Previous changes made to input files
Moved the changes to input files into a news format.
| Sep-2008 | Added the following to the biology input file: C_PB_T15 0.0 Clearance rate of pelagic bact mg3(mg N)-1d-1 0.0002 - 0.004 C_BB_T15 0.0 Clearance rate of sed bact mg3(mg N)-1d-1 0.0002 - 0.004 | Generalising the biology input file parsing |
| 30-sep-2008 | flagcullPIN becomes flagfishPIN in harvest input file | Need to generalise the fisheries input file parsing |
| 01-Oct-2008 | Fisheries. Added flagfishBD 0 1=fishing of deposit feeders, 0=off 0 flagfishMA 0 1=fishing of macroalgae, 0=off 0 also flag_access_thru_wc_BD 0 1=can access deposit feeders through the water column, 0=no 0 flag_access_thru_wc_MA 0 1=can access macroalgae through the water column, 0=no 0 | Trying to generalise the fisheries input file parsing |
| 27 October 2008 | Added to biology input file: invading_sp_model (set this to 1 for now as 0=no invader and more complex options of 2 or more don’t work yet) InvaderIndex (invading species guild index, which I guess you get from the list in the functionalgroup.csv) minInvaderAge (minimum cohort entering as invading species - 0 for urchins as only have one cohort) maxInvaderAge (maximum cohort entering as invading species - again I guess 0 is most appropriate here) InvaderEntryBox (box ID for first box invading species arrives in) InvaderMinDepth (minimum depth invading species tolerates) InvaderMaxDepth (maximum depth invading species tolerates) InvaderStartDay (day invading species enters the system) InvaderEndDay (day invading species stops entering the system) InvaderScalar (increase per year of invading species - so what to scale original biomass by to represent invading species entering) InvaderSpeed (speed of spread of invading species) | Beth has added the following additional parameters to the biological input files to support invading species |
| 05-Nov-2008 | Changed the KUP, KLP and KDEP species parameters in the biology input file to functional group values instead of a mixture of functional groups and groups of functional groups like deepfish. Example change is the following: KLP was: KLP_fish 0.00001 Lower prey selection size limit for fish 0.005 KLP_deepfish 0.00001 Lower prey selection size limit for deepwater fish (FMN, FDO) 0.005 KLP_otherfish 0.00001 Lower prey selection size limit for other (FDD) fish 0.005 KLP_tuna 0.00001 Lower prey selection size limit for tuna (FVT and FVO) 0.005 KLP_shark 0.00001 Lower prey selection size limit for sharks 0.005 KLP_bird 0.00001 Lower prey selection size limit for seabirds 0.005 KLP_baleen 1.0e-10 Lower prey selection size limit for baleen whales 0.0001 KLP_whale 1.0e-8 Lower prey selection size limit for toothed whale 0.0001 KLP_mammal 0.000008 Lower prey selection size limit for mammals 0.0001 KLP_CEP 0.0001 Lower prey selection size limit for cephalopods 0.005 KLP_ZG 0.0001 Lower prey selection size limit for gelatinous zooplankton 0.001 KLP_BMS 0.0000001 Lower prey selection size limit for gelatinous zooplankton 0.001 and is now: #Gape size for vertebrates, to determine available prey fish groups KLP_FPS 0.00001 KLP_FPL 0.00001 KLP_FPO 0.00001 KLP_FVD 0.00001 KLP_FVV 0.00001 KLP_FVS 