file upload

MICP_Kinetics.py

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+"""kinetics of microbially induced calcium carbonate precipitation(MICP)."""
+
+import phreeqpy.iphreeqc.phreeqc_dll as phreeqc_mod
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+phreeqc = phreeqc_mod.IPhreeqc('/usr/local/lib/libiphreeqc.so')
+
+initial_conditions = """
+#-------------------------------------------
+SOLUTION_MASTER_SPECIES
+    Urea Urea  0 CO(NH2)2 60.06 
+    
+SOLUTION_SPECIES 
+Urea = Urea
+        log_k  0 
+        Vm  14.5
+Cl- + H+ = HCl
+        log_k   0.7
+        delta_h 0       kcal
+        -gamma  0       0.06
+Cl- + Ca+2 = CaCl+
+        log_k   0.3
+        delta_h 0       kcal
+        -gamma  0       0.06
+2Cl- + Ca+2 = CaCl2
+        log_k   .66
+        delta_h 0       kcal
+        -gamma  0       0.06
+#---------------------------------------------
+
+SOLUTION 1
+      Urea 1
+      Ca 1
+      Cl 2
+      -units 	mol/kgw
+      -pH 	7	charge_balance
+
+Rates
+    Ureolysis
+    -START
+    10 REM PARM(1) = biomass density in CFU/l
+    20 if (M <= 0) then goto 40                                              
+    30 rate = PARM(1)*6.4e-12 /3600 * mol("Urea") / (mol("Urea") + .3)
+    40 moles = rate * TIME                                                   
+    50 save moles                                                            
+    -END
+
+    Calcite
+    -START
+    10  REM PARM(1) = specific surface area of calcite, cm^2/mol
+    20  REM PARM(2) = exponent for M/M0
+    30  si_cc = SI("Calcite")
+    40  IF (M <= 0  and si_cc < 0) THEN GOTO 100
+    50  k1 = 1.55e-6 #mol/m2/s
+    60  k2 = 5.01E-01 #mol/m2/s
+    70  IF M0 > 0 THEN area = PARM(1)*M0*(M/M0)^PARM(2) ELSE area = PARM(1)*M #area(m²)
+    80  rate = area * (k1 + ACT("H+")* k2) * (1 - 10^(si_cc)) #mol/s
+    90  moles = rate * TIME 
+    100 SAVE moles
+    -END
+
+Kinetics 1 #Ureolysis 
+    Ureolysis
+        -formula AmmH+ 2 CO3-2 1 Urea -1 H2O -2
+        -parms 1.58e9 
+    Calcite
+        -m0   .04 # mol/L # same as lb
+        -parms 1.1e1   0.6
+       -steps 900000 s in 100 steps 
+ 
+USER_PUNCH
+    -heading  soln_vol 
+    -START
+    10 punch soln_vol
+    -END
+
+SELECTED_OUTPUT
+    -step    true
+    -distance fasle
+    -state  false
+    -sim    false
+    -soln   false
+    -pe     false
+    -time   true
+    -pH 
+    -tot    Ca Urea 
+    -kinetic_reactants Calcite Ureolysis
+    -si calcite
+
+END
+"""
+np.set_printoptions(precision=2)
+pd.set_option('display.precision', 2)
+
+phreeqc.load_database(r"/home/amin/phreeqc_databases/Amm_biozement.dat")
+phreeqc.run_string(initial_conditions)
+output = phreeqc.get_selected_output_array()
+table = pd.DataFrame(output[1:], columns=output[0])
+print("\n")
+print(table)
+
+dk_Calcite = table['dk_Calcite'][1:]
+k_Calcite = table['k_Calcite'][1:]
+dk_Ureolysis = table['dk_Ureolysis'][1:]
+time = table['time'][1:]
+step = table['step'][1:]
+R_p = dk_Calcite/time/step
+R_u = -dk_Ureolysis/time/step
+sv_calcite = 36.9 # specific volume of calcite (cm³/mol)
+tot_v = table['soln_vol'][1:] + k_Calcite*sv_calcite/1000 # total volume in litre
+
+fig, ax = plt.subplots()
+ax.plot(time / 3600, R_p / R_u)
+ax.set(xlabel='time(h)', ylabel='$R_p/R_u$')
+
+plt.show()