WIP: change base class hierarchy

I want to properly accomodate postprocessing codes, so I need something
more general than `direct_numerical_simulation`.

bfps/cpp/full_code/code_base.cpp

+#include "code_base.hpp"
+#include "scope_timer.hpp"
+
+code_base::code_base(
+        const MPI_Comm COMMUNICATOR,
+        const std::string &simulation_name):
+    comm(COMMUNICATOR),
+    simname(simulation_name)
+{
+    MPI_Comm_rank(this->comm, &this->myrank);
+    MPI_Comm_size(this->comm, &this->nprocs);
+    this->stop_code_now = false;
+}
+
+int code_base::check_stopping_condition(void)
+{
+    if (myrank == 0)
+    {
+        std::string fname = (
+                std::string("stop_") +
+                std::string(this->simname));
+        {
+            struct stat file_buffer;
+            this->stop_code_now = (
+                    stat(fname.c_str(), &file_buffer) == 0);
+        }
+    }
+    MPI_Bcast(
+            &this->stop_code_now,
+            1,
+            MPI_C_BOOL,
+            0,
+            MPI_COMM_WORLD);
+    return EXIT_SUCCESS;
+}
+

bfps/cpp/full_code/code_base.hpp

+/**********************************************************************
+*                                                                     *
+*  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 CODE_BASE_HPP
+#define CODE_BASE_HPP
+
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include "base.hpp"
+
+class code_base
+{
+    private:
+        clock_t time0, time1;
+    public:
+        int myrank, nprocs;
+        MPI_Comm comm;
+
+        std::string simname;
+
+        bool stop_code_now;
+
+        int nx;
+        int ny;
+        int nz;
+        int dealias_type;
+        double dkx;
+        double dky;
+        double dkz;
+
+        code_base(
+                const MPI_Comm COMMUNICATOR,
+                const std::string &simulation_name);
+        virtual ~code_base(){}
+
+        int check_stopping_condition(void);
+
+        int start_simple_timer(void)
+        {
+            this->time0 = clock();
+            return EXIT_SUCCESS;
+        }
+
+        int print_simple_timer(void)
+        {
+            this->time1 = clock();
+            double local_time_difference = ((
+                    (unsigned int)(this->time1 - this->time0)) /
+                    ((double)CLOCKS_PER_SEC));
+            double time_difference = 0.0;
+            MPI_Allreduce(
+                    &local_time_difference,
+                    &time_difference,
+                    1,
+                    MPI_DOUBLE,
+                    MPI_SUM,
+                    MPI_COMM_WORLD);
+            if (this->myrank == 0)
+                std::cout << "iteration " << this->iteration <<
+                             " took " << time_difference/this->nprocs <<
+                             " seconds" << std::endl;
+            if (this->myrank == 0)
+                std::cerr << "iteration " << this->iteration <<
+                             " took " << time_difference/this->nprocs <<
+                             " seconds" << std::endl;
+            this->time0 = this->time1;
+            return EXIT_SUCCESS;
+        }
+};
+
+#endif//CODE_BASE_HPP
+

bfps/cpp/full_code/direct_numerical_simulation.cpp

@@ -3,64 +3,15 @@
 #include <sys/stat.h>
 #include "direct_numerical_simulation.hpp"
 #include "scope_timer.hpp"
-
-int grow_single_dataset(hid_t dset, int tincrement)
-{
-    int ndims;
-    hsize_t space;
-    space = H5Dget_space(dset);
-    ndims = H5Sget_simple_extent_ndims(space);
-    hsize_t *dims = new hsize_t[ndims];
-    H5Sget_simple_extent_dims(space, dims, NULL);
-    dims[0] += tincrement;
-    H5Dset_extent(dset, dims);
-    H5Sclose(space);
-    delete[] dims;
-    return EXIT_SUCCESS;
-}
-
-herr_t grow_dataset_visitor(
-    hid_t o_id,
-    const char *name,
-    const H5O_info_t *info,
-    void *op_data)
-{
-    if (info->type == H5O_TYPE_DATASET)
-    {
-        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
-        grow_single_dataset(dset, *((int*)(op_data)));
-        H5Dclose(dset);
-    }
-    return EXIT_SUCCESS;
-}
-
-direct_numerical_simulation::direct_numerical_simulation(
-        const MPI_Comm COMMUNICATOR,
-        const std::string &simulation_name):
-    comm(COMMUNICATOR),
-    simname(simulation_name)
-{
-    MPI_Comm_rank(this->comm, &this->myrank);
-    MPI_Comm_size(this->comm, &this->nprocs);
-    this->stop_code_now = false;
-}
+#include "hdf5_tools.hpp"
 
