6685
SVN commit message
Adding PGMSY and aging of contaminants
Changed paths: M /Atlantis/trunk/atlantis/ConvertAtlantis/atAssesstoXML.c M /Atlantis/trunk/atlantis/ConvertAtlantis/atCreateXML.c M /Atlantis/trunk/atlantis/ConvertAtlantis/atRunXML.c M /Atlantis/trunk/atlantis/atSS3Link/atSS3DataGen.c M /Atlantis/trunk/atlantis/atSS3Link/atSS3LinkIO.c M /Atlantis/trunk/atlantis/atassess/atAssessTierSetup.c M /Atlantis/trunk/atlantis/atassess/atassessParamIO.c M /Atlantis/trunk/atlantis/atecology/additionalTracer.c M /Atlantis/trunk/atlantis/atecology/atContaminants.c M /Atlantis/trunk/atlantis/atecology/atGroupProcesses.c M /Atlantis/trunk/atlantis/atecology/atannualbiology.c M /Atlantis/trunk/atlantis/atecology/atbiolmessage.c M /Atlantis/trunk/atlantis/atecology/atbiolsetup.c M /Atlantis/trunk/atlantis/atecology/atdemography.c M /Atlantis/trunk/atlantis/atecology/atecology.c M /Atlantis/trunk/atlantis/atecology/atmigration.c M /Atlantis/trunk/atlantis/atecology/atmovement.c M /Atlantis/trunk/atlantis/atecology/include/atContaminants.h M /Atlantis/trunk/atlantis/atharvest/atHarvest.c M /Atlantis/trunk/atlantis/atharvest/atHarvestParamIO.c M /Atlantis/trunk/atlantis/atharvest/atHarvestSetup.c M /Atlantis/trunk/atlantis/atharvest/include/atHarvest.h M /Atlantis/trunk/atlantis/atharvest/include/atHarvestPrivate.h M /Atlantis/trunk/atlantis/atlantisUtil/atUtil.c M /Atlantis/trunk/atlantis/atlantisUtil/atUtilGroupIO.c M /Atlantis/trunk/atlantis/atlantisUtil/atUtilXML.c M /Atlantis/trunk/atlantis/atlantisUtil/include/atFunctGroup.h M /Atlantis/trunk/atlantis/atlantismain/include/atlantisboxmodel.h M /Atlantis/trunk/atlantis/atmanage/atManageAnnual.c M /Atlantis/trunk/atlantis/atmanage/atManageTier.c M /Atlantis/trunk/atlantis/atmanage/atSS3assess.c
Atlantis model used: Atlantis Model for Puget Sound https://github.com/hmorzaria/psatlantismodel commit 87031b7
Atlantis revision comments
Version 6685
Date pulled: September 27, 2023
OS: Ubuntu 18.04.6 LTS
Environment: Linux
Modeler: Hem Nalini Morzaria-Luna
Notes
- Function CKsimulator is returning an error in atSS3DataGen.c commented out lines 85-89
/* if(bm->CloseKinEst->UseCloseKin && FunctGroupArray[groupIndex].isCloseKin) { GetCloseKinNum(bm, groupIndex, yearIndex); CKsimulator(bm, groupIndex, yearIndex); bm->CloseKinEst[groupIndex].nCKsampled++; } */
Model behavior
Code compiled. Segmentation fault ~day 200
Detailed comparison with previous version
Left is new version, right is old version. Versions are separated by |
Versions compared 6685 6681
` FILE COMPARED atassess/atassess_2013.vcxproj.bec
FILE COMPARED atassess/atassessParamIO.c < //Initialise_PGMSY(bm); < < if (speciesParamStructArray[sp].paramType == SP_I | if (FunctGroupArray[sp].speciesParams[MultispAsse if ((FunctGroupArray[sp].speciesParams[Multis | bm->PGMSY_on = TRUE; bm->PGMSY_on = TRUE; | // Make sure the R file is in place // Make sure the R file is in place < fprintf(bm->logFile,“Set PGMSY_on as %s h | } | if ((FunctGroupArray[sp].isFished == TRUE) && (b } | bm->RBCestimation.earliestYr = bm->RBCestimat if ((FunctGroupArray[sp].isFished == TRUE) & < bm->RBCestimation.earliestYr = bm->RBCest < } < > Util_XML_Read_Species_RBCParam(bm, fileName, childGroupin < <
FILE COMPARED atassess/atAssessTierSetup.c fprintf(bm->logFile, “Initiaised propcatch, propcatch < < > printf(”%s free got to here A“, FunctGroupArray[gro > > printf(”%s free got to here B“, FunctGroupArray[gro >
> printf(”%s free got to here C“, FunctGroupArray[gro > > printf(”%s free got to here C1“, FunctGroupArra >
> printf(”%s free got to here C2“, FunctGroupArra >
> printf(”%s free got to here C3“, FunctGroupArra >
> printf(”%s free got to here C4“, FunctGroupArra >
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> printf(”%s free got to here D“, FunctGroupArray > printf(”%s free got to here E“, FunctGroupArray[gro > > printf(”%s free got to here F“, FunctGroupArray[gro >
> printf(”%s free got to here G“, FunctGroupArray[gro >
> printf(”%s free got to here H“, FunctGroupArray[gro >
