From 6df4f5ac20ebef5c315a701e2088e32edd677508 Mon Sep 17 00:00:00 2001
From: Cristian C Lalescu <Cristian.Lalescu@ds.mpg.de>
Date: Tue, 3 Apr 2018 17:45:35 +0200
Subject: [PATCH] add test interpolation code that compiles
---
bfps/cpp/full_code/test_interpolation.cpp | 162 ++++++++++++++++++++++
bfps/cpp/full_code/test_interpolation.hpp | 53 +++++++
setup.py | 1 +
3 files changed, 216 insertions(+)
create mode 100644 bfps/cpp/full_code/test_interpolation.cpp
create mode 100644 bfps/cpp/full_code/test_interpolation.hpp
diff --git a/bfps/cpp/full_code/test_interpolation.cpp b/bfps/cpp/full_code/test_interpolation.cpp
new file mode 100644
index 00000000..e93cd3eb
--- /dev/null
+++ b/bfps/cpp/full_code/test_interpolation.cpp
@@ -0,0 +1,162 @@
+#include "full_code/test_interpolation.hpp"
+
+
+template <typename rnumber>
+int test_interpolation<rnumber>::read_parameters(void)
+{
+ this->test::read_parameters();
+ hid_t parameter_file;
+ hid_t dset, memtype, space;
+ char fname[256];
+ hsize_t dims[1];
+ char *string_data;
+ sprintf(fname, "%s.h5", this->simname.c_str());
+ this->nparticles = hdf5_tools::read_value<int>(
+ parameter_file, "/parameters/nparticles");
+ this->tracers0_integration_steps = hdf5_tools::read_value<int>(
+ parameter_file, "/parameters/tracers0_integration_steps");
+ this->tracers0_neighbours = hdf5_tools::read_value<int>(
+ parameter_file, "/parameters/tracers0_neighbours");
+ this->tracers0_smoothness = hdf5_tools::read_value<int>(
+ parameter_file, "/parameters/tracers0_smoothness");
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int test_interpolation<rnumber>::initialize(void)
+{
+ this->test::initialize();
+
+ this->vorticity = new field<rnumber, FFTW, THREE>(
+ this->nx, this->ny, this->nz,
+ this->comm,
+ DEFAULT_FFTW_FLAG);
+
+ this->velocity = new field<rnumber, FFTW, THREE>(
+ this->nx, this->ny, this->nz,
+ this->comm,
+ DEFAULT_FFTW_FLAG);
+
+ this->nabla_u = new field<rnumber, FFTW, THREExTHREE>(
+ this->nx, this->ny, this->nz,
+ this->comm,
+ DEFAULT_FFTW_FLAG);
+
+ this->kk = new kspace<FFTW, SMOOTH>(
+ this->vorticity->clayout, this->dkx, this->dky, this->dkz);
+
+ if (this->myrank == 0)
+ {
+ hid_t stat_file = H5Fopen(
+ (this->simname + std::string(".h5")).c_str(),
+ H5F_ACC_RDWR,
+ H5P_DEFAULT);
+ this->kk->store(stat_file);
+ H5Fclose(stat_file);
+ }
+
+ this->ps = particles_system_builder(
+ this->velocity, // (field object)
+ this->kk, // (kspace object, contains dkx, dky, dkz)
+ this->tracers0_integration_steps, // to check coherency between parameters and hdf input file (nb rhs)
+ (long long int)nparticles, // to check coherency between parameters and hdf input file
+ this->simname + "_input.h5", // particles input filename
+ std::string("/tracers0/state/0"), // dataset name for initial input
+ std::string("/tracers0/rhs/0") , // dataset name for initial input
+ this->tracers0_neighbours, // parameter (interpolation no neighbours)
+ this->tracers0_smoothness, // parameter
+ this->comm,
+ 1);
+ this->particles_output_writer_mpi = new particles_output_hdf5<
+ long long int, double, 3>(
+ MPI_COMM_WORLD,
+ "tracers0",
+ nparticles,
+ this->tracers0_integration_steps);
+ this->particles_sample_writer_mpi = new particles_output_sampling_hdf5<
+ long long int, double, 3>(
+ MPI_COMM_WORLD,
+ this->ps->getGlobalNbParticles(),
+ (this->simname + "_output.h5"),
+ "tracers0",
+ "position/0");
+
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int test_interpolation<rnumber>::finalize(void)
+{
+ delete this->nabla_u;
+ delete this->velocity;
+ delete this->vorticity;
+ this->ps.release();
+ this->test::finalize();
+ delete this->kk;
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int test_interpolation<rnumber>::do_work()
