diff --git a/bfps/DNS.py b/bfps/DNS.py
index c7d77956d1364ea9e743c93da83e4c4151e1006a..e6ace758a1f6efb240cfa0655cc661a83a1ab6e2 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):
@@ -168,6 +148,11 @@ class DNS(_code):
self.NSVEp_extra_parameters['tracers0_integration_steps'] = int(4)
self.NSVEp_extra_parameters['tracers0_neighbours'] = int(1)
self.NSVEp_extra_parameters['tracers0_smoothness'] = int(1)
+ self.NSVEp_extra_parameters['tracers0_enable_p2p'] = int(0)
+ self.NSVEp_extra_parameters['tracers0_enable_inner'] = int(0)
+ self.NSVEp_extra_parameters['tracers0_enable_vorticity_omega'] = int(0)
+ self.NSVEp_extra_parameters['tracers0_cutoff'] = float(1)
+ self.NSVEp_extra_parameters['tracers0_inner_v0'] = float(1)
#self.extra_parameters = {}
#for key in ['NSVE', 'NSVE_no_output', 'NSVEparticles', 'NSVEparticles_no_output', 'NSVEcomplex_particles']:
# self.extra_parameters[key] = {}
diff --git a/bfps/cpp/full_code/NSVE.cpp b/bfps/cpp/full_code/NSVE.cpp
index e8bf9fd2e9786bd5df8a4c9d7dc9b37e15de85c1..d9cb72a220aaf6cb124cb37f827373f9a44b03ac 100644
--- a/bfps/cpp/full_code/NSVE.cpp
+++ b/bfps/cpp/full_code/NSVE.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int NSVE<rnumber>::initialize(void)
{
+ TIMEZONE("NSVE::initialize");
this->read_iteration();
this->read_parameters();
if (this->myrank == 0)
@@ -67,6 +68,7 @@ int NSVE<rnumber>::initialize(void)
template <typename rnumber>
int NSVE<rnumber>::step(void)
{
+ TIMEZONE("NSVE::step");
this->fs->step(this->dt);
this->iteration = this->fs->iteration;
return EXIT_SUCCESS;
@@ -75,6 +77,7 @@ int NSVE<rnumber>::step(void)
template <typename rnumber>
int NSVE<rnumber>::write_checkpoint(void)
{
+ TIMEZONE("NSVE::write_checkpoint");
this->fs->io_checkpoint(false);
this->checkpoint = this->fs->checkpoint;
this->write_iteration();
@@ -84,6 +87,7 @@ int NSVE<rnumber>::write_checkpoint(void)
template <typename rnumber>
int NSVE<rnumber>::finalize(void)
{
+ TIMEZONE("NSVE::finalize");
if (this->myrank == 0)
H5Fclose(this->stat_file);
delete this->fs;
@@ -104,6 +108,7 @@ int NSVE<rnumber>::finalize(void)
template <typename rnumber>
int NSVE<rnumber>::do_stats()
{
+ TIMEZONE("NSVE::do_stats");
if (!(this->iteration % this->niter_stat == 0))
return EXIT_SUCCESS;
hid_t stat_group;
@@ -137,6 +142,29 @@ 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->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/NSVE_field_stats.cpp b/bfps/cpp/full_code/NSVE_field_stats.cpp
index 7e33acf93644208d292c5d8df66653f4bb7b806f..15980a20141a563be08ad0b28a3190b3e9e1c17c 100644
--- a/bfps/cpp/full_code/NSVE_field_stats.cpp
+++ b/bfps/cpp/full_code/NSVE_field_stats.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int NSVE_field_stats<rnumber>::initialize(void)
{
+ TIMEZONE("NSVE_field_stats::initialize");
this->postprocess::read_parameters();
this->vorticity = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
@@ -49,6 +50,7 @@ int NSVE_field_stats<rnumber>::initialize(void)
template <typename rnumber>
int NSVE_field_stats<rnumber>::read_current_cvorticity(void)
{
+ TIMEZONE("NSVE_field_stats::read_current_cvorticity");
this->vorticity->real_space_representation = false;
if (this->bin_IO != NULL)
{
@@ -76,6 +78,7 @@ int NSVE_field_stats<rnumber>::read_current_cvorticity(void)
template <typename rnumber>
int NSVE_field_stats<rnumber>::finalize(void)
{
+ TIMEZONE("NSVE_field_stats::finalize");
if (this->bin_IO != NULL)
delete this->bin_IO;
delete this->vorticity;
@@ -85,6 +88,7 @@ int NSVE_field_stats<rnumber>::finalize(void)
template <typename rnumber>
int NSVE_field_stats<rnumber>::work_on_current_iteration(void)
{
+ TIMEZONE("NSVE_field_stats::work_on_current_iteration");
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/NSVE_no_output.hpp b/bfps/cpp/full_code/NSVE_no_output.hpp
index 0047a45a02dd58ae8934f78fdd8d804424ae817c..045db08ec74b74206973e0dfbcb30716d62be0de 100644
--- a/bfps/cpp/full_code/NSVE_no_output.hpp
+++ b/bfps/cpp/full_code/NSVE_no_output.hpp
@@ -1,3 +1,29 @@
+/**********************************************************************
+* *
+* 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 NSVE_NO_OUTPUT_HPP
#define NSVE_NO_OUTPUT_HPP
@@ -16,9 +42,9 @@ class NSVE_no_output: public NSVE<rnumber>
~NSVE_no_output(){}
int write_checkpoint(void)
{
- return 0;
+ TIMEZONE("NSVE_no_output::write_checkpoint");
+ return EXIT_SUCCESS;
}
- int read_parameters(void);
};
#endif//NSVE_NO_OUTPUT_HPP
diff --git a/bfps/cpp/full_code/NSVEcomplex_particles.cpp b/bfps/cpp/full_code/NSVEcomplex_particles.cpp
