finalize test of particle cloud code

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)

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',

bfps/test/test_bfps_NSVEparticles.py

 #! /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

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__':