From 218346542ca6fe0d31da34ae0228625a7e2022d4 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Thu, 6 Mar 2025 15:58:07 -0700 Subject: [PATCH 1/5] Remove LGPL, Add Apache2.0 Also mention the license explicitly in the README. --- LICENSE.md | 157 ---------------------------------------- LICENSE.txt | 202 ++++++++++++++++++++++++++++++++++++++++++++++++++++ README.md | 7 ++ 3 files changed, 209 insertions(+), 157 deletions(-) delete mode 100644 LICENSE.md create mode 100644 LICENSE.txt diff --git a/LICENSE.md b/LICENSE.md deleted file mode 100644 index 0927556b5..000000000 --- a/LICENSE.md +++ /dev/null @@ -1,157 +0,0 @@ -### GNU LESSER GENERAL PUBLIC LICENSE - -Version 3, 29 June 2007 - -Copyright (C) 2007 Free Software Foundation, Inc. - - -Everyone is permitted to copy and distribute verbatim copies of this -license document, but changing it is not allowed. - -This version of the GNU Lesser General Public License incorporates the -terms and conditions of version 3 of the GNU General Public License, -supplemented by the additional permissions listed below. - -#### 0. Additional Definitions. - -As used herein, "this License" refers to version 3 of the GNU Lesser -General Public License, and the "GNU GPL" refers to version 3 of the -GNU General Public License. - -"The Library" refers to a covered work governed by this License, other -than an Application or a Combined Work as defined below. - -An "Application" is any work that makes use of an interface provided -by the Library, but which is not otherwise based on the Library. -Defining a subclass of a class defined by the Library is deemed a mode -of using an interface provided by the Library. - -A "Combined Work" is a work produced by combining or linking an -Application with the Library. The particular version of the Library -with which the Combined Work was made is also called the "Linked -Version". - -The "Minimal Corresponding Source" for a Combined Work means the -Corresponding Source for the Combined Work, excluding any source code -for portions of the Combined Work that, considered in isolation, are -based on the Application, and not on the Linked Version. - -The "Corresponding Application Code" for a Combined Work means the -object code and/or source code for the Application, including any data -and utility programs needed for reproducing the Combined Work from the -Application, but excluding the System Libraries of the Combined Work. - -#### 1. Exception to Section 3 of the GNU GPL. - -You may convey a covered work under sections 3 and 4 of this License -without being bound by section 3 of the GNU GPL. - -#### 2. Conveying Modified Versions. - -If you modify a copy of the Library, and, in your modifications, a -facility refers to a function or data to be supplied by an Application -that uses the facility (other than as an argument passed when the -facility is invoked), then you may convey a copy of the modified -version: - -- a) under this License, provided that you make a good faith effort - to ensure that, in the event an Application does not supply the - function or data, the facility still operates, and performs - whatever part of its purpose remains meaningful, or -- b) under the GNU GPL, with none of the additional permissions of - this License applicable to that copy. - -#### 3. Object Code Incorporating Material from Library Header Files. - -The object code form of an Application may incorporate material from a -header file that is part of the Library. You may convey such object -code under terms of your choice, provided that, if the incorporated -material is not limited to numerical parameters, data structure -layouts and accessors, or small macros, inline functions and templates -(ten or fewer lines in length), you do both of the following: - -- a) Give prominent notice with each copy of the object code that - the Library is used in it and that the Library and its use are - covered by this License. -- b) Accompany the object code with a copy of the GNU GPL and this - license document. - -#### 4. Combined Works. - -You may convey a Combined Work under terms of your choice that, taken -together, effectively do not restrict modification of the portions of -the Library contained in the Combined Work and reverse engineering for -debugging such modifications, if you also do each of the following: - -- a) Give prominent notice with each copy of the Combined Work that - the Library is used in it and that the Library and its use are - covered by this License. -- b) Accompany the Combined Work with a copy of the GNU GPL and this - license document. -- c) For a Combined Work that displays copyright notices during - execution, include the copyright notice for the Library among - these notices, as well as a reference directing the user to the - copies of the GNU GPL and this license document. -- d) Do one of the following: - - 0) Convey the Minimal Corresponding Source under the terms of - this License, and the Corresponding Application Code in a form - suitable for, and under terms that permit, the