From 89a5e91521b38b64cb51ea8acf7b8fb41da74137 Mon Sep 17 00:00:00 2001
From: Chichi Lalescu <chichilalescu@gmail.com>
Date: Sat, 8 Sep 2018 21:52:03 +0200
Subject: [PATCH] partial move read_parameters to cpp files
NSVEparticles test works.
---
bfps/DNS.py | 20 -------------
bfps/cpp/full_code/NSVE.cpp | 22 ++++++++++++++
bfps/cpp/full_code/NSVEparticles.cpp | 14 +++++++++
bfps/cpp/full_code/code_base.cpp | 14 +++++++++
bfps/cpp/full_code/code_base.hpp | 1 +
.../full_code/direct_numerical_simulation.cpp | 11 +++++++
.../full_code/direct_numerical_simulation.hpp | 1 +
setup.py | 29 +++++++------------
8 files changed, 74 insertions(+), 38 deletions(-)
diff --git a/bfps/DNS.py b/bfps/DNS.py
index c7d77956..e6ef006a 100644
--- a/bfps/DNS.py
+++ b/bfps/DNS.py
@@ -116,26 +116,6 @@ class DNS(_code):
with open(self.name + '.cpp', 'w') as outfile:
outfile.write(self.version_message + '\n\n')
outfile.write(self.includes + '\n\n')
- outfile.write(
- self.cread_pars(
- template_class = '{0}<rnumber>::'.format(self.dns_type),
- template_prefix = 'template <typename rnumber> ',
- simname_variable = 'this->simname.c_str()',
- prepend_this = True) +
- '\n\n')
- for rnumber in ['float', 'double']:
- outfile.write(self.cread_pars(
- template_class = '{0}<{1}>::'.format(self.dns_type, rnumber),
- template_prefix = 'template '.format(rnumber),
- just_declaration = True) + '\n\n')
- if self.dns_type in ['NSVEparticles', 'NSVE_no_output', 'NSVEparticles_no_output', 'NSVEcomplex_particles', 'NSVEp_extra_sampling']:
- outfile.write('template <typename rnumber> int NSVE<rnumber>::read_parameters(){return EXIT_SUCCESS;}\n')
- outfile.write('template int NSVE<float>::read_parameters();\n')
- outfile.write('template int NSVE<double>::read_parameters();\n\n')
- if self.dns_type in ['NSVEparticles_no_output', 'NSVEp_extra_sampling']:
- outfile.write('template <typename rnumber> int NSVEparticles<rnumber>::read_parameters(){return EXIT_SUCCESS;}\n')
- outfile.write('template int NSVEparticles<float>::read_parameters();\n')
- outfile.write('template int NSVEparticles<double>::read_parameters();\n\n')
outfile.write(self.main + '\n')
return None
def generate_default_parameters(self):
diff --git a/bfps/cpp/full_code/NSVE.cpp b/bfps/cpp/full_code/NSVE.cpp
index e8bf9fd2..ce0a9544 100644
--- a/bfps/cpp/full_code/NSVE.cpp
+++ b/bfps/cpp/full_code/NSVE.cpp
@@ -137,6 +137,28 @@ int NSVE<rnumber>::do_stats()
return EXIT_SUCCESS;
}
+template <typename rnumber>
+int NSVE<rnumber>::read_parameters(void)
+{
+ this->direct_numerical_simulation::read_parameters();
+ hid_t parameter_file = H5Fopen((this->simname + ".h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ this->nu = hdf5_tools::read_value<double>(parameter_file, "parameters/nu");
+ this->dt = hdf5_tools::read_value<double>(parameter_file, "parameters/dt");
+ this->fmode = hdf5_tools::read_value<int>(parameter_file, "parameters/fmode");
+ this->famplitude = hdf5_tools::read_value<double>(parameter_file, "parameters/famplitude");
+ this->friction_coefficient = hdf5_tools::read_value<double>(parameter_file, "parameters/friction_coefficient");
+ this->fk0 = hdf5_tools::read_value<double>(parameter_file, "parameters/fk0");
+ this->fk1 = hdf5_tools::read_value<double>(parameter_file, "parameters/fk1");
+ this->energy = hdf5_tools::read_value<double>(parameter_file, "parameters/energy");
+ this->histogram_bins = hdf5_tools::read_value<int>(parameter_file, "parameters/histogram_bins");
+ this->max_velocity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_velocity_estimate");
+ this->max_vorticity_estimate = hdf5_tools::read_value<double>(parameter_file, "parameters/max_vorticity_estimate");
+ std::string tmp = hdf5_tools::read_string(parameter_file, "parameters/forcing_type");
+ snprintf(this->forcing_type, 511, "%s", tmp.c_str());
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
+
template class NSVE<float>;
template class NSVE<double>;
diff --git a/bfps/cpp/full_code/NSVEparticles.cpp b/bfps/cpp/full_code/NSVEparticles.cpp
index bbdd96c3..78f3d6a0 100644
--- a/bfps/cpp/full_code/NSVEparticles.cpp
+++ b/bfps/cpp/full_code/NSVEparticles.cpp
@@ -142,6 +142,20 @@ int NSVEparticles<rnumber>::do_stats()
return EXIT_SUCCESS;
}
+template <typename rnumber>
+int NSVEparticles<rnumber>::read_parameters(void)
+{
+ this->NSVE<rnumber>::read_parameters();
+ hid_t parameter_file = H5Fopen((this->simname + ".h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ this->niter_part = hdf5_tools::read_value<int>(parameter_file, "parameters/niter_part");
+ 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 class NSVEparticles<float>;