> printf(”%s free got to here I“, FunctGroupArray[gro > > printf(”%s free got to here J“, FunctGroupArray[gro >
> if(bm->RBCestimation.Catch_by_Metier) > free4d(bm->RBCestimation.Catch_by_Metier); if(bm->RBCestimation.Catch_by_Metier) < free4d(bm->RBCestimation.Catch_by_Metier); < < int nLen, nt, mid; | int nLen, nt; > /* TODO: FIX - Filler on metiers to fisheries - read mid = bm->RBCestimation.speciesRPFleetToMetier[m] | bm->RBCestimation.speciesMetierToRPFleet[groupInd bm->RBCestimation.speciesMetierToRPFleet[groupInd | bm->RBCestimation.speciesRPFleetToMetier[m][group strcpy(bm->RBCestimation.metierArray[mid].metierC | strcpy(bm->RBCestimation.metierArray[m].metierCod bm->RBCestimation.metierArray[mid].PGMSYlinks = P | bm->RBCestimation.metierArray[m].PGMSYlinks = PGM
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
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 > //double Calculate_Phosphorus_Uptake(MSEBoxModel bm, int gui > // > // double uptake; > // //double P0 = FunctGroupArray[guild].speciesParams[P_ > // //double P1 = FunctGroupArray[guild].speciesParams[P_ > // double PValue = biomass PRatio; > // //double growth =PValue * mum * hN_sp * hI_sp * eddy_ > // > // uptake = grow * PRatio; //PValue * mum * hN_sp * hI_s > // //uptake = growth * FunctGroupArray[guild].speciesPar > // > // /* Save the uptake value for later */ > // FunctGroupArray[guild].uptakeP = uptake; > // > // return uptake; > //} > |
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fprintf(bm->logFile, “%s-%d B < < |
//if(sp == 5 && tracerIndex = < |
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// | / //if(amount > 0 && tracerIndex == c_id && toG | if(amount > 0 && tracerIndex == c_id && toGui if(amount > 0 && toGuild == 0){ < } | }/ /**/ <
FILE COMPARED atecology/atannualbiology.c < /** < //if (do_debug && (bm->which_check == species)) { < if (species == 33) { < fprintf(bm->logFile,“Doing %s stock %d, ngene < FunctGroupArray[species].groupCode, stock_id, < EMBRYO[species].Larvae[stock_id][ngene][qid]) < } < / < < < / < //if (do_debug && (bm->which_check == species)) { < if (species == 33) { < fprintf(bm->logFile,”Initialisation, species %s, rec < } < **/ <
FILE COMPARED atecology/atbiolmessage.c > /* Write time */ > fprintf(fid, “Time: %e”, bm->dayt); >
FILE COMPARED atecology/atbiology.c
FILE COMPARED atecology/atBiologyXMLParamIO.c bm->flagtempdepend_move = (int) Util_XML_Read_Value(f | bm->flagtempdepend = (int) Util_XML_Read_Value(fileNa bm->flagtempdepend_reprod = (int) Util_XML_Read_Value(fil < if (bm->flagtempdepend_move) { | if (bm->flagtempdepend) { if (bm->flagtempdepend_reprod) { | if (bm->flagtempdepend) { MIGRATION[sp].ReprodAllowed = Util_Alloc_Init_2D_Int( < < MIGRATION[sp].ReprodAllowedPrm = Util_Alloc_Init_2D_I |
FILE COMPARED atecology/atbiolsetup.c foundchrt = 0; < foundchrt = chrt; < i_free2d(MIGRATION[sp].ReprodAllowed); < i_free2d(MIGRATION[sp].ReprodAllowedPrm); < totden_check = Util_Alloc_Init_2D_Double(totdensize, bm-> <
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 int Group_Transfer_Contaminant(MSEBoxModel bm, BoxLayerValue | int Group_Transfer_Contaminant(MSEBoxModel bm, BoxLayerValue double cGroupLevel, transfer, totalBiomass, amt_excha | double cGroupLevel, transfer, totalBiomass, propEaten /* If the amount transfered is zero don’t do anything | /* If the amount eaten is zero don’t do anything if (amountTransfer == 0.0) | if (amountEaten == 0.0) quit(“Group_Transfer_Contaminant - from group %s-%d, | quit(”Group_Transfer_Contaminant - to group %s-%d, fr /* Work out the proportion transfered / | / Work out the proportion eaten / amountTransfer = amountTransfer / (totalBiomass + sma | propEaten = amountEaten / (totalBiomass + sma if(!initialBiomass) // No actual transfer possible | if(!initialBiomass) // No actual consumption possibl amountTransfer = amountTransfer / (totalBiomass + sma | propEaten = amountEaten / (totalBiomass + sma if (amountTransfer > 1.0) { | if (propEaten > 1.0) { amountTransfer = 1.0; | propEaten = 1.0; if ((isnan(propTransfer)) || (propTransfer > 