user to - recombine or relink the Application with a modified version of - the Linked Version to produce a modified Combined Work, in the - manner specified by section 6 of the GNU GPL for conveying - Corresponding Source. - - 1) Use a suitable shared library mechanism for linking with - the Library. A suitable mechanism is one that (a) uses at run - time a copy of the Library already present on the user's - computer system, and (b) will operate properly with a modified - version of the Library that is interface-compatible with the - Linked Version. -- e) Provide Installation Information, but only if you would - otherwise be required to provide such information under section 6 - of the GNU GPL, and only to the extent that such information is - necessary to install and execute a modified version of the - Combined Work produced by recombining or relinking the Application - with a modified version of the Linked Version. (If you use option - 4d0, the Installation Information must accompany the Minimal - Corresponding Source and Corresponding Application Code. If you - use option 4d1, you must provide the Installation Information in - the manner specified by section 6 of the GNU GPL for conveying - Corresponding Source.) - -#### 5. Combined Libraries. - -You may place library facilities that are a work based on the Library -side by side in a single library together with other library -facilities that are not Applications and are not covered by this -License, and convey such a combined library under terms of your -choice, if you do both of the following: - -- a) Accompany the combined library with a copy of the same work - based on the Library, uncombined with any other library - facilities, conveyed under the terms of this License. -- b) Give prominent notice with the combined library that part of it - is a work based on the Library, and explaining where to find the - accompanying uncombined form of the same work. - -#### 6. Revised Versions of the GNU Lesser General Public License. - -The Free Software Foundation may publish revised and/or new versions -of the GNU Lesser 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 address new problems or concerns. - -Each version is given a distinguishing version number. If the Library -as you received it specifies that a certain numbered version of the -GNU Lesser General Public License "or any later version" applies to -it, you have the option of following the terms and conditions either -of that published version or of any later version published by the -Free Software Foundation. If the Library as you received it does not -specify a version number of the GNU Lesser General Public License, you -may choose any version of the GNU Lesser General Public License ever -published by the Free Software Foundation. - -If the Library as you received it specifies that a proxy can decide -whether future versions of the GNU Lesser General Public License shall -apply, that proxy's public statement of acceptance of any version is -permanent authorization for you to choose that version for the -Library. diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 000000000..d64569567 --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,202 @@ + + Apache License + Version 2.0, January 2004 + http://www.apache.org/licenses/ + + TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION + + 1. Definitions. + + "License" shall mean the terms and conditions for use, reproduction, + and distribution as defined by Sections 1 through 9 of this document. + + "Licensor" shall mean the copyright owner or entity authorized by + the copyright owner that is granting the License. + + "Legal Entity" shall mean the union of the acting entity and all + other entities that control, are controlled by, or are under common + control with that entity. For the purposes of this definition, + "control" means (i) the power, direct or indirect, to cause the + direction or management of such entity, whether by contract or + otherwise, or (ii) ownership of fifty percent (50%) or more of the + outstanding shares, or (iii) beneficial ownership of such entity. + + "You" (or "Your") shall mean an individual or Legal Entity + exercising permissions granted by this License. + + "Source" form shall mean the preferred form for making modifications, + including but not limited to software source code, documentation + source, and configuration files. + + "Object" form shall mean any form resulting from mechanical + transformation or translation of a Source form, including but + not limited to compiled object code, generated documentation, + and conversions to other media types. + + "Work" shall mean the work of authorship, whether in Source or + Object form, made available under the License, as indicated by a + copyright notice that is included in or attached to the work + (an example is provided in the Appendix below). + + "Derivative Works" shall mean any work, whether in Source or Object + form, that is based on (or derived from) the Work and for which the + editorial