Atlantis-Ecosystem-Model · cecilieha · May 6, 2026 · Apr 23, 2026 · Apr 24, 2026 · Apr 24, 2026
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,121 @@
+# Terms and Conditions for Access to and Use of CSIRO Environmental Modelling Suite (EMS) Software
+
+### ATLANTIS SOURCE CODE ACADEMIC LICENCE AGREEMENT 
+
+### IMPORTANT – PLEASE READ CAREFULLY
+
+**Your access to and use of the Atlantis ecosystem modelling software code on this site, and all associated libraries (“the Software”), is subject to the following terms of use.** 
+
+**This is an agreement between CSIRO and the user entity listed below “you” regarding the Atlantis software source code provided to you under this agreement ("Software").  CSIRO requests that you confirm your agreement to these terms by signing this agreement, however you are deemed to agree to the terms of this agreement by installing and / or using the Software, regardless of whether you sign them.**
+
+Signed by:			
+
+For and on behalf of: 	
+
+
+
+### BY USING THIS SOFTWARE YOU ARE ACCEPTING,  AND WILL BE BOUND BY, THESE TERMS:
+
+#### Registration
+Prior to accessing the Software, we recommend you register with CSIRO your name and email address via emailing <a href="mailto:atlantis@csiro.au?subject=Atlantis%20InQuiry">email the developers</a>. If the link doesn't autoconnect to email for you please check if you have a pop-up blocker turned on in your browser. Alternatively, right click on the text "email to developers" and select the option "copy email". 
+
+#### 1.	Definitions
+1.1.	‘CSIRO’ means the Commonwealth Scientific and Industrial Research Organisation (ABN 41 687 119 230).
+
+1.2.	‘Improvement’ means any enhancement, adaptation or modification to or a new release or version of the Software which provides for a technical improvement or error correction.  For clarity, an Improvement does not need to have improved or additional functionality or performance).
+
+1.3.	‘IP’ means any rights in any copyright work (including any work or item created in the future), patentable invention, design, circuit layout, new plant variety, trademark, know-how or trade secret.
+
+1.4.	‘Manual’ means any instructions or documentation (in electronic or hard copy form) which CSIRO may provide to you to assist with installation and / or use of the Software.
+
+1.5.	'Permitted Use' means bona fide evaluation, research and teaching purposes, but not including commercial use.
+
+
+#### 2.	Licence
+CSIRO grants you a non-exclusive, non-transferable licence (with no right to grant sublicenses) to use and make Improvements to the Software (and Manual) for the Permitted Use.  
+
+#### 3.	Restrictions on use
+You must not without CSIRO’s prior written consent:
+
+3.1.	use the Software for any purpose other than the Permitted Use;
+
+3.2.	integrate or combine the Software with other software subject to the GNU GPL licence or any other licence terms which would conflict with this agreement; or
+
+3.3.	use it to develop a commercial copycat or functionally equivalent software or derivative software based on the IP embodied in the Software, except in the course of exercising your rights under clause 6.1. 
+
+#### 4. Installation and support
+4.1	You are responsible for installing and using the Software on suitable hardware and acknowledge you will need to write additional software in order to make the Software interoperate with your hardware and/or other software, libraries and datasets.  
+
+4.2	CSIRO is not obligated to provide you with any maintenance, support or other services in relation to the Software
+
+### 5.	Improvements
+5.1.	You are permitted to make Improvements to the Software and you will own the IP in such Improvements.
+
+5.2.	You grant CSIRO a non-exclusive, worldwide, royalty-free, perpetual, irrevocable licence (including a right of sub-licence) to use, reproduce, adapt and distribute any of your Improvements that are committed into the Atlantis code repositories for the purposes of bona fide evaluation, research (including funded contract research) and teaching purposes, but not including commercial use.
+
+5.3.	If CSIRO makes Improvements to the Software, CSIRO will own the IP in all such Improvements.  CSIRO may in its discretion provide such Improvements to you, via the Atlantis code repositories, in which case those Improvements will be deemed to be part of the Software licensed to you under this agreement.
