guilhem_lavaux/cosmotool
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'master' of file:///home/guilhem/Dropbox/gitRoot/CosmoToolbox

Browse Source
This commit is contained in:
Guilhem Lavaux 2010-09-22 21:26:07 -04:00
commit e9a9d64924
15 changed files with 1046 additions and 119 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

39
CMakeLists.txt Normal file
View File

@ -0,0 +1,39 @@
cmake_minimum_required(VERSION 2.6)
project(CosmoToolbox)
option(BUILD_SHARED_LIBS "Build shared libraries." OFF)
find_path(NETCDF_INCLUDE_PATH NAMES netcdf.h)
find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
find_library(NETCDF_LIBRARY netcdf)
find_library(NETCDFCPP_LIBRARY netcdf_c++)
find_library(GSL_LIBRARY gsl)
find_library(GSLCBLAS_LIBRARY gslcblas)
include(FindPackageHandleStandardArgs)
set(NETCDF_FIND_REQUIRED TRUE)
set(GSL_FIND_REQUIRED TRUE)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(NetCDF DEFAULT_MSG NETCDF_LIBRARY NETCDFCPP_LIBRARY NETCDF_INCLUDE_PATH)
FIND_PACKAGE_HANDLE_STANDARD_ARGS(GSL DEFAULT_MSG GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
# CPACK Configuration
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "0")
SET(CPACK_PACKAGE_VERSION_PATCH "0")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${GalaxExplorer_VERSION_MAJOR}.${GalaxExplorer_VERSION_MINOR}")
SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
SET(CPACK_SOURCE_IGNORE_FILES
"/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
add_subdirectory(src)
add_subdirectory(sample)
include(CPack)