revisions, annotations, elaborations, or other modifications + represent, as a whole, an original work of authorship. For the purposes + of this License, Derivative Works shall not include works that remain + separable from, or merely link (or bind by name) to the interfaces of, + the Work and Derivative Works thereof. + + "Contribution" shall mean any work of authorship, including + the original version of the Work and any modifications or additions + to that Work or Derivative Works thereof, that is intentionally + submitted to Licensor for inclusion in the Work by the copyright owner + or by an individual or Legal Entity authorized to submit on behalf of + the copyright owner. For the purposes of this definition, "submitted" + means any form of electronic, verbal, or written communication sent + to the Licensor or its representatives, including but not limited to + communication on electronic mailing lists, source code control systems, + and issue tracking systems that are managed by, or on behalf of, the + Licensor for the purpose of discussing and improving the Work, but + excluding communication that is conspicuously marked or otherwise + designated in writing by the copyright owner as "Not a Contribution." + + "Contributor" shall mean Licensor and any individual or Legal Entity + on behalf of whom a Contribution has been received by Licensor and + subsequently incorporated within the Work. + + 2. Grant of Copyright License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + copyright license to reproduce, prepare Derivative Works of, + publicly display, publicly perform, sublicense, and distribute the + Work and such Derivative Works in Source or Object form. + + 3. Grant of Patent License. Subject to the terms and conditions of + this License, each Contributor hereby grants to You a perpetual, + worldwide, non-exclusive, no-charge, royalty-free, irrevocable + (except as stated in this section) patent license to make, have made, + use, offer to sell, sell, import, and otherwise transfer the Work, + where such license applies only to those patent claims licensable + by such Contributor that are necessarily infringed by their + Contribution(s) alone or by combination of their Contribution(s) + with the Work to which such Contribution(s) was submitted. If You + institute patent litigation against any entity (including a + cross-claim or counterclaim in a lawsuit) alleging that the Work + or a Contribution incorporated within the Work constitutes direct + or contributory patent infringement, then any patent licenses + granted to You under this License for that Work shall terminate + as of the date such litigation is filed. + + 4. Redistribution. You may reproduce and distribute copies of the + Work or Derivative Works thereof in any medium, with or without + modifications, and in Source or Object form, provided that You + meet the following conditions: + + (a) You must give any other recipients of the Work or + Derivative Works a copy of this License; and + + (b) You must cause any modified files to carry prominent notices + stating that You changed the files; and + + (c) You must retain, in the Source form of any Derivative Works + that You distribute, all copyright, patent, trademark, and + attribution notices from the Source form of the Work, + excluding those notices that do not pertain to any part of + the Derivative Works; and + + (d) If the Work includes a "NOTICE" text file as part of its + distribution, then any Derivative Works that You distribute must + include a readable copy of the attribution notices contained + within such NOTICE file, excluding those notices that do not + pertain to any part of the Derivative Works, in at least one + of the following places: within a NOTICE text file distributed + as part of the Derivative Works; within the Source form or + documentation, if provided along with the Derivative Works; or, + within a display generated by the Derivative Works, if and + wherever such third-party notices normally appear. The contents + of the NOTICE file are for informational purposes only and + do not modify the License. You may add Your own attribution + notices within Derivative Works that You distribute, alongside + or as an addendum to the NOTICE text from the Work, provided + that such additional attribution notices cannot be construed + as modifying the License. + + You may add Your own copyright statement to Your modifications and + may provide additional or different license terms and conditions + for use, reproduction, or distribution of Your modifications, or + for any such Derivative Works as a whole, provided Your use, + reproduction, and distribution of the Work otherwise complies with + the conditions stated in this License. + + 5. Submission of Contributions. Unless You explicitly state otherwise, + any Contribution intentionally submitted for inclusion in the Work + by You to the Licensor shall be under the terms and conditions of + this License, without any additional terms or conditions. + Notwithstanding