index 93d0edc17e24925b25513dd3a4832f687255329a..81c6cd5ff37443fb110a0feb46a0858d274d4489 100644
--- a/bfps/cpp/full_code/NSVEcomplex_particles.cpp
+++ b/bfps/cpp/full_code/NSVEcomplex_particles.cpp
@@ -1,3 +1,29 @@
+/**********************************************************************
+* *
+* 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 *
+* *
+**********************************************************************/
+
+
+
#include <string>
#include <cmath>
#include "NSVEcomplex_particles.hpp"
@@ -9,6 +35,7 @@
template <typename rnumber>
int NSVEcomplex_particles<rnumber>::initialize(void)
{
+ TIMEZONE("NSVEcomplex_particles::initialize");
this->NSVE<rnumber>::initialize();
p2p_computer<double, long long int> current_p2p_computer;
@@ -63,6 +90,7 @@ int NSVEcomplex_particles<rnumber>::initialize(void)
template <typename rnumber>
int NSVEcomplex_particles<rnumber>::step(void)
{
+ TIMEZONE("NSVEcomplex_particles::step");
this->fs->compute_velocity(this->fs->cvorticity);
this->fs->cvelocity->ift();
if(enable_vorticity_omega){
@@ -80,6 +108,7 @@ int NSVEcomplex_particles<rnumber>::step(void)
template <typename rnumber>
int NSVEcomplex_particles<rnumber>::write_checkpoint(void)
{
+ TIMEZONE("NSVEcomplex_particles::write_checkpoint");
this->NSVE<rnumber>::write_checkpoint();
this->particles_output_writer_mpi->open_file(this->fs->get_current_fname());
// TODO P2P write particle data too
@@ -96,6 +125,7 @@ int NSVEcomplex_particles<rnumber>::write_checkpoint(void)
template <typename rnumber>
int NSVEcomplex_particles<rnumber>::finalize(void)
{
+ TIMEZONE("NSVEcomplex_particles::finalize");
delete this->nabla_u;
delete this->particles_output_writer_mpi;
delete this->particles_sample_writer_mpi;
@@ -109,6 +139,7 @@ int NSVEcomplex_particles<rnumber>::finalize(void)
template <typename rnumber>
int NSVEcomplex_particles<rnumber>::do_stats()
{
+ TIMEZONE("NSVEcomplex_particles::do_stats");
/// perform fluid stats
this->NSVE<rnumber>::do_stats();
@@ -184,6 +215,30 @@ int NSVEcomplex_particles<rnumber>::do_stats()
this->ps->getLocalNbParticles(),
this->ps->get_step_idx()-1);
+ // deallocate temporary data array
+ // TODO: is it required/safe to call the release method here?
+ //pdata.release();
+
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVEcomplex_particles<rnumber>::read_parameters(void)
+{
+ TIMEZONE("NSVEcomplex_particles::read_parameters");
+ 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");
+ this->enable_p2p = hdf5_tools::read_value<int>(parameter_file, "parameters/tracers0_enable_p2p");
+ this->enable_inner = hdf5_tools::read_value<int>(parameter_file, "parameters/tracers0_enable_inner");
+ this->enable_vorticity_omega = hdf5_tools::read_value<int>(parameter_file, "parameters/tracers0_enable_vorticity_omega");
+ this->cutoff = hdf5_tools::read_value<double>(parameter_file, "parameters/tracers0_cutoff");
+ this->inner_v0 = hdf5_tools::read_value<double>(parameter_file, "parameters/tracers0_inner_v0");
+ H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/NSVEp_extra_sampling.cpp b/bfps/cpp/full_code/NSVEp_extra_sampling.cpp
index 3d002d341e26ba547ef4c6ecc47769923e41b8f8..22357510d2683f4a88f4af7a5371d74fdd45043d 100644
--- a/bfps/cpp/full_code/NSVEp_extra_sampling.cpp
+++ b/bfps/cpp/full_code/NSVEp_extra_sampling.cpp
@@ -5,6 +5,7 @@
template <typename rnumber>
int NSVEp_extra_sampling<rnumber>::initialize(void)
{
+ TIMEZONE("NSVEp_extra_sampling::initialize");
this->NSVEparticles<rnumber>::initialize();
/// allocate grad vel field
@@ -30,6 +31,7 @@ int NSVEp_extra_sampling<rnumber>::initialize(void)
template <typename rnumber>
int NSVEp_extra_sampling<rnumber>::finalize(void)
{
+ TIMEZONE("NSVEp_extra_sampling::finalize");
delete this->nabla_u;
delete this->pressure;
delete this->nabla_p;
@@ -41,6 +43,7 @@ int NSVEp_extra_sampling<rnumber>::finalize(void)
template <typename rnumber>
int NSVEp_extra_sampling<rnumber>::do_stats()
{
+ TIMEZONE("NSVEp_extra_sampling::do_stats");
this->NSVEparticles<rnumber>::do_stats();
if (!(this->iteration % this->niter_part == 0))
return EXIT_SUCCESS;
diff --git a/bfps/cpp/full_code/NSVEparticles.cpp b/bfps/cpp/full_code/NSVEparticles.cpp
index bbdd96c36f05eb1b8dd755dfc59c9f2a1f98d49d..b09e32805bbfb61469926be9f9d1b259066f9080 100644
--- a/bfps/cpp/full_code/NSVEparticles.cpp
+++ b/bfps/cpp/full_code/NSVEparticles.cpp
@@ -1,3 +1,6 @@
+
+
+
#include <string>
#include <cmath>
#include "NSVEparticles.hpp"
@@ -6,6 +9,7 @@
