   Input file: ../examples/ex15
  Output file: ex15.out
Database file: ../examples/ex15.dat

------------------
Reading data base.
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	SOLUTION_MASTER_SPECIES
	SOLUTION_SPECIES
	END
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Reading input data for simulation 1.
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	TITLE Example 15.--1D Transport: Kinetic Biodegradation, Cell Growth, and Sorption
	***********
	PLEASE NOTE: This problem requires database file ex15.dat!!
	***********
	PRINT
	        reset false
			status false
	SOLUTION 0 Pulse solution with NTA and cobalt
	        units umol/L
	        pH      6
	        C       .49
	        O(0)    62.5 
	        Nta     5.23
	        Co      5.23
	        Na      1000
	        Cl      1000
	SOLUTION 1-10 Background solution initially filling column
	        units umol/L
	        pH      6
	        C       .49
	        O(0)    62.5 
	        Na      1000
	        Cl      1000
	COPY solution 0 100 # for use later on, and in
	COPY solution 1 101 # 20 cells model
	END
	RATES Rate expressions for the four kinetic reactions
	        HNTA-2
	        start
	10 Ks = 7.64e-7
	20 Ka = 6.25e-6
	30 qm = 1.407e-3/3600
	40 f1 = MOL("HNta-2")/(Ks + MOL("HNta-2"))
	50 f2 = MOL("O2")/(Ka + MOL("O2"))
	60 rate = -qm * KIN("Biomass") * f1 * f2 
	70 moles = rate * TIME
	80 PUT(rate, 1)   # save the rate for use in Biomass rate calculation
	90 SAVE moles
	        end
	        Biomass
	        start
	10 Y = 65.14
	20 b = 0.00208/3600
	30 rate = GET(1)  # uses rate calculated in HTNA-2 rate calculation
	40 rate = -Y*rate -b*M
	50 moles = -rate * TIME
	60 if (M + moles) < 0 then moles = -M
	70 SAVE moles
	        end
	        Co_sorption
	        start
	10 km = 1/3600
	20 kd = 5.07e-3
	30 solids = 3.75e3
	40 rate = -km*(MOL("Co+2") - (M/solids)/kd)
	50 moles = rate * TIME
	60 if (M - moles) < 0 then moles = M
	70 SAVE moles
	        end
	        CoNta_sorption
	        start
	10 km = 1/3600
	20 kd = 5.33e-4
	30 solids = 3.75e3
	40 rate = -km*(MOL("CoNta-") - (M/solids)/kd)
	50 moles = rate * TIME
	60 if (M - moles) < 0 then moles = M
	70 SAVE moles
	        end
	KINETICS 1-10 Four kinetic reactions for all cells
	        HNTA-2
	                formula C -3.12 H -1.968 O -4.848 N -0.424 Nta 1.
	        Biomass
	                formula        H 0.0
	                m              1.36e-4
	        Co_sorption
	                formula CoCl2
	                m      0.0
	                tol 1e-11
	        CoNta_sorption
	                formula NaCoNta
	                m      0.0
	                tol 1e-11
	COPY kinetics 1 101 # to use with 20 cells                
	END
	SELECTED_OUTPUT
	        file   ex15.sel
	        molalities    Nta-3 CoNta- HNta-2 Co+2
	USER_PUNCH
	        headings        hours   Co_sorb CoNta_sorb      Biomass
	        start
	  10 punch TOTAL_TIME/3600 + 3600/2/3600
	  20 punch KIN("Co_sorption")/3.75e3
	  30 punch KIN("CoNta_sorption")/3.75e3
	  40 punch KIN("Biomass")
	USER_GRAPH 1 Example 15
	        -headings 10_cells: Co+2 CoNTA- HNTA-2 pH
	        -chart_title "Kinetic Biodegradation, Cell Growth, and Sorption: Dissolved Species"
	        -axis_titles "Time, in hours" "Micromoles per kilogram water" "pH"
	        -axis_scale x_axis 0 75
	        -axis_scale y_axis 0 4
	        -axis_scale secondary_y_axis 5.799 6.8 0.2 0.1
	        -plot_concentration_vs t
	        -start
	  10 x = TOTAL_TIME/3600 + 3600/2/3600
	  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
	  30 PLOT_XY x, MOL("Co+2") * 1e6, color = Red, line_width = 0, symbol_size = 4
	  40 PLOT_XY x, MOL("CoNta-") * 1e6, color = Green, line_width = 0, symbol_size = 4
	  50 PLOT_XY x, MOL("HNta-2") * 1e6, color = Blue, line_width = 0, symbol_size = 4
	  60 PLOT_XY x, -LA("H+"), y-axis = 2, color = Magenta, line_width = 0, symbol_size = 4
	        -end
	USER_GRAPH 2 Example 15
	        -headings 10_cells: Co+2 CoNTA- Biomass
	        -chart_title "Kinetic Biodegradation, Cell Growth, and Sorption: Sorbed Species"
	        -axis_titles "Time, in hours"  "Nanomoles per kilogram water"              "Biomass, in milligrams per liter"
	        -axis_scale x_axis 0 75
	        -axis_scale y_axis 0 2
	        -axis_scale secondary_y_axis 0 0.4
	        -plot_concentration_vs t
	        -start
	  10 x = TOTAL_TIME/3600 + 3600/2/3600
	  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
	  30 PLOT_XY x, KIN("Co_sorption") / 3.75e3 * 1e9, color = Red, line_width = 0, symbol_size = 4
	  40 PLOT_XY x, KIN("CoNta_sorption") / 3.75e3 * 1e9, color = Green, line_width = 0,        symbol_size = 4
	  50 PLOT_XY x, KIN("Biomass") * 1e3, y-axis = 2, color = Magenta, line_width = 0,        symbol_size = 4
	        -end          -end
	TRANSPORT First 20 hours have NTA and cobalt in infilling solution
	        cells                10
	        lengths              10*1
	        shifts               20
	        time_step            3600
	        flow_direction       forward
	        boundary_conditions  flux flux
	        dispersivities       10*.05
	        correct_disp         true
	        diffusion_coefficient 0.0
	        punch_cells          10
	        punch_frequency      1
	        print_cells          10
	        print_frequency      5
	COPY solution 101 0 # initial column solution becomes influent
	END

