Merge branch 'master' of bitbucket.org:glavaux/cosmotool
This commit is contained in:
Guilhem Lavaux
commit
f3c459d9f6
5
.gitignore
vendored
5
.gitignore
vendored
@ -1,4 +1,9 @@
|
||||
*~
|
||||
.eggs/
|
||||
dist/
|
||||
wheelhouse/
|
||||
cosmotool.egg-info/
|
||||
build/
|
||||
*.o
|
||||
*.prog
|
||||
*.pyc
|
||||
|
||||
@ -54,8 +54,8 @@ IF(YORICK_SUPPORT)
|
||||
ENDIF((EXISTS ${NETCDFCPP_INCLUDE_PATH}/netcdf AND ${NETCDFCPP_LIBRARY} MATCHES "netcdf_c\\+\\+4") OR (INTERNAL_NETCDF))
|
||||
ENDIF(YORICK_SUPPORT)
|
||||
|
||||
find_program(CYTHON cython3 cython)
|
||||
find_library(ZLIB z)
|
||||
find_program(CYTHON NAMES cython3 cython)
|
||||
find_library(ZLIB_LIBRARY z)
|
||||
find_library(DL_LIBRARY dl)
|
||||
find_library(MATH_LIBRARY m)
|
||||
|
||||
@ -70,8 +70,8 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
|
||||
SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
|
||||
SET(CPACK_RESOURCE_FILE_LICENSE "${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${EXTRA_VERSION}")
|
||||
SET(CPACK_PACKAGE_VERSION_MINOR "1")
|
||||
SET(CPACK_PACKAGE_VERSION_PATCH "1${EXTRA_VERSION}")
|
||||
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
|
||||
SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
|
||||
SET(CPACK_SOURCE_IGNORE_FILES
|
||||
|
||||
508
LICENCE.txt
Normal file
508
LICENCE.txt
Normal file
@ -0,0 +1,508 @@
|
||||
Copyright (C) 2009-2020 Guilhem Lavaux
|
||||
|
||||
|
||||
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.
|
||||
169
MANIFEST.in
Normal file
169
MANIFEST.in
Normal file
@ -0,0 +1,169 @@
|
||||
include .gitignore
|
||||
include CMakeLists.txt
|
||||
include FindNumPy.cmake
|
||||
include FindPyLibs.cmake
|
||||
include GetGitRevisionDescription.cmake
|
||||
include GetGitRevisionDescription.cmake.in
|
||||
include LICENCE.txt
|
||||
include LICENCE_CeCILL_V2
|
||||
include README.md
|
||||
include build_tools/gather_sources.py
|
||||
include color_msg.cmake
|
||||
include doc/Makefile
|
||||
include doc/make.bat
|
||||
include doc/source/conf.py
|
||||
include doc/source/cpplibrary.rst
|
||||
include doc/source/index.rst
|
||||
include doc/source/intro.rst
|
||||
include doc/source/pythonmodule.rst
|
||||
include external/external_build.cmake
|
||||
include external/libsharp-6077806.tar.gz
|
||||
include external/omptl-20120422.tar.bz2
|
||||
include external/patch-omptl
|
||||
include python/CMakeLists.txt
|
||||
include python/_cosmo_bispectrum.cpp
|
||||
include python/_cosmo_cic.pyx
|
||||
include python/_cosmo_power.pyx
|
||||
include python/_cosmotool.pyx
|
||||
include python/_fast_interp.pyx
|
||||
include python/_project.pyx
|
||||
include python/copy.pxd
|
||||
include python/cosmotool/__init__.py
|
||||
include python/cosmotool/bispectrum.py
|
||||
include python/cosmotool/borg.py
|
||||
include python/cosmotool/cic.py
|
||||
include python/cosmotool/cl_cic.py
|
||||
include python/cosmotool/config.py.in
|
||||
include python/cosmotool/ctpv.py
|
||||
include python/cosmotool/fftw.py
|
||||
include python/cosmotool/grafic.py
|
||||
include python/cosmotool/simu.py
|
||||
include python/cosmotool/smooth.py
|
||||
include python/cosmotool/timing.py
|
||||
include python/cppHelper.hpp
|
||||
include python/dummy.c
|
||||
include python/project_tool.hpp
|
||||
include python/safe_gadget.hpp
|
||||
include python_sample/build_2lpt_ksz.py
|
||||
include python_sample/build_2lpt_skymap.py
|
||||
include python_sample/build_dipole_ksz_from_galaxies.py
|
||||
include python_sample/build_nbody_ksz.py
|
||||
include python_sample/build_nbody_ksz_from_galaxies.py
|
||||
include python_sample/build_nbody_skymap.py
|
||||
include python_sample/gen_2lpt_asmooth.py
|
||||
include python_sample/gen_2lpt_density.py
|
||||
include python_sample/icgen/__init__.py
|
||||
include python_sample/icgen/borgadaptor.py
|
||||
include python_sample/icgen/borgicgen.py
|
||||
include python_sample/icgen/cosmogrowth.py
|
||||
include python_sample/icgen/gen_ic_from_borg.py
|
||||
include python_sample/icgen/test_ic_from_borg.py
|
||||
include python_sample/icgen/test_whitify.py
|
||||
include python_sample/ksz/__init__.py
|
||||
include python_sample/ksz/constants.py
|
||||
include python_sample/ksz/gal_prof.py
|
||||
include python_sample/ramsesToArray.py
|
||||
include python_sample/test_bispectrum.py
|
||||
include python_sample/test_spheric_proj.py
|
||||
include sample/CMakeLists.txt
|
||||
include sample/Hartmann_Matrix.txt
|
||||
include sample/gadgetToArray.cpp
|
||||
include sample/gadgetToDensity.cpp
|
||||
include sample/graficToDensity.cpp
|
||||
include sample/simple3DFilter.cpp
|
||||
include sample/simpleDistanceFilter.cpp
|
||||
include sample/testAlgo.cpp
|
||||
include sample/testBQueue.cpp
|
||||
include sample/testBSP.cpp
|
||||
include sample/testDelaunay.cpp
|
||||
include sample/testEskow.cpp