+
+### 6.	IP Rights
+6.1.	As between CSIRO and you, CSIRO retains full ownership of the IP in the Software and the Manual.
+
+6.2.	You acknowledge that the Software contains third party software, and that your use under this agreement may be subject to additional conditions disclosed in the source code of the Software provided to you. 
+
+6.3.	Redistributions of source code must retain the copyright notice: Copyright (c) 2017 Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230. All rights reserved, this list of conditions and the following disclaimer.
+
+6.4		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.
+
+6.5		Neither the name of CSIRO nor the names of its contributors may be used to endorse or promote products derived from this Software without specific prior written permission of CSIRO.
+
+### 7.	Use of CSIRO name
+7.1.	You must not use CSIRO’s name or trade marks in a manner that suggests that CSIRO endorses, or is associated with your research activities or your business, products or services without prior approval by CSIRO.
+
+### 8.	Licence fee
+8.1.	CSIRO is making the Software available to you free of charge in consideration of you fulfilling your promises under this agreement. 
+
+### 9.	Limitation of liability 
+Without limiting the disclaimer set out below:
+
+9.1.	Your exercise of rights under this agreement is at your sole risk.  The Software and Manual (if any) are supplied to you on an “as is” basis.  You acknowledge that the Software and Manual may have inherent defects or deficiencies which cause interruptions, errors or downtime.  You are solely responsible for ensuring that the Software is suitable for your purposes.  You assume all risk for any liabilities, expenses, losses, damages and costs directly or indirectly arising from your use of or reliance on the Software. 
+
+9.2.	To the full extent permitted by applicable law:
+
+9.2.1	CSIRO expressly disclaims and excludes all warranties of any kind, whether express or implied, including, but not limited to implied warranties of merchantability, fitness for a particular purpose and non-infringement of intellectual property rights, except insofar as the exclusion of any implied warranties would contravene the law or cause any part of this agreement to be void (“non-excludable implied warranties”); and
+
+9.2.2	CSIRO does not warrant that use of the Software will not infringe any third party rights.
+
+9.2.3	CSIRO makes no warranty to representation that the Software is free of bugs or inherent defects or deficiencies which cause interruptions errors or downtime nor is CSIRO under any obligation to release bug fixes or any improvements or further releases of the Software, other than as may be required under clause 5.  If CSIRO does make improvements then it may in its discretion supply them on this Site in which case those improvements are subject to these terms and conditions. 
+
+9.2.4	In no event will CSIRO be liable to you on any legal theory (including, without limitation, negligence) for any loss or damage whatsoever, including (without limitation) loss of production or operation time; loss, damage or corruption of data or records; or loss of anticipated savings, opportunity, revenue, profit or goodwill, or other economic loss; or any special, incidental, consequential, punitive or exemplary damages arising out of or in connection with this agreement or the use of the Software, even if you have advised of the possibility of such damages.
+
+9.3.	CSIRO’s maximum liability to you for breach of any term of this licence or of any non-excludable implied warranties is limited, at CSIRO’s option, to either repairing or re-supplying the Software or the payment of the cost of repairing or re-supplying the Software.
+
+9.4		CSIRO does not provide any assurance that the Software and its outputs or any derivatives are suitable for any use or purpose.  You are responsible for ensuring the Software (and outputs or derivatives) is suitable for your own use or purpose, including compatibility with your computer programs or equipment as applicable.  Any use of the Software (and outputs or derivatives) is at your own risk.  
+
+***
+
+  **DISCLAIMER:**  
+