template <typename rnumber>
int NSVEparticles<rnumber>::initialize(void)
{
+ TIMEZONE("NSVEparticles::intialize");
this->NSVE<rnumber>::initialize();
this->pressure = new field<rnumber, FFTW, ONE>(
this->fs->cvelocity->rlayout->sizes[2],
@@ -45,6 +49,7 @@ int NSVEparticles<rnumber>::initialize(void)
template <typename rnumber>
int NSVEparticles<rnumber>::step(void)
{
+ TIMEZONE("NSVEparticles::step");
this->fs->compute_velocity(this->fs->cvorticity);
this->fs->cvelocity->ift();
this->ps->completeLoop(this->dt);
@@ -55,6 +60,7 @@ int NSVEparticles<rnumber>::step(void)
template <typename rnumber>
int NSVEparticles<rnumber>::write_checkpoint(void)
{
+ TIMEZONE("NSVEparticles::write_checkpoint");
this->NSVE<rnumber>::write_checkpoint();
this->particles_output_writer_mpi->open_file(this->fs->get_current_fname());
this->particles_output_writer_mpi->template save<3>(
@@ -70,6 +76,7 @@ int NSVEparticles<rnumber>::write_checkpoint(void)
template <typename rnumber>
int NSVEparticles<rnumber>::finalize(void)
{
+ TIMEZONE("NSVEparticles::finalize");
delete this->pressure;
this->ps.release();
delete this->particles_output_writer_mpi;
@@ -84,6 +91,7 @@ int NSVEparticles<rnumber>::finalize(void)
template <typename rnumber>
int NSVEparticles<rnumber>::do_stats()
{
+ TIMEZONE("NSVEparticles::do_stats");
/// fluid stats go here
this->NSVE<rnumber>::do_stats();
@@ -142,6 +150,21 @@ int NSVEparticles<rnumber>::do_stats()
return EXIT_SUCCESS;
}
+template <typename rnumber>
+int NSVEparticles<rnumber>::read_parameters(void)
+{
+ TIMEZONE("NSVEparticles::read_parameters");
+ 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/NSVEparticles_no_output.hpp b/bfps/cpp/full_code/NSVEparticles_no_output.hpp
index 264fd75ac9b0628aff167d018d888030b7029a35..5b9d5e15e00fd1b2d8551995e99e0a157339925c 100644
--- a/bfps/cpp/full_code/NSVEparticles_no_output.hpp
+++ b/bfps/cpp/full_code/NSVEparticles_no_output.hpp
@@ -16,9 +16,9 @@ class NSVEparticles_no_output: public NSVEparticles<rnumber>
~NSVEparticles_no_output(){}
int write_checkpoint(void)
{
- return 0;
+ TIMEZONE("NSVEparticles_no_output::write_checkpoint");
+ return EXIT_SUCCESS;
}
- int read_parameters(void);
};
#endif//NSVEPARTICLES_NO_OUTPUT_HPP
diff --git a/bfps/cpp/full_code/code_base.cpp b/bfps/cpp/full_code/code_base.cpp
index 1b06fe8e66a4180034b9f6a494a1a432ae5ea3f9..a6487c726de44b018392128f955ccebf7e7100a1 100644
--- a/bfps/cpp/full_code/code_base.cpp
+++ b/bfps/cpp/full_code/code_base.cpp
@@ -1,12 +1,42 @@
+/**********************************************************************
+* *
+* 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 *
+* *
+**********************************************************************/
+
+
+
+#define NDEBUG
+
#include "code_base.hpp"
#include "scope_timer.hpp"
+
code_base::code_base(
const MPI_Comm COMMUNICATOR,
const std::string &simulation_name):
comm(COMMUNICATOR),
simname(simulation_name)
{
+ TIMEZONE("code_base::code_base");
MPI_Comm_rank(this->comm, &this->myrank);
MPI_Comm_size(this->comm, &this->nprocs);
this->stop_code_now = false;
@@ -14,6 +44,7 @@ code_base::code_base(
int code_base::check_stopping_condition(void)
{
+ TIMEZONE("code_base::check_stopping_condition");
if (myrank == 0)
{
std::string fname = (
@@ -34,3 +65,18 @@ int code_base::check_stopping_condition(void)
return EXIT_SUCCESS;
}
+int code_base::read_parameters(void)
+{
+ TIMEZONE("code_base::read_parameters");
+ 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 cf0521e2b7383edf925e1129d4fa4a931a55efe4..5ec4260dbfbaaa8ea4e123d8a38b680c0df121eb 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 edc2f99497a21368c63348167190dc6c64b44712..c0b0441e5b274cbe088b6fd0903823c6d17b2076 100644
--- a/bfps/cpp/full_code/direct_numerical_simulation.cpp
+++ b/bfps/cpp/full_code/direct_numerical_simulation.cpp
@@ -8,6 +8,7 @@
int direct_numerical_simulation::grow_file_datasets()
{
+ TIMEZONE("direct_numerical_simulation::grow_file_datasets");
return hdf5_tools::grow_file_datasets(
this->stat_file,
"statistics",
@@ -16,6 +17,7 @@ int direct_numerical_simulation::grow_file_datasets()
int direct_numerical_simulation::read_iteration(void)
{
+ TIMEZONE("direct_numerical_simulation::read_iteration");
/* read iteration */
hid_t dset;
hid_t iteration_file = H5Fopen(
@@ -56,6 +58,7 @@ int direct_numerical_simulation::read_iteration(void)
int direct_numerical_simulation::write_iteration(void)
{
+ TIMEZONE("direct_numerical_simulation::write_iteration");
if (this->myrank == 0)
{
