v6707

image

New parameters to add No new parameters

SVN commit message

r6707 | ful083 | 2024-03-30 07:20:31 -0700 (Sat, 30 Mar 2024) | 3 lines Changed paths: M /Atlantis/trunk/atlantis/ConvertAtlantis/atBioltoXML.c M /Atlantis/trunk/atlantis/ConvertAtlantis/atManagetoXML.c

Added contaminant handling

See blog entry on contaminants for list of additional parameters

Atlantis model used: Atlantis Model for Puget Sound https://github.com/hmorzaria/psatlantismodel commit 87031b7

Atlantis revision comments

Version 6707

Date pulled: May 15, 2024

OS: Ubuntu 20.04 LTS

Environment: Linux

Modeler: Hem Nalini Morzaria-Luna

Notes

Model behavior

Does not compile, error in atphysics.c

Code changes

Versions compared 6707 6706 FILE COMPARED atassess/atassess_2013.vcxproj.bec

FILE COMPARED atassess/atassessParamIO.c

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FILE COMPARED atassess/doolittle.c

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FILE COMPARED atbrokerlink/atBrokerLinkInit.c

FILE COMPARED atbrokerlink/Deserialiser.c

FILE COMPARED atbrokerlink/ImportExportData.c

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FILE COMPARED atbrokerlink/requests.pb-c.c

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FILE COMPARED atCLAMLink/atCLAMComm.c

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FILE COMPARED atCLAMLink/atCLAMLinkIO.c

FILE COMPARED atCLAMLink/atCLAMLinkSetup.c

FILE COMPARED atCLAMLink/atCLAMManage.c

FILE COMPARED atecology/additionalTracer.c

FILE COMPARED atecology/atannualbiology.c

FILE COMPARED atecology/atbiolmessage.c

FILE COMPARED atecology/atbiology.c

FILE COMPARED atecology/atBiologyXMLParamIO.c

FILE COMPARED atecology/atbiolsetup.c

FILE COMPARED atecology/atbiolUtil.c

FILE COMPARED atecology/atbiophysics.c

FILE COMPARED atecology/atBuildTracer.c

FILE COMPARED atecology/atcalibtools.c

FILE COMPARED atecology/atContaminants.c

FILE COMPARED atecology/atcoral.c

FILE COMPARED atecology/atdemography.c

FILE COMPARED atecology/atdiversity.c

FILE COMPARED atecology/atecology_2013.vcxproj.bec

FILE COMPARED atecology/atecology.c

FILE COMPARED atecology/atecologyts.c

FILE COMPARED atecology/atexternalpop.c

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FILE COMPARED atecology/atfluxbreakdown.c

FILE COMPARED atecology/atForcedMovement.c

FILE COMPARED atecology/atGroupProcesses.c

FILE COMPARED atecology/atIceProcesses.c

FILE COMPARED atecology/atImposeRecruit.c

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FILE COMPARED atecology/atmacrophytes.c

FILE COMPARED atecology/atmigration.c

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FILE COMPARED atecology/atNutrient.c

FILE COMPARED atecology/atPhysChemIO.c

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FILE COMPARED atecology/atq10.c

FILE COMPARED atecology/attime.c

FILE COMPARED atecology/atvertprocesses.c

FILE COMPARED atecology/dump.c

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FILE COMPARED ateconomic/ateconeffort.c

FILE COMPARED ateconomic/ateconhelp.c

FILE COMPARED ateconomic/ateconindicator.c

FILE COMPARED ateconomic/ateconio.c

FILE COMPARED ateconomic/ateconomic_2013.vcxproj.bec

FILE COMPARED ateconomic/ateconomic.c

FILE COMPARED ateconomic/atEconomicAnnual.c

FILE COMPARED ateconomic/ateconomicsetup.c

FILE COMPARED ateconomic/atEconomicUtil.c

FILE COMPARED ateconomic/ateconParamIO.c

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FILE COMPARED ateconomic/ateconts.c