|
||||
include sample/testHDF5.cpp
|
||||
include sample/testInterpolate.cpp
|
||||
include sample/testNewton.cpp
|
||||
include sample/testPool.cpp
|
||||
include sample/testReadFlash.cpp
|
||||
include sample/testSmooth.cpp
|
||||
include sample/test_cosmopower.cpp
|
||||
include sample/test_fft_calls.cpp
|
||||
include sample/test_healpix_calls.cpp
|
||||
include sample/testkd.cpp
|
||||
include sample/testkd2.cpp
|
||||
include sample/testkd3.cpp
|
||||
include setup.py
|
||||
include src/CMakeLists.txt
|
||||
include src/algo.hpp
|
||||
include src/bqueue.hpp
|
||||
include src/bqueue.tcc
|
||||
include src/bsp_simple.hpp
|
||||
include src/bsp_simple.tcc
|
||||
include src/cic.cpp
|
||||
include src/cic.hpp
|
||||
include src/config.hpp
|
||||
include src/cosmopower.cpp
|
||||
include src/cosmopower.hpp
|
||||
include src/dinterpolate.hpp
|
||||
include src/dinterpolate.tcc
|
||||
include src/eskow.hpp
|
||||
include src/field.hpp
|
||||
include src/fixArray.hpp
|
||||
include src/fortran.cpp
|
||||
include src/fortran.hpp
|
||||
include src/fourier/base_types.hpp
|
||||
include src/fourier/details/euclidian_maps.hpp
|
||||
include src/fourier/details/euclidian_spectrum_1d.hpp
|
||||
include src/fourier/details/euclidian_spectrum_1d_bin.hpp
|
||||
include src/fourier/details/euclidian_transform.hpp
|
||||
include src/fourier/details/healpix_alms.hpp
|
||||
include src/fourier/details/healpix_map.hpp
|
||||
include src/fourier/details/healpix_spectrum.hpp
|
||||
include src/fourier/details/healpix_transform.hpp
|
||||
include src/fourier/details/healpix_utility.hpp
|
||||
include src/fourier/euclidian.hpp
|
||||
include src/fourier/fft/fftw_calls.hpp
|
||||
include src/fourier/fft/fftw_calls_mpi.hpp
|
||||
include src/fourier/fft/fftw_complex.hpp
|
||||
include src/fourier/healpix.hpp
|
||||
include src/growthFactor.cpp
|
||||
include src/growthFactor.hpp
|
||||
include src/h5_readFlash.cpp
|
||||
include src/h5_readFlash.hpp
|
||||
include src/hdf5_array.hpp
|
||||
include src/hdf5_flash.h
|
||||
include src/interpolate.cpp
|
||||
include src/interpolate.hpp
|
||||
include src/interpolate3d.hpp
|
||||
include src/kdtree_leaf.hpp
|
||||
include src/kdtree_leaf.tcc
|
||||
include src/kdtree_splitters.hpp
|
||||
include src/loadFlash.cpp
|
||||
include src/loadFlash.hpp
|
||||
include src/loadFlash_dummy.cpp
|
||||
include src/loadGadget.cpp
|
||||
include src/loadGadget.hpp
|
||||
include src/loadRamses.cpp
|
||||
include src/loadRamses.hpp
|
||||
include src/loadSimu.hpp
|
||||
include src/load_data.cpp
|
||||
include src/load_data.hpp
|
||||
include src/mach.hpp
|
||||
include src/miniargs.cpp
|
||||
include src/miniargs.hpp
|
||||
include src/mykdtree.hpp
|
||||
include src/mykdtree.tcc
|
||||
include src/newton.hpp
|
||||
include src/octTree.hpp
|
||||
include src/octTree.tcc
|
||||
include src/openmp.hpp
|
||||
include src/pool.hpp
|
||||
include src/powerSpectrum.cpp
|
||||
include src/powerSpectrum.hpp
|
||||
include src/replicateGenerator.hpp
|
||||
include src/sparseGrid.hpp
|
||||
include src/sparseGrid.tcc
|
||||
include src/sphSmooth.hpp
|
||||
include src/sphSmooth.tcc
|
||||
include src/symbol_visible.hpp
|
||||
include src/tf_fit.hpp
|
||||
include src/yorick.hpp
|
||||
include src/yorick_nc3.cpp
|
||||
include src/yorick_nc4.cpp
|
||||
35
builder/build-wheels.sh
Executable file
35
builder/build-wheels.sh
Executable file
@ -0,0 +1,35 @@
|
||||
#!/bin/bash
|
||||
set -e -x
|
||||
|
||||
CC=cc
|
||||
CXX=c++
|
||||
|
||||
export CC CXX
|
||||
|
||||
# Install a system package required by our library
|
||||
#yum install -y atlas-devel
|
||||
yum install -y cmake3 gsl-devel zlib-devel
|
||||
|
||||
ln -fs /usr/bin/cmake3 /usr/bin/cmake
|
||||
|
||||
|
||||
ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38 cp39-cp39"
|
||||
|
||||
# Compile wheels
|
||||
for pkg in $ALL_PYTHON; do
|
||||
PYBIN=/opt/python/${pkg}/bin
|
||||
# "${PYBIN}/pip" install -r /io/dev-requirements.txt
|
||||
"${PYBIN}/pip" install -r /io/requirements.txt
|
||||
"${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
|
||||
done
|
||||
|
||||
# Bundle external shared libraries into the wheels
|
||||
for whl in wheelhouse/*.whl; do
|
||||
auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/
|
||||
done
|
||||
|
||||
# Install packages and test
|
||||
for pkg in $ALL_PYTHON; do
|
||||
PYBIN=/opt/python/${pkg}/bin
|
||||
"${PYBIN}/pip" install cosmotool --no-index -f /io/wheelhouse
|
||||
done
|
||||
12
builder/start.sh
Executable file
12
builder/start.sh
Executable file
@ -0,0 +1,12 @@
|
||||
#!/bin/bash
|
||||
|
||||
d=$(pwd)
|
||||
if test x"$(basename $d)" = xbuilder; then
|
||||
d=${d}/../
|
||||
fi
|
||||
if ! [ -e ${d}/setup.py ] ; then
|
||||
echo "Unknown directory. Please move to the root of cosmotool source tree."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
