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*To*: <dlpark@xxxxxxxx>*Subject*: Phreeqc Files: Using KINETICS block*From*: Jennifer Tonkin <jtonkin@xxxxxxxxxxxxxxxx>*Date*: Tue, 12 Jun 2001 17:30:05 -0700 (PDT)

David, Hi -- I've been working with Jim Murray using PHREEQC for our Environmental Modeling class. I think the class went pretty well; with some fits and starts we definitely learned a lot more about the problem implementation, especially using the TRANSPORT block. We ran into the following problem trying to use the KINETICS block: One of our students was working on a final project, her input files are below (the simplest one first). She was trying to model an exponential growth, and was running into the problem where PHREEQC was taking a long time to do this calculation (it shouldn't take too long to do this?) and her values were maxing out at whatever value she chose for the "formula" for the organic matter, e.g., "phyto" and "12" in her first file. We weren't sure if this was a coding problem, i.e., PHREEQC just doesn't like the big numbers or if we just set up the problem wrong. Any input you have would be very helpful. Thanks again, Jennifer ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Jennifer W. Tonkin Ph.D. Candidate University of Washington Department of Chemistry Box 351700 Seattle, WA 98195-1700 Office: 416 Ocean Sciences Building E-mail: jtonkin@xxxxxxxxxxxxxxxx Tel: (206) 543-0632 Fax: (206) 685-3351 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ---------- Forwarded message ---------- Date: Fri, 1 Jun 2001 19:39:06 -0700 (PDT) From: erin jennifer breckel <ebreckel@xxxxxxxxxxxxxxxx> To: Jennifer Tonkin <jtonkin@xxxxxxxxxxxxxxxx> Subject: phreeqc files Hey Jennifer. Here are the three files I've been playing around with. They are the really stripped donw version, one with everything and multiple rate blocks, and one with everything and a single rate block. Thanks for taking the time to look at these for me. Erin DATABASE C:\PROGRAM FILES\USGS\PHREEQCI2.3\phreeqc.dat TITLE NPZ Model (Simple Version) SOLUTION_MASTER_SPECIES Phyto Phyto 0.0 Phyto 1.0 Zoo Zoo 0.0 Zoo 1.0 Ntot Ntot 0.0 Ntot 1.0 SOLUTION_SPECIES Phyto = Phyto log_k 0.0 Zoo = Zoo log_k 0.0 Ntot = Ntot log_k 0.0 SOLUTION 1 temp 25 pH 8.1 pe 4 redox pe units mmol/l #mmol/m^3 density 1 Phyto 0.2268 Ntot 12.11 Zoo 0.1134 -water 1 # kg RATES Phytoplankton -start 1 rem PARM(1) = phyto photosynthetic rate (day^-1) 2 rem PARM(2) = uptake half saturation constant (mmol N/m^3) 3 rem PARM(3) = grazing max specific ingestion rate (day^-1) 4 rem PARM(4) = half sat constant for grazer ingestion (mmol N/m^3) 5 rem PARM(5) = grazing