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Commit 66ab2a6e authored by Cristian Lalescu's avatar Cristian Lalescu
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add broken distributed particles

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bfps/cpp/distributed_particles.cpp 0 → 100644
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View file @ 66ab2a6e
/**********************************************************************
* *
* 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 *
* *
**********************************************************************/
//#define NDEBUG
#include <cmath>
#include <cassert>
#include <cstring>
#include <string>
#include <sstream>
#include "base.hpp"
#include "distributed_particles.hpp"
#include "fftw_tools.hpp"
extern int myrank, nprocs;
template <int particle_type, class rnumber, int interp_neighbours>
distributed_particles<particle_type, rnumber, interp_neighbours>::distributed_particles(
const char *NAME,
interpolator<rnumber, interp_neighbours> *FIELD,
const int NPARTICLES,
const int TRAJ_SKIP,
const int INTEGRATION_STEPS)
{
switch(particle_type)
{
case VELOCITY_TRACER:
this->ncomponents = 3;
break;
default:
this->ncomponents = 3;
break;
}
assert((INTEGRATION_STEPS <= 6) &&
(INTEGRATION_STEPS >= 1));
strncpy(this->name, NAME, 256);
this->nparticles = NPARTICLES;
this->vel = FIELD;
this->integration_steps = INTEGRATION_STEPS;
this->traj_skip = TRAJ_SKIP;
this->myrank = this->vel->descriptor->myrank;
this->nprocs = this->vel->descriptor->nprocs;
this->comm = this->vel->descriptor->comm;
}
template <int particle_type, class rnumber, int interp_neighbours>
distributed_particles<particle_type, rnumber, interp_neighbours>::~distributed_particles()
{
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::roll_rhs()
{
for (int i=this->integration_steps-2; i>=0; i--)
rhs[i+1] = rhs[i];
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::AdamsBashforth(
const int nsteps)
{
this->roll_rhs();
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::step()
{
this->AdamsBashforth((this->iteration < this->integration_steps) ?
this->iteration+1 :
this->integration_steps);
this->iteration++;
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::read(
const hid_t data_file_id)
{
double *temp = new double[this->nparticles*this->ncomponents];
if (this->myrank == 0)
{
std::string temp_string = (std::string("/") +
std::string(this->name) +
std::string("/state"));
hid_t dset = H5Dopen(data_file_id, temp_string.c_str(), H5P_DEFAULT);
hid_t mspace, rspace;
hsize_t count[4], offset[4];
rspace = H5Dget_space(dset);
H5Sget_simple_extent_dims(rspace, count, NULL);
count[0] = 1;
offset[0] = this->iteration / this->traj_skip;
offset[1] = 0;
offset[2] = 0;
mspace = H5Screate_simple(3, count, NULL);
H5Sselect_hyperslab(rspace, H5S_SELECT_SET, offset, NULL, count, NULL);
H5Dread(dset, H5T_NATIVE_DOUBLE, mspace, rspace, H5P_DEFAULT, temp);
H5Sclose(mspace);
H5Sclose(rspace);
H5Dclose(dset);
}
MPI_Bcast(
temp,
this->nparticles*this->ncomponents,
MPI_DOUBLE,
0,
this->comm);
//if (this->myrank == 0)
//{
// if (this->iteration > 0)
// {
// temp_string = (std::string("/") +
// std::string(this->name) +
// std::string("/rhs"));
// dset = H5Dopen(data_file_id, temp_string.c_str(), H5P_DEFAULT);
// rspace = H5Dget_space(dset);
// H5Sget_simple_extent_dims(rspace, count, NULL);
// //reading from last available position
// offset[0] = count[0] - 1;
// offset[3] = 0;
// count[0] = 1;
// count[1] = 1;
// mspace = H5Screate_simple(4, count, NULL);
// for (int i=0; i<this->integration_steps; i++)
// {
// offset[1] = i;
// H5Sselect_hyperslab(rspace, H5S_SELECT_SET, offset, NULL, count, NULL);
// H5Dread(dset, H5T_NATIVE_DOUBLE, mspace, rspace, H5P_DEFAULT, this->rhs[i]);
// }
// H5Sclose(mspace);
// H5Sclose(rspace);
// H5Dclose(dset);
// }
//}
//MPI_Bcast(
// temp,
// this->array_size,
// MPI_DOUBLE,
// 0,
// this->comm);
//for (int i = 0; i<this->integration_steps; i++)
// MPI_Bcast(
// this->rhs[i],
// this->array_size,
// MPI_DOUBLE,
// 0,
// this->comm);
delete[] temp;
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::write(
const hid_t data_file_id,
const char *dset_name,
const double *data)
{
//std::string temp_string = (std::string(this->name) +
// std::string("/") +
// std::string(dset_name));
//hid_t dset = H5Dopen(data_file_id, temp_string.c_str(), H5P_DEFAULT);
//hid_t mspace, wspace;
//hsize_t count[3], offset[3];
//wspace = H5Dget_space(dset);
