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Phreeqc Files: Using KINETICS block



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




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