v6715

New parameters to add No new parameters

SVN commit message

r6715 | ful083 | 2024-05-06 15:54:49 -0700 (Mon, 06 May 2024) | 1 line Changed paths: M /Atlantis/trunk/atlantis/atecology/atq10.c M /Atlantis/trunk/atlantis/atharvest/atHarvestImposedCatch.c M /Atlantis/trunk/atlantis/atlantismain/include/atlantisboxmodel.h

Up dated the q!0 to include a new CEATTLE option (setting 3 for q10_method)

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

Atlantis revision comments

Version 6715

Date pulled: May 15, 2024

OS: Ubuntu 20.04 LTS

Environment: Linux

Modeler: Hem Nalini Morzaria-Luna

Notes

Model behavior

Not compiled

Code changes

Versions compared 6715 6707 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

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

FILE COMPARED atecology/atbiolmessage.c double start_N = 0.0, natDead_N = 0.0, mort_scale = 0.0, | double start_N = 0.0, natDead_N = 0.0, mort_scale = 0 // double total = 0.0; < //total += natDead_N; | total += natDead_N; int sp, cohort, i, k; | int sp, cohort, this_cohort, i, k; //int this_cohort;; < //this_cohort = 0; | this_cohort = 0; //this_cohort++; | this_cohort++;

FILE COMPARED atecology/atbiology.c localWCTracers[i] = 0.0; < // Do nothing here now | localWCTracers[i] = 0.0; //localWCTracers[i] = 0.0; Moved outside the if s < for (i = 0; i < bm->ntracer; i++) { | for (i = 0; i < bm->ntracer; i++) if (!(_finite(localTracer[i]))) { | if (!(_finite(localTracer[i]))) fprintf(llogfp, “day %e, box %d-%d %s (%d) starts | fprintf(llogfp,”day %e, box %d-%d %s } < } <

FILE COMPARED atecology/atBiologyXMLParamIO.c bm->contam_sig_uptake_const = Util_XML_Read_Value(fileNam < bm->flag_detritus_contam = Util_XML_Read_Value(fileName, < < //fprintf(bm->logFile, “contam_sig_uptake_const starts: % < < int maxnum, num_migs; | int maxnum, num_migs, use_nyears; //int use_nyears; // Was used previously but not anymore < //use_nyears = 1; | use_nyears = 1; //use_nyears = nyears; | use_nyears = nyears;

FILE COMPARED atecology/atbiolsetup.c Util_Usage(1); | Util_Usage(); int ij, n, sp, k, flag_sp, sp_stock_type, stock_id, nreg, | int ij, n, sp, k, flag_sp, sp_stock_type, stock_id, nreg, //int stage; < //stage = FunctGroupA | stage = FunctGroupArr //stage = FunctGroupArray[fgI | stage = FunctGroupArray[fgInd

FILE COMPARED atecology/atbiolUtil.c

FILE COMPARED atecology/atbiophysics.c

FILE COMPARED atecology/atBuildTracer.c

FILE COMPARED atecology/atcalibtools.c int qid, recdate, spmigrate; | int qid, recdate, spmigrate, pid; //int pid; < //pid = Funct | pid = FunctGr >

