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Commit 8b2867ce authored by Chichi Lalescu's avatar Chichi Lalescu
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generate initial conditions forparticles with orientation

parent 6f214d33
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1 merge request!23WIP: Feature/use cmake
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with 35 additions and 11 deletions
bfps/DNS.py
+ 35
− 11
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...@@ -127,7 +127,7 @@ class DNS(_code): ...@@ -127,7 +127,7 @@ class DNS(_code):
template_class = '{0}<{1}>::'.format(self.dns_type, rnumber), template_class = '{0}<{1}>::'.format(self.dns_type, rnumber),
template_prefix = 'template '.format(rnumber), template_prefix = 'template '.format(rnumber),
just_declaration = True) + '\n\n') just_declaration = True) + '\n\n')
if self.dns_type in ['NSVEparticles', 'NSVE_no_output', 'NSVEparticles_no_output']: if self.dns_type in ['NSVEparticles', 'NSVE_no_output', 'NSVEparticles_no_output', 'NSVEparticlesP2P']:
outfile.write('template <typename rnumber> int NSVE<rnumber>::read_parameters(){return EXIT_SUCCESS;}\n') outfile.write('template <typename rnumber> int NSVE<rnumber>::read_parameters(){return EXIT_SUCCESS;}\n')
outfile.write('template int NSVE<float>::read_parameters();\n') outfile.write('template int NSVE<float>::read_parameters();\n')
outfile.write('template int NSVE<double>::read_parameters();\n\n') outfile.write('template int NSVE<double>::read_parameters();\n\n')
...@@ -377,7 +377,7 @@ class DNS(_code): ...@@ -377,7 +377,7 @@ class DNS(_code):
assert (self.parameters['niter_todo'] % self.parameters['niter_stat'] == 0) assert (self.parameters['niter_todo'] % self.parameters['niter_stat'] == 0)
assert (self.parameters['niter_todo'] % self.parameters['niter_out'] == 0) assert (self.parameters['niter_todo'] % self.parameters['niter_out'] == 0)
assert (self.parameters['niter_out'] % self.parameters['niter_stat'] == 0) assert (self.parameters['niter_out'] % self.parameters['niter_stat'] == 0)
if self.dns_type in ['NSVEparticles_no_output', 'NSVEparticles']: if self.dns_type in ['NSVEparticles_no_output', 'NSVEparticlesP2P', 'NSVEparticles']:
assert (self.parameters['niter_todo'] % self.parameters['niter_part'] == 0) assert (self.parameters['niter_todo'] % self.parameters['niter_part'] == 0)
assert (self.parameters['niter_out'] % self.parameters['niter_part'] == 0) assert (self.parameters['niter_out'] % self.parameters['niter_part'] == 0)
_code.write_par(self, iter0 = iter0) _code.write_par(self, iter0 = iter0)
...@@ -432,6 +432,9 @@ class DNS(_code): ...@@ -432,6 +432,9 @@ class DNS(_code):
number_of_particles = 1 number_of_particles = 1
for val in pbase_shape[1:]: for val in pbase_shape[1:]:
number_of_particles *= val number_of_particles *= val
ncomponents = 3
if self.dns_type in ['NSVEparticlesP2P']:
ncomponents = 6
with h5py.File(self.get_checkpoint_0_fname(), 'a') as ofile: with h5py.File(self.get_checkpoint_0_fname(), 'a') as ofile:
s = 0 s = 0
ofile.create_group('tracers{0}'.format(s)) ofile.create_group('tracers{0}'.format(s))
...@@ -442,13 +445,13 @@ class DNS(_code): ...@@ -442,13 +445,13 @@ class DNS(_code):
shape = ( shape = (
(self.parameters['tracers{0}_integration_steps'.format(s)],) + (self.parameters['tracers{0}_integration_steps'.format(s)],) +
pbase_shape + pbase_shape +
(3,)), (ncomponents,)),
dtype = np.float) dtype = np.float)
ofile['tracers{0}/state'.format(s)].create_dataset( ofile['tracers{0}/state'.format(s)].create_dataset(
'0', '0',
shape = ( shape = (
pbase_shape + pbase_shape +
(3,)), (ncomponents,)),
dtype = np.float) dtype = np.float)
return None return None
def job_parser_arguments( def job_parser_arguments(
...@@ -621,6 +624,17 @@ class DNS(_code): ...@@ -621,6 +624,17 @@ class DNS(_code):
self.parameters_to_parser_arguments( self.parameters_to_parser_arguments(
parser_NSVEp2, parser_NSVEp2,