+  EXCEPT AS EXPRESSLY STATED IN THIS AGREEMENT AND TO THE FULL EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE IS PROVIDED "AS-IS". CSIRO MAKES NO REPRESENTATIONS, WARRANTIES OR CONDITIONS OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY REPRESENTATIONS, WARRANTIES OR CONDITIONS REGARDING THE CONTENTS OR ACCURACY OF THE SOFTWARE, OR OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NON-INFRINGEMENT, THE ABSENCE OF LATENT OR OTHER DEFECTS, OR THE PRESENCE OR ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE.
+
+  TO THE FULL EXTENT PERMITTED BY APPLICABLE LAW, IN NO EVENT SHALL CSIRO BE LIABLE ON ANY LEGAL THEORY (INCLUDING, WITHOUT LIMITATION, IN AN ACTION FOR BREACH OF CONTRACT, NEGLIGENCE OR OTHERWISE) FOR ANY CLAIM, LOSS, DAMAGES OR OTHER LIABILITY HOWSOEVER INCURRED.  WITHOUT LIMITING THE SCOPE OF THE PREVIOUS SENTENCE THE EXCLUSION OF LIABILITY SHALL INCLUDE: LOSS OF PRODUCTION OR OPERATION TIME, LOSS, DAMAGE OR CORRUPTION OF DATA OR RECORDS; OR LOSS OF ANTICIPATED SAVINGS, OPPORTUNITY, REVENUE, PROFIT OR GOODWILL, OR OTHER ECONOMIC LOSS; OR ANY SPECIAL, INCIDENTAL, INDIRECT, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES, ARISING OUT OF OR IN CONNECTION WITH THIS AGREEMENT, ACCESS OF THE SOFTWARE OR ANY OTHER DEALINGS WITH THE SOFTWARE, EVEN IF CSIRO HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH CLAIM, LOSS, DAMAGES OR OTHER LIABILITY.
+
+  APPLICABLE LEGISLATION SUCH AS THE AUSTRALIAN CONSUMER LAW MAY APPLY REPRESENTATIONS, WARRANTIES, OR CONDITIONS, OR IMPOSES OBLIGATIONS OR LIABILITY ON CSIRO THAT CANNOT BE EXCLUDED, RESTRICTED OR MODIFIED TO THE FULL EXTENT SET OUT IN THE EXPRESS TERMS OF THIS CLAUSE ABOVE "CONSUMER GUARANTEES".  TO THE EXTENT THAT SUCH CONSUMER GUARANTEES CONTINUE TO APPLY, THEN TO THE FULL EXTENT PERMITTED BY THE APPLICABLE LEGISLATION, THE LIABILITY OF CSIRO UNDER THE RELEVANT CONSUMER GUARANTEE IS LIMITED (WHERE PERMITTED AT CSIRO’S OPTION) TO ONE OF FOLLOWING REMEDIES OR SUBSTANTIALLY EQUIVALENT REMEDIES:
+
+  (i)	THE REPLACEMENT OF THE SOFTWARE, THE SUPPLY OF EQUIVALENT SOFTWARE, OR SUPPLYING RELEVANT SERVICES AGAIN;  
+  (ii)	THE REPAIR OF THE SOFTWARE;  
+  (iii)	THE PAYMENT OF THE COST OF REPLACING THE SOFTWARE, OF ACQUIRING EQUIVALENT SOFTWARE, HAVING THE RELEVANT SERVICES SUPPLIED AGAIN, OR HAVING THE SOFTWARE REPAIRED.
+
+  IN THIS CLAUSE, CSIRO INCLUDES ANY THIRD PARTY AUTHOR OR OWNER OF ANY PART OF THE SOFTWARE OR MATERIAL DISTRIBUTED WITH IT.  CSIRO MAY ENFORCE ANY RIGHTS ON BEHALF OF THE RELEVANT THIRD PARTY.
+
+***
+
+#### 10. Dispute and Governing Law
+10.1.	This agreement records our entire agreement and supersedes all earlier agreements and representations that may have been made by either party about the Software and Manual. Any provision of this licence which is illegal, void or unenforceable will be ineffective to the extent only of that illegality, voidness or unenforceability without invalidating the remaining provisions of this licence. This licence is governed by the laws applicable in the State of Victoria, Australia. 
+
+10.2	If there is a dispute between CSIRO and you which concerns these terms and conditions, each party must negotiate in good faith to resolve the dispute. Any dispute that cannot be resolved must be referred to the Australian Commercial Disputes Centre for arbitration in accordance with the Centre’s guidelines on arbitration. The decision of the arbitrator (including any award as to costs) will be final and binding. 
+
+10.3.	If there is a disagreement between you and CSIRO that cannot be resolved then the matter must be referred to the Australian Commercial Disputes Centre for arbitration in accordance with the Centre’s Guidelines on Arbitration.  The decision of the arbitrator (including any award as to costs) will be final and binding.  
+
+10.4	If part or all of any clause of these terms and conditions is illegal or unenforceable it will be severed from this agreement and will not affect the continued operation of the remaining clauses. 
+
+10.5	These terms and conditions are governed by the laws of Victoria, Australia and the parties submit to the non-exclusive jurisdiction of the courts of that State in relation to any proceedings under or relating to them.
diff --git a/README.md b/README.md
@@ -1,14 +1,26 @@
 # Atlantis
 <img width="120" height="130" alt="Atlantis_1" src="https://github.com/user-attachments/assets/4d2d9337-03f4-4f34-a4d2-48ad4c78ff86" />
 