506
LICENCE_CeCILL_V2 Normal file
View File

@ -0,0 +1,506 @@
CeCILL FREE SOFTWARE LICENSE AGREEMENT
Notice
This Agreement is a Free Software license agreement that is the result
of discussions between its authors in order to ensure compliance with
the two main principles guiding its drafting:
* firstly, compliance with the principles governing the distribution
of Free Software: access to source code, broad rights granted to
users,
* secondly, the election of a governing law, French law, with which
it is conformant, both as regards the law of torts and
intellectual property law, and the protection that it offers to
both authors and holders of the economic rights over software.
The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
license are:
Commissariat à l'Energie Atomique - CEA, a public scientific, technical
and industrial research establishment, having its principal place of
business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
Centre National de la Recherche Scientifique - CNRS, a public scientific
and technological establishment, having its principal place of business
at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
Institut National de Recherche en Informatique et en Automatique -
INRIA, a public scientific and technological establishment, having its
principal place of business at Domaine de Voluceau, Rocquencourt, BP
105, 78153 Le Chesnay cedex, France.
Preamble
The purpose of this Free Software license agreement is to grant users
the right to modify and redistribute the software governed by this
license within the framework of an open source distribution model.
The exercising of these rights is conditional upon certain obligations
for users so as to preserve this status for all subsequent redistributions.
In consideration of access to the source code and the 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 only have limited liability.
In this respect, the risks associated with loading, using, modifying
and/or developing or reproducing the software by the user are brought to
the user's attention, given its Free Software status, which may make it
complicated to use, with the result that its use is reserved for
developers and experienced professionals having in-depth computer
knowledge. Users are therefore encouraged to load and test the
suitability of the software 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 of
security. This Agreement may be freely reproduced and published,
provided it is not altered, and that no provisions are either added or
removed herefrom.
This Agreement may apply to any or all software for which the holder of
the economic rights decides to submit the use thereof to its provisions.
Article 1 - DEFINITIONS
For the purpose of this Agreement, when the following expressions
commence with a capital letter, they shall have the following meaning:
Agreement: means this license agreement, and its possible subsequent
versions and annexes.
Software: means the software in its Object Code and/or Source Code form
and, where applicable, its documentation, "as is" when the Licensee
accepts the Agreement.
Initial Software: means the Software in its Source Code and possibly its
Object Code form and, where applicable, its documentation, "as is" when
it is first distributed under the terms and conditions of the Agreement.
Modified Software: means the Software modified by at least one
Contribution.
Source Code: means all the Software's instructions and program lines to
which access is required so as to modify the Software.
Object Code: means the binary files originating from the compilation of
the Source Code.
Holder: means the holder(s) of the economic rights over the Initial
Software.
Licensee: means the Software user(s) having accepted the Agreement.
Contributor: means a Licensee having made at least one Contribution.
Licensor: means the Holder, or any other individual or legal entity, who
distributes the Software under the Agreement.
Contribution: means any or all modifications, corrections, translations,
adaptations and/or new functions integrated into the Software by any or
all Contributors, as well as any or all Internal Modules.
Module: means a set of sources files including their documentation that
enables supplementary functions or services in addition to those offered
by the Software.
External Module: means any or all Modules, not derived from the
Software, so that this Module and the Software run in separate address
spaces, with one calling the other when they are run.
Internal Module: means any or all Module, connected to the Software so
that they both execute in the same address space.
GNU GPL: means the GNU General Public License version 2 or any
subsequent version, as published by the Free Software Foundation Inc.
Parties: mean both the Licensee and the Licensor.
These expressions may be used both in singular and plural form.
Article 2 - PURPOSE
The purpose of the Agreement is the grant by the Licensor to the
Licensee of a non-exclusive, transferable and worldwide license for the
Software as set forth in Article 5 hereinafter for the whole term of the
protection granted by the rights over said Software.
Article 3 - ACCEPTANCE
3.1 The Licensee shall be deemed as having accepted the terms and
conditions of this Agreement upon the occurrence of the first of the
following events:
* (i) loading the Software by any or all means, notably, by
downloading from a remote server, or by loading from a physical
medium;
* (ii) the first time the Licensee exercises any of the rights
granted hereunder.
3.2 One copy of the Agreement, containing a notice relating to the
characteristics of the Software, to the limited warranty, and to the
fact that its use is restricted to experienced users has been provided
to the Licensee prior to its acceptance as set forth in Article 3.1
hereinabove, and the Licensee hereby acknowledges that it has read and
understood it.
Article 4 - EFFECTIVE DATE AND TERM
4.1 EFFECTIVE DATE
The Agreement shall become effective on the date when it is accepted by
the Licensee as set forth in Article 3.1.
4.2 TERM
The Agreement shall remain in force for the entire legal term of
protection of the economic rights over the Software.
Article 5 - SCOPE OF RIGHTS GRANTED
The Licensor hereby grants to the Licensee, who accepts, the following
rights over the Software for any or all use, and for the term of the
Agreement, on the basis of the terms and conditions set forth hereinafter.
Besides, if the Licensor owns or comes to own one or more patents
protecting all or part of the functions of the Software or of its
components, the Licensor undertakes not to enforce the rights granted by
these patents against successive Licensees using, exploiting or
modifying the Software. If these patents are transferred, the Licensor
