diff --git a/uppsrc/plugin/Eigen/COPYING.BSD b/uppsrc/plugin/Eigen/COPYING.BSD
new file mode 100644
index 000000000..11971ffe2
--- /dev/null
+++ b/uppsrc/plugin/Eigen/COPYING.BSD
@@ -0,0 +1,26 @@
+/*
+ Copyright (c) 2011, Intel Corporation. All rights reserved.
+
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above copyright notice,
+ this list of conditions and the following disclaimer in the documentation
+ and/or other materials provided with the distribution.
+ * Neither the name of Intel Corporation nor the names of its contributors may
+ be used to endorse or promote products derived from this software without
+ specific prior written permission.
+
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+*/
\ No newline at end of file
diff --git a/uppsrc/plugin/Eigen/COPYING.GPL b/uppsrc/plugin/Eigen/COPYING.GPL
index 0e4fa8aaf..94a9ed024 100644
--- a/uppsrc/plugin/Eigen/COPYING.GPL
+++ b/uppsrc/plugin/Eigen/COPYING.GPL
@@ -1,165 +1,674 @@
- GNU LESSER GENERAL PUBLIC LICENSE
+ GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
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of this license document, but changing it is not allowed.
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diff --git a/uppsrc/plugin/Eigen/COPYING.LGPL b/uppsrc/plugin/Eigen/COPYING.LGPL
index 94a9ed024..4362b4915 100644
--- a/uppsrc/plugin/Eigen/COPYING.LGPL
+++ b/uppsrc/plugin/Eigen/COPYING.LGPL
@@ -1,674 +1,502 @@
- GNU GENERAL PUBLIC LICENSE
- Version 3, 29 June 2007
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
- Copyright (C) 2007 Free Software Foundation, Inc.
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
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Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
+[This is the first released version of the Lesser GPL. It also counts
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+KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE
+LIBRARY IS WITH YOU. SHOULD THE LIBRARY PROVE DEFECTIVE, YOU ASSUME
+THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
- THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
-APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
-HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
-OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
-IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
-ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
-
- 16. Limitation of Liability.
-
- IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
-THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
-GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
-USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
-DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
-PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
-EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
-SUCH DAMAGES.
-
- 17. Interpretation of Sections 15 and 16.
-
- If the disclaimer of warranty and limitation of liability provided
-above cannot be given local legal effect according to their terms,
-reviewing courts shall apply local law that most closely approximates
-an absolute waiver of all civil liability in connection with the
-Program, unless a warranty or assumption of liability accompanies a
-copy of the Program in return for a fee.
+ 16. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN
+WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY
+AND/OR REDISTRIBUTE THE LIBRARY AS PERMITTED ABOVE, BE LIABLE TO YOU
+FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR
+CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE
+LIBRARY (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING
+RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A
+FAILURE OF THE LIBRARY TO OPERATE WITH ANY OTHER SOFTWARE), EVEN IF
+SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGES.
END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Libraries
- How to Apply These Terms to Your New Programs
+ If you develop a new library, and you want it to be of the greatest
+possible use to the public, we recommend making it free software that
+everyone can redistribute and change. You can do so by permitting
+redistribution under these terms (or, alternatively, under the terms of the
+ordinary General Public License).
- If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
+ To apply these terms, attach the following notices to the library. It is
+safest to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least the
+"copyright" line and a pointer to where the full notice is found.
- To do so, attach the following notices to the program. It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-
+
Copyright (C)
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
- This program is distributed in the hope that it will be useful,
+ This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Also add information on how to contact you by electronic and paper mail.
- If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the library, if
+necessary. Here is a sample; alter the names:
- Copyright (C)
- This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
- This is free software, and you are welcome to redistribute it
- under certain conditions; type `show c' for details.
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the
+ library `Frob' (a library for tweaking knobs) written by James Random Hacker.
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
+ , 1 April 1990
+ Ty Coon, President of Vice
- You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
- The GNU General Public License does not permit incorporating your program
-into proprietary programs. If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library. If this is what you want to do, use the GNU Lesser General
-Public License instead of this License. But first, please read
-.
+That's all there is to it!
diff --git a/uppsrc/plugin/Eigen/COPYING.MINPACK b/uppsrc/plugin/Eigen/COPYING.MINPACK
new file mode 100644
index 000000000..11d8a9a6c
--- /dev/null
+++ b/uppsrc/plugin/Eigen/COPYING.MINPACK
@@ -0,0 +1,52 @@
+Minpack Copyright Notice (1999) University of Chicago. All rights reserved
+
+Redistribution and use in source and binary forms, with or
+without modification, are permitted provided that the
+following conditions are met:
+
+1. Redistributions of source code must retain the above
+copyright notice, this list of conditions and the following
+disclaimer.
+
+2. Redistributions in binary form must reproduce the above
+copyright notice, this list of conditions and the following
+disclaimer in the documentation and/or other materials
+provided with the distribution.
+
+3. The end-user documentation included with the
+redistribution, if any, must include the following
+acknowledgment:
+
+ "This product includes software developed by the
+ University of Chicago, as Operator of Argonne National
+ Laboratory.
+
+Alternately, this acknowledgment may appear in the software
+itself, if and wherever such third-party acknowledgments
+normally appear.
