From ff410a694f3867bd1a75ff862ccfd374117bf0c9 Mon Sep 17 00:00:00 2001
From: Berenger Bramas <bbramas@mpcdf.mpg.de>
Date: Fri, 19 May 2017 12:38:06 +0200
Subject: [PATCH] Update to have nparticles from system
---
bfps/cpp/full_code/NSVEparticles.cpp | 4 +-
.../particles/abstract_particles_system.hpp | 4 ++
.../particles_output_sampling_hdf5.hpp | 2 +-
bfps/cpp/particles/particles_sampling.hpp | 37 +++++++++----------
bfps/cpp/particles/particles_system.hpp | 12 +++++-
.../particles/particles_system_builder.hpp | 1 +
6 files changed, 37 insertions(+), 23 deletions(-)
diff --git a/bfps/cpp/full_code/NSVEparticles.cpp b/bfps/cpp/full_code/NSVEparticles.cpp
index 35cbf47d..aa655275 100644
--- a/bfps/cpp/full_code/NSVEparticles.cpp
+++ b/bfps/cpp/full_code/NSVEparticles.cpp
@@ -74,8 +74,8 @@ int NSVEparticles<rnumber>::do_stats()
// sample_from_particles_system(*this->fs->cvelocity,// field to save TODO
// this->ps,
// 0, // hdf5 datagroup TODO
-// "TODO", // dataset basename TODO
-// this->particles_output_writer_mpi->getTotalNbParticles());
+// "TODO" // dataset basename TODO
+// );
// }
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/particles/abstract_particles_system.hpp b/bfps/cpp/particles/abstract_particles_system.hpp
index 6961eabc..1c8592f3 100644
--- a/bfps/cpp/particles/abstract_particles_system.hpp
+++ b/bfps/cpp/particles/abstract_particles_system.hpp
@@ -32,8 +32,12 @@ public:
virtual partsize_t getLocalNbParticles() const = 0;
+ virtual partsize_t getGlobalNbParticles() const = 0;
+
virtual int getNbRhs() const = 0;
+ virtual int get_step_idx() const = 0;
+
//- Not generic to enable sampling begin
virtual void sample_compute_field(const field<float, FFTW, ONE>& sample_field,
real_number sample_rhs[]) = 0;
diff --git a/bfps/cpp/particles/particles_output_sampling_hdf5.hpp b/bfps/cpp/particles/particles_output_sampling_hdf5.hpp
index 7e9a54dd..bcf734d6 100644
--- a/bfps/cpp/particles/particles_output_sampling_hdf5.hpp
+++ b/bfps/cpp/particles/particles_output_sampling_hdf5.hpp
@@ -60,7 +60,7 @@ public:
{
assert(size_particle_rhs >= 0);
const hsize_t datacount[3] = {hsize_t(Parent::getNbRhs()),
- hsize_t(Parent::total_nb_particles),
+ hsize_t(Parent::getTotalNbParticles()),
hsize_t(size_particle_rhs)};
hid_t dataspace = H5Screate_simple(3, datacount, NULL);
assert(dataspace >= 0);
diff --git a/bfps/cpp/particles/particles_sampling.hpp b/bfps/cpp/particles/particles_sampling.hpp
index cc987f69..c71c1a01 100644
--- a/bfps/cpp/particles/particles_sampling.hpp
+++ b/bfps/cpp/particles/particles_sampling.hpp
@@ -15,25 +15,24 @@ template <class partsize_t, class particles_rnumber, class rnumber, field_backen
void sample_from_particles_system(const field<rnumber, be, fc>& in_field, // a pointer to a field<rnumber, FFTW, fc>
std::unique_ptr<abstract_particles_system<partsize_t, particles_rnumber>>& ps, // a pointer to an particles_system<double>
hid_t gid, // an hid_t identifying an HDF5 group
- const std::string& fname,
- const partsize_t totalNbParticles){
-// const int size_particle_rhs = ncomp(fc);
-// const partsize_t nb_particles = ps->getLocalNbParticles();
-// std::unique_ptr<particles_rnumber[]> sample_rhs(new particles_rnumber[size_particle_rhs*nb_particles]);
-
-// ps->sample_compute_field(in_field, sample_rhs.get());
-
-// const std::string datasetname = fname + std::string("/") + std::to_string(ps->step_idx);
-
