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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 | 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/ .
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS 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.
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. 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. The memtestG80 library
5. thread_mpi
6. Blas
7. Lapack
8. Subset of Boost C++ library
9. Google Test and Google Mock
10. Sun XDR implementation (External Data Representation)
11. Sun FDLIBM (Freely Distributable Maths Library)
12. Random123
13. md5
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.
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) 2001-2014, The GROMACS development team.
The Debian packaging, consisting of files in the debian/ directory, is
copyright (C) 2005-2014 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. 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 General Public License,
available at http://www.gnu.org/licenses/lgpl-3.0.txt or on this system at
'/usr/share/common-licenses/LGPL-3'.
5. 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.
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.
12. Random123
============================================
Copyright 2010-2012, D. E. Shaw Research.
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 D. E. Shaw Research 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.
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
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