//H5Sget_simple_extent_dims(wspace, count, NULL);
//count[0] = 1;
//offset[0] = this->iteration / this->traj_skip;
//offset[1] = 0;
//offset[2] = 0;
//mspace = H5Screate_simple(3, count, NULL);
//H5Sselect_hyperslab(wspace, H5S_SELECT_SET, offset, NULL, count, NULL);
//H5Dwrite(dset, H5T_NATIVE_DOUBLE, mspace, wspace, H5P_DEFAULT, data);
//H5Sclose(mspace);
//H5Sclose(wspace);
//H5Dclose(dset);
}
template <int particle_type, class rnumber, int interp_neighbours>
void distributed_particles<particle_type, rnumber, interp_neighbours>::write(
const hid_t data_file_id,
const bool write_rhs)
{
//if (this->myrank == 0)
//{
// this->write(data_file_id, "state", this->state);
// if (write_rhs)
// {
// std::string temp_string = (
// std::string("/") +
// std::string(this->name) +
// std::string("/rhs"));
// hid_t dset = H5Dopen(data_file_id, temp_string.c_str(), H5P_DEFAULT);
// hid_t wspace = H5Dget_space(dset);
// hsize_t count[4], offset[4];
// H5Sget_simple_extent_dims(wspace, count, NULL);
// //writing to last available position
// offset[0] = count[0] - 1;
// offset[1] = 0;
// offset[2] = 0;
// offset[3] = 0;
// count[0] = 1;
// count[1] = 1;
// hid_t mspace = H5Screate_simple(4, count, NULL);
// for (int i=0; i<this->integration_steps; i++)
// {
// offset[1] = i;
// H5Sselect_hyperslab(wspace, H5S_SELECT_SET, offset, NULL, count, NULL);
// H5Dwrite(dset, H5T_NATIVE_DOUBLE, mspace, wspace, H5P_DEFAULT, this->rhs[i]);
// }
// H5Sclose(mspace);
// H5Sclose(wspace);
// H5Dclose(dset);
// }
//}
}
/*****************************************************************************/
template class distributed_particles<VELOCITY_TRACER, float, 1>;
template class distributed_particles<VELOCITY_TRACER, float, 2>;
template class distributed_particles<VELOCITY_TRACER, float, 3>;
template class distributed_particles<VELOCITY_TRACER, float, 4>;
template class distributed_particles<VELOCITY_TRACER, float, 5>;
template class distributed_particles<VELOCITY_TRACER, float, 6>;
template class distributed_particles<VELOCITY_TRACER, double, 1>;
template class distributed_particles<VELOCITY_TRACER, double, 2>;
template class distributed_particles<VELOCITY_TRACER, double, 3>;
template class distributed_particles<VELOCITY_TRACER, double, 4>;
template class distributed_particles<VELOCITY_TRACER, double, 5>;
template class distributed_particles<VELOCITY_TRACER, double, 6>;
/*****************************************************************************/
bfps/cpp/distributed_particles.hpp 0 → 100644
+ 91
− 0
View file @ 66ab2a6e
/**********************************************************************
* *
* 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 *
* *
**********************************************************************/
#include <stdio.h>
#include <stdlib.h>
#include <iostream>
#include <unordered_map>
#include <hdf5.h>
#include "base.hpp"
#include "particles_base.hpp"
#include "fluid_solver_base.hpp"
#include "interpolator.hpp"
#ifndef PARTICLES
#define PARTICLES
template <int particle_type, class rnumber, int interp_neighbours>
class distributed_particles
{
public:
int myrank, nprocs;
MPI_Comm comm;
std::unordered_map<int, single_particle_state<particle_type> > state;
std::unordered_map<int, single_particle_state<particle_type> > rhs[6];
int nparticles;
int ncomponents;
int integration_steps;
int traj_skip;
// this class only works with buffered interpolator
interpolator<rnumber, interp_neighbours> *vel;
/* simulation parameters */
char name[256];
int iteration;
double dt;
/* methods */
/* constructor and destructor.
* allocate and deallocate:
* this->state
* this->rhs
* */
distributed_particles(
const char *NAME,
interpolator<rnumber, interp_neighbours> *FIELD,
const int NPARTICLES,
const int TRAJ_SKIP,
const int INTEGRATION_STEPS = 2);
~distributed_particles();
void sample(interpolator<rnumber, interp_neighbours> *field, double *y);
/* input/output */
void read(const hid_t data_file_id);
void write(const hid_t data_file_id, const char *dset_name, const double *data);
void write(const hid_t data_file_id, const bool write_rhs = true);
/* solvers */
void step();
void roll_rhs();
void AdamsBashforth(const int nsteps);
};
#endif//PARTICLES
setup.py
+ 1
− 0
View file @ 66ab2a6e
......@@ -98,6 +98,7 @@ src_file_list = ['field_descriptor',
'rFFTW_particles',
'interpolator',
'particles',
'distributed_particles',
'fftw_tools',
'spline_n1',
'spline_n2',
......
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