guilhem_lavaux/vide_public
0
0
Fork 0
mirror of https://bitbucket.org/cosmicvoids/vide_public.git synced 2025-07-04 15:21:11 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions

Updated CosmoTool to last revision for support of KDTree with periodic boundaries

Browse source
This commit is contained in:
Guilhem Lavaux 2013-03-05 22:43:20 -05:00
parent 6dc5cf8cc9
commit bea9fbdef4
3 changed files with 448 additions and 0 deletions
Download patch file Download diff file Expand all files Collapse all files

161
external/cosmotool/build_tools/gather_sources.py vendored Normal file
View file

@ -0,0 +1,161 @@
#+
# This is CosmoTool (./build_tools/gather_sources.py) -- Copyright (C) Guilhem Lavaux (2007-2013)
#
# guilhem.lavaux@gmail.com
#
# This software is a computer program whose purpose is to provide a toolbox for cosmological
# data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
#+
import shutil
import tempfile
import re
from git import Repo,Tree,Blob
def apply_license(license, relimit, filename):
header = re.sub(r'@FILENAME@', filename, license)
f = file(filename)
lines = f.read()
f.close()
lines = re.sub(relimit, '', lines)
lines = header + lines
with tempfile.NamedTemporaryFile(delete=False) as tmp_sources:
tmp_sources.write(lines)
shutil.move(tmp_sources.name, filename)
def apply_python_license(filename):
license="""#+
# This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2013)
#
# guilhem.lavaux@gmail.com
#
# This software is a computer program whose purpose is to provide a toolbox for cosmological
# data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
#
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
#
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
#
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
#
# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
#+
"""
print("Shell/Python file: %s" % filename)
relimit=r'^#\+\n(#.*\n)*#\+\n'
apply_license(license, relimit, filename)
def apply_cpp_license(filename):
license="""/*+
This is CosmoTool (@FILENAME@) -- Copyright (C) Guilhem Lavaux (2007-2013)
guilhem.lavaux@gmail.com
This software is a computer program whose purpose is to provide a toolbox for cosmological
data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
+*/
"""
relimit = r'^(?s)/\*\+.*\+\*/'
print("C++ file: %s" % filename)
apply_license(license, relimit, filename)
def analyze_tree(prefix, t):
for ename,entry in t.items():
if ename == 'external' or ename == 'zobov':
continue
if type(entry) == Tree:
analyze_tree(prefix + "/" + ename, entry)
elif type(entry) == Blob:
if ename == './src/hdf5_flash.h' or ename == './src/h5_readFlash.cpp' or ename == './src/h5_readFlash.hpp':
continue
if re.match(".*\.(sh|py|pyx)$",ename) != None:
fname=prefix+"/"+ename
apply_python_license(fname)
if re.match('.*\.(cpp|hpp|h)$', ename) != None:
fname=prefix+"/"+ename
apply_cpp_license(fname)
if __name__=="__main__":
repo = Repo(".")
assert repo.bare == False
t = repo.tree()
analyze_tree(".", t)

