fix sampling file space error

bfps/DNS.py

@@ -784,10 +784,15 @@ class DNS(_code):
     def generate_tracer_state(
             self,
             rseed = None,
-            species = 0):
+            species = 0,
+            integration_steps = None,
+            ncomponents = 3):
         try:
-            ncomponents = 3
-            if self.dns_type in ['NSVEcomplex_particles']:
+            if type(integration_steps) == type(None):
+                integration_steps = self.NSVEp_extra_parameters['tracers0_integration_steps']
+            if 'tracers{0}_integration_steps'.format(species) in self.parameters.keys():
+                integration_steps = self.parameters['tracers{0}_integration_steps'.format(species)]
+            if self.dns_type == 'NSVEcomplex_particles' and species == 0:
                 ncomponents = 6
             with h5py.File(self.get_checkpoint_0_fname(), 'a') as data_file:
                 nn = self.parameters['nparticles']
@@ -797,9 +802,7 @@ class DNS(_code):
                     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,)),
+                        shape = (integration_steps, nn, ncomponents,),
                         dtype = np.float)
                 dset = data_file['tracers{0}/state'.format(species)].create_dataset(
                         '0',

bfps/cpp/full_code/NSVEparticles.cpp

-
-
-
-
-//#define NDEBUG
+/**********************************************************************
+*                                                                     *
+*  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                                 *
+*                                                                     *
+**********************************************************************/
+
+
+
+#define NDEBUG
 
 #include <string>
 #include <cmath>

bfps/cpp/particles/particles_output_hdf5.hpp

@@ -242,6 +242,7 @@ public:
             variable_used_only_in_assert(rethdf);
             assert(rethdf >= 0);
 
+            DEBUG_MSG("before writing state\n");
             herr_t	status = H5Dwrite(
                     dataset_id,
                     type_id,
@@ -257,6 +258,7 @@ public:
             assert(rethdf >= 0);
             rethdf = H5Sclose(filespace);
             assert(rethdf >= 0);
+            DEBUG_MSG("after writing state\n");
         }
         {
             assert(size_particle_rhs >= 0);
@@ -304,6 +306,7 @@ public:
                 variable_used_only_in_assert(rethdf);
                 assert(rethdf >= 0);
 
+                DEBUG_MSG("before writing rhs %d\n", idx_rhs);
                 herr_t	status = H5Dwrite(
                         dataset_id,
                         type_id,
@@ -317,6 +320,7 @@ public:
                 assert(rethdf >= 0);
                 rethdf = H5Sclose(memspace);
                 assert(rethdf >= 0);
+                DEBUG_MSG("after writing rhs %d\n", idx_rhs);
             }
             int rethdf = H5Dclose(dataset_id);
             variable_used_only_in_assert(rethdf);

bfps/cpp/particles/particles_output_sampling_hdf5.hpp

@@ -216,7 +216,7 @@ public:
             hid_t memspace = H5Screate_simple(2, count, NULL);
             assert(memspace >= 0);
 
-            const hsize_t file_count[2] = {hsize_t(Parent::getTotalNbParticles()), size_particle_positions};
+            const hsize_t file_count[2] = {hsize_t(Parent::getTotalNbParticles()), size_particle_rhs};
             hid_t filespace = H5Screate_simple(2, file_count, NULL);
             assert(filespace >= 0);
             int rethdf = H5Sselect_hyperslab(