hid_t dset = H5Dopen(
@@ -88,6 +91,7 @@ int direct_numerical_simulation::write_iteration(void)
int direct_numerical_simulation::main_loop(void)
{
+ TIMEZONE("direct_numerical_simulation::main_loop");
this->start_simple_timer();
int max_iter = (this->iteration + this->niter_todo -
(this->iteration % this->niter_todo));
@@ -117,3 +121,15 @@ int direct_numerical_simulation::main_loop(void)
return EXIT_SUCCESS;
}
+int direct_numerical_simulation::read_parameters(void)
+{
+ TIMEZONE("direct_numerical_simulation::read_parameters");
+ 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 8050bb045b29acf29d655273f7dff310dd10d0fa..15ab698a1128fd836b74b100b9a79d5c6d67d12f 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/bfps/cpp/full_code/field_output_test.cpp b/bfps/cpp/full_code/field_output_test.cpp
index f54400647bee3d8b05d7ef4dc58b9a90998ac184..30df4e7512bec3c08325fe156b21789f80882f54 100644
--- a/bfps/cpp/full_code/field_output_test.cpp
+++ b/bfps/cpp/full_code/field_output_test.cpp
@@ -8,6 +8,7 @@
template <typename rnumber>
int field_output_test<rnumber>::initialize(void)
{
+ TIMEZONE("field_output_test::initialize");
this->read_parameters();
return EXIT_SUCCESS;
}
@@ -15,12 +16,14 @@ int field_output_test<rnumber>::initialize(void)
template <typename rnumber>
int field_output_test<rnumber>::finalize(void)
{
+ TIMEZONE("field_output_test::finalize");
return EXIT_SUCCESS;
}
template <typename rnumber>
int field_output_test<rnumber>::read_parameters()
{
+ TIMEZONE("field_output_test::read_parameters");
this->test::read_parameters();
return EXIT_SUCCESS;
}
@@ -28,6 +31,7 @@ int field_output_test<rnumber>::read_parameters()
template <typename rnumber>
int field_output_test<rnumber>::do_work(void)
{
+ TIMEZONE("field_output_test::do_work");
// allocate
field<rnumber, FFTW, ONE> *scal_field = new field<rnumber, FFTW, ONE>(
this->nx, this->ny, this->nz,
diff --git a/bfps/cpp/full_code/field_single_to_double.cpp b/bfps/cpp/full_code/field_single_to_double.cpp
index bb34abd22ca3d629a2b05e1d3e0a94b903010610..92976ecfb3ff32dc798a2f6f4b17bfd44441a158 100644
--- a/bfps/cpp/full_code/field_single_to_double.cpp
+++ b/bfps/cpp/full_code/field_single_to_double.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int field_single_to_double<rnumber>::initialize(void)
{
+ TIMEZONE("field_single_to_double::intialize");
this->NSVE_field_stats<rnumber>::initialize();
DEBUG_MSG("after NSVE_field_stats::initialize\n");
this->kk = new kspace<FFTW, SMOOTH>(
@@ -47,7 +48,7 @@ int field_single_to_double<rnumber>::initialize(void)
template <typename rnumber>
int field_single_to_double<rnumber>::work_on_current_iteration(void)
{
- DEBUG_MSG("entered field_single_to_double::work_on_current_iteration\n");
+ TIMEZONE("field_single_to_double::work_on_current_iteration");
this->read_current_cvorticity();
// using CLOOP as opposed to a global std::copy because CLOOP
@@ -83,6 +84,7 @@ int field_single_to_double<rnumber>::work_on_current_iteration(void)
template <typename rnumber>
int field_single_to_double<rnumber>::finalize(void)
{
+ TIMEZONE("field_single_to_double::finalize");
delete this->vec_field_double;
delete this->kk;
return EXIT_SUCCESS;
diff --git a/bfps/cpp/full_code/field_test.cpp b/bfps/cpp/full_code/field_test.cpp
index 5c323e547900cc2e52561c0df16748659a7006b6..1627bc4088581468ebedab585db7ca9d6519d3a3 100644
--- a/bfps/cpp/full_code/field_test.cpp
+++ b/bfps/cpp/full_code/field_test.cpp
@@ -8,6 +8,7 @@
template <typename rnumber>
int field_test<rnumber>::initialize(void)
{
+ TIMEZONE("field_test::initialize");
this->read_parameters();
return EXIT_SUCCESS;
}
@@ -15,23 +16,22 @@ int field_test<rnumber>::initialize(void)
template <typename rnumber>
int field_test<rnumber>::finalize(void)
{
+ TIMEZONE("field_test::finalize");
+ this->read_parameters();
return EXIT_SUCCESS;
}
template <typename rnumber>
int field_test<rnumber>::read_parameters()
{
+ TIMEZONE("field_test::read_parameters");
this->test::read_parameters();
// in case any parameters are needed, this is where they should be read
- hid_t parameter_file;
- hid_t dset;
- parameter_file = H5Fopen(
+ hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
- dset = H5Dopen(parameter_file, "/parameters/filter_length", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->filter_length);
- H5Dclose(dset);
+ this->filter_length = hdf5_tools::read_value<double>(parameter_file, "/parameters/filter_length");
H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