+
+4. WARRANTY DISCLAIMER. THE SOFTWARE IS SUPPLIED "AS IS"
+WITHOUT WARRANTY OF ANY KIND. THE COPYRIGHT HOLDER, THE
+UNITED STATES, THE UNITED STATES DEPARTMENT OF ENERGY, AND
+THEIR EMPLOYEES: (1) DISCLAIM ANY WARRANTIES, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES
+OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, TITLE
+OR NON-INFRINGEMENT, (2) DO NOT ASSUME ANY LEGAL LIABILITY
+OR RESPONSIBILITY FOR THE ACCURACY, COMPLETENESS, OR
+USEFULNESS OF THE SOFTWARE, (3) DO NOT REPRESENT THAT USE OF
+THE SOFTWARE WOULD NOT INFRINGE PRIVATELY OWNED RIGHTS, (4)
+DO NOT WARRANT THAT THE SOFTWARE WILL FUNCTION
+UNINTERRUPTED, THAT IT IS ERROR-FREE OR THAT ANY ERRORS WILL
+BE CORRECTED.
+
+5. LIMITATION OF LIABILITY. IN NO EVENT WILL THE COPYRIGHT
+HOLDER, THE UNITED STATES, THE UNITED STATES DEPARTMENT OF
+ENERGY, OR THEIR EMPLOYEES: BE LIABLE FOR ANY INDIRECT,
+INCIDENTAL, CONSEQUENTIAL, SPECIAL OR PUNITIVE DAMAGES OF
+ANY KIND OR NATURE, INCLUDING BUT NOT LIMITED TO LOSS OF
+PROFITS OR LOSS OF DATA, FOR ANY REASON WHATSOEVER, WHETHER
+SUCH LIABILITY IS ASSERTED ON THE BASIS OF CONTRACT, TORT
+(INCLUDING NEGLIGENCE OR STRICT LIABILITY), OR OTHERWISE,
+EVEN IF ANY OF SAID PARTIES HAS BEEN WARNED OF THE
+POSSIBILITY OF SUCH LOSS OR DAMAGES.
+
diff --git a/uppsrc/plugin/Eigen/COPYING.MPL2 b/uppsrc/plugin/Eigen/COPYING.MPL2
new file mode 100644
index 000000000..14e2f777f
--- /dev/null
+++ b/uppsrc/plugin/Eigen/COPYING.MPL2
@@ -0,0 +1,373 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+ means each individual or legal entity that creates, contributes to
+ the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+ means the combination of the Contributions of others (if any) used
+ by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+ means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+ means Source Code Form to which the initial Contributor has attached
+ the notice in Exhibit A, the Executable Form of such Source Code
+ Form, and Modifications of such Source Code Form, in each case
+ including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+ means
+
+ (a) that the initial Contributor has attached the notice described
+ in Exhibit B to the Covered Software; or
+
+ (b) that the Covered Software was made available under the terms of
+ version 1.1 or earlier of the License, but not also under the
+ terms of a Secondary License.
+
+1.6. "Executable Form"
+ means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+ means a work that combines Covered Software with other material, in
+ a separate file or files, that is not Covered Software.
+
+1.8. "License"
+ means this document.
+
+1.9. "Licensable"
+ means having the right to grant, to the maximum extent possible,
+ whether at the time of the initial grant or subsequently, any and
+ all of the rights conveyed by this License.
+
+1.10. "Modifications"
+ means any of the following:
+
+ (a) any file in Source Code Form that results from an addition to,
+ deletion from, or modification of the contents of Covered
+ Software; or
+
+ (b) any new file in Source Code Form that contains any Covered
+ Software.
+
+1.11. "Patent Claims" of a Contributor
+ means any patent claim(s), including without limitation, method,
+ process, and apparatus claims, in any patent Licensable by such
+ Contributor that would be infringed, but for the grant of the
+ License, by the making, using, selling, offering for sale, having
+ made, import, or transfer of either its Contributions or its
+ Contributor Version.
+
+1.12. "Secondary License"
+ means either the GNU General Public License, Version 2.0, the GNU
+ Lesser General Public License, Version 2.1, the GNU Affero General
+ Public License, Version 3.0, or any later versions of those
+ licenses.
