HPx

RATES
pyrite
-mybasic
-start
 #1 REM parm(1) k_0 mol/dm�/s
 mole = 0
 if SR("pyrite") < 1 then 
     MolarVolume = phase_vm("pyrite")
     phi0 = m0()*MolarVolume # initial bulk volume
     phi = m()*MolarVolume
     k_red = (phi/phi0)^(2/3)
     k = k_red*parm(1)/conv_t("s") # to convert from time units s to the time units of the HYDRUS GUI
     rate = k*(1 - SR("pyrite"))
     mole = rate*time()
     if (mole > m()) then mole = m()
 endif
 save(mole)
-end

solution 1001 initial condition mobile phase
-temp 25
-units mol/kgw
-pH 7 
-pe -2.5
Al 2.59E-8
Ca 1.43E-2
K 9E-3
C 1E-3 CO2(g) -2.6038
Cl 1.14E-3
Si 1.93E-3
S(6) 1E-3 charge
Fe 1.45E-4
end
solution 3001 boundary condition
-temp 25
-units mol/kgw
-pH 5
-redox O(-2)/O(0)
Al 1.28E-8
Ca 1.9E-3
K 8.7E-3
C 1E-3 CO2(g) -3.49894
Cl 1.14E-3
Si 1.99E-4
O(0) 1E-3 O2(g) -0.68
S 1E-3 charge
Fe 5E-7
end
gas_phase 3001 boundary condition
-temp 25
-fixed_volume 1
-boundary_layer 1 m
CO2(g) 3.17E-4
O2(g) 0.21
end

KINETICS 1001 
-material 1
pyrite
 -parms 3E-10 #mol /l / s 
 -m0 0.083682
#-cvode true
-rk 6
#-bad_step_max 1000
gas_phase 1-@_NODES
-fixed_volume
CO2(g) 0.0
O2(g) 0.0
-equilibrate with solution 1001

rt_output
-profile gnuplot
selected_output
-totals Fe(2) Fe(3) S(6) S(-2)
-pH
-pe
-si pyrite
user_punch
-headings Distance volpyr pO2 pCO2
-plot_titles "volume fraction pyrite" "pO_2" "pCO_2"
-plot_units "-"  "atm" "atm"
-mybasic 
-start
 punch(-dist())
 punch(kin("pyrite")*phase_vm("pyrite")/1000)
 punch(sr("O2(g)"),sr("CO2(g)"))
-end

GLOBAL_VARIABLE Profiles$  "nod_inf_chem.out"
GLOBAL_VARIABLE HP2015$  "Figure 3 - HP1.txt"
GLOBAL_VARIABLE MIN3P$  "Figure 3 - MIN3P.txt"
SELECTED_GRAPH
-start
 set linestyle 1 lc "red" lw 3 
 set linestyle 2 lc "blue" lw 3 
  set linestyle 3 lc "green" lw 3 
 set size ratio 1.25
 set linestyle 51 lc "black" lw 2 pi 8 dt 3

 tCreated = 'Created with @_HPVERSION$ on @_DATE$ - @_TIME$ '
 set label 1 tCreated at graph 1, screen 0.98 right font ",6" textcolor "gray40"
 tProj = '@_PROJECTNAME$ '
 set label 2 tProj at graph 1, screen 0.02 right font ",6" textcolor "gray40"
 
 set yrange [5:0]
 set ylabel "Depth [m]"
 set key inside bottom
 set size 1,0.95
 set xtics scale 1.5,1 
 set object 1 polygon  from graph 0,0.5 to graph 1,0.5 fc rgb "grey80"
 set object 2 polygon from graph 0.75,0.5 to graph 0.735,0.52  to graph 0.765,0.52 fillstyle solid 0.5 noborder
-end