FILE COMPARED ateconomic/ateffortquota.c

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FILE COMPARED atharvest/atharvest_2013.vcxproj.bec

FILE COMPARED atharvest/atHarvest.c

FILE COMPARED atharvest/atHarvestAnnual.c

FILE COMPARED atharvest/atHarvestCatch.c

FILE COMPARED atharvest/atHarvestDiscards.c

FILE COMPARED atharvest/atHarvestImposedCatch.c

FILE COMPARED atharvest/atHarvestIndex.c

FILE COMPARED atharvest/atHarvestIO.c

FILE COMPARED atharvest/atHarvestParamIO.c

FILE COMPARED atharvest/atHarvestSetup.c

FILE COMPARED atharvest/atHarvestTS.c

FILE COMPARED atimplementation/atimplementation_2013.vcxproj.bec

FILE COMPARED atimplementation/atImplementationAnnual.c

FILE COMPARED atimplementation/atImplementationParamIO.c

FILE COMPARED atimplementation/atImplementationSetup.c

FILE COMPARED atlantismain/atlantismain.c

FILE COMPARED atlantismain/atlantisMerged.pc

FILE COMPARED atlantisUtil/atlantisUtil_2013.vcxproj.bec

FILE COMPARED atlantisUtil/atUtil.c

FILE COMPARED atlantisUtil/atUtilArray.c

FILE COMPARED atlantisUtil/atUtilFisheryIO.c

FILE COMPARED atlantisUtil/atUtilFisheryXML.c

FILE COMPARED atlantisUtil/atUtilGroupIO.c

FILE COMPARED atlantisUtil/atUtilhelp.c

FILE COMPARED atlantisUtil/atUtilIO.c

FILE COMPARED atlantisUtil/atUtilUnix.c

FILE COMPARED atlantisUtil/atUtilXML.c

FILE COMPARED atlink/atComms.c

FILE COMPARED atlink/atlinkconversion.c

FILE COMPARED atlink/atlinkexport.c

FILE COMPARED atlink/atlinkimport.c

FILE COMPARED atmanage/atmanage_2013.vcxproj.bec

FILE COMPARED atmanage/atManage.c

FILE COMPARED atmanage/atManageAnnual.c

FILE COMPARED atmanage/atManageIndex.c

FILE COMPARED atmanage/atManageIO.c

FILE COMPARED atmanage/atManageMPATS.c

FILE COMPARED atmanage/atManageParamIO.c

FILE COMPARED atmanage/atManageSetup.c

FILE COMPARED atmanage/atManageTier.c

FILE COMPARED atmanage/atPGMSY.c

FILE COMPARED atmanage/atRlink.c

FILE COMPARED atmanage/atRlinkRAssess.c

FILE COMPARED atmanage/atRlinkRBC.c

FILE COMPARED atmanage/atRlinkRedus.c

FILE COMPARED atmanage/atSS3assess.c

FILE COMPARED atphysics/atagetracerIO.c

FILE COMPARED atphysics/atbioirrig.c

FILE COMPARED atphysics/atbioturb.c

FILE COMPARED atphysics/atboundary.c

FILE COMPARED atphysics/atdecay.c

FILE COMPARED atphysics/atdeposition.c

FILE COMPARED atphysics/atdiagIO.c

FILE COMPARED atphysics/atdietIO.c

FILE COMPARED atphysics/atepiIO.c

FILE COMPARED atphysics/atfishstatIO.c

FILE COMPARED atphysics/atgas.c

FILE COMPARED atphysics/atgeomIO.c

FILE COMPARED atphysics/athdiff.c

FILE COMPARED atphysics/athydromod.c

FILE COMPARED atphysics/aticeIO.c

FILE COMPARED atphysics/atindex.c

FILE COMPARED atphysics/atLandIO.c

FILE COMPARED atphysics/atparamIO.c

FILE COMPARED atphysics/atphysics_2013.vcxproj.bec

FILE COMPARED atphysics/atphysics.c

FILE COMPARED atphysics/atPhysicsModule.c

FILE COMPARED atphysics/atphysIO.c

FILE COMPARED atphysics/atprofile.c

FILE COMPARED atphysics/atreadbm.c

FILE COMPARED atphysics/atsaturation.c

FILE COMPARED atphysics/atsedprops.c

FILE COMPARED atphysics/atsettle.c

