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Fix(#87): add box-level discard and rec-catch tracers once per box #91

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Fix(#87): add box-level discard and rec-catch tracers once per box #91

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47 changes: 26 additions & 21 deletions atlantis/atharvest/atHarvest.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1851,32 +1851,37 @@ void Harvest_Update_Total_Catch(MSEBoxModel *bm, double *FishTracers, int habita
All weights converted from mg N to t.
*/

for (guild = 0; guild < bm->K_num_tot_sp; guild++) {
if (habitat == WC || (habitat == EPIFAUNA && (FunctGroupArray[guild].isVertebrate == FALSE && FunctGroupArray[guild].habitatType != WC))) {
if (FunctGroupArray[guild].isFished == TRUE) {
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
/* Catch by fishery tracers */
FishTracers[FunctGroupArray[guild].CaughtByFisheryTracers[nf]] += bm->Catch[bm->current_box][guild][nf][bm->current_layer] * bm->X_CN * mg_2_tonne;

/* Total Rec Catch tracers */
//TODO: Sum over all rec fisheries.
FishTracers[FunctGroupArray[guild].totRecCatchTracer] += bm->RecCatch[bm->current_box][guild][nf] * bm->X_CN * mg_2_tonne;
/* Layer-indexed catch: adding once per layer is correct */
for (guild = 0; guild < bm->K_num_tot_sp; guild++) {
if (habitat == WC || (habitat == EPIFAUNA && (FunctGroupArray[guild].isVertebrate == FALSE && FunctGroupArray[guild].habitatType != WC))) {
if (FunctGroupArray[guild].isFished == TRUE) {
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
FishTracers[FunctGroupArray[guild].CaughtByFisheryTracers[nf]] += bm->Catch[bm->current_box][guild][nf][bm->current_layer] * bm->X_CN * mg_2_tonne;
}
FishTracers[FunctGroupArray[guild].totCatchTracer] += bm->totcatch[guild] * bm->X_CN * mg_2_tonne;
}
/* Total Catch tracers */
FishTracers[FunctGroupArray[guild].totCatchTracer] += bm->totcatch[guild] * bm->X_CN * mg_2_tonne;
}
if (FunctGroupArray[guild].isImpacted == TRUE) {
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
/* Discards by fishery tracers */
FishTracers[FunctGroupArray[guild].DiscardedByFisheryTracers[nf]] += bm->Discards[bm->current_box][guild][nf] * bm->X_CN * mg_2_tonne;
}

/* Total Discards */
FishTracers[FunctGroupArray[guild].totDiscardsTracer] += bm->totdiscards[guild] * bm->X_CN * mg_2_tonne;
}

/* Box-level discards and rec catch (no layer index): add once per box.
Water-column groups at layer 0 (the last layer processed);
epibenthic invertebrates in the EPIFAUNA call. */
for (guild = 0; guild < bm->K_num_tot_sp; guild++) {
int epiGroup = (FunctGroupArray[guild].isVertebrate == FALSE && FunctGroupArray[guild].habitatType != WC);
if ((habitat == WC && !bm->current_layer && !epiGroup) || (habitat == EPIFAUNA && epiGroup)) {
if (FunctGroupArray[guild].isFished == TRUE) {
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
FishTracers[FunctGroupArray[guild].totRecCatchTracer] += bm->RecCatch[bm->current_box][guild][nf] * bm->X_CN * mg_2_tonne;
}
}
if (FunctGroupArray[guild].isImpacted == TRUE) {
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
FishTracers[FunctGroupArray[guild].DiscardedByFisheryTracers[nf]] += bm->Discards[bm->current_box][guild][nf] * bm->X_CN * mg_2_tonne;
}
FishTracers[FunctGroupArray[guild].totDiscardsTracer] += bm->totdiscards[guild] * bm->X_CN * mg_2_tonne;
}
}
}
}
if (!bm->current_layer && (habitat == WC)) { // So read in at the end of every box as FCcaught reinitialised before new box calculations done
/* Total Effort tracers */
for (nf = 0; nf < bm->K_num_fisheries; nf++) {
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