v6704

New parameters to add No new parameters

SVN commit message

r6704 | ful083 | 2024-02-16 22:22:07 -0800 (Fri, 16 Feb 2024) | 1 line Changed paths: M /Atlantis/trunk/atlantis/atmanage/atManageAnnual.c

Changed reference to flagusingRedusR_HCR_id to overall model variable bm->usingRedus_R_HCR

---

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

Atlantis revision comments

Version 6704

Date pulled: February 29, 2024

OS: Ubuntu 20.04 LTS

Environment: Linux

Modeler: Hem Nalini Morzaria-Luna

Notes

Model behavior

Code compiled and runs to 5 years

Code changes

Specific code changes relative to v6702

FILE COMPARED atecology/atannualbiology.c > / > / quit(“EMBRYO[%s].next_larvae | quit(”EMBRYO[%s].next_larvae

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/atdemography.c warn(“Time: %e Zeroing temperature sensitivity fo | warn(”Time: %e Zeroing temperature sensitivity fo

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].speciesParams | //matage = (int) (FunctGroupArray[sp].speciesPara 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 for (n = 0; n < FunctGroupArray[sp].numCohortsXnu | Util_Init_1D_Double(totboxden, (bm->K_num_max_coh /* 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(“Time: %e Zeroing temperature sensit | warn(”Ecology_Total_Verts_And_Migration: 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(“Time: %e Zeroing temperature sensitivit | warn(”Ecology_Invert_Migration: Time: %e Zero If not zero the entry. Simialrly for salinity | If not zero the entry. Similarly 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(Func | } else if(Fun }else{ | } else { >
warn(“Time: %e Zeroing temperature sensitivity fo | warn(”Invade_Spread: Time: %e Zeroing temperature > int flagcontract_sp, contract_sp; > double pH_scale = 0.0; warn(“Time: %e Zeroing temperature sensitivity fo | warn(”Check_Conditions: Time: %e Zeroing temperat > / 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(“Time: %e Zeroing temperature sensitivity fo | warn(”Check_Realloc_Conditions: Time: %e Zeroing

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

FILE COMPARED atlantismain/atlantismain.c > void Util_Usage(); > if (verbose > 1) | printf(“Call ecology”); | if (verbose > 1) { > printf(“Call ecology”); > fflush(stdout); > fflush(stderr); > } > bm.dtsz_stored = bm.dt;

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

FILE COMPARED atmanage/atRlinkRAssess.c printf(“Creating %s”,fname); | printf(“Init_RAssess_File: Creating %s”,fname); >
> printf(“Run_RAssess for species %s idR %d RAssessRuseScri

FILE COMPARED atphysics/attracerIO.c >
> //fprintf(bm->logFile, “readBMTracerD quit(”readBMTracerDat | quit(“readBMTracerDat >
> //fprintf(bm->logFile,”readBMTracerData - bo

FILE COMPARED atphysics/attransport.c