entos academic user agreement

ENTOS SOFTWARE TERMS OF USE (ACADEMIC USERS)

 

This user agreement (“Agreement”) is between California Institute of Technology, a not-for-profit California corporation, located at 1200 E. California Blvd., Pasadena, California 91125 (“Caltech”) and you, an individual (“User” or “You”). Caltech will allow You to use entos Version 0.7.1: An Ab Initio Molecular Dynamics Software Simulation Package (“Software”), which is protected under copyright laws, patent laws and applicable international intellectual property treaties. All rights not specifically granted in this Agreement are reserved to Caltech and to the University of Bristol, a corporation incorporated in England and Wales by Royal Charter with registration number RC000648, whose principal offices are at Beacon House, Queens Road, Bristol, BS8 1QU, UK, (“Bristol”; together with Caltech the “Copyright Owners”). The User may use the Software on the following terms: 

 

1. Caltech hereby grants You the right to use the Software through this website for non-commercial, academic research purposes only.The Software may only be accessed by You. You agree not to grant access to the Software to any other individual or entity without the prior written permission of Caltech. You hereby certify that You will use the Software for non-commercial, academic research purposes only and are affiliated with a non-profit research institution.

 

2. The Software is experimental in nature and is being made available for use “as is”. This Agreement does not include any technical or other type of support.

 

3. None of the output from the Software provided may be used in commercial products or services directly or indirectly unless a license agreement is executed between Caltech and User granting the right to use output from the Software in commercial products or services.

 

4. You agree not to download or reproduce the Software or create derivative works based on the Software.

 

5. THE SOFTWARE AND/OR RELATED MATERIALS ARE PROVIDED BY THE COPYRIGHT OWNERS AND THE UNITED STATES GOVERNMENT “AS-IS”

 

USER BEARS ALL RISK RELATING TO QUALITY AND PERFORMANCE OF THE SOFTWARE AND/OR RELATED MATERIALS, AND AGREES TO INDEMNIFY THE COPYRIGHT OWNERS FOR ALL THIRD-PARTY CLAIMS RESULTING FROM THE ACTIONS OF USER IN THE USE OF THE SOFTWARE.

 

6. Third-party open source code may have been incorporated into the Software. Copyright and terms of use for this third-party source code are described in Exhibit A, the terms and conditions of which are hereby incorporated by reference into this Agreement, and Licensee agrees to such terms and conditions.

 

7. All right, title, and interest in and to all data, information, and inventions that result from use of the Software by You shall vest in and belong to You.  For any publications that reference the Software, You agree to include the following citation:

"entos: A quantum molecular simulation package." F. R. Manby, T. F. Miller III, P. J. Bygrave, F. Ding, T. Dresselhaus, F. A. Batista-Romero, A. Buccheri, C. Bungey, S. J. R. Lee, R. Meli, K. Miyamoto, C. Steinmann, T. Tsuchiya, M. Welborn, T. Wiles, and Z. Williams, ChemRxiv.7762646 (2019). DOI: 10.26434/chemrxiv.7762646.v2

 

8. This Agreement shall be governed by the laws of the State of California, and any action brought hereunder shall be within the State of California.

 

9. By clicking Agree and Continue above, You agree to abide by all the terms and conditions of this Agreement.

EXHIBIT A

THIRD PARTY SOURCE CODE

libecpint: MIT License

 

Copyright (c) 2017 Robert A. Shaw

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.

Catch2: Boost Software License – Version 1.0 – August 17, 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.

 

libxc: Mozilla Public License Version 2.0
 

A copy of this license can be found on the world-wide web by navigating a web browser to the URL 
https://www.mozilla.org/en-US/MPL/2.0/
 

gsl: Copyright (c) 2015 Microsoft Corporation. All rights reserved. 

 

This code is licensed under the MIT License (MIT). 

 

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. 

 

Armadillo: Apache License, Version 2.0
 

A copy of this license can be found on the world-wide web by navigating a web browser to the URL https://www.apache.org/licenses/LICENSE-2.0
 

Intel TBB: Apache License, Version 2.0 

A copy of this license can be found on the world-wide web by navigating a web browser to the URL https://www.apache.org/licenses/LICENSE-2.0

 

Libcint Copyright © 2012, Qiming Sun 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.

libirc: MIT License

 

Copyright (c) 2017-2019 Rocco Meli, Peter Bygrave

 

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.

OpenMM

Currently only MIT-licensed components are used in Entos, but the full openmm license file is as follows:

OpenMM was developed by Simbios, the NIH National Center for Physics-Based Simulation of Biological Structures at Stanford, funded under the NIH Roadmap for Medical Research, grant U54 GM072970. See https://simtk.org.

 

Portions copyright � 2008-2019 Stanford University and the Authors.

 

There are several licenses which cover different parts of OpenMM as described below.

 

1. API, Reference Platform, CPU Platform

 

The OpenMM API, the Reference Platform, and the CPU platform may be used under the terms of the MIT License: 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, 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 IN THE SOFTWARE.

 

2. CUDA and OpenCL Platforms

 

The CUDA Platform and OpenCL Platform may be used under the terms of the GNU Lesser General Public License. A copy of this license may be found in the accompanying file "LGPL.txt". It in turn incorporates the terms of the GNU General Public License, which may be found in the accompanying file "GPL.txt".

