diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 0000000..6a1a591 --- /dev/null +++ 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 email the developers. 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 index d24ed7a..6d3a11f 100644 --- a/README.md +++ b/README.md @@ -1,14 +1,26 @@ # Atlantis Atlantis_1 +[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 email the developers. + +>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 email the developers. 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) | | - +| 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 | | | | | -| | English Channel | | | | | -| | Lake Victoria | | | | | +| | English Channel | France | | | | +| | Lake Victoria | Kenya, Uganda and Tanzania | | | | | NGOC | Northern Gulf of California | Mexico | [Hem Nalini Morzaria-Luna](https://github.com/hmorzaria) | NA | NA | +| | Guam | USA | | | | -[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 index 0a034e7..4ed379e 100644 --- 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 index 20dc97b..a60c6d2 100644 --- 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@ diff --git a/atlantis/atCLAMLink/Makefile.in b/atlantis/atCLAMLink/Makefile.in index d10be0e..be1d538 100644 --- a/atlantis/atCLAMLink/Makefile.in +++ b/atlantis/atCLAMLink/Makefile.in @@ -280,6 +280,7 @@ 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@ @@ -365,7 +366,10 @@ 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 = libatCLAMLink.a c_sources = atCLAMManage.c atCLAMLinkIO.c atCLAMComm.c atCLAMLinkSetup.c atCLAMImplement.c h_sources = $(top_srcdir)/atCLAMLink/include/atCLAMLink.h diff --git a/atlantis/atSS3Link/Makefile.in b/atlantis/atSS3Link/Makefile.in index a585dbd..847772c 100644 --- a/atlantis/atSS3Link/Makefile.in +++ b/atlantis/atSS3Link/Makefile.in @@ -280,6 +280,7 @@ 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@ @@ -365,7 +366,10 @@ 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 = libatSS3Link.a c_sources = atSS3Link.c atSS3LinkIO.c atSS3DataGen.c atSS3Util.c atCloseKin.c diff --git a/atlantis/atassess/Makefile.in b/atlantis/atassess/Makefile.in index 8c46093..24f907d 100644 --- a/atlantis/atassess/Makefile.in +++ b/atlantis/atassess/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 = libatassess.a libatassess_adir = $(includedir)/atassess libatassess_a_SOURCES = atclassical.c atindices.c atsample.c atsurvey.c \ diff --git a/atlantis/atbrokerlink/Makefile.in b/atlantis/atbrokerlink/Makefile.in index 4a51e9c..3d7ed34 100644 --- a/atlantis/atbrokerlink/Makefile.in +++ b/atlantis/atbrokerlink/Makefile.in @@ -276,6 +276,7 @@ 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@ @@ -361,7 +362,10 @@ 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 = libbrokerlink.a libbrokerlink_adir = $(includedir)/atbrokerlink libbrokerlink_a_SOURCES = requests.pb-c.h requests.pb-c.c responses.pb-c.h responses.pb-c.c \ diff --git a/atlantis/atecology/Makefile.in b/atlantis/atecology/Makefile.in index 4a0b694..e742b83 100644 --- a/atlantis/atecology/Makefile.in +++ b/atlantis/atecology/Makefile.in @@ -307,6 +307,7 @@ 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@ @@ -392,7 +393,10 @@ 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 = libatecology.a libatecology_adir = $(includedir)/atecology libatecology_a_SOURCES = atbiolUtil.c atannualbiology.c atbiolmessage.c atbiology.c atbiolsetup.c \ diff --git a/atlantis/atecology/atdemography.c b/atlantis/atecology/atdemography.c index 34f6d0f..3e7eea9 100644 --- a/atlantis/atecology/atdemography.c +++ b/atlantis/atecology/atdemography.c @@ -115,7 +115,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota //double lostden = 0; double dennow, CHLa, KWSR_sp, KWRR_sp, enviro_scalar, this_prop_ageup, plankton, vertdistrib, starting_num, new_num, amt, sp_AgeClassSize; - + //printf("Created Vertebrate Reproduction arrays\n"); if (verbose > 1) @@ -142,7 +142,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota } else { do_debug = 0; } - + /******************************************************************************* Get initial values for vertebrate vectors */ @@ -156,7 +156,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota VERTinfo[bm->which_check][cohort][DEN_id]); } } - + /******************************************************************************* Get plankton values in case have plankton based reproduction */ @@ -170,24 +170,24 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota for (species = 0; species < bm->K_num_tot_sp; species++) { if ((FunctGroupArray[species].speciesParams[flag_id] == TRUE) && ((FunctGroupArray[species].isVertebrate == TRUE) || (FunctGroupArray[species].groupAgeType == AGE_STRUCTURED))) { - + // Reinitialise for this species Util_Init_1D_Int(active_den, bm->K_num_max_cohort * bm->K_num_max_genetypes, 0); - + if ((bm->which_check == species) && (((bm->current_box == bm->checkbox) || (bm->checkbox > bm->nbox)) && (bm->dayt >= bm->checkstart))) do_debug = 1; else do_debug = 0; - + //if ((FunctGroupArray[species].numSpawns > 1) || (FunctGroupArray[species].groupType == FISH_INVERT)) // do_debug = 1; - + //if (bm->which_check == species) // do_debug = 1; //if ((species == 44) || (species == 64)) // do_debug = 1; - + /** Initialisation **/ /* Define num_cohorts = FunctGroupArray[species].numCohorts so that when use it as index to call value from vector have already corrected for the fact index starts at 0 not 1. @@ -216,7 +216,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota need_recupdate = 0; semelparous_migrants = 0; semelparous_parents = 0; - + /* If species in model and active then proceed */ if (flagSP && sp_active) { EMBRYO[species].recruiting_now = 0; @@ -224,7 +224,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota /** Spawning **/ sp_checkday = EMBRYO[species].next_spawn_any_age; - + /** //if (do_debug && (bm->which_check == species)) //if ((FunctGroupArray[species].groupType == MAMMAL) || (FunctGroupArray[species].groupType == FISH_INVERT)) @@ -233,9 +233,9 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota fprintf(llogfp, "Time: %e overall_checkday: %d, spawn_check_day: %d, ageday: %d for sp %s sp_checkday: %d\n", bm->dayt, overall_checkday, sp_checkday, EMBRYO[species].next_age_any_age, FunctGroupArray[species].groupCode, sp_checkday); } **/ - + if (overall_checkday == sp_checkday) { - + done_something = 1; /* Initalise TotSpawn for new values from current time step - needs to be reset for every box-layer as is the total spawn for that box-layer and added to EMBRYO.Larvae[] */ for (ngene = 0; ngene < sp_numGeneTypes; ngene++) { @@ -252,7 +252,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota Find_Evolution_Stats(bm, species, llogfp, 0); Find_Evolution_Shift(bm, species, llogfp); Do_Evolution(bm, species, llogfp); - + /* External to model spawning */ Ecology_Do_External_Age_Structured_Spawning(bm, species, flagmother, do_debug, &semelparous_migrants, llogfp); @@ -264,7 +264,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota /* Apply an semelparous reproductive deaths */ Apply_Semelparous_Deaths(bm, species, do_debug, semelparous_migrants, semelparous_parents, llogfp); - + /* Now spawning is started turn the switch off (so any once off events not repeated) */ EMBRYO[species].readytospawn[stock_id] = 0; } else { @@ -272,7 +272,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota EMBRYO[species].IndSpawn[cohort] = 0; } } - + /* Reset spawning readiness - can't do it at the time due to multiple layer handling */ if (overall_checkday == (sp_checkday + 1)) { done_something = 1; @@ -290,15 +290,15 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota /* Get vertical position in the water column */ vertdistrib = Get_Vertical_Recruit_Position(species, wclayer, maxdeep, totaldeep); - + /* Check for final recruit distribution */ Find_Final_Recruit_Distribution(bm, species, enviro_scalar, vertdistrib, wclayer, stock_id, do_debug, llogfp); } - + /** Do record keeping and diagostic tracking **/ if (overall_checkday == (sp_checkday + 2)) { done_something = 1; - + qid = EMBRYO[species].next_larvae; if(EMBRYO[species].SpawnRecruitOverlap && EMBRYO[species].CounterNotDone) qid++; @@ -326,11 +326,11 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota Update_Spawn_Queue(bm, species, cohort, maxstock_id, do_debug, llogfp); } } - + /******* Aging and Settlement of new young ******/ Util_Init_1D_Double(lostden_zero, bm->K_num_max_genetypes, 0.0); sp_checkday = EMBRYO[species].next_age_any_age; - + /* Find any recruits settling in this timestep */ Get_Settlers(bm, species, wclayer, stock_id, &recruits_arrive, do_debug, llogfp); @@ -339,18 +339,18 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota fprintf(llogfp, "Time: %e box%d-%d %s has sp_checkday %d vs overall_checkday %d\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, sp_checkday, overall_checkday); } */ - + /* Start aging */ if (overall_checkday == sp_checkday) { done_something = 1; - + Init_Aging_Arrays(bm, species, stock_id, maxstock_id, llogfp); - + /* Turn switch on to let groups age */ for (cohort = (int)floor((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { shiftVERTON[species][cohort]++; } - + if (bm->flagsenesce && (sp_AgeClassSize >= 1.0)) { /* If assuming senescence - not necessary if each age phase represents < 1 year */ senesce_on = 1; @@ -358,20 +358,20 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota /* The oldest age group doesn't age up. */ senesce_on = 0; } - + /** if (do_debug && (bm->which_check == species)) { fprintf(llogfp, "Time: %e, %s senesce_on: %d\n", bm->dayt, FunctGroupArray[species].groupCode, senesce_on); } **/ - + /* Iterate of cohorts and calculate number aging up - starting with evolutionary shifts */ Do_Phenotyic_Expression(bm, species, llogfp); Do_Aging_Update_Trait(bm, species, llogfp); - + for (cohort = (int)floor((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { basecohort = (int)floor (cohort / sp_numGeneTypes); - + /** if (do_debug && (bm->which_check == species)) { //if ((FunctGroupArray[species].groupType == MAMMAL) || (FunctGroupArray[species].groupType == FISH_INVERT)) { @@ -385,9 +385,9 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota /* Skip to next cohort as oldest don't age away in this option or the cohort not aging now */ continue; } - + dennow = Get_Numbers_Aging(bm, species, cohort, active_den, lostden_zero, &this_prop_ageup, do_debug, llogfp); - + /* Update numbers to age and local distribution */ Update_Aging_Numbers(bm, species, cohort, stock_id, dennow, this_prop_ageup, do_debug, llogfp); @@ -398,7 +398,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota Update_Age_Queue(bm, species, cohort, do_debug, llogfp); } - + /* Set flag to indicate need age distribution update */ need_update = 1; @@ -406,7 +406,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota age-structured information due to aging */ need_matupdate = 1; } - + /** //if (do_debug && (bm->which_check == species)) { //if ((FunctGroupArray[species].groupType == MAMMAL) || (FunctGroupArray[species].groupType == FISH_INVERT)) { @@ -422,7 +422,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota moving target - not 100% correct probably but much easier to deal with) */ if (EMBRYO[species].recruiting_now) { done_something = 1; - + /** if (do_debug && (bm->which_check == species)) { //if ((FunctGroupArray[species].groupType == MAMMAL) || (FunctGroupArray[species].groupType == FISH_INVERT)) { @@ -441,9 +441,9 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota so don't need to update age distribution */ if ((bm->current_box == bm->last_box) && (!bm->current_layer)) FunctGroupArray[species].speciesParams[firstrecday_id] = 0; - + } - + /* Update flags */ FunctGroupArray[species].speciesParams[need_update_id] = need_update; FunctGroupArray[species].speciesParams[need_recupdate_id] = need_recupdate; @@ -451,12 +451,12 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota cohort = 0; /* Update sizes of smallest age class - calculate new sn and rn */ - + if (bm->flag_modify_KWSR) { KWSR_sp = Get_Recruit_Size_Forcing(bm, species, do_debug, llogfp); KWRR_sp = KWSR_sp * FunctGroupArray[species].X_RS[cohort]; } - + FunctGroupArray[species].speciesParams[suckler_contam_today_id] = 1; // Only zeroed if recruits actively arriving if (recruits_arrive) { /* Update sizes of smallest age class - calculate new sn and rn */ @@ -467,7 +467,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota new_num += starting_num; shiftVERT[species][cohort][SN_id] = (KWSR_sp * EMBRYO[species].recruitSPden[ngene] + VERTinfo[species][cohort][SN_id] * starting_num) / (new_num + small_num); shiftVERT[species][cohort][RN_id] = (KWRR_sp * EMBRYO[species].recruitSPden[ngene] + (VERTinfo[species][cohort][RN_id] - EMBRYO[species].IndSpawn[cohort]) * starting_num) / (new_num + small_num); - + if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Apply_Settler_Contaminants(bm, species, cohort, starting_num, new_num, EMBRYO[species].next_recruit); FunctGroupArray[species].speciesParams[suckler_contam_today_id] = 0; // As getting transfer at birth so don't double up @@ -477,11 +477,11 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota if((EMBRYO[species].recruitSPden[ngene] > 0) || (lostden_zero[ngene] != 0.0)){ active_den[cohort] = 1; } - + /** //if (do_debug && (bm->which_check == species) && (EMBRYO[species].recruitSPden[ngene] > 0) ) { //fprintf(bm->logFile, "VERTinfo[species][cohort][DEN_id] = %e\n", VERTinfo[species][cohort][DEN_id]); - + if (do_debug && (EMBRYO[species].recruitSPden[ngene] > 0)) { //if (EMBRYO[species].recruitSPden[ngene] > 0) { fprintf(llogfp, "Time: %e, box%d %s ngene: %d shiftVERT-SN: %e, KWSR_sp: %e, recruitSPden: %e, VERTinfo-SN: %e, starting_num: %e, new_num: %e (VERTden: %e, lostdenzero: %e)\n", bm->dayt, bm->current_box, FunctGroupArray[species].groupCode, ngene, shiftVERT[species][cohort][SN_id], KWSR_sp, EMBRYO[species].recruitSPden[ngene], VERTinfo[species][cohort][SN_id], starting_num, new_num, VERTinfo[species][cohort][DEN_id], lostden_zero[ngene]); @@ -499,7 +499,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota for (i = 0; i < (FunctGroupArray[species].numCohortsXnumGenes); i++) { basecohort = (int)(floor (i / sp_numGeneTypes)); ngene = i - (basecohort * sp_numGeneTypes); - + if (shiftVERT[species][i][DEN_id] > 0) { fprintf(llogfp, "day: %e, %s-%d box: %d, layer %d, shiftDEN-%d %e\n", bm->dayt, FunctGroupArray[species].groupCode, i, bm->current_box, wclayer, i, shiftVERT[species][i][DEN_id]); @@ -510,14 +510,14 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota } } **/ - + /* Update local dPools */ if(done_something){ for (i = 0; i < (FunctGroupArray[species].numCohortsXnumGenes); i++) { Update_Local_dPool(bm, species, i, EMBRYO[species].IndSpawn[i], EMBRYO[species].recruitSPden, sp_numGeneTypes, localWCTracers, do_debug, llogfp); } } - + /* Update age distributions - only do at end for typical group, but do it every box for site attached */ need_update = (int) (FunctGroupArray[species].speciesParams[need_update_id]); if (bm->flagagestruct && need_update && (((bm->current_box == bm->last_box) && (!bm->current_layer)) @@ -544,7 +544,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota } } } - + return; } @@ -560,7 +560,7 @@ void Vertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int tota double Ecology_Age_Structured_Spawn(int species, double KSPA_SP, double FSP_SP, double RSprop_SP, double SN, double RN, double FSPB_SP, double X_RS, int repcost, FILE *llogfp) { double WforS, Wgt, Spwn, Wgtcheck, RepCost; double RN_buf = 0.999999999; - + if(repcost) { // NOTE: parameters are overloaded - FSP is constant for reproduction cost and KSPA is the exponent here RepCost = FSP_SP * pow(SN, KSPA_SP); @@ -586,13 +586,13 @@ double Ecology_Age_Structured_Spawn(int species, double KSPA_SP, double FSP_SP, Spwn = RN; } } - + // Sanity check if (Spwn > RN) Spwn = RN * RN_buf; //fprintf(llogfp, "%s repcost %d SN: %e RN: %e KSPA_SP %e FSP_SP: %e RSprop_SP: %e FSPB_SP: %e X_RS: %e Spwn: %e\n", FunctGroupArray[species].groupCode, repcost, SN, RN, KSPA_SP, FSP_SP, RSprop_SP, FSPB_SP, X_RS, Spwn); - + return (Spwn); } @@ -643,7 +643,7 @@ int Ecology_Sp_Active(MSEBoxModel *bm, int species, FILE *llogfp) { } } else if(FunctGroupArray[species].groupAgeType == AGE_STRUCTURED_BIOMASS) { sp_active = bm->flagday; - } + } } return sp_active; } @@ -658,7 +658,7 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in int basecohort; int sp_numGeneTypes = (int) (FunctGroupArray[species].numGeneTypes); int overall_checkday = (int) (floor(bm->dayt)); - + Util_Init_1D_Int(ngene_done, bm->K_num_max_genetypes, 0); Util_Init_1D_Int(not_finished, bm->K_num_max_genetypes, 0); @@ -669,13 +669,13 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in //if((bm->dayt >= bm->checkstart) && (bm->which_check == species)) // do_debug = 1; - + //if ((FunctGroupArray[species].numSpawns > 1) || (FunctGroupArray[species].groupType == FISH_INVERT)) // do_debug = 1; //if (bm->which_check == species) // do_debug = 1; - + //printf("Creating Init Spawn arrays\n"); /* If no embryos there can be no recruits */ @@ -685,21 +685,21 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in if ((bm->current_box == bm->last_box) && (!bm->current_layer)) { for(chrt = 0; chrt < FunctGroupArray[species].numCohortsXnumGenes; chrt++) { - + basecohort = (int)(floor (chrt / sp_numGeneTypes)); ngene = chrt - (basecohort * sp_numGeneTypes); - + /** if (do_debug && (species == bm->which_check)) { fprintf(llogfp, "Time: %e %s-%d has overall_checkday: %d StartDay: %d EndDay: %d next_recruit: %d Larvae: %e\n", bm->dayt, FunctGroupArray[species].groupCode, chrt, overall_checkday, EMBRYO[species].StartDay[chrt][EMBRYO[species].next_recruit], EMBRYO[species].EndDay[chrt][EMBRYO[species].next_recruit], EMBRYO[species].next_recruit, EMBRYO[species].Larvae[0][0][EMBRYO[species].next_recruit]); } **/ - + if(( overall_checkday > EMBRYO[species].StartDay[chrt][EMBRYO[species].next_recruit] ) && ( overall_checkday <= EMBRYO[species].EndDay[chrt][EMBRYO[species].next_recruit])) { if(ngene_done[ngene] < 1) { not_finished[ngene] = 0; for (i = 0; i < maxstock_id; i++) { - + /** //if (do_debug && (species == bm->which_check)) { if (species == 52) { @@ -717,7 +717,7 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in if (not_finished[ngene] < 1) { /* If all settlers arrived then need to reset */ EMBRYO[species].EndDay[chrt][EMBRYO[species].next_recruit] = overall_checkday; - + /** //if (do_debug && (species == bm->which_check)) { if (species == 52) { @@ -750,7 +750,7 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in bm->dayt, FunctGroupArray[species].groupCode, EMBRYO[species].next_larvae, EMBRYO[species].next_recruit); } **/ - + ngene_done[ngene] = 2; // Step 2 done } } @@ -768,7 +768,7 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in bm->tot_SSB[species] = 0.0; // Reinitialise CounterNotDone in case need to spawn mid recruitment EMBRYO[species].CounterNotDone = 1; - + //fprintf(llogfp, "Time: %e, %s has -- CounterNotDone reset to 1\n", bm->dayt, FunctGroupArray[species].groupCode); } @@ -779,7 +779,7 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in fprintf(llogfp, "Ending Init Spawns\n"); } */ - + return; } @@ -792,19 +792,19 @@ void Ecology_Init_Spawn_Params(MSEBoxModel *bm, int species, int maxstock_id, in */ void Update_Age_Queue(MSEBoxModel *bm, int species, int cohort, int do_debug, FILE *llogfp) { int chrt, day_to_check; - + if ((bm->current_box == bm->last_box) && (!bm->current_layer) && !cohort){ /* Shuffle Aging Queue to next entry - only do once per species and as counter counting down do it for the youngest (as last) */ EMBRYO[species].next_age++; day_to_check = MAXINT; for(chrt = 0; chrt < FunctGroupArray[species].numCohortsXnumGenes; chrt++) { - + if ((EMBRYO[species].Age_Now[chrt][EMBRYO[species].next_age] > bm->dayt) && (day_to_check > EMBRYO[species].Age_Now[chrt][EMBRYO[species].next_age])) day_to_check = EMBRYO[species].Age_Now[chrt][EMBRYO[species].next_age]; } EMBRYO[species].next_age_any_age = day_to_check; - + /** //if (bm->which_check == species) { fprintf(llogfp, "Time: %e, %s-%d has next_age_id: %d next_age date: %d\n", bm->dayt, @@ -827,21 +827,21 @@ void Update_Spawn_Queue(MSEBoxModel *bm, int species, int cohort, int maxstock_i if ((bm->current_box == bm->last_box) && (!bm->current_layer) && (cohort == (FunctGroupArray[species].numCohortsXnumGenes - 1))){ EMBRYO[species].next_spawn++; EMBRYO[species].CounterNotDone = 1; - + day_to_check = MAXINT; for(chrt = 0; chrt < FunctGroupArray[species].numCohortsXnumGenes; chrt++) { if ((EMBRYO[species].Spawn_Now[chrt][EMBRYO[species].next_spawn] > bm->dayt) && (day_to_check > EMBRYO[species].Spawn_Now[chrt][EMBRYO[species].next_spawn])) day_to_check = EMBRYO[species].Spawn_Now[chrt][EMBRYO[species].next_spawn]; } EMBRYO[species].next_spawn_any_age = day_to_check; - + /* Zero statistic storing */ for (ngene = 0; ngene < FunctGroupArray[species].numGeneTypes; ngene++){ for (i = 0; i < maxstock_id; i++) { totrecruit[species][i][ngene] = 0.0; } } - + /* if (do_debug && (bm->which_check == species)){ fprintf(llogfp, "Time: %e, %s-%d has next_spawn: %d\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, EMBRYO[species].next_spawn); @@ -876,12 +876,12 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i int basecohort = 0; int flag_allow_spawn = 1; *semelparous_migrants = 0; - + if(verbose) printf("Ecology_Do_External_Age_Structured_Spawning for %s\n", FunctGroupArray[species].groupCode); - + //fprintf(llogfp, "Time: %e, %s-%d box%d-%d Spawn_Now: %d (next_spawn: %d) overall_checkday: %d recruitType: %d\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, bm->current_box, bm->current_layer, EMBRYO[species].Spawn_Now[cohort][EMBRYO[species].next_spawn], EMBRYO[species].next_spawn, overall_checkday, FunctGroupArray[sp].recruitType); - + /* If spawn outside model and in first dynamic box then add in spawning due to migrants */ if ((FunctGroupArray[species].externalReproducer) && ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer))) { for (cohort = ((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { @@ -890,7 +890,7 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i recieve_ngene = ngene; //fprintf(llogfp, "Time: %e, %s-%d Spawn_Now: %d (next_spawn: %d) overall_checkday: %d\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, EMBRYO[species].Spawn_Now[cohort][EMBRYO[species].next_spawn], EMBRYO[species].next_spawn, overall_checkday); - + if(EMBRYO[species].Spawn_Now[cohort][EMBRYO[species].next_spawn] != overall_checkday) continue; // As not the cohort spawning @@ -904,7 +904,7 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i } else { allowed_to_spawn = 0; } - + //fprintf(llogfp, "Time: %e, %s-%d allowed_to_spawn A: %d\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, allowed_to_spawn); if (!allowed_to_spawn) // If not big enough to spawn skip ahead @@ -920,24 +920,24 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i for (mid = MIGRATION[species].num_in_queue_done; mid < MIGRATION[species].num_in_queue; mid++) { flag_allow_spawn = MIGRATION[species].ReprodAllowed[cohort][mid]; if (flag_allow_spawn && (MIGRATION[species].DEN[cohort][mid] > bm->min_dens)) { - + /* for those species with size-based age of maturity, check the age class is big enough to spawn */ Wgt = MIGRATION[species].SN[cohort][mid] + MIGRATION[species].RN[cohort][mid]; li = Ecology_Get_Size(bm, species, Wgt, cohort); if (li < FunctGroupArray[species].speciesParams[min_li_mat_id]) { allowed_to_spawn = 0; } - + //fprintf(llogfp, "Time: %e, %s cohort %d allowed_to_spawn B: %d\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, allowed_to_spawn); if (!allowed_to_spawn) // If not big enough to spawn skip ahead continue; - + step1 = Ecology_Age_Structured_Spawn(species, KSPA_sp, FSP_sp, RSprop_sp, MIGRATION[species].SN[cohort][mid], MIGRATION[species].RN[cohort][mid], FunctGroupArray[species].scaled_FSPB[cohort], FunctGroupArray[species].X_RS[cohort], bm->flag_repcostSpawn, llogfp); MigIndSpawn = FunctGroupArray[species].scaled_FSPB[cohort] * step1; - + //fprintf(llogfp, "Time: %e, %s cohort %d mid: %d MigIndSpawn: %e FSPB: %e step1: %e\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, mid, MigIndSpawn, FunctGroupArray[species].scaled_FSPB[cohort], step1); - + thisSSB = (MIGRATION[species].RN[cohort][mid] + MIGRATION[species].SN[cohort][mid]) * MIGRATION[species].DEN[cohort][mid]; bm->tot_SSB[species] += FunctGroupArray[species].scaled_FSPB[cohort] * thisSSB; @@ -946,10 +946,10 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i EMBRYO[species].TotSpawn[recieve_ngene] += MigIndSpawn * MIGRATION[species].DEN[cohort][mid]; MIGRATION[species].RN[cohort][mid] -= MigIndSpawn; // Mass lost in spawning - - if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ + + /* if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ quit("Have not coded contaminant transfer for externally reproducing species - if you get this message contact teh developer group and ask them to sort this for you.... if it involves salmon Beth may swear, don't worry she will be fine after a bowl of ice cream\n"); - } + } */ /* If semelparous reproduction */ if (flagmother < 0) { @@ -959,7 +959,7 @@ void Ecology_Do_External_Age_Structured_Spawning(MSEBoxModel *bm, int species, i if (isnan(MIGRATION[species].RN[cohort][mid])) { quit("Time %e - during external spawning of %s cohort %d mid: %d have got NAN RN: %e SN: %e MigIndSpawn: %e scaled_FSPB: %e step1: %e DEN: %e\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, mid, MIGRATION[species].RN[cohort][mid], MIGRATION[species].SN[cohort][mid], MigIndSpawn, FunctGroupArray[species].scaled_FSPB[cohort], step1, MIGRATION[species].DEN[cohort][mid]); } - + /** //if (do_debug) { if (species == 33) { @@ -1031,20 +1031,20 @@ void Ecology_Do_Internal_Age_Structured_Spawning(MSEBoxModel *bm, int species, i /* Animals in this box spawn */ step1 = Ecology_Age_Structured_Spawn(species, KSPA_sp, FSP_sp, RSprop_sp, VERTinfo[species][cohort][SN_id], VERTinfo[species][cohort][RN_id], FunctGroupArray[species].scaled_FSPB[cohort], FunctGroupArray[species].X_RS[cohort], bm->flag_repcostSpawn, llogfp); EMBRYO[species].IndSpawn[cohort] = FunctGroupArray[species].scaled_FSPB[cohort] * step1; - + thisSSB = (VERTinfo[species][cohort][RN_id] + VERTinfo[species][cohort][SN_id]) * VERTinfo[species][cohort][DEN_id]; bm->tot_SSB[species] += FunctGroupArray[species].scaled_FSPB[cohort] * thisSSB; if(bm->flag_do_evolution) { recieve_ngene = Do_Inheritance(bm, species, ngene, basecohort, cohort, llogfp); } - + if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ if(EMBRYO[species].IndSpawn[cohort] > 0) { // Only transfer contaminants if actually producing any spawn Get_Parental_Contaminants(bm, species, cohort, flagmother, VERTinfo[species][cohort][DEN_id]); } } - + EMBRYO[species].TotSpawn[recieve_ngene] += EMBRYO[species].IndSpawn[cohort] * VERTinfo[species][cohort][DEN_id]; /** @@ -1056,7 +1056,7 @@ void Ecology_Do_Internal_Age_Structured_Spawning(MSEBoxModel *bm, int species, i FunctGroupArray[species].scaled_FSPB[cohort], VERTinfo[species][cohort][SN_id], VERTinfo[species][cohort][RN_id], FSP_sp, KSPA_sp, step1); } **/ - + /* If semelparous reproduction */ if (flagmother < 0) { *semelparous_parents = 1; @@ -1073,36 +1073,36 @@ void Ecology_Do_Internal_Age_Structured_Spawning(MSEBoxModel *bm, int species, i */ void Apply_Semelparous_Deaths(MSEBoxModel *bm, int species, int do_debug, int semelparous_migrants, int semelparous_parents, FILE *llogfp) { int cohort, qid; - + for (cohort = ((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { - + if(FunctGroupArray[species].scaled_FSPB[cohort] > 0.0) { /* If semelparous external reproduction */ if (semelparous_migrants) { for (qid = MIGRATION[species].num_in_queue_done; qid < MIGRATION[species].num_in_queue; qid++) { fprintf(llogfp,"Time: %e %s-%d qid: %d has starting MIGRATION_den_expect: %e", bm->dayt, FunctGroupArray[species].groupCode, cohort, qid, MIGRATION[species].DEN[cohort][qid]); - + MIGRATION[species].DEN[cohort][qid] *= (1.0 - FunctGroupArray[species].scaled_FSPB[cohort]); - + fprintf(llogfp," ending: %e as scaled_FSPB: %e\n", MIGRATION[species].DEN[cohort][qid], FunctGroupArray[species].scaled_FSPB[cohort]); } } - + /* If semelparous reproduction internal to the model domain */ if (semelparous_parents) { fprintf(llogfp,"Time: %e %s-%d current_box: %d has DEN: %e and shiftDEN: %e ", bm->dayt, FunctGroupArray[species].groupCode, cohort, bm->current_box, VERTinfo[species][cohort][DEN_id], shiftVERT[species][cohort][DEN_id]); - + /* In case need to do aging correct adult abundance directly */ VERTinfo[species][cohort][DEN_id] *= (1.0 - FunctGroupArray[species].scaled_FSPB[cohort]); - + /* If not at same time aging then need to update the shift values - no need to multiply by (1.0 - FunctGroupArray[species].scaled_FSPB[cohort]) here as already applied that above */ shiftVERT[species][cohort][DEN_id] = VERTinfo[species][cohort][DEN_id]; shiftVERTON[species][cohort]++; - + fprintf(llogfp," DEN ending: %e shift ending: %e as scaled_FSPB: %e\n", VERTinfo[species][cohort][DEN_id], shiftVERT[species][cohort][DEN_id], FunctGroupArray[species].scaled_FSPB[cohort]); } @@ -1134,7 +1134,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl qid++; if (qid > (EMBRYO[species].num_in_larval_queue - 1)) qid = EMBRYO[species].num_in_larval_queue - 1; - + /** if (species == 33) fprintf(llogfp, "Time: %e %s has qid %d as next_larvae %d SpawnRecruitOverlap %d CounterNotDone %d and next_larve %d \n", bm->dayt, FunctGroupArray[species].groupCode, qid, EMBRYO[species].next_larvae, EMBRYO[species].SpawnRecruitOverlap, EMBRYO[species].CounterNotDone, EMBRYO[species].next_larvae); @@ -1151,10 +1151,10 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl EMBRYO[species].Larvae[stock_id][ngene][qid] = 0; } } - + /**/ - - + + for(ngene = 0; ngene < sp_numGeneTypes; ngene++){ switch (recruit_sp) { case no_recruit: @@ -1163,19 +1163,19 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl case const_recruit: /* Fixed set of constants */ if (EMBRYO[species].readytospawn[stock_id] == 1) EMBRYO[species].Larvae[stock_id][ngene][qid] = KDENR_sp / ng; - + /* if (species == 52) { fprintf(llogfp, "Time: %e box%d-%d %s larvae %e KDENR: %e ng: %e\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, EMBRYO[species].Larvae[stock_id][ngene][qid], KDENR_sp, ng); } */ - + break; case chl_recruit: /* Proportional to primary productivity */ EMBRYO[species].Larvae[stock_id][ngene][qid] += recSTOCK[species][stock_id] * PP_sp * bm->cell_vol * (CHLa / bm->ref_chl); - + //fprintf(llogfp, "Time: %e box%d-%d %s larvae %e P_sp: %e cell_vol: %e CHLa: %e ref_chl: %e\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, EMBRYO[species].Larvae[stock_id][ngene][qid], PP_sp, bm->cell_vol, CHLa, bm->ref_chl); - + break; case rand_recruit: /* Random - follows lognormal */ if (EMBRYO[species].readytospawn[stock_id] == 1) @@ -1206,7 +1206,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl //if (do_debug && (bm->which_check == species)) { if (species == 33) { fprintf(llogfp,"Doing %s stock %d, ngene: %d, qid: %d, TotSpawn: %e, Larvae: %e\n", - FunctGroupArray[species].groupCode, stock_id, ngene, qid, EMBRYO[species].TotSpawn[ngene], + FunctGroupArray[species].groupCode, stock_id, ngene, qid, EMBRYO[species].TotSpawn[ngene], EMBRYO[species].Larvae[stock_id][ngene][qid]); } **/ @@ -1225,7 +1225,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl } **/ } - + if ((FunctGroupArray[species].externalReproducer) && ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer))) { for (cohort = ((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { for (mid = MIGRATION[species].num_in_queue_done; mid < MIGRATION[species].num_in_queue; mid++) { @@ -1233,7 +1233,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl EMBRYO[species].Larvae[stock_id][ngene][qid] += KDENR_sp * FunctGroupArray[species].scaled_FSPB[cohort] * MIGRATION[species].DEN[cohort][mid]; FunctGroupArray[species].speciesParams[recruit_qid_id] = qid; - + /** if (do_debug && (bm->which_check == species)) { fprintf(llogfp,"Time: %e %s ngene: %d, qid: %d, mid: %d, cohort: %d, KDENR: %e, scaledFSPB: %e, MIGRATIONden: %e, Larvae: %e\n", bm->dayt, FunctGroupArray[species].groupCode, ngene, qid, mid, cohort, KDENR_sp, FunctGroupArray[species].scaled_FSPB[cohort], MIGRATION[species].DEN[cohort][mid], EMBRYO[species].Larvae[stock_id][ngene][qid]); @@ -1248,7 +1248,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl case ts_recruit:/* Read in timeseries of recruitment */ if (EMBRYO[species].readytospawn[stock_id] == 1) { EMBRYO[species].Larvae[stock_id][ngene][qid] = tsEval(bm->tsRecruit, tsrecruitid, bm->t); - + /** //if (do_debug && (bm->which_check == species)) fprintf(llogfp, "Time: %e %s ngene: %d stock: %d qid: %d with Larvae: %e and time t: %e\n", bm->dayt, FunctGroupArray[species].groupCode, ngene, stock_id, qid, EMBRYO[species].Larvae[stock_id][ngene][qid], bm->t); @@ -1264,12 +1264,12 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl cohort = (FunctGroupArray[species].numGeneTypes * bcohort) + ngene; EMBRYO[species].Larvae[stock_id][ngene][qid] += VERTinfo[species][cohort][DEN_id] * FunctGroupArray[species].scaled_FSPB[cohort] * (VERTinfo[species][cohort][SN_id] + VERTinfo[species][cohort][RN_id]) * bm->X_CN * mg_2_tonne; } - + if ((FunctGroupArray[species].externalReproducer) && ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer))) { for (cohort = ((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { for (mid = MIGRATION[species].num_in_queue_done; mid < MIGRATION[species].num_in_queue; mid++) { if(MIGRATION[species].DEN[cohort][mid] > bm->min_dens){ - + EMBRYO[species].Larvae[stock_id][ngene][qid] += MIGRATION[species].DEN[cohort][mid] * FunctGroupArray[species].scaled_FSPB[cohort] * (MIGRATION[species].SN[cohort][mid] + MIGRATION[species].RN[cohort][mid]) * bm->X_CN * mg_2_tonne; FunctGroupArray[species].speciesParams[recruit_qid_id] = qid; } @@ -1284,12 +1284,12 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl EMBRYO[species].Larvae[stock_id][ngene][qid] += FunctGroupArray[species].scaled_FSPB[cohort] * VERTinfo[species][cohort][DEN_id]; } - + if ((FunctGroupArray[species].externalReproducer) && ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer))) { for (cohort = ((FunctGroupArray[species].numCohortsXnumGenes) - 1); cohort >= 0; cohort--) { for (mid = MIGRATION[species].num_in_queue_done; mid < MIGRATION[species].num_in_queue; mid++) { if(MIGRATION[species].DEN[cohort][mid] > bm->min_dens){ - + EMBRYO[species].Larvae[stock_id][ngene][qid] += FunctGroupArray[species].scaled_FSPB[cohort] * MIGRATION[species].DEN[cohort][mid]; FunctGroupArray[species].speciesParams[recruit_qid_id] = qid; } @@ -1303,7 +1303,7 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl quit("No such flagrecruit defined for vertebrates (i.e. value must be between 1 ands 10 at present)\n"); break; } - + stocking_sp = (int) (FunctGroupArray[species].speciesParams[flagstocking_id]); if (stocking_sp) { /* Read in timeseries of number of recruits added due to stocking - assume all genotypes get the same number of recruits */ @@ -1321,16 +1321,16 @@ void Ecology_Find_Embryoes(MSEBoxModel *bm, int species, int stock_id, double pl EMBRYO[species].Larvae[stock_id][ngene][qid], EMBRYO[species].TotSpawn[ngene], recruit_sp); } **/ - + if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Store_Recruit_Contaminants(bm, species, stock_id, ngene, qid); } } - + if (bm->flag_do_evolution){ /* Redistribute larvae across based on evolutiomn curve if necesary */ Evolution_Curve(bm, species, stock_id, qid, do_debug, llogfp); } - + return; } @@ -1375,7 +1375,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F /* if(((bm->current_box == bm->checkbox) || (bm->checkbox > bm->nbox)) && (bm->dayt >= bm->checkstart) && (bm->which_check == species)) do_debug = 1; - + if ((FunctGroupArray[species].numSpawns > 1) || (FunctGroupArray[species].groupType == FISH_INVERT)) do_debug = 1; @@ -1398,7 +1398,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F case ts_recruit:/* Read in timeseries of recruitment */ case multiple_ts_recruit: /* Read in timeseries of recruitment */ temprec = EMBRYO[species].Larvae[stock_id][ngene][qid]; - + /** //if (do_debug) { //if (species == 33) { @@ -1406,7 +1406,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F fprintf( llogfp, "Time: %e, box%d-%d, species %s, ngene: %d, stock: %d, qid: %d, temprec: %e, Larvae: %e\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, ngene, stock_id, qid, temprec, EMBRYO[species].Larvae[stock_id][ngene][qid]); } **/ - + break; case BevHolt_recruit: /* Beverton-Holt stock-recruit relationship - Atlantis basic version (mix numbers and biomass) */ temprec = (recSTOCK[species][stock_id] * BHalpha_sp * EMBRYO[species].Larvae[stock_id][ngene][qid] / (BHbeta_sp + bm->totfishpop[species] * stock_prop[species][stock_id])); @@ -1417,7 +1417,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F if (species == 33) { fprintf( llogfp, "Time: %e, box%d-%d, species %s, ngene: %d, stock: %d, temprec: %e, recSTOCK: %e, BHalpha: %e, Larvae: %e, BHbeta: %e, totfish: %e, stock_prop: %e)\n", - bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, + bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, ngene, stock_id, temprec, recSTOCK[species][stock_id], BHalpha_sp, EMBRYO[species].Larvae[stock_id][ngene][qid], BHbeta_sp, bm->totfishpop[species], stock_prop[species][stock_id]); @@ -1457,7 +1457,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F break; case Ricker_recruit: /* Ricker */ temprec = bm->totfishpop[species] * stock_prop[species][stock_id] * exp(recSTOCK[species][stock_id] * Ralpha_sp * (1.0 - bm->totfishpop[species] * stock_prop[species][stock_id] / Rbeta_sp)); - + /** if (do_debug && (bm->which_check == species)) { fprintf( llogfp, "Time: %e, box%d-%d, species %s, ngene: %d, stock: %d, temprec: %e, totfishpop: %e, stock_prop: %e, recSTOCK: %e, Ralpha: %e, Larvae: %e, Rbeta: %e\n", @@ -1466,7 +1466,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F EMBRYO[species].Larvae[stock_id][ngene][qid], Rbeta_sp); } **/ - + break; case SSB_BevHolt_recruit: /* Standard Beverton-Holt stock-recruit relationship */ temprec = (recSTOCK[species][stock_id] * BHalpha_sp * bm->totfishpop[species] * stock_prop[species][stock_id] / (BHbeta_sp + bm->totfishpop[species] * stock_prop[species][stock_id])); @@ -1503,7 +1503,7 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F bm->airtemp_index = tsEvalR(bm->thermal_index, bm->tindex_id, bm->t, bm->tindex_rewindid); bm->airT_rate_index = tsEvalR(bm->rate_index, bm->rindex_id, bm->t, bm->rindex_rewindid); current_ICE = Get_Ice_Rating(bm, species); - + this_stock = bm->tot_SSB[species] * stock_prop[species][stock_id]; prod_alpha = FunctGroupArray[species].speciesParams[prod_alpha_id]; @@ -1512,9 +1512,9 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F temp_coefft = FunctGroupArray[species].speciesParams[temp_coefft_id]; rate_coefft = FunctGroupArray[species].speciesParams[rate_coefft_id]; wind_coefft = FunctGroupArray[species].speciesParams[wind_coefft_id]; - + recruit_var = FunctGroupArray[species].speciesParams[recruit_var_id]; - + step1 = prod_alpha - dd_beta1 * this_stock * dd_beta2 * current_ICE + temp_coefft * bm->airtemp_index + rate_coefft * bm->airT_rate_index + recruit_var * 0.5; if(bm->track_wind) { step1 += (wind_coefft * current_WIND); @@ -1532,13 +1532,13 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F larval_scalar = Larval_Mortality(bm, species, stock_id, llogfp); temprec *= larval_scalar; } - + // Check for any stochasticity added to this recruitment if ( FunctGroupArray[species].speciesParams[flag_recruit_stochastic_id] > 0) { step1 = temprec; temprec = Util_Normx_Result(step1, norm_sigma); } - + // Store the final number of recruits EMBRYO[species].BulkRecruits[ngene] = temprec; @@ -1552,13 +1552,13 @@ void Get_Recruits(MSEBoxModel *bm, int species, int stock_id, double plankton, F EMBRYO[species].BulkRecruits[ngene], temprec, EMBRYO[species].Larvae[stock_id][ngene][qid], qid); } **/ - + if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Get_Recruit_Contaminants(bm, species, ngene, stock_id, qid); } - + } - + return; } @@ -1572,7 +1572,7 @@ double Larval_Mortality(MSEBoxModel *bm, int species, int stock_id, FILE *llogfp double dependbiom = bm->totfishpop[dependsp_id]; double depend_scalar = FunctGroupArray[species].speciesParams[intersp_depend_scale_id]; double ans = 0.0; - + if (depend_type == intersp_linear) { // Directly proportional ans = depend_scalar * dependbiom; } else if (depend_type == intersp_inverse) { // Indirectly proportional @@ -1606,7 +1606,7 @@ double Get_Enviro_Recruit_Forcing(MSEBoxModel *bm, int species, int do_debug, FI double Tscalar = 1.0; double recCcorr = 1.0; //int recruit_sp = (int) (FunctGroupArray[species].speciesParams[flagrecruit_id]); - + if(!bm->flagtempdepend_reprod) { // Have turned off temperature dependent movement if(temp_sensitive_sp && bm->newmonth) { warn("Time: %e Zeroing temperature sensitivity for reproduction of %s even though flagtempsensitive %d as flagtempdepend_move = %d\n", bm->dayt, FunctGroupArray[species].groupCode, temp_sensitive_sp, bm->flagtempdepend_move); @@ -1705,7 +1705,7 @@ double Get_Enviro_Recruit_Forcing(MSEBoxModel *bm, int species, int do_debug, FI FunctGroupArray[species].groupCode, H2Otemp, min_spawntemp_sp, max_spawntemp_sp, current_SALT, min_spawnsalt_sp, max_spawnsalt_sp); } **/ - + return enviro_scalar; } @@ -1713,15 +1713,15 @@ double Get_Recruit_Size_Forcing(MSEBoxModel *bm, int species, int do_debug, FILE int KWSRforceid = (int) (FunctGroupArray[species].speciesParams[KWSRforce_id]); double KWSR_sp = FunctGroupArray[species].speciesParams[KWSR_id]; double KWSR_force = 0.0; - + /* Forcing */ if (bm->flag_modify_KWSR && (KWSRforceid > -1)) { KWSR_force = tsEval(bm->KWSR_force, KWSRforceid, bm->t); - + if (bm->flag_modify_KWSR == scale_KWSR) KWSR_force *= KWSR_sp; } - + return KWSR_force; } @@ -1736,7 +1736,7 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, double KWRR_sp = FunctGroupArray[species].speciesParams[KWRR_id]; int larval_queue_extension = FunctGroupArray[species].speciesParams[larval_queue_extension_id]; //int cohort_recruit_entry = FunctGroupArray[species].speciesParams[cohort_recruit_entry_id]; - + //fprintf(bm->logFile, "Time: %e %s box%d-%d (vs first_box %d, top_layer %d) numGeneTypes: %d Recruit_Migration recruitType: %d num_in_queue: %d externalReproducer: %d\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, bm->current_layer, bm->first_box, bm->top_layer, sp_numGeneTypes, FunctGroupArray[species].recruitType, MIGRATION[species].num_in_queue, FunctGroupArray[species].externalReproducer); if((FunctGroupArray[species].externalReproducer && (FunctGroupArray[species].recruitType != external_spawn_local_recruit)) || (FunctGroupArray[species].recruitType == external_recruit)) { @@ -1744,9 +1744,9 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, for(ngene = 0; ngene < sp_numGeneTypes; ngene++){ for (mid = 0; mid < MIGRATION[species].num_in_queue; mid++) { - + fprintf(bm->logFile, "Time: %e %s RecruitQueueMatch: %d\n", bm->dayt, FunctGroupArray[species].groupCode, MIGRATION[species].RecruitQueueMatch[mid]); - + if (MIGRATION[species].RecruitQueueMatch[mid] > 0) { if (bm->flag_modify_KWSR) { KWSR_sp = Get_Recruit_Size_Forcing(bm, species, do_debug, llogfp); @@ -1757,7 +1757,7 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, recruit_outside = 0; thisday = EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit]; - + /** if(do_debug) { fprintf(bm->logFile, "Time: %e %s mid: %d Return_Now = %d, Leave_Now = %d, thisday: %d\n", bm->dayt, FunctGroupArray[species].groupCode, mid, MIGRATION[species].Return_Now[mid], MIGRATION[species].Leave_Now[mid], thisday); @@ -1770,7 +1770,7 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, if ( thisday > MIGRATION[species].Return_Now[mid]) continue; // Skip ahead if time is alredy past the migration time /**/ - + /* Outside the model when recruitment happens */ if ((MIGRATION[species].Return_Now[mid] >= thisday) && (MIGRATION[species].Leave_Now[mid] <= thisday)) { recruit_outside = 1; @@ -1778,19 +1778,19 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, FunctGroupArray[species].speciesParams[direct_recruit_entry_id] = 0; direct_recruit_entry = 1; } - + /** //if(do_debug) { if ((species == 26) || (species == 35) || (species == 64)) { fprintf(bm->logFile, "Time: %e %s-%d mid: %d recruit_outside = %d, MIGRATION.recruit = %e (leave: %d return: %d start_return_chrt: %d direct_recruit_entry: %e)\n", bm->dayt, FunctGroupArray[species].groupCode, ngene, mid, recruit_outside, MIGRATION[species].recruit[ngene][mid], MIGRATION[species].Leave_Now[mid], MIGRATION[species].Return_Now[mid], MIGRATION[species].start_return_chrt[mid], FunctGroupArray[species].speciesParams[direct_recruit_entry_id]); } **/ - + if (recruit_outside && (!direct_recruit_entry)) { oldDEN = MIGRATION[species].DEN[ngene][mid]; oldSN = MIGRATION[species].SN[ngene][mid]; oldRN = MIGRATION[species].RN[ngene][mid]; - + embryo_recruits = 0.0; if(larval_queue_extension) { for (lid = 0; lid < larval_queue_extension; lid++) { @@ -1807,19 +1807,19 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, //orig_den = MIGRATION[species].DEN[ngene][mid]; MIGRATION[species].DEN[ngene][mid] += (MIGRATION[species].recruit[ngene][mid] + embryo_recruits); // As all in youngest cohort maps to ngene not cohort in Migration //MIGRATION[species].recruit[ngene][mid] = EMBRYO[species].BulkRecruits[ngene] * enviro_scalar; - + // Update size here too - used to reset to KMIG each year, but that is erroneous MIGRATION[species].SN[ngene][mid] = (oldSN * oldDEN + KWSR_sp * MIGRATION[species].recruit[ngene][mid]) / (MIGRATION[species].recruit[ngene][mid] + oldDEN + small_num); MIGRATION[species].RN[ngene][mid] = (oldRN * oldDEN + KWRR_sp * MIGRATION[species].recruit[ngene][mid]) / (MIGRATION[species].recruit[ngene][mid] + oldDEN + small_num); - + //fprintf(bm->logFile, "Time: %e %s-%d mid: %d now MigDEN: %e as MIGrecruit: %e MigYOY: %e embryo_recruits: %e with SN: %e and RN: %e\n", bm->dayt, FunctGroupArray[species].groupCode, ngene, mid, MIGRATION[species].DEN[ngene][mid], MIGRATION[species].recruit[ngene][mid], MIGRATION[species].MigYOY[ngene][mid], embryo_recruits, MIGRATION[species].SN[ngene][mid], MIGRATION[species].RN[ngene][mid]); if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Get_SettlerMigrant_Contaminants(bm, species, ngene, mid, oldDEN, MIGRATION[species].recruit[ngene][mid]); } - + // Reset now passed across MIGRATION[species].recruit[ngene][mid] = 0; } @@ -1829,7 +1829,7 @@ void Recruit_Migration(MSEBoxModel *bm, int species, int wclayer, int stock_id, } } } - + return; } @@ -1846,23 +1846,23 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro double recruitment_scalar; double hab_scalar = Get_Habitat_Mediated_Recruit_Scalar(bm, species, llogfp); enviro_scalar *= hab_scalar; - + //double KWSR_sp = FunctGroupArray[species].speciesParams[KWSR_id]; //double KWRR_sp = FunctGroupArray[species].speciesParams[KWRR_id]; //double oldDEN, oldSN, oldRN; - + if(EMBRYO[species].SpawnRecruitOverlap && EMBRYO[species].CounterNotDone) qid++; /* Recruitment scaling due to external files - added for Cam for the GOC model */ recruitment_scalar = Ecology_Get_Recruitment_Scalar(bm, species); - + /** if (bm->debug == debug_external_scaling && (bm->which_check == species)) { fprintf(bm->logFile, "Time: %e, External recruitment scaling of group %s in box %d:%d. Scaling - %e. Spawning numbers before scaling = %e, after = %e\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, bm->current_layer, recruitment_scalar, enviro_scalar, enviro_scalar * recruitment_scalar ); } - + if (species == 0){ fprintf(llogfp, "Time: %e %s has qid %d as next_recruit %d SpawnRecruitOverlap %d CounterNotDone %d\n", bm->dayt, FunctGroupArray[species].groupCode, qid, EMBRYO[species].next_recruit, EMBRYO[species].SpawnRecruitOverlap, EMBRYO[species].CounterNotDone); } @@ -1899,7 +1899,7 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro fprintf(llogfp,"Time: %e, %s box%d-%d ngene: %d, qid: %d, totrecruit: %e num_rec: %e (Bulkrecruits: %e, enviro_scalar: %e, vdistrib: %e, hdistrib: %e)\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, wclayer, ngene, qid, totrecruit[species][stock_id][ngene], EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid], EMBRYO[species].BulkRecruits[ngene], enviro_scalar, vertdistrib, bm->recruit_hdistrib[ngene][bm->current_box][species]); } **/ - + break; case external_recruit: if ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer)) { @@ -1910,8 +1910,8 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro if (mid < 0) { // See AlignVsMigration() for how this is set recruit_outside = 0; } - - + + /** thisday = EMBRYO[species].StartDay[ngene][qid]; @@ -1920,7 +1920,7 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro bm->dayt, FunctGroupArray[species].groupCode, ngene, mid, thisday, MIGRATION[species].Leave_Now[mid], MIGRATION[species].Return_Now[mid], recruit_outside); } **/ - + if (recruit_outside) { //oldDEN = MIGRATION[species].DEN[ngene][mid]; //oldSN = MIGRATION[species].SN[ngene][mid]; @@ -1934,7 +1934,7 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro // Update size here too - used to reset to KMIG each year, but that is erroneous //MIGRATION[species].SN[ngene][mid] = (oldSN * oldDEN + KWSR_sp * EMBRYO[species].BulkRecruits[ngene] * enviro_scalar) / (EMBRYO[species].BulkRecruits[ngene] * enviro_scalar + oldDEN + small_num); //MIGRATION[species].RN[ngene][mid] = (oldRN * oldDEN + KWRR_sp * EMBRYO[species].BulkRecruits[ngene] * enviro_scalar) / (EMBRYO[species].BulkRecruits[ngene] * enviro_scalar + oldDEN + small_num); - + /** //if ((species == 64) || (species == 69)) { if (species == 52) { @@ -1947,7 +1947,7 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro MIGRATION[species].recruit[ngene][mid] = 0; EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid] = EMBRYO[species].BulkRecruits[ngene] * enviro_scalar * vertdistrib * bm->recruit_hdistrib[ngene][bm->current_box][species]; totrecruit[species][stock_id][ngene] += EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid]; - + /** //if ((species == 64) || (species == 69)) { fprintf(bm->logFile, "Time: %e %s ngene: %d qid: %d box: %d-%d num_recruit: %e BulkRecruits: %e enviro_scalar: %e vertdistrib: %e hdistrib: %e\n", @@ -1984,13 +1984,13 @@ void Find_Final_Recruit_Distribution(MSEBoxModel *bm, int species, double enviro } EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][qid] = EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid]; - - + + /* Now find the contaminant content */ if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Set_Recruit_Final_Contaminants(bm, wclayer, species, ngene, mid, qid, recruit_outside); } - + /** //if (do_debug && (bm->which_check == species)) { //if (species == 33) { @@ -2061,7 +2061,7 @@ void Sanity_Check_Recruits(MSEBoxModel *bm, int species, FILE *llogfp){ int maxstock_id = FunctGroupArray[species].numStocks; int sp_numGeneTypes = (int) (FunctGroupArray[species].numGeneTypes); int qid = EMBRYO[species].next_larvae; - + if (recruit_sp == fixed_linear_recruit) { for(ij=0; ij < bm->nbox; ij++){ if(bm->boxes[ij].type != BOUNDARY) { @@ -2072,7 +2072,7 @@ void Sanity_Check_Recruits(MSEBoxModel *bm, int species, FILE *llogfp){ } } } - + for ( i = 0; i < maxstock_id; i++) { for(ngene = 0; ngene < sp_numGeneTypes; ngene++){ KDENR_sp = KDENR[species][i]; @@ -2087,7 +2087,7 @@ void Sanity_Check_Recruits(MSEBoxModel *bm, int species, FILE *llogfp){ } } } - + return; } @@ -2107,7 +2107,7 @@ void Store_Recruitment_Diagnostics(MSEBoxModel *bm, int species, int use_aggrega int ngene = 0, i = 0, stock_id = 0, den, k, mid, thisday, recruit_outside = 0; //int stage; int fished_chrt = 0; - + Util_Init_1D_Double(yoy, bm->K_num_max_genetypes, 0.0); /* yoy = young of the year */ @@ -2117,7 +2117,7 @@ void Store_Recruitment_Diagnostics(MSEBoxModel *bm, int species, int use_aggrega KWSR_sp = Get_Recruit_Size_Forcing(bm, species, do_debug, llogfp); KWRR_sp = KWSR_sp * FunctGroupArray[species].X_RS[ngene]; } - + //yoysum += EMBRYO[species].Larvae[i][ngene][qid]; yoy[ngene] += EMBRYO[species].Larvae[i][ngene][qid]; if (use_aggregate) { @@ -2125,19 +2125,19 @@ void Store_Recruitment_Diagnostics(MSEBoxModel *bm, int species, int use_aggrega } else { tot_yoy[species][i] = (EMBRYO[species].Larvae[i][ngene][qid] * (KWRR_sp + KWSR_sp)); } - + if(FunctGroupArray[species].externalReproducer){ for (mid = MIGRATION[species].num_in_queue_done; mid < MIGRATION[species].num_in_queue; mid++) { recruit_outside = 0; - + thisday = EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit]; //stage = FunctGroupArray[species].cohort_stage[ngene]; - + /* Outside the model when recruitment happens */ if ((MIGRATION[species].Return_Now[mid] >= thisday) && (MIGRATION[species].Leave_Now[mid] <= thisday)) { recruit_outside = 1; } - + if (recruit_outside) { tot_yoy[species][i] += MIGRATION[species].recruit[ngene][mid] * (KWRR_sp + KWSR_sp); } @@ -2223,11 +2223,11 @@ void Store_Recruitment_Diagnostics(MSEBoxModel *bm, int species, int use_aggrega bm->calcTrackedMort[species][ngene][k][ongoingF_id] = 0.0; bm->calcTrackedMort[species][ngene][k][start_id] = 0.0; - + if (!k) { FunctGroupArray[species].min_B[ngene] = MAXDOUBLE; FunctGroupArray[species].max_B[ngene] = MINDOUBLE; - + if(FunctGroupArray[species].groupAgeType == AGE_STRUCTURED) { FunctGroupArray[species].min_wgt[ngene] = MAXDOUBLE; FunctGroupArray[species].max_wgt[ngene] = MINDOUBLE; @@ -2284,7 +2284,7 @@ void Store_Recruitment_Diagnostics(MSEBoxModel *bm, int species, int use_aggrega /* Set starting cohort size for pseduo assessment */ bm->calcNstart[species][expect_id] = biomass; bm->calcNstartPerPred[species][expect_id] = biomass; - + // Mark diet updated FunctGroupArray[species].updatedDiet = 1; @@ -2308,11 +2308,11 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * //int do_debug2; int sp_checkday = (int)(bm->dayt); *recruits_arrive = 0; - + if(verbose) { printf("Doing Get_Settlers for %s\n", FunctGroupArray[species].groupCode); } - + /* If recruit within the same year do so now */ for (ngene = 0; ngene < sp_numGeneTypes; ngene ++) { /** @@ -2322,10 +2322,10 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * bm->dayt, FunctGroupArray[species].groupCode, ngene, EMBRYO[species].next_recruit, EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit], EMBRYO[species].EndDay[ngene][EMBRYO[species].next_recruit], sp_checkday, EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit]); } **/ - + if ((sp_checkday >= EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit]) && (sp_checkday < EMBRYO[species].EndDay[ngene][EMBRYO[species].next_recruit])) { Dayj = bm->dayt - EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit]; - + /* Flat recruitment distribution through recruitment period */ if (flagtrecruitdistrib) { recruits_coming = EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit] / EMBRYO[species].RecruitPeriod[EMBRYO[species].next_recruit]; @@ -2350,13 +2350,13 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * } **/ } - + if (FunctGroupArray[species].recruitType == external_recruit) { /* Recruiting into te MIGRATION array */ this_ID = EMBRYO[species].migIDmatch[EMBRYO[species].next_recruit]; MIGRATION[species].recruit[ngene][this_ID] = recruits_coming; FunctGroupArray[species].speciesParams[direct_recruit_entry_id] = 1; - + /** if (species == 33) { fprintf(llogfp, "Time: %e, get settlers %s box%d wclayer: %d num_recruits: %e, period: %e, recruits_coming: %e MIGRATION.recruit[this_ID: %d]: %e\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, wclayer, EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit], EMBRYO[species].RecruitPeriod[EMBRYO[species].next_recruit], recruits_coming, EMBRYO[species].recruitSPden[ngene], this_ID, MIGRATION[species].recruit[ngene][this_ID]); @@ -2366,7 +2366,7 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * } else { /* Recruiting within the model domain */ EMBRYO[species].recruitSPden[ngene] = recruits_coming; - + /** if (species == 33) { fprintf(llogfp, "Time: %e, get settlers %s box%d wclayer: %d num_recruits: %e, period: %e, recruits_coming: %e recruitSPden: %e\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, wclayer, EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit], EMBRYO[species].RecruitPeriod[EMBRYO[species].next_recruit], recruits_coming, EMBRYO[species].recruitSPden[ngene]); @@ -2379,7 +2379,7 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * //EMBRYO[species].Larvae[stock_id][ngene][EMBRYO[species].next_recruit] -= recruits_coming; EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit] -= recruits_coming; *recruits_arrive = 1; - + //fprintf(llogfp, "Time: %e, %s box%d-%d stock %d ngene %d next_reruit: %d setting remaining Larvae: %e\n", bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, wclayer, stock_id, ngene, EMBRYO[species].next_recruit, EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit]); } @@ -2390,26 +2390,26 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * fprintf(llogfp, "Time: %e, %s ngene: %d, qid (next_recruit): %d StartDay: %d, EndDay: %d, sp_checkday: %d, recruitSPden: %e, remaining larvae: %e, num_recruits%d-%d: %e, temprec: %e, RecruitPeriod: %e, flagtrecruitdistrib: %d\n", bm->dayt, FunctGroupArray[species].groupCode, ngene, EMBRYO[species].next_recruit, EMBRYO[species].StartDay[ngene][EMBRYO[species].next_recruit], EMBRYO[species].EndDay[ngene][EMBRYO[species].next_recruit], sp_checkday, EMBRYO[species].recruitSPden[ngene], EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit], bm->current_box, wclayer, EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit], temprec, EMBRYO[species].RecruitPeriod[EMBRYO[species].next_recruit], flagtrecruitdistrib); } **/ - + if (EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit] < 0.0) { - + /** //if (do_debug && (bm->which_check == species)) { if ((species == 33) || (species == 32)) { fprintf(llogfp,"Time: %e %s stock: %d, ngene: %d, out of larvae in box%d-%d as larvae : %e so larvae RESET\n", bm->dayt, FunctGroupArray[species].groupCode, stock_id, ngene, bm->current_box, bm->current_layer, EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit]); } **/ - + /** Reset EMBRYO information and finalise settling**/ EMBRYO[species].num_recruits_updating[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit] = 0.0; EMBRYO[species].EndDay[ngene][EMBRYO[species].next_recruit] = bm->dayt + 1; - + } if (FunctGroupArray[species].speciesParams[firstrecday_id]) { EMBRYO[species].recruiting_now = 1; } - + } else { FunctGroupArray[species].speciesParams[firstrecday_id] = 1; EMBRYO[species].recruitSPden[ngene] = 0.0; @@ -2421,7 +2421,7 @@ void Get_Settlers(MSEBoxModel *bm, int species, int wclayer, int stock_id, int * **/ } - + if(bm->track_contaminants && bm->flag_contamMaternalTransfer){ Get_Settler_Contaminants(bm, wclayer, species, ngene, EMBRYO[species].next_recruit, EMBRYO[species].recruitSPden[ngene]); } @@ -2443,12 +2443,12 @@ void Init_Aging_Arrays(MSEBoxModel *bm, int species, int stock_id, int maxstock_ int sp_ddepend_move = (int)(FunctGroupArray[species].speciesParams[ddepend_move_id]); int sp_AgeClassSize = FunctGroupArray[species].ageClassSize; int qid; - + /* if(verbose) printf(" Doing Init_Aging_Arrays - %s current_box %d first_box %d current_layer %d top_layer %d\n", FunctGroupArray[species].groupCode, bm->current_box, bm->first_box, bm->current_layer, bm->top_layer); */ - + /* Initialise aging arrays - once if no site attachment, per box if there is site_attachment */ if ((bm->current_box == bm->first_box) && (bm->current_layer == bm->top_layer)) { for (cohort = 0; cohort < FunctGroupArray[species].numCohortsXnumGenes; cohort++) { @@ -2457,21 +2457,21 @@ void Init_Aging_Arrays(MSEBoxModel *bm, int species, int stock_id, int maxstock_ FunctGroupArray[species].agingVERT[cohort][i][DEN_id] = 0.0; FunctGroupArray[species].agingVERT[cohort][i][SN_id] = 0.0; FunctGroupArray[species].agingVERT[cohort][i][RN_id] = 0.0; - + /* if (species == 22) { fprintf(llogfp,"Time: %e %s-%d stock %d agingVERT zeroed\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, i); } */ } - + if (sp_ddepend_move != 1) { for (nc = 0; nc < sp_AgeClassSize; nc++) { bm->tempPopRatio[i][species][cohort][nc] = 0.0; } } } - + for (qid = MIGRATION[species].num_in_queue_done; qid < MIGRATION[species].num_in_queue; qid++) { MIGRATION[species].aging[cohort][qid] = 0.0; } @@ -2507,7 +2507,7 @@ double Get_Proportion_Aging(MSEBoxModel *bm, int species, int cohort, int do_deb p_ageup = 1.0 / sp_AgeSize; if (p_ageup > 1.0) p_ageup = 1.0; - + } else { /* If non-homogeneous distribution, determine proportion to age-up */ i = (int) (sp_AgeSize - 1); @@ -2523,7 +2523,7 @@ double Get_Proportion_Aging(MSEBoxModel *bm, int species, int cohort, int do_deb if (do_debug && (bm->which_check == species)) { fprintf(llogfp, "Time: %e p_ageup: %e sp: %s cohort: %d boxPopRatio: %e sp_AgeSize: %e\n", bm->dayt, p_ageup, FunctGroupArray[species].groupCode, cohort, FunctGroupArray[species].boxPopRatio[bm->current_box][bm->current_layer][cohort][i], sp_AgeSize); **/ - + if ((p_ageup < 0) || (!_finite(p_ageup)) || (p_ageup > 1)){ fprintf(llogfp, "p_ageup: %e, sp: %s, cohort: %d, i: %d is IMPOSSIBLE?! (boxPopRatio[%d][%d][%d][%d]: %e)\n", p_ageup, FunctGroupArray[species].groupCode, cohort, i, bm->current_box, bm->current_layer, cohort, i, FunctGroupArray[species].boxPopRatio[bm->current_box][bm->current_layer][cohort][i]); quit("p_ageup: %e, sp: %s, cohort: %d, i: %d is IMPOSSIBLE?! (boxPopRatio[%d][%d][%d][%d]: %e)\n", p_ageup, FunctGroupArray[species].groupCode, cohort, i, @@ -2565,7 +2565,7 @@ double Get_Numbers_Aging(MSEBoxModel *bm, int species, int cohort, int *active_d FunctGroupArray[species].groupCode, cohort, shiftVERT[species][cohort][DEN_id], num_aging, VERTinfo[species][cohort][DEN_id]); } **/ - + // Find number aging into the age-gene bin (well it will be age+1 but the +1 transition is done in Update_Aging_Numbers() to be consistent with non-evolution case dennow = 0.0; for (ng = 0; ng < FunctGroupArray[species].numGeneTypes; ng++){ @@ -2607,7 +2607,7 @@ double Get_Numbers_Aging(MSEBoxModel *bm, int species, int cohort, int *active_d shiftVERTON[species][cohort]); } **/ - + // Used to assume that as iterating down last lostden was for the youngest ageclass, // now storing it explicitly, just to be safe (and storing one value per gene type - see lostden_zero). if(lostden > 0) @@ -2678,7 +2678,7 @@ void Update_Aging_Numbers(MSEBoxModel *bm, int species, int cohort, int stock_id fprintf(llogfp, "Time: %e, box%d-%d %s-chrt_aged_into %d stock: %d, agingDEN: %e, agingSN: %e, agingRN: %e dennow: %e\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, nextcid, stock_id, FunctGroupArray[species].agingVERT[nextcid][stock_id][DEN_id], FunctGroupArray[species].agingVERT[nextcid][stock_id][SN_id], FunctGroupArray[species].agingVERT[nextcid][stock_id][RN_id], dennow); } **/ - + if(bm->track_contaminants){ Age_Contaminants_Store(bm, species, cohort, nextcid, dennow, this_p_ageup); } @@ -2715,11 +2715,11 @@ void Update_Migration_Array(MSEBoxModel *bm, int species, int cohort, int maxsto //double mxs = (double)(maxstock_id); //do_debug = 1; - + if ((bm->current_box != bm->first_box) || (bm->current_layer != bm->top_layer)){ return; // As only want to do this once } - + /* Have replaced previous detailed and somewhat painful handling of aging in the MIGRATION array by having single entry per migration queue rather than trying to overload per cohort */ if (spmigrate) { if (FunctGroupArray[species].isVertebrate == TRUE){ @@ -2735,17 +2735,17 @@ void Update_Migration_Array(MSEBoxModel *bm, int species, int cohort, int maxsto } else { p_ageup = shiftVERT[species][cohort][RN_id]; // p_ageup stored here for biomass pool age structured groups } - + oldden = MIGRATION[species].DEN[nextcid][qid]; oldSN = MIGRATION[species].SN[nextcid][qid]; oldRN = MIGRATION[species].RN[nextcid][qid]; - + newSN = MIGRATION[species].SN[cohort][qid]; newRN = MIGRATION[species].RN[cohort][qid]; num_aging = (p_ageup * MIGRATION[species].DEN[cohort][qid]); /* Update size - + Start with size scalar - only needed if not using external pop code to update size explicitly */ sizeScalar = 1.0; @@ -2755,47 +2755,47 @@ void Update_Migration_Array(MSEBoxModel *bm, int species, int cohort, int maxsto sizeScalar = 1.0 + (MIGRATION[species].growth[qid] / growth_period); } } - + MIGRATION[species].SN[nextcid][qid] = (oldden * oldSN + num_aging * newSN * sizeScalar) / (oldden + num_aging + small_num); MIGRATION[species].RN[nextcid][qid] = (oldden * oldRN + num_aging * newRN * sizeScalar) / (oldden + num_aging + small_num); - + if(bm->track_contaminants){ Age_MigrantContaminants_Update(bm, species, nextcid, cohort, qid, oldden, num_aging); } - + /* Update numbers */ MIGRATION[species].DEN[nextcid][qid] += num_aging; MIGRATION[species].DEN[cohort][qid] -= num_aging; - + MIGRATION[species].aging[nextcid][qid] = num_aging; - + if (MIGRATION[species].DEN[nextcid][qid] > 0) { MIGRATION[species].cohort_migrating[nextcid][qid] = 1; - } - + } + /* Not doing this as getting double migration - as enter ok, and not checked when leave this is proabably ok if (!MIGRATION[species].cohort_migrating[nextcid][qid]) { MIGRATION[species].cohort_migrating[nextcid][qid] = 1; // Update so allowed to migrate in the movement code } */ - + /** //if (do_debug) { if (species == 33) { fprintf(llogfp,"Time: %e box%d-%d %s-%d qid: %d p_ageup: %e, DEN: %e nextDEN: %e (num_in_queue: %d)\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, cohort, qid, p_ageup, MIGRATION[species].DEN[cohort][qid], MIGRATION[species].DEN[nextcid][qid], MIGRATION[species].num_in_queue); } **/ - + } } else { for (qid = MIGRATION[species].num_in_queue_done; qid < MIGRATION[species].num_in_queue; qid++) { - + if( (FunctGroupArray[species].speciesParams[flagkeep_plusgroup_id] > 0) && (bm->dayt < MIGRATION[species].Return_Now[qid])) { // Do nothing as want to keep a plus group that hasn't returned to the model yet } else { MIGRATION[species].DEN[cohort][qid] *= (1.0 - p_ageup); // So have aging out of system handled } - + /** if (species == 33) { fprintf(llogfp,"Time: %e box%d-%d %s-%d qid: %d p_ageup: %e, DEN: %e\n", bm->dayt, bm->current_box, bm->current_layer, FunctGroupArray[species].groupCode, cohort, qid, p_ageup, MIGRATION[species].DEN[cohort][qid]); @@ -2816,9 +2816,9 @@ void Get_Latest_Additions(MSEBoxModel *bm, int wclayer, int species, int maxstoc int i = 0, nc = 0, cohort = 0, migstock_id = 0, ngene = 0, qid = 0, mxk = 0; //int stage = 0; double sp_AgeClassSize = (double)(FunctGroupArray[species].ageClassSize); - int sp_numGeneTypes = (int) (FunctGroupArray[species].numGeneTypes); + int sp_numGeneTypes = (int) (FunctGroupArray[species].numGeneTypes); Util_Init_1D_Double(coming_SPden, bm->K_num_max_genetypes, 0.0); - + /* Get total settlers that are in the process of arriving */ for ( ngene = 0; ngene < sp_numGeneTypes; ngene++ ){ coming_SPden[ngene] = EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][EMBRYO[species].next_recruit]; @@ -2894,7 +2894,7 @@ void Get_Latest_Additions(MSEBoxModel *bm, int wclayer, int species, int maxstoc } } } - + return; } @@ -2902,7 +2902,7 @@ void Get_Latest_Additions(MSEBoxModel *bm, int wclayer, int species, int maxstoc * \brief Update the Local tracers - the cohort index used to be i in the original code when was all in one routine * */ -void Update_Local_dPool(MSEBoxModel *bm, int species, int cohort, double Spawned_Matter, double *recruitDEN, +void Update_Local_dPool(MSEBoxModel *bm, int species, int cohort, double Spawned_Matter, double *recruitDEN, int sp_numGeneTypes, double *localWCTracers, int do_debug, FILE *llogfp) { int vids = FunctGroupArray[species].structNTracers[cohort]; int vidr = FunctGroupArray[species].resNTracers[cohort]; @@ -2915,7 +2915,7 @@ void Update_Local_dPool(MSEBoxModel *bm, int species, int cohort, double Spawned /** if (do_debug && (bm->which_check == species)) { fprintf(llogfp, "Time: %e, %s-%d starting Pool: %e with SN: %e, RN: %e with shiftden: %e and Spawned_Matter: %e\n", bm->dayt, - FunctGroupArray[species].groupCode, cohort, + FunctGroupArray[species].groupCode, cohort, localWCTracers[vidd], localWCTracers[vids], localWCTracers[vidr], shiftVERT[species][cohort][DEN_id], Spawned_Matter); } **/ @@ -2954,7 +2954,7 @@ void Update_Local_dPool(MSEBoxModel *bm, int species, int cohort, double Spawned } } - + /** if ((do_debug && (shiftVERT[species][cohort][DEN_id] > 0.0)) || (!_finite(localWCTracers[vidd]))) { fprintf(llogfp, "Time: %e %s-%d newPool: %e (%e) with SN: %e RN: %e (Spawned_Matter: %e shiftDEN: %e)\n", @@ -2993,18 +2993,18 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe Util_Init_1D_Int(stock_done, bm->K_num_stocks_per_sp, 0); Util_Init_1D_Double(totsum, bm->K_num_stocks_per_sp, 0.0); Util_Init_1D_Double(totksum, bm->K_num_stocks_per_sp, 0.0); - + /* - + if(((bm->nbox < bm->checkbox) || (bm->current_box == bm->checkbox)) && (bm->dayt > bm->checkstart) && (bm->which_check == species)) do_debug = 1; - + if ((FunctGroupArray[species].numSpawns > 1) || (FunctGroupArray[species].groupType == FISH_INVERT)) do_debug = 1; if (bm->which_check == species) do_debug = 1; - + if((bm->which_check == species) && (bm->dayt >= bm->checkstart)) do_debug = 1; @@ -3183,7 +3183,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe bm->tempPopRatio[stock_id][species][cohort][k] /= totksum[stock_id]; } } - + /* If site attached update local age distribution */ for (k = 0; k < classize; k++) { FunctGroupArray[species].boxPopRatio[bm->current_box][bm->current_layer][cohort][k] = bm->tempPopRatio[stock_id][species][cohort][k]; @@ -3244,7 +3244,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe if(rec_related) bm->tempPopRatio[i][species][cohort][k] = recVERTpopratio[i][species][cohort][k]; totsum[i] += bm->tempPopRatio[i][species][cohort][k]; - + /** if(do_debug){ fprintf(llogfp,"Time: %e step 1 %s-%d stock %d k: %d tempPopRatio: %e (recVERTpopratio: %e) totsum %e allgone: %d\n", @@ -3274,7 +3274,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe if (bm->tempPopRatio[i][species][cohort][k] > maxvalue) maxvalue = bm->tempPopRatio[i][species][cohort][k]; - + /** if(do_debug){ fprintf(llogfp,"Time: %e step 2 %s-%d stock %d k: %d tempPopRatio: %e totsum %e\n", @@ -3304,7 +3304,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe } totksum[i] += bm->tempPopRatio[i][species][cohort][k]; - + /* if(do_debug){ fprintf(llogfp,"Time: %e step 4 %s-%d stock %d classize: %d tempPopRatio: %e totksum %e\n", @@ -3323,11 +3323,11 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe } if (totksum[i] != 1) { - + /* Renormalise */ for (k = 0; k < classize; k++) { bm->tempPopRatio[i][species][cohort][k] /= totksum[i]; - + /** if(do_debug){ fprintf(llogfp,"Time: %e step 5 renormalising %s-%d stock %d classize %d tempPopRatio: %e totksum %e\n", @@ -3352,7 +3352,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe for (b = 0; b < classize; b++) { FunctGroupArray[species].boxPopRatio[ij][k][cohort][b] = bm->tempPopRatio[stock_id][species][cohort][b]; - + if(!_finite(FunctGroupArray[species].boxPopRatio[ij][k][cohort][b])){ quit("boxPopRatio for %s-%d in box%d-%d sub-chort (b) %d is NAN as tempPopRatio for stock_id %d = %e MIGRATIONaging may hold more\n", FunctGroupArray[species].groupCode, cohort, ij, k, b, stock_id, bm->tempPopRatio[stock_id][species][cohort][b]); @@ -3375,7 +3375,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe } } } - + // Update migrators so nhave an appropriate proportion assigned to aging event on return if (MIGRATION[species].num_in_queue > 0) { for (cohort = 0; cohort < NumCohort; cohort++) { @@ -3390,7 +3390,7 @@ void Update_Age_Distrib(MSEBoxModel *bm, int species, int stock_id, int sp_ddepe } } } - + /* If aging alone then ended, if has to recruit also then set flag to -1 to signal already done age distribution recalculation */ @@ -3542,7 +3542,7 @@ void Determine_Stock_Prop(MSEBoxModel *bm, int species, int maxstock_id, int who stock_prop[species][stock_id] += bm->stock_struct_prop[species][n][stock_id] * scale; overall_tot += bm->stock_struct_prop[species][n][stock_id] * scale; } - + } /* Find total amount */ @@ -3633,29 +3633,29 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { //do_debug = 0; //if(species == 7) // do_debug = 1; - + if (FunctGroupArray[species].speciesParams[flag_id] == TRUE && FunctGroupArray[species].isVertebrate == TRUE) { Util_Init_1D_Double(tot_new_mat, bm->K_num_max_cohort * bm->K_num_max_genetypes, 0.0); //Util_Init_1D_Int(mig_status, bm->K_num_max_stages, 0); - + /** if((bm->dayt >= bm->checkstart) && (sp == bm->which_check)) do_debug = 1; else do_debug = 0; - + if (bm->which_check == species) do_debug = 1; - + if ((FunctGroupArray[species].numSpawns > 1) || (FunctGroupArray[species].groupType == FISH_INVERT)) do_debug = 1; - + if((bm->dayt >= bm->checkstart) && (species == bm->which_check)) do_debug = 1; if ((species == 64) || (species == 69)) do_debug = 1; - + if((bm->dayt >= bm->checkstart) && (species == bm->which_check)) do_debug = 1; **/ @@ -3671,7 +3671,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { if(bm->M_est_method == Z_and_F_based) { Record_End_Num(bm, species); } - + /* Initialise aging in general */ for (cohort = 0; cohort < FunctGroupArray[species].numCohortsXnumGenes; cohort++) { for (k = 0; k < maxstock; k++) { @@ -3708,11 +3708,11 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { /* Determine proportion of the population that is currently outside the model domain */ if (sp_mignum) { - + // Was for (cohort = (((FunctGroupArray[species].numCohorts - 1) * FunctGroupArray[species].numGeneTypes) - 1); cohort > -1 ; cohort--) // I think can actually be as written below but keeping it here for reference just in case - - + + for (cohort = FunctGroupArray[species].numCohortsXnumGenes - 1; cohort > -1 ; cohort--) { // Running backwards so don't need embedded stage check to see different migration status for mig_status (if run forward then get wrong answer for young_in_old_out as not done the later stages when do the younger finalmig = 0; avgsn = 0; @@ -3722,36 +3722,36 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { nextcid = cid + FunctGroupArray[species].numGeneTypes; //stage = FunctGroupArray[species].cohort_stage[cohort]; //next_stage = FunctGroupArray[species].cohort_stage[nextcid]; - + // For each migration group? num_in_MIG_total = 0.0; for (qid = MIGRATION[species].num_in_queue_done; qid < MIGRATION[species].num_in_queue; qid++) { num_in_MIG = MIGRATION[species].DEN[cohort][qid]; num_in_MIG_total += MIGRATION[species].DEN[cohort][qid]; - + // Does prop_mig[cohort] have to be handled as migration_den[cohort+1] - as put against agingDEN which already cast to [cohort+1]? I don't think so as called form main loop so aging will have happened already on previous iteration of the model // #TODO: check this assumption re cohort vs cohrot+1 MIGRATION[species].prop_mig[cohort][qid] = num_in_MIG / (totden[species][cohort] + num_in_MIG + small_num); } - + MIGRATION[species].totprop_mig[cohort] += num_in_MIG_total / (totden[species][cohort] + num_in_MIG_total + small_num); - + if (MIGRATION[species].totprop_mig[cohort] > 1.0) MIGRATION[species].totprop_mig[cohort] = 1.0; /* Allocate those who would age-up into an age class outside the model domain to the Migration array. Only do this if juveniles becoming adults and one away while the other isn't - + Do allocation of aging into Migration array only when appropriate - i.e. juveniles in model domain and adults not. If both outside model domain then code in Update_Migration_Array() will handle it. Also if juveniles are outside the domain and the adults are inside then this is dealt with in Update_Migration_Array() too - see logic discussion in Update_Migration_Array() - + By default mat_transition_thresh should be something high like 0.99 and juv_transition_thresh something lower like 0.1 or 0.5 etc, so this only comes into play when the majority of the adult popualtion is outside the model and juveniles not, but made them variables so more easily adjusted as needed - + */ if ((cohort < age_mat) && (nextcid >= age_mat)) { if ((MIGRATION[species].totprop_mig[cohort] < bm->juv_transition_thresh) && (MIGRATION[species].totprop_mig[nextcid] > bm->mat_transition_thresh)) { @@ -3762,11 +3762,11 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { fprintf(llogfp, "Time: %e, Looking at %s-%d with totprop_mig-%d (juv) %e totprop_mig-%d (mat): %e juv_transition_thresh: %e mat_transition_thresh: %e\n", bm->dayt, FunctGroupArray[species].groupCode, cohort, MIGRATION[species].totprop_mig[cohort], MIGRATION[species].totprop_mig[nextcid],bm->juv_transition_thresh, bm->mat_transition_thresh); } **/ - + // #TODO: Do we need to use MIGRATION[species].all_go[cohort][qid] here? if (FunctGroupArray[species].agingVERT[cohort][k][DEN_id] > 0) { warn("Juveniles have to suddenly flee domain as age for %s (time: %e)\n", FunctGroupArray[species].groupCode, bm->dayt); // Warngin as doesn't really make sense to have to do this - + for (k = 0; k < maxstock; k++) { oldden = MIGRATION[species].DEN[nextcid][qid]; oldSN = MIGRATION[species].SN[nextcid][qid]; @@ -3818,7 +3818,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { **/ } } - + /* Apply newly mature individuals accordingly */ //totsum = 0; for (cohort = 1; cohort < FunctGroupArray[species].numCohortsXnumGenes; cohort++) { @@ -3835,7 +3835,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { denup = (1.0 - MIGRATION[species].totprop_mig[cohort]) * FunctGroupArray[species].agingVERT[cohort][stock_id][DEN_id] * FunctGroupArray[species].AGEnewden[cohort][0][ij] * spSTOCKprop[stock_id][cohort] / AGE_stock_struct_prop[species][cohort][stock_id]; - + if (denup < 0.0) denup = 0.0; @@ -3849,7 +3849,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { bm->boxes[ij].tr[0][rn] = (dennow * rnnow + FunctGroupArray[species].agingVERT[cohort][stock_id][RN_id] * denup) / nextden; } bm->boxes[ij].tr[0][den] = nextden; - + if ((do_debug) || (!