undertakes to have the transferees subscribe to the obligations set
forth in this paragraph.
5.1 RIGHT OF USE
The Licensee is authorized to use the Software, without any limitation
as to its fields of application, with it being hereinafter specified
that this comprises:
1. permanent or temporary reproduction of all or part of the Software
by any or all means and in any or all form.
2. loading, displaying, running, or storing the Software on any or
all medium.
3. entitlement to observe, study or test its operation so as to
determine the ideas and principles behind any or all constituent
elements of said Software. This shall apply when the Licensee
carries out any or all loading, displaying, running, transmission
or storage operation as regards the Software, that it is entitled
to carry out hereunder.
5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
The right to make Contributions includes the right to translate, adapt,
arrange, or make any or all modifications to the Software, and the right
to reproduce the resulting software.
The Licensee is authorized to make any or all Contributions to the
Software provided that it includes an explicit notice that it is the
author of said Contribution and indicates the date of the creation thereof.
5.3 RIGHT OF DISTRIBUTION
In particular, the right of distribution includes the right to publish,
transmit and communicate the Software to the general public on any or
all medium, and by any or all means, and the right to market, either in
consideration of a fee, or free of charge, one or more copies of the
Software by any means.
The Licensee is further authorized to distribute copies of the modified
or unmodified Software to third parties according to the terms and
conditions set forth hereinafter.
5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
The Licensee is authorized to distribute true copies of the Software in
Source Code or Object Code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:
1. a copy of the Agreement,
2. a notice relating to the limitation of both the Licensor's
warranty and liability as set forth in Articles 8 and 9,
and that, in the event that only the Object Code of the Software is
redistributed, the Licensee allows future Licensees unhindered access to
the full Source Code of the Software by indicating how to access it, it
being understood that the additional cost of acquiring the Source Code
shall not exceed the cost of transferring the data.
5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
When the Licensee makes a Contribution to the Software, the terms and
conditions for the distribution of the resulting Modified Software
become subject to all the provisions of this Agreement.
The Licensee is authorized to distribute the Modified Software, in
source code or object code form, provided that said distribution
complies with all the provisions of the Agreement and is accompanied by:
1. a copy of the Agreement,
2. a notice relating to the limitation of both the Licensor's
warranty and liability as set forth in Articles 8 and 9,
and that, in the event that only the object code of the Modified
Software is redistributed, the Licensee allows future Licensees
unhindered access to the full source code of the Modified Software by
indicating how to access it, it being understood that the additional
cost of acquiring the source code shall not exceed the cost of
transferring the data.
5.3.3 DISTRIBUTION OF EXTERNAL MODULES
When the Licensee has developed an External Module, the terms and
conditions of this Agreement do not apply to said External Module, that
may be distributed under a separate license agreement.
5.3.4 COMPATIBILITY WITH THE GNU GPL
The Licensee can include a code that is subject to the provisions of one
of the versions of the GNU GPL in the Modified or unmodified Software,
and distribute that entire code under the terms of the same version of
the GNU GPL.
The Licensee can include the Modified or unmodified Software in a code
that is subject to the provisions of one of the versions of the GNU GPL,
and distribute that entire code under the terms of the same version of
the GNU GPL.
Article 6 - INTELLECTUAL PROPERTY
6.1 OVER THE INITIAL SOFTWARE
The Holder owns the economic rights over the Initial Software. Any or
all use of the Initial Software is subject to compliance with the terms
and conditions under which the Holder has elected to distribute its work
and no one shall be entitled to modify the terms and conditions for the
distribution of said Initial Software.
The Holder undertakes that the Initial Software will remain ruled at
least by this Agreement, for the duration set forth in Article 4.2.
6.2 OVER THE CONTRIBUTIONS
The Licensee who develops a Contribution is the owner of the
intellectual property rights over this Contribution as defined by
applicable law.
6.3 OVER THE EXTERNAL MODULES
The Licensee who develops an External Module is the owner of the
intellectual property rights over this External Module as defined by
applicable law and is free to choose the type of agreement that shall
govern its distribution.
6.4 JOINT PROVISIONS
The Licensee expressly undertakes:
1. not to remove, or modify, in any manner, the intellectual property
notices attached to the Software;
2. to reproduce said notices, in an identical manner, in the copies
of the Software modified or not.
The Licensee undertakes not to directly or indirectly infringe the
intellectual property rights of the Holder and/or Contributors on the
Software and to take, where applicable, vis-à-vis its staff, any and all
measures required to ensure respect of said intellectual property rights
of the Holder and/or Contributors.
Article 7 - RELATED SERVICES
7.1 Under no circumstances shall the Agreement oblige the Licensor to
provide technical assistance or maintenance services for the Software.
However, the Licensor is entitled to offer this type of services. The
terms and conditions of such technical assistance, and/or such
maintenance, shall be set forth in a separate instrument. Only the
Licensor offering said maintenance and/or technical assistance services
shall incur liability therefor.
7.2 Similarly, any Licensor is entitled to offer to its licensees, under
its sole responsibility, a warranty, that shall only be binding upon
itself, for the redistribution of the Software and/or the Modified
Software, under terms and conditions that it is free to decide. Said
warranty, and the financial terms and conditions of its application,
shall be subject of a separate instrument executed between the Licensor
and the Licensee.
Article 8 - LIABILITY
8.1 Subject to the provisions of Article 8.2, the Licensee shall be
entitled to claim compensation for any direct loss it may have suffered
from the Software as a result of a fault on the part of the relevant