+[Atlantis](https://research.csiro.au/atlantis/home/about-atlantis/) is software for modeling marine ecosystems, including spatial and temporal dynamics. This ecosystem model considers all parts of marine ecosystems – biophysical, economic, and social. Originally focused on the biophysical world and then on fisheries, it has grown to be used for cumulative impacts and climate-related questions.
+Developed by [Dr. Beth Fulton](https://people.csiro.au/F/B/Beth-Fulton.aspx) at the Commonwealth Scientific and Industrial Research Organization
+
+More information on Atlantis can be found at the links below or at [Atlantis_example_and_instructions](https://github.com/Atlantis-Ecosystem-Model/Atlantis_example_and_instructions/)
+
+**Attention!**
+>Atlantis is a living piece of software. If you would like to know more, please go to the [Atlantis research page](https://research.csiro.au/atlantis) or  <a href="mailto:atlantis@csiro.au?subject=Atlantis%20InQuiry">email the developers</a>.
+
+>To get the most out of Atlantis, it is strongly recommended that you register with the developers so we can support you and connect you with the user community. To do that <a href="mailto:atlantis@csiro.au?subject=Atlantis%20InQuiry">email the developers</a>. If the link doesn't autoconnect to your email, please check whether your pop-up blocker is turned on in your browser. Alternatively, right-click the text "email to developers" and select "copy email". The manual and the wiki are available from the links below. Note that the wiki is kept as an archive and is no longer updated. All current information is found in the manual.
+
+#### License ####
+This project is licensed under the CSIRO open-source License - see the [LICENSE.md](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/blob/main/LICENSE.md) file for details. The software is free to use, but please still register with the developers so they know who they are supporting. When you send the email, please be sure it includes your name, affiliation, and a brief line explaining why you are interested. This is important for us to provide you with the best possible support - it will not affect access, which is free of charge regardless.
+
+
 Atlantis current release [Atlantis v3.6721](https://github.com/Atlantis-Ecosystem-Model/AtlantisTrunk/releases/tag/3.6721)
 #### Version numbering: atlantis_major_release.atlantis_version
-Atlantis major release represents a significant change in the code, often not backwards compatible 
 
