v6706

image

New parameters to add No new parameters

SVN commit message

r6706 | ful083 | 2024-03-30 07:17:22 -0700 (Sat, 30 Mar 2024) | 1 line Changed paths: M /Atlantis/trunk/atlantis/sjwlib/diffusion.c M /Atlantis/trunk/atlantis/sjwlib/include/sjwlib.h

Sorting compile issues

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

Atlantis revision comments

Version 6706

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 6706 6704 FILE COMPARED atassess/atassess_2013.vcxproj.bec

FILE COMPARED atassess/atassessParamIO.c

FILE COMPARED atassess/atAssessTierSetup.c

FILE COMPARED atassess/atattribute.c

FILE COMPARED atassess/atclassical.c

FILE COMPARED atassess/atdatareading.c

FILE COMPARED atassess/atdiet.c

FILE COMPARED atassess/atindices.c

FILE COMPARED atassess/atnetwork.c

FILE COMPARED atassess/atsample.c

FILE COMPARED atassess/atsamplesetup.c

FILE COMPARED atassess/atsolve.c

FILE COMPARED atassess/atsurvey.c

FILE COMPARED atassess/atwriting.c

FILE COMPARED atassess/doolittle.c

FILE COMPARED atassess/unit_lower_triangular.c

FILE COMPARED atassess/upper_triangular.c

FILE COMPARED atbrokerlink/atBrokerLinkInit.c Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage();

FILE COMPARED atbrokerlink/Deserialiser.c

FILE COMPARED atbrokerlink/ImportExportData.c

FILE COMPARED atbrokerlink/LinkageInterface.c

FILE COMPARED atbrokerlink/network.c

FILE COMPARED atbrokerlink/NetworkError.c

FILE COMPARED atbrokerlink/requests.pb-c.c

FILE COMPARED atbrokerlink/responses.pb-c.c

FILE COMPARED atCLAMLink/atCLAMComm.c

FILE COMPARED atCLAMLink/atCLAMImplement.c

FILE COMPARED atCLAMLink/atCLAMLink.c

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 /* < */ < quit(“EMBRYO[%s].next_larvae | quit(”EMBRYO[%s].next_larvae

FILE COMPARED atecology/atbiolmessage.c

FILE COMPARED atecology/atbiology.c if (verbose > 0){ | if (verbose > 0) printf(“processing box %d”, pBox->n); | printf(“processing box %d”, pBox->n); fflush(stdout); < fflush(stderr); < } < if(!bm->dtsz_stored) { < bm->dtsz_stored = dt; < } < <

FILE COMPARED atecology/atBiologyXMLParamIO.c

FILE COMPARED atecology/atbiolsetup.c fprintf(llogfp, “totboxden created with dimension bm->K_n < <

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 warn(“Time: %e Zeroing temperature sensitivity fo | warn(”Time: %e Zeroing temperature sensitivity fo

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

FILE COMPARED atecology/atExternalScalar.c

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

FILE COMPARED atecology/atLandProcess.c

FILE COMPARED atecology/atmacrophytes.c

FILE COMPARED atecology/atmigration.c //int matage; | int matage; //int last_return = -1; | int last_return = -1; //matage = (int) (FunctGroupArray[sp].speciesPara | matage = (int) (FunctGroupArray[sp].speciesParams //last_return = -1; | last_return = -1; /** Error check printout ** | /** Error check printout / / | // / | // / | // / | // / | /**/