podman run -ti --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh
|
||||
1
conda/build.sh
Normal file
1
conda/build.sh
Normal file
@ -0,0 +1 @@
|
||||
$PYTHON setup.py install
|
||||
7
conda/conda_build_config.yaml
Normal file
7
conda/conda_build_config.yaml
Normal file
@ -0,0 +1,7 @@
|
||||
python:
|
||||
- 3.7
|
||||
- 3.8
|
||||
|
||||
numpy:
|
||||
- 1.11
|
||||
- 1.19
|
||||
38
conda/meta.yaml
Normal file
38
conda/meta.yaml
Normal file
@ -0,0 +1,38 @@
|
||||
package:
|
||||
name: cosmotool
|
||||
version: "1.0.0a7"
|
||||
|
||||
source:
|
||||
git_rev: 7fce73e
|
||||
git_url: https://bitbucket.org/glavaux/cosmotool
|
||||
|
||||
requirements:
|
||||
build:
|
||||
- numpy >=1.11
|
||||
- gcc_linux-64
|
||||
- gxx_linux-64
|
||||
- python
|
||||
- setuptools
|
||||
- cython
|
||||
- healpy
|
||||
- numexpr
|
||||
- cffi
|
||||
- pyfftw
|
||||
- gsl
|
||||
- h5py
|
||||
|
||||
run:
|
||||
- numpy
|
||||
- python
|
||||
- healpy
|
||||
- numexpr
|
||||
- cffi
|
||||
- pyfftw
|
||||
- h5py
|
||||
|
||||
test:
|
||||
imports:
|
||||
- cosmotool
|
||||
|
||||
about:
|
||||
home: https://bitbucket.org/glavaux/cosmotool
|
||||
56
external/external_build.cmake
vendored
56
external/external_build.cmake
vendored
@ -2,8 +2,8 @@ include(FindOpenMP)
|
||||
|
||||
OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
|
||||
|
||||
SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from")
|
||||
SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from")
|
||||
SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from")
|
||||
SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from")
|
||||
SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
|
||||
SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from")
|
||||
SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from")
|
||||
@ -56,19 +56,19 @@ if (ENABLE_SHARP)
|
||||
IF(NOT ENABLE_OPENMP)
|
||||
SET(SHARP_OPENMP --disable-openmp)
|
||||
ENDIF()
|
||||
ExternalProject_Add(sharp
|
||||
URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
|
||||
PREFIX ${BUILD_PREFIX}/sharp-prefix
|
||||
BUILD_IN_SOURCE 1
|
||||
CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
|
||||
BUILD_COMMAND ${CMAKE_MAKE_PROGRAM}
|
||||
INSTALL_COMMAND echo "No install"
|
||||
)
|
||||
SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a)
|
||||
SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a)
|
||||
SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a)
|
||||
SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY})
|
||||
SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include)
|
||||
ExternalProject_Add(sharp
|
||||
URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
|
||||
PREFIX ${BUILD_PREFIX}/sharp-prefix
|
||||
BUILD_IN_SOURCE 1
|
||||
CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
|
||||
INSTALL_COMMAND echo "No install"
|
||||
BUILD_BYPRODUCTS ${SHARP_LIBRARIES}
|
||||
)
|
||||
endif (ENABLE_SHARP)
|
||||
|
||||
|
||||
@ -246,10 +246,23 @@ if (INTERNAL_BOOST)
|
||||
set(Boost_DEP boost)
|
||||
|
||||
ELSE (INTERNAL_BOOST)
|
||||
find_package(Boost 1.53 QUIET)
|
||||
set(Boost_DEP)
|
||||
find_package(Boost 1.69 QUIET)
|
||||
if (Boost_VERSION)
|
||||
if (${Boost_VERSION} VERSION_GREATER 1000)
|
||||
math(EXPR TMP_MAJOR "${Boost_VERSION} / 100000")
|
||||
math(EXPR TMP_MINOR "(${Boost_VERSION} - ${TMP_MAJOR} * 100000) / 100")
|
||||
math(EXPR TMP_PATCHLEVEL "${Boost_VERSION} - ${TMP_MAJOR} * 100000 - ${TMP_MINOR} * 100")
|
||||
set(Boost_VERSION ${TMP_MAJOR}.${TMP_MINOR}.${TMP_PATCHLEVEL})
|
||||
ENDIF()
|
||||
if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0)
|
||||
set(Boost_DEP Boost::boost)
|
||||
set(Boost_TARGET Boost::boost)
|
||||
endif()
|
||||
endif()
|
||||
if (NOT Boost_FOUND)
|
||||
cmessage(CWARNING "Boost >= 1.53 was not found")
|
||||
cmessage(CWARNING "Boost >= 1.69 was not found")
|
||||
else()
|
||||
cmessage(STATUS "Boost has been found (version=${Boost_VERSION}), Boost_TARGET=${Boost_Target}")
|
||||
endif()
|
||||
endif (INTERNAL_BOOST)
|
||||
mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES)
|
||||
@ -278,13 +291,19 @@ IF(INTERNAL_GSL)
|
||||
set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
|
||||
SET(cosmotool_DEPS ${cosmotool_DEPS} gsl)
|
||||
ELSE(INTERNAL_GSL)
|
||||
find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
|
||||
find_library(GSL_LIBRARY gsl)
|
||||
find_library(GSLCBLAS_LIBRARY gslcblas)
|
||||
IF (NOT DEFINED GSL_LIBRARY OR NOT GSL_LIBRARY)
|
||||
find_library(GSL_LIBRARY gsl)
|
||||
ENDIF()
|
||||
IF (NOT DEFINED GSL_INCLUDE_PATH OR NOT GSL_INCLUDE_PATH)
|
||||
find_path(GSL_INCLUDE_PATH NAMES gsl/gsl_blas.h)
|
||||
ENDIF()
|
||||
IF (NOT DEFINED GSL_CBLAS_LIBRARY OR NOT GSL_CBLAS_LIBRARY)
|
||||
find_library(GSLCBLAS_LIBRARY gslcblas)