-Atlantis version represents smaller fixes and new features and follows the historical versioning, which is detailed in the [historical CHANGELOG](https://atlantis-ecosystem-model.github.io/atlantis-wiki/changelog.html#section-1)  
+An Atlantis major release represents a significant change to the code, often not backward-compatible. 
 
-[Atlantis](https://research.csiro.au/atlantis/home/about-atlantis/) is an ecosystem model that considers all parts of marine ecosystems – biophysical, economic, and social. Originally focused on the biophysical world and then on fisheries, it has grown to be used for cumulative impacts and climate-related questions.
-Developed by [Dr. Beth Fulton](https://people.csiro.au/F/B/Beth-Fulton.aspx) at the Commonwealth Scientific and Industrial Research Organization
+The Atlantis version represents smaller fixes and new features and follows the historical versioning, which is detailed in the [historical CHANGELOG](https://atlantis-ecosystem-model.github.io/atlantis-wiki/changelog.html#section-1)  
 
 ### [Atlantis ecosystem model documentation](https://atlantis-ecosystem-model.github.io/AtlantisManual/)
 
@@ -30,21 +42,22 @@ Developed by [Dr. Beth Fulton](https://people.csiro.au/F/B/Beth-Fulton.aspx) at
 |  | South Australia | Australia | [Beth Fulton](https://github.com/eafulton) | NA |
 |  | Salish Sea | Canada | [Raisha Lovindeer](https://github.com/raishalovindeer) | NA |
 | AMPS | Puget Sound | USA; Canada | [Hem Nalini Morzaria-Luna](https://github.com/hmorzaria) | NA |
-|  | Southern Benguela | South Africa |  | NA |
+|  | Southern Benguela | South Africa | [Kelly Cisneros](https://github.com/kortegac) | NA |
 |  | Tasman and Golden Bays | New Zealand |  | NA |
 |  | Korean Peninsula | South Korea | [Junggil Seo]() | NA |
 |  | Chatham Rise | New Zealand | [Vidette McGregor](https://github.com/mcgregorv)  | NA |
 |  | Gulf of Alaska | USA | [Alberto Rovellini](https://github.com/somros)  | <https://github.com/somros/AtlantisGOA_Base> |
-
+| LMAM | Lake Michigan | USA | [Kevin Cazelles](https://github.com/kevcaz)| | 
 
 ### Atlantis Models not currently maintained
 
 | Model Name | Region | Country | Contact | GitHub URL | URL Publication |
 |----|----|----|----|----|----|
 |  | Baltic |  |  |  | <https://doi.org/10.1371/journal.pone.0199168> |
-|  | English Channel |  |  |  | <http://dx.doi.org/10.1016/j.ecss.2016.10.016> |
-|  | Lake Victoria |  |  |  | <http://dx.doi.org/10.1016/j.envsoft.2016.09.019> |
+|  | English Channel | France |  |  | <http://dx.doi.org/10.1016/j.ecss.2016.10.016> |
+|  | Lake Victoria | Kenya, Uganda and Tanzania |  |  | <http://dx.doi.org/10.1016/j.envsoft.2016.09.019> |
 | NGOC | Northern Gulf of California | Mexico | [Hem Nalini Morzaria-Luna](https://github.com/hmorzaria) | NA | NA |
+|  | Guam | USA |  |  | <https://repository.library.noaa.gov/view/noaa/893> |
 
 
-[CSIRO](https://research.csiro.au/atlantis/home/usage-to-date/) documents many of these models, their intended uses, and the types of questions the model is being used to address.
+[CSIRO](https://research.csiro.au/atlantis/home/usage-to-date/) documents many of these models, their intended uses, and the types of questions the models are being used to address.
diff --git a/atlantis/ConvertAtlantis/Makefile.in b/atlantis/ConvertAtlantis/Makefile.in
@@ -282,6 +282,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@
@@ -367,7 +368,10 @@ GCCVERSION = $(shell gcc --version | grep ^gcc | sed 's/^.* //g')
 #-Wconversion
 WARN = -Wall -Wextra -Wno-unused-parameter -Wuninitialized \
 	-Warray-bounds $(am__append_1)
-AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN)
+
+#fetching repo version from git
+AM_CFLAGS = $(DEFINES) $(INCLUDES) $(DBG) $(OPT) $(EF) $(PG) $(WARN) \
+	-DRELEASE_VERSION=\"$(RELEASE_VERSION)\"
 lib_LIBRARIES = libatConvertAtlantis.a
 libatConvertAtlantis_adir = $(includedir)/ConvertAtlantis
 libatConvertAtlantis_a_SOURCES = atBioltoXML.c atCreateXML.c convertXML.h atHarvesttoXML.c atManagetoXML.c atImplementationtoXML.c atAssesstoXML.c \

diff --git a/atlantis/Makefile.in b/atlantis/Makefile.in
@@ -252,6 +252,7 @@ PACKAGE_URL = @PACKAGE_URL@
 PACKAGE_VERSION = @PACKAGE_VERSION@
 PATH_SEPARATOR = @PATH_SEPARATOR@
 RANLIB = @RANLIB@
+RELEASE_VERSION = @RELEASE_VERSION@
 SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 STRIP = @STRIP@