From 8d88006bbcbcb9d05e1b25f6a7f2b5b268bc0346 Mon Sep 17 00:00:00 2001
From: Chichi Lalescu <chichilalescu@gmail.com>
Date: Thu, 25 May 2017 21:45:53 +0200
Subject: [PATCH] real space conversion works
---
bfps/PP.py | 10 ++-
bfps/cpp/full_code/NSVE_field_stats.cpp | 94 ++++++++++++++++++++
bfps/cpp/full_code/NSVE_field_stats.hpp | 63 +++++++++++++
bfps/cpp/full_code/get_rfields.cpp | 93 +++++++++++++++++++
bfps/cpp/full_code/get_rfields.hpp | 61 +++++++++++++
bfps/cpp/full_code/native_binary_to_hdf5.cpp | 1 +
bfps/cpp/full_code/postprocess.cpp | 3 +-
setup.py | 2 +
8 files changed, 325 insertions(+), 2 deletions(-)
create mode 100644 bfps/cpp/full_code/NSVE_field_stats.cpp
create mode 100644 bfps/cpp/full_code/NSVE_field_stats.hpp
create mode 100644 bfps/cpp/full_code/get_rfields.cpp
create mode 100644 bfps/cpp/full_code/get_rfields.hpp
diff --git a/bfps/PP.py b/bfps/PP.py
index ffa0b2da..71c67286 100644
--- a/bfps/PP.py
+++ b/bfps/PP.py
@@ -451,6 +451,12 @@ class PP(_code):
self.simulation_parser_arguments(parser_native_binary_to_hdf5)
self.job_parser_arguments(parser_native_binary_to_hdf5)
self.parameters_to_parser_arguments(parser_native_binary_to_hdf5)
+ parser_get_rfields = subparsers.add_parser(
+ 'get_rfields',
+ help = 'get real space velocity field')
+ self.simulation_parser_arguments(parser_get_rfields)
+ self.job_parser_arguments(parser_get_rfields)
+ self.parameters_to_parser_arguments(parser_get_rfields)
return None
def prepare_launch(
self,
@@ -671,6 +677,8 @@ class PP(_code):
njobs = opt.njobs,
hours = opt.minutes // 60,
minutes = opt.minutes % 60,
- no_submit = opt.no_submit)
+ no_submit = opt.no_submit,
+ err_file = 'err_' + self.dns_type,
+ out_file = 'out_' + self.dns_type)
return None
diff --git a/bfps/cpp/full_code/NSVE_field_stats.cpp b/bfps/cpp/full_code/NSVE_field_stats.cpp
new file mode 100644
index 00000000..344cf2ce
--- /dev/null
+++ b/bfps/cpp/full_code/NSVE_field_stats.cpp
@@ -0,0 +1,94 @@
+#include <string>
+#include <cmath>
+#include "NSVE_field_stats.hpp"
+#include "scope_timer.hpp"
+
+
+template <typename rnumber>
+int NSVE_field_stats<rnumber>::initialize(void)
+{
+ this->postprocess::read_parameters();
+ this->vorticity = new field<rnumber, FFTW, THREE>(
+ nx, ny, nz,
+ this->comm,
+ DEFAULT_FFTW_FLAG);
+ this->vorticity->real_space_representation = false;
+ hid_t parameter_file = H5Fopen(
+ (this->simname + std::string(".h5")).c_str(),
+ H5F_ACC_RDONLY,
+ H5P_DEFAULT);
+ if (!H5Lexists(parameter_file, "field_dtype", H5P_DEFAULT))
+ this->bin_IO = NULL;
+ else
+ {
+ hid_t dset = H5Dopen(parameter_file, "field_dtype", H5P_DEFAULT);
+ hid_t space = H5Dget_space(dset);
+ hid_t memtype = H5Dget_type(dset);
+ char *string_data = (char*)malloc(256);
+ H5Dread(dset, memtype, H5S_ALL, H5S_ALL, H5P_DEFAULT, &string_data);
+ // check that we're using the correct data type
+ // field_dtype SHOULD be something like "<f4", "<f8", ">f4", ">f8"
+ // first character is ordering, which is machine specific
+ // for the other two I am checking that they have the correct values
+ assert(string_data[1] == 'f');
+ assert(string_data[2] == '0' + sizeof(rnumber));
+ free(string_data);
+ H5Sclose(space);
+ H5Tclose(memtype);
+ H5Dclose(dset);
+ this->bin_IO = new field_binary_IO<rnumber, COMPLEX, THREE>(
+ this->vorticity->clayout->sizes,
+ this->vorticity->clayout->subsizes,
+ this->vorticity->clayout->starts,
+ this->vorticity->clayout->comm);
+ }
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE_field_stats<rnumber>::read_current_cvorticity(void)
+{
+ this->vorticity->real_space_representation = false;
+ if (this->bin_IO != NULL)
+ {
+ char itername[16];