threshold (mmol N/m^3) 6 rem PARM(6) = diffusivity (m^2/day) 7 rem PARM(7) = mixed layer depth (m) 10 Phyto = TOT("Phyto") 20 Growth = (PARM(1)*Phyto) 50 moles = (Growth) * (TIME/24) 200 SAVE moles -end KINETICS 1 Phytoplankton -parms 0.93 0.5 1.3 0.2142 0.126 7.344 60 -formula Phyto 12 -steps 8765 in 1461 steps INCREMENTAL_REACTIONS true SELECTED_OUTPUT -file Npz_h.sel -reset false -molalities Phyto -time END DATABASE C:\PROGRAM FILES\USGS\PHREEQCI2.3\phreeqc.dat TITLE NPZ Model (Multiple Rate Blocks) SOLUTION_MASTER_SPECIES Phyto Phyto 0.0 Phyto 1.0 Zoo Zoo 0.0 Zoo 1.0 Ntot Ntot 0.0 Ntot 1.0 SOLUTION_SPECIES Phyto = Phyto log_k 0.0 Zoo = Zoo log_k 0.0 Ntot = Ntot log_k 0.0 SOLUTION 1 temp 25 pH 8.1 pe 4 redox pe units mmol/l #mmol/m^3 density 1 Phyto 0.2268 Ntot 12.11 Zoo 0.1134 -water 1 # kg RATES Phytoplankton -start 1 rem PARM(1) = phyto photosynthetic rate (day^-1) 2 rem PARM(2) = uptake half saturation constant (mmol N/m^3) 3 rem PARM(3) = grazing max specific ingestion rate (day^-1) 4 rem PARM(4) = half sat constant for grazer ingestion (mmol N/m^3) 5 rem PARM(5) = grazing threshold (mmol N/m^3) 6 rem PARM(6) = diffusivity (m^2/day) 7 rem PARM(7) = mixed layer depth (m) 10 Phyto = TOT("Phyto") 20 Growth = ((PARM(1)*Ntot*Phyto)/(PARM(2)+Ntot)) 30 Grazing = ((PARM(3)*max(Phyto-PARM(5),0)*Zoo)/(PARM(4)+Phyto-PARM(5))) 40 Diffusion = (Phyto*PARM(6))/(PARM(7)*PARM(7)) 50 moles = (Growth) * (TIME/24) 200 SAVE moles -end Zooplankton -start 1 rem PARM(1) = grazer growth efficiency 2 rem PARM(2) = grazing max specific ingestion rate (day^-1) 3 rem PARM(3) = grazing threshold (mmol N/m^3) 4 rem PARM(4) = half sat constant for grazer ingestion (mmol N/m^3) 5 rem PARM(5) = predation rate (day^-1) 6 rem PARM(6) = diffusivity (m^2/day) 7 rem PARM(7) = mixed layer depth (m) 10 Zoo = TOT("Zoo") 20 Growth = (PARM(1)*PARM(2)*max(Phyto-PARM(3),0)*Zoo)/(PARM(4)+Phyto-PARM(3)) 30 Predation = PARM(5)*Zoo 40 Diffusion = (Zoo*PARM(6))/(PARM(7)*PARM(7)) 50 moles = (Growth) * (TIME/24) 200 SAVE moles -end Nitrogen -start 1 rem PARM(1) = phyto photosynthetic rate (day^-1) 2 rem PARM(2) = uptake half saturation constant (mmol N/m^3) 3 rem PARM(3) = grazing max specific ingestion rate (day^-1) 4 rem PARM(4) = half sat constant for grazer ingestion (mmol N/m^3) 5 rem PARM(5) = grazing threshold (mmol N/m^3) 6 rem PARM(6) = diffusivity (m^2/day) 7 rem PARM(7) = mixed layer depth (m) 8 rem PARM(8) = Nitrogen concentration at 120 m depth (mmol N/m^3) 15 Ntot = TOT("Ntot") 20 Uptake = ((PARM(1)*Ntot*Phyto)/(PARM(2)+Ntot)) 30 Remineral = (0.3*(PARM(3)*max(Phyto-PARM(5),0)*Zoo)/(PARM(4)+Phyto-PARM(5))) 40 Diffusion = ((PARM(6))/(PARM(7)*PARM(7)))*(PARM(8)-Ntot) 