+{
+ std::string fname = this->simname + std::string("_input.h5");
+ // read vorticity field
+ this->vorticity->io(
+ fname,
+ "vorticity",
+ 0, true);
+
+ // compute velocity
+ invert_curl(this->kk, this->vorticity, this->velocity);
+
+ // compute velocity gradient
+ compute_gradient(this->kk, this->velocity, this->nabla_u);
+
+ // go to real space
+ this->vorticity->ift();
+ this->velocity->ift();
+ this->nabla_u->ift();
+
+ // allocate interpolation arrays
+ std::unique_ptr<double[]> p3data(new double[3*this->ps->getLocalNbParticles()]);
+ std::unique_ptr<double[]> p9data(new double[9*this->ps->getLocalNbParticles()]);
+
+ /// sample velocity at particles' position
+ this->ps->sample_compute_field(*this->velocity, p3data.get());
+ this->particles_sample_writer_mpi->template save_dataset<3>(
+ "tracers0",
+ "velocity",
+ this->ps->getParticlesState(),
+ &p9data,
+ this->ps->getParticlesIndexes(),
+ this->ps->getLocalNbParticles(),
+ this->ps->get_step_idx()-1);
+ /// sample vorticity at particles' position
+ this->ps->sample_compute_field(*this->vorticity, p3data.get());
+ this->particles_sample_writer_mpi->template save_dataset<3>(
+ "tracers0",
+ "vorticity",
+ this->ps->getParticlesState(),
+ &p9data,
+ this->ps->getParticlesIndexes(),
+ this->ps->getLocalNbParticles(),
+ this->ps->get_step_idx()-1);
+ /// sample velocity gradient at particles' position
+ this->ps->sample_compute_field(*this->nabla_u, p9data.get());
+ this->particles_sample_writer_mpi->template save_dataset<9>(
+ "tracers0",
+ "velocity_gradient",
+ this->ps->getParticlesState(),
+ &p9data,
+ this->ps->getParticlesIndexes(),
+ this->ps->getLocalNbParticles(),
+ this->ps->get_step_idx()-1);
+
+ // no need to deallocate because we used "unique_ptr"
+ return EXIT_SUCCESS;
+}
+
+template class test_interpolation<float>;
+template class test_interpolation<double>;
+
diff --git a/bfps/cpp/full_code/test_interpolation.hpp b/bfps/cpp/full_code/test_interpolation.hpp
new file mode 100644
index 00000000..e8be247c
--- /dev/null
+++ b/bfps/cpp/full_code/test_interpolation.hpp
@@ -0,0 +1,53 @@
+#ifndef TEST_INTERPOLATION_HPP
+#define TEST_INTERPOLATION_HPP
+
+
+
+#include <cstdlib>
+#include "base.hpp"
+#include "kspace.hpp"
+#include "full_code/test.hpp"
+#include "particles/particles_system_builder.hpp"
+#include "particles/particles_output_hdf5.hpp"
+#include "particles/particles_sampling.hpp"
+
+/** \brief Interpolation tester.
+ *
+ */
+
+template <typename rnumber>
+class test_interpolation: public test
+{
+ public:
+ int nparticles;
+ int tracers0_integration_steps;
+ int tracers0_neighbours;
+ int tracers0_smoothness;
+
+ std::unique_ptr<abstract_particles_system<long long int, double>> ps;
+
+ particles_output_hdf5<long long int, double,3> *particles_output_writer_mpi;
+ particles_output_sampling_hdf5<long long int, double, 3> *particles_sample_writer_mpi;
+
+ field<rnumber, FFTW, THREE> *velocity, *vorticity;
+ field<rnumber, FFTW, THREExTHREE> *nabla_u;
+
+ kspace<FFTW, SMOOTH> *kk;
+
+ test_interpolation(
+ const MPI_Comm COMMUNICATOR,
+ const std::string &simulation_name):
+ test(
+ COMMUNICATOR,
+ simulation_name){}
+ ~test_interpolation(){}
+
+ int initialize(void);
+ int do_work(void);
+ int finalize(void);
+
+ int read_parameters(void);
+};
+
+#endif//TEST_INTERPOLATION_HPP
+
diff --git a/setup.py b/setup.py
index 9511a92d..350bccf2 100644
--- a/setup.py
+++ b/setup.py
@@ -94,6 +94,7 @@ src_file_list = ['full_code/NSVEcomplex_particles',
'full_code/filter_test',
'full_code/field_test',
'full_code/field_output_test',
+ 'full_code/test_interpolation',
'hdf5_tools',
'full_code/get_rfields',
'full_code/resize',
--
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