+ sprintf(itername, "i%.5x", this->iteration);
+ std::string native_binary_fname = (
+ this->simname +
+ std::string("_cvorticity_") +
+ std::string(itername));
+ this->bin_IO->read(
+ native_binary_fname,
+ this->vorticity->get_cdata());
+ }
+ else
+ {
+ this->vorticity->io(
+ this->simname + std::string("_fields.h5"),
+ "vorticity",
+ this->iteration,
+ true);
+ }
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE_field_stats<rnumber>::finalize(void)
+{
+ if (this->bin_IO != NULL)
+ delete this->bin_IO;
+ delete this->vorticity;
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int NSVE_field_stats<rnumber>::work_on_current_iteration(void)
+{
+ DEBUG_MSG("entered NSVE_field_stats::work_on_current_iteration\n");
+ return EXIT_SUCCESS;
+}
+
+template class NSVE_field_stats<float>;
+template class NSVE_field_stats<double>;
+
diff --git a/bfps/cpp/full_code/NSVE_field_stats.hpp b/bfps/cpp/full_code/NSVE_field_stats.hpp
new file mode 100644
index 00000000..d544c0c7
--- /dev/null
+++ b/bfps/cpp/full_code/NSVE_field_stats.hpp
@@ -0,0 +1,63 @@
+/**********************************************************************
+* *
+* 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_FIELD_STATS_HPP
+#define NSVE_FIELD_STATS_HPP
+
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <vector>
+#include "base.hpp"
+#include "field.hpp"
+#include "field_binary_IO.hpp"
+#include "full_code/postprocess.hpp"
+
+template <typename rnumber>
+class NSVE_field_stats: public postprocess
+{
+ private:
+ field_binary_IO<rnumber, COMPLEX, THREE> *bin_IO;
+ public:
+ field<rnumber, FFTW, THREE> *vorticity;
+
+ NSVE_field_stats(
+ const MPI_Comm COMMUNICATOR,
+ const std::string &simulation_name):
+ postprocess(
+ COMMUNICATOR,
+ simulation_name){}
+ virtual ~NSVE_field_stats(){}
+
+ virtual int initialize(void);
+ virtual int work_on_current_iteration(void);
+ virtual int finalize(void);
+
+ int read_current_cvorticity(void);
+};
+
+#endif//NSVE_FIELD_STATS_HPP
+
diff --git a/bfps/cpp/full_code/get_rfields.cpp b/bfps/cpp/full_code/get_rfields.cpp
new file mode 100644
index 00000000..0df8b564
--- /dev/null
+++ b/bfps/cpp/full_code/get_rfields.cpp
@@ -0,0 +1,93 @@
+#include <string>
+#include <cmath>
+#include "get_rfields.hpp"
+#include "scope_timer.hpp"
+
+
+template <typename rnumber>
+int get_rfields<rnumber>::initialize(void)
+{
+ this->NSVE_field_stats<rnumber>::initialize();
+ this->kk = new kspace<FFTW, SMOOTH>(
+ this->vorticity->clayout, this->dkx, this->dky, this->dkz);
+ hid_t parameter_file = H5Fopen(
+ (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->checkpoints_per_file = 1;
+ this->iteration_list = hdf5_tools::read_vector<int>(
+ parameter_file,
+ "/get_rfields/iteration_list");
+ H5Fclose(parameter_file);
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int get_rfields<rnumber>::work_on_current_iteration(void)
+{
+ DEBUG_MSG("entered get_rfields::work_on_current_iteration\n");
+ this->read_current_cvorticity();
+ field<rnumber, FFTW, THREE> *vel = new field<rnumber, FFTW, THREE>(
+ this->nx, this->ny, this->nz,
+ this->comm,
+ this->vorticity->fftw_plan_rigor);
+
+ vel->real_space_representation = false;
+ this->kk->CLOOP_K2(
+ [&](ptrdiff_t cindex,
+ ptrdiff_t xindex,
+ ptrdiff_t yindex,
+ ptrdiff_t zindex,
+ double k2){
+ if (k2 <= this->kk->kM2 && k2 > 0)
+ {
+ vel->cval(cindex,0,0) = -(this->kk->ky[yindex]*this->vorticity->cval(cindex,2,1) - this->kk->kz[zindex]*this->vorticity->cval(cindex,1,1)) / k2;
+ vel->cval(cindex,0,1) = (this->kk->ky[yindex]*this->vorticity->cval(cindex,2,0) - this->kk->kz[zindex]*this->vorticity->cval(cindex,1,0)) / k2;