+
+1.13. "Source Code Form"
+ means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+ means an individual or a legal entity exercising rights under this
+ License. For legal entities, "You" includes any entity that
+ controls, is controlled by, or is under common control with You. For
+ purposes of this definition, "control" means (a) the power, direct
+ or indirect, to cause the direction or management of such entity,
+ whether by contract or otherwise, or (b) ownership of more than
+ fifty percent (50%) of the outstanding shares or beneficial
+ ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+ Licensable by such Contributor to use, reproduce, make available,
+ modify, display, perform, distribute, and otherwise exploit its
+ Contributions, either on an unmodified basis, with Modifications, or
+ as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+ for sale, have made, import, and otherwise transfer either its
+ Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+ or
+
+(b) for infringements caused by: (i) Your and any other third party's
+ modifications of Covered Software, or (ii) the combination of its
+ Contributions with other software (except as part of its Contributor
+ Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+ its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+ Form, as described in Section 3.1, and You must inform recipients of
+ the Executable Form how they can obtain a copy of such Source Code
+ Form by reasonable means in a timely manner, at a charge no more
+ than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+ License, or sublicense it under different terms, provided that the
+ license for the Executable Form does not attempt to limit or alter
+ the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+* *
+* 6. Disclaimer of Warranty *
+* ------------------------- *
+* *
+* Covered Software is provided under this License on an "as is" *
+* basis, without warranty of any kind, either expressed, implied, or *
+* statutory, including, without limitation, warranties that the *
+* Covered Software is free of defects, merchantable, fit for a *
+* particular purpose or non-infringing. The entire risk as to the *
+* quality and performance of the Covered Software is with You. *
+* Should any Covered Software prove defective in any respect, You *
+* (not any Contributor) assume the cost of any necessary servicing, *
+* repair, or correction. This disclaimer of warranty constitutes an *
+* essential part of this License. No use of any Covered Software is *
+* authorized under this License except under this disclaimer. *
+* *
+************************************************************************
+
+************************************************************************
+* *
+* 7. Limitation of Liability *
+* -------------------------- *
+* *
+* Under no circumstances and under no legal theory, whether tort *
+* (including negligence), contract, or otherwise, shall any *
+* Contributor, or anyone who distributes Covered Software as *
+* permitted above, be liable to You for any direct, indirect, *
+* special, incidental, or consequential damages of any character *
+* including, without limitation, damages for lost profits, loss of *
+* goodwill, work stoppage, computer failure or malfunction, or any *
+* and all other commercial damages or losses, even if such party *
+* shall have been informed of the possibility of such damages. This *
+* limitation of liability shall not apply to liability for death or *
+* personal injury resulting from such party's negligence to the *
+* extent applicable law prohibits such limitation. Some *
+* jurisdictions do not allow the exclusion or limitation of *
+* incidental or consequential damages, so this exclusion and *
+* limitation may not apply to You. *
+* *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+ This Source Code Form is subject to the terms of the Mozilla Public
+ License, v. 2.0. If a copy of the MPL was not distributed with this
+ file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+ This Source Code Form is "Incompatible With Secondary Licenses", as
+ defined by the Mozilla Public License, v. 2.0.
diff --git a/uppsrc/plugin/Eigen/COPYING.README b/uppsrc/plugin/Eigen/COPYING.README
new file mode 100644
index 000000000..de5b63215
--- /dev/null
+++ b/uppsrc/plugin/Eigen/COPYING.README
@@ -0,0 +1,18 @@
+Eigen is primarily MPL2 licensed. See COPYING.MPL2 and these links:
+ http://www.mozilla.org/MPL/2.0/
+ http://www.mozilla.org/MPL/2.0/FAQ.html
+
+Some files contain third-party code under BSD or LGPL licenses, whence the other
+COPYING.* files here.
+
+All the LGPL code is either LGPL 2.1-only, or LGPL 2.1-or-later.
+For this reason, the COPYING.LGPL file contains the LGPL 2.1 text.
+
+If you want to guarantee that the Eigen code that you are #including is licensed
+under the MPL2 and possibly more permissive licenses (like BSD), #define this
+preprocessor symbol:
+ EIGEN_MPL2_ONLY
+For example, with most compilers, you could add this to your project CXXFLAGS:
+ -DEIGEN_MPL2_ONLY
+This will cause a compilation error to be generated if you #include any code that is
+LGPL licensed.