187
external/cosmotool/sample/testkd3.cpp vendored Normal file
View file

@ -0,0 +1,187 @@
/*+
This is CosmoTool (./sample/testkd3.cpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
guilhem.lavaux@gmail.com
This software is a computer program whose purpose is to provide a toolbox for cosmological
data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
+*/
#include <ctime>
#include <cassert>
#include <cstdlib>
#include <iostream>
#include <fstream>
#define __KD_TREE_NUMNODES
#include "mykdtree.hpp"
#include "kdtree_splitters.hpp"
#include <limits>
#define NTRY 30
#define NGB 24
#define ND 3
using namespace std;
using namespace CosmoTool;
typedef KDTree<ND,char,ComputePrecision,KD_homogeneous_cell_splitter<ND, char> > MyTree;
//typedef KDTree<ND,char,ComputePrecision > MyTree;
typedef KDCell<ND,char> MyCell;
static double periodic(double a)
{
while (a < -0.5)
a+=1;
while (a > 0.5)
a -= 1;
return a;
}
MyCell *findNearest(MyTree::coords& xc, MyCell *cells, uint32_t Ncells)
{
MyCell *near2 = 0;
double R2 = INFINITY;
for (int i = 0; i < Ncells; i++)
{
double d2 = 0;
for (int j = 0; j < ND; j++)
{
double delta = periodic(xc[j]-cells[i].coord[j]);
d2 += delta*delta;
}
if (d2 < R2)
{
near2 = &cells[i];
R2 = d2;
}
}
return near2;
}
int main()
{
uint32_t Ncells = 3000000;
MyCell *cells = new MyCell[Ncells];
for (int i = 0; i < Ncells; i++)
{
cells[i].active = true;
for (int l = 0; l < ND; l++)
cells[i].coord[l] = drand48();
}
// Check timing
clock_t startTimer = clock();
MyTree tree(cells, Ncells);
clock_t endTimer = clock();
tree.setPeriodic(true, 1.0);
clock_t delta = endTimer-startTimer;
double myTime = delta*1.0/CLOCKS_PER_SEC * 1.0;
cout << "KDTree build = " << myTime << " s" << endl;
MyTree::coords *xc = new MyTree::coords[NTRY];
cout << "Generating seeds..." << endl;
for (int k = 0; k < NTRY; k++)
{
for (int l = 0; l < ND; l++)
xc[k][l] = drand48();
}
// Check consistency
cout << "Check consistency..." << endl;
MyCell **ngb = new MyCell *[NGB];
double *distances = new double[NGB];
ofstream fngb("nearest.txt");
for (int k = 0; k < NTRY; k++) {
cout << "Seed = " << xc[k][0] << " " << xc[k][1] << " " << xc[k][2] << endl;
tree.getNearestNeighbours(xc[k], NGB, ngb, distances);
int last = -1;
for (uint32_t i = 0; i < NGB; i++)
{
if (ngb[i] == 0)
continue;
last = i;
double d2 = 0;
for (int l = 0; l < 3; l++)
d2 += ({double delta = periodic(xc[k][l] - ngb[i]->coord[l]); delta*delta;});
fngb << ngb[i]->coord[0] << " " << ngb[i]->coord[1] << " " << ngb[i]->coord[2] << " " << sqrt(d2) << " " << sqrt(distances[i]) << endl;
}
fngb << endl << endl;
double farther_dist = distances[last];
for (uint32_t i = 0; i < Ncells; i++)
{
bool found = false;
// If the points is not in the list, it means it is farther than the farthest point
for (int j =0; j < NGB; j++)
{
if (&cells[i] == ngb[j]) {
found = true;
break;
}
}
double dist_to_seed = 0;
for (int l = 0; l < 3; l++)
{
double delta = periodic(xc[k][l]-cells[i].coord[l]);
dist_to_seed += delta*delta;
}
double delta_epsilon = fabs(farther_dist/dist_to_seed-1);
if (!found)
{
if (dist_to_seed <= farther_dist &&
delta_epsilon > 1000*sqrt(numeric_limits<double>::epsilon()))
{
cout << "SHOULD BE IN (d=" << dist_to_seed << "): Failed iteration " << k << " particle " << i << " (farthest=" << sqrt(farther_dist) << ")" << endl;
cout << "delta_epsilon = " << delta_epsilon << endl;
abort();
}
}
else
{
if (dist_to_seed > farther_dist &&
delta_epsilon > 1000*sqrt(numeric_limits<double>::epsilon()))
{
cout << "SHOULD BE OUT (d=" << sqrt(dist_to_seed) << "): Failed iteration " << k << " particle " << i << " (farthest=" << sqrt(farther_dist) << ")" << endl;
cout << "delta_epsilon = " << delta_epsilon << " epsilon = " << 100*sqrt(numeric_limits<double>::epsilon()) << endl;
abort();
}
}
}
}
return 0;
}

100
external/cosmotool/src/replicateGenerator.hpp vendored Normal file
View file

@ -0,0 +1,100 @@
/*+
This is CosmoTool (./src/replicateGenerator.hpp) -- Copyright (C) Guilhem Lavaux (2007-2013)
guilhem.lavaux@gmail.com
This software is a computer program whose purpose is to provide a toolbox for cosmological
data analysis (e.g. filters, generalized Fourier transforms, power spectra, ...)
This software is governed by the CeCILL license under French law and
abiding by the rules of distribution of free software. You can use,
modify and/ or redistribute the software under the terms of the CeCILL
license as circulated by CEA, CNRS and INRIA at the following URL
"http://www.cecill.info".
As a counterpart to the access to the source code and rights to copy,
modify and redistribute granted by the license, users are provided only
with a limited warranty and the software's author, the holder of the
economic rights, and the successive licensors have only limited
liability.
In this respect, the user's attention is drawn to the risks associated
with loading, using, modifying and/or developing or reproducing the
software by the user in light of its specific status of free software,
that may mean that it is complicated to manipulate, and that also
therefore means that it is reserved for developers and experienced
professionals having in-depth computer knowledge. Users are therefore
encouraged to load and test the software's suitability as regards their
requirements in conditions enabling the security of their systems and/or
data to be ensured and, more generally, to use and operate it in the
same conditions as regards security.
The fact that you are presently reading this means that you have had
knowledge of the CeCILL license and that you accept its terms.
+*/
#ifndef __REPLICATE_GENERATOR_HPP
#define __REPLICATE_GENERATOR_HPP
#include <algorithm>
#include "algo.hpp"
namespace CosmoTool
{
template<typename Coord, int N>
class ReplicateGenerator
{
public:
typedef Coord Coords[N];
Coord replicate;
ReplicateGenerator(const Coords& x, Coord shift)
{
face = 0;
replicate = shift;
numFaces = spower<N,long>(3);
std::copy(x, x+N, x_base);
if (!next())
abort();
}
bool next()
{
if (face == numFaces)
return false;
face++;
bool no_move = true;
int q_face = face;
for (int i = 0; i < N; i++)
{
int c_face;
c_face = q_face % 3;
q_face /= 3;
x_shifted[i] = x_base[i] + (c_face-1)*replicate;
no_move = no_move && (c_face == 1);
}
if (no_move)
return next();
return true;
}
const Coord *getPosition()
{
return x_shifted;
}
void getPosition(Coords& x_out)
{
std::copy(x_shifted, x_shifted+N, x_out);
}
private:
Coord x_shifted[N], x_base[N];
long face, numFaces;
};
};
#endif