Add missing defines to PKG_CFLAGS

[gromacs.git] / COPYING

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entire whole, and thus to each and every part regardless of who wrote it.

Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
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collective works based on the Program.

In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.

  3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:

    a) Accompany it with the complete corresponding machine-readable
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    years, to give any third party, for a charge no more than your
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    c) Accompany it with the information you received as to the offer
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    received the program in object code or executable form with such
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The source code for a work means the preferred form of the work for
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  4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License.  Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
parties remain in full compliance.

  5. You are not required to accept this License, since you have not
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prohibited by law if you do not accept this License.  Therefore, by
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Program), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Program or works based on it.

  6. Each time you redistribute the Program (or any work based on the
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You are not responsible for enforcing compliance by third parties to
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  7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
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may not distribute the Program at all.  For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.

If any portion of this section is held invalid or unenforceable under
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to distribute software through any other system and a licensee cannot
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This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.

  8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
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the limitation as if written in the body of this License.

  9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time.  Such new versions will
be similar in spirit to the present version, but may differ in detail to
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specifies a version number of this License which applies to it and "any
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either of that version or of any later version published by the Free
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Foundation.

  10. If you wish to incorporate parts of the Program into other free
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                            NO WARRANTY

  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, 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
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WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
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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
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                     END OF TERMS AND CONDITIONS

            How to Apply These Terms to Your New Programs

  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 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
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.

    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>

    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 2 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License along
    with this program; 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 is interactive, make it output a short notice like this
when it starts in an interactive mode:

    Gnomovision version 69, Copyright (C) year name of author
    Gnomovision 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.

The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License.  Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.

You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary.  Here is a sample; alter the names:

  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
  `Gnomovision' (which makes passes at compilers) written by James Hacker.

  <signature of Ty Coon>, 1 April 1989
  Ty Coon, President of Vice

This 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.

2. Trajectory file reading using VMD plugins
============================================

   Files: include/molfile_plugin.h
          include/vmddlopen.h
          include/vmdplugin.h
          src/gmxlib/vmddlopen.c
          src/gmxlib/vmdio.c

                (C) Copyright 1995-2009 The Board of Trustees of the
                            University of Illinois
                             All Rights Reserved

Developed by:           Theoretical and Computational Biophysics Group
                        University of Illinois at Urbana-Champaign
                        http://www.ks.uiuc.edu/

Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the Software), to deal with
the Software without restriction, including without limitation the rights to
use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is furnished to
do so, subject to the following conditions:

Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimers.

Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimers in the documentation
and/or other materials provided with the distribution.

Neither the names of Theoretical and Computational Biophysics Group,
University of Illinois at Urbana-Champaign, nor the names of its contributors
may be used to endorse or promote products derived from this Software without
specific prior written permission.

THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL
THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS WITH THE SOFTWARE.

3. Internal FFT (ffpack)
========================

   Files: src/mdlib/fftpack.c

Copyright (c) 2005-2011, NumPy Developers.
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 the NumPy Developers nor the names of any
       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.

fftpack.c : A set of FFT routines in C.
Algorithmically based on Fortran-77 FFTPACK by Paul N. Swarztrauber (Version 4, 1985).

4. The memtestG80 library
=========================

The memtestG80 library, written by Imran Haque, is Copyright 2009 Stanford University,
covered by the LGPL license. It may be used under the following terms:

IN NO EVENT SHALL STANFORD UNIVERSITY BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, 
SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF
THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF STANFORD UNIVERSITY HAS BEEN 
ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

STANFORD UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED 
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. 
THE SOFTWARE AND ACCOMPANYING DOCUMENTATION PROVIDED HEREUNDER IS PROVIDED "AS IS". 
Folding@home HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
OR MODIFICATIONS.

Restrictions:

You may use this software on a computer system only if you own the system or have the 
written permission of the owner.

You may not alter the software or associated data files. 

Certain builds of this software incorporate by linkage code from the libintl
and libiconv libraries, which are covered by the Library GNU Public License,
available at http://www.gnu.org/licenses/lgpl-3.0.txt.

5. thread_mpi
=============

Copyright (c) 2009-2012, Sander Pronk & Erik Lindahl.
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) Neither the name of the <organization> 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 US ''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 <copyright holder> 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.

If you want to redistribute modifications, please consider that
scientific software is very special. Version control is crucial -
bugs must be traceable. We will be happy to consider code for
inclusion in the official distribution, but derived work should not
be called official thread_mpi.

6. Blas
=======

These files are semi-automatic translations by f2c from the original netlib BLAS library.
The source has been modified to (mostly) use modern C formatting, and to get rid of
compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and
not the reference BLAS implementation.

The reference BLAS implementation is available from http://www.netlib.org/blas

BLAS does not come with a formal named "license", but a general statement that

"The reference BLAS is a freely-available software package. It is available from netlib
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."

While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
our modified BLAS files as the original netlib versions, so do what you want with them.
However, be warned that we have only tested that they to the right thing in the cases used
in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
better idea to use the full reference implementation.

Erik Lindahl, 2008-10-07.

7. Lapack
=========

These files are semi-automatic translations by f2c from the original netlib LAPACK library.
The source has been modified to (mostly) use modern C formatting, and to get rid of
compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and
not the reference LAPACK implementation.

The reference LAPACK implementation is available from http://www.netlib.org/lapack

LAPACK does not come with a formal named "license", but a general statement saying:

"The reference LAPACK is a freely-available software package. It is available from netlib
via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
packages (and has been). We only ask that proper credit be given to the authors."

While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
our modified LAPACK files as the original netlib versions, so do what you want with them.

However, be warned that we have only tested that they to the right thing in the cases used
in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
better idea to use the full reference implementation.

Erik Lindahl, 2008-10-07.

8. OpenMM (binary distributions only)
=====================================

There are several licenses which cover different parts of OpenMM as described
in the file openmm/licenses/Licenses.txt accompanying the binary distribution.