diff --git a/uppsrc/plugin/Eigen/Eigen.cpp b/uppsrc/plugin/Eigen/Eigen.cpp
index cc5dcc96a..ffa4628a1 100644
--- a/uppsrc/plugin/Eigen/Eigen.cpp
+++ b/uppsrc/plugin/Eigen/Eigen.cpp
@@ -1 +1,3 @@
-// Dummy file just to get a lib
+// Just a dummy file to compile
+
+
diff --git a/uppsrc/plugin/Eigen/Eigen.h b/uppsrc/plugin/Eigen/Eigen.h
index 7b43f8a62..d7c794dca 100644
--- a/uppsrc/plugin/Eigen/Eigen.h
+++ b/uppsrc/plugin/Eigen/Eigen.h
@@ -11,8 +11,119 @@
#define EIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT
#endif
+#ifndef _DEBUG
#define EIGEN_NO_DEBUG
+#endif
+#define EIGEN_EXCEPTIONS
+
+//#undef Success
#include "Eigen/Eigen"
+
+NAMESPACE_UPP
+
+template
+void Xmlize(XmlIO &xml, Eigen::Matrix &mat) {
+ if(xml.IsStoring()) {
+ Size sz(mat.cols(), mat.rows());
+ xml ("Size", sz);
+ for(int r = 0; r < mat.rows(); r++)
+ for(int c = 0; c < mat.cols(); c++) {
+ T data = mat(r, c);
+ xml.Attr("item", data);
+ }
+ } else {
+ Size sz;
+ xml ("Size", sz);
+ mat.resize(sz.cy, sz.cx);
+ int r = 0;
+ int c = 0;
+ for(int i = 1; i < xml->GetCount(); i++) {
+ T data;
+ xml.Attr("item", data);
+ mat(r, c) = data;
+ ++c;
+ if (c == sz.cx) {
+ c = 0;
+ r++;
+ }
+ if (r == sz.cy)
+ break;
+ }
+ }
+}
+
+template
+void Xmlize(XmlIO &xml, Eigen::Matrix &vec) {
+ if(xml.IsStoring()) {
+ int sz = vec.size();
+ xml ("Size", sz);
+ for(int r = 0; r < vec.size(); r++) {
+ T data = vec(r);
+ xml.Attr("item", data);
+ }
+ } else {
+ int sz;
+ xml ("Size", sz);
+ vec.resize(sz);
+ int r = 0;
+ for(int i = 1; i < xml->GetCount(); i++) {
+ T data;
+ xml.Attr("item", data);
+ vec(r) = data;
+ ++r;
+ if (r == sz)
+ break;
+ }
+ }
+}
+
+template
+void Jsonize(JsonIO &xml, Eigen::Matrix &mat) {
+ if(xml.IsStoring()) {
+ Size sz(mat.cols(), mat.rows());
+ xml.Set(sz);
+ for(int r = 0; r < mat.rows(); r++)
+ for(int c = 0; c < mat.cols(); c++) {
+ T data = mat(r, c);
+ xml.Set(data);
+ }
+ } else {
+ Size sz = xml.Get();
+ mat.resize(sz.cy, sz.cx);
+ int r = 0;
+ int c = 0;
+ for(int i = 0; i < sz.cy*sz.cx; i++) {
+ T data = xml.Get();
+ mat(r, c) = data;
+ ++c;
+ if (c == sz.cx) {
+ c = 0;
+ r++;
+ }
+ if (r == sz.cy)
+ break;
+ }
+ }
+}
+
+template
+void Jsonize(JsonIO &xml, Eigen::Matrix &vec) {
+ Vector vector;
+ if(xml.IsStoring()) {
+ vector.SetCount(vec.size());
+ for (int i = 0; i < vec.size(); ++i)
+ vector[i] = vec(i);
+ xml("vector", vector);
+ } else {
+ xml("vector", vector);
+ vec.resize(vector.GetCount());
+ for (int i = 0; i < vec.size(); ++i)
+ vec(i) = vector[i];
+ }
+}
+
+END_UPP_NAMESPACE
+
#endif
diff --git a/uppsrc/plugin/Eigen/Eigen.upp b/uppsrc/plugin/Eigen/Eigen.upp
index 97931c1d7..72ce093e4 100644
--- a/uppsrc/plugin/Eigen/Eigen.upp
+++ b/uppsrc/plugin/Eigen/Eigen.upp
@@ -12,8 +12,6 @@ file
Eigen.h,
ToStringPlugin.h,
srcdoc.tpp,
- COPYING.GPL,
- COPYING.LGPL,
Eigen readonly separator,
Eigen/Array highlight cpp,
Eigen/Core highlight cpp,
@@ -329,5 +327,12 @@ file
unsupported/Eigen/src/SparseExtra/SparseLLT.h,
unsupported/Eigen/src/SparseExtra/SparseLU.h,
unsupported/Eigen/src/SparseExtra/SuperLUSupport.h,
- unsupported/Eigen/src/SparseExtra/UmfPackSupport.h;
+ unsupported/Eigen/src/SparseExtra/UmfPackSupport.h,
+ License readonly separator,
+ COPYING.README,
+ COPYING.BSD,
+ COPYING.MINPACK,
+ COPYING.MPL2,
+ COPYING.GPL,
+ COPYING.LGPL;
diff --git a/uppsrc/plugin/Eigen/Eigen/CMakeLists.txt b/uppsrc/plugin/Eigen/Eigen/CMakeLists.txt
new file mode 100644
index 000000000..a92dd6f6c
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/CMakeLists.txt
@@ -0,0 +1,19 @@
+include(RegexUtils)
+test_escape_string_as_regex()
+
+file(GLOB Eigen_directory_files "*")
+
+escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+foreach(f ${Eigen_directory_files})
+ if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/src")
+ list(APPEND Eigen_directory_files_to_install ${f})
+ endif()
+endforeach(f ${Eigen_directory_files})
+
+install(FILES
+ ${Eigen_directory_files_to_install}
+ DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
+ )
+
+add_subdirectory(src)
diff --git a/uppsrc/plugin/Eigen/Eigen/Cholesky b/uppsrc/plugin/Eigen/Eigen/Cholesky
index 53f7bf911..f727f5d89 100644
--- a/uppsrc/plugin/Eigen/Eigen/Cholesky
+++ b/uppsrc/plugin/Eigen/Eigen/Cholesky
@@ -5,8 +5,6 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
/** \defgroup Cholesky_Module Cholesky module
*
*
@@ -24,8 +22,9 @@ namespace Eigen {
#include "src/misc/Solve.h"
#include "src/Cholesky/LLT.h"
#include "src/Cholesky/LDLT.h"
-
-} // namespace Eigen
+#ifdef EIGEN_USE_LAPACKE
+#include "src/Cholesky/LLT_MKL.h"
+#endif
#include "src/Core/util/ReenableStupidWarnings.h"
diff --git a/uppsrc/plugin/Eigen/Eigen/CholmodSupport b/uppsrc/plugin/Eigen/Eigen/CholmodSupport
new file mode 100644
index 000000000..745b884e7
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/CholmodSupport
@@ -0,0 +1,45 @@
+#ifndef EIGEN_CHOLMODSUPPORT_MODULE_H
+#define EIGEN_CHOLMODSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+extern "C" {
+ #include
+}
+
+/** \ingroup Support_modules
+ * \defgroup CholmodSupport_Module CholmodSupport module
+ *
+ * This module provides an interface to the Cholmod library which is part of the suitesparse package.
