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Commit 11fa51cb authored by Cristian Lalescu's avatar Cristian Lalescu
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Merge branch 'feature/particle-API' into develop

parents 66b02365 553a7bb8
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bfps/NavierStokes.py
View file @ 11fa51cb
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bfps/cpp/rFFTW_interpolator.cpp
View file @ 11fa51cb
......@@ -32,15 +32,13 @@
template <class rnumber, int interp_neighbours>
rFFTW_interpolator<rnumber, interp_neighbours>::rFFTW_interpolator(
fluid_solver_base<rnumber> *fs,
base_polynomial_values BETA_POLYS)
base_polynomial_values BETA_POLYS,
rnumber *FIELD)
{
this->descriptor = fs->rd;
this->field_size = 2*fs->cd->local_size;
this->compute_beta = BETA_POLYS;
if (sizeof(rnumber) == 4)
this->field = (rnumber*)((void*)fftwf_alloc_real(this->field_size));
else if (sizeof(rnumber) == 8)
this->field = (rnumber*)((void*)fftw_alloc_real(this->field_size));
this->field = FIELD;
// compute dx, dy, dz;
this->dx = 4*acos(0) / (fs->dkx*this->descriptor->sizes[2]);
......@@ -59,24 +57,9 @@ rFFTW_interpolator<rnumber, interp_neighbours>::rFFTW_interpolator(
template <class rnumber, int interp_neighbours>
rFFTW_interpolator<rnumber, interp_neighbours>::~rFFTW_interpolator()
{
if (sizeof(rnumber) == 4)
fftwf_free((float*)((void*)this->field));
else if (sizeof(rnumber) == 8)
fftw_free((double*)((void*)this->field));
delete[] this->compute;
}
template <class rnumber, int interp_neighbours>
int rFFTW_interpolator<rnumber, interp_neighbours>::read_rFFTW(void *void_src)
{
rnumber *src = (rnumber*)void_src;
/* do big copy of middle stuff */
std::copy(src,
src + this->field_size,
this->field);
return EXIT_SUCCESS;
}
template <class rnumber, int interp_neighbours>
void rFFTW_interpolator<rnumber, interp_neighbours>::get_grid_coordinates(
const int nparticles,
......
bfps/cpp/rFFTW_interpolator.hpp
View file @ 11fa51cb
......@@ -60,7 +60,8 @@ class rFFTW_interpolator
rFFTW_interpolator(
fluid_solver_base<rnumber> *FSOLVER,
base_polynomial_values BETA_POLYS);
base_polynomial_values BETA_POLYS,
rnumber *FIELD_DATA);
~rFFTW_interpolator();
/* map real locations to grid coordinates */
......@@ -83,7 +84,6 @@ class rFFTW_interpolator
const double *__restrict__ xx,
double *__restrict__ dest,
const int *deriv = NULL);
int read_rFFTW(void *src);
};
#endif//RFFTW_INTERPOLATOR
......