1.0)) { | if ((isnan(propEaten)) || (propEaten > 1.0)) { fprintf(stderr, “Group_Transfer_Contaminant g | fprintf(stderr,”Group_Transfer_Contaminant g if ((isnan(propTransfer)) || (propTransfer > 1.0) | if ((isnan(propEaten)) || (propEaten > 1.0)) { fprintf(stderr, “Time: %e box %d-%d case %d G | fprintf(stderr,”Time: %e box %d-%d case %d G //transfer = cGroupLevel amountTran | transfer = cGroupLevel * propEaten / transfer = cGroupLevel * amountTransfer; // Actu < quit(“Group_Transfer_Contamin | quit(”Group_Transfer_Contamin FunctGroupArr | FunctGroupArr fprintf(bm->logFile, “prey = %s, to %s-%d | fprintf(bm->logFile,”prey = %s, to %s-%d amt_exchanged = amountTransfer * dtsz; | amt_exchanged = amountEaten * dtsz; < } < < void Age_Contaminants_Store(MSEBoxModel bm, int sp, int coho < int cIndex, cid; < double cGroupLevel; < < for (cIndex = 0; cIndex < bm->num_contaminants; cIndex++) < cid = FunctGroupArray[sp].contaminantTracers[cohort][ < cGroupLevel = bm->boxes[bm->current_box].tr[bm->curre < FunctGroupArray[sp].agingContam[nextcid][cIndex] = cG < bm->boxes[bm->current_box].tr[bm->current_layer][cid] < // Remove it here so transferred to next class with a < < } < } < < void Age_Contaminants_Update(MSEBoxModel bm, int sp, int coh < int cIndex, cid; < double cGroupLevel; < < for (cIndex = 0; cIndex < bm->num_contaminants; cIndex++) < cid = FunctGroupArray[sp].contaminantTracers[cohort][ < cGroupLevel = bm->boxes[bm->current_box].tr[bm->curre < < bm->boxes[ij].tr[k][cid] += FunctGroupArray[sp].aging < // Add stuff being transferred < } <
FILE COMPARED atecology/atcoral.c
FILE COMPARED atecology/atdemography.c void Update_Aging_Numbers(MSEBoxModel bm, int species, int c | void Update_Aging_Numbers(MSEBoxModel bm, int species, int c double Get_Numbers_Aging(MSEBoxModel bm, int species, int co | double Get_Numbers_Aging(MSEBoxModel bm, int species, int co double dennow, CHLa, KWSR_sp, KWRR_sp, enviro_scalar, thi | double dennow, CHLa, KWSR_sp, KWRR_sp, enviro_scalar, dennow = Get_Numbers_Aging(bm, specie | dennow = Get_Numbers_Aging(bm, specie Update_Aging_Numbers(bm, species, coh | Update_Aging_Numbers(bm, species, coh int flag_allow_spawn = 1; < flag_allow_spawn = MIGRATION[species].ReprodA | if (MIGRATION[species].DEN[cohort][mid] > bm- if (flag_allow_spawn && (MIGRATION[species].D < if (species == 33) { | if (species == 52) { fprintf(llogfp, “Time: %e, %s cohort | fprintf(llogfp,”Time: %e, %s cohort //if (do_debug ) { | if (do_debug ) { if (species == 33) { | fprintf(llogfp, “Time: %e, %s , cohor fprintf(llogfp,”Time: %e, %s cohort < if (species == 33) { | if ((species == 33) || (species == 32)) { if (species == 33) { | //if (species == 33) { > if (species == 52) { temprec = (recSTOCK[species][stock_id | temprec = (recSTOCK[species][stock_id > * stock_prop[species] if (species == 33) { | if ((species == 33) || (species == 32)) { if (species == 33) { | if ((species == 33) || (species == 32)) { < if(!bm->flagtempdepend_reprod) { // Have turned off tempe < if(temp_sensitive_sp && bm->newmonth) { < warn(“Time: %e Zeroing temperature sensitivity fo < } < temp_sensitive_sp = 0; < } < < if (species == 33) { | //if (species == 33) { > if ((species == 33) || (species == 32)) { if (species == 33) { | //if (species == 33) { //if (species == 52) { | if (species == 52) { /** | //fprintf(llogfp,”Time: %e, get settlers %s if (species == 33) { < fprintf(llogfp, “Time: %e, get settlers %s bo < } < / < if (species == 33) { | if (species == 52) { / | /**/ double Get_Numbers_Aging(MSEBoxModel bm, int species, int co | double Get_Numbers_Aging(MSEBoxModel bm, int species, int co < void Update_Aging_Numbers(MSEBoxModel bm, int species, int c | void Update_Aging_Numbers(MSEBoxModel bm, int species, int c < if(bm->track_contaminants){ < Age_Contaminants_Store(bm, species, cohort, nextc < } < < if(bm->track_contaminants < Age_Contaminants_Upda < } < double flag_allow_spawn = 1.0; < flag_allow_spawn = (double)(MIGRATION[species].Re | MigSpawn = spawn_active * prop_mat * MigSpawn = flag_allow_spawn * spawn_a <