FILE COMPARED atecology/atContaminants.c double flux, uptakeSum = 0, cLevel = 0, amt_after_dec | double flux, uptakeSum, cLevel, amt_after_decay; amt_after_decay = (cLevel / bm->dtsz_stored) - bm | amt_after_decay = cLevel - bm->contaminantStructu double flux = 0; | double flux; int cIndex, groupIndex, cohort; | int cIndex, groupIndex, cohort, pid; //int pid; < /* < fprintf(bm->logFile, “Time: %e box%d-%d running - test pr | //fprintf(bm->logFile,”Time: %e box%d-%d running - test printf(“Time: %e box%d-%d running - test propContam %s-% | //printf(”Time: %e box%d-%d running - test propContam %s- / < double cGroupLevel, transfer, totalBiomass, propLost | double cGroupLevel, transfer, totalBiomass, propLost; transfer = cGroupLevel propLost * bm->conta | transfer = cGroupLevel * propLost * bm->conta fprintf(bm->logFile, “Gain_Contam transfer > 0 – | fprintf(bm->logFile,”Time: %e %s-%d in box %d-%d double cLevel = 0, uptake_rate = 0, cUptake = 0, cGro | double cLevel, uptake_rate, cUptake = 0, cGroupLevel, case sigmoidal_uptake_id: /* The Richards | case sigmoidal_uptake_id: /* The sigmoida if (FunctGroupArray[sp].isOncePerDt = < time_step = dtsz; < } else if ((it_count == 1) && (FunctG < time_step = bm->dt; < } else { < time_step = 0; < } < < if ((time_step > 0) && (uptake_rate > < /* Have the calculate the actual < contam_sig_uptake_const set to 0 < / < < //fprintf(bm->logFile,“Time: %e b < < Cnew = pow((pow(cLevel,(1.0 - bm- < cUptake = (Cnew - cGroupLevel) / < //cUptake = 0; < } else { < cUptake = 0.0; < } < break; < case invitro_sigmoid_id: /* The InVitro v < fprintf(bm->logFile,”Time: %e box%d-%d %s | fprintf(bm->logFile,“Time: %e box%d-%d %s if(!cUptake) { | if(!cUptake) continue; | continue; } < /* < fprintf(bm->logFile,”Time: %e at end of Species_Contam_U | //fprintf(bm->logFile, “Time: %e at end of Species_Contam printf(”Time: %e end of Species_Contam_Uptake for box%d-% | //printf(“Time: %e end of Species_Contam_Uptake for box%d / < double cGroupLevel = 0, transfer, totalBiomass, amt_excha | double cGroupLevel, transfer, totalBiomass, amt_excha > >
> double tracerArray; < //double newValue; < double local_cGroupLevel, decay_constant; < < tracerArray = getTracerArray(boxLayerInfo, habitat); < < local_cGroupLevel = tracerArray[FunctGroupArr < newValue = local_cGroupLevel pow(0.5, time_ | newValue = cGroupLevel * pow(0.5, time_step / bm->contaminantStructure[cIndex]->sp_amount_d | bm->contaminantStructure[cIndex]->sp_amount_d < /* Alternative code – Using the decay consta < decay_constant = (log(2))/bm->contaminantStru < newValue = local_cGroupLevel * decay_constant < bm->contaminantStructure[cIndex]->sp_amount_d < / < < //fprintf(bm->logFile,“Time: %e %s-%d contami < < double step1, step2, chronicLevel = 0, cGroupLevel = 0; | double step1, step2, chronicLevel, cGroupLevel; int contamIndex, pid = 0; | int contamIndex, pid; double contam_interaction_coefft = 0, contam_scalar = 1.0 | double contam_interaction_coefft, contam_scalar; if (!bm->flag_contamInteractModel) { | if (!bm->flag_contamInteractModel) } < if (bm->flag_contamOnlyAmplify && (cum_contam_scalar < 1. | if (bm->flag_contamOnlyAmplify && (cum_contam_scalar < 1. } < double cGroupLevel = 0, cEnvLevel, conc_amplif = 1.0, cPo | double cGroupLevel = 0, cEnvLevel, chronicLevel, conc_amp //double chronicLevel; < if (cGroupLevel <= 0) { | if (cGroupLevel <= 0) // Nothing to worr // Nothing to worry about < } < / < | /*

FILE COMPARED atecology/atcoral.c

FILE COMPARED atecology/atdemography.c double oldDEN, oldSN, oldRN, embryo_recruits; | double oldDEN, oldSN, oldRN, embryo_recruits, orig_den; //double orig_den; < //orig_den = MIGRATION[specie | orig_den = MIGRATION[species] //fprintf(bm->logFile, “Time: | fprintf(bm->logFile,”Time: % int recruit_outside = 0; | int recruit_outside = 0, leave_stage = 0; //int thisday = 0; | int thisday = 0; > thisday = EMBRYO[species].Sta > leave_stage = FunctGroupArray[species].cohort thisday = EMBRYO[species].StartDay[ngene][qid < < //double yoysum = 0.0; | double yoysum = 0.0, biomass, chrt_biomass; double biomass, chrt_biomass; < int ngene = 0, i = 0, stock_id = 0, den, k, mid, this | int ngene = 0, i = 0, stock_id = 0, den, k, mid, this //int stage; < //yoysum += EMBRYO[species].Larvae[i] | yoysum += EMBRYO[species].Larvae[i][n //stage = FunctGroupArray[species].cohort | stage = FunctGroupArray[species].cohort_s int ij, k, stock_id, species, cohort, age_mat, sn, rn, de | int ij, k, stock_id, species, cohort, age_mat, sn, rn //int stage, next_stage; < //stage = FunctGroupArray[species].co | stage = FunctGroupArray[species].coho //next_stage = FunctGroupArray[specie | next_stage = FunctGroupArray[species] int recruit_outside = 0, cohort = 0, bcohort = 0; | int recruit_outside = 0, pid = 0, cohort = 0, bcohort int mid = 0, pid; | int mid = 0;

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 //double distrib_last_qrt, distrib_qrt, distrib_next_qrt; | double distrib_last_qrt, distrib_qrt, distrib_next_qrt; /* < fprintf(llogfp, “Ecology_Update_Move_Entr | //fprintf(llogfp,”Ecology_Update_Move_En */ <