self.NSVEp_extra_parameters) self.NSVEp_extra_parameters)
parser_NSVEp2p = subparsers.add_parser(
'NSVEparticlesP2P',
help = 'plain Navier-Stokes vorticity formulation, with basic fluid tracers')
self.simulation_parser_arguments(parser_NSVEp2p)
self.job_parser_arguments(parser_NSVEp2p)
self.particle_parser_arguments(parser_NSVEp2p)
self.parameters_to_parser_arguments(parser_NSVEp2p)
self.parameters_to_parser_arguments(
parser_NSVEp2p,
self.NSVEp_extra_parameters)
return None return None
def prepare_launch( def prepare_launch(
self, self,
...@@ -656,7 +670,7 @@ class DNS(_code): ...@@ -656,7 +670,7 @@ class DNS(_code):
self.dns_type = opt.DNS_class self.dns_type = opt.DNS_class
self.name = self.dns_type + '-' + self.fluid_precision + '-v' + bfps.__version__ self.name = self.dns_type + '-' + self.fluid_precision + '-v' + bfps.__version__
# merge parameters if needed # merge parameters if needed
if self.dns_type in ['NSVEparticles', 'NSVEparticles_no_output']: if self.dns_type in ['NSVEparticles', 'NSVEparticlesP2P', 'NSVEparticles_no_output']:
for k in self.NSVEp_extra_parameters.keys(): for k in self.NSVEp_extra_parameters.keys():
self.parameters[k] = self.NSVEp_extra_parameters[k] self.parameters[k] = self.NSVEp_extra_parameters[k]
if type(extra_parameters) != type(None): if type(extra_parameters) != type(None):
...@@ -690,7 +704,7 @@ class DNS(_code): ...@@ -690,7 +704,7 @@ class DNS(_code):
# hardcoded FFTW complex representation size # hardcoded FFTW complex representation size
field_size = 3*(opt.nx+2)*opt.ny*opt.nz*self.fluid_dtype.itemsize field_size = 3*(opt.nx+2)*opt.ny*opt.nz*self.fluid_dtype.itemsize
checkpoint_size = field_size checkpoint_size = field_size
if self.dns_type in ['NSVEparticles', 'NSVEparticles_no_output']: if self.dns_type in ['NSVEparticles', 'NSVEparticlesP2P', 'NSVEparticles_no_output']:
rhs_size = self.parameters['tracers0_integration_steps'] rhs_size = self.parameters['tracers0_integration_steps']
if type(opt.tracers0_integration_steps) != type(None): if type(opt.tracers0_integration_steps) != type(None):
rhs_size = opt.tracers0_integration_steps rhs_size = opt.tracers0_integration_steps
...@@ -726,14 +740,24 @@ class DNS(_code): ...@@ -726,14 +740,24 @@ class DNS(_code):
nn = self.parameters['nparticles'] nn = self.parameters['nparticles']
cc = int(0) cc = int(0)
batch_size = int(1e6) batch_size = int(1e6)
def get_random_phases(npoints):
return np.random.random(
(npoints, 3))*2*np.pi
def get_random_versors(npoints):
bla = np.random.normal(
size = (npoints, 3))
bla /= np.sum(bla**2, axis = 1)[:, None]
return bla
while nn > 0: while nn > 0:
if nn > batch_size: if nn > batch_size:
dset[cc*batch_size:(cc+1)*batch_size] = np.random.random( dset[cc*batch_size:(cc+1)*batch_size, :3] = get_random_phases(batch_size)
(batch_size, 3))*2*np.pi if dset.shape[1] == 6:
dset[cc*batch_size:(cc+1)*batch_size, 3:] = get_random_versors(batch_size)
nn -= batch_size nn -= batch_size
else: else:
dset[cc*batch_size:cc*batch_size+nn] = np.random.random( dset[cc*batch_size:cc*batch_size+nn, :3] = get_random_phases(nn)
(nn, 3))*2*np.pi if dset.shape[1] == 6:
dset[cc*batch_size:cc*batch_size+nn, 3:] = get_random_versors(nn)
nn = 0 nn = 0
cc += 1 cc += 1
return None return None
...@@ -943,7 +967,7 @@ class DNS(_code): ...@@ -943,7 +967,7 @@ class DNS(_code):
# particle_initial_condition[..., 2] += onedarray[None, :, None, None] # particle_initial_condition[..., 2] += onedarray[None, :, None, None]
self.write_par( self.write_par(
particle_ic = None) particle_ic = None)
if self.dns_type in ['NSVEparticles', 'NSVEparticles_no_output']: if self.dns_type in ['NSVEparticles', 'NSVEparticlesP2P', 'NSVEparticles_no_output']:
self.generate_particle_data(opt = opt) self.generate_particle_data(opt = opt)
self.run( self.run(
nb_processes = opt.nb_processes, nb_processes = opt.nb_processes,
......
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