|
||||
ENDIF()
|
||||
|
||||
set(GSL_LIBRARIES ${GSL_LIBRARY} ${GSLCBLAS_LIBRARY})
|
||||
|
||||
ENDIF(INTERNAL_GSL)
|
||||
|
||||
mark_as_advanced(GSL_LIBRARY GSLCBLAS_LIBRARY GSL_INCLUDE_PATH)
|
||||
|
||||
|
||||
@ -337,7 +356,7 @@ ENDIF(INTERNAL_FFTW)
|
||||
IF (INTERNAL_EIGEN)
|
||||
ExternalProject_Add(eigen
|
||||
URL ${EIGEN_URL}
|
||||
URL_HASH SHA256=04f8a4fa4afedaae721c1a1c756afeea20d3cdef0ce3293982cf1c518f178502
|
||||
URL_HASH MD5=b9e98a200d2455f06db9c661c5610496
|
||||
PREFIX ${BUILD_PREFIX}/eigen-prefix
|
||||
CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
|
||||
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
|
||||
@ -375,6 +394,7 @@ ExternalProject_Add(omptl
|
||||
BUILD_COMMAND echo "No build"
|
||||
PATCH_COMMAND patch -p1 -t -N < ${CMAKE_SOURCE_DIR}/external/patch-omptl
|
||||
INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${EXT_INSTALL}/include/omptl
|
||||
BUILD_BYPRODUCTS ${EXT_INSTALL}/include/omptl
|
||||
)
|
||||
include_directories(${EXT_INSTALL}/include)
|
||||
##include_directories(${OMPTL_BUILD_DIR}/src/)
|
||||
|
||||
@ -30,6 +30,10 @@ IF(CYTHON)
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx
|
||||
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_project.pyx ${CMAKE_CURRENT_SOURCE_DIR}/project_tool.hpp )
|
||||
|
||||
add_custom_command(
|
||||
OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp
|
||||
COMMAND ${CYTHON} --cplus -o ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx
|
||||
DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/_cosmomath.pyx )
|
||||
ENDIF(CYTHON)
|
||||
|
||||
|
||||
@ -38,25 +42,27 @@ add_library(_cosmo_power MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_power.cpp)
|
||||
add_library(_cosmo_cic MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmo_cic.cpp)
|
||||
add_library(_fast_interp MODULE ${CMAKE_CURRENT_BINARY_DIR}/_fast_interp.cpp)
|
||||
add_library(_project MODULE ${CMAKE_CURRENT_BINARY_DIR}/_project.cpp)
|
||||
add_library(_cosmomath MODULE ${CMAKE_CURRENT_BINARY_DIR}/_cosmomath.cpp)
|
||||
target_include_directories(_cosmotool PRIVATE ${PYTHON_INCLUDES})
|
||||
target_include_directories(_cosmo_power PRIVATE ${PYTHON_INCLUDES})
|
||||
target_include_directories(_cosmo_cic PRIVATE ${PYTHON_INCLUDES})
|
||||
target_include_directories(_fast_interp PRIVATE ${PYTHON_INCLUDES})
|
||||
target_include_directories(_project PRIVATE ${PYTHON_INCLUDES})
|
||||
|
||||
target_include_directories(_cosmomath PRIVATE ${PYTHON_INCLUDES})
|
||||
|
||||
SET(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} -Bsymbolic-functions")
|
||||
if(APPLE)
|
||||
set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup")
|
||||
endif()
|
||||
|
||||
target_link_libraries(_cosmotool ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_power ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_cic ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmotool PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_power PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmo_cic PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_cosmomath PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES})
|
||||
target_link_libraries(_project )
|
||||
target_link_libraries(_fast_interp ${CosmoTool_local} )
|
||||
target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} )
|
||||
|
||||
SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp )
|
||||
SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath)
|
||||
|
||||
if (Boost_FOUND)
|
||||
message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")
|
||||
|
||||
45
python/_cosmomath.pyx
Normal file
45
python/_cosmomath.pyx
Normal file
@ -0,0 +1,45 @@
|
||||
#cython: language_level=3
|
||||
import numpy as np
|
||||
cimport numpy as np
|
||||
|
||||
np.import_array()
|
||||
np.import_ufunc()
|
||||
|
||||
cdef extern from "sys/types.h":
|
||||
ctypedef np.int64_t int64_t
|
||||
|
||||
cdef extern from "numpy/npy_common.h":
|
||||
ctypedef npy_intp
|
||||
|
||||
cdef extern from "special_math.hpp" namespace "CosmoTool":
|
||||
T log_modified_bessel_first_kind[T](T v, T z) nogil except +
|
||||
|
||||
cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
|
||||
void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)
|
||||
|
||||
|
||||
cdef np.PyUFuncGenericFunction loop_func[1]
|
||||
cdef char input_output_types[3]
|
||||
cdef void *elementwise_funcs[1]
|
||||
|
||||
loop_func[0] = <np.PyUFuncGenericFunction>parallel_ufunc_dd_d[double,npy_intp]
|
||||
|
||||
input_output_types[0] = np.NPY_DOUBLE
|
||||
input_output_types[1] = np.NPY_DOUBLE
|
||||
input_output_types[2] = np.NPY_DOUBLE
|
||||
|
||||
elementwise_funcs[0] = <void*>log_modified_bessel_first_kind[double]
|
||||
|
||||
log_modified_I = np.PyUFunc_FromFuncAndData(
|
||||
loop_func,
|
||||
elementwise_funcs,