FILE COMPARED atecology/atGroupProcesses.c if(bm->flag_detritus_contam) { | Gain_Contaminants(bm, boxLayerInfo, WC, WC, guild Gain_Contaminants(bm, boxLayerInfo, WC, WC, g < } < if(bm->flag_detritus_contam) { // If allowing tra | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerInfo, < } < if(bm->flag_detritus_contam) { | Gain_Contaminants(bm, boxLayerInfo, S Gain_Contaminants(bm, boxLayerInfo, SED, SED, | } < | Group_Transfer_Contaminant(bm, boxLay if(bm->flag_detritus_contam) { // If allowing tr | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerInfo, < Group_Transfer_Contaminant(bm, boxLayerInfo, < } < } else if(bm->flag_detritus_contam) { | } else { if(bm->flag_detritus_contam) { | Gain_Contaminants(bm, boxLaye Gain_Contaminants(bm, boxLayerInfo, EPIFA < } < if(bm->flag_detritus_contam) { // If allowing tra | Group_Transfer_Contaminant(bm, boxLayerInfo, EPIF Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerInfo, |
| Group_Transfer_Contaminant(bm, boxLayerInfo, EPIF Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerInfo, < } < Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLayerInfo, Group_Transfer_Contaminant(bm, boxLay | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLay | Group_Transfer_Contaminant(bm, boxLay Group_Transfer_Contaminant(bm, boxLayerIn | Group_Transfer_Contaminant(bm, boxLayerIn Group_Transfer_Contam | Group_Transfer_Contam Group_Transfer_Contaminant(bm, boxLayerIn | Group_Transfer_Contaminant(bm, boxLayerIn Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLayerInfo, if(bm->flag_benthos_sediment_link) { | if(bm->flag_benthos_sediment_link) realised_mum = area_hab; | realised_mum = area_hab; } < Group_Transfer_Contaminant(bm, boxLayerInfo, | Group_Transfer_Contaminant(bm, boxLayerInfo, Group_Transfer_Contaminant(bm | Group_Transfer_Contaminant(bm double biomass, eatBiomass, hO_SP, area_hab, NumSp, x_Sp, | double biomass, eatBiomass, hO_SP, area_hab, NumSp, x if(bm->flag_benthos_sediment_link) { | if(bm->flag_benthos_sediment_link) } else { < realised_mum = FunctGroupArray[guild].scaled_mum[ < } < < if(guild == bm->which_check) { | if(guild == bm->which_check) } < realised_mum, FunctGroupArray[guild].speciesParam | FunctGroupArray[guild].scaled double biomass, eatBiomass, BB_scale, hO_SP, depth_sc | double biomass, eatBiomass, BB_scale, hO_SP, depth_sc if(bm->flag_benthos_sediment_link) { | if(bm->flag_benthos_sediment_link) realised_mum = area_hab; | realised_mum = area_hab; } else { < realised_mum = FunctGroupArray[guild].scaled_mum[ < } < realised_mum, FunctGroupArray[guild].speciesParam | FunctGroupArray[guild].scaled Group_Transfer_Contaminant(bm, boxLayerInfo, habi | Group_Transfer_Contaminant(bm, boxLayerInfo, habi Group_Transfer_Contaminant(bm, boxLay | Group_Transfer_Contaminant(bm, boxLay

FILE COMPARED atecology/atIceProcesses.c /* | // if(i == 0){ if(i == 0){ | // lighttop = lightbot; /* Surface ic lighttop = lightbot; // Surface ic | // }else{ } else { | // lighttop = light_surf * (1.0 - albedo lighttop = light_surf * (1.0 - albedo | // } | // } if(i < (ice->currentnz - 1)){ | lighttop = light_surf * (1.0 - albedo | // if(i < (ice->currentnz - 1)){ } | // lighttop = light_surf * (1.0 - albedo */ | // } >