Licensor, subject to providing evidence thereof.
8.2 The Licensor's liability is limited to the commitments made under
this Agreement and shall not be incurred as a result of in particular:
(i) loss due the Licensee's total or partial failure to fulfill its
obligations, (ii) direct or consequential loss that is suffered by the
Licensee due to the use or performance of the Software, and (iii) more
generally, any consequential loss. In particular the Parties expressly
agree that any or all pecuniary or business loss (i.e. loss of data,
loss of profits, operating loss, loss of customers or orders,
opportunity cost, any disturbance to business activities) or any or all
legal proceedings instituted against the Licensee by a third party,
shall constitute consequential loss and shall not provide entitlement to
any or all compensation from the Licensor.
Article 9 - WARRANTY
9.1 The Licensee acknowledges that the scientific and technical
state-of-the-art when the Software was distributed did not enable all
possible uses to be tested and verified, nor for the presence of
possible defects to be detected. In this respect, the Licensee's
attention has been drawn to the risks associated with loading, using,
modifying and/or developing and reproducing the Software which are
reserved for experienced users.
The Licensee shall be responsible for verifying, by any or all means,
the suitability of the product for its requirements, its good working
order, and for ensuring that it shall not cause damage to either persons
or properties.
9.2 The Licensor hereby represents, in good faith, that it is entitled
to grant all the rights over the Software (including in particular the
rights set forth in Article 5).
9.3 The Licensee acknowledges that the Software is supplied "as is" by
the Licensor without any other express or tacit warranty, other than
that provided for in Article 9.2 and, in particular, without any warranty
as to its commercial value, its secured, safe, innovative or relevant
nature.
Specifically, the Licensor does not warrant that the Software is free
from any error, that it will operate without interruption, that it will
be compatible with the Licensee's own equipment and software
configuration, nor that it will meet the Licensee's requirements.
9.4 The Licensor does not either expressly or tacitly warrant that the
Software does not infringe any third party intellectual property right
relating to a patent, software or any other property right. Therefore,
the Licensor disclaims any and all liability towards the Licensee
arising out of any or all proceedings for infringement that may be
instituted in respect of the use, modification and redistribution of the
Software. Nevertheless, should such proceedings be instituted against
the Licensee, the Licensor shall provide it with technical and legal
assistance for its defense. Such technical and legal assistance shall be
decided on a case-by-case basis between the relevant Licensor and the
Licensee pursuant to a memorandum of understanding. The Licensor
disclaims any and all liability as regards the Licensee's use of the
name of the Software. No warranty is given as regards the existence of
prior rights over the name of the Software or as regards the existence
of a trademark.
Article 10 - TERMINATION
10.1 In the event of a breach by the Licensee of its obligations
hereunder, the Licensor may automatically terminate this Agreement
thirty (30) days after notice has been sent to the Licensee and has
remained ineffective.
10.2 A Licensee whose Agreement is terminated shall no longer be
authorized to use, modify or distribute the Software. However, any
licenses that it may have granted prior to termination of the Agreement
shall remain valid subject to their having been granted in compliance
with the terms and conditions hereof.
Article 11 - MISCELLANEOUS
11.1 EXCUSABLE EVENTS
Neither Party shall be liable for any or all delay, or failure to
perform the Agreement, that may be attributable to an event of force
majeure, an act of God or an outside cause, such as defective
functioning or interruptions of the electricity or telecommunications
networks, network paralysis following a virus attack, intervention by
government authorities, natural disasters, water damage, earthquakes,
fire, explosions, strikes and labor unrest, war, etc.
11.2 Any failure by either Party, on one or more occasions, to invoke
one or more of the provisions hereof, shall under no circumstances be
interpreted as being a waiver by the interested Party of its right to
invoke said provision(s) subsequently.
11.3 The Agreement cancels and replaces any or all previous agreements,
whether written or oral, between the Parties and having the same
purpose, and constitutes the entirety of the agreement between said
Parties concerning said purpose. No supplement or modification to the
terms and conditions hereof shall be effective as between the Parties
unless it is made in writing and signed by their duly authorized
representatives.
11.4 In the event that one or more of the provisions hereof were to
conflict with a current or future applicable act or legislative text,
said act or legislative text shall prevail, and the Parties shall make
the necessary amendments so as to comply with said act or legislative
text. All other provisions shall remain effective. Similarly, invalidity
of a provision of the Agreement, for any reason whatsoever, shall not
cause the Agreement as a whole to be invalid.
11.5 LANGUAGE
The Agreement is drafted in both French and English and both versions
are deemed authentic.
Article 12 - NEW VERSIONS OF THE AGREEMENT
12.1 Any person is authorized to duplicate and distribute copies of this
Agreement.
12.2 So as to ensure coherence, the wording of this Agreement is
protected and may only be modified by the authors of the License, who
reserve the right to periodically publish updates or new versions of the
Agreement, each with a separate number. These subsequent versions may
address new issues encountered by Free Software.
12.3 Any Software distributed under a given version of the Agreement may
only be subsequently distributed under the same version of the Agreement
or a subsequent version, subject to the provisions of Article 5.3.4.
Article 13 - GOVERNING LAW AND JURISDICTION
13.1 The Agreement is governed by French law. The Parties agree to
endeavor to seek an amicable solution to any disagreements or disputes
that may arise during the performance of the Agreement.
13.2 Failing an amicable solution within two (2) months as from their
occurrence, and unless emergency proceedings are necessary, the
disagreements or disputes shall be referred to the Paris Courts having
jurisdiction, by the more diligent Party.
Version 2.0 dated 2006-09-05.