|
||||
input_output_types,
|
||||
1, # number of supported input types
|
||||
2, # number of input args
|
||||
1, # number of output args
|
||||
0, # `identity` element, never mind this
|
||||
"log_modified_bessel_first_kind", # function name
|
||||
"log_modified_bessel_first_kind(v: Float, z: Float) -> Float", # docstring
|
||||
0 # unused
|
||||
)
|
||||
|
||||
@ -513,7 +513,8 @@ def writeGadget(str filename, object simulation):
|
||||
simdata.TotalNumPart = NumPart
|
||||
simdata.NumPart = NumPart
|
||||
|
||||
cxx_writeGadget(filename, &simdata)
|
||||
filename_b = bytes(filename, 'utf-8')
|
||||
cxx_writeGadget(filename_b, &simdata)
|
||||
|
||||
def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadMass = False):
|
||||
""" loadRamses(basepath, snapshot_id, cpu_id, doublePrecision = False, loadPosition = True, loadVelocity = False)
|
||||
|
||||
@ -3,6 +3,7 @@ from ._project import *
|
||||
from ._cosmo_power import *
|
||||
from ._cosmo_cic import *
|
||||
from ._fast_interp import *
|
||||
from ._cosmomath import *
|
||||
from .grafic import writeGrafic, writeWhitePhase, readGrafic, readWhitePhase
|
||||
from .borg import read_borg_vol
|
||||
from .cic import cicParticles
|
||||
|
||||
@ -87,7 +87,7 @@ class ProgrammableParticleHistoryLoad(object):
|
||||
class ProgrammableDensityLoad(object):
|
||||
|
||||
@staticmethod
|
||||
def main_script(source, density, extents=None, aname="default"):
|
||||
def main_script(source, density, extents=None, aname="default", extra_arrays={}):
|
||||
import vtk
|
||||
from vtk.util import numpy_support
|
||||
|
||||
@ -116,6 +116,11 @@ class ProgrammableDensityLoad(object):
|
||||
arr = numpy_support.numpy_to_vtk(density.transpose().astype(np.float64).ravel(), deep=1)
|
||||
arr.SetName(aname)
|
||||
ido.GetPointData().AddArray(arr)
|
||||
|
||||
for k in extra_arrays.keys():
|
||||
arr = numpy_support.numpy_to_vtk(extra_arrays[k].transpose().astype(np.float64).ravel(), deep=1)
|
||||
arr.SetName(k)
|
||||
ido.GetPointData().AddArray(arr)
|
||||
|
||||
@staticmethod
|
||||
def request_information(source, density=None, dims=None):
|
||||
|
||||
@ -98,12 +98,12 @@ def simpleWriteGadget(filename, positions, boxsize=1.0, Hubble=100, Omega_M=0.30
|
||||
|
||||
s.positions = positions
|
||||
|
||||
if velocities:
|
||||
if velocities is not None:
|
||||
s.velocities = velocities
|
||||
else:
|
||||
s.velocities = [np.zeros(positions[0].size,dtype=np.float32)]*3
|
||||
|
||||
if identifiers:
|
||||
if identifiers is not None:
|
||||
s.identifiers = identifiers
|
||||
else:
|
||||
s.identifiers = np.arange(positions[0].size, dtype=np.int64)
|
||||
|
||||
1
python/dummy.c
Normal file
1
python/dummy.c
Normal file
@ -0,0 +1 @@
|
||||
static void dummyFunc() {}
|
||||
5
requirements.txt
Normal file
5
requirements.txt
Normal file
@ -0,0 +1,5 @@
|
||||
numpy
|
||||
cffi
|
||||
numexpr
|
||||
pyfftw
|
||||
cython
|
||||
@ -114,6 +114,9 @@ if (Boost_FOUND)
|
||||
add_dependencies(graficToDensity ${all_deps})
|
||||
endif()
|
||||
endif()
|
||||
|
||||
add_executable(test_special test_special.cpp)
|
||||
target_link_libraries(test_special ${tolink})
|
||||
endif (Boost_FOUND)
|
||||
|
||||
IF (ENABLE_OPENMP AND YORICK_SUPPORT)
|
||||
|
||||
12
sample/test_special.cpp
Normal file
12
sample/test_special.cpp
Normal file
@ -0,0 +1,12 @@
|
||||
#include <iostream>
|
||||
#include "special_math.hpp"
|
||||
|
||||
int main()
|
||||
{
|
||||
|
||||
std::cout << CosmoTool::log1p_exp(2.0) << std::endl;
|
||||
|
||||
std::cout << CosmoTool::log_modified_bessel_first_kind(100.0, 0.1) << std::endl;
|
||||
return 0;
|
||||
}
|
||||
|
||||
16
setup.py
16
setup.py
@ -21,7 +21,7 @@ class CMakeExtension(Extension):
|
||||
doesn't try to build your sources for you
|
||||
"""
|
||||
|
||||
def __init__(self, name, sources=[]):
|
||||
def __init__(self, name, sources=["python/dummy.c"]):
|
||||
|
||||
super().__init__(name = name, sources = sources)
|
||||
|
||||
@ -156,9 +156,8 @@ class BuildCMakeExt(build_ext):
|
||||
|
||||
cython_code = os.path.join(str(build_dir.absolute()),'mycython')
|
||||
with open(cython_code, mode="wt") as ff:
|
||||
ff.write(f"#!{sys.executable}\n"
|
||||
"from Cython.Compiler.Main import setuptools_main\n"
|
||||
"setuptools_main()")
|
||||
ff.write("#!/bin/sh\n"
|
||||
f"{sys.executable} -c 'from Cython.Compiler.Main import setuptools_main; setuptools_main()' $@")
|
||||
os.chmod(cython_code, stat.S_IXUSR|stat.S_IWUSR|stat.S_IRUSR|stat.S_IRGRP)
|
||||
|
||||
# Now that the necessary directories are created, build
|
||||
@ -169,6 +168,7 @@ class BuildCMakeExt(build_ext):
|
||||
# Below is just an example set of arguments for building Blender as a Python module
|
||||
|
||||
self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
|
||||
'-DCMAKE_C_COMPILER=' + os.environ["CC"], "-DCMAKE_CXX_COMPILER=" + os.environ["CXX"],