FILE COMPARED atecology/atImposeRecruit.c

FILE COMPARED atecology/atLandProcess.c

FILE COMPARED atecology/atmacrophytes.c

FILE COMPARED atecology/atmigration.c

FILE COMPARED atecology/atmovement.c

FILE COMPARED atecology/atNutrient.c

FILE COMPARED atecology/atPhysChemIO.c

FILE COMPARED atecology/atprocess.c

FILE COMPARED atecology/atq10.c FunctGroupArray[sp].TcorrEff = FunctGroupArray[sp].Tc < double step1, step2, step3, step4, stepA, stepB, step | double step1, step2; double temp_const_A = 0.0, temp_const_B = 0.0; | double temp_const_A = 0.0; int q10flag = (int)(FunctGroupArray[sp].speciesParams[q10 < switch (q10flag) { | if (FunctGroupArray[sp].speciesParams[q10_met case base_q10_id: /* Basic q10 relationship / | ans = (double)pow(FunctGroupArray[sp].species | // Equation from Gary G - Tdep_di=log case humped_griffith_q10_id: / Humped shape from | temp_const_A = (double) FunctGroupArr // Equation from Gary G - Tdep_di=log(2)0.85 | opt_temp = (double) FunctGroupArray[s temp_const_A = (double) FunctGroupArray[sp].s | step1 = log(2) temp_const_A * pow(b opt_temp = (double) FunctGroupArray[sp].speci | step2 = exp(-bm->temp_const_C * (pow( step1 = log(2) * temp_const_A * pow(bm->temp_ | current_corr = current_temp - opt_te step2 = exp(-bm->temp_const_C (pow(fabs(cur | current_corr = current_temp - opt_temp; | ans = step1 step2; | ans = step1 * step2; | // fprintf(bm->logFile, “FunctGr | // fprintf(llogfp,”ParameterQ10 // fprintf(bm->logFile, “Funct | // fprintf(llogfp,”ParameterQ | } else { break; | ans = (double)pow(FunctGroupArray[sp] case Heinichen_q10_id: < /* Equation 4 from Heinichen et al. referenci < // Tau = 2.71^(25.55-(0.63/((0.0000863TinK[i < step1 = 0.0000863 (current_temp + 273.15); < step2 = 25.55 - (0.63 / step1); // Caren adde < < step3 = exp(step2); < < /* < if(sp == 45) { < fprintf(bm->logFile, “Tau check: Day: %e, S < } < / < < opt_temp = FunctGroupArray[sp].speciesParams[ < < // Equation #5 from Heinichen et al. 2022 < stepA = 0.0000863 (opt_temp + 273.15); < stepB = 25.55 - (0.63 / stepA); < stepC = exp(stepB); < < ans = 1.0 / (step3 / stepC); //scaled Tau < < /* < if(sp == 45) { < fprintf(bm->logFile,”Scaled Tau check: Day < } < / < < break; < case CEATTLE_q10_id: < // Equation from Wisconsin model used in CEAT < temp_const_A = (double) FunctGroupArray[sp].s < opt_temp = (double) FunctGroupArray[sp].speci < temp_const_B = (double) FunctGroupArray[sp].s < < step1 = log(temp_const_A)(temp_const_B - opt < step2 = log(temp_const_A)(temp_const_B - opt < step3 = (pow(step2, 2) pow((1 + pow((1 + 40 < step4 = (temp_const_B - current_temp)/(temp_c < < ans = pow(step4, step3) * exp(step3 * (1 - st < < break; < default: < quit(“How got here as code option not possibl < // Always has to be non-negative, but don’t make it zero < if((ans < 0.0) || (!ans) || isnan(ans)) < ans = small_num; < < double TscalarEff = 1.0; < if((FunctGroupArray[sp].Tcorr * pHscalar) < 1 | if((FunctGroupArray[sp].Tcorr Tscalar = FunctGroupArray[sp].Tcorr * pHs | Tscalar = FunctGroupA } else { | else Tscalar = 1.0 / (FunctGroupArray[sp].Tcor | Tscalar = 1.0 / (Func } < < TscalarEff = 1.0 / (FunctGroupArray[sp].Tcorr < if ((sp_q10eff == poorer_when | if ((sp_q10eff == 1) && (bm-> } else if ((sp_q10eff == poor | } else if ((sp_q10eff == 2) & } else if ((sp_q10eff == vers | } FunctGroupArray[sp].speciesParams[E1_id] | FunctGroupArray[sp].speciesParams[E2_id] < FunctGroupArray[sp].speciesParams[E3_id] < FunctGroupArray[sp].speciesParams[E4_id] < } <

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 int nf, ns, sp, b, ij, do_debug, do_debug_base, nreg; | int nf, ns, sp, b, ij, do_debug, do_debug_base, nreg, int do_debug_quota = 0; <

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 quit(“No such case (%d) for flagimposecatch f | quit(”No such case (%d) for flagimposecatch f

FILE COMPARED atharvest/atHarvestIndex.c

FILE COMPARED atharvest/atHarvestIO.c

FILE COMPARED atharvest/atHarvestParamIO.c

FILE COMPARED atharvest/atHarvestSetup.c bm->EffortModelsActive = 0; < < if((bm->FISHERYprms[nf][flageffortmodel_id] > 0) || ( < bm->EffortModelsActive = 1; < } <

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 Arguments: See Util_Usage(1) routine below for explanat | Arguments: See Util_Usage() routine below for explanati void Util_Usage(int dummy); | void Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); if( argc < 2 ) Util_Usage(1); | if( argc < 2 ) Util_Usage(); if( argc < 2 ) Util_Usage(1); | if( argc < 2 ) Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage(); void Util_Usage(int dummy) { | void Util_Usage() {

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 Util_Usage(1); | Util_Usage(); Util_Usage(1); | Util_Usage();