FILE COMPARED atecology/atdiversity.c
FILE COMPARED atecology/atecology_2013.vcxproj.bec
FILE COMPARED atecology/atecology.c boxLayerInfo- | boxLayerInfo- >
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 // TODO: I think this is a bug and hangover from | if (bm->flag_replicated_old_PPmort) { | /* Zero out the mortality value so we /* Zero out the mortality value so we can use | FunctGroupArray[guild].mortality[0] = FunctGroupArray[guild].mortality[0] = 0.0; < } < boxLayerInfo->DetritusProd[habitatTyp | boxLayerInfo->DetritusProd[habitatTyp //fprintf(bm->logFile,“Calling Group_Transfer | //fprintf(bm->logFile,”Calling Group_Transfer Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLayerInfo, // TODO: I think this is a bug and hangover from | /* Zero out the mortality value so we if (bm->flag_replicated_old_PPmort) { | FunctGroupArray[guild].mortality[0] = /* Zero out the mortality value so we can use | FunctGroupArray[guild].mortality[0] = 0.0; < } < < boxLayerInfo->DetritusProd[WC][DLdet_ | boxLayerInfo->DetritusProd[WC][DLdet_ Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLayerInfo,
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 | MIGRATION[sp].ReprodAllowed[cohort][c < MIGRATION[sp].ReprodAllowed[cohort][curre < if ((sp == 33) || ((sp > 8) && (sp < 12))) { | //if ((sp == 33) || ((sp > 8) && (sp < 12))) { } | //} // | / //if (bm->debug && (bm->which_check == sp | if (bm->debug && (bm->which_check == sp)) if (sp == 33) { < // | / |
// | //fprintf(llogfp,“%s-%d age_away: %d vs num_aging_eve if (sp == 33) { < fprintf(llogfp,”%s-%d age_away: %d vs num_aging_e < } < // < /** | /* //if ((sp == 48) || (sp == 63) || (sp == 64)) | if ((sp == 48) || (sp == 63) || (sp == 64)) { if (sp == 33) { | fprintf(bm->logFile, “Init_Migration_Age_ fprintf(bm->logFile,”Init_Migration_Age_ < **/ | */ fprintf(bm->logFile, “Init_Migration_Age_ | fprintf(bm->logFile,”Init_Migration_Age_
FILE COMPARED atecology/atmovement.c if (bm->flagtempdepend_move || bm->flagsaltdepend || | if (bm->flagtempdepend || bm->flagsaltdepend || bm->f Util_Init_2D_Double(totden_check, bm->K_num_tot_sp, bm->K < //sp = bm->which_check; | if ((bm->which_check <= bm->K_num_tot_sp)){ sp = 33; | if (FunctGroupArray[bm->which_check].isVertebrate == if ((sp <= bm->K_num_tot_sp)){ < if (FunctGroupArray[sp].isVertebrate == TRUE) { < for (n = 0; n | for (n = 0; n den = | den = fprintf(llogfp, “START Time: %e, | fprintf(llogfp,”START Time: %e, | if (verbose > 0) | for (sp = 0; sp < bm->K_num_tot_sp; sp++) { printf(“Doing vertebrate movement”); < < for (sp = 0; sp < bm->K_num_tot_sp; sp++) { < /** | / if (sp == 33) { | if (sp == 35) { / | // if (sp == 33) { | if ((sp == 33) || (sp == 32)) { / | // if (sp == 33) { | if (sp == 35) { / | **/ if (sp == 33) { | if (sp == 35) { < if (verbose > 0) < printf(“Doing movement for %s”, FunctGroupArray < < | /* Normalise proportion of total abundance in eac | /* Normalise proportion of total abun /* If non present (less than one individual prese | /* If non present (less than one indi | for (n = 0; n < FunctGroupArray[sp].numCohortsXnu | for (n = 0; n < FunctGroupArray[sp].n | /* Note that this use of growth rate and clearanc | /* Note that this use of growth rate | age_mat = (int) (FunctGroupArray[sp].speciesParam | age_mat = (int) (FunctGroupArray[sp]. if(!bm->flagtempdepend_move) { // Have turned off < if(temp_sensitive_sp && bm->newmonth) { < warn(“Time: %e Zeroing temperature sensit < } < temp_sensitive_sp = 0; < } < < /* Replicate old bec_dev results on existing mode | /* Replicate old bec_dev results on e bearlive = (int) (FunctGroupArray[sp].speciesPara | bearlive = (int) (FunctGroupArray[sp] /* Make parameter adjustments due to acidificatio | /* Make parameter adjustments due to | if (sp_ddepend_move > perscribed_move || FunctGro | if (sp_ddepend_move > perscribed_move /* If using ‘sticky’ density dependent movement s | /* If using ‘sticky’ density dependen /* Do final summation (in all cases) / | / Do final summation (in all cases) | | /* Final movement allocations - including migrati | /* Final movement allocations - inclu if (sp == 33) { | if ((sp == 33) || > if (sp == 33) { | if ((sp == 33) || if (sp == 33) { | if ((sp == 33) || if (sp == 33) { | if ((sp == 33) || totden_check[sp][n] += totden[sp] < /* Finalise migration now all boxes iterated thro | /* Finalise migration now all boxes i //sp = bm->which_check; | if ((bm->which_check <= bm->K_num_tot_sp)){ sp = 33; | if (FunctGroupArray[bm->which_check].isVertebrate == if (sp <= bm->K_num_tot_sp){ < if (FunctGroupArray[sp].isVertebrate == TRUE) { < for (n = 0; n < FunctGroupArray[sp].n | for (n = 0; n < FunctGroupArray[bm->w den = FunctGroupArray[sp].NumsTra | den = FunctGroupArray[bm->which_c fprintf(llogfp,”END END Time: %e | fprintf(llogfp, “END END Time: %e < if (verbose > 0) | if (bm->flagtempdepend || bm->flagsaltdepend || bm->flagO printf(”Doing invertebrate movement“); < < if (bm->flagtempdepend_move || bm->flagsaltdepend || bm-> < > if (verbose) > printf(”Dealing with invertebrate movement” > if(!bm->flagtempdepend_move) { // Have turned off tem < if(temp_sensitive_sp && bm->newmonth) { < warn(“Time: %e Zeroing temperature sensitivit < } < temp_sensitive_sp = 0; < } < < if(!bm->flagtempdepend_move) { // Have turned off tempera < if(temp_sensitive_sp && bm->newmonth) { < warn(”Time: %e Zeroing temperature sensitivity fo < } < temp_sensitive_sp = 0; < } < < if (bm->flagtempdepend_move) { | if (bm->flagtempdepend) { < if(!bm->flagtempdepend_move) { // Have turned off tempera < if(temp_sensitive_sp && bm->newmonth) { < warn(“Time: %e Zeroing temperature sensitivity fo < } < temp_sensitive_sp = 0; < } < < if(!bm->flagtempdepend_move) { // Have turned off tempera < if(temp_sensitive_sp && bm->newmonth) { < warn(”Time: %e Zeroing temperature sensitivity fo < } < temp_sensitive_sp = 0; < } <
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
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 |
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stage = FunctGroupArray[sp].cohor < sel = | sel = sel = bm->selectivity[sp][nf][stage] + addlsm | sel = selectivity[sp][nf][stage] + addlsm; sel_lsm = bm->selectivity[sp][nf][juv | sel_lsm = selectivity[sp][nf][juv_id] sel = bm->selectivity[sp][nf] | sel = selectivity[sp][nf][adu
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 readGroupAgeGroupFisheryParamXML(bm, fileName | readGroupAgeGroupFisheryParamXML(bm, fileName readGroupAgeGroupFisheryParamXML(bm, fileName | readGroupAgeGroupFisheryParamXML(bm, fileName
FILE COMPARED atharvest/atHarvestSetup.c bm->selectivity[sp][i | selectivity[sp][i][b] free3d(bm->selectivity); | free3d(selectivity); bm->selectivity = Util_Alloc_Init_3D_Double(bm->K_num | selectivity = Util_Alloc_Init_3D_Double(2, bm->K_num_
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 Ecology_Update_Move_Entry(bm, logfp); // Not in fish < > Ecology_Update_Move_Entry(bm, logfp);
FILE COMPARED atlantismain/atlantisMerged.pc
FILE COMPARED atlantisUtil/atlantisUtil_2013.vcxproj.bec
FILE COMPARED atlantisUtil/atUtil.c sprintf(paramStrings[q10_optimal_temp_id], “%s”, “q10_opt | sprintf(paramStrings[q10_optimal_temp_id],”%s”, “q10 > sprintf(paramStrings[q10_method_id],”%s”, “q10_metho sprintf(RBCParamStrings[trigger_threshold_id],”%s”, “tri <
FILE COMPARED atlantisUtil/atUtilArray.c
FILE COMPARED atlantisUtil/atUtilFisheryIO.c
FILE COMPARED atlantisUtil/atUtilFisheryXML.c
FILE COMPARED atlantisUtil/atUtilGroupIO.c FunctGroupArray[i].agingContam = Util_Alloc_Init_ < free2d(FunctGroupArray[i].agingContam); <
FILE COMPARED atlantisUtil/atUtilhelp.c
FILE COMPARED atlantisUtil/atUtilIO.c
FILE COMPARED atlantisUtil/atUtilUnix.c
FILE COMPARED atlantisUtil/atUtilXML.c { “FLAG_Q10_METHOD”, q10_method_id, “^q10_met | {”FLAG_Q10_METHOD”, q10_method_id, “^q10_met
{ "FLAG_TRIGTHRESH", trigger_threshold_id, "^trigger_
<FILE COMPARED atlink/atComms.c
FILE COMPARED atlink/atlinkconversion.c
FILE COMPARED atlink/atlinkexport.c
FILE COMPARED atlink/atlinkimport.c
FILE COMPARED atmanage/atCloseKin.c
FILE COMPARED atmanage/atmanage_2013.vcxproj.bec