-fig_nr 1
-fig_group "KM - SS -ARD01"
-fig_variabletype "Mayer et al - 2015 - Fig 3"
-fig_name "pH pe"
-fig_type "yx"
-fig_y same depth_[m] Distance
-fig_x pH <ds "@HP2015$ " k "pH HP1 (2015)" ls 1>
-fig_x pH <ds "@MIN3P$ " k "pH MIN3P" ls 1 dt 2>
-fig_sx pe <ds "@HP2015$ " k "pe HP1 (2015)" ls 2>
-fig_sx pe <ds "@MIN3P$ " k "pe MIN3P" ls 2 dt 2>
-fig_x pH <ds "@Profiles$ " k "HPx" i 10 ls 51 style linespoints y 1>
-fig_sx pe <ds "@Profiles$ " vk false i 10 ls 51 style linespoints y 1>
-fig_start
 set x2tics 10 out border out scale 1.5,1 
 set mx2tics 2
 set x2range [-5:25]
 set xtics 1
 set xrange [1:7]
 set xlabel "pH"
 set x2label "pe"
-fig_end 

-fig_nr 2
-fig_group "KM - SS -ARD01"
-fig_variabletype "Mayer et al - 2015 - Fig 3"
-fig_name "pyrite"
-fig_type "yx"
-fig_y same depth_[m] Distance
-fig_x pyrite_volume_fraction <ds "@HP2015$ " k "HP1 (2015)" ls 1>
-fig_x pyrite_volume_fraction <ds "@MIN3P$ " k "MIN3P" ls 2>
-fig_x volpyr <ds "@Profiles$ " k "HPx" i 10 ls 51 style linespoints y 1>
-fig_start
 set xlabel "/Symbol f_{pyrite}"
 set xtics 0.001
 set xrange [0:0.003]
 set key left
-fig_end 

-fig_nr 3
-fig_group "KM - SS -ARD01"
-fig_variabletype "Mayer et al - 2015 - Fig 3"
-fig_name "Fe S"
-fig_type "yx"
-fig_y same depth_[m] Distance
-fig_x SO4_[mol_L-1] <ds "@HP2015$ " k "S(6) HP1 (2015)" ls 1>
-fig_x SO4_[mol_L-1] <ds "@MIN3P$ " k "S(6) MIN3P" ls 1 dt 2>
-fig_sx Fe(II)_mol_L-1] <ds "@HP2015$ " k "Fe(2) HP1 (2015)" ls 2>
-fig_sx Fe(II)_mol_L-1] <ds "@MIN3P$ " k "Fe(2) MIN3P" ls 2 dt 2>
-fig_sx Fe(III)_[mol_L-1] <ds "@HP2015$ " k "Fe(3) HP1 (2015)" ls 3>
-fig_sx Fe(III)_[mol_L-1] <ds "@MIN3P$ " k "Fe(3) MIN3P" ls 3 dt 2>
-fig_x S(6) <ds "@Profiles$ " k "HPx" i 10 ls 51 style linespoints y 1>
-fig_sx Fe(2) <ds "@Profiles$ " vk false i 10 ls 51 style linespoints y 1>
-fig_sx Fe(3) <ds "@Profiles$ " vk false i 10 ls 51 style linespoints y 1>
-fig_start
 set x2tics 0.01 out border out scale 1.5,1 
 set mx2tics 2
 set x2range [0:0.05]
 set xtics 0.02
 set xrange [0:0.08]
 set xlabel "S(6) [mol L^{-1]"
 set x2label "Fe(2), Fe(3) [mol L^{-1]"
 set key left
-fig_end 

-fig_nr 4
-fig_group "KM - SS -ARD01"
-fig_variabletype "Mayer et al - 2015 - Fig 3"
-fig_name "O2"
-fig_type "yx"
-fig_y same depth_[m] Distance
-fig_x pO2_[atm] <ds "@HP2015$ " k "HP1 (2015)" ls 1>
-fig_x pO2_[atm] <ds "@MIN3P$ " k "MIN3P" ls 2>
-fig_x pO2 <ds "@Profiles$ " k "HPx" i 10 ls 51 style linespoints y 1>
-fig_start
 set xlabel "p_{O_2} [atm]"
 set xtics 0.05
 set xrange [0:0.25]
-fig_end