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 if(bm->flagStoreShotCPUE) { | if(bm->flagStoreShotCPUE) } | if(bm->flagStoreCPUE) if(bm->flagStoreCPUE) { < } < if(bm->EffortModelsActive) { | for (nf = 0; nf < bm->K_num_fisheries; nf++) { for (nf = 0; nf < bm->K_num_fisheries; nf++) { | Harvest_Set_Harvest_Index(bm, nf, checkdone_i Harvest_Set_Harvest_Index(bm, nf, checkdone_id, 0 | for (ij = 0; ij < ncells; ij++) { for (ij = 0; ij < ncells; ij++) { | bm->CumEffort[nf][ij] += bm->Effort[i bm->CumEffort[nf][ij] += bm->Effort[ij][nf]; | bm->OldEffort[ij][nf] = bm->Effort[ij bm->OldEffort[ij][nf] = bm->Effort[ij][nf]; | bm->totOldEffort[nf] += bm->OldEffort bm->totOldEffort[nf] += bm->OldEffort[ij][nf] | bm->Effort[ij][nf] = 0.0; bm->Effort[ij][nf] = 0.0; | bm->TempCPUE[ij][nf] = 0.0; bm->TempCPUE[ij][nf] = 0.0; | | / / | if (do_debug && (nf == bm->which_flee if (do_debug && (nf == bm->which_fleet)) { | fprintf(llogfp, “Time: %e, %s fprintf(llogfp,”Time: %e, %s-%d, effort: %e | bm->Effort[ij bm->Effort[ij][nf], bm->OldEffort[ij][nf], b | } } | / / | | } } | scale_effort[nf] = 0; scale_effort[nf] = 0; | bm->totCPUE[nf] = 0; bm->totCPUE[nf] = 0; | } } < } < for (nstock = 0; nstock < FunctGroupArray[sp].num | for (nstock = 0; nstock < FunctGroupA bm->RegionalData[sp][nstock][reg_catch_id] = | bm->RegionalData[sp][nstock][ } < if(!bm->EffortModelsActive) { < // Check MPAs active or not then jump out - need MPA < if (bm->dayt != bm->predayt) { < for (fishery_id = 0; fishery_id < bm->K_num_fishe < Check_For_Active_MPA(bm, fishery_id); < } < } < return; < } < < /* Determine effort model type / < flagspeffortmodel = (int) (bm->FISHERYprms[nf < < if (!flagspeffortmodel) { < continue; < } < < // If have active effort model then continue < if (bm->dayt != bm->predayt) { | if (bm->dayt != bm->predayt) } < / Check if fishery activated and if no set to zero a | /* Check if fishery activated and if no set to zero if (((!flagspeffortmodel) && ((!mEff[fishery_ | if ((!flagspeffortmodel) && ((!mEff[fishery_i > for (ij = 0; ij < bm->nbox; ij++) { > bm->Effort[ij][fishery_id] = > } > continue; > } > > / Only continue if fishery active this time > if (!bm->FISHERYprms[fishery_id][fisheriesact /* Before do spatially explicit management identi | /* Before do spatially explicit management identi int flagfcmpa, ij, k, sp, cohort, cIndex, ad, adbox; | int flagfcmpa, ij, k, sp; double temp_scale, temp_scale2, catch_check, cGroupLe | double temp_scale, temp_scale2, catch_check; double tracerArray; < > } / Check for contaminant based closures */ < if(bm->track_contaminants) { < < switch (bm->flag_contam_fisheries_mgmt) { < case no_closures: // Nothing to do < break; < case set_closures: // Closed for a set period < if((bm->dayt >= bm->contam_fishery_closur < bm->MPA[ij][fishery_id] = 1.0 - bm->C < } < break; < case conc_based: // Based on concentration in < tracerArray = boxLayerInfo->localWCTracer < for (sp = 0; sp < bm->K_num_tot_sp; sp++) < for(cohort = 0; cohort < FunctGroupAr < for (cIndex = 0; cIndex < bm->num < cGroupLevel = tracerArray[Fun < < thresh_level = bm->contaminan < if (cGroupLevel > thresh_leve < if (!bm->contam_fishery_c < bm->MPA[ij][fishery_i < } else { // Close immedia < bm->MPA[ij][fishery_i < for (ad = 0; ad < bm- < adbox = bm->boxes < bm->MPA[adbox][fi < } < } < < // Break loop as already < sp = bm->K_num_tot_sp; < } < } < } < } < break; < default: < quit(“This (%d) setting for flag_contam_f < break; < } < } < } < <