FILE COMPARED atmanage/atManage.c
FILE COMPARED atmanage/atManageAnnual.c > // Call PGMSY first as does own species assessments - so > if (bm->PGMSY_on) { > Call_PGMSY(bm, year, llogfp); > } >
// Under single species assessments - for single spec | if ((int)(bm->RBCestimation.RBCspeciesParam[sp][Multi if((bm->UsingRAssess == 1) && (FunctGroupArray[sp].is | // Do nothing as covered in multispecies call - P > } else { > // Under single species assessments > if((bm->UsingRAssess == 1) && (FunctGroupArray[sp Do_RAssess(bm, sp, year, llogfp); | Do_RAssess(bm, sp, year, llogfp); quit(“How get here as R link not active so set Us | quit(”How get here as R link not active so se } else if(bm->useRBCTiers) { | } else if(bm->useRBCTiers) { CallTierAssessment(bm, sp, year, llogfp); | CallTierAssessment(bm, sp, year, llogfp); } else { | } else { AMS_Tiered_Assessment(bm, sp, llogfp); | AMS_Tiered_Assessment(bm, sp, llogfp); > } |
fprintf(bm->logFile, “Time: %e year: %d Getting read to d < < if (bm->PGMSY_on) { < Call_PGMSY(bm, year, llogfp); < } <
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 printf(“Generating data during the non-assessment per | printf(”Generating data“); printf(”Generating data during the assessment period < printf(“Entering assessment rourine for %s”, FunctG < < printf(“Finished assessment process for %s”, FunctG < | double current_catch = 0, tac_change, cpue_ratio; double current_catch = 0, tac_change, cpue_ratio; < | int Nregions = (int)(bm->RBCestimation.RBCspeciesPara int Nregions = (int)(bm->RBCestimation.RBCspeciesParam[sp < int nf, nreg, CPUEfleet, assess_flag_sp, nfishery, index1 | int nf, nreg, CPUEfleet, assess_flag_sp, nfishery, in printf(“DoTierAssessment %s with year: %d with nYears: %d | < printf(”Doing Tiered Assessment for %s FunctGroupArra | printf(“Doing Tiered Assessment”); /******* Find total old TAC *******/ | Util_Init_2D_Double(bm->RBCestimation.RBCspeciesArray[spe > Util_Init_3D_Double(bm->RBCestimation.RBCspeciesArray[spe > Util_Init_1D_Double(bm->RBCestimation.RBCspeciesArray[spe > Util_Init_2D_Double(bm->RBCestimation.RBCspeciesArray[spe > > /******* Find total old TAC *******/ < printf(“Got here E”); < printf(“Doing Tiered Assessment - Deal with old TAcs and < < if(year > bm->RBCestimation.RBCspeciesParam[species][Asse | if(bm->RBCestimation.RBCspeciesParam[species][isTriggerSp | breakout = trigger_species_breakout(bm, species, year // Only do this if after first year of the assessment | if(breakout > 0) { if(bm->RBCestimation.RBCspeciesParam[species][isTrigg | // Nothing to do as uses tier from speciesParams[ | } else { printf(”Checking trigger breakout for %s“, Func | // Rollover so overwrite tier | tier = sp_rollover; breakout = trigger_species_breakout(bm, species, < if(breakout > 0) { < // Nothing to do as uses tier from speciesPar < } else { < // Rollover so overwrite tier < tier = sp_rollover; < } < printf(”Doing Tiered Assessment - check for rollover“); < < printf(”Doing Tiered Assessment - start assessment of spe < < int nPast = (int)(bm->RBCestimation.RBCspeciesParam[speci < int InitnYears = bm->RBCestimation.nFuture + nPast; < < printf(“Doing Tier_averages - initalise popcatch and avpr | / < Util_Init_2D_Double(bm->RBCestimation.RBCspeciesArray[spe < Util_Init_3D_Double(bm->RBCestimation.RBCspeciesArray[spe < Util_Init_1D_Double(bm->RBCestimation.RBCspeciesArray[spe < Util_Init_2D_Double(bm->RBCestimation.RBCspeciesArray[spe < < / < fprintf(bm->logFile,”DoMultiStockAssessment Time: %e yea < < fprintf(bm->logFile, “DoMultiStockAssessment Time < < < printf(”Checking if %s is prevAssessment %e“, FunctGrou < < printf(”About to do Market test for %s“, FunctGroupArra < < < printf(”Doing test for %s - r %d f %d rbcYear: %d < < < printf(“About to do test for %s vs threshold %e for this_ < < if (lastC > (bm->RBCestimation.RBCspeciesParam[sp][trigge | if (lastC > (bm->RBCestimation.RBCspeciesParam[sp][trigge } < printf(”About to do print to logfile %s with TACcaptured < < printf(“About to do stock test for %s”, FunctGroupArray < < printf(“About to do 10year test for %s”, FunctGroupArra < < printf(“For %s no incr check and return”, FunctGroupArr < < fprintf(bm->logFile,“Time: %e year: %d %s CalculateNonInd < < fprintf(bm->logFile,”Time: %e year: %d %s vs %s I | fprintf(bm->logFile,“Time: %e year: %d %s Indicat < fprintf(bm->logFile,”Time: %e year: %d %s avg Indicat <