@@ -39,6 +39,7 @@ int field_test<rnumber>::read_parameters()
template <typename rnumber>
int field_test<rnumber>::do_work(void)
{
+ TIMEZONE("field_test::do_work");
// allocate
field<rnumber, FFTW, ONE> *scal_field = new field<rnumber, FFTW, ONE>(
this->nx, this->ny, this->nz,
diff --git a/bfps/cpp/full_code/filter_test.cpp b/bfps/cpp/full_code/filter_test.cpp
index 80c4f83db69106c533e4ef21cecdf5874a24a06e..4db13843fa8f69db77f8a15cbd0563feb087dfcf 100644
--- a/bfps/cpp/full_code/filter_test.cpp
+++ b/bfps/cpp/full_code/filter_test.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int filter_test<rnumber>::initialize(void)
{
+ TIMEZONE("filter_test::initialize");
this->read_parameters();
this->scal_field = new field<rnumber, FFTW, ONE>(
nx, ny, nz,
@@ -30,6 +31,7 @@ int filter_test<rnumber>::initialize(void)
template <typename rnumber>
int filter_test<rnumber>::finalize(void)
{
+ TIMEZONE("filter_test::finalize");
delete this->scal_field;
delete this->kk;
return EXIT_SUCCESS;
@@ -38,16 +40,13 @@ int filter_test<rnumber>::finalize(void)
template <typename rnumber>
int filter_test<rnumber>::read_parameters()
{
+ TIMEZONE("filter_test::read_parameters");
this->test::read_parameters();
- hid_t parameter_file;
- hid_t dset;
- parameter_file = H5Fopen(
+ hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
- dset = H5Dopen(parameter_file, "/parameters/filter_length", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->filter_length);
- H5Dclose(dset);
+ this->filter_length = hdf5_tools::read_value<double>(parameter_file, "/parameters/filter_length");
H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
@@ -56,6 +55,7 @@ template <typename rnumber>
int filter_test<rnumber>::reset_field(
int dimension)
{
+ TIMEZONE("filter_test::reset_field");
this->scal_field->real_space_representation = true;
*this->scal_field = 0.0;
if (this->scal_field->rlayout->starts[0] == 0)
@@ -95,6 +95,7 @@ int filter_test<rnumber>::reset_field(
template <typename rnumber>
int filter_test<rnumber>::do_work(void)
{
+ TIMEZONE("filter_test::do_work");
std::string filename = this->simname + std::string("_fields.h5");
for (int dimension = 0; dimension < 3; dimension++)
{
diff --git a/bfps/cpp/full_code/get_rfields.cpp b/bfps/cpp/full_code/get_rfields.cpp
index 3986b5f9de93cdeb83341402750dc05bf7e4b695..376a265946cb4682a619040a1c907f5f2abbd8e1 100644
--- a/bfps/cpp/full_code/get_rfields.cpp
+++ b/bfps/cpp/full_code/get_rfields.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int get_rfields<rnumber>::initialize(void)
{
+ TIMEZONE("get_rfields::initialize");
this->NSVE_field_stats<rnumber>::initialize();
DEBUG_MSG("after NSVE_field_stats::initialize\n");
this->kk = new kspace<FFTW, SMOOTH>(
@@ -15,23 +16,15 @@ int get_rfields<rnumber>::initialize(void)
(this->simname + std::string(".h5")).c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
- hid_t dset = H5Dopen(parameter_file, "/parameters/niter_out", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->niter_out);
- H5Dclose(dset);
- if (H5Lexists(parameter_file, "/parameters/checkpoints_per_file", H5P_DEFAULT))
- {
- dset = H5Dopen(parameter_file, "/parameters/checkpoints_per_file", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->checkpoints_per_file);
- H5Dclose(dset);
- }
- else
+ this->niter_out = hdf5_tools::read_value<int>(parameter_file, "/parameters/niter_out");
+ this->checkpoints_per_file = hdf5_tools::read_value<int>(parameter_file, "/parameters/checkpoints_per_file");
+ if (this->checkpoints_per_file == INT_MAX) // value returned if dataset does not exist
this->checkpoints_per_file = 1;
H5Fclose(parameter_file);
parameter_file = H5Fopen(
(this->simname + std::string("_post.h5")).c_str(),
H5F_ACC_RDONLY,
H5P_DEFAULT);
- DEBUG_MSG("before read_vector\n");
this->iteration_list = hdf5_tools::read_vector<int>(
parameter_file,
"/get_rfields/parameters/iteration_list");
@@ -42,7 +35,7 @@ int get_rfields<rnumber>::initialize(void)
template <typename rnumber>
int get_rfields<rnumber>::work_on_current_iteration(void)
{
- DEBUG_MSG("entered get_rfields::work_on_current_iteration\n");
+ TIMEZONE("get_rfields::work_on_current_iteration");
this->read_current_cvorticity();
field<rnumber, FFTW, THREE> *vel = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
@@ -97,6 +90,7 @@ int get_rfields<rnumber>::work_on_current_iteration(void)
template <typename rnumber>
int get_rfields<rnumber>::finalize(void)
{
+ TIMEZONE("get_rfields::finalize");
delete this->kk;
this->NSVE_field_stats<rnumber>::finalize();