|
||||
'-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
|
||||
'-DINTERNAL_HDF5=ON','-DINTERNAL_NETCDF=ON',
|
||||
'-DBUILD_PYTHON=ON', '-DINSTALL_PYTHON_LOCAL=OFF',
|
||||
@ -218,10 +218,11 @@ class BuildCMakeExt(build_ext):
|
||||
CosmoTool_extension = CMakeExtension(name="cosmotool")
|
||||
|
||||
setup(name='cosmotool',
|
||||
version='1.0.0a2',
|
||||
version='1.1.1',
|
||||
packages=["cosmotool"],
|
||||
package_dir={'cosmotool': 'python/cosmotool'},
|
||||
setup_requires=['cython','cffi','numexpr'],
|
||||
install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],
|
||||
setup_requires=['cython','cffi','numpy','numexpr'],
|
||||
ext_modules=[CosmoTool_extension],
|
||||
description='A small cosmotool box of useful functions',
|
||||
long_description=open("./README.md", 'r').read(),
|
||||
@ -241,5 +242,6 @@ setup(name='cosmotool',
|
||||
'build_ext': BuildCMakeExt,
|
||||
'install_data': InstallCMakeLibsData,
|
||||
'install_lib': InstallCMakeLibs,
|
||||
}
|
||||
},
|
||||
python_requires='>=3.6'
|
||||
)
|
||||
|
||||
@ -72,14 +72,14 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS}
|
||||
|
||||
include_directories(${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src)
|
||||
|
||||
set(CosmoTool_LIBS ${GSL_LIBRARIES})
|
||||
set(CosmoTool_LIBS ${GSL_LIBRARIES} ${Boost_TARGET})
|
||||
if(YORICK_SUPPORT)
|
||||
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES})
|
||||
include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH})
|
||||
endif(YORICK_SUPPORT)
|
||||
|
||||
if (HDF5_FOUND)
|
||||
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB})
|
||||
set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB_LIBRARY})
|
||||
message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}")
|
||||
endif (HDF5_FOUND)
|
||||
|
||||
@ -92,11 +92,13 @@ if (BUILD_SHARED_LIBS)
|
||||
add_library(CosmoTool_static STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
|
||||
target_link_libraries(CosmoTool_static)
|
||||
set_property(TARGET CosmoTool_static PROPERTY POSITION_INDEPENDENT_CODE ON)
|
||||
add_dependencies(CosmoTool_static ${cosmotool_DEPS})
|
||||
endif(BUILD_STATIC_LIBS)
|
||||
else (BUILD_SHARED_LIBS)
|
||||
add_library(CosmoTool STATIC ${CosmoTool_SRCS} $<TARGET_OBJECTS:CosmoHDF5>)
|
||||
target_link_libraries(CosmoTool)
|
||||
target_link_libraries(CosmoTool ${CosmoTool_LIBS})
|
||||
set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON)
|
||||
add_dependencies(CosmoTool ${cosmotool_DEPS})
|
||||
endif (BUILD_SHARED_LIBS)
|
||||
|
||||
IF(NOT COSMOTOOL_PYTHON_PACKAGING)
|
||||
|
||||
@ -93,6 +93,6 @@ namespace CosmoTool
|
||||
|
||||
|
||||
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -165,6 +165,6 @@ namespace CosmoTool
|
||||
FilesystemFullException()
|
||||
: Exception() {}
|
||||
};
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
@ -114,6 +114,9 @@ public: \
|
||||
static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, int sign, unsigned flags) { \
|
||||
return prefix ## _plan_dft_3d(Nx, Ny, Nz, in, out, sign, flags); \
|
||||
} \
|
||||
static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, int sign, unsigned flags) { \
|
||||
return prefix ## _plan_dft_2d(Nx, Ny, in, out, sign, flags); \
|
||||
} \
|
||||
static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \
|
||||
}
|
||||
|
||||
|
||||
@ -97,6 +97,9 @@ public: \
|
||||
static plan_type plan_dft_3d(int Nx, int Ny, int Nz, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \
|
||||
return prefix ## _mpi_plan_dft_3d(Nx, Ny, Nz, in, out, comm, sign, flags); \
|
||||
} \
|
||||
static plan_type plan_dft_2d(int Nx, int Ny, complex_type *in, complex_type *out, MPI_Comm comm, int sign, unsigned flags) { \
|
||||
return prefix ## _mpi_plan_dft_2d(Nx, Ny, in, out, comm, sign, flags); \
|
||||
} \
|
||||
static void destroy_plan(plan_type plan) { prefix ## _destroy_plan(plan); } \
|
||||
}
|
||||
|
||||
|
||||
@ -78,8 +78,6 @@ namespace CosmoTool {
|
||||
}
|
||||
};
|
||||
|
||||
//, typename boost::enable_if<boost::is_same<T, tl> >::type> \
|
||||
//
|
||||
#define HDF5_TYPE(tl, thdf5) \
|
||||
template<typename T> struct get_hdf5_data_type<T, typename boost::enable_if<boost::is_same<T,tl> >::type > \
|
||||
{ static H5::DataType type() { return H5::PredType::thdf5; }; }
|
||||
@ -122,7 +120,7 @@ namespace CosmoTool {
|
||||
|
||||
template<>
|
||||
struct hdf5_extent_gen<0> {
|
||||
static inline boost::multi_array_types::extent_gen build(hsize_t *d)
|
||||
static inline boost::multi_array_types::extent_gen build(hsize_t *)
|
||||
{
|
||||
return boost::extents;
|
||||
}
|
||||
@ -513,7 +511,7 @@ namespace CosmoTool { \
|
||||
}; \
|
||||
};
|
||||
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
||||
@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms.