-// particles_output_sampling_hdf5<partsize_t, particles_rnumber, 3, size_particle_rhs> outputclass(MPI_COMM_WORLD,
-// totalNbParticles,
-// gid,
-// datasetname);
-// outputclass.save(ps->getParticlesPositions(),
-// &sample_rhs,
-// ps->getParticlesIndexes(),
-// ps->getLocalNbParticles(),
-// in_field->iteration);
+ const std::string& fname){
+ const int size_particle_rhs = ncomp(fc);
+ const partsize_t nb_particles = ps->getLocalNbParticles();
+ std::unique_ptr<particles_rnumber[]> sample_rhs(new particles_rnumber[size_particle_rhs*nb_particles]);
+
+ ps->sample_compute_field(in_field, sample_rhs.get());
+
+ const std::string datasetname = fname + std::string("/") + std::to_string(ps->get_step_idx());
+
+ particles_output_sampling_hdf5<partsize_t, particles_rnumber, 3, size_particle_rhs> outputclass(MPI_COMM_WORLD,
+ ps->getGlobalNbParticles(),
+ gid,
+ datasetname);
+ outputclass.save(ps->getParticlesPositions(),
+ &sample_rhs,
+ ps->getParticlesIndexes(),
+ ps->getLocalNbParticles(),
+ ps->get_step_idx());
}
#endif
diff --git a/bfps/cpp/particles/particles_system.hpp b/bfps/cpp/particles/particles_system.hpp
index 1e5ec2dd..02767a8b 100644
--- a/bfps/cpp/particles/particles_system.hpp
+++ b/bfps/cpp/particles/particles_system.hpp
@@ -42,6 +42,7 @@ class particles_system : public abstract_particles_system<partsize_t, real_numbe
std::unique_ptr<real_number[]> my_particles_positions;
std::unique_ptr<partsize_t[]> my_particles_positions_indexes;
partsize_t my_nb_particles;
+ const partsize_t total_nb_particles;
std::vector<std::unique_ptr<real_number[]>> my_particles_rhs;
int step_idx;
@@ -55,6 +56,7 @@ public:
const std::array<size_t,3>& in_local_field_offset,
const field_class& in_field,
MPI_Comm in_mpi_com,
+ const partsize_t in_total_nb_particles,
const int in_current_iteration = 1)
: mpi_com(in_mpi_com),
current_partition_interval({in_local_field_offset[IDX_Z], in_local_field_offset[IDX_Z] + in_local_field_dims[IDX_Z]}),
@@ -67,7 +69,7 @@ public:
default_field(in_field),
spatial_box_width(in_spatial_box_width), spatial_partition_width(in_spatial_partition_width),
my_spatial_low_limit(in_my_spatial_low_limit), my_spatial_up_limit(in_my_spatial_up_limit),
- my_nb_particles(0), step_idx(in_current_iteration){
+ my_nb_particles(0), total_nb_particles(in_total_nb_particles), step_idx(in_current_iteration){
current_my_nb_particles_per_partition.reset(new partsize_t[partition_interval_size]);
current_offset_particles_for_partition.reset(new partsize_t[partition_interval_size+1]);
@@ -190,6 +192,10 @@ public:
step_idx += 1;
}
+ int get_step_idx() const final {
+ return step_idx;
+ }
+
void shift_rhs_vectors() final {
if(my_particles_rhs.size()){
std::unique_ptr<real_number[]> next_current(std::move(my_particles_rhs.back()));
@@ -226,6 +232,10 @@ public:
return my_nb_particles;
}
+ partsize_t getGlobalNbParticles() const final {
+ return total_nb_particles;
+ }
+
int getNbRhs() const final {
return int(my_particles_rhs.size());
}
diff --git a/bfps/cpp/particles/particles_system_builder.hpp b/bfps/cpp/particles/particles_system_builder.hpp
index 321f6d20..7a2d49c0 100644
--- a/bfps/cpp/particles/particles_system_builder.hpp
+++ b/bfps/cpp/particles/particles_system_builder.hpp
@@ -206,6 +206,7 @@ struct particles_system_build_container {
local_field_offset,
(*fs_field),
mpi_comm,
+ nparticles,
in_current_iteration);
// Load particles from hdf5
--
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