return EXIT_SUCCESS;
diff --git a/bfps/cpp/full_code/joint_acc_vel_stats.cpp b/bfps/cpp/full_code/joint_acc_vel_stats.cpp
index e4f4d5d40772292f44c7e776dcd4d1b82c4ce222..1c28527e5986e12a5d66151a5623194e4ffab3aa 100644
--- a/bfps/cpp/full_code/joint_acc_vel_stats.cpp
+++ b/bfps/cpp/full_code/joint_acc_vel_stats.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int joint_acc_vel_stats<rnumber>::initialize(void)
{
+ TIMEZONE("joint_acc_vel_stats::initialize");
this->NSVE_field_stats<rnumber>::initialize();
this->kk = new kspace<FFTW, SMOOTH>(
this->vorticity->clayout, this->dkx, this->dky, this->dkz);
@@ -85,7 +86,7 @@ int joint_acc_vel_stats<rnumber>::initialize(void)
template <typename rnumber>
int joint_acc_vel_stats<rnumber>::work_on_current_iteration(void)
{
- DEBUG_MSG("entered joint_acc_vel_stats::work_on_current_iteration\n");
+ TIMEZONE("joint_acc_vel_stats::work_on_current_iteration");
/// read current vorticity, place it in this->ve->cvorticity
this->read_current_cvorticity();
*this->ve->cvorticity = this->vorticity->get_cdata();
@@ -156,6 +157,7 @@ int joint_acc_vel_stats<rnumber>::work_on_current_iteration(void)
template <typename rnumber>
int joint_acc_vel_stats<rnumber>::finalize(void)
{
+ DEBUG_MSG("entered joint_acc_vel_stats::finalize\n");
delete this->ve;
delete this->kk;
if (this->myrank == 0)
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.cpp b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
index 7774e2dea9012394c389858038e8ca82674256d7..fb5a39c2af8a88a158df679ad27ce0f08fab37f8 100644
--- a/bfps/cpp/full_code/native_binary_to_hdf5.cpp
+++ b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int native_binary_to_hdf5<rnumber>::initialize(void)
{
+ TIMEZONE("native_binary_to_hdf5::initialize");
this->read_parameters();
this->vec_field = new field<rnumber, FFTW, THREE>(
nx, ny, nz,
@@ -24,6 +25,7 @@ int native_binary_to_hdf5<rnumber>::initialize(void)
template <typename rnumber>
int native_binary_to_hdf5<rnumber>::work_on_current_iteration(void)
{
+ TIMEZONE("native_binary_to_hdf5::work_on_current_iteration");
char itername[16];
sprintf(itername, "i%.5x", this->iteration);
std::string native_binary_fname = (
@@ -45,6 +47,7 @@ int native_binary_to_hdf5<rnumber>::work_on_current_iteration(void)
template <typename rnumber>
int native_binary_to_hdf5<rnumber>::finalize(void)
{
+ TIMEZONE("native_binary_to_hdf5::finalize");
delete this->bin_IO;
delete this->vec_field;
return EXIT_SUCCESS;
@@ -53,6 +56,7 @@ int native_binary_to_hdf5<rnumber>::finalize(void)
template <typename rnumber>
int native_binary_to_hdf5<rnumber>::read_parameters(void)
{
+ TIMEZONE("native_binary_to_hdf5::read_parameters");
this->postprocess::read_parameters();
hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
diff --git a/bfps/cpp/full_code/postprocess.cpp b/bfps/cpp/full_code/postprocess.cpp
index cb04a030123f3f5ecaa501ca11b22511d1a8ca84..13bee7009e3d8d03e0f2ce10c8a3c1706318b460 100644
--- a/bfps/cpp/full_code/postprocess.cpp
+++ b/bfps/cpp/full_code/postprocess.cpp
@@ -8,6 +8,7 @@
int postprocess::main_loop(void)
{
+ TIMEZONE("postprocess::main_loop");
this->start_simple_timer();
for (unsigned int iteration_counter = 0;
iteration_counter < iteration_list.size();
@@ -33,41 +34,20 @@ int postprocess::main_loop(void)
int postprocess::read_parameters()
{
- hid_t parameter_file;
- char fname[256];
- sprintf(fname, "%s.h5", this->simname.c_str());
- parameter_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
- this->dealias_type = hdf5_tools::read_value<int>(
- parameter_file, "/parameters/dealias_type");
- 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->dt = hdf5_tools::read_value<double>(
- parameter_file, "/parameters/dt");
- 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->fmode = hdf5_tools::read_value<int>(
- parameter_file, "/parameters/fmode");
- sprintf(this->forcing_type, "%s",
- hdf5_tools::read_string(parameter_file, "/parameters/forcing_type").c_str());
- this->nu = hdf5_tools::read_value<double>(
- parameter_file, "/parameters/nu");
- 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");
+ TIMEZONE("postprocess::read_parameters");
+ this->code_base::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");
+ 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 0;
+ return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/postprocess.hpp b/bfps/cpp/full_code/postprocess.hpp
index 660e561a1ddba6b355ee5ecf49c5cea1b7153eff..65e6eadd1fd05615eb69cb7d8ca1754abd1b7e42 100644