0.00001 KLP_FVT 0.00001 KLP_FVO 0.00001 KLP_FVB 0.00001 KLP_FMM 0.00001 KLP_FMN 0.00001 KLP_FBP 0.00001 KLP_FDD 0.00001 KLP_FDS 0.00001 KLP_FDB 0.00001 KLP_FDC 0.00001 KLP_FDO 0.00001 KLP_FDE 0.00001 KLP_FDF 0.00001 KLP_FDP 0.00001 KLP_FDM 0.00001 KLP_SHD 0.00001 KLP_SHC 0.00001 KLP_SHP 0.00001 KLP_SHB 0.00001 KLP_SHR 0.00001 KLP_SSK 0.00001 KLP_SB 0.00001 KLP_SP 0.00001 KLP_REP 0.00001 KLP_PIN 0.000008 KLP_WDG 0.000008 KLP_WHB 1.00E-10 KLP_WHT 1.00E-08 KLP_WHS 1.00E-08 KLP_PL 0 KLP_PS 0 KLP_DF 0 KLP_MA 0 KLP_MB 0 KLP_SG 0 KLP_ZG 0.0001 KLP_ZL 0 KLP_ZM 0 KLP_ZS 0 KLP_PB 0 KLP_BB 0 KLP_BO 0 KLP_BD 0 KLP_BC 0 KLP_BFS 0 KLP_BFD 0 KLP_BFF 0 KLP_BG 0 KLP_BMS 0.0000001 KLP_BMD 0.0000001 KLP_BML 0.0000001 KLP_CEP 0.0001 KLP_PWN 0.0000001 KUP was: KUP_fish 0.42 Upper prey selection size limit for fish 0.2 - 0.4 KUP_deepfish 0.6 Upper prey selection size limit for deepwater fish (FDO) 0.2 - 0.6 KUP_otherfish 0.95 Upper prey selection size limit for other fish (FDD) 0.2 - 0.6 KUP_mesopelag 0.9 Upper prey selection size limit for mesopelagic fish (FMM, FMN) 0.2 - 0.6 KUP_shark 0.4 Upper prey selection size limit for sharks 0.2 - 0.4 KUP_bird 0.25 Upper prey selection size limit for seabirds (lower as fly off) 0.1 - 0.2 KUP_baleen 2.0e-6 Upper prey selection size limit for baleen whales 0.0001 KUP_whale 15.0 Upper prey selection size limit for toothed whales 0.2 - 15.0 KUP_mammal 0.4 Upper prey selection size limit for other mammals 0.2 - 0.4 KUP_CEP 0.4 Upper prey selection size limit for cephalopods 0.2 - 0.4 KUP_ZG 0.5 Upper prey selection size limit for gelatinous zooplankton 0.2 - 0.7 KUP_BMS 0.1 Upper prey selection size limit for gelatinous zooplankton 0.2 - 0.7 and is now: KUP_FPS 0.42 KUP_FPL 0.42 KUP_FPO 0.42 KUP_FVD 0.42 KUP_FVV 0.42 KUP_FVS 0.42 KUP_FVT 0.42 KUP_FVO 0.42 KUP_FVB 0.42 KUP_FMM 0.9 KUP_FMN 0.9 KUP_FBP 0.42 KUP_FDD 0.95 KUP_FDS 0.42 KUP_FDB 0.42 KUP_FDC 0.42 KUP_FDO 0.6 KUP_FDE 0.42 KUP_FDF 0.42 KUP_FDP 0.42 KUP_FDM 0.42 KUP_SHD 0.4 KUP_SHC 0.4 KUP_SHP 0.4 KUP_SHB 0.4 KUP_SHR 0.4 KUP_SSK 0.4 KUP_SB 0.25 KUP_SP 0.42 KUP_REP 0.4 KUP_PIN 0.4 KUP_WDG 0.4 KUP_WHB 2.00E-06 KUP_WHT 15 KUP_WHS 15 KUP_PL 0 KUP_PS 0 KUP_DF 0 KUP_MA 0 KUP_MB 0 KUP_SG 0 KUP_ZG 0.5 KUP_ZL 0 KUP_ZM 0 KUP_ZS 0 KUP_PB 0 KUP_BB 0 KUP_BO 0 KUP_BD 0 KUP_BC 0 KUP_BFS 0 KUP_BFD 0 KUP_BFF 0 KUP_BG 0 KUP_BMS 0.1 KUP_BMD 0.1 KUP_BML 0.1 KUP_CEP 0.4 KUP_PWN 0.1 KDEP was: #Depth consumers can dig “into,” are found down to in the sediment KDEP_BFS 0.003 Sediment penetration depth of shallow filter feeders m 0.003 KDEP_BFF 0.003 Sediment penetration depth of other filter feeders m 0.003 KDEP_BFD 0.003 Sediment penetration depth of deep filter feeders m 0.003 KDEP_BO 0.03 Sediment penetration depth of meiobenthos m 0.03 KDEP_BD 0.1 Sediment penetration depth of deposit feeder m 0.01 - 0.3 KDEP_BC 0.1 Sediment penetration depth of infaunal carniv m 0.01 - 0.3 KDEP_BG 0.005 Sediment penetration depth of benth grazers m 0.001 - 0.01 KDEP_BMS 0.001 Sediment penetration depth of shallow macrozoobenthos m 0.00001 - 0.002 KDEP_BMD 0.001 Sediment penetration depth of deep macrozoobenthos m 0.00001 - 0.002 KDEP_BML 0.001 Sediment penetration depth of megazoobenthos m 0.00001 - 0.002 KDEP_CEP 