+ * It provides the two following main factorization classes:
+ * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+ * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
+ *
+ * For the sake of completeness, this module also propose the two following classes:
+ * - class CholmodSimplicialLLT
+ * - class CholmodSimplicialLDLT
+ * Note that these classes does not bring any particular advantage compared to the built-in
+ * SimplicialLLT and SimplicialLDLT factorization classes.
+ *
+ * \code
+ * #include
+ * \endcode
+ *
+ * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies.
+ * The dependencies depend on how cholmod has been compiled.
+ * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
+ *
+ */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/CholmodSupport/CholmodSupport.h"
+
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
+
diff --git a/uppsrc/plugin/Eigen/Eigen/Core b/uppsrc/plugin/Eigen/Eigen/Core
index 6e855427c..d48017022 100644
--- a/uppsrc/plugin/Eigen/Eigen/Core
+++ b/uppsrc/plugin/Eigen/Eigen/Core
@@ -4,24 +4,9 @@
// Copyright (C) 2008 Gael Guennebaud
// Copyright (C) 2007-2011 Benoit Jacob
//
-// Eigen is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 3 of the License, or (at your option) any later version.
-//
-// Alternatively, you can redistribute it and/or
-// modify it under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 2 of
-// the License, or (at your option) any later version.
-//
-// Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
-// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License and a copy of the GNU General Public License along with
-// Eigen. If not, see .
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
#ifndef EIGEN_CORE_H
#define EIGEN_CORE_H
@@ -34,6 +19,12 @@
// defined e.g. EIGEN_DONT_ALIGN) so it needs to be done before we do anything with vectorization.
#include "src/Core/util/Macros.h"
+#include
+
+// this include file manages BLAS and MKL related macros
+// and inclusion of their respective header files
+#include "src/Core/util/MKL_support.h"
+
// if alignment is disabled, then disable vectorization. Note: EIGEN_ALIGN is the proper check, it takes into
// account both the user's will (EIGEN_DONT_ALIGN) and our own platform checks
#if !EIGEN_ALIGN
@@ -136,7 +127,7 @@
#endif
// MSVC for windows mobile does not have the errno.h file
-#if !(defined(_MSC_VER) && defined(_WIN32_WCE))
+#if !(defined(_MSC_VER) && defined(_WIN32_WCE)) && !defined(__ARMCC_VERSION)
#define EIGEN_HAS_ERRNO
#endif
@@ -146,7 +137,6 @@
#include
#include
#include
-#include
#include
#include
#include
@@ -167,7 +157,7 @@
#include
#endif
-#if (defined(_CPPUNWIND) || defined(__EXCEPTIONS)) && !defined(EIGEN_NO_EXCEPTIONS)
+#if defined(_CPPUNWIND) || defined(__EXCEPTIONS)
#define EIGEN_EXCEPTIONS
#endif
@@ -175,9 +165,6 @@
#include
#endif
-// defined in bits/termios.h
-#undef B0
-
/** \brief Namespace containing all symbols from the %Eigen library. */
namespace Eigen {
@@ -201,6 +188,8 @@ inline static const char *SimdInstructionSetsInUse(void) {
#endif
}
+} // end namespace Eigen
+
#define STAGE10_FULL_EIGEN2_API 10
#define STAGE20_RESOLVE_API_CONFLICTS 20
#define STAGE30_FULL_EIGEN3_API 30
@@ -247,6 +236,10 @@ using std::ptrdiff_t;
* \endcode
*/
+/** \defgroup Support_modules Support modules [category]
+ * Category of modules which add support for external libraries.
+ */
+
#include "src/Core/util/Constants.h"
#include "src/Core/util/ForwardDeclarations.h"
#include "src/Core/util/Meta.h"
@@ -318,15 +311,15 @@ using std::ptrdiff_t;
#include "src/Core/CommaInitializer.h"
#include "src/Core/Flagged.h"
#include "src/Core/ProductBase.h"
-#include "src/Core/Product.h"
+#include "src/Core/GeneralProduct.h"
#include "src/Core/TriangularMatrix.h"
#include "src/Core/SelfAdjointView.h"
-#include "src/Core/SolveTriangular.h"
+#include "src/Core/products/GeneralBlockPanelKernel.h"
#include "src/Core/products/Parallelizer.h"
#include "src/Core/products/CoeffBasedProduct.h"
-#include "src/Core/products/GeneralBlockPanelKernel.h"
#include "src/Core/products/GeneralMatrixVector.h"
#include "src/Core/products/GeneralMatrixMatrix.h"
+#include "src/Core/SolveTriangular.h"
#include "src/Core/products/GeneralMatrixMatrixTriangular.h"
#include "src/Core/products/SelfadjointMatrixVector.h"
#include "src/Core/products/SelfadjointMatrixMatrix.h"
@@ -347,7 +340,20 @@ using std::ptrdiff_t;
#include "src/Core/ArrayBase.h"
#include "src/Core/ArrayWrapper.h"
-} // namespace Eigen
+#ifdef EIGEN_USE_BLAS
+#include "src/Core/products/GeneralMatrixMatrix_MKL.h"
+#include "src/Core/products/GeneralMatrixVector_MKL.h"
+#include "src/Core/products/GeneralMatrixMatrixTriangular_MKL.h"
+#include "src/Core/products/SelfadjointMatrixMatrix_MKL.h"
+#include "src/Core/products/SelfadjointMatrixVector_MKL.h"
+#include "src/Core/products/TriangularMatrixMatrix_MKL.h"
+#include "src/Core/products/TriangularMatrixVector_MKL.h"
+#include "src/Core/products/TriangularSolverMatrix_MKL.h"
+#endif // EIGEN_USE_BLAS
+
+#ifdef EIGEN_USE_MKL_VML
+#include "src/Core/Assign_MKL.h"
+#endif
#include "src/Core/GlobalFunctions.h"
diff --git a/uppsrc/plugin/Eigen/Eigen/Eigen2Support b/uppsrc/plugin/Eigen/Eigen/Eigen2Support
index d96592a8d..36156d29a 100644
--- a/uppsrc/plugin/Eigen/Eigen/Eigen2Support
+++ b/uppsrc/plugin/Eigen/Eigen/Eigen2Support
@@ -3,24 +3,9 @@
//
// Copyright (C) 2009 Gael Guennebaud
//
-// Eigen is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 3 of the License, or (at your option) any later version.