_finite(bm->boxes[ij].tr[0][den]))) { fprintf(llogfp, "Update1-Land Time: %e, box%d-%d %s-chrt%d, dennow: %e, snnow: %e, aging-stock%d-SN: %e, denup: %e, nextden: %e\n", bm->dayt, ij, 0, FunctGroupArray[species].groupCode, cohort, dennow, snnow, stock_id, @@ -3862,7 +3862,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { FunctGroupArray[species].groupCode, cohort, bm->boxes[ij].tr[0][den] / (dennow + small_num), bm->boxes[ij].tr[0][sn] / snnow, bm->boxes[ij].tr[0][rn] / rnnow); } - + if((!_finite(bm->boxes[ij].tr[0][den]))){ quit("Ecology_Update_Vert_Cohorts %s-%d has nan numbers in box %d-%d\n", FunctGroupArray[species].groupCode, cohort, ij, 0); } @@ -3879,7 +3879,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { bm->boxes[ij].tr[0][sn] = snnow; if (sp_AgeSize < 1 && bm->boxes[ij].tr[0][rn] < bm->min_pool * 10.0) bm->boxes[ij].tr[0][rn] = rnnow; - + /* Note that age distributions have already been updated in Vertebrate_Reproduction */ } else if (bm->boxes[ij].type != BOUNDARY) { @@ -3914,7 +3914,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { if (denup < 0.0) denup = 0.0; - + nextden = bm->boxes[ij].tr[k][den] + denup + small_num; dennow = bm->boxes[ij].tr[k][den]; snnow = bm->boxes[ij].tr[k][sn]; @@ -3923,7 +3923,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { if (nextden > 0 && MIGRATION[species].totprop_mig[cohort] < 0.99) { bm->boxes[ij].tr[k][sn] = (dennow * snnow + FunctGroupArray[species].agingVERT[cohort][stock_id][SN_id] * denup) / nextden; bm->boxes[ij].tr[k][rn] = (dennow * rnnow + FunctGroupArray[species].agingVERT[cohort][stock_id][RN_id] * denup) / nextden; - + if(bm->track_contaminants){ Age_Contaminants_Update(bm, species, cohort, denup, dennow, nextden, ij, k); } @@ -3944,7 +3944,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { if((!_finite(bm->boxes[ij].tr[k][den])) || (bm->boxes[ij].tr[k][den] < 0.0)){ quit("Ecology_Update_Vert_Cohorts %s-%d has nan numbers or is a negative in box %d-%d\n", FunctGroupArray[species].groupCode, cohort, ij, k); } - + /** //if ((species == 64) || (species == 69)) { //if (species == 22) { @@ -3974,7 +3974,7 @@ void Ecology_Update_Vertebrate_Cohorts(MSEBoxModel *bm, FILE *llogfp) { bm->boxes[ij].tr[k][sn] = snnow; if (sp_AgeSize < 1 && bm->boxes[ij].tr[k][rn] < bm->min_pool * 10.0) bm->boxes[ij].tr[k][rn] = rnnow; - + /* Note that age distributions have already been updated in Vertebrate_Reproduction */ } } @@ -4027,7 +4027,7 @@ void Record_End_Num(MSEBoxModel *bm, int species) { int ij, k, cohort, stock_id, den, fished_chrt; double chrt_biomass; double biomass = 0.0; - + for(cohort = FunctGroupArray[species].numGeneTypes; cohortcalcTrackedMort[species][cohort][stock_id][endNum_id] = 0.0; } - + if(FunctGroupArray[species].groupAgeType == AGE_STRUCTURED) { den = FunctGroupArray[species].NumsTracers[cohort]; for (ij = 0; ij < bm->nbox; ij++) { @@ -4045,9 +4045,9 @@ void Record_End_Num(MSEBoxModel *bm, int species) { for (k = 0; k < bm->boxes[ij].nz; k++) { if (fished_chrt == cohort ) biomass += bm->boxes[ij].tr[k][den]; - + stock_id = bm->group_stock[species][ij][k]; - + bm->calcTrackedMort[species][cohort][stock_id][endNum_id] += bm->boxes[ij].tr[k][den]; } } @@ -4057,15 +4057,15 @@ void Record_End_Num(MSEBoxModel *bm, int species) { for (ij = 0; ij < bm->nbox; ij++) { // Loop through each pelagic layer for (k = 0; k < bm->boxes[ij].nz; k++) { - + stock_id = bm->group_stock[species][ij][k]; - + chrt_biomass = bm->boxes[ij].tr[k][den] * bm->boxes[ij].dz[k] * bm->boxes[ij].area * FunctGroupArray[species].habitatCoeffs[WC]; bm->calcTrackedMort[species][cohort][stock_id][endNum_id] += chrt_biomass; } // Set relk for sediment and epibenthos by assuming its the one in deepest vertical layer stock_id = bm->group_stock[species][ij][0]; // As assuming k = 0 - + // Loop through each sediment layer for (k = 0; k < bm->boxes[ij].sm.nz; k++) { chrt_biomass = bm->boxes[ij].sm.tr[k][den] * bm->boxes[ij].sm.dz[k] * bm->boxes[ij].area * FunctGroupArray[species].habitatCoeffs[SED]; @@ -4079,7 +4079,7 @@ void Record_End_Num(MSEBoxModel *bm, int species) { } } } - + return; } @@ -4146,17 +4146,17 @@ void Reset_Mortality(MSEBoxModel *bm, int species) { bm->calcTrackedPredMort[species][cohort][k][pred][final_id] = bm->calcTrackedPredMort[species][cohort][k][pred][ongoing_id] / (bm->calcTrackedMort[species][cohort][k][start_id] + small_num); bm->calcTrackedPredMort[species][cohort][k][pred][ongoing_id] = 0.0; } - + bm->calcTrackedMort[species][cohort][k][ongoingM1_id] = 0.0; bm->calcTrackedMort[species][cohort][k][ongoingM2_id] = 0.0; bm->calcTrackedMort[species][cohort][k][ongoingF_id] = 0.0; bm->calcTrackedMort[species][cohort][k][start_id] = 0.0; - + if (!k) { FunctGroupArray[species].min_B[cohort] = MAXDOUBLE; FunctGroupArray[species].max_B[cohort] = MINDOUBLE; - + if(FunctGroupArray[species].groupAgeType == AGE_STRUCTURED) { FunctGroupArray[species].min_wgt[cohort] = MAXDOUBLE; FunctGroupArray[species].max_wgt[cohort] = MINDOUBLE; @@ -4211,7 +4211,7 @@ void Reset_Mortality(MSEBoxModel *bm, int species) { } bm->calcNstart[species][expect_id] = biomass; bm->calcNstartPerPred[species][expect_id] = biomass; - + FunctGroupArray[species].updatedDiet = 2; return; @@ -4256,10 +4256,10 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to do_debug = 1; } else do_debug = 0; - + //if(((bm->current_box == bm->checkbox) || (bm->dayt >= bm->checkstart)) && (bm->which_check == species)) // do_debug = 1; - + //if (bm->which_check == species) // do_debug = 1; @@ -4334,10 +4334,10 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to /* if (do_debug && (bm->which_check == species)) - fprintf(llogfp, "day %d, %s-%d box: %d-%d starting_biom: %e, sp_Spawn_Now = %d, sp_Age_Now: %d, spawn_day: %d, age_day: %d, overall_checkday: %d, sp_spawnday: %d, additional_day: %d, stuff_to_do: %d\n", + fprintf(llogfp, "day %d, %s-%d box: %d-%d starting_biom: %e, sp_Spawn_Now = %d, sp_Age_Now: %d, spawn_day: %d, age_day: %d, overall_checkday: %d, sp_spawnday: %d, additional_day: %d, stuff_to_do: %d\n", overall_checkday, FunctGroupArray[species].groupCode, cohort, bm->current_box, bm->current_layer, this_biom, sp_Spawn_Now, sp_Age_Now, EMBRYO[species].Spawn_Now[cohort][EMBRYO[species].next_spawn], EMBRYO[species].Age_Now[cohort][EMBRYO[species].next_age], overall_checkday, sp_spawnday, additional_day, stuff_to_do); */ - + if (!sp_Spawn_Now && !sp_Age_Now && !stuff_to_do) { /* Not spawning or aging now so don't do anything */ continue; @@ -4362,7 +4362,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if (do_debug && (bm->which_check == species)) fprintf(llogfp, "%s-%d box: %d-%d, spawning_biomass = %e spawn_active: %e this_biom: %e, scaled_FSPB: %e\n", FunctGroupArray[species].groupCode, cohort, bm->current_box, bm->current_layer, spawning_biomass, spawn_active, this_biom, FunctGroupArray[species].scaled_FSPB[cohort]); */ - + /* Spawning - internal to model domain */ Ecology_Find_Invert_Spawn(bm, species, spawning_biomass, stock_id, plankton, CHLa, llogfp); @@ -4377,7 +4377,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if (do_debug && (bm->which_check == species)) fprintf(llogfp, "%s-%d box: %d-%d, overall_checkday: %d, sp_spawnday: %d, additional_day: %d\n", FunctGroupArray[species].groupCode, cohort, bm->current_box, bm->current_layer, overall_checkday, sp_spawnday, additional_day); */ - + /* Reset spawning readiness - can't do it at the time due to multiple layer handling */ if (overall_checkday == (sp_spawnday + additional_day)) { EMBRYO[species].readytospawn[stock_id] = 2; // Reset so ready for next spawning event (now this one is done) @@ -4392,7 +4392,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if (do_debug && (bm->which_check == species)) fprintf(llogfp, "%s-%d box: %d-%d, spawned_biomass = %e ", FunctGroupArray[species].groupCode, cohort, bm->current_box, bm->current_layer, spawned_biomass); */ - + /* Check for environmental effects */ enviro_scalar = 1.0; enviro_scalar = Get_Enviro_Recruit_Forcing(bm, species, do_debug, llogfp); @@ -4402,7 +4402,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if (do_debug && (bm->which_check == species)) fprintf(llogfp, "enviro_scalar = %e ", enviro_scalar); */ - + /* Check for vertical distribution of new recruits */ if (FunctGroupArray[species].recruitType) { vertdistrib = 1.0; @@ -4423,7 +4423,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if (do_debug && (bm->which_check == species)) fprintf(llogfp, "vertdistrib = %e\n", vertdistrib); */ - + Find_Final_Invert_Recruit_Distribtuion(bm, species, ngene, qid, stock_id, spawned_biomass, wclayer, llogfp); /* Update yoy sum - only if localised recruit as all other cases done in Store_Recruitment_Diagnostics() */ @@ -4477,7 +4477,7 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to if(bm->M_est_method == Z_and_F_based) { Record_End_Num(bm, species); } - + Init_Aging_Arrays(bm, species, stock_id, maxstock_id, llogfp); /* Add the cohort that is maturing (if senescent they will just age out of the system and die) */ @@ -4493,10 +4493,10 @@ void Invertebrate_Reproduction(MSEBoxModel *bm, int wclayer, int maxdeep, int to /* if (do_debug && (bm->which_check == species)) - fprintf(llogfp," %s-%d (bc %d vs nc %d) biomass_newly_mature: %e, this_biom: %e, p_ageup: %e\n", + fprintf(llogfp," %s-%d (bc %d vs nc %d) biomass_newly_mature: %e, this_biom: %e, p_ageup: %e\n", FunctGroupArray[species].groupCode, cohort, basecohort, num_cohorts, biomass_newly_mature, this_biom, p_ageup); */ - + /* Did something */ did_something = 1; } @@ -4611,7 +4611,7 @@ void Ecology_Find_Invert_Spawn(MSEBoxModel *bm, int species, double spawning_bio boxkey_id = bm->BoxKeyMap[bm->current_box][rects_key_id]; EMBRYO[species].Larvae[stock_id][ngene][qid] += Get_Imposed_MultRecruits(bm, species, do_debug, boxkey_id, llogfp); } - + if (FunctGroupArray[species].recruitType) EMBRYO[species].Larvae[stock_id][ngene][qid] = local_spawn_biomass; // Local biomass sets the number of recruits else @@ -4685,7 +4685,7 @@ double Ecology_Find_Invert_Recruits(MSEBoxModel *bm, int species, int ngene, int stock_scalar1 = recSTOCK[species][stock_id]; pop_spawning_biomass = bm->totfishpop[species] * stock_prop[species][stock_id]; } - + //if (bm->which_check == species) // do_debug = 1; @@ -4740,7 +4740,7 @@ double Ecology_Find_Invert_Recruits(MSEBoxModel *bm, int species, int ngene, int // force_recover_recruit); break; case Ricker_recruit: /* Ricker */ - case SSB_ricker: /* SSB based ricker version - for senescent and short lived species */ + case SSB_ricker: /* SSB based ricker version - for senescent and short lived species */ spawned_biomass = pop_spawning_biomass * exp(stock_scalar1 * Ralpha_sp * (1.0 - pop_spawning_biomass / Rbeta_sp)); break; case jackknife_recruit: /* Jackknife spawning function - sum up spawning stock biomass */ @@ -4766,7 +4766,7 @@ double Ecology_Find_Invert_Recruits(MSEBoxModel *bm, int species, int ngene, int step1 = spawned_biomass; spawned_biomass = Util_Normx_Result(step1, norm_sigma); } - + if (do_debug && (bm->which_check == species)) fprintf(llogfp,"%s has recruit_sp: %d, spawned_biomass %e\n", FunctGroupArray[species].groupCode, recruit_sp, spawned_biomass); @@ -4830,7 +4830,7 @@ void Ecology_Update_Invert_Cohorts(MSEBoxModel *bm, FILE *llogfp) { bm->calcTrackedMort[species][n][k][ongoingM2_id] = 0.0; bm->calcTrackedMort[species][n][k][ongoingF_id] = 0.0; bm->calcTrackedMort[species][n][k][start_id] = 0.0; - + FunctGroupArray[species].min_B[n] = MAXDOUBLE; FunctGroupArray[species].max_B[n] = MINDOUBLE; @@ -4864,7 +4864,7 @@ void Ecology_Update_Invert_Cohorts(MSEBoxModel *bm, FILE *llogfp) { } bm->calcNstart[species][expect_id] = biomass; bm->calcNstartPerPred[species][expect_id] = biomass; - + FunctGroupArray[species].updatedDiet = 1; } @@ -4876,10 +4876,10 @@ void Ecology_Update_Invert_Cohorts(MSEBoxModel *bm, FILE *llogfp) { FunctGroupArray[species].speciesParams[need_matupdate_id] = 0; } } - + } } - + return; } @@ -4907,7 +4907,7 @@ void Find_Final_Invert_Recruit_Distribtuion(MSEBoxModel *bm, int species, int ng EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid] = hab_scalar * spawned_biomass * bm->recruit_hdistrib[ngene][bm->current_box][species]; totrecruit[species][stock_id][ngene] += EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid]; - + /* if(EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid] > 0){ fprintf(llogfp,"Time: %e box%d-%d %s ngene: %d, qid: %d, num_rec: %e, hab_scalar: %e, spawned_biomass: %e, hdistrib: %e, totrecruit: %e\n", @@ -4919,7 +4919,7 @@ void Find_Final_Invert_Recruit_Distribtuion(MSEBoxModel *bm, int species, int ng case at_parent_location: EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid] = hab_scalar * spawned_biomass; totrecruit[species][stock_id][ngene] += EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid]; - + /* fprintf(llogfp,"Time: %e box%d-%d %s ngene: %d, qid: %d, num_rec: %e, hab_scalar: %e, spawned_biomass: %e, totrecruit: %e\n", bm->dayt, bm->current_box, wclayer, FunctGroupArray[species].groupCode, ngene, qid, EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid], @@ -4938,7 +4938,7 @@ void Find_Final_Invert_Recruit_Distribtuion(MSEBoxModel *bm, int species, int ng //thisday = (double)(EMBRYO[species].Spawn_Now[cohort][EMBRYO[species].next_spawn]); thisday = (double)EMBRYO[species].StartDay[cohort][EMBRYO[species].next_recruit]; //pid = FunctGroupArray[species].cohort_stage[cohort]; - + /* Recruit while outside the model */ if ((MIGRATION[species].Return_Now[mid] >= thisday) && (MIGRATION[species].Leave_Now[mid] <= thisday)) { recruit_outside = 1; @@ -4950,7 +4950,7 @@ void Find_Final_Invert_Recruit_Distribtuion(MSEBoxModel *bm, int species, int ng } else { MIGRATION[species].recruit[ngene][mid] = 0; } - + /** if ((species == 26) || (species == 35) || (species == 64)) { fprintf(llogfp,"Time: %e box%d-%d %s ngene: %d, mid: %d, MIGden: %e, MIGrecruit: %e, hab_scalar: %e, spawned_biomass: %e, totrecruit: %e\n", @@ -4987,8 +4987,8 @@ void Find_Final_Invert_Recruit_Distribtuion(MSEBoxModel *bm, int species, int ng break; } /* - fprintf(llogfp,"%s case: %d, qid: %d, spawned_biomass: %e, num_rec: %e\n", - FunctGroupArray[species].groupCode,FunctGroupArray[species].recruitType, qid, spawned_biomass, + fprintf(llogfp,"%s case: %d, qid: %d, spawned_biomass: %e, num_rec: %e\n", + FunctGroupArray[species].groupCode,FunctGroupArray[species].recruitType, qid, spawned_biomass, EMBRYO[species].num_recruits[bm->current_box][wclayer][ngene][qid]); */ } @@ -5031,7 +5031,7 @@ void Update_Invert_Aging(MSEBoxModel *bm, double *localWCTracers, int species, i /* for (i = 0; i < FunctGroupArray[species].numCohortsXnumGenes; i++) { - fprintf(llogfp, "Time: %e %s-%d box%d-%d biom_start: %e\n", + fprintf(llogfp, "Time: %e %s-%d box%d-%d biom_start: %e\n", bm->dayt, FunctGroupArray[species].groupCode, i, bm->current_box, bm->current_layer, localWCTracers[FunctGroupArray[species].totNTracers[i]]); } */ @@ -5112,12 +5112,12 @@ void Update_Invert_Aging(MSEBoxModel *bm, double *localWCTracers, int species, i } } */ - + /* Lose those aging up and any contributions to spawning */ localWCTracers[FunctGroupArray[species].totNTracers[cohort]] -= ((biomass_newly_mature + spawning_biomass_contrib) / tracer_correction); /* Gain newly aged up * Note: Originally had no terminal entry below just skipped this addition if (basecohort == num_cohorts) - * However added in terminal age class step below so can have multi-year age cohorts for biomass pools + * However added in terminal age class step below so can have multi-year age cohorts for biomass pools */ localWCTracers[FunctGroupArray[species].totNTracers[nextcid]] += (biomass_newly_mature / tracer_correction); /* Gain new recruits */ @@ -5136,7 +5136,7 @@ void Update_Invert_Aging(MSEBoxModel *bm, double *localWCTracers, int species, i bm->dayt, FunctGroupArray[species].groupCode, bm->current_box, bm->current_layer, cohort, ngene, sp_numGeneTypes, nextcid, new_settled_biomass/tracer_correction, biomass_newly_mature/tracer_correction, biomass_terminal_class/tracer_correction, spawning_biomass_contrib/tracer_correction); for (i = 0; i < FunctGroupArray[species].numCohortsXnumGenes; i++) { - fprintf(llogfp, "Time: %e %s-%d box%d-%d biom_end: %e\n", + fprintf(llogfp, "Time: %e %s-%d box%d-%d biom_end: %e\n", bm->dayt, FunctGroupArray[species].groupCode, i, bm->current_box, bm->current_layer, localWCTracers[FunctGroupArray[species].totNTracers[i]]); } } @@ -5154,7 +5154,7 @@ void Update_Invert_Cohorts(MSEBoxModel *bm, int species, int stock_id, int maxst int i = 0, k = 0, classize = 1, sp_recruitpeak = 0, cohort = 0, qid; double totksum = 0, sp_recruitRange = 0, this_totsum = 0, maxvalue = 0; double sp_AgeClassSize = (double)(FunctGroupArray[species].ageClassSize); - + if ((int) (sp_AgeClassSize) == 0) classize = 1; else @@ -5210,7 +5210,7 @@ void Update_Invert_Cohorts(MSEBoxModel *bm, int species, int stock_id, int maxst } else { bm->tempPopRatio[stock_id][species][cohort][k] /= (this_totsum + small_num); } - + if (bm->tempPopRatio[stock_id][species][cohort][k] > maxvalue) { maxvalue = bm->tempPopRatio[stock_id][species][cohort][k]; } diff --git a/atlantis/ateconomic/Makefile.in b/atlantis/ateconomic/Makefile.in index 82fe19d..e38e8b9 100644 --- a/atlantis/ateconomic/Makefile.in +++ b/atlantis/ateconomic/Makefile.in @@ -283,6 +283,7 @@ 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@ @@ -368,7 +369,10 @@ 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 = libateconomic.a libateconomic_adir = $(includedir)/ateconomic libateconomic_a_SOURCES = ateconindicator.c ateconomic.c ateconomicsetup.c \ diff --git a/atlantis/atharvest/Makefile.in b/atlantis/atharvest/Makefile.in index 45c4562..28cb5ef 100644 --- a/atlantis/atharvest/Makefile.in +++ b/atlantis/atharvest/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 = libatharvest.a libatharvest_adir = $(includedir)/atharvest libatharvest_a_SOURCES = atHarvestAnnual.c atHarvest.c atHarvestIndex.c atHarvestIO.c atHarvestTS.c \ diff --git a/atlantis/atimplementation/Makefile.in b/atlantis/atimplementation/Makefile.in index a245cfd..dcb92eb 100644 --- a/atlantis/atimplementation/Makefile.in +++ b/atlantis/atimplementation/Makefile.in @@ -278,6 +278,7 @@ 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@ @@ -363,7 +364,10 @@ 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 = libatimplementation.a libatimplementation_adir = $(includedir)/atimplementation c_sources = atImplementationAnnual.c atImplementationSetup.c atImplementationParamIO.c diff --git a/atlantis/atlantisUtil/Makefile.in b/atlantis/atlantisUtil/Makefile.in index 8714877..5078e14 100644 --- a/atlantis/atlantisUtil/Makefile.in +++ b/atlantis/atlantisUtil/Makefile.in @@ -281,6 +281,7 @@ 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@ @@ -366,7 +367,10 @@ 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 = libatlantisutil.a libatlantisutil_adir = $(includedir)/atlantisUtil libatlantisutil_a_SOURCES = atUtilhelp.c atUtil.c atUtilArray.c atUtilUnix.c atUtilIO.c atUtilGroupIO.c atUtilXML.c atUtilFisheryIO.c \ diff --git a/atlantis/atlantismain/Makefile.in b/atlantis/atlantismain/Makefile.in index 63038b0..4a8ab62 100644 --- a/atlantis/atlantismain/Makefile.in +++ b/atlantis/atlantismain/Makefile.in @@ -284,6 +284,7 @@ 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@ @@ -369,7 +370,10 @@ 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)\" atlantisMergeddir = $(includedir)/atlantismain atlantisMerged_SOURCES = atlantismain.c atlantisboxmodel.h atlantisMerged_LDADD = -latlantisutil -latassess -latphysics \ diff --git a/atlantis/atlink/Makefile.in b/atlantis/atlink/Makefile.in index 873a003..ac2b9a7 100644 --- a/atlantis/atlink/Makefile.in +++ b/atlantis/atlink/Makefile.in @@ -274,6 +274,7 @@ 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@ @@ -359,7 +360,10 @@ 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 = libatlink.a libatlink_adir = $(includedir)/atlink libatlink_a_SOURCES = atComms.c atlinkconversion.o atlinkexport.c atlinkimport.c atComms.h atlink.h atLinkModule.h diff --git a/atlantis/atmanage/Makefile.in b/atlantis/atmanage/Makefile.in index 2cac1e6..4fb867d 100644 --- a/atlantis/atmanage/Makefile.in +++ b/atlantis/atmanage/Makefile.in @@ -280,6 +280,7 @@ 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@ @@ -365,7 +366,10 @@ 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 = libatmanage.a libatmanage_adir = $(includedir)/atmanage libatmanage_a_SOURCES = atManageAnnual.c atManage.c \ diff --git a/atlantis/atphysics/Makefile.in b/atlantis/atphysics/Makefile.in index ddd6cad..7e87e31 100644 --- a/atlantis/atphysics/Makefile.in +++ b/atlantis/atphysics/Makefile.in @@ -301,6 +301,7 @@ 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@ @@ -386,7 +387,10 @@ 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 = libatphysics.a libatphysics_adir = $(includedir)/atphysics libatphysics_a_SOURCES = atbioirrig.c atbioturb.c atboundary.c atdecay.c atdeposition.c \ diff --git a/atlantis/config.h.in b/atlantis/config.h.in index 411831d..d465ed9 100644 --- a/atlantis/config.h.in +++ b/atlantis/config.h.in @@ -134,6 +134,9 @@ /* Define to the version of this package. */ #undef PACKAGE_VERSION +/* Release version */ +#undef RELEASE_VERSION + /* Define as the return type of signal handlers (`int' or `void'). */ #undef RETSIGTYPE diff --git a/atlantis/configure b/atlantis/configure index 1b55c2a..15a1755 100755 --- a/atlantis/configure +++ b/atlantis/configure @@ -661,6 +661,7 @@ OS_LINUX_FALSE OS_LINUX_TRUE GCC_GE_730_FALSE GCC_GE_730_TRUE +RELEASE_VERSION LIBOBJS host_os host_vendor @@ -7309,6 +7310,103 @@ then : fi +#fetching release tag from git +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for release version" >&5 +printf %s "checking for release version... " >&6; } +RELEASE_VERSION=$(git describe --tags 2>/dev/null || echo "unknown") +#RELEASE_VERSION=$(git describe --tags --abbrev=0 2>/dev/null || echo "unknown") +{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $RELEASE_VERSION" >&5 +printf "%s\n" "$RELEASE_VERSION" >&6; } + +printf "%s\n" "#define RELEASE_VERSION \"$RELEASE_VERSION\"" >>confdefs.h + + + +if test "x$ac_cv_func_vprintf" = xno +then : + ac_fn_c_check_func "$LINENO" "_doprnt" "ac_cv_func__doprnt" +if test "x$ac_cv_func__doprnt" = xyes +then : + +printf "%s\n" "#define HAVE_DOPRNT 1" >>confdefs.h + +fi + +fi +ac_fn_c_check_func "$LINENO" "floor" "ac_cv_func_floor" +if test "x$ac_cv_func_floor" = xyes +then : + printf "%s\n" "#define HAVE_FLOOR 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "localtime_r" "ac_cv_func_localtime_r" +if test "x$ac_cv_func_localtime_r" = xyes +then : + printf "%s\n" "#define HAVE_LOCALTIME_R 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "memset" "ac_cv_func_memset" +if test "x$ac_cv_func_memset" = xyes +then : + printf "%s\n" "#define HAVE_MEMSET 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "pow" "ac_cv_func_pow" +if test "x$ac_cv_func_pow" = xyes +then : + printf "%s\n" "#define HAVE_POW 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "regcomp" "ac_cv_func_regcomp" +if test "x$ac_cv_func_regcomp" = xyes +then : + printf "%s\n" "#define HAVE_REGCOMP 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "sqrt" "ac_cv_func_sqrt" +if test "x$ac_cv_func_sqrt" = xyes +then : + printf "%s\n" "#define HAVE_SQRT 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strcasecmp" "ac_cv_func_strcasecmp" +if test "x$ac_cv_func_strcasecmp" = xyes +then : + printf "%s\n" "#define HAVE_STRCASECMP 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strchr" "ac_cv_func_strchr" +if test "x$ac_cv_func_strchr" = xyes +then : + printf "%s\n" "#define HAVE_STRCHR 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strdup" "ac_cv_func_strdup" +if test "x$ac_cv_func_strdup" = xyes +then : + printf "%s\n" "#define HAVE_STRDUP 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strerror" "ac_cv_func_strerror" +if test "x$ac_cv_func_strerror" = xyes +then : + printf "%s\n" "#define HAVE_STRERROR 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strncasecmp" "ac_cv_func_strncasecmp" +if test "x$ac_cv_func_strncasecmp" = xyes +then : + printf "%s\n" "#define HAVE_STRNCASECMP 1" >>confdefs.h + +fi +ac_fn_c_check_func "$LINENO" "strstr" "ac_cv_func_strstr" +if test "x$ac_cv_func_strstr" = xyes +then : + printf "%s\n" "#define HAVE_STRSTR 1" >>confdefs.h + +fi + +# if test `gcc -dumpversion | gawk '{print $1>=7?"1":"0"}'` = 1; then diff --git a/atlantis/sjwlib/Makefile.in b/atlantis/sjwlib/Makefile.in index 26cd2de..53ea8eb 100644 --- a/atlantis/sjwlib/Makefile.in +++ b/atlantis/sjwlib/Makefile.in @@ -308,6 +308,7 @@ 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@ @@ -393,7 +394,10 @@ 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)\" h_sources = $(top_srcdir)/sjwlib/include/datafile.h \ $(top_srcdir)/sjwlib/include/gridlib.h \ $(top_srcdir)/sjwlib/include/mapproj.h \