WIP implement static velocity field

cpp/full_code/static.cpp

+/******************************************************************************
+*                                                                             *
+*  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>
+#include "static_field.hpp"
+#include "scope_timer.hpp"
+#include "fftw_tools.hpp"
+
+
+template <typename rnumber>
+int static_field<rnumber>::initialize(void)
+{
+    TIMEZONE("static_file::initialize");
+    this->read_iteration();
+    this->read_parameters();
+    if (this->myrank == 0)
+    {
+        // set caching parameters
+        hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
+        herr_t cache_err = H5Pset_cache(fapl, 0, 521, 134217728, 1.0);
+        variable_used_only_in_assert(cache_err);
+        DEBUG_MSG("when setting stat_file cache I got %d\n", cache_err);
+        this->stat_file = H5Fopen(
+                (this->simname + ".h5").c_str(),
+                H5F_ACC_RDWR,
+                fapl);
+    }
+    int data_file_problem;
+    if (this->myrank == 0)
+        data_file_problem = this->grow_file_datasets();
+    MPI_Bcast(&data_file_problem, 1, MPI_INT, 0, this->comm);
+    if (data_file_problem > 0)
+    {
+        std::cerr <<
+            data_file_problem <<
+            " problems growing file datasets.\ntrying to exit now." <<
+            std::endl;
+        return EXIT_FAILURE;
+    }
+   
+    this->vorticity = new field<rnumber, FFTW, THREE>(
+            nx, ny, nz,
+            this->comm,
+	    fftw_planner_string_to_flag[this->fftw_plan_rigor]);
+
+    this->stat_vel = new field<rnumber, FFTW, THREE>(
+            nx, ny, nz,
+            this->comm,
+	    fftw_planner_string_to_flag[this->fftw_plan_rigor]);
+    //reading initial field which is either default or a specified source field
+    this->vorticity->io(
+	    this->simname + std::string(".h5"),
+	    "vorticity",
+	    this->iteration,
+	    true);
+    this->kk = new kspace<FFTW, SMOOTH>(
+            this->vorticity->clayout, this->dkx, this->dky, this->dkz);
+
+    // compute the velocity field and store 
+    invert_curl(
+        this->kk,
+        this->vorticity,
+        stat_vel_field);
+    // transform velocity field to real space
+    this->stat_vel->ift();
+
+    return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE<rnumber>::step(void)
+{
+   return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE<rnumber>::write_checkpoint(void)
+{
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE<rnumber>::finalize(void)
+{
+    TIMEZONE("NSVE::finalize");
+    if (this->myrank == 0)
+        H5Fclose(this->stat_file);
+    delete this->vorticity;
+    delete this->stat_vel;
+    delete this->kk;
+    return EXIT_SUCCESS;
+}
+
+/** \brief Compute standard statistics for velocity and vorticity fields.
+ *
+ *  IMPORTANT: at the end of this subroutine, `this->fs->cvelocity` contains
+ *  the Fourier space representation of the velocity field, and
+ *  `this->tmp_vec_field` contains the real space representation of the
+ *  velocity field.
+ *  This behavior is relied upon in the `NSVEparticles` class, so please
+ *  don't break it.
+ */
+
+template <typename rnumber>
+int NSVE<rnumber>::do_stats()
+{
+   return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE<rnumber>::read_parameters(void)
+{
+  TIMEZONE("NSVE::read_parameters");
+    this->direct_numerical_simulation::read_parameters();
+    hid_t parameter_file = H5Fopen((this->simname + ".h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+    this->fftw_plan_rigor = hdf5_tools::read_string(parameter_file, "parameters/fftw_plan_rigor");
+    H5Fclose(parameter_file);
+    return EXIT_SUCCESS;
+}
+
+template class NSVE<float>;
+template class NSVE<double>;
+

cpp/full_code/static.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 STATIC_FIELD_HPP
+#define STATIC_FIELD_HPP
+
+
+
+#include <cstdlib>
+#include "base.hpp"
+#include "full_code/direct_numerical_simulation.hpp"
+
+template <typename rnumber>
+class static_field: public direct_numerical_simulation
+{
+    public:
+
+        /* parameters that are read in read_parameters */
+        std::string fftw_plan_rigor;
+
+        /* other stuff */
+        kspace<FFTW, SMOOTH> *kk;
+        field<rnumber, FFTW, THREE> *velocity;
+        field<rnumber, FFTW, THREE> *stat_vel;
+
+
+        static_field(
+                const MPI_Comm COMMUNICATOR,
+                const std::string &simulation_name):
+            direct_numerical_simulation(
+                    COMMUNICATOR,
+                    simulation_name){}
+        ~static_field(){}
+
+        int initialize(void);
+        int step(void);
+        int finalize(void);
+
+        virtual int read_parameters(void);
+        int write_checkpoint(void);
+        int do_stats(void);
+};
+
+#endif//STATIC_FIELD_HPP
+