--- a/bfps/cpp/full_code/postprocess.hpp
+++ b/bfps/cpp/full_code/postprocess.hpp
@@ -46,6 +46,7 @@ class postprocess: public code_base
double friction_coefficient;
double fk0;
double fk1;
+ double energy;
int fmode;
char forcing_type[512];
double nu;
diff --git a/bfps/cpp/full_code/resize.cpp b/bfps/cpp/full_code/resize.cpp
index 41d68ef725ab89c9ad2d55e5f9cc014844294b71..de555a7436786d7ffdfd6a1b7206d74850065b6b 100644
--- a/bfps/cpp/full_code/resize.cpp
+++ b/bfps/cpp/full_code/resize.cpp
@@ -7,6 +7,7 @@
template <typename rnumber>
int resize<rnumber>::initialize(void)
{
+ TIMEZONE("resize::initialize");
this->NSVE_field_stats<rnumber>::initialize();
DEBUG_MSG("after NSVE_field_stats::initialize\n");
hid_t parameter_file = H5Fopen(
@@ -46,7 +47,7 @@ int resize<rnumber>::initialize(void)
template <typename rnumber>
int resize<rnumber>::work_on_current_iteration(void)
{
- DEBUG_MSG("entered resize::work_on_current_iteration\n");
+ TIMEZONE("resize::work_on_current_iteration");
this->read_current_cvorticity();
std::string fname = (
@@ -64,6 +65,7 @@ int resize<rnumber>::work_on_current_iteration(void)
template <typename rnumber>
int resize<rnumber>::finalize(void)
{
+ TIMEZONE("resize::finalize");
delete this->new_field;
this->NSVE_field_stats<rnumber>::finalize();
return EXIT_SUCCESS;
diff --git a/bfps/cpp/full_code/symmetrize_test.cpp b/bfps/cpp/full_code/symmetrize_test.cpp
index 3b4cd5a5b7304e233735cab87f603b5e164ef0eb..821161da846a323721c07ed47a7c66d9efea78f0 100644
--- a/bfps/cpp/full_code/symmetrize_test.cpp
+++ b/bfps/cpp/full_code/symmetrize_test.cpp
@@ -8,6 +8,7 @@
template <typename rnumber>
int symmetrize_test<rnumber>::initialize(void)
{
+ TIMEZONE("symmetrize_test::initialize");
this->read_parameters();
return EXIT_SUCCESS;
}
@@ -15,12 +16,14 @@ int symmetrize_test<rnumber>::initialize(void)
template <typename rnumber>
int symmetrize_test<rnumber>::finalize(void)
{
+ TIMEZONE("symmetrize_test::finalize");
return EXIT_SUCCESS;
}
template <typename rnumber>
int symmetrize_test<rnumber>::read_parameters()
{
+ TIMEZONE("symmetrize_test::read_parameters");
this->test::read_parameters();
hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
@@ -35,6 +38,7 @@ int symmetrize_test<rnumber>::read_parameters()
template <typename rnumber>
int symmetrize_test<rnumber>::do_work(void)
{
+ TIMEZONE("symmetrize_test::do_work");
// allocate
DEBUG_MSG("about to allocate field0\n");
field<rnumber, FFTW, THREE> *test_field0 = new field<rnumber, FFTW, THREE>(
diff --git a/bfps/cpp/full_code/test.cpp b/bfps/cpp/full_code/test.cpp
index 9c2e4e6744b4ecd8945615da730c9dcd14382e78..aa909362df050c95282fd9c7de66de3d8a1acc34 100644
--- a/bfps/cpp/full_code/test.cpp
+++ b/bfps/cpp/full_code/test.cpp
@@ -8,9 +8,7 @@
int test::main_loop(void)
{
- #ifdef USE_TIMINGOUTPUT
- TIMEZONE("test::main_loop");
- #endif
+ TIMEZONE("test::main_loop");
this->start_simple_timer();
this->do_work();
this->print_simple_timer(
@@ -18,36 +16,3 @@ int test::main_loop(void)
return EXIT_SUCCESS;
}
-
-int test::read_parameters()
-{
- hid_t parameter_file;
- hid_t dset;
- char fname[256];
- sprintf(fname, "%s.h5", this->simname.c_str());
- parameter_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
- dset = H5Dopen(parameter_file, "/parameters/dealias_type", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->dealias_type);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/dkx", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->dkx);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/dky", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->dky);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/dkz", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_DOUBLE, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->dkz);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/nx", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->nx);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/ny", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->ny);
- H5Dclose(dset);
- dset = H5Dopen(parameter_file, "/parameters/nz", H5P_DEFAULT);
- H5Dread(dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &this->nz);
- H5Dclose(dset);
- H5Fclose(parameter_file);
- return 0;
-}
-
diff --git a/bfps/cpp/full_code/test.hpp b/bfps/cpp/full_code/test.hpp
index 134a01512b3fd836a8ac4d40068b3954752c4844..96ddaf8104f1dd3d050b4acf16a68dbcd539b290 100644
--- a/bfps/cpp/full_code/test.hpp
+++ b/bfps/cpp/full_code/test.hpp
@@ -56,7 +56,6 @@ class test: public code_base