 

3. SIMD-oriented Fast Mersenne Twister (SFMT)

 

OpenMM uses the SFMT library which is copyright 2006-2007 Mutsuo Saito, Makoto Matsumoto and Hiroshima University. It may be used under the following terms:

 

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 Hiroshima University 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.

 

4. Hilbert Curve

 

OpenMM uses an implementation of Hilbert curves which is copyright 1998-2000 Rice University. It may be used under the following terms:

 

This software is copyrighted by Rice University. It may be freely copied, modified, and redistributed, provided that the copyright notice is preserved on all copies.

 

There is no warranty or other guarantee of fitness for this software, it is provided solely "as is". Bug reports or fixes may be sent to the author, who may or may not act on them as he desires.

 

You may include this software in a program or other software product, but must display the notice:

 

Hilbert Curve implementation copyright 1998, Rice University

 

in any place where the end-user would see your own copyright.

 

If you modify this software, you should include a notice giving the name of the person performing the modification, the date of modification, and the reason for such modification.

 

5. AsmJit

 

OpenMM uses the AsmJit library which is copyright 2008-2014 by Petr Kobalicek. It may be used under the following terms:

 

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.

 

6. PdbxReader

 

OpenMM uses the PDBx/mmCIF parser written by John Westbrook. It is distributed under the Creative Commons Attribution 3.0 Unported license. For details, see https://creativecommons.org/licenses/by/3.0. This library was modified to move it inside the simtk.openmm.app.internal module.

 

7. irrXML

 

OpenMM uses the irrXML library which is copyright 2002-2005 Nikolaus Gebhardt. It may be used under the following terms:

 

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.

 

8. L-BFGS

 

OpenMM uses the L-BFGS library by Jorge Nocedal and Naoaki Okazaki. It may be used under the following license:

 

Copyright (c) 1990, Jorge Nocedal

Copyright (c) 2007-2010 Naoaki Okazaki

All rights reserved.

 

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.

Hungarian Algorithm

https://github.com/mcximing/hungarian-algorithm-cpp

 

Copyright (c) 2016, mcximing 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.

Intel® Math Kernel Library

 

Intel Simplified Software License (Version February 2020)

Use and Redistribution. You may use and redistribute the software (the “Software”), without modification, provided the following conditions are met:

  • Redistributions must reproduce the above copyright notice and the following terms of use in the Software and in the documentation and/or other materials provided with the distribution.

  • Neither the name of Intel nor the names of its suppliers may be used to endorse or promote products derived from this Software without specific prior written permission.

  • No reverse engineering, decompilation, or disassembly of this Software is permitted.

 

Limited patent license. Intel grants you a world-wide, royalty-free, non-exclusive license under patents it now or hereafter owns or controls to make, have made, use, import, offer to sell and sell (“Utilize”) this Software, but solely to the extent that any such patent is necessary to Utilize the Software alone. The patent license shall not apply to any combinations which include this software. No hardware per se is licensed hereunder.

Third party programs. The Software may contain Third Party Programs. “Third Party Programs” are third party software, open source software or other Intel software listed in the “third-party-programs.txt” or other similarly named text file that is included with the Software. Third Party Programs, even if included with the distribution of the Software, may be governed by separate license terms, including without limitation, third party license terms, open source software notices and terms, and/or other Intel software license terms. These separate license terms may govern your use of the Third Party Programs.

DISCLAIMER. THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, AND NON-INFRINGEMENT ARE DISCLAIMED. THIS SOFTWARE IS NOT INTENDED FOR USE IN SYSTEMS OR APPLICATIONS WHERE FAILURE OF THE SOFTWARE MAY CAUSE PERSONAL INJURY OR DEATH AND YOU AGREE THAT YOU ARE FULLY RESPONSIBLE FOR ANY CLAIMS, COSTS, DAMAGES, EXPENSES, AND ATTORNEYS’ FEES ARISING OUT OF ANY SUCH USE, EVEN IF ANY CLAIM ALLEGES THAT INTEL WAS NEGLIGENT REGARDING THE DESIGN OR MANUFACTURE OF THE MATERIALS.

LIMITATION OF LIABILITY. IN NO EVENT WILL INTEL 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. YOU AGREE TO INDEMNIFY AND HOLD INTEL HARMLESS AGAINST ANY CLAIMS AND EXPENSES RESULTING FROM YOUR USE OR UNAUTHORIZED USE OF THE SOFTWARE.

No support. Intel may make changes to the Software, at any time without notice, and is not obligated to support, update or provide training for the Software.

Termination. Intel may terminate your right to use the Software in the event of your breach of this Agreement and you fail to cure the breach within a reasonable period of time.

Feedback. Should you provide Intel with comments, modifications, corrections, enhancements or other input (“Feedback”) related to the Software Intel will be free to use, disclose, reproduce, license or otherwise distribute or exploit the Feedback in its sole discretion without any obligations or restrictions of any kind, including without limitation, intellectual property rights or licensing obligations.

Compliance with laws. You agree to comply with all relevant laws and regulations governing your use, transfer, import or export (or prohibition thereof) of the Software.

Governing law. All disputes will be governed by the laws of the United States of America and the State of Delaware without reference to conflict of law principles and subject to the exclusive jurisdiction of the state or federal courts sitting in the State of Delaware, and each party agrees that it submits to the personal jurisdiction and venue of those courts and waives any objections. The United Nations Convention on Contracts for the International Sale of Goods (1980) is specifically excluded and will not apply to the Software.

*Other names and brands may be claimed as the property of others.

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