0.003 Sediment penetration depth of cephalopods m 0.003 KDEP_PWN 0.001 Sediment penetration depth of prawns m 0.00001 - 0.002 KDEP_Demfish 1.0 Sediment penetration depth of demersal fish m 0.00001 - 0.002 KDEP_Pelfish 1.0 Sediment penetration depth of pelagic fish m 0.00001 - 0.002 KDEP_SB 0.05 Sediment penetration depth of seabirds m 0.01 - 0.3 KDEP_SHD 0.08 Sediment penetration depth of demersal sharks m 0.001 - 0.01 KDEP_PIN 0.001 Sediment penetration depth of pinnipeds m 0.00001 - 0.002 and is now: KDEP_FPS 1 KDEP_FPL 1 KDEP_FPO 1 KDEP_FVD 1 KDEP_FVV 1 KDEP_FVS 1 KDEP_FVT 1 KDEP_FVO 1 KDEP_FVB 1 KDEP_FMM 1 KDEP_FMN 1 KDEP_FBP 1 KDEP_FDD 1 KDEP_FDS 1 KDEP_FDB 1 KDEP_FDC 1 KDEP_FDO 1 KDEP_FDE 1 KDEP_FDF 1 KDEP_FDP 1 KDEP_FDM 1 KDEP_SHD 0.08 KDEP_SHC 0.08 KDEP_SHP 0.08 KDEP_SHB 0.08 KDEP_SHR 0.08 KDEP_SSK 0.08 KDEP_SB 0.05 KDEP_SP 0.001 KDEP_REP 0.08 KDEP_PIN 0.001 KDEP_WDG 0.001 KDEP_WHB 0.001 KDEP_WHT 0.001 KDEP_WHS 0.001 KDEP_PL 0 KDEP_PS 0 KDEP_DF 0 KDEP_MA 0 KDEP_MB 0 KDEP_SG 0 KDEP_ZG 0 KDEP_ZL 0 KDEP_ZM 0 KDEP_ZS 0 KDEP_PB 0 KDEP_BB 0 KDEP_BO 0.03 KDEP_BD 0.1 KDEP_BC 0.1 KDEP_BFS 0.003 KDEP_BFD 0.003 KDEP_BFF 0.003 KDEP_BG 0.005 KDEP_BMS 0.001 KDEP_BMD 0.001 KDEP_BML 0.001 KDEP_CEP 0.003 KDEP_PWN 0.001 Correction The KDEP_SP value should be the same as the value for fixh. ie 1. | This simplifies the Atlantis code and adds additional flexibility in the model input parameters |
| 18th November | Added the following to the run.prm file: K_num_catchqueue 1 Added to the fisheries input file #Threshold CPUE above which invest in more effort kg d-1 midwcCEP_mEff_thresh_top 0.0 jigCEP_mEff_thresh_top 0.0 midwcFP_mEff_thresh_top 0.0 dredgeBFS_mEff_thresh_top 0.0 netFD_mEff_thresh_top 0.0 netSH_mEff_thresh_top 0.0 plineFVO_mEff_thresh_top 0.0 pseineFVO_mEff_thresh_top 0.0 pseineFP_mEff_thresh_top 0.0. trapBMS_mEff_thresh_top 0.0 trapFD_mEff_thresh_top 0.0 dtrawlBMS_mEff_thresh_top 0.0 dtrawlCEP_mEff_thresh_top 0.0 dtrawlFD_mEff_thresh_top 0.0 dtrawlFDB_mEff_thresh_top 0.0 dtrawlFDO_mEff_thresh_top 0.0 midwcFD_mEff_thresh_top 0.0 dseineFDB_mEff_thresh_top 0.0 dlineFD_mEff_thresh_top 0.0 dlineFVS_mEff_thresh_top 0.0 dlineSH_mEff_thresh_top 0.0 diveBG_mEff_thresh_top 0.0 pseineFVS_mEff_thresh_top 0.0 cullPIN_mEff_thresh_top 0.0 REC_mEff_thresh_top 0.0 ptrawlPWN_mEff_thresh_top 0.0 dtrawlFBP_mEff_thresh_top 0.0 midwcZL_mEff_thresh_top 0.0 trapFDE_mEff_thresh_top 0.0 dlineFDE_mEff_thresh_top 0.0 netFDE_mEff_thresh_top 0.0 midwcPWN_mEff_thresh_top 0.0 mowMA_mEff_thresh_top 0.0 #Proportional increase/decrease in effort in effort if outside CPUE thresholds #Effort decrease will be (1-mEff_prop) and increase will be (1+mEff_prop) midwcCEP_mEff_shift 0.0 jigCEP_mEff_shift 0.0 midwcFP_mEff_shift 0.0 dredgeBFS_mEff_shift 0.0 netFD_mEff_shift 0.0 netSH_mEff_shift 0.0 plineFVO_mEff_shift 0.0 pseineFVO_mEff_shift 0.0 pseineFP_mEff_shift 0.0 trapBMS_mEff_shift 0.0 trapFD_mEff_shift 0.0 dtrawlBMS_mEff_shift 0.0 dtrawlCEP_mEff_shift 0.0 dtrawlFD_mEff_shift 0.0 dtrawlFDB_mEff_shift 0.0 dtrawlFDO_mEff_shift 0.0 midwcFD_mEff_shift 0.0 dseineFDB_mEff_shift 0.0 dlineFD_mEff_shift 0.0 dlineFVS_mEff_shift 0.0 dlineSH_mEff_shift 0.0 diveBG_mEff_shift 0.0 pseineFVS_mEff_shift 0.0 cullPIN_mEff_shift 0.0 REC_mEff_shift 0.0 ptrawlPWN_mEff_shift 0.0 dtrawlFBP_mEff_shift 0.0 midwcZL_mEff_shift 0.0 trapFDE_mEff_shift 0.0 dlineFDE_mEff_shift 0.0 netFDE_mEff_shift 0.0 midwcPWN_mEff_shift 0.0 mowMA_mEff_shift 0.0 | This allows for CPUE related effort model (simple increase/decrease based on whether CPUE outside defined band) |