FILE COMPARED atmanage/atManageAnnual.c int sp, nf, flag_sp, co_sp, co_sp2, co_TYPE, dont_sca | int sp, nf, flag_sp, co_sp, co_sp2, co_TYPE, dont_sca /* If doing pseudo assessments go do them now / < do_assessing = 1; < if (bm->pseudo_assess || bm->useRBCTiers || bm->do_TACass < do_assessing = 1; < } else if (!bm->do_TACassessing) { // used to be “else i < do_assessing = 0; < } < < if ((bm->thisyear > 0) || (!do_assessing)){ | if (bm->thisyear > 0) { > /* If doing pseudo assessments go do them now / > do_assess = 1; > if (bm->pseudo_assess || bm->useRBCTiers || bm->do_TA > do_assess = 1; > } else if (!bm->do_TACassessing) { // used to be ”el > do_assess = 0; > } > if (!do_assessing) { | if (!do_assess) { < // Allow for F based assessment rule her etoo, judt in ca < if ((bm->thisyear > 0) && do_assessing){ < Check_F_Harvest_Control_Rule(bm, llogfp); < Check_Ecosystem_F_Harvest_Control_Rule(bm, llogfp); < } < case tier13: < double FTARG, F_rescale, Fcurr, calcF, Fstep1, this_mFC, | double FTARG, F_rescale, Fcurr, calcF, Fstep1, this_mFC, > double Braw = bm->totfishpop[sp] bm->X_CN * mg_2_tonne; > double Bcurr = Assess_Add_Error(bm, er_case, Braw, est_bi >
double FrefLim = FunctGroupArray[sp].speciesParams[FrefLi < < double Braw, Bcurr; < if(!do_assess) { // Where do_assess set at atlantismain. < Braw = bm->totfishpop[sp] * bm->X_CN * mg_2_tonne; < Bcurr = Assess_Add_Error(bm, er_case, Braw, est_bias, < } else { < Bcurr = bm->NAssess[sp][est_med_stock_id]; < Fcurr = bm->NAssess[sp][est_Fcurr_id]; < M = bm->NAssess[sp][est_M_id]; < } < < //FINISH THIS < < fprintf(llogfp,”The HCR refernce poitns are as follows: | fprintf(llogfp, “BrefA: %e, BrefB: %e, Blim: %e, FrefLim: < < >
> // This is the old method - not used anymore // // This is the old method - not used anymore // | // TODO: This should be F from calcTrackedMort | if (update_date > 182) { // TODO: This should be F from calcTrackedMort | // If restarted records within last 6 months use prev if (update_date > 182) { | start_N = bm->calcNstart[sp][hist_id]; // If restarted records within last 6 months use previou | catch_N = bm->calcFnum[sp][hist_id]; start_N = bm->calcNstart[sp][hist_id]; | mort_scale = 1.0; catch_N = bm->calcFnum[sp][hist_id]; | } else { mort_scale = 1.0; | // If restart records early each year then current re } else { | start_N = bm->calcNstart[sp][expect_id]; // If restart records early each year then current recor | catch_N = bm->calcFnum[sp][expect_id]; start_N = bm->calcNstart[sp][expect_id]; | mort_scale = 365.0 / (365.0 - update_date); catch_N = bm->calcFnum[sp][expect_id]; | } mort_scale = 365.0 / (365.0 - update_date); < } < if (start_N < 0) | if (start_N < 0) start_N = 1; | start_N = 1; if (catch_N < 0) | if (catch_N < 0) catch_N = 0; | catch_N = 0; |
Fcurr = catch_N / (start_N + small_num); // T | Fcurr = catch_N / (start_N + small_num); // TO Fcurr = mort_scale; | Fcurr = mort_scale; |
/ | / |
| switch (tier) { | if (tier < tier8) { // So not US (tier8) or Norway (tier case tier0: // Intentional flow throgh for all these | /* Tier 1 - Best quantitative assessment available / case tier1: | if (Bcurr >= BrefA) { case tier2: | / Greater than BrefA (e.g. B48) so use F48 / case tier3: | FTARG = FrefA; case tier4: | //FTARG = Fcurr; case tier5: | } else if ((Bcurr < BrefA) && (Bcurr >= BrefB)) { case tier6: | / Less than BrefA and greater than BrefB (e.g. B case tier7: | FTARG = FrefA; case dyntier4: | } else if ((Bcurr < BrefB) && (Bcurr > Blim)) { case dyntier1B0: | /* Less than BrefB and greater than Blim (e.g. B2 case sp_rollover: // So not US (tier8) or Norway (tie | FTARG = FrefA * ((Bcurr - Blim) / (BrefB - Blim)) if (Bcurr >= BrefA) { | } else { /* Greater than BrefA (e.g. B48) so use F48 * | /* Less