FILE COMPARED atecology/atmovement.c double clear, E1_sp, spSpeed, this_HowFar, vertdistri | double clear, E1_sp, spSpeed, this_HowFar, vertdistri Util_Init_1D_Double(totboxden, (bm->K_num_max_coh | for (n = 0; n < FunctGroupArray[sp].numCohortsXnu > /* Initialise totnumber being > totboxden[n] = 0.0; > } > min_temp_sp = FunctGroupArray[sp].spe > max_temp_sp = FunctGroupArray[sp].spe > min_salt_sp = FunctGroupArray[sp].spe > max_salt_sp = FunctGroupArray[sp].spe warn(“Ecology_Total_Verts_And_Migration: | warn(”Time: %e Zeroing temperature sensit > min_temp_sp += contract_sp * > max_temp_sp -= contract_sp * > double totboxden[invert_biosum + 1]; < Util_Init_1D_Double(totboxden, (bm->K_num_max_cohort < < if ((FunctGroupArray[sp].isVertebrate == TRUE) || (Fu < continue; < } < < warn(“Ecology_Invert_Migration: Time: %e Zero | warn(”Time: %e Zeroing temperature sensitivit If not zero the entry. Similarly for salinity | If not zero the entry. Simialrly for salinity > / / Dedicated invertebrate movements / | // Dedicated invertebrate movements if( flagcontract_sp && (pH_scale > 0.0)) { | if( flagcontract_sp && (pH_scale > 0.0)) { | amt = 0; < > amt = 0; / | / / | / < < < distinction between vertebrate | distinction between vertebrate > / If not zero the entry. Si | If not zero the entry. Si > / < / | / / | / / | / to zero - divide by volume | to zero - divide by volume < for (k = 1; k < bm->boxes[ij] |
} < / | / < < > < if(FunctGroup | if(FunctGroup } else if(Fun | }else if(Func } else { | }else{ < warn(“Invade_Spread: Time: %e Zeroing temperature | warn(”Time: %e Zeroing temperature sensitivity fo int flagcontract_sp, contract_sp; < double pH_scale = 0.0; < warn(“Check_Conditions: Time: %e Zeroing temperat | warn(”Time: %e Zeroing temperature sensitivity fo / Make parameter adjustments due to acidification / < flagcontract_sp = (int)FunctGroupArray[sp].speciesParams[ < pH_scale = (FunctGroupArray[sp].pHcorr - 1.0); < if( flagcontract_sp && (pH_scale > 0.0)) { < contract_sp = (int)FunctGroupArray[sp].speciesParams[ < min_temp_sp += contract_sp pH_scale; < max_temp_sp -= contract_sp * pH_scale; < } < < warn(“Check_Realloc_Conditions: Time: %e Zeroing | warn(”Time: %e Zeroing temperature sensitivity fo

FILE COMPARED atecology/atNutrient.c

FILE COMPARED atecology/atPhysChemIO.c

FILE COMPARED atecology/atprocess.c

FILE COMPARED atecology/atq10.c

FILE COMPARED atecology/attime.c

FILE COMPARED atecology/atvertprocesses.c eatBact = eatBactPB + eatBactBB + eatIceBact; | eatBact = eatBactPB + eatBactBB;

FILE COMPARED atecology/dump.c

FILE COMPARED atecology/init.c

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

FILE COMPARED ateconomic/ateconresponse.c

FILE COMPARED ateconomic/ateconts.c

FILE COMPARED ateconomic/ateffortquota.c

FILE COMPARED ateconomic/atquota.c

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 double EFF_scale1 = 0.0, EFF_scale2 = 0.0, EFF_scale3 | double EFF_scale1 = 0.0, EFF_scale2 = 0.0, EFF_scale3 > FC_likeREEF, FC_likeFLAT, FC_likeSOFT > otherFC_likeSOFT, otherFC_dempel, dem } else if (flagmanage > stock_adapt_mgmt){ | } /* TAC-check needed so discard if over TAC amount < dummy = TAC_Check(bm, fishery_id, flagmanage, llo < } < } else if (flagmanage == stock_adapt_mgmt) { | } else if (flagmanage == stock_adapt_mgmt) } < if (bm->FISHERYprms[fishery_id][use_msy_effort_id]) { | if (bm->FISHERYprms[fishery_id][use_msy_effort_id]) } <