|
||||
+*/
|
||||
|
||||
#include <sys/types.h>
|
||||
#include "/usr/include/regex.h"
|
||||
#include <regex.h>
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
|
||||
30
src/numpy_adaptors.hpp
Normal file
30
src/numpy_adaptors.hpp
Normal file
@ -0,0 +1,30 @@
|
||||
#ifndef __COSMOTOOL_NUMPY_ADAPTOR_HPP
|
||||
#define __COSMOTOOL_NUMPY_ADAPTOR_HPP
|
||||
|
||||
namespace CosmoTool {
|
||||
|
||||
template<typename T, typename IT>
|
||||
void parallel_ufunc_dd_d(char **args, IT* dimensions, IT* steps, void *func) {
|
||||
IT i;
|
||||
IT n = dimensions[0];
|
||||
char *in = args[0], *in2 = args[1], *out = args[2];
|
||||
IT in_step = steps[0], in2_step = steps[1], out_step = steps[2];
|
||||
|
||||
double tmp;
|
||||
typedef double (*F_t)(double,double);
|
||||
|
||||
F_t f = (F_t)func;
|
||||
|
||||
#pragma omp parallel for schedule(static)
|
||||
for (i = 0; i < n; i++) {
|
||||
T *out_t = (T *)(out + i * out_step);
|
||||
T *in_t = (T *)(in + i * in_step);
|
||||
T *in2_t = (T *)(in2 + i * in2_step);
|
||||
*out_t = f(*in_t, *in2_t);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
231
src/special_math.hpp
Normal file
231
src/special_math.hpp
Normal file
@ -0,0 +1,231 @@
|
||||
// Original code derived from Boost and is distributed here
|
||||
// under the Boost license (licenses/boost-license.txt)
|
||||
// Copyright (c) 2006 Xiaogang Zhang
|
||||
// Copyright (c) 2007, 2017 John Maddock
|
||||
// Secondary code copyright by its author and is distributed here
|
||||
// under the BSD-3 license (LICENSE.md). Derived from
|
||||
// stan/math/prim/fun/log_modified_bessel_first_kind.hpp
|
||||
|
||||
#ifndef __COSMOTOOL_SPECIAL_MATH_HPP
|
||||
#define __COSMOTOOL_SPECIAL_MATH_HPP
|
||||
|
||||
#include "algo.hpp"
|
||||
#include <boost/math/constants/constants.hpp>
|
||||
#include <boost/math/tools/rational.hpp>
|
||||
#include <cmath>
|
||||
#include <limits>
|
||||
|
||||
// Taken and adapted from
|
||||
// https://github.com/stan-dev/math/blob/develop/stan/math/prim/fun/log_modified_bessel_first_kind.hpp
|
||||
|
||||
namespace CosmoTool {
|
||||
|
||||
template <typename T> T log1p_exp(T x) {
|
||||
if (x > T(0)) {
|
||||
return x + std::log1p(std::exp(-x));
|
||||
}
|
||||
return std::log1p(std::exp(x));
|
||||
}
|
||||
|
||||
template <typename T> T multiply_log(T a, T b) {
|
||||
if (a == 0 && b == 0)
|
||||
return 0;
|
||||
return a * std::log(b);
|
||||
}
|
||||
|
||||
template <typename T> T inf() { return std::numeric_limits<T>::infinity(); }
|
||||
|
||||
template <typename T> T log_sum_exp(T const a, T const b) {
|
||||
if (a == -inf<T>()) {
|
||||
return b;
|
||||
}
|
||||
if (a == inf<T>() && b == inf<T>()) {
|
||||
return inf<T>();
|
||||
}
|
||||
if (a > b) {
|
||||
return a + log1p_exp(b - a);
|
||||
}
|
||||
return b + log1p_exp(a - b);
|
||||
}
|
||||
|
||||
/* Log of the modified Bessel function of the first kind,
|
||||
* which is better known as the Bessel I function. See
|
||||
* modified_bessel_first_kind.hpp for the function definition.
|
||||
* The derivatives are known to be incorrect for v = 0 because a
|
||||
* simple constant 0 is returned.
|
||||
*
|
||||
* @tparam T common type for calculation
|
||||
* @param v Order, can be a non-integer but must be at least -1
|
||||
* @param z Real non-negative number
|
||||
* @throws std::domain_error if either v or z is NaN, z is
|
||||
* negative, or v is less than -1
|
||||
* @return log of Bessel I function
|
||||
*/
|
||||
template <typename T> T log_modified_bessel_first_kind(T const v, T const z) {
|
||||
using boost::math::tools::evaluate_polynomial;
|
||||
using std::log;
|
||||
using std::pow;
|
||||
using std::sqrt;
|
||||
static const double LOG_TWO = std::log(2.0);
|
||||
static const double EPSILON = std::numeric_limits<double>::epsilon();
|
||||
static const double TWO_PI = 2.0 * boost::math::constants::pi<double>();
|
||||
|
||||
if (z == 0) {
|
||||
if (v == 0) {
|
||||
return 0.0;
|
||||
}
|
||||
if (v > 0) {
|
||||
return -std::numeric_limits<T>::infinity();
|
||||
}
|
||||
return std::numeric_limits<T>::infinity();
|
||||
}
|
||||
if (std::isinf(z)) {
|
||||
return z;
|
||||
}
|
||||
if (v == 0) {
|
||||
// Modified Bessel function of the first kind of order zero
|
||||
// we use the approximating forms derived in:
|
||||
// "Rational Approximations for the Modified Bessel Function of the
|
||||
// First Kind -- I0(x) for Computations with Double Precision"
|
||||
// by Pavel Holoborodko, see
|
||||
// http://www.advanpix.com/2015/11/11/rational-approximations-for-the-modified-bessel-function-of-the-first-kind-i0-computations-double-precision
|
||||
// The actual coefficients used are [Boost's] own, and extend
|
||||
// Pavel's work to precisions other than double.