-//
-// Alternatively, you can redistribute it and/or
-// modify it under the terms of the GNU General Public License as
-// published by the Free Software Foundation; either version 2 of
-// the License, or (at your option) any later version.
-//
-// Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
-// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
-// GNU General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License and a copy of the GNU General Public License along with
-// Eigen. If not, see .
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
#ifndef EIGEN2SUPPORT_H
#define EIGEN2SUPPORT_H
@@ -31,9 +16,8 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
-/** \defgroup Eigen2Support_Module Eigen2 support module
+/** \ingroup Support_modules
+ * \defgroup Eigen2Support_Module Eigen2 support module
* This module provides a couple of deprecated functions improving the compatibility with Eigen2.
*
* To use it, define EIGEN2_SUPPORT before including any Eigen header
@@ -56,13 +40,29 @@ namespace Eigen {
#include "src/Eigen2Support/MathFunctions.h"
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
// Eigen2 used to include iostream
#include
+#define EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, SizeSuffix) \
+using Eigen::Matrix##SizeSuffix##TypeSuffix; \
+using Eigen::Vector##SizeSuffix##TypeSuffix; \
+using Eigen::RowVector##SizeSuffix##TypeSuffix;
+
+#define EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(TypeSuffix) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 2) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 3) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, 4) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE_AND_SIZE(TypeSuffix, X) \
+
+#define EIGEN_USING_MATRIX_TYPEDEFS \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(i) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(f) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(d) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cf) \
+EIGEN_USING_MATRIX_TYPEDEFS_FOR_TYPE(cd)
+
#define USING_PART_OF_NAMESPACE_EIGEN \
EIGEN_USING_MATRIX_TYPEDEFS \
using Eigen::Matrix; \
diff --git a/uppsrc/plugin/Eigen/Eigen/Eigenvalues b/uppsrc/plugin/Eigen/Eigen/Eigenvalues
index 250c0f466..af99ccd1f 100644
--- a/uppsrc/plugin/Eigen/Eigen/Eigenvalues
+++ b/uppsrc/plugin/Eigen/Eigen/Eigenvalues
@@ -9,8 +9,7 @@
#include "Jacobi"
#include "Householder"
#include "LU"
-
-namespace Eigen {
+#include "Geometry"
/** \defgroup Eigenvalues_Module Eigenvalues module
*
@@ -35,8 +34,11 @@ namespace Eigen {
#include "src/Eigenvalues/ComplexSchur.h"
#include "src/Eigenvalues/ComplexEigenSolver.h"
#include "src/Eigenvalues/MatrixBaseEigenvalues.h"
-
-} // namespace Eigen
+#ifdef EIGEN_USE_LAPACKE
+#include "src/Eigenvalues/RealSchur_MKL.h"
+#include "src/Eigenvalues/ComplexSchur_MKL.h"
+#include "src/Eigenvalues/SelfAdjointEigenSolver_MKL.h"
+#endif
#include "src/Core/util/ReenableStupidWarnings.h"
diff --git a/uppsrc/plugin/Eigen/Eigen/Geometry b/uppsrc/plugin/Eigen/Eigen/Geometry
index 78277c0c5..efd9d4504 100644
--- a/uppsrc/plugin/Eigen/Eigen/Geometry
+++ b/uppsrc/plugin/Eigen/Eigen/Geometry
@@ -13,8 +13,6 @@
#define M_PI 3.14159265358979323846
#endif
-namespace Eigen {
-
/** \defgroup Geometry_Module Geometry module
*
*
@@ -58,8 +56,6 @@ namespace Eigen {
#include "src/Eigen2Support/Geometry/All.h"
#endif
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN_GEOMETRY_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/Householder b/uppsrc/plugin/Eigen/Eigen/Householder
index 6b86cf65c..6e348db5c 100644
--- a/uppsrc/plugin/Eigen/Eigen/Householder
+++ b/uppsrc/plugin/Eigen/Eigen/Householder
@@ -5,8 +5,6 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
/** \defgroup Householder_Module Householder module
* This module provides Householder transformations.