50 moles = (-Uptake) * (TIME/24) 200 SAVE moles -end KINETICS 1 Phytoplankton -parms 0.93 0.5 1.3 0.2142 0.126 7.344 60 -formula Phyto 1 Zooplankton -parms 0.3 1.3 0.126 0.2142 0.07 7.344 60 -formula Zoo 1 Nitrogen -parms 0.93 0.5 1.3 0.2142 0.126 7.344 60 23 -formula Ntot 1 -steps 8765 in 1461 steps INCREMENTAL_REACTIONS true SELECTED_OUTPUT -file Npz_g.sel -reset false -molalities Phyto Zoo Ntot -time END DATABASE C:\PROGRAM FILES\USGS\PHREEQCI2.3\phreeqc.dat TITLE NPZ Model (1 RATE BLOCK) SOLUTION_MASTER_SPECIES Phyto Phyto 0.0 Phyto 1.0 Zoo Zoo 0.0 Zoo 1.0 Ntot Ntot 0.0 Ntot 1.0 SOLUTION_SPECIES Phyto = Phyto log_k 0.0 Zoo = Zoo log_k 0.0 Ntot = Ntot log_k 0.0 SOLUTION 1 temp 25 pH 8.1 pe 4 redox pe units mmol/l #mmol/m^3 density 1 Phyto 0.2268 Ntot 12.1 Zoo 0.1134 -water 1 # kg RATES Npz -start 1 rem PARM(1) = phyto photosynthetic rate (day^-1) 2 rem PARM(2) = uptake half saturation constant (mmol N/m^3) 3 rem PARM(3) = grazing max specific ingestion rate (day^-1) 4 rem PARM(4) = half sat constant for grazer ingestion (mmol N/m^3) 5 rem PARM(5) = grazing threshold (mmol N/m^3) 6 rem PARM(6) = diffusivity (m^2/day) 7 rem PARM(7) = mixed layer depth (m) 8 rem PARM(8) = grazer growth efficiency 9 rem PARM(9) = predation rate (day^-1) 10 rem PARM(10) = Nitrogen concentration at 120 m depth (mmol N/m^3) 15 Phyto = TOT("Phyto") 20 Pgrowth = ((PARM(1)*Ntot*Phyto)/(PARM(2)+Ntot)) 30 Pgrazing = ((PARM(3)*max(Phyto-PARM(5),0)*Zoo)/(PARM(4)+Phyto-PARM(5))) 40 Pdiffusion = (Phyto*PARM(6))/(PARM(7)*PARM(7)) 50 Phytom = (Pgrowth - Pgrazing - Pdiffusion) * (TIME/86400) 60 Zoo = TOT("Zoo") 70 Zgrowth = (PARM(8)*PARM(3)*max(Phyto-PARM(5),0)*Zoo)/(PARM(4)+Phyto-PARM(5)) 80 Zpredation = PARM(9)*Zoo 90 ZDiffusion = (Zoo*PARM(6))/(PARM(7)*PARM(7)) 100 Zoom = (Zgrowth - Zpredation - Zdiffusion) * (TIME/86400) 110 Ntot = TOT("Ntot") 120 Nuptake = ((PARM(1)*Ntot*Phyto)/(PARM(2)+Ntot)) 130 Nremineral = (0.3*(PARM(3)*max(Phyto-PARM(5),0)*Zoo)/(PARM(4)+Phyto-PARM(5))) 140 Ndiffusion = ((PARM(6))/(PARM(7)*PARM(7)))*(PARM(10)-Ntot) 150 Ntotm = (-Nuptake + Nremineral + Ndiffusion) * (TIME/86400) 200 SAVE Phytom Zoom Ntotm -end KINETICS 1 Npz -formula Phyto 1 Zoo 1 Ntot 1 -parms 0.93 0.5 1.3 0.2142 0.126 7.344 60 0.3 0.07 23 -steps 31556926 in 1461 steps INCREMENTAL_REACTIONS true SELECTED_OUTPUT -file Npz_f.sel -reset false -user_punch true USER_PUNCH -heading Days Phyto Zoo Ntot -start 10 PUNCH SIM_TIME/3600/24 20 PUNCH MOL("Phyto") 30 PUNCH MOL("Zoo") 40 PUNCH MOL("Ntot") -end END

**Follow-Ups**:**Re: Phreeqc Files: Using KINETICS block***From:*David L Parkhurst

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