diff --git a/bfps/DNS.py b/bfps/DNS.py
index dd75854d9e7aa3a61c47e680a6a4b4a93dd51239..ffcaea49772e8a26f12c7983ecb86ec3abd3a1d0 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -791,13 +791,17 @@ class DNS(_code):
ncomponents = 6
with h5py.File(self.get_checkpoint_0_fname(), 'a') as data_file:
nn = self.parameters['nparticles']
+ if not 'tracers{0}'.format(species) in data_file.keys():
+ data_file.create_group('tracers{0}'.format(species))
+ data_file.create_group('tracers{0}/rhs'.format(species))
+ data_file.create_group('tracers{0}/state'.format(species))
data_file['tracers{0}/rhs'.format(species)].create_dataset(
'0',
shape = (
(self.parameters['tracers{0}_integration_steps'.format(species)],) +
(nn, ncomponents,)),
dtype = np.float)
- dset = data_file['tracers{0}/state'.format(s)].create_dataset(
+ dset = data_file['tracers{0}/state'.format(species)].create_dataset(
'0',
shape = (nn, ncomponents,),
dtype = np.float)
@@ -958,12 +962,6 @@ class DNS(_code):
self,
opt = None):
if self.parameters['nparticles'] > 0:
- with h5py.File(self.get_checkpoint_0_fname(), 'a') as ofile:
- s = 0
- if not 'tracers{0}'.format(s) in ofile.keys():
- ofile.create_group('tracers{0}'.format(s))
- ofile.create_group('tracers{0}/rhs'.format(s))
- ofile.create_group('tracers{0}/state'.format(s))
self.generate_tracer_state(
species = 0,
rseed = opt.particle_rand_seed)
diff --git a/bfps/__main__.py b/bfps/__main__.py
index 16a7cf7d099c49a39368a8ff09cb05bf890feb6f..cf269edbaea91acd4b3de595782b92e32e1cbd3b 100644
--- a/bfps/__main__.py
+++ b/bfps/__main__.py
@@ -33,7 +33,7 @@ from .PP import PP
from .TEST import TEST
def main():
- parser = argparse.ArgumentParser(prog = 'bfps')
+ parser = argparse.ArgumentParser(prog = 'bfps', conflict_handler = 'resolve')
parser.add_argument(
'-v', '--version',
action = 'version',
diff --git a/bfps/test/test_bfps_NSVEparticles.py b/bfps/test/test_bfps_NSVEparticles.py
index f914ad7dbfa7f23466c19cfba64f730b9e4cda45..fe1e7875a651b17dd9180f3cbe6d6bfe1f1b5c27 100644
--- a/bfps/test/test_bfps_NSVEparticles.py
+++ b/bfps/test/test_bfps_NSVEparticles.py
@@ -1,4 +1,29 @@
#! /usr/bin/env python
+#######################################################################
+# #
+# Copyright 2019 Max Planck Institute #
+# for Dynamics and Self-Organization #
+# #
+# This file is part of bfps. #
+# #
+# bfps 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 3 of the License, #
+# or (at your option) any later version. #
+# #
+# bfps 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 bfps. If not, see <http://www.gnu.org/licenses/> #
+# #
+# Contact: Cristian.Lalescu@ds.mpg.de #
+# #
+#######################################################################
+
+
import os
import numpy as np
diff --git a/bfps/test/test_particle_clouds.py b/bfps/test/test_particle_clouds.py
index 1a890495ca263b4f317722c0fb6cfe4a22d57f87..5d2045390f51e7f529f78a3eb7037acb3fcae3b9 100644
--- a/bfps/test/test_particle_clouds.py
+++ b/bfps/test/test_particle_clouds.py
@@ -33,15 +33,22 @@ import sys
import bfps
from bfps import DNS
+
def main():
- nclouds = 4
- nparticles_per_cloud = 3
+ nclouds = 10
+ nparticles_per_cloud = 1000
nparticles = nclouds*nparticles_per_cloud
niterations = 32
c = DNS()
+ c.dns_type = 'NSVEparticles'
+ c.parameters['nparticles'] = nparticles
+ c.parameters['tracers1_integration_steps'] = 4
+ c.generate_tracer_state(rseed = 2, species = 1)
+ del c.parameters['nparticles']
+ del c.parameters['tracers1_integration_steps']
ic_file = h5py.File(c.get_checkpoint_0_fname(), 'a')
- ic_file['tracers0/state/0'] = np.random.random((nclouds, nparticles_per_cloud, 3))
- ic_file['tracers0/rhs/0'] = np.zeros((2, nclouds, nparticles_per_cloud, 3))
+ ic_file['tracers0/state/0'] = ic_file['tracers1/state/0'].value.reshape(nclouds, nparticles_per_cloud, 3)
+ ic_file['tracers0/rhs/0'] = ic_file['tracers1/rhs/0'].value.reshape(4, nclouds, nparticles_per_cloud, 3)
ic_file.close()
c.launch(
['NSVEparticles',
@@ -57,8 +64,28 @@ def main():
'--niter_out', '{0}'.format(niterations),
'--niter_stat', '1',
'--nparticles', '{0}'.format(nparticles),
- '--tracers0_integration_steps', '2',
+ '--njobs', '2',
'--wd', './'])
+ f0 = h5py.File(
+ os.path.join(
+ os.path.join(bfps.lib_dir, 'test'),
+ 'B32p1e4_checkpoint_0.h5'),
+ 'r')
+ f1 = h5py.File(c.get_checkpoint_0_fname(), 'r')
+ for iteration in [0, 32, 64]:
+ field0 = f0['vorticity/complex/{0}'.format(iteration)].value
+ field1 = f1['vorticity/complex/{0}'.format(iteration)].value
+ field_error = np.max(np.abs(field0 - field1))
+ x0 = f0['tracers0/state/{0}'.format(iteration)].value
+ x1 = f1['tracers0/state/{0}'.format(iteration)].value.reshape(x0.shape)
+ traj_error = np.max(np.abs(x0 - x1))
+ y0 = f0['tracers0/rhs/{0}'.format(iteration)].value
+ y1 = f1['tracers0/rhs/{0}'.format(iteration)].value.reshape(y0.shape)
+ rhs_error = np.max(np.abs(y0 - y1))
+ assert(field_error < 1e-5)
+ assert(traj_error < 1e-5)
+ assert(rhs_error < 1e-5)
+ print('SUCCESS! Basic test passed.')
return None
if __name__ == '__main__':