*
@@ -19,8 +17,6 @@ namespace Eigen {
#include "src/Householder/HouseholderSequence.h"
#include "src/Householder/BlockHouseholder.h"
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN_HOUSEHOLDER_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/IterativeLinearSolvers b/uppsrc/plugin/Eigen/Eigen/IterativeLinearSolvers
new file mode 100644
index 000000000..315c2dd1e
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/IterativeLinearSolvers
@@ -0,0 +1,40 @@
+#ifndef EIGEN_ITERATIVELINEARSOLVERS_MODULE_H
+#define EIGEN_ITERATIVELINEARSOLVERS_MODULE_H
+
+#include "SparseCore"
+#include "OrderingMethods"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \ingroup Sparse_modules
+ * \defgroup IterativeLinearSolvers_Module IterativeLinearSolvers module
+ *
+ * This module currently provides iterative methods to solve problems of the form \c A \c x = \c b, where \c A is a squared matrix, usually very large and sparse.
+ * Those solvers are accessible via the following classes:
+ * - ConjugateGradient for selfadjoint (hermitian) matrices,
+ * - BiCGSTAB for general square matrices.
+ *
+ * These iterative solvers are associated with some preconditioners:
+ * - IdentityPreconditioner - not really useful
+ * - DiagonalPreconditioner - also called JAcobi preconditioner, work very well on diagonal dominant matrices.
+ * - IncompleteILUT - incomplete LU factorization with dual thresholding
+ *
+ * Such problems can also be solved using the direct sparse decomposition modules: SparseCholesky, CholmodSupport, UmfPackSupport, SuperLUSupport.
+ *
+ * \code
+ * #include
+ * \endcode
+ */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/IterativeLinearSolvers/IterativeSolverBase.h"
+#include "src/IterativeLinearSolvers/BasicPreconditioners.h"
+#include "src/IterativeLinearSolvers/ConjugateGradient.h"
+#include "src/IterativeLinearSolvers/BiCGSTAB.h"
+#include "src/IterativeLinearSolvers/IncompleteLUT.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_ITERATIVELINEARSOLVERS_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/Jacobi b/uppsrc/plugin/Eigen/Eigen/Jacobi
index afa676813..ba8a4dc36 100644
--- a/uppsrc/plugin/Eigen/Eigen/Jacobi
+++ b/uppsrc/plugin/Eigen/Eigen/Jacobi
@@ -5,8 +5,6 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
/** \defgroup Jacobi_Module Jacobi module
* This module provides Jacobi and Givens rotations.
*
@@ -21,8 +19,6 @@ namespace Eigen {
#include "src/Jacobi/Jacobi.h"
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN_JACOBI_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/LU b/uppsrc/plugin/Eigen/Eigen/LU
index 226f88ca3..db5795504 100644
--- a/uppsrc/plugin/Eigen/Eigen/LU
+++ b/uppsrc/plugin/Eigen/Eigen/LU
@@ -5,8 +5,6 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
/** \defgroup LU_Module LU module
* This module includes %LU decomposition and related notions such as matrix inversion and determinant.
* This module defines the following MatrixBase methods:
@@ -23,6 +21,9 @@ namespace Eigen {
#include "src/misc/Image.h"
#include "src/LU/FullPivLU.h"
#include "src/LU/PartialPivLU.h"
+#ifdef EIGEN_USE_LAPACKE
+#include "src/LU/PartialPivLU_MKL.h"
+#endif
#include "src/LU/Determinant.h"
#include "src/LU/Inverse.h"
@@ -34,8 +35,6 @@ namespace Eigen {
#include "src/Eigen2Support/LU.h"
#endif
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN_LU_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/LeastSquares b/uppsrc/plugin/Eigen/Eigen/LeastSquares
index 93a6302dc..35137c25d 100644
--- a/uppsrc/plugin/Eigen/Eigen/LeastSquares
+++ b/uppsrc/plugin/Eigen/Eigen/LeastSquares
@@ -15,8 +15,6 @@
#include "Eigenvalues"
#include "Geometry"
-namespace Eigen {
-
/** \defgroup LeastSquares_Module LeastSquares module
* This module provides linear regression and related features.
*
@@ -27,8 +25,6 @@ namespace Eigen {
#include "src/Eigen2Support/LeastSquares.h"
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN2_SUPPORT
diff --git a/uppsrc/plugin/Eigen/Eigen/OrderingMethods b/uppsrc/plugin/Eigen/Eigen/OrderingMethods
new file mode 100644
index 000000000..1e2d87452
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/OrderingMethods
@@ -0,0 +1,23 @@
+#ifndef EIGEN_ORDERINGMETHODS_MODULE_H
+#define EIGEN_ORDERINGMETHODS_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \ingroup Sparse_modules
+ * \defgroup OrderingMethods_Module OrderingMethods module
+ *
+ * This module is currently for internal use only.
+ *
+ *
+ * \code
+ * #include
+ * \endcode
+ */
+
+#include "src/OrderingMethods/Amd.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_ORDERINGMETHODS_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/PaStiXSupport b/uppsrc/plugin/Eigen/Eigen/PaStiXSupport
new file mode 100644
index 000000000..7c616ee5e
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/PaStiXSupport
@@ -0,0 +1,46 @@
+#ifndef EIGEN_PASTIXSUPPORT_MODULE_H
+#define EIGEN_PASTIXSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include
+extern "C" {
+#include
+#include
+}
+
+#ifdef complex
+#undef complex
+#endif
+
+/** \ingroup Support_modules
+ * \defgroup PaStiXSupport_Module PaStiXSupport module
+ *
+ * This module provides an interface to the PaSTiX library.