virtual int finalize(void) = 0;
int main_loop(void);
- virtual int read_parameters(void);
};
#endif//TEST_HPP
diff --git a/bfps/cpp/full_code/test_interpolation.cpp b/bfps/cpp/full_code/test_interpolation.cpp
index b194d372f6b40916bcd64ff8268a44694b0465d0..5ef11de44b6f6a36ab6827facae3c637b702bc58 100644
--- a/bfps/cpp/full_code/test_interpolation.cpp
+++ b/bfps/cpp/full_code/test_interpolation.cpp
@@ -4,6 +4,7 @@
template <typename rnumber>
int test_interpolation<rnumber>::read_parameters(void)
{
+ TIMEZONE("test_interpolation::read_parameters");
this->test::read_parameters();
hid_t parameter_file = H5Fopen(
(this->simname + std::string(".h5")).c_str(),
@@ -24,6 +25,7 @@ int test_interpolation<rnumber>::read_parameters(void)
template <typename rnumber>
int test_interpolation<rnumber>::initialize(void)
{
+ TIMEZONE("test_interpolation::initialize");
this->read_parameters();
this->vorticity = new field<rnumber, FFTW, THREE>(
this->nx, this->ny, this->nz,
@@ -86,6 +88,7 @@ int test_interpolation<rnumber>::initialize(void)
template <typename rnumber>
int test_interpolation<rnumber>::finalize(void)
{
+ TIMEZONE("test_interpolation::finalize");
delete this->nabla_u;
delete this->velocity;
delete this->vorticity;
@@ -99,6 +102,7 @@ int test_interpolation<rnumber>::finalize(void)
template <typename rnumber>
int test_interpolation<rnumber>::do_work()
{
+ TIMEZONE("test_interpolation::do_work");
*this->nabla_u = 0.0;
this->velocity->real_space_representation = false;
this->vorticity->real_space_representation = false;
diff --git a/bfps/cpp/scope_timer.hpp b/bfps/cpp/scope_timer.hpp
index 2c48e2eda06ded74e668825181f0444eef22f647..890f522c415d7a102a0fff25c5292502cbcb459c 100644
--- a/bfps/cpp/scope_timer.hpp
+++ b/bfps/cpp/scope_timer.hpp
@@ -791,7 +791,8 @@ extern EventManager global_timer_manager;
#define TIMEZONE(NAME) \
ScopeEvent TIMEZONE_Core_Pre_Merge(____TIMEZONE_AUTO_ID, __LINE__)( \
- NAME, global_timer_manager, ScopeEventUniqueKey);
+ NAME, global_timer_manager, ScopeEventUniqueKey); \
+ DEBUG_MSG((NAME + std::string("\n")).c_str());
#define TIMEZONE_MULTI_REF(NAME) \
ScopeEvent TIMEZONE_Core_Pre_Merge(____TIMEZONE_AUTO_ID, __LINE__)( \
NAME, global_timer_manager, ScopeEventMultiRefKey);
diff --git a/cpp_build.py b/cpp_build.py
new file mode 100644
index 0000000000000000000000000000000000000000..a312191aadd3c54d1f5461823e4d39fe54355e79
--- /dev/null
+++ b/cpp_build.py
@@ -0,0 +1,85 @@
+#######################################################################
+# #
+# Copyright 2015 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 #
+# #
+#######################################################################
+
+
+
+import os
+import subprocess
+
+src_file_list = ['hdf5_tools',
+ 'full_code/get_rfields',
+ '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',
+ 'full_code/NSVEparticles',
+ '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',
+ 'fftw_tools',
+ 'spline_n1',
+ 'spline_n2',
+ 'spline_n3',
+ 'spline_n4',
+ 'spline_n5',
+ 'spline_n6',
+ 'spline_n7',
+ 'spline_n8',
+ 'spline_n9',
+ 'spline_n10',
+ 'Lagrange_polys',
+ 'scope_timer']
+
+def get_dependency_list():
+ ofile = open('dependencies.txt', 'w')
+ for src_file in src_file_list:
+ p = subprocess.Popen(
+ ['g++', '-Ibfps/cpp', '-MM', 'bfps/cpp/' + src_file + '.cpp'],
+ stdout = subprocess.PIPE)
+ out, err = p.communicate()
+ p.terminate()
+ deps = str(out, 'ASCII').replace('\\\n', '')
+ print(deps.split()[0])
+ ofile.write(' '.join(deps.split()[1:]) + '\n')
+ ofile.close()
+ return None
+
+if __name__ == '__main__':
+ #pass
+ get_dependency_list()
+
diff --git a/setup.py b/setup.py
index 7889c927cb10d0eb66d14bc422d4ba4d8436d5e8..b427ebe77ab86ec8be96b3a751a97600c629df53 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 = [
diff --git a/tests/run_all_tests.sh b/tests/run_all_tests.sh
new file mode 100644
index 0000000000000000000000000000000000000000..7865a8a3d9a3b7d56194b0dcda2bc24925aaeafd
--- /dev/null
+++ b/tests/run_all_tests.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -e
+
+bfps.test_fftw
+bfps.test_Parseval
+bfps.test_NSVEparticles
+
+# test postprocessing
+bfps PP field_single_to_double --simname dns_nsveparticles --iter0 32 --iter1 32
+bfps PP get_rfields --simname dns_nsveparticles --iter0 0 --iter1 64
+bfps PP joint_acc_vel_stats --simname dns_nsveparticles --iter0 0 --iter1 64
+bfps PP resize --simname dns_nsveparticles --new_nx 96 --new_ny 96 --new_nz 96 --new_simname dns_nsveparticles_resized