diff --git a/bfps/NavierStokes.py b/bfps/NavierStokes.py
index a075074fb4233e842a9055f74f074dec532dc694..6c0c8b3a5b7c37a21482755344f8548323d7a442 100644
--- a/bfps/NavierStokes.py
+++ b/bfps/NavierStokes.py
@@ -51,6 +51,19 @@ class NavierStokes(_fluid_particle_base):
simname = simname,
dtype = fluid_precision,
use_fftw_wisdom = use_fftw_wisdom)
+ self.parameters['nu'] = 0.1
+ self.parameters['fmode'] = 1
+ self.parameters['famplitude'] = 0.5
+ self.parameters['fk0'] = 1.5
+ self.parameters['fk1'] = 3.0
+ self.parameters['forcing_type'] = 'linear'
+ self.parameters['histogram_bins'] = 256
+ self.parameters['max_velocity_estimate'] = 1.0
+ self.parameters['max_vorticity_estimate'] = 1.0
+ self.parameters['QR2D_histogram_bins'] = 64
+ self.parameters['max_trS2_estimate'] = 1.0
+ self.parameters['max_Q_estimate'] = 1.0
+ self.parameters['max_R_estimate'] = 1.0
self.file_datasets_grow = """
//begincpp
std::string temp_string;
@@ -718,6 +731,83 @@ class NavierStokes(_fluid_particle_base):
with h5py.File(os.path.join(self.work_dir, self.simname + '.h5'), 'r+') as ofile:
kspace = self.get_kspace()
nshells = kspace['nshell'].shape[0]
+ for k in ['velocity', 'vorticity']:
+ time_chunk = 2**20//(8*3*self.parameters['nx'])
+ time_chunk = max(time_chunk, 1)
+ ofile.create_dataset('statistics/xlines/' + k,
+ (1, self.parameters['nx'], 3),
+ chunks = (time_chunk, self.parameters['nx'], 3),
+ maxshape = (None, self.parameters['nx'], 3),
+ dtype = self.dtype,
+ compression = 'gzip')
+ time_chunk = 2**20//(8*3*3*nshells)
+ time_chunk = max(time_chunk, 1)
+ ofile.create_dataset('statistics/spectra/' + k + '_' + k,
+ (1, nshells, 3, 3),
+ chunks = (time_chunk, nshells, 3, 3),
+ maxshape = (None, nshells, 3, 3),
+ dtype = np.float64,
+ compression = 'gzip')
+ time_chunk = 2**20//(8*4*10)
+ time_chunk = max(time_chunk, 1)
+ a = ofile.create_dataset('statistics/moments/' + k,
+ (1, 10, 4),
+ chunks = (time_chunk, 10, 4),
+ maxshape = (None, 10, 4),
+ dtype = np.float64,
+ compression = 'gzip')
+ time_chunk = 2**20//(8*4*self.parameters['histogram_bins'])
+ time_chunk = max(time_chunk, 1)
+ ofile.create_dataset('statistics/histograms/' + k,
+ (1,
+ self.parameters['histogram_bins'],
+ 4),
+ chunks = (time_chunk,
+ self.parameters['histogram_bins'],
+ 4),
+ maxshape = (None,
+ self.parameters['histogram_bins'],
+ 4),
+ dtype = np.int64,
+ compression = 'gzip')
+ for s in range(self.particle_species):
+ 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(
+ '/particles/tracers{0}/velocity'.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)
if self.QR_stats_on:
time_chunk = 2**20//(8*3*self.parameters['histogram_bins'])
time_chunk = max(time_chunk, 1)
diff --git a/bfps/_fluid_base.py b/bfps/_fluid_base.py
index 31bd4d318ed239191bc63d1af9c524c36a954aa7..4e1a6c6c7824e44c656124fda1e7374666bd21ad 100644
--- a/bfps/_fluid_base.py
+++ b/bfps/_fluid_base.py
@@ -70,19 +70,6 @@ class _fluid_particle_base(_code):
self.parameters['niter_out'] = 1024
self.parameters['nparticles'] = 0
self.parameters['dt'] = 0.01
- self.parameters['nu'] = 0.1
- self.parameters['fmode'] = 1
- self.parameters['famplitude'] = 0.5
- self.parameters['fk0'] = 1.5
- self.parameters['fk1'] = 3.0
- self.parameters['forcing_type'] = 'linear'
- self.parameters['histogram_bins'] = 256
- self.parameters['max_velocity_estimate'] = 1.0
- self.parameters['max_vorticity_estimate'] = 1.0
- self.parameters['QR2D_histogram_bins'] = 64
- self.parameters['max_trS2_estimate'] = 1.0
- self.parameters['max_Q_estimate'] = 1.0
- self.parameters['max_R_estimate'] = 1.0
self.fluid_includes = '#include "fluid_solver.hpp"\n'
self.fluid_variables = ''
self.fluid_definitions = ''
@@ -403,83 +390,6 @@ class _fluid_particle_base(_code):
for k in kspace.keys():
ofile['kspace/' + k] = kspace[k]
nshells = kspace['nshell'].shape[0]
- for k in ['velocity', 'vorticity']:
- time_chunk = 2**20//(8*3*self.parameters['nx'])
- time_chunk = max(time_chunk, 1)
- ofile.create_dataset('statistics/xlines/' + k,
- (1, self.parameters['nx'], 3),
- chunks = (time_chunk, self.parameters['nx'], 3),
- maxshape = (None, self.parameters['nx'], 3),
- dtype = self.dtype,
- compression = 'gzip')
- time_chunk = 2**20//(8*3*3*nshells)
- time_chunk = max(time_chunk, 1)
- ofile.create_dataset('statistics/spectra/' + k + '_' + k,
- (1, nshells, 3, 3),
- chunks = (time_chunk, nshells, 3, 3),
- maxshape = (None, nshells, 3, 3),
- dtype = np.float64,
- compression = 'gzip')
- time_chunk = 2**20//(8*4*10)
- time_chunk = max(time_chunk, 1)
- a = ofile.create_dataset('statistics/moments/' + k,
- (1, 10, 4),
- chunks = (time_chunk, 10, 4),
- maxshape = (None, 10, 4),
- dtype = np.float64,
- compression = 'gzip')
- time_chunk = 2**20//(8*4*self.parameters['histogram_bins'])
- time_chunk = max(time_chunk, 1)
- ofile.create_dataset('statistics/histograms/' + k,
- (1,
- self.parameters['histogram_bins'],
- 4),
- chunks = (time_chunk,
- self.parameters['histogram_bins'],
- 4),
- maxshape = (None,
- self.parameters['histogram_bins'],
- 4),
- dtype = np.int64,
- compression = 'gzip')
- for s in range(self.particle_species):
- 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(
- '/particles/tracers{0}/velocity'.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