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 int Create_Dir_SS3(MSEBoxModel bm, int sp, int year, FILE l < // Name: Create_Dir_SS3 < // Creating a directory for the SS activity - done here to tr < // occur before the write occurs < // < // called by: SS330Assessment < // created: Aug 2023 Beth Fuliton < // < //*********************************************************** < int Create_Dir_SS3(MSEBoxModel bm, int sp, int year, FILE l < < char dirName[STRLEN]; < int ret = 0; < < struct stat st = {0}; < < /* Create directory / < sprintf(dirName, “%s_SS3_sim_%d_year_%d”, FunctGroupArray < < if (stat(dirName, &st) == -1) { < printf(“Creating %s”, dirName); < ret = mkdir(dirName, 0777); // Was S_IRWXU instead o < } < < / Change directory into the new directory - lets skip th < //pass your path in the function < ret = chdir(dirName); < // if the change of directory was successful it will prin < if (ret < 0) < quit(“SS330Assessment: chdir change of directory to % < else < printf(”SS330Assessment: chdir change of directory to < < / < < if (ret < 0) { < printf(“Error: %s”, strerror(errno)); < quit(“Create_Dir_SS3: make directory to %s not succes < } < < return ret; < } < < //*********************************************************** < // < // called by: | // // calls: | // called by : // created: Oct 2019 Rich Little | // calls : > // created :Oct 2019 Rich Little printf(”Starting SS330Assessment”); | / Create directory / > ret = mkdir(dirName, S_IRWXU); > > / Change directory into the new directory / > //pass your path in the function > ret = chdir(dirName); > /if the change of directory was successful it will print > if (ret < 0) > quit(“SS330Assessment: chdir change of directory to % > else > printf(”SS330Assessment: chdir change of directory to < /* Create directory */ < ret = Create_Dir_SS3(bm, sp, year, llogfp); // Failure t < < // read max convergence criterion | // read max convergence criterion } else { | } else { // read next year+1 catches from report.sso | // read next year+1 catches from report.sso > if (bm->RBCestimation.RBCspeciesParam[sp][AssessFail_id]) | if (bm->RBCestimation.RBCspeciesParam[sp][AssessFail_id]) bm->RBCestimation.RBCspeciesArray[sp].NassessFail++; < >
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 bm->flag_replicated_old_PPmort = (int) Util_XML_Read_Valu < <
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/atSS3DataGen.c void RecordHistF(MSEBoxModel bm, int sp, int iyr); < / if(bm->CloseKinEst->UseCloseKin && FunctGroupArray[ | if(bm->CloseKinEst->UseCloseKin && FunctGroupArray[gr } / | } // Store historical F < RecordHistF(bm, groupIndex, yearIndex); < < return; < } < < //********************************************************** < // < // Name: RecordHistF < // Description: store F based on recorded catch and effort d < // and get average of the 5 most recent years < // < // created : September 2023 Beth Fulton < // < //*********************************************************** < void RecordHistF(MSEBoxModel bm, int sp, int iyr) { < int minYr, maxYr, ij, k, nf, n, r, sn, rn, den, stage, pi < double avgPeriod = 0.0; < double fishableBiomass = 0.0, avgF = 0.0, avgC = 0.0, spb < < for (ij = 0; ij < bm->nbox; ij++) { < if (bm->boxes[ij].type != BOUNDARY) { < for (k = 0; k < bm->boxes[ij].nz; k++) { < bm->cell_vol = bm->boxes[ij].area bm->boxes < < switch (FunctGroupArray[sp].groupAgeType) { < case AGE_STRUCTURED: < for (n = 0; n < FunctGroupArray[sp].numCo < sn = FunctGroupArray[sp].structNTrace < rn = FunctGroupArray[sp].resNTracers[ < den = FunctGroupArray[sp].NumsTracers < stage = FunctGroupArray[sp].cohort_st < spbiom = (bm->boxes[ij].tr[k][sn] + b < < /* Consideration per fishery / < for (nf = 0; nf < bm->K_num_fisheries < sel = bm->selectivity[sp][nf][sta < q = bm->SP_FISHERYprms[sp][nf][q_ < < fishableBiomass += sel q * spbi < } < } < break; < case AGE_STRUCTURED_BIOMASS: < for (n = 0; n < FunctGroupArray[sp].numCo < pid = FunctGroupArray[sp].totNTracers < stage = FunctGroupArray[sp].cohort_st < spbiom = bm->boxes[ij].tr[k][pid]; < < /* Consideration per fishery / < for (nf = 0; nf < bm->K_num_fisheries < sel = bm->selectivity[sp][nf][sta < q = bm->SP_FISHERYprms[sp][nf][q_ < < fishableBiomass += sel q * spbi < } < } < break; < case BIOMASS: < /* Do nothing / < pid = FunctGroupArray[sp].totNTracers[0]; < spbiom = bm->boxes[ij].tr[k][pid]; < < / Consideration per fishery / < for (nf = 0; nf < bm->K_num_fisheries; nf < sel = bm->selectivity[sp][nf][0]; < q = bm->SP_FISHERYprms[sp][nf][q_id]; < } < fishableBiomass += sel q * spbiom; < < break; < } < } < } < } < < for (nf = 0; nf < bm->K_num_fisheries; nf++) { < bm->RBCestimation.RBCspeciesArray[sp].Fhist[nf][iyr] < for (r = 0; r < bm->RBCestimation.RBCspeciesParam[sp] < bm->RBCestimation.RBCspeciesArray[sp].Fhist[nf][i < < } < } < < // Calculate the averages - over teh review period, which < minYr = iyr - bm->RBCestimation.ReviewPeriod; < avgPeriod = 0.0; < if (minYr < 0) { < minYr = 0; < } < < avgF = 0.0; < avgC = 0.0; < for (ij = minYr; ij < (iyr + 1); ij++) { < for (nf = 0; nf < bm->K_num_fisheries; nf++) { < avgF += bm->RBCestimation.RBCspeciesArray[sp].Fhi < for (r = 0; r < bm->RBCestimation.RBCspeciesParam < avgC += bm->RBCestimation.RBCspeciesArray[sp] < } < } < avgPeriod += 1.0; < } < avgF /= avgPeriod; < avgC /= avgPeriod; < < bm->RBCestimation.RBCspeciesParam[sp][F_5yrAvg_id] = avgF < bm->RBCestimation.RBCspeciesParam[sp][Catch_5yrAvg_id] = <
FILE COMPARED atSS3Link/atSS3Link_2013.vcxproj.bec
FILE COMPARED atSS3Link/atSS3Link.c
FILE COMPARED atSS3Link/atSS3LinkIO.c if ((fiddat = fopen(outputFileName, “w”)) == NULL) { | if ((fiddat = fopen(outputFileName, “r”)) == NULL) { if ((fidctl = fopen(outputFileName, “w”)) == NULL) { | if ((fidctl = fopen(outputFileName, “r”)) == NULL) { if ((fidss = fopen(outputFileName, “w”)) == NULL) { | if ((fidss = fopen(outputFileName, “r”)) == NULL) { quit(“SS selectivity pattern (%d) for %s fleet %d | quit(”SS selectivity pattern not coded in“);
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 Create_RBC_Species_ParamXML(bm, fileName, fp, childGroupi < Create_RBC_Species_ParamXML(bm, fileName, fp, childGroupi <
FILE COMPARED ConvertAtlantis/atBioltoXML.c Util_XML_Parse_Create_Node(fp, fileName, groupingNode | Util_XML_Parse_Create_Node(fp, fileName, groupingNode
Util_XML_Parse_Create_Node(fp, fileName, groupingNode, "f
<
Util_XML_Get_Value_Integer(fileName, ATLANTIS_ATTRIBUTE,
| Util_XML_Get_Value_Integer(fileName, ATLANTIS_ATTRIBUTE,
Util_XML_Get_Value_Integer(fileName, ATLANTIS_ATTRIBUTE,
| if (bm->flagtempdepend) {
<
if (bm->flagtempdepend_move) {
<
| if (bm->flagtempdepend) {
if (bm->flagtempdepend_reprod) {
<
int numExpectedTokens = 17;
| int numExpectedTokens = 16;
<
/* Whether can reproduce while outside the model
<
varStr = strtok(NULL, seps);
<
Util_XML_Create_Node(ATLANTIS_ATTRIBUTE, groupNod
<
int start_stage, migrationID, start_tofy, end_tofy, mig_p
| int start_stage, migrationID, start_tofy, end_tofy, mig_p
Util_XML_Get_Value_Integer(convertedXMLFileName,
|
<
MIGRATION[speciesIndex].ReprodAllowedPrm[start_st
<FILE COMPARED ConvertAtlantis/atCreateXML.c case trigger_threshold_id: <
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 // Old verion when had fixed limit to the number of f | Parse_File( // Parse_File( bm, fp, fileName, groupingNode, “Companion | bm, Parse_File( bm, fp, fileName, groupingNode,”CompanionSpe | fp, > fileName, > groupingNode, > “CompanionSpecies”, > “^co_sp_[A-Z]{2,3}”, > “Identity of companions in companion >”“, XML_TYPE_INTEGERARRAY, -1, TRUE,
FILE COMPARED ConvertAtlantis/atRunXML.c Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “f < <
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
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 `