Calculating transport: 10 (mobile) cells, 20 shifts, 1 mixruns...

	TRANSPORT Last 55 hours with background infilling solution
	        shifts               55
	COPY cell 100 0 # for the 20 cell model...
	COPY cell 101 1-20
	END

Calculating transport: 10 (mobile) cells, 55 shifts, 1 mixruns...

	USER_PUNCH
	        start
	  10 punch TOTAL_TIME/3600 + 3600/4/3600
	  20 punch KIN("Co_sorption")/3.75e3
	  30 punch KIN("CoNta_sorption")/3.75e3
	  40 punch KIN("Biomass")
	        end
	USER_GRAPH 1
	        -headings 20_cells: Co+2 CoNTA- HNTA-2 pH
	        -start
	  10 x = TOTAL_TIME/3600 + 3600/4/3600
	  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
	  30 PLOT_XY x, MOL("Co+2") * 1e6, color = Red, symbol_size = 0
	  40 PLOT_XY x, MOL("CoNta-") * 1e6, color = Green, symbol_size = 0
	  50 PLOT_XY x, MOL("HNta-2") * 1e6, color = Blue, symbol_size = 0
	  60 PLOT_XY x, -LA("H+"), y-axis = 2, color = Magenta, symbol_size = 0
	        -end
	USER_GRAPH 2
	        -headings 20_cells: Co+2 CoNTA- Biomass
	        -start
	  10 x = TOTAL_TIME/3600 + 3600/4/3600
	  20 PLOT_XY -1, -1, line_width = 0, symbol_size = 0
	  30 PLOT_XY x, KIN("Co_sorption") / 3.75e3 * 1e9, color = Red, symbol_size = 0
	  40 PLOT_XY x, KIN("CoNta_sorption") / 3.75e3 * 1e9, color = Green, symbol_size = 0
	  60 PLOT_XY x, KIN("Biomass") * 1e3, y-axis = 2, color = Magenta, symbol_size = 0
	        -end        
	TRANSPORT First 20 hours have NTA and cobalt in infilling solution
	        cells                20
	        lengths              20*0.5
	        shifts               40
	        initial_time         0
	        time_step            1800
	        flow_direction       forward
	        boundary_conditions  flux  flux
	        dispersivities       20*.05
	        correct_disp         true
	        diffusion_coefficient 0.0
	        punch_cells          20
	        punch_frequency      2
	        print_cells          20
	        print_frequency      10
	COPY cell 101 0
	END
WARNING: USER_PUNCH: Headings count does not match number of calls to PUNCH.


Calculating transport: 20 (mobile) cells, 40 shifts, 1 mixruns...

	TRANSPORT Last 55 hours with background infilling solution
	        shifts               110
	END

Calculating transport: 20 (mobile) cells, 110 shifts, 1 mixruns...