+ * PaSTiX is a general \b supernodal, \b parallel and \b opensource sparse solver.
+ * It provides the two following main factorization classes:
+ * - class PastixLLT : a supernodal, parallel LLt Cholesky factorization.
+ * - class PastixLDLT: a supernodal, parallel LDLt Cholesky factorization.
+ * - class PastixLU : a supernodal, parallel LU factorization (optimized for a symmetric pattern).
+ *
+ * \code
+ * #include
+ * \endcode
+ *
+ * In order to use this module, the PaSTiX headers must be accessible from the include paths, and your binary must be linked to the PaSTiX library and its dependencies.
+ * The dependencies depend on how PaSTiX has been compiled.
+ * For a cmake based project, you can use our FindPaSTiX.cmake module to help you in this task.
+ *
+ */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/PaStiXSupport/PaStiXSupport.h"
+
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_PASTIXSUPPORT_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/PardisoSupport b/uppsrc/plugin/Eigen/Eigen/PardisoSupport
new file mode 100644
index 000000000..99330ce7a
--- /dev/null
+++ b/uppsrc/plugin/Eigen/Eigen/PardisoSupport
@@ -0,0 +1,30 @@
+#ifndef EIGEN_PARDISOSUPPORT_MODULE_H
+#define EIGEN_PARDISOSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include
+
+#include
+
+/** \ingroup Support_modules
+ * \defgroup PardisoSupport_Module PardisoSupport module
+ *
+ * This module brings support for the Intel(R) MKL PARDISO direct sparse solvers.
+ *
+ * \code
+ * #include
+ * \endcode
+ *
+ * In order to use this module, the MKL headers must be accessible from the include paths, and your binary must be linked to the MKL library and its dependencies.
+ * See this \ref TopicUsingIntelMKL "page" for more information on MKL-Eigen integration.
+ *
+ */
+
+#include "src/PardisoSupport/PardisoSupport.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_PARDISOSUPPORT_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/QR b/uppsrc/plugin/Eigen/Eigen/QR
index 97c1788ee..ac5b02693 100644
--- a/uppsrc/plugin/Eigen/Eigen/QR
+++ b/uppsrc/plugin/Eigen/Eigen/QR
@@ -9,8 +9,6 @@
#include "Jacobi"
#include "Householder"
-namespace Eigen {
-
/** \defgroup QR_Module QR module
*
*
@@ -28,13 +26,15 @@ namespace Eigen {
#include "src/QR/HouseholderQR.h"
#include "src/QR/FullPivHouseholderQR.h"
#include "src/QR/ColPivHouseholderQR.h"
+#ifdef EIGEN_USE_LAPACKE
+#include "src/QR/HouseholderQR_MKL.h"
+#include "src/QR/ColPivHouseholderQR_MKL.h"
+#endif
#ifdef EIGEN2_SUPPORT
#include "src/Eigen2Support/QR.h"
#endif
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#ifdef EIGEN2_SUPPORT
diff --git a/uppsrc/plugin/Eigen/Eigen/SVD b/uppsrc/plugin/Eigen/Eigen/SVD
index d24471fd7..fd310017a 100644
--- a/uppsrc/plugin/Eigen/Eigen/SVD
+++ b/uppsrc/plugin/Eigen/Eigen/SVD
@@ -7,15 +7,13 @@
#include "src/Core/util/DisableStupidWarnings.h"
-namespace Eigen {
-
/** \defgroup SVD_Module SVD module
*
*
*
- * This module provides SVD decomposition for (currently) real matrices.
+ * This module provides SVD decomposition for matrices (both real and complex).
* This decomposition is accessible via the following MatrixBase method:
- * - MatrixBase::svd()
+ * - MatrixBase::jacobiSvd()
*
* \code
* #include
@@ -24,14 +22,15 @@ namespace Eigen {
#include "src/misc/Solve.h"
#include "src/SVD/JacobiSVD.h"
+#if defined(EIGEN_USE_LAPACKE) && !defined(EIGEN_USE_LAPACKE_STRICT)
+#include "src/SVD/JacobiSVD_MKL.h"
+#endif
#include "src/SVD/UpperBidiagonalization.h"
#ifdef EIGEN2_SUPPORT
#include "src/Eigen2Support/SVD.h"
#endif
-} // namespace Eigen
-
#include "src/Core/util/ReenableStupidWarnings.h"
#endif // EIGEN_SVD_MODULE_H
diff --git a/uppsrc/plugin/Eigen/Eigen/Sparse b/uppsrc/plugin/Eigen/Eigen/Sparse
index 7425b3a41..2d1757172 100644
--- a/uppsrc/plugin/Eigen/Eigen/Sparse
+++ b/uppsrc/plugin/Eigen/Eigen/Sparse
@@ -1,69 +1,23 @@
#ifndef EIGEN_SPARSE_MODULE_H
#define EIGEN_SPARSE_MODULE_H
-#include "Core"
-
-#include "src/Core/util/DisableStupidWarnings.h"
-
-#include
-#include