bfps/fluid_base.py
View file @ 11fa51cb
......@@ -130,9 +130,10 @@ class fluid_particle_base(bfps.code):
'hsize_t dset;\n')
for key in ['state', 'velocity', 'acceleration']:
self.definitions += ('full_name = (std::string(name) + std::string("/{0}"));\n'.format(key) +
'if (H5Lexists(g_id, full_name.c_str(), H5P_DEFAULT))\n{\n' +
'dset = H5Dopen(g_id, full_name.c_str(), H5P_DEFAULT);\n' +
'grow_single_dataset(dset, niter_todo/niter_part);\n' +
'H5Dclose(dset);\n')
'H5Dclose(dset);\n}\n')
self.definitions += ('full_name = (std::string(name) + std::string("/rhs"));\n' +
'if (H5Lexists(g_id, full_name.c_str(), H5P_DEFAULT))\n{\n' +
'dset = H5Dopen(g_id, full_name.c_str(), H5P_DEFAULT);\n' +
......@@ -445,25 +446,24 @@ class fluid_particle_base(bfps.code):
dtype = np.int64,
compression = 'gzip')
for s in range(self.particle_species):
if self.parameters['tracers{0}_integration_method'.format(s)] == 'AdamsBashforth':
time_chunk = 2**20 // (8*3*
self.parameters['nparticles']*
self.parameters['tracers{0}_integration_steps'.format(s)])
time_chunk = max(time_chunk, 1)
ofile.create_dataset('particles/tracers{0}/rhs'.format(s),
(1,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
maxshape = (None,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
chunks = (time_chunk,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
dtype = np.float64)
time_chunk = 2**20 // (8*3*
self.parameters['nparticles']*
self.parameters['tracers{0}_integration_steps'.format(s)])
time_chunk = max(time_chunk, 1)
ofile.create_dataset('particles/tracers{0}/rhs'.format(s),
(1,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
maxshape = (None,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
chunks = (time_chunk,
self.parameters['tracers{0}_integration_steps'.format(s)],
self.parameters['nparticles'],
3),
dtype = np.float64)
time_chunk = 2**20 // (8*3*self.parameters['nparticles'])
time_chunk = max(time_chunk, 1)
ofile.create_dataset(
......@@ -474,14 +474,15 @@ class fluid_particle_base(bfps.code):
chunks = (time_chunk, self.parameters['nparticles'], 3),
maxshape = (None, self.parameters['nparticles'], 3),
dtype = np.float64)
ofile.create_dataset(
'/particles/tracers{0}/acceleration'.format(s),
(1,
self.parameters['nparticles'],
3),
chunks = (time_chunk, self.parameters['nparticles'], 3),
maxshape = (None, self.parameters['nparticles'], 3),
dtype = np.float64)
if self.parameters['tracers{0}_acc_on'.format(s)]:
ofile.create_dataset(
'/particles/tracers{0}/acceleration'.format(s),
(1,
self.parameters['nparticles'],
3),
chunks = (time_chunk, self.parameters['nparticles'], 3),
maxshape = (None, self.parameters['nparticles'], 3),
dtype = np.float64)
ofile.close()
return None
done.txt
View file @ 11fa51cb
......@@ -6,3 +6,7 @@ x 2015-12-26 call interpolation only when needed @optimizati
x 2015-12-26 clean up tox files, make sure all tests run @tests +v1.0
x 2016-01-03 check divfree function
x 2016-01-03 compute kMeta(t) as well
x 2016-01-03 split library into core and extra @optimization +v1.0
x 2016-01-07 FFTW interpolator doesn't need its own field @optimization +v1.0 +particle_api
x 2016-01-08 simplify tracer/field addition mechanism @design +v1.0 +particle_api
x 2016-01-08 add stat choice parameter to add_particles @design +v1.0 +particle_api
tests/base.py
View file @ 11fa51cb
......@@ -102,29 +102,19 @@ def launch(
c.parameters['famplitude'] = 0.2
c.fill_up_fluid_code()
if c.parameters['nparticles'] > 0:
c.add_particle_fields(
name = 'regular',
c.add_3D_rFFTW_field(name = 'rFFTW_acc')
c.add_interpolator(
name = 'spline',
neighbours = opt.neighbours,
smoothness = opt.smoothness)
c.add_particle_fields(kcut = 'fs->kM/2', name = 'filtered', neighbours = opt.neighbours)
c.add_particles(
kcut = 'fs->kM/2',
integration_steps = 1,
fields_name = 'filtered')
#for integr_steps in range(1, 7):
# c.add_particles(
# integration_steps = integr_steps,
# neighbours = opt.neighbours,
# smoothness = opt.smoothness,
# fields_name = 'regular')
for info in [(2, 'AdamsBashforth'),