51
lib/Makefile
View File

@ -1,51 +0,0 @@
SHLIBS= libCosmoTool.so
SOURCES= loadRamses.cpp yorick.cpp miniargs.cpp fortran.cpp interpolate.cpp load_data.cpp powerSpectrum.cpp octTree.cpp loadGadget.cpp
LIBS= -lnetcdf_c++ -lnetcdf -lgsl -lgslcblas -lm
include config.mk
VPATH=../src
all: $(SHLIBS)
libCosmoTool.so: loadRamses.o yorick.o miniargs.o fortran.o interpolate.o load_data.o powerSpectrum.o octTree.o loadGadget.o
depend: $(SOURCES)
@echo "[DEPENDS] $^"
@$(CC) $(CPPFLAGS) -M -MM $^ > .mydepends
install:
@mkdir -p ../install/lib
@mkdir -p ../install/include/CosmoTool
@echo "Copying libraries"
@cp libCosmoTool.so ../install/lib
@echo "Copying header files"
@cp ../src/*.hpp ../install/include/CosmoTool
@cp ../src/*.tcc ../install/include/CosmoTool
distclean: clean
@rm -f .mydepends
clean:
@rm -f *.o
@rm -f $(PROGS)
.mydepends: depend Makefile config.mk
%.so:
@echo "[LINK SHARED] $@"
@$(CXX) -shared -o $@ $^ $(LDFLAGS) $(LIBS)
%.prog:
@echo "[L] $@"
@$(CXX) -o $@ $^ $(LDFLAGS) $(LIBS)
%.o: %.c
@echo "[C] $< ..."
@$(CC) -c -fPIC -o $@ $< $(CPPFLAGS) $(CFLAGS)
%.o: %.cpp
@echo "[C++] $< ..."
@$(CXX) -c -fPIC -o $@ $< $(CPPFLAGS) $(CXXFLAGS)
include .mydepends