 
 int direct_numerical_simulation::grow_file_datasets()
 {
-    int file_problems = 0;
-
-    hid_t group;
-    group = H5Gopen(this->stat_file, "/statistics", H5P_DEFAULT);
-    int tincrement = this->niter_todo / this->niter_stat;
-    H5Ovisit(
-            group,
-            H5_INDEX_NAME,
-            H5_ITER_NATIVE,
-            grow_dataset_visitor,
-            &tincrement);
-    H5Gclose(group);
-    return file_problems;
+    return hdf5_tools::grow_file_datasets(
+            this->stat_file,
+            "statistics",
+            this->niter_todo / this->niter_stat);
 }
 
 int direct_numerical_simulation::read_iteration(void)
@@ -164,25 +115,3 @@ int direct_numerical_simulation::main_loop(void)
     return EXIT_SUCCESS;
 }
 
-int direct_numerical_simulation::check_stopping_condition(void)
-{
-    if (myrank == 0)
-    {
-        std::string fname = (
-                std::string("stop_") +
-                std::string(this->simname));
-        {
-            struct stat file_buffer;
-            this->stop_code_now = (
-                    stat(fname.c_str(), &file_buffer) == 0);
-        }
-    }
-    MPI_Bcast(
-            &this->stop_code_now,
-            1,
-            MPI_C_BOOL,
-            0,
-            MPI_COMM_WORLD);
-    return EXIT_SUCCESS;
-}
-

bfps/cpp/full_code/direct_numerical_simulation.hpp

@@ -31,45 +31,24 @@
 #include <sys/types.h>
 #include <sys/stat.h>
 #include "base.hpp"
+#include "full_code/code_base.hpp"
 
-int grow_single_dataset(hid_t dset, int tincrement);
-
-herr_t grow_dataset_visitor(
-    hid_t o_id,
-    const char *name,
-    const H5O_info_t *info,
-    void *op_data);
-
-class direct_numerical_simulation
+class direct_numerical_simulation: public code_base
 {
-    private:
-        clock_t time0, time1;
     public:
-        int myrank, nprocs;
-        MPI_Comm comm;
-
-        std::string simname;
-
         int iteration, checkpoint;
         int checkpoints_per_file;
         int niter_out;
         int niter_stat;
         int niter_todo;
         hid_t stat_file;
-        bool stop_code_now;
-
-
-        int nx;
-        int ny;
-        int nz;
-        int dealias_type;
-        double dkx;
-        double dky;
-        double dkz;
 
         direct_numerical_simulation(
                 const MPI_Comm COMMUNICATOR,
-                const std::string &simulation_name);
+                const std::string &simulation_name):
+            code_base(
+                    COMMUNICATOR,
+                    simulation_name){}
         virtual ~direct_numerical_simulation(){}
 
         virtual int write_checkpoint(void) = 0;
@@ -82,39 +61,6 @@ class direct_numerical_simulation
         int read_iteration(void);
         int write_iteration(void);
         int grow_file_datasets(void);
-        int check_stopping_condition(void);
-
-        int start_simple_timer(void)
-        {
-            this->time0 = clock();
-            return EXIT_SUCCESS;
-        }
-
-        int print_simple_timer(void)
-        {
-            this->time1 = clock();
-            double local_time_difference = ((
-                    (unsigned int)(this->time1 - this->time0)) /
-                    ((double)CLOCKS_PER_SEC));
-            double time_difference = 0.0;
-            MPI_Allreduce(
-                    &local_time_difference,
-                    &time_difference,
-                    1,
-                    MPI_DOUBLE,
-                    MPI_SUM,
-                    MPI_COMM_WORLD);
-            if (this->myrank == 0)
-                std::cout << "iteration " << this->iteration <<
-                             " took " << time_difference/this->nprocs <<
-                             " seconds" << std::endl;
-            if (this->myrank == 0)
-                std::cerr << "iteration " << this->iteration <<
-                             " took " << time_difference/this->nprocs <<
-                             " seconds" << std::endl;
-            this->time0 = this->time1;
-            return EXIT_SUCCESS;
-        }
 };
 
