add methods to sample to file

CMakeLists.txt

@@ -472,7 +472,7 @@ if (BUILD_TESTING)
     ### basic particle functionality
     add_test(
         NAME test_tracer_set
-        COMMAND turtle TEST test_tracer_set  -n 32 --np 2 --ntpp 2
+        COMMAND turtle TEST test_tracer_set  -n 32 --np 2 --ntpp 2 --simname tracer_set_testsim
         WORKING_DIRECTORY ${TEST_OUTPUT_DIRECTORY})
     ### compare DNS output to stored results
     add_test(

cpp/particles/interpolation/abstract_particle_set.hpp

@@ -32,6 +32,7 @@
 #include <memory>
 #include "field.hpp"
 #include "particles/p2p/p2p_distr_mpi.hpp"
+#include "particles/particles_sampling.hpp"
 
 
 
@@ -154,6 +155,70 @@ class abstract_particle_set
                     this->getParticleIndex());
             return EXIT_SUCCESS;
         }
+
+        template <typename field_rnumber,
+                  field_backend be,
+                  field_components fc>
+        int sample(
+                field<field_rnumber, be, fc> *field_to_sample,
+                particles_output_sampling_hdf5<partsize_t, particle_rnumber, 3> *particle_sample_writer,
+                const std::string species_name,
+                const std::string field_name,
+                const int iteration)
+        {
+            // set file layout
+            particle_sample_writer->setParticleFileLayout(this->getParticleFileLayout());
+            // allocate position array
+            std::unique_ptr<particle_rnumber[]> xx = this->extractFromParticleState(0, 3);
+            // allocate temporary array
+            std::unique_ptr<particle_rnumber[]> pdata(new particle_rnumber[ncomp(fc)*this->getLocalNumberOfParticles()]);
+            // clean up temporary array
+            std::fill_n(pdata.get(), ncomp(fc)*this->getLocalNumberOfParticles(), 0);
+            this->sample(*field_to_sample, pdata.get());
+            particle_sample_writer->template save_dataset<ncomp(fc)>(
+                    species_name,
+                    field_name,
+                    xx.get(),
+                    &pdata,
+                    this->getParticleIndex(),
+                    this->getLocalNumberOfParticles(),
+                    iteration);
+            // deallocate temporary array
+            delete[] pdata.release();
+            // deallocate position array
+            delete[] xx.release();
+            return EXIT_SUCCESS;
+        }
+
+        int sample_state_triple(
+                const int i0,
+                particles_output_sampling_hdf5<partsize_t, particle_rnumber, 3> *particle_sample_writer,
+                const std::string species_name,
+                const std::string field_name,
+                const int iteration)
+        {
+            assert(i0 >= 0);
+            assert(i0 <= this->getStateSize()-3);
+            // set file layout
+            particle_sample_writer->setParticleFileLayout(this->getParticleFileLayout());
+            // allocate position array
+            std::unique_ptr<particle_rnumber[]> xx = this->extractFromParticleState(0, 3);
+            // allocate temporary array
+            std::unique_ptr<particle_rnumber[]> yy = this->extractFromParticleState(i0, i0+3);
+            particle_sample_writer->template save_dataset<3>(
+                    species_name,
+                    field_name,
+                    xx.get(),
+                    &yy,
+                    this->getParticleIndex(),
+                    this->getLocalNumberOfParticles(),
+                    iteration);
+            // deallocate temporary array
+            delete[] yy.release();
+            // deallocate position array
+            delete[] xx.release();
+            return EXIT_SUCCESS;
+        }
 };
 
 #endif//ABSTRACT_PARTICLE_SET_HPP