libgromacs3 2018.1-1 / usr / share / doc / libgromacs3 / copyright

Copyright (c) 2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,
by the GROMACS development team, led by Mark Abraham, David van der Spoel, Berk
Hess, and Erik Lindahl, and including many others, as listed in the AUTHORS
file in the top-level source directory and at http://www.gromacs.org.

If you want to redistribute modifications to GROMACS, 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 must not be called official GROMACS. Details are found
in the README & COPYING files - if they are missing, get the
official version at http://www.gromacs.org.

To help us fund GROMACS development, we humbly ask that you cite
the research papers on the package. Check out http://www.gromacs.org.

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

This Debian-packaged version of GROMACS was assembled by Nicholas Breen
<nbreen@debian.org> and others from the original sources at
http://www.gromacs.org/ .

A detailed list of Gromacs contributors is available at
http://www.gromacs.org/About_Gromacs/People

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


GROMACS is free software, distributed under the GNU Lesser General
Public License (LGPL) Version 2.1 or (at your option) any later
version. See section 1 for details. GROMACS includes optional code
covered by several different licences as described below.  The
GROMACS package in its entirety may be copied, modified or
distributed according to the conditions described in section 1.
However, in the interests of clarity and completeness, some
individual parts of GROMACS that can be used under their respective
licenses are also noted here.

This file contains the licenses for the following bodies of code:
1. GROMACS
2. Trajectory file reading using VMD plugins
3. Internal FFT (fftpack)
4. thread_mpi
5. Blas
6. Lapack
7. Parts of Boost C++ library
8. Google Test and Google Mock
9. Sun XDR implementation (External Data Representation)
10. Sun FDLIBM (Freely Distributable Maths Library)
11. ThreeFry Random Engine
12. Gamma distribution from libc++
13. md5
14. lmfit

Our chosen method for packaging distributions (CPack) only permits a
package to have a single license file, so we are unfortunately forced
to combine all of this information into a single license file. Sorry
about that.

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

1. GROMACS
==========

As our use of the LGPL conveys upon a licensee the option to
redistribute the library under the terms of the plain GPL, we must
include a copy of that GPL for their reference. The applicable GPL
license comes after the applicable LGPL license in this file.

On Debian systems, the full text of the LGPL v2.1 can be found in
'/usr/share/common-licenses/LGPL-2.1', and the full text of the GPL
v2 can be found in '/usr/share/common-licenses/GPL-2'.

Copyright:

    Copyright (c) 1991-2001, University of Groningen, The Netherlands.
    Copyright (c) 2001-2018, The GROMACS development team.

The Debian packaging, consisting of files in the debian/ directory, is
copyright (C) 2005-2018 Nicholas Breen <nbreen@debian.org> and the Debichem
Team, and is licensed under the GPL v2 or (at your discretion) any later
version, as referenced above.  As an exclusion, copyright for files in the
debian/man/ subdirectory are held by the GROMACS development team under the
same licensing conditions as GROMACS proper.

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. thread_mpi
=============

   Files: src/external/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.

5. 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 do 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.

6. 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 do 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. Parts of Boost C++ library
=============================

   Files: src/gromacs/utility/current_function.h
          src/gromacs/utility/path.cpp

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.

8. 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.


9. 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


10. 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.


11. ThreeFry Random Engine
============================================

Based on proposed Boost implementations by
a) John Salmon, Copyright 2010-2014 by D. E. Shaw Research
b) Thijs van den Berg, Copyright (c) 2014 M.A. (Thijs) van den Berg

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.

12. Gamma distribution from libc++
============================================

Copyright (c) The LLVM compiler infrastructure

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in 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:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

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
AUTHORS 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 IN
THE SOFTWARE.


13. md5
============================================

Copyright (C) 1999, 2002 Aladdin Enterprises.  All rights reserved.

This software is provided 'as-is', without any express or implied
warranty.  In no event will the authors be held liable for any damages
arising from the use of this software.

Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:

1. The origin of this software must not be misrepresented; you must not
  claim that you wrote the original software. If you use this software
  in a product, an acknowledgment in the product documentation would be
  appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be
  misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.

L. Peter Deutsch
ghost@aladdin.com

14. lmfit
============================================
The package lmfit is distributed under the FreeBSD License:

--
  Copyright (c) 1980-1999 University of Chicago,
                          as operator of Argonne National Laboratory
  Copyright (c) 2004-2013 Joachim Wuttke, Forschungszentrum Juelich GmbH

  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.

  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 holder 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.
--