 #endif//DIRECT_NUMERICAL_SIMULATION_HPP

bfps/cpp/full_code/hdf5_tools.cpp

+#include "hdf5_tools.hpp"
+
+int hdf5_tools::grow_single_dataset(hid_t dset, int tincrement)
+{
+    int ndims;
+    hsize_t space;
+    space = H5Dget_space(dset);
+    ndims = H5Sget_simple_extent_ndims(space);
+    hsize_t *dims = new hsize_t[ndims];
+    H5Sget_simple_extent_dims(space, dims, NULL);
+    dims[0] += tincrement;
+    H5Dset_extent(dset, dims);
+    H5Sclose(space);
+    delete[] dims;
+    return EXIT_SUCCESS;
+}
+
+herr_t hdf5_tools::grow_dataset_visitor(
+    hid_t o_id,
+    const char *name,
+    const H5O_info_t *info,
+    void *op_data)
+{
+    if (info->type == H5O_TYPE_DATASET)
+    {
+        hsize_t dset = H5Dopen(o_id, name, H5P_DEFAULT);
+        grow_single_dataset(dset, *((int*)(op_data)));
+        H5Dclose(dset);
+    }
+    return EXIT_SUCCESS;
+}
+
+
+int hdf5_tools::grow_file_datasets(
+        const hid_t stat_file,
+        const std::string group_name,
+        const int tincrement)
+{
+    int file_problems = 0;
+
+    hid_t group;
+    group = H5Gopen(stat_file, group_name.c_str(), H5P_DEFAULT);
+    H5Ovisit(
+            group,
+            H5_INDEX_NAME,
+            H5_ITER_NATIVE,
+            grow_dataset_visitor,
+            &tincrement);
+    H5Gclose(group);
+    return file_problems;
+}
+

bfps/cpp/full_code/hdf5_tools.hpp

+/**********************************************************************
+*                                                                     *
+*  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 HDF5_TOOLS_HPP
+#define HDF5_TOOLS_HPP
+
+#include "base.hpp"
+
+namespace hdf5_tools
+{
+    int grow_single_dataset(
+            hid_t dset,
+            int tincrement);
+
+    herr_t grow_dataset_visitor(
+        hid_t o_id,
+        const char *name,
+        const H5O_info_t *info,
+        void *op_data);
+
+    int grow_file_datasets(
+            const hid_t stat_file,
+            const std::string group_name,
+            const int tincrement);
+}
+
+#endif//HDF5_TOOLS_HPP
+

bfps/cpp/full_code/ppNSVE.cpp

@@ -35,6 +35,36 @@ int NSVEparticles<rnumber>::do_stats()
     return EXIT_SUCCESS;
 }
 
+template <typename rnumber>
+int direct_numerical_simulation::main_loop(void)
+{
+    this->start_simple_timer();
+    int max_iter = (this->iteration + this->niter_todo -
+                    (this->iteration % this->niter_todo));
+    for (; this->iteration < max_iter;)
+    {
+    #ifdef USE_TIMINGOUTPUT
+        const std::string loopLabel = ("code::main_start::loop-" +
+                                       std::to_string(this->iteration));
+        TIMEZONE(loopLabel.c_str());
+    #endif
+        this->do_stats();
+
+        this->step();
+        if (this->iteration % this->niter_out == 0)
+            this->write_checkpoint();
+        this->check_stopping_condition();
+        if (this->stop_code_now)
+            break;
+        this->print_simple_timer();
+    }
+    this->do_stats();
+    this->print_simple_timer();
+    if (this->iteration % this->niter_out != 0)
+        this->write_checkpoint();
+    return EXIT_SUCCESS;
+}
+
 template class NSVEparticles<float>;
 template class NSVEparticles<double>;
 

bfps/cpp/full_code/ppNSVE.hpp

@@ -39,8 +39,6 @@ template <typename rnumber>
 class ppNSVE: public NSVE<rnumber>
 {
     public:
-
-
         ppNSVE(
                 const MPI_Comm COMMUNICATOR,
                 const std::string &simulation_name):

setup.py

@@ -90,6 +90,8 @@ print('This is bfps version ' + VERSION)
 ### lists of files and MANIFEST.in
 src_file_list = ['full_code/ppNSVE',
                  'field_binary_IO',
+                 'full_code/hdf5_tools',
+                 'full_code/code_base',
                  'full_code/direct_numerical_simulation',
                  'full_code/NSVE',
                  'full_code/NSVEparticles',