Fixes to filename shell completions

[gromacs/AngularHB.git] / COPYING

GROMACS is free software, distributed under the GNU Lesser General
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This file contains the licenses for the following bodies of code:
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==========

As our use of the LGPL conveys upon a licensee the option to
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============================================

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That's all there is to it!

============================================

                    GNU GENERAL PUBLIC LICENSE
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distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
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Thus, it is not the intent of this section to claim rights or contest
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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
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  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
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  4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License.  Any attempt
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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
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  5. You are not required to accept this License, since you have not
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all its terms and conditions for copying, distributing or modifying
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  6. Each time you redistribute the Program (or any work based on the
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  7. If, as a consequence of a court judgment or allegation of patent
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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
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This section is intended to make thoroughly clear what is believed to
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  8. If the distribution and/or use of the Program is restricted in
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may add an explicit geographical distribution limitation excluding
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  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
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Each version is given a distinguishing version number.  If the Program
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either of that version or of any later version published by the Free
Software Foundation.  If the Program does not specify a version number of
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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
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
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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: src/external/vmd_molfile/
          src/gromacs/fileio/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/external/fftpack/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
=========================

   Files: src/gromacs/gmxlib/gpu_utils/memtestG80_core.*

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
=============

   Files: src/gromacs/legacyheaders/thread_mpi/
          src/gromacs/gmxlib/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 LGPL, 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 LGPL, 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. Subset of Boost C++ library
==============================

   Files: src/external/boost/boost/*

Boost Software License - Version 1.0 - August 17th, 2003

Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (the "Software") to use, reproduce, display, distribute,
execute, and transmit the Software, and to prepare derivative works of the
Software, and to permit third-parties to whom the Software is furnished to
do so, all subject to the following:

The copyright notices in the Software and this entire statement, including
the above license grant, this restriction and the following disclaimer,
must be included in all copies of the Software, in whole or in part, and
all derivative works of the Software, unless such copies or derivative
works are solely in the form of machine-executable object code generated by
a source language processor.

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, TITLE AND NON-INFRINGEMENT. IN NO EVENT
SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.

9. Google Test and Google Mock
===============================

   Files: src/external/gmock-1.7.0/*

Copyright 2008, Google Inc.
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 Google Inc. 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.


10. Sun Extensible Data Representation routines (XDR)
=====================================================

    Files: src/gromacs/fileio/gmx_system_xdr.c

Sun RPC is a product of Sun Microsystems, Inc. and is provided for
unrestricted use provided that this legend is included on all tape
media and as a part of the software program in whole or part.  Users
may copy or modify Sun RPC without charge, but are not authorized
to license or distribute it to anyone else except as part of a product or
program developed by the user.

SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.

Sun RPC is provided with no support and without any obligation on the
part of Sun Microsystems, Inc. to assist in its use, correction,
modification or enhancement.

SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
OR ANY PART THEREOF.

In no event will Sun Microsystems, Inc. be liable for any lost revenue
or profits or other special, indirect and consequential damages, even if
Sun has been advised of the possibility of such damages.

Sun Microsystems, Inc.
2550 Garcia Avenue
Mountain View, California  94043


11. Sun FDLIBM (Freely Distributable Maths Library)
===================================================

    Files: src/gromacs/math/utilities.c

Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved.

Developed at SunSoft, a Sun Microsystems, Inc. business.
Permission to use, copy, modify, and distribute this
software is freely granted, provided that this notice
is preserved.