FILE COMPARED atmanage/atManageAnnual.c if (FunctGroupArray[sp].isVertebrate == TRUE) { | if (FunctGroupArray[sp].isVertebrate Assess_Pseudo_Estimate_Prm(bm, sp, llogfp); | Assess_Pseudo_Estimate_Prm(bm } else { | else return; | return; } < if (FunctGroupArray[sp].speciesParams[flagFonly_id]) | if (FunctGroupArray[sp].speciesParams[flagFon return; | return; } < if(FunctGroupArray[sp].speciesParams[tac_resetcount_i | if(FunctGroupArray[sp].speciesParams[tac_rese return; | return; } < if(bm->usingRedus_R_HCR) { // Used to say < | if(FunctGroupArray[sp].speciesParams[flagusing if(bm->usingRedus_R_HCR) { // Used to say < | if(FunctGroupArray[sp].speciesParams[flagusin double FTARG, F_rescale, Fcurr, calcF, Fstep1, this_mFC, | double FTARG, F_rescale, Fcurr, calcM, calcF, Fstep1, thi //double calcM; < //calcM = 0.0; | calcM = 0.0; //calcM += (bm->calcTrackedMort[sp][nc][k][finalM | calcM += (bm->calcTrackedMort[sp][nc][k][finalM1_ //calcM /= counter; | calcM /= counter;

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 printf(“Init_RAssess_File: Creating %s”,fname); | printf(“Creating %s”,fname); < printf(“Run_RAssess for species %s idR %d RAssessRuseScri <

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 < //fprintf(bm->logFile, “readBMTracerD < quit(”readBMTracerDat | quit(“readBMTracerDat < //fprintf(bm->logFile,”readBMTracerData - bo <

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

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

FILE COMPARED ConvertAtlantis/atRunXML.c

FILE COMPARED ConvertAtlantis/ConvertAtlantis_2013.vcxproj.bec

FILE COMPARED externalLibs/win32_vs_dll_4.0.1-beta3.tar/netcdf.inc

FILE COMPARED netcdf/include/netcdf.inc

FILE COMPARED sjwlib/cfft.c

FILE COMPARED sjwlib/colourtable.c

FILE COMPARED sjwlib/contour.c

FILE COMPARED sjwlib/convertFileFormats.c

FILE COMPARED sjwlib/datafile.c

FILE COMPARED sjwlib/decay.c

FILE COMPARED sjwlib/dfcoords.c

FILE COMPARED sjwlib/dfeval.c

FILE COMPARED sjwlib/diffusion.c void free_diffusion1d(int dummy) { | void free_diffusion1d() {

FILE COMPARED sjwlib/drandom.c

FILE COMPARED sjwlib/ellipt_coord.c

FILE COMPARED sjwlib/erfc.c

FILE COMPARED sjwlib/geodetic.c

FILE COMPARED sjwlib/gridangle.c

FILE COMPARED sjwlib/gridmetric.c

FILE COMPARED sjwlib/gridmisc.c

FILE COMPARED sjwlib/keyfile.c

FILE COMPARED sjwlib/libsjwlib.pc

FILE COMPARED sjwlib/mapproj.c

FILE COMPARED sjwlib/memory.c

FILE COMPARED sjwlib/netcdf.c

FILE COMPARED sjwlib/nrcdflib.c

FILE COMPARED sjwlib/pointsourcesink.c

FILE COMPARED sjwlib/polar_coord.c

FILE COMPARED sjwlib/polyline.c

FILE COMPARED sjwlib/ppbfetch.c

FILE COMPARED sjwlib/ptrack.c

FILE COMPARED sjwlib/quit.c

FILE COMPARED sjwlib/rect_coord.c

FILE COMPARED sjwlib/sjwlib_2013.vcxproj.bec

FILE COMPARED sjwlib/spline.c

FILE COMPARED sjwlib/text_input.c

FILE COMPARED sjwlib/time.c

FILE COMPARED sjwlib/timeseries.c

FILE COMPARED sjwlib/txt_param.c

FILE COMPARED sjwlib/vgrid.c

FILE COMPARED sjwlib/warn.c

FILE COMPARED sjwlib/waterprops.c

FILE COMPARED sjwlib/weight_fn.c

FILE COMPARED sjwlib/win32.c

FILE COMPARED sjwlib/xytoij.c