6
lib/config.mk
View File

@ -1,6 +0,0 @@
CC=gcc
CXX=g++
CFLAGS=-ggdb -O0
CXXFLAGS=-ggdb -O0
LDFLAGS=
CPPFLAGS=

20
sample/CMakeLists.txt Normal file
View File

@ -0,0 +1,20 @@
SET(tolink CosmoTool ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
include_directories(${CMAKE_SOURCE_DIR}/src)
add_executable(testBQueue testBQueue.cpp)
target_link_libraries(testBQueue ${tolink})
add_executable(testInterpolate testInterpolate.cpp)
target_link_libraries(testInterpolate ${tolink})
add_executable(testSmooth testSmooth.cpp)
target_link_libraries(testSmooth ${tolink})
add_executable(testkd testkd.cpp)
target_link_libraries(testkd ${tolink})
add_executable(testkd2 testkd2.cpp)
target_link_libraries(testkd2 ${tolink})
add_executable(testDelaunay testDelaunay.cpp)
target_link_libraries(testDelaunay ${tolink})

2
sample/testBQueue.cpp
View File

@ -5,7 +5,7 @@ using namespace std;
int main(int argc, char **argv)
{
CosmoTool::BoundedQueue<int,int,100000> bq(4);
CosmoTool::BoundedQueue<int,int> bq(4, 100000.);
for (int i = 10; i >= 0; i--)
{

28
sample/testDelaunay.cpp Normal file
View File

@ -0,0 +1,28 @@
#include <iostream>
#include "dinterpolate.hpp"
#define NX 10
#define NY 10
using namespace std;
using namespace CosmoTool;
typedef DelaunayInterpolate<double,double,2> myTriangle;
int main()
{
myTriangle::CoordType pos[] = { {0,0}, {1,0}, {0,1}, {1, 1} } ;
double vals[] = { 0, 1, 1, 0 };
uint32_t simplex[] = { 0, 1, 2, 3, 1, 2 };
myTriangle t(&pos[0], &vals[0], &simplex[0], 4, 2);
for (uint32_t iy = 0; iy <= NY; iy++) {
for (uint32_t ix = 0; ix <= NX; ix++) {
myTriangle::CoordType inter = { ix *1.0/ NX, iy *1.0/NY };
cout << inter[1] << " " << inter[0] << " " << t.computeValue(inter) << endl;
}
cout << endl;
}
return 0;
}

30
sample/testInterpolate.cpp Normal file
View File

@ -0,0 +1,30 @@
#include <iostream>
#include "interpolate3d.hpp"
using namespace std;
using namespace CosmoTool;
int main()
{
VectorField<float,2> *vectors = new VectorField<float,2>[8];
for (int i = 0; i < 2; i++)
for (int j = 0; j < 2; j++)
for (int k = 0; k < 2; k++)
{
int idx = i + 2*(j + 2*k);
vectors[idx].vec[0] = i;
vectors[idx].vec[1] = j;
}
GridSampler<VectorField<float,2> > sampler(vectors, 2, 2, 2, 2);
Interpolate3D<GridSampler<VectorField<float,2> > > inter(sampler);
VectorField<float,2> v = inter.get(0.5,0.5,0.5);
VectorField<float,2> v2 = inter.get(1.5,1.5,1.5);
cout << v.vec[0] << " " << v.vec[1] << endl;
cout << v2.vec[0] << " " << v2.vec[1] << endl;
return 0;
}

68
sample/testSmooth.cpp Normal file
View File

@ -0,0 +1,68 @@
#include <iostream>
#include "sphSmooth.hpp"
#include "yorick.hpp"
#include "mykdtree.hpp"
using namespace std;
using namespace CosmoTool;
#define NX 1024
#define ND 2
typedef SPHSmooth<char,ND> MySmooth;
typedef MySmooth::SPHTree MyTree;
typedef MySmooth::SPHNode MyNode;
typedef MySmooth::SPHCell MyCell;
double unit_fun(const char& c)
{
return 1.0;
}
int main()
{
uint32_t Ncells = 10000;
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();
cells[i].val.weight = 0;
}
MyTree tree(cells, Ncells);
MySmooth smooth(&tree, 16);
for (uint32_t iy = 0; iy < NX; iy++)
{
cout << "iy=" << iy << endl;
for (uint32_t ix = 0; ix < NX; ix++)
{
MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
smooth.fetchNeighbours(c);
smooth.addGridSite(c);
}
}
uint32_t dims[] = { NX, NX };
ProgressiveOutput<ComputePrecision> out =
ProgressiveOutput<ComputePrecision>::saveArrayProgressive("out.nc", dims, 2);
for (uint32_t iy = 0; iy < NX; iy++)
{
cout << "iy=" << iy << endl;
for (uint32_t ix = 0; ix < NX; ix++)
{
MyTree::coords c = { 1.0*ix/NX, 1.0*iy/NX };
smooth.fetchNeighbours(c);
out.put(smooth.computeSmoothedValue(c, unit_fun));
}
}
return 0;
}