(3, 'AdamsBashforth'),
(4, 'AdamsBashforth'),
(6, 'AdamsBashforth')]:
c.add_particles(
integration_steps = info[0],
integration_method = info[1],
fields_name = 'regular')
kcut = ['fs->kM/2', 'fs->kM/3'],
integration_steps = 3,
interpolator = 'spline')
c.add_particles(
integration_steps = [2, 3, 4, 6],
interpolator = 'spline',
acc_name = 'rFFTW_acc')
c.finalize_code()
c.write_src()
c.write_par()
......@@ -158,6 +148,8 @@ def launch(
def acceleration_test(c, m = 3, species = 0):
if not c.parameters['tracers{0}_acc_on'.format(species)]:
return None
import numpy as np
import matplotlib.pyplot as plt
from bfps.tools import get_fornberg_coeffs
......@@ -182,13 +174,12 @@ def acceleration_test(c, m = 3, species = 0):
pid = np.argmin(SNR(num_acc1, acc[n+1:-n-1]))
pars = d['parameters']
to_print = (
'integration={0}, steps={1}, interp={2}, neighbours={3}, '.format(
pars['tracers{0}_integration_method'.format(species)].value,
'steps={0}, interp={1}, neighbours={2}, '.format(
pars['tracers{0}_integration_steps'.format(species)].value,
pars[str(pars['tracers{0}_field'.format(species)].value) + '_type'].value,
pars[str(pars['tracers{0}_field'.format(species)].value) + '_neighbours'].value))
if 'spline' in pars['tracers{0}_field'.format(species)].value:
to_print += 'smoothness = {0}, '.format(pars[str(pars['tracers{0}_field'.format(species)].value) + '_smoothness'].value)
pars[str(pars['tracers{0}_interpolator'.format(species)].value) + '_type'].value,
pars[str(pars['tracers{0}_interpolator'.format(species)].value) + '_neighbours'].value))
if 'spline' in pars['tracers{0}_interpolator'.format(species)].value:
to_print += 'smoothness = {0}, '.format(pars[str(pars['tracers{0}_interpolator'.format(species)].value) + '_smoothness'].value)
to_print += (
'SNR d1p-vel={0:.3f}, d1v-acc={1:.3f}, d2p-acc={2:.3f}'.format(
np.mean(SNR(num_vel1, vel[n+1:-n-1])),
......
todo.txt
View file @ 11fa51cb
(B) FFTW interpolator doesn't need its own field @optimization +v1.0
(B) compute z polynomials only when needed @optimization +v1.0
(B) compute z polynomials only when needed @optimization +v1.0
(B) read https://www.xsede.org/documents/271087/369161/ExtScale-Koziol.pdf @optimization @HDF5 +I/O
(B) set up mechanism for adding in new PDEs @design +v2.0 +alternate_algorithms
(B) split library into core and extra @optimization +v1.0
(B) tweak HDF5 settings @optimization @HDF5 +I/O
(B) use less memory @optimization
(C) clean up machine_settings mess @design @documentation +v2.0
(C) code overview @documentation
(C) move stat I/O to cpp lib @design @HDF5
(C) test involving hydrodynamic similarity @tests
(C) use HDF5 io for fields @design @HDF5 +I/O
(D) generalize interpolation comparison test @tests
(D) test anisotropic grids @tests
(D) test non-cubic domains @tests
(D) tests should not overwrite other tests (tox_full) @tests
(E) add u-equation algorithm for testing purposes @tests +alternate_algorithms
(E) pure python DNS addon: pros and cons @tests +alternate_algorithms
(B) set up mechanism for adding in new PDEs @design +v2.0 +alternate_algorithms
(B) tweak HDF5 settings @optimization @HDF5 +I/O
(B) use less memory @optimization
(C) clean up machine_settings mess @design @documentation +v2.0
(C) code overview @documentation
(C) move stat I/O to cpp lib @design @HDF5
(C) test involving hydrodynamic similarity @tests
(C) use HDF5 io for fields @design @HDF5 +I/O
(D) generalize interpolation comparison test @tests
(D) generate separate lib(s) with extra classes @tests +alternate_algorithms
(D) test anisotropic grids @tests
(D) test non-cubic domains @tests
(D) tests should not overwrite other tests (tox_full) @tests
(E) add u-equation algorithm for testing purposes @tests +alternate_algorithms
(E) pure python DNS addon: pros and cons @tests +alternate_algorithms
(F) add switch to turn off simulation
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