than Blim so set F = 0 / FTARG = FrefA; | FTARG = 0; //FTARG = Fcurr; | } } else if ((Bcurr < BrefA) && (Bcurr >= BrefB)) { | } else { / Less than BrefA and greater than BrefB (e. | /* Tier 8 version of the broken stick - how its appli FTARG = FrefA; | if (Bcurr >= BrefA) { } else if ((Bcurr < BrefB) && (Bcurr > Blim)) { | /* Greater than BrefA (e.g. B48) so fish at a hig /* Less than BrefB and greater than Blim (e.g | FTARG = FrefH; FTARG = FrefA * ((Bcurr - Blim) / (BrefB - Bl | } else if ((Bcurr < BrefA) && (Bcurr >= BrefB)) { } else { | /* Less than BrefA and greater than BrefB (e.g. B /* Less than Blim so set F = 0 / | FTARG = FrefA; FTARG = 0; | } else if ((Bcurr < BrefB) && (Bcurr > Blim)) { } | / Less than BrefB and greater than Blim (e.g. B2 break; | FTARG = FrefA * ((Bcurr - Blim) / (BrefB - Blim)) case tier8: // Tier 8 version of the broken stick - h | } else { case tier9: | /* Less than Blim so set F = 0 / if (Bcurr >= BrefA) { | FTARG = 0; / Greater than BrefA (e.g. B48) so fish at a | } FTARG = FrefH; | } else if ((Bcurr < BrefA) && (Bcurr >= BrefB)) { < /* Less than BrefA and greater than BrefB (e. < FTARG = FrefA; < } else if ((Bcurr < BrefB) && (Bcurr > Blim)) { < /* Less than BrefB and greater than Blim (e.g < Formulate updated to allow for FrefLme to < FTARG = ((FrefLim * (BrefB - Bcurr) + FrefA * < } else { < /* Less than Blim so set F = FrefLim (typical < FTARG = FrefLim; < } < break; < case tier13: // Icelandic escapement approach < if (Bcurr > Blim) { < /* Bigger than Blim so set F rate / < FTARG = 1 - (Blim / BrefB); < } else { < / Less than Blim so set F = 0 / < FTARG = 0; < } < break; < default: < quit(”Per_Sp_Frescale: We do not have any code fo < break; < } else { | } else if (tier != tier8) { switch (tier) { | Fstep1 = Fcurr / (FunctGroupArray[sp].speciesParams[m case tier0: // Intentional flow throgh for al | if (tier != tier9) { case tier1: | F_rescale = Fstep1 (FTARG / (Fcurr + small_num) case tier2: | } else { case tier3: | F_rescale = Fstep1 * (FTARG / (FrefA + small_num) case tier4: < case tier5: < case tier6: < case tier7: < case dyntier4: < case dyntier1B0: < case sp_rollover: < case tier13: < Fstep1 = Fcurr / (FunctGroupArray[sp].species < F_rescale = Fstep1 * (FTARG / (Fcurr + small_ < break; < case tier9: // Norwegian way of doing it - to avo < Fstep1 = Fcurr / (FunctGroupArray[sp].species < F_rescale = Fstep1 * (FTARG / (FrefA + small_ < break; < case tier8: < /* In tier 8 version rescaling vs FrefA - alt < so just in case the user has not entered Fre < this_mFC = FunctGroupArray[sp].speciesParams[ < Fstep1 = FrefA / this_mFC; < F_rescale = Fstep1 * (FTARG / (FrefA + small_ < break; < default: < quit(”Per_Sp_Frescale: We do not have any cod < break; < > } else { > / In tier 8 version rescaling vs FrefA - although ap > so just in case the user has not entered FrefA for m > this_mFC = FunctGroupArray[sp].speciesParams[maxmFC_i > Fstep1 = FrefA / this_mFC; > F_rescale = Fstep1 * (FTARG / (FrefA + small_num));
WriteAnnBrokenStickFile(bm, sp, nf, tier, FrefLim | WriteAnnBrokenStickFile(bm, sp, nf, Fcurr, FTARG, double FrefLim = FunctGroupArray[sp].speciesParams[FrefLi | < fprintf(llogfp, “The HCR refernce poitns are as follows: < fprintf(llogfp,”BrefA: %e, BrefB: %e, Blim: %e, FrefLim: < /* Less than BrefB and greater than Blim (e.g. B2 | /* Less than BrefB and greater than Blim (e.g. B2 Formulate updated to allow for FrefLme to be n | FTARG = FrefA * ((Bcurr - Blim) / (BrefB - Blim)) FTARG = ((FrefLim * (BrefB - Bcurr) + FrefA * (Bc < /* Less than Blim so set F = FrefLim (typicall ab | /* Less than Blim so set F = 0 */ FTARG = FrefLim; | FTARG = 0; > WriteAnnBrokenStickFile(bm, othersp, nf, tier | WriteAnnBrokenStickFile(bm, othersp, nf, Fcur