template class NSVEparticles<double>;
diff --git a/bfps/cpp/full_code/code_base.cpp b/bfps/cpp/full_code/code_base.cpp
index 1b06fe8e..32fe9c1c 100644
--- a/bfps/cpp/full_code/code_base.cpp
+++ b/bfps/cpp/full_code/code_base.cpp
@@ -34,3 +34,17 @@ int code_base::check_stopping_condition(void)
return EXIT_SUCCESS;
}
+int code_base::read_parameters(void)
+{
+ hid_t parameter_file = H5Fopen((this->simname + ".h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ this->dkx = hdf5_tools::read_value<double>(parameter_file, "parameters/dkx");
+ this->dky = hdf5_tools::read_value<double>(parameter_file, "parameters/dky");
+ this->dkz = hdf5_tools::read_value<double>(parameter_file, "parameters/dkz");
+ this->nx = hdf5_tools::read_value<int>(parameter_file, "parameters/nx");
+ this->ny = hdf5_tools::read_value<int>(parameter_file, "parameters/ny");
+ this->nz = hdf5_tools::read_value<int>(parameter_file, "parameters/nz");
+ this->dealias_type = hdf5_tools::read_value<int>(parameter_file, "parameters/dealias_type");
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
+
diff --git a/bfps/cpp/full_code/code_base.hpp b/bfps/cpp/full_code/code_base.hpp
index cf0521e2..5ec4260d 100644
--- a/bfps/cpp/full_code/code_base.hpp
+++ b/bfps/cpp/full_code/code_base.hpp
@@ -108,6 +108,7 @@ class code_base
return EXIT_SUCCESS;
}
+ virtual int read_parameters(void);
virtual int initialize(void) = 0;
virtual int main_loop(void) = 0;
virtual int finalize(void) = 0;
diff --git a/bfps/cpp/full_code/direct_numerical_simulation.cpp b/bfps/cpp/full_code/direct_numerical_simulation.cpp
index edc2f994..f763cde9 100644
--- a/bfps/cpp/full_code/direct_numerical_simulation.cpp
+++ b/bfps/cpp/full_code/direct_numerical_simulation.cpp
@@ -117,3 +117,14 @@ int direct_numerical_simulation::main_loop(void)
return EXIT_SUCCESS;
}
+int direct_numerical_simulation::read_parameters(void)
+{
+ this->code_base::read_parameters();
+ hid_t parameter_file = H5Fopen((this->simname + ".h5").c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+ this->checkpoints_per_file = hdf5_tools::read_value<int>(parameter_file, "parameters/checkpoints_per_file");
+ this->niter_out = hdf5_tools::read_value<int>(parameter_file, "parameters/niter_out");
+ this->niter_stat = hdf5_tools::read_value<int>(parameter_file, "parameters/niter_stat");
+ this->niter_todo = hdf5_tools::read_value<int>(parameter_file, "parameters/niter_todo");
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
diff --git a/bfps/cpp/full_code/direct_numerical_simulation.hpp b/bfps/cpp/full_code/direct_numerical_simulation.hpp
index 8050bb04..15ab698a 100644
--- a/bfps/cpp/full_code/direct_numerical_simulation.hpp
+++ b/bfps/cpp/full_code/direct_numerical_simulation.hpp
@@ -51,6 +51,7 @@ class direct_numerical_simulation: public code_base
simulation_name){}
virtual ~direct_numerical_simulation(){}
+ virtual int read_parameters(void);
virtual int write_checkpoint(void) = 0;
virtual int initialize(void) = 0;
virtual int step(void) = 0;
diff --git a/setup.py b/setup.py
index 7889c927..b427ebe7 100644
--- a/setup.py
+++ b/setup.py
@@ -88,40 +88,29 @@ print('This is bfps version ' + VERSION)
### lists of files and MANIFEST.in
-src_file_list = ['full_code/NSVEcomplex_particles',
+src_file_list = [
+ 'full_code/code_base',
+ 'full_code/direct_numerical_simulation',
+ 'full_code/NSVE',
'full_code/joint_acc_vel_stats',
'full_code/test',
'full_code/filter_test',
'full_code/field_test',
'full_code/symmetrize_test',
'full_code/field_output_test',
- 'full_code/test_interpolation',
- 'hdf5_tools',
'full_code/get_rfields',
'full_code/field_single_to_double',
'full_code/resize',
'full_code/NSVE_field_stats',
'full_code/native_binary_to_hdf5',
'full_code/postprocess',
- 'full_code/code_base',
- 'full_code/direct_numerical_simulation',
- 'full_code/NSVE',
- 'field_binary_IO',
- 'vorticity_equation',
'field',
'kspace',
'field_layout',
- 'field_descriptor',
- 'rFFTW_distributed_particles',
- 'distributed_particles',
- 'particles',
- 'particles_base',
- 'rFFTW_interpolator',
- 'interpolator',
- 'interpolator_base',
- 'fluid_solver',
- 'fluid_solver_base',
+ 'hdf5_tools',
'fftw_tools',
+ 'vorticity_equation',
+ 'field_binary_IO',
'spline_n1',
'spline_n2',
'spline_n3',
@@ -134,7 +123,11 @@ src_file_list = ['full_code/NSVEcomplex_particles',
'spline_n10',
'Lagrange_polys',
'scope_timer',
+ 'interpolator',
+ 'interpolator_base',
+ 'full_code/test_interpolation',
'full_code/NSVEparticles',
+ 'full_code/NSVEcomplex_particles',
'full_code/NSVEp_extra_sampling']
particle_headers = [
--
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