45
src/CMakeLists.txt Normal file
View File

@ -0,0 +1,45 @@
SET(CosmoTool_SRCS
fortran.cpp
interpolate.cpp
load_data.cpp
loadGadget.cpp
loadRamses.cpp
octTree.cpp
powerSpectrum.cpp
yorick.cpp
miniargs.cpp
)
SET(CosmoTool_SRCS ${CosmoTool_SRCS}
bqueue.hpp
config.hpp
dinterpolate.hpp
field.hpp
fixArray.hpp
fortran.hpp
interpolate3d.hpp
interpolate.hpp
kdtree_leaf.hpp
load_data.hpp
loadGadget.hpp
loadRamses.hpp
loadSimu.hpp
miniargs.hpp
mykdtree.hpp
octTree.hpp
powerSpectrum.hpp
sparseGrid.hpp
sphSmooth.hpp
yorick.hpp
)
add_library(CosmoTool ${CosmoTool_SRCS})
target_link_libraries(CosmoTool ${NETCDF_LIBRARY} ${NETCDFCPP_LIBRARY} ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
install(TARGETS CosmoTool
LIBRARY DESTINATION lib
ARCHIVE DESTINATION lib)
install(DIRECTORY . DESTINATION include/CosmoTool
FILES_MATCHING PATTERN "*.hpp")
install(DIRECTORY . DESTINATION include/CosmoTool
FILES_MATCHING PATTERN "*.tcc")

165
src/loadGadget.cpp
View File

@ -1,3 +1,4 @@
#include <iostream>
#include <assert.h>
#include <stdio.h>
#include <stdlib.h>
@ -6,6 +7,7 @@
#include "fortran.hpp"
using namespace CosmoTool;
using namespace std;
PurePositionData *CosmoTool::loadGadgetPosition(const char *fname)
{
@ -93,33 +95,54 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
return 0;
}
f->beginCheckpoint();
for (int i = 0; i < 6; i++)
h.npart[i] = f->readInt32();
for (int i = 0; i < 6; i++)
h.mass[i] = f->readReal64();
data->time = h.time = f->readReal64();
h.redshift = f->readReal64();
h.flag_sfr = f->readInt32();
h.flag_feedback = f->readInt32();
for (int i = 0; i < 6; i++)
h.npartTotal[i] = f->readInt32();
h.flag_cooling = f->readInt32();
h.num_files = f->readInt32();
data->BoxSize = h.BoxSize = f->readReal64();
h.Omega0 = f->readReal64();
h.OmegaLambda = f->readReal64();
h.HubbleParam = f->readReal64();
f->endCheckpoint(true);
long NumPart = 0, NumPartTotal = 0;
for(int k=0; k<5; k++)
try
{
NumPart += h.npart[k];
NumPartTotal += (id < 0) ? h.npart[k] : h.npartTotal[k];
f->beginCheckpoint();
for (int i = 0; i < 6; i++)
h.npart[i] = f->readInt32();
for (int i = 0; i < 6; i++)
h.mass[i] = f->readReal64();
data->time = h.time = f->readReal64();
h.redshift = f->readReal64();
h.flag_sfr = f->readInt32();
h.flag_feedback = f->readInt32();
for (int i = 0; i < 6; i++)
h.npartTotal[i] = f->readInt32();
h.flag_cooling = f->readInt32();
h.num_files = f->readInt32();
data->BoxSize = h.BoxSize = f->readReal64();
h.Omega0 = f->readReal64();
h.OmegaLambda = f->readReal64();
h.HubbleParam = f->readReal64();
f->endCheckpoint(true);
for(int k=0; k<6; k++)
{
NumPart += h.npart[k];
NumPartTotal += (id < 0) ? h.npart[k] : h.npartTotal[k];
}
data->NumPart = NumPart;
data->TotalNumPart = NumPartTotal;
}
catch (const InvalidUnformattedAccess& e)
{
cerr << "Invalid format while reading header" << endl;
delete data;
delete f;
return 0;
}
if (loadflags & NEED_TYPE)
{
int p = 0;
data->type = new int[data->NumPart];
for (int k = 0; k < 6; k++)
for (int n = 0; n < h.npart[k]; n++,p++)
data->type[p] = k;
}
data->NumPart = NumPart;
data->TotalNumPart = NumPartTotal;
if (loadflags & NEED_POSITION) {
@ -131,16 +154,26 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
}
}
f->beginCheckpoint();
for(int k = 0, p = 0; k < 5; k++) {
for(int n = 0; n < h.npart[k]; n++) {
data->Pos[0][p] = f->readReal32();
data->Pos[1][p] = f->readReal32();
data->Pos[2][p] = f->readReal32();
p++;
try
{
f->beginCheckpoint();
for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) {
data->Pos[0][p] = f->readReal32();
data->Pos[1][p] = f->readReal32();
data->Pos[2][p] = f->readReal32();
p++;
}
}
f->endCheckpoint();
}
catch (const InvalidUnformattedAccess& e)
{
cerr << "Invalid format while reading positions" << endl;
delete f;
delete data;
return 0;
}
}
f->endCheckpoint();
} else {
// Skip positions
@ -153,21 +186,32 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
data->Vel[i] = new float[data->NumPart];
if (data->Vel[i] == 0)
{
delete f;
delete data;
return 0;
}
}
f->beginCheckpoint();
for(int k = 0, p = 0; k < 5; k++) {
for(int n = 0; n < h.npart[k]; n++) {
data->Vel[0][p] = f->readReal32();
data->Vel[1][p] = f->readReal32();
data->Vel[2][p] = f->readReal32();
p++;
try
{
f->beginCheckpoint();
for(int k = 0, p = 0; k < 6; k++) {
for(int n = 0; n < h.npart[k]; n++) {
data->Vel[0][p] = f->readReal32();
data->Vel[1][p] = f->readReal32();
data->Vel[2][p] = f->readReal32();
p++;
}
}
f->endCheckpoint();
}
catch (const InvalidUnformattedAccess& e)
{
cerr << "Invalid format while reading velocities" << endl;
delete f;
delete data;
return 0;
}
}
f->endCheckpoint();
// TODO: FIX THE UNITS OF THESE FUNKY VELOCITIES !!!
} else {
@ -177,23 +221,34 @@ SimuData *CosmoTool::loadGadgetMulti(const char *fname, int id, int loadflags)
// Skip ids
if (loadflags & NEED_GADGET_ID) {
f->beginCheckpoint();
data->Id = new int[data->NumPart];
if (data->Id == 0)
try
{
f->beginCheckpoint();
data->Id = new int[data->NumPart];
if (data->Id == 0)
{
delete f;
delete data;
return 0;
}
for(int k = 0, p = 0; k < 6; k++)
{
for(int n = 0; n < h.npart[k]; n++)
{
data->Id[p] = f->readInt32();
p++;
}
}
f->endCheckpoint();
}
catch (const InvalidUnformattedAccess& e)
{
cerr << "Invalid formatted while reading ID" << endl;
delete f;
delete data;
return 0;
}
for(int k = 0, p = 0; k < 6; k++)
{
for(int n = 0; n < h.npart[k]; n++)
{
data->Id[p] = f->readInt32();
p++;
}
}
f->endCheckpoint();
} else {
f->skip(2*4);
for (int k = 0; k < 6; k++)

