diff --git a/bfps/cpp/full_code/NSVE.cpp b/bfps/cpp/full_code/NSVE.cpp
index 0b82a781fb73f850fc39e4386d6dbb4a5e5ef5df..9c40968a66f050c318222690a94b273488e46b61 100644
--- a/bfps/cpp/full_code/NSVE.cpp
+++ b/bfps/cpp/full_code/NSVE.cpp
@@ -36,11 +36,11 @@ int NSVE<rnumber>::initialize(void)
simname.c_str(),
nx, ny, nz,
dkx, dky, dkz,
- FFTW_MEASURE);
+ DEFAULT_FFTW_FLAG);
this->tmp_vec_field = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
this->comm,
- FFTW_MEASURE);
+ DEFAULT_FFTW_FLAG);
this->fs->checkpoints_per_file = checkpoints_per_file;
diff --git a/bfps/cpp/full_code/code_base.hpp b/bfps/cpp/full_code/code_base.hpp
index 6fc29ff113e227a440b5101b9b9d515eb913e75d..08a234b755b01a8fa53c6c50d30a315070af9a1e 100644
--- a/bfps/cpp/full_code/code_base.hpp
+++ b/bfps/cpp/full_code/code_base.hpp
@@ -41,6 +41,7 @@ class code_base
MPI_Comm comm;
std::string simname;
+ int iteration;
bool stop_code_now;
@@ -91,6 +92,10 @@ class code_base
this->time0 = this->time1;
return EXIT_SUCCESS;
}
+
+ virtual int initialize(void) = 0;
+ virtual int main_loop(void) = 0;
+ virtual int finalize(void) = 0;
};
#endif//CODE_BASE_HPP
diff --git a/bfps/cpp/full_code/direct_numerical_simulation.hpp b/bfps/cpp/full_code/direct_numerical_simulation.hpp
index 978f91b2e8c7da389368514b5c5011ada5bdfba5..8050bb045b29acf29d655273f7dff310dd10d0fa 100644
--- a/bfps/cpp/full_code/direct_numerical_simulation.hpp
+++ b/bfps/cpp/full_code/direct_numerical_simulation.hpp
@@ -36,7 +36,7 @@
class direct_numerical_simulation: public code_base
{
public:
- int iteration, checkpoint;
+ int checkpoint;
int checkpoints_per_file;
int niter_out;
int niter_stat;
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.cpp b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..ee1b6f9d8f3787c57a77fa8e50ae7965b1d99ef6
--- /dev/null
+++ b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
@@ -0,0 +1,33 @@
+#include <string>
+#include <cmath>
+#include "native_binary_to_hdf5.hpp"
+#include "scope_timer.hpp"
+
+
+template <typename rnumber>
+int native_binary_to_hdf5<rnumber>::initialize(void)
+{
+ this->read_parameters();
+ this->vec_field = new field<rnumber, FFTW, THREE>(
+ nx, ny, nz,
+ this->comm,
+ DEFAULT_FFTW_FLAG);
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int native_binary_to_hdf5<rnumber>::work_on_current_iteration(void)
+{
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int native_binary_to_hdf5<rnumber>::finalize(void)
+{
+ delete this->vec_field;
+ return EXIT_SUCCESS;
+}
+
+template class native_binary_to_hdf5<float>;
+template class native_binary_to_hdf5<double>;
+
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.hpp b/bfps/cpp/full_code/native_binary_to_hdf5.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..2235e4fca2644e3b49ab979005d007e6a3f4f45d
--- /dev/null
+++ b/bfps/cpp/full_code/native_binary_to_hdf5.hpp
@@ -0,0 +1,60 @@
+/**********************************************************************
+* *
+* Copyright 2017 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 *
+* *
+**********************************************************************/
+
+
+
+#ifndef NATIVE_BINARY_TO_HDF5_HPP
+#define NATIVE_BINARY_TO_HDF5_HPP
+
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <vector>
+#include "base.hpp"
+#include "field.hpp"
+#include "full_code/postprocess.hpp"
+
+template <typename rnumber>
+class native_binary_to_hdf5: public postprocess
+{
+ public:
+
+ field<rnumber, FFTW, THREE> *vec_field;
+
+ native_binary_to_hdf5(
+ const MPI_Comm COMMUNICATOR,
+ const std::string &simulation_name):
+ postprocess(
+ COMMUNICATOR,
+ simulation_name){}
+ virtual ~native_binary_to_hdf5(){}
+
+ int initialize(void);
+ int work_on_current_iteration(void);
+ int finalize(void);
+ virtual int read_parameters(void);
+};
+
+#endif//NATIVE_BINARY_TO_HDF5_HPP
+
diff --git a/bfps/cpp/full_code/postprocess.cpp b/bfps/cpp/full_code/postprocess.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..3c6eed59921afa17c3b7c4fa048df41f42eef350
--- /dev/null
+++ b/bfps/cpp/full_code/postprocess.cpp
@@ -0,0 +1,28 @@
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "scope_timer.hpp"
+#include "hdf5_tools.hpp"
+#include "full_code/postprocess.hpp"
+
+
+int postprocess::main_loop(void)
+{
+ this->start_simple_timer();
+ for (unsigned int iteration_counter = 0;
+ iteration_counter < iteration_list.size();
+ iteration_counter++)
+ {
+ this->iteration = iteration_list[iteration_counter];
+ #ifdef USE_TIMINGOUTPUT
+ const std::string loopLabel = ("postprocess::main_loop-" +
+ std::to_string(this->iteration));
+ TIMEZONE(loopLabel.c_str());
+ #endif
+ this->work_on_current_iteration();
+ this->print_simple_timer(
+ "iteration " + std::to_string(this->iteration));
+ }
+ return EXIT_SUCCESS;
+}
+
diff --git a/bfps/cpp/full_code/postprocess.hpp b/bfps/cpp/full_code/postprocess.hpp
new file mode 100644
index 0000000000000000000000000000000000000000..5d3e578d7dad0975fe47848e1f6224442a219b80
--- /dev/null
+++ b/bfps/cpp/full_code/postprocess.hpp
@@ -0,0 +1,59 @@
+/**********************************************************************
+* *
+* Copyright 2017 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 *
+* *
+**********************************************************************/
+
+
+
+#ifndef POSTPROCESS_HPP
+#define POSTPROCESS_HPP
+
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <vector>
+#include "base.hpp"
+#include "full_code/code_base.hpp"
+
+class postprocess: public code_base
+{
+ public:
+ std::vector<int> iteration_list;
+ hid_t stat_file;
+
+ postprocess(
+ const MPI_Comm COMMUNICATOR,
+ const std::string &simulation_name):
+ code_base(
+ COMMUNICATOR,
+ simulation_name){}
+ virtual ~postprocess(){}
+
+ virtual int initialize(void) = 0;
+ virtual int work_on_current_iteration(void) = 0;
+ virtual int finalize(void) = 0;
+
+ int main_loop(void);
+};
+
+#endif//POSTPROCESS_HPP
+
diff --git a/setup.py b/setup.py
index f9574c84c1e40b4feca307793ece98c191a8cedf..cd2dd02aa8e0828c4484bd6155afef87c2911f60 100644
--- a/setup.py
+++ b/setup.py
@@ -89,6 +89,8 @@ print('This is bfps version ' + VERSION)
### lists of files and MANIFEST.in
src_file_list = ['hdf5_tools',
+ 'full_code/native_binary_to_hdf5',
+ 'full_code/postprocess',
'full_code/code_base',
'full_code/direct_numerical_simulation',
'full_code/NSVE',