fs->iteration = iteration;
fs->read('v', 'c'); fs->read('v', 'c');
if (fs->cd->myrank == 0)
{{
hid_t dset = H5Dopen(stat_file, "kspace/ksample_indices", H5P_DEFAULT);
hid_t rspace;
rspace = H5Dget_space(dset);
hsize_t count[2];
H5Sget_simple_extent_dims(rspace, count, NULL);
H5Sclose(rspace);
nksamples = count[0];
kindices = new int[nksamples*2];
H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, kindices);
H5Dclose(dset);
typedef struct {{
double re; /*real part*/
double im; /*imaginary part*/
}} tmp_complex_type;
H5T_field_complex = H5Tcreate(H5T_COMPOUND, sizeof(tmp_complex_type));
H5Tinsert(H5T_field_complex, "r", HOFFSET(tmp_complex_type, re), {2});
H5Tinsert(H5T_field_complex, "i", HOFFSET(tmp_complex_type, im), {2});
}}
//endcpp //endcpp
""".format(self.C_dtype, self.fftw_plan_rigor) """.format(self.C_dtype, self.fftw_plan_rigor, field_H5T)
if not self.frozen_fields: if not self.frozen_fields:
self.fluid_loop = 'fs->step(dt);\n' self.fluid_loop = 'fs->step(dt);\n'
else: else:
...@@ -230,7 +286,12 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base): ...@@ -230,7 +286,12 @@ class NavierStokes(bfps.fluid_base.fluid_particle_base):
self.fluid_output + '\n}\n') self.fluid_output + '\n}\n')
self.fluid_end = ('if (fs->iteration % niter_out != 0)\n{\n' + self.fluid_end = ('if (fs->iteration % niter_out != 0)\n{\n' +
self.fluid_output + '\n}\n' + self.fluid_output + '\n}\n' +
'delete fs;\n') 'delete fs;\n' +
'if (fs->cd->myrank == 0)\n' +
'{\n' +
'delete[] kindices;\n' +
'H5Tclose(H5T_field_complex);\n' +
'}\n')
return None return None
def add_particle_fields( def add_particle_fields(
self, self,
......
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