| 6th December | Added to the run.prm flagannual_Mest 1 # Write out mortality per predator annually (1) or not (0) | This identifies how often want mortality per predator indices |
| 8th December | Added to the harvest.prm # This sets the start date of a fishery in days after the start of the run midwcCEP_tStart 0 jigCEP_tStart 0 midwcFP_tStart 0 dredgeBFS_tStart 0 netFD_tStart 0 netSH_tStart 0 plineFVO_tStart 0 pseineFVO_tStart 0 pseineFP_tStart 0 trapBMS_tStart 0 trapFD_tStart 0 dtrawlBMS_tStart 0 dtrawlCEP_tStart 0 dtrawlFD_tStart 0 dtrawlFDB_tStart 0 dtrawlFDO_tStart 0 midwcFD_tStart 0 dseineFDB_tStart 0 dlineFD_tStart 0 dlineFVS_tStart 0 dlineSH_tStart 0 diveBG_tStart 0 pseineFVS_tStart 0 cullPIN_tStart 0 REC_tStart 0 ptrawlPWN_tStart 0 dtrawlFBP_tStart 0 midwcZL_tStart 0 trapFDE_tStart 0 dlineFDE_tStart 0 netFDE_tStart 0 midwcPWN_tStart 0 mowMA_tStart 0 # This sets the end date of a fishery in days after the start of the run midwcCEP_tEnd 1000000000 jigCEP_tEnd 1000000000 midwcFP_tEnd 1000000000 dredgeBFS_tEnd 1000000000 netFD_tEnd 1000000000 netSH_tEnd 1000000000 plineFVO_tEnd 1000000000 pseineFVO_tEnd 1000000000 pseineFP_tEnd 1000000000 trapBMS_tEnd 1000000000 trapFD_tEnd 1000000000 dtrawlBMS_tEnd 1000000000 dtrawlCEP_tEnd 1000000000 dtrawlFD_tEnd 1000000000 dtrawlFDB_tEnd 1000000000 dtrawlFDO_tEnd 1000000000 midwcFD_tEnd 1000000000 dseineFDB_tEnd 1000000000 dlineFD_tEnd 1000000000 dlineFVS_tEnd 1000000000 dlineSH_tEnd 1000000000 diveBG_tEnd 1000000000 pseineFVS_tEnd 1000000000 cullPIN_tEnd 1000000000 REC_tEnd 1000000000 ptrawlPWN_tEnd 1000000000 dtrawlFBP_tEnd 1000000000 midwcZL_tEnd 1000000000 trapFDE_tEnd 1000000000 dlineFDE_tEnd 1000000000 netFDE_tEnd 1000000000 midwcPWN_tEnd 1000000000 mowMA_tEnd 1000000000 | This allows for fisheries to be started after model starts or stops before model end run |
| 20th Dec 2008 | min_channel_depth added to biol.prm | It is the minimum depth of estuarine channels (so in tidal movements can have groups move on/off flats with the tides) |
| 22 Dec 2008 | Added the following to the biology input file flagDC 1 DC: 1 = on, 0 = off 1 | |
| 05 Jan 2009 | Added the following to the run input file and removed it from the assess input file K_num_detritus 6 # Total number of detritus groups in the model (labile and refractory; water column and sediments) | The bm->K_num_macrofauna is calculated based on this value in atParamIO.c. |
| 07 Apr 2009 | Added the following to the biology input file; lim_sun_hours 0 # Variable daylength: 0=no (i.e. always 12 hours), 1=yes (changes with season and latitude) add swr_scalar 0.45 # Proportion of shortwave radiation available to photosynthesis | If yes is chosen a projection (so lat-long can be related to x-y) is needed in the bgm file and the swr_scalar value must be included in the biol.prm file so that get correct surface irradiance calculated |