|
||||
|
||||
if (z < 7.75) {
|
||||
// Bessel I0 over[10 ^ -16, 7.75]
|
||||
// Max error in interpolated form : 3.042e-18
|
||||
// Max Error found at double precision = Poly : 5.106609e-16
|
||||
// Cheb : 5.239199e-16
|
||||
static const double P[] = {
|
||||
1.00000000000000000e+00, 2.49999999999999909e-01,
|
||||
2.77777777777782257e-02, 1.73611111111023792e-03,
|
||||
6.94444444453352521e-05, 1.92901234513219920e-06,
|
||||
3.93675991102510739e-08, 6.15118672704439289e-10,
|
||||
7.59407002058973446e-12, 7.59389793369836367e-14,
|
||||
6.27767773636292611e-16, 4.34709704153272287e-18,
|
||||
2.63417742690109154e-20, 1.13943037744822825e-22,
|
||||
9.07926920085624812e-25};
|
||||
return log1p_exp(multiply_log(2.0, z) - log(4.0) +
|
||||
log(evaluate_polynomial(P, 0.25 * square(z))));
|
||||
}
|
||||
if (z < 500) {
|
||||
// Max error in interpolated form : 1.685e-16
|
||||
// Max Error found at double precision = Poly : 2.575063e-16
|
||||
// Cheb : 2.247615e+00
|
||||
static const double P[] = {
|
||||
3.98942280401425088e-01, 4.98677850604961985e-02,
|
||||
2.80506233928312623e-02, 2.92211225166047873e-02,
|
||||
4.44207299493659561e-02, 1.30970574605856719e-01,
|
||||
-3.35052280231727022e+00, 2.33025711583514727e+02,
|
||||
-1.13366350697172355e+04, 4.24057674317867331e+05,
|
||||
-1.23157028595698731e+07, 2.80231938155267516e+08,
|
||||
-5.01883999713777929e+09, 7.08029243015109113e+10,
|
||||
-7.84261082124811106e+11, 6.76825737854096565e+12,
|
||||
-4.49034849696138065e+13, 2.24155239966958995e+14,
|
||||
-8.13426467865659318e+14, 2.02391097391687777e+15,
|
||||
-3.08675715295370878e+15, 2.17587543863819074e+15};
|
||||
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
|
||||
}
|
||||
// Max error in interpolated form : 2.437e-18
|
||||
// Max Error found at double precision = Poly : 1.216719e-16
|
||||
static const double P[] = {3.98942280401432905e-01, 4.98677850491434560e-02,
|
||||
2.80506308916506102e-02, 2.92179096853915176e-02,
|
||||
4.53371208762579442e-02};
|
||||
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
|
||||
}
|
||||
if (v == 1) { // WARNING: will not autodiff for v = 1 correctly
|
||||
// modified from Boost's bessel_i1_imp in the double precision case
|
||||
// see credits above in the v == 0 case
|
||||
if (z < 7.75) {
|
||||
// Bessel I0 over[10 ^ -16, 7.75]
|
||||
// Max error in interpolated form: 5.639e-17
|
||||
// Max Error found at double precision = Poly: 1.795559e-16
|
||||
|
||||
static const double P[] = {
|
||||
8.333333333333333803e-02, 6.944444444444341983e-03,
|
||||
3.472222222225921045e-04, 1.157407407354987232e-05,
|
||||
2.755731926254790268e-07, 4.920949692800671435e-09,
|
||||
6.834657311305621830e-11, 7.593969849687574339e-13,
|
||||
6.904822652741917551e-15, 5.220157095351373194e-17,
|
||||
3.410720494727771276e-19, 1.625212890947171108e-21,
|
||||
1.332898928162290861e-23};
|
||||
T a = square(z) * 0.25;
|
||||
T Q[3] = {1, 0.5, evaluate_polynomial(P, a)};
|
||||
return log(z) + log(evaluate_polynomial(Q, a)) - LOG_TWO;
|
||||
}
|
||||
if (z < 500) {
|
||||
// Max error in interpolated form: 1.796e-16
|
||||
// Max Error found at double precision = Poly: 2.898731e-16
|
||||
|
||||
static const double P[] = {
|
||||
3.989422804014406054e-01, -1.496033551613111533e-01,
|
||||
-4.675104253598537322e-02, -4.090895951581637791e-02,
|
||||
-5.719036414430205390e-02, -1.528189554374492735e-01,
|
||||
3.458284470977172076e+00, -2.426181371595021021e+02,
|
||||
1.178785865993440669e+04, -4.404655582443487334e+05,
|
||||
1.277677779341446497e+07, -2.903390398236656519e+08,
|
||||
5.192386898222206474e+09, -7.313784438967834057e+10,
|
||||
8.087824484994859552e+11, -6.967602516005787001e+12,
|
||||
4.614040809616582764e+13, -2.298849639457172489e+14,
|
||||
8.325554073334618015e+14, -2.067285045778906105e+15,
|
||||
3.146401654361325073e+15, -2.213318202179221945e+15};
|
||||
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
|
||||
}
|
||||
// Max error in interpolated form: 1.320e-19
|
||||
// Max Error found at double precision = Poly: 7.065357e-17
|
||||
static const double P[] = {
|
||||
3.989422804014314820e-01, -1.496033551467584157e-01,
|
||||
-4.675105322571775911e-02, -4.090421597376992892e-02,
|
||||
-5.843630344778927582e-02};
|
||||
return z + log(evaluate_polynomial(P, 1 / z)) - multiply_log(0.5, z);
|
||||
}
|
||||
if (z > 100) {
|
||||
// Boost does something like this in asymptotic_bessel_i_large_x
|
||||
T lim = pow((square(v) + 2.5) / (2 * z), 3) / 24;
|
||||
if (lim < (EPSILON * 10)) {
|
||||
T s = 1;
|
||||
T mu = 4 * square(v);
|
||||
T ex = 8 * z;
|
||||
T num = mu - 1;
|
||||
T denom = ex;
|
||||
s -= num / denom;
|
||||
num *= mu - 9;
|
||||
denom *= ex * 2;
|
||||
s += num / denom;
|
||||
num *= mu - 25;
|
||||
denom *= ex * 3;
|
||||
s -= num / denom;
|
||||
s = z - log(sqrt(z * TWO_PI)) + log(s);
|
||||
return s;
|
||||
}
|
||||
}
|
||||
|
||||
T log_half_z = log(0.5 * z);
|
||||
T lgam = (v > -1) ? lgamma(v + 1.0) : 0;
|
||||
T lcons = (2.0 + v) * log_half_z;
|
||||
T out;
|
||||
if (v > -1) {
|
||||
out = log_sum_exp(v * log_half_z - lgam, lcons - lgamma(v + 2));
|
||||
lgam += log1p(v);
|
||||
} else {
|
||||
out = lcons;
|
||||
}
|
||||
|
||||
double m = 2;
|
||||
double lfac = 0;
|
||||
T old_out;
|
||||
do {
|
||||
lfac += log(m);
|
||||
lgam += log(v + m);
|
||||
lcons += 2 * log_half_z;
|
||||
old_out = out;
|
||||
out = log_sum_exp(out, lcons - lfac - lgam); // underflows eventually
|
||||
m++;
|
||||
} while (out > old_out || out < old_out);
|
||||
return out;
|
||||
}
|
||||
|
||||
} // namespace CosmoTool
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue
Block a user