the above, nothing herein shall supersede or modify + the terms of any separate license agreement you may have executed + with Licensor regarding such Contributions. + + 6. Trademarks. This License does not grant permission to use the trade + names, trademarks, service marks, or product names of the Licensor, + except as required for reasonable and customary use in describing the + origin of the Work and reproducing the content of the NOTICE file. + + 7. Disclaimer of Warranty. Unless required by applicable law or + agreed to in writing, Licensor provides the Work (and each + Contributor provides its Contributions) on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or + implied, including, without limitation, any warranties or conditions + of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A + PARTICULAR PURPOSE. You are solely responsible for determining the + appropriateness of using or redistributing the Work and assume any + risks associated with Your exercise of permissions under this License. + + 8. Limitation of Liability. In no event and under no legal theory, + whether in tort (including negligence), contract, or otherwise, + unless required by applicable law (such as deliberate and grossly + negligent acts) or agreed to in writing, shall any Contributor be + liable to You for damages, including any direct, indirect, special, + incidental, or consequential damages of any character arising as a + result of this License or out of the use or inability to use the + Work (including but not limited to damages for loss of goodwill, + work stoppage, computer failure or malfunction, or any and all + other commercial damages or losses), even if such Contributor + has been advised of the possibility of such damages. + + 9. Accepting Warranty or Additional Liability. While redistributing + the Work or Derivative Works thereof, You may choose to offer, + and charge a fee for, acceptance of support, warranty, indemnity, + or other liability obligations and/or rights consistent with this + License. However, in accepting such obligations, You may act only + on Your own behalf and on Your sole responsibility, not on behalf + of any other Contributor, and only if You agree to indemnify, + defend, and hold each Contributor harmless for any liability + incurred by, or claims asserted against, such Contributor by reason + of your accepting any such warranty or additional liability. + + END OF TERMS AND CONDITIONS + + APPENDIX: How to apply the Apache License to your work. + + To apply the Apache License to your work, attach the following + boilerplate notice, with the fields enclosed by brackets "[]" + replaced with your own identifying information. (Don't include + the brackets!) The text should be enclosed in the appropriate + comment syntax for the file format. We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright [yyyy] [name of copyright owner] + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md index 78af0d981..2b13a4147 100644 --- a/README.md +++ b/README.md @@ -279,3 +279,10 @@ diffusivity varies with different Richardson numbers. The fifth driver reads in tidal energy flux and buoyancy frequency data from an input data set and computes diffusivities in a column based on these physical values. + +LICENSE +------- + +[![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0) + +CVMix is [licensed](LICENSE.txt) under Apache 2.0. From 9b7d7514a214990db803bf01204389d97bda3ca1 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Mon, 10 Mar 2025 13:09:46 -0600 Subject: [PATCH 2/5] Update edit date and KPP test description --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2b13a4147..dafd0fd82 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -Last update: July 23, 2014 +Last update: March 10, 2025 -------------------------- @@ -257,7 +257,7 @@ in the salt fingering regime and one in the diffusive convective instability regime. In each case, the stratification parameter is set and then the temperature and salinity diffusivity coefficients are computed. -The third driver runs a set of 6 tests for KPP boundary layer mixing: +The third driver runs a set of seven tests for KPP boundary layer mixing: 1. Compute the boundary layer depth for a column with a given HMIX (HBLT should = |HMIX|+2) 2. Compute shape function coefficients with G(0) = G(1) = G'(1) = 0 and G'(0) @@ -270,6 +270,7 @@ The third driver runs a set of 6 tests for KPP boundary layer mixing: 6. Compute velocity scales (a) when surface buoyancy flux is 0 and friction is positive; and (b) when surface buoyancy flux is negative and friction velocity is 0. + 7. Compute bulk Richardson number from buoyancy and zonal wind data, using `StokesMOST` The fourth driver sets up a single column using the shear mixing formula found in the Large, et al. KPP paper. For this test, each level is a different local From 0cf87216e44f94188da19bcc19ebef62a4dfa063 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Tue, 11 Mar 2025 13:19:46 -0600 Subject: [PATCH 3/5] Add LLVM exception to