FILE COMPARED atphysics/atsourcesink.c

FILE COMPARED atphysics/atsummaryIO.c

FILE COMPARED atphysics/atsuspension.c

FILE COMPARED atphysics/atswr.c

FILE COMPARED atphysics/attempsalt.c

FILE COMPARED atphysics/attracerIO.c

FILE COMPARED atphysics/attransport.c

FILE COMPARED atphysics/atvdiff.c

FILE COMPARED atphysics/atvertgeom.c

FILE COMPARED atphysics/atvmix.c

FILE COMPARED atSS3Link/atCloseKin.c

FILE COMPARED atSS3Link/atSS3DataGen.c

FILE COMPARED atSS3Link/atSS3Link_2013.vcxproj.bec

FILE COMPARED atSS3Link/atSS3Link.c

FILE COMPARED atSS3Link/atSS3LinkIO.c

FILE COMPARED atSS3Link/atSS3Test.c

FILE COMPARED atSS3Link/atSS3Util.c

FILE COMPARED build_hpc

FILE COMPARED configure_mac

FILE COMPARED configure.ac

FILE COMPARED ConvertAtlantis/atAssesstoXML.c

FILE COMPARED ConvertAtlantis/atBioltoXML.c Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “c <

                              <
Util_XML_Parse_Create_Node(fp, fileName, groupingNode, "f
                              <
    
                              <

FILE COMPARED ConvertAtlantis/atCreateXML.c

FILE COMPARED ConvertAtlantis/atEconomicXML.c

FILE COMPARED ConvertAtlantis/atFisheriesXML.c

FILE COMPARED ConvertAtlantis/atGroupsXML.c

FILE COMPARED ConvertAtlantis/atHarvesttoXML.c

FILE COMPARED ConvertAtlantis/atImplementationtoXML.c

FILE COMPARED ConvertAtlantis/atManagetoXML.c /* Fisheries contaminant management / < void ContaminantFisheryXML(MSEBoxModel bm, FILE fp, char f < int cIndex; < char varStr[STRLEN*2]; < char longStr[2*STRLEN]; < < xmlNodePtr groupingNode; < groupingNode = Util_XML_Create_Node(ATLANTIS_ATTRIBUTE_SU < < /* not sure this is going to give the correct array lengt < Util_XML_Create_Node_Next_Line( < fp, < fileName, < groupingNode, < “ContamClosed”, < “Sites closed due to a contaminant spill”, < ““, XML_TYPE_BOOLEANARRAY); < < Util_XML_Parse_Create_Node(fp, fileName, groupingNode,”f < Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “c < Util_XML_Parse_Create_Node(fp, fileName, groupingNode,”c < Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “c < < Util_XML_Parse_Create_Node(fp, fileName, groupingNode,”c < Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “f < < < for(cIndex = 0; cIndex < bm->num_contaminants; cIndex++){ < sprintf(varStr,”%s_fishery_thresh_level”, bm->contam < sprintf(longStr, “Concentration of ontaminant %s wher < Util_XML_Parse_Create_Node(fp, fileName, groupingNode < } < < } < < < if(bm->track_contaminants) { < ContaminantFisheryXML(bm, fp, fileName, doc, rootnode < } <

FILE COMPARED ConvertAtlantis/atRunXML.c

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FILE COMPARED sjwlib/nrcdflib.c

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FILE COMPARED sjwlib/polar_coord.c

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FILE COMPARED sjwlib/txt_param.c

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FILE COMPARED sjwlib/waterprops.c

FILE COMPARED sjwlib/weight_fn.c

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FILE COMPARED sjwlib/xytoij.c