FILE COMPARED atmanage/atManageIndex.c

FILE COMPARED atmanage/atManageIO.c > > fprintf(fid,“Tier”); | fprintf(fid,“FrefLim”); | fprintf(fid, “FCurr”); fprintf(fid,“FrefA”); | fprintf(fid,“FrefH”); | fprintf(fid, “FTARG”); fprintf(fid,“Blim”); | fprintf(fid,“BrefB”); < fprintf(fid,“BrefA”); < fprintf(fid,“FCurr”); < fprintf(fid,“FTARG”); < > > void WriteAnnBrokenStickFile(MSEBoxModel bm, int species, i | void WriteAnnBrokenStickFile(MSEBoxModel bm, int species, i fprintf(annBrokenfp, “%e %s %s %d %e %e %e %e %e %e % | fprintf(annBrokenfp,”%e %s %s %e %e %e %e“, bm->da

FILE COMPARED atmanage/atManageMPATS.c

FILE COMPARED atmanage/atManageParamIO.c if( Util_XML_Read_Array_Double(ATLANTIS_ATTRIBUTE, fil < quit(“Error: Unable to find parameter ‘TAC_Parameters < } < < < /* Read the Seasonal Fishery xml nodes / | / Create the Seasonal Fishery xml ndoes / / Read the ryke based Fishery xml nodes / | / Create the Seasonal Fishery xml ndoes / / Read the contaminant Fishery xml ndoes / < void readContaminantFisheryXML(MSEBoxModel bm, char fileNam < int i, cIndex; < xmlNodePtr groupingNode; < char varStr[STRLEN*2]; < double values = 0; < char errorString[STRLEN]; < sprintf(errorString, “%s/Fishery_Contaminant_Parameters”, < < groupingNode = Util_XML_Get_Node(ATLANTIS_ATTRIBUTE_SUB_G < if (groupingNode == NULL) < quit(“readContaminantFisheryXML: %s attribute group n < < if(Util_XML_Read_Array_Double(ATLANTIS_ATTRIBUTE, fileNam < quit(”Error: Unable to find parameter’%s/ContamClose < } < < for (i = 0; i < bm->nbox; i++) { < bm->ContamClosed[i] = values[i]; < } < free(values); < < bm->flag_contam_fisheries_mgmt = Util_XML_Read_Value(file < bm->contam_fishery_closure_day = Util_XML_Read_Value(file < bm->contam_fishery_closure_period = Util_XML_Read_Value(f < bm->contam_fishery_closure_option = Util_XML_Read_Value(f < < for(cIndex = 0; cIndex < bm->num_contaminants; cIndex++){ < sprintf(varStr,”%s_fishery_thresh_level”, bm->contam < bm->contaminantStructure[cIndex]->fishery_thresh_leve < } < < } < < if(bm->track_contaminants){ < readContaminantFisheryXML(bm, filename, inputDoc->chi < } <

FILE COMPARED atmanage/atManageSetup.c FunctGroupArray[sp].speciesParams[FrefLim_id] = F < free1d(FrefLimi); < < free1d(bm->ContamClosed); < bm->ContamClosed = Util_Alloc_Init_1D_Double(bm->nbox, 0. < <

FILE COMPARED atmanage/atManageTier.c case tier13: // Icealndic escapement method < case tier13: // —————- tier 13 Iceland esc <

FILE COMPARED atmanage/atPGMSY.c

FILE COMPARED atmanage/atRlink.c int initRedus(int ans) | int initRedus()

FILE COMPARED atmanage/atRlinkRAssess.c

FILE COMPARED atmanage/atRlinkRBC.c

FILE COMPARED atmanage/atRlinkRedus.c int initRedus(int ans) | int initRedus()

FILE COMPARED atmanage/atSS3assess.c free(cwd); // TODO: This correct or cause dump? | free(cwd);

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 fprintf(bm->logFile,“Doing deposition in box %d”); | sed_layer_coords(sm); sed_layer_coords(sm, bm->logFile); <

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 free_diffusion1d(1); | free_diffusion1d();

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 if (propInput->prop_vid < 0) { | if (propInput->prop_vid < 0) quit(“open_phyprop: no %s variable in %s”, propInpu | quit(“open_phyprop: no %s variable in %s”, } | <

FILE COMPARED atphysics/attracerIO.c /* | //int pid = FunctGroupArray[8].contamPropTracers[3][0]; int pid = FunctGroupArray[8].contamPropTracers[3][0]; | //fprintf(bm->logFile, “Time: %e at start of writeBMTrace fprintf(bm->logFile,”Time: %e at start of writeBMTracerD | */ < <

FILE COMPARED atphysics/attransport.c

FILE COMPARED atphysics/atvdiff.c

FILE COMPARED atphysics/atvertgeom.c //fprintf(bm->logFile, “box: %d”, b); < < sed_layer_coords(sm, llogfp); | sed_layer_coords(sm); void sed_layer_coords(SedModel sm, FILE llogfp) | void sed_layer_coords(SedModel *sm) < //fprintf(llogfp, “topk: %d sm->dz[0]: %e”, sm->topk, sm < < < //fprintf(llogfp, “but ends sm->dz[0] %e ”, sm->dz[0]); <

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 Util_XML_Create_Node_Next_Line(fp, fileName, childGroupin < < > Util_XML_Parse_Create_Node(fp, fileName, groupingNode, “c > Util_XML_Parse_Create_Node(fp, fileName, groupingNode,”f > >

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

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