174
src/loadRamses.cpp
View File

@ -203,7 +203,7 @@ int readInfoFile(const char *basename, int outputId, InfoData& info)
ostringstream ss_fname;
ss_fname << basename << "/info_" << setfill('0') << setw(5) << outputId << ".txt";
cout << "Opening info file " << ss_fname.str() << endl;
// cout << "Opening info file " << ss_fname.str() << endl;
ifstream infile(ss_fname.str().c_str());
if (!infile)
return 0;
@ -255,6 +255,178 @@ int readInfoFile(const char *basename, int outputId, InfoData& info)
return 1;
}
CosmoTool::SimuData *CosmoTool::loadRamsesSimu(const char *basename, int outputId, int cpuid, int flags)
{
CosmoTool::SimuData *data = new CosmoTool::SimuData();
int id = 1;
uint32_t totPart = 0;
int nCpu = 0;
InfoData info;
static const double CM_IN_MPC = 3.08e24;
if (!readInfoFile(basename, outputId, info))
return 0;
double hubble = info.aexp*info.aexp/info.unit_t / (1e5/CM_IN_MPC);
double L0 = info.boxSize*info.unitLength*hubble/100/CM_IN_MPC/info.aexp;
double unit_vel = L0*hubble/info.aexp;
while (1)
{
ostringstream ss_fname;
ss_fname << basename << "/part_" << setfill('0') << setw(5) << outputId << ".out" << setfill('0') << setw(5) << id;
string fname = ss_fname.str();
try
{
UnformattedRead infile(fname);
int ndim, nPar;
infile.beginCheckpoint();
nCpu = max(1,infile.readInt32());
infile.endCheckpoint();
infile.beginCheckpoint();
ndim = infile.readInt32();
infile.endCheckpoint();
infile.beginCheckpoint();
nPar = infile.readInt32();
infile.endCheckpoint();
totPart += nPar;
id++;
}
catch (const NoSuchFileException& e)
{
break;
}
}
data->BoxSize = L0;
data->time = info.aexp;
data->NumPart = 0;
data->TotalNumPart = totPart;
if (cpuid < 0)
cpuid = 1;
else cpuid++;
uint32_t curPos = 0;
ostringstream ss_fname;
ss_fname << basename << "/part_" << setfill('0') << setw(5) << outputId << ".out" << setfill('0') << setw(5) << cpuid;
string fname = ss_fname.str();
try
{
UnformattedRead infile(fname);
int nCpu, ndim, nPar;
infile.beginCheckpoint();
nCpu = infile.readInt32();
infile.endCheckpoint();
infile.beginCheckpoint();
ndim = infile.readInt32();
infile.endCheckpoint();
infile.beginCheckpoint();
data->NumPart = nPar = infile.readInt32();
infile.endCheckpoint();
if (flags & NEED_POSITION)
{
data->Pos[0] = new float[nPar];
data->Pos[1] = new float[nPar];
data->Pos[2] = new float[nPar];
}
if (flags & NEED_VELOCITY)
{
data->Vel[0] = new float[nPar];
data->Vel[1] = new float[nPar];
data->Vel[2] = new float[nPar];
}
if (flags & NEED_GADGET_ID)
{
data->Id = new int[nPar];
}
for (int k = 0; k < 3; k++)
{
infile.beginCheckpoint();
if (flags & NEED_POSITION)
{
for (uint32_t i = 0; i < nPar; i++)
{
data->Pos[k][i] = infile.readReal32();
data->Pos[k][i] *= data->BoxSize;
}
infile.endCheckpoint();
}
else
infile.endCheckpoint(true);
}
for (int k = 0; k < 3; k++) {
infile.beginCheckpoint();
if (flags & NEED_VELOCITY)
{
for (uint32_t i = 0; i < nPar; i++)
{
data->Vel[k][i] = infile.readReal32();
data->Vel[k][i] *= unit_vel;
}
infile.endCheckpoint();
}
else
infile.endCheckpoint(true);
}
float minMass = INFINITY;
infile.beginCheckpoint();
for (uint32_t i = nPar; i > 0; i--)
{
float dummyF = infile.readReal32();
if (dummyF < minMass) minMass = dummyF;
}
infile.endCheckpoint();
infile.beginCheckpoint();
if (flags & NEED_GADGET_ID)
{
for (uint32_t i = 0; i < nPar; i++)
data->Id[i] = infile.readInt32();
infile.endCheckpoint();
}
else
infile.endCheckpoint(true);
curPos += nPar;
}
catch (const NoSuchFileException& e)
{
cerr << "No such file " << fname << endl;
delete data;
return 0;
}
return data;
}
CosmoTool::PurePositionData *CosmoTool::loadRamsesPosition(const char *basename, int outputId, bool quiet)
{
PurePositionData *gd = (PurePositionData *)malloc(sizeof(PurePositionData));

3
src/loadRamses.hpp
View File

@ -2,6 +2,7 @@
#define _LOAD_RAMSES_HPP
#include "load_data.hpp"
#include "loadSimu.hpp"
namespace CosmoTool {
@ -10,6 +11,8 @@ namespace CosmoTool {
PhaseSpaceData *loadRamsesPhase(const char *fname, int id, bool quiet = false);
PhaseSpaceDataID *loadRamsesPhase1(const char *fname, int id, int cpuid, bool quiet = false);
SimuData *loadRamsesSimu(const char *basename, int id, int cpuid, int flags);
};
#endif

7
src/loadSimu.hpp
View File

@ -7,7 +7,7 @@ namespace CosmoTool
static const int NEED_GADGET_ID = 1;
static const int NEED_POSITION = 2;
static const int NEED_VELOCITY = 4;
static const int NEED_TYPE = 8;
class SimuData
{
@ -20,8 +20,9 @@ namespace CosmoTool
int *Id;
float *Pos[3];
float *Vel[3];
int *type;
public:
SimuData() : Id(0),NumPart(0) { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
SimuData() : Id(0),NumPart(0),type(0) { Pos[0]=Pos[1]=Pos[2]=0; Vel[0]=Vel[1]=Vel[2]=0; }
~SimuData()
{
for (int j = 0; j < 3; j++)
@ -31,6 +32,8 @@ namespace CosmoTool
if (Vel[j])
delete[] Vel[j];
}
if (type)
delete[] type;
if (Id)
delete[] Id;
}

17
src/octTree.cpp
View File

@ -9,12 +9,27 @@ using namespace CosmoTool;
//#define VERBOSE
static uint32_t mypow(uint32_t i, uint32_t p)
{
if (p == 0)
return 1;
else if (p == 1)
return i;
uint32_t k = p/2;
uint32_t j = mypow(i, k);
if (2*k==p)
return j*j;
else
return j*j*i;
}
OctTree::OctTree(const FCoordinates *particles, octPtr numParticles,
uint32_t maxMeanTreeDepth, uint32_t maxAbsoluteDepth,
uint32_t threshold)
{
cout << "MeanTree=" << maxMeanTreeDepth << endl;
numCells = pow(8, maxMeanTreeDepth);
numCells = mypow(8, maxMeanTreeDepth);
assert(numCells < invalidOctCell);
//#ifdef VERBOSE
cerr << "Allocating " << numCells << " octtree cells" << endl;