+ vel->cval(cindex,1,0) = -(this->kk->kz[zindex]*this->vorticity->cval(cindex,0,1) - this->kk->kx[xindex]*this->vorticity->cval(cindex,2,1)) / k2;
+ vel->cval(cindex,1,1) = (this->kk->kz[zindex]*this->vorticity->cval(cindex,0,0) - this->kk->kx[xindex]*this->vorticity->cval(cindex,2,0)) / k2;
+ vel->cval(cindex,2,0) = -(this->kk->kx[xindex]*this->vorticity->cval(cindex,1,1) - this->kk->ky[yindex]*this->vorticity->cval(cindex,0,1)) / k2;
+ vel->cval(cindex,2,1) = (this->kk->kx[xindex]*this->vorticity->cval(cindex,1,0) - this->kk->ky[yindex]*this->vorticity->cval(cindex,0,0)) / k2;
+ }
+ else
+ std::fill_n((rnumber*)(vel->get_cdata()+3*cindex), 6, 0.0);
+ }
+ );
+ vel->symmetrize();
+ vel->ift();
+
+ std::string fname = (
+ this->simname +
+ std::string("_checkpoint_") +
+ std::to_string(this->iteration / (this->niter_out*this->checkpoints_per_file)) +
+ std::string(".h5"));
+ vel->io(
+ fname,
+ "velocity",
+ this->iteration,
+ false);
+
+ delete vel;
+ return EXIT_SUCCESS;
+}
+
+template <typename rnumber>
+int get_rfields<rnumber>::finalize(void)
+{
+ delete this->kk;
+ this->NSVE_field_stats<rnumber>::finalize();
+ return EXIT_SUCCESS;
+}
+
+template class get_rfields<float>;
+template class get_rfields<double>;
+
diff --git a/bfps/cpp/full_code/get_rfields.hpp b/bfps/cpp/full_code/get_rfields.hpp
new file mode 100644
index 00000000..ae669aa3
--- /dev/null
+++ b/bfps/cpp/full_code/get_rfields.hpp
@@ -0,0 +1,61 @@
+/**********************************************************************
+* *
+* 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 GET_RFIELDS_HPP
+#define GET_RFIELDS_HPP
+
+#include <cstdlib>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <vector>
+#include "base.hpp"
+#include "field.hpp"
+#include "field_binary_IO.hpp"
+#include "full_code/NSVE_field_stats.hpp"
+
+template <typename rnumber>
+class get_rfields: public NSVE_field_stats<rnumber>
+{
+ public:
+ int checkpoints_per_file;
+ int niter_out;
+ kspace<FFTW, SMOOTH> *kk;
+
+ get_rfields(
+ const MPI_Comm COMMUNICATOR,
+ const std::string &simulation_name):
+ NSVE_field_stats<rnumber>(
+ COMMUNICATOR,
+ simulation_name){}
+ virtual ~get_rfields(){}
+
+ int initialize(void);
+ int work_on_current_iteration(void);
+ int finalize(void);
+};
+
+#endif//GET_RFIELDS_HPP
+
diff --git a/bfps/cpp/full_code/native_binary_to_hdf5.cpp b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
index 78a29add..7774e2de 100644
--- a/bfps/cpp/full_code/native_binary_to_hdf5.cpp
+++ b/bfps/cpp/full_code/native_binary_to_hdf5.cpp
@@ -61,6 +61,7 @@ int native_binary_to_hdf5<rnumber>::read_parameters(void)
this->iteration_list = hdf5_tools::read_vector<int>(
parameter_file,
"/native_binary_to_hdf5/iteration_list");
+ H5Fclose(parameter_file);
return EXIT_SUCCESS;
}
diff --git a/bfps/cpp/full_code/postprocess.cpp b/bfps/cpp/full_code/postprocess.cpp
index 193dafeb..05242f39 100644
--- a/bfps/cpp/full_code/postprocess.cpp
+++ b/bfps/cpp/full_code/postprocess.cpp
@@ -8,6 +8,8 @@
int postprocess::main_loop(void)
{
+ DEBUG_MSG("entered postprocess::main_loop\n");
+ DEBUG_MSG("interation_list.size = %d\n", iteration_list.size());
this->start_simple_timer();
for (unsigned int iteration_counter = 0;
iteration_counter < iteration_list.size();
@@ -32,7 +34,6 @@ int postprocess::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());
parameter_file = H5Fopen(fname, H5F_ACC_RDONLY, H5P_DEFAULT);
diff --git a/setup.py b/setup.py
index cd2dd02a..1178f547 100644
--- a/setup.py
+++ b/setup.py
@@ -89,6 +89,8 @@ print('This is bfps version ' + VERSION)
### lists of files and MANIFEST.in
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',
--
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