license Also filled in the copyright template in the license file. --- LICENSE.txt | 18 +++++++++++++++++- README.md | 2 +- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index d64569567..7c0ff2817 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -187,7 +187,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright [yyyy] [name of copyright owner] + Copyright 2025 CVMix developers Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -200,3 +200,19 @@ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. + +---- LLVM Exceptions to the Apache 2.0 License ---- + +As an exception, if, as a result of your compiling your source code, portions +of this Software are embedded into an Object form of such source code, you +may redistribute such embedded portions in such Object form without complying +with the conditions of Sections 4(a), 4(b) and 4(d) of the License. + +In addition, if you combine or link compiled forms of this Software with +software that is licensed under the GPLv2 ("Combined Software") and if a +court of competent jurisdiction determines that the patent provision (Section +3), the indemnity provision (Section 9) or other Section of the License +conflicts with the conditions of the GPLv2, you may retroactively and +prospectively choose to deem waived or otherwise exclude such Section(s) of +the License, but only in their entirety and only with respect to the Combined +Software. \ No newline at end of file diff --git a/README.md b/README.md index dafd0fd82..fa6e5fcbc 100644 --- a/README.md +++ b/README.md @@ -286,4 +286,4 @@ LICENSE [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0) -CVMix is [licensed](LICENSE.txt) under Apache 2.0. +CVMix is [licensed](LICENSE.txt) under Apache 2.0 with the [LLVM exception](https://lwn.net/Articles/701155/) to explicitly allow it to be included in projects licensed under GPLv2. From c6637a0d30910b7d1db7df733490d492770b2920 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Wed, 2 Apr 2025 14:04:40 -0600 Subject: [PATCH 4/5] Update copyright in the license Also update the README to give GFDL and LANL credit for creating CVMix --- LICENSE.txt | 2 +- README.md | 13 ++++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index 7c0ff2817..448b29ca3 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -187,7 +187,7 @@ same "printed page" as the copyright notice for easier identification within third-party archives. - Copyright 2025 CVMix developers + Copyright 2012-2025 University Corporation for Atmospheric Research (UCAR) Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/README.md b/README.md index fa6e5fcbc..8feab4ac9 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,19 @@ -Last update: March 10, 2025 +Last update: April 2, 2025 -------------------------- - CVMix is a transparent, robust, flexible, and well-documented open source -Fortran library for parameterizing ocean vertical mixing processes. It contains -the following first-order closures: +Fortran library for parameterizing ocean vertical mixing processes. +It began as a collaboration among NOAA's Geophysical Fluid Dynamics Laboratory +(GFDL), DOE's Los Alamos National Lab (LANL), and NSF's National Center +for Atmospheric Research (NCAR). + +CVMix contains the following first-order closures: 1. Background [time-independent] mixing, including the Bryan and Lewis (1979) parameterization 2. Convective mixing (both density-based and the Brunt-Vaisala scheme) 3. Double diffusion mixing, as described in Large, et al. (1994) and modified according to Danabasoglu, et al. (2006) -4. The KPP boundary layer mixing scheme from Large, et al. 1994 +4. The KPP boundary layer mixing scheme from Large, et al. (1994) 5. Shear [Richardson number-based] mixing, including both Pacanowski and Philander (1981) and the shear mixing used in Large, et al. (1994) 6. Tidal mixing, which currently only offers the method described in Simmons, From c38ddb7ebdd2d58c517b63a99bbdc8e348732db2 Mon Sep 17 00:00:00 2001 From: Michael Levy Date: Sat, 17 May 2025 09:05:03 -0600 Subject: [PATCH 5/5] More explicit explanation of LLVM exception Mention GOTM by name, and also give permission for including code as part of the scientific publication process --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 8feab4ac9..bebc12573 100644 --- a/README.md +++ b/README.md @@ -289,4 +289,5 @@ LICENSE [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://www.apache.org/licenses/LICENSE-2.0) -CVMix is [licensed](LICENSE.txt) under Apache 2.0 with the [LLVM exception](https://lwn.net/Articles/701155/) to explicitly allow it to be included in projects licensed under GPLv2. +CVMix is [licensed](LICENSE.txt) under Apache 2.0 with the [LLVM exception](https://lwn.net/Articles/701155/) to explicitly allow it to be included in and distributed with projects licensed under GPLv2 such as the General Ocean Turbulence Model ([GOTM](https://gotm.net/portfolio/)). +This exception also allows such projects to publish the CVMix source code as supplementary material to scientific journal articles.