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final finish up for making the repo public
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Kiran Vaddi committed Aug 15, 2020
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2 changes: 1 addition & 1 deletion Readme.md
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Expand Up @@ -91,7 +91,7 @@ This will plot the following:
## Notebooks
This repository is shipped few useful [notebooks](https://github.com/kiranvad/pyMECSim/tree/master/notebooks).
* [Cyclic Voltammetry Simulation Example for Single Electron Transfer Mechanism](https://github.com/kiranvad/pyMECSim/blob/master/notebooks/Cyclic%20Voltammetry%20Simulation%20Example%20for%20Single%20Electron%20Transfer%20Mechanism.ipynb) -- that examplains all the possible use case of the simulator on a simple one electron transfer mehcanism
* [Kinetic Zone Diagram](https://github.com/kiranvad/pyMECSim/blob/master/notebooks/Kinetic%20Zone%20%Diagram.ipynb) -- exmaple explaining how to generate various CV curves in the [kinetic zone diagram](https://www.nature.com/articles/s41570-017-0039/figures/2)
* [Kinetic Zone Diagram](/notebooks/Kinetic%20Zone%20Diagram.ipynb) -- exmaple explaining how to generate various CV curves in the [kinetic zone diagram](https://www.nature.com/articles/s41570-017-0039/figures/2)
## Notes
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242 changes: 61 additions & 181 deletions pymecsim/EC_Model.fin
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36,868 changes: 32,770 additions & 4,098 deletions pymecsim/EC_Model.tvc
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36,878 changes: 32,775 additions & 4,103 deletions pymecsim/MECSimOutput_Pot.txt
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23 changes: 10 additions & 13 deletions pymecsim/Master.inp
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@@ -1,10 +1,10 @@
2.98e+02 !T
0.00e+00 !Rh
5.00e-01 !E_start
-5.00e-01 !E_rev
5.10e-01 !E_start
-5.10e-01 !E_rev
1 !num_cycles
1.00e+00 !scan_rate
12 !points in time across n cycle
7.50e-02 !scan_rate
15 !points in time across n cycle
0 ! correct vscan and freq for DigiPot/FFT
1 ! output type: 0=E,i,t; 1=DigiPot compatible
0 ! EC type: 0 = Butler-Volmer, 1 = Marcus theory
Expand Down Expand Up @@ -35,18 +35,15 @@
1.00e-05 ! nu_RDE
1 ! number of AC sources to add (keep 1 with zero amplitude if want DC only)
0.00e+00, 1.80e+01 ! AC sin wave: amp (mV), freq(Hz) (REPEAT)
4 ! Number of species
1.00e-06, 1.00e-05, 0 ! P
0.00e+00, 1.00e-05, 0 ! Q
1.00e-05, 1.00e-05, 0 ! A
0.00e+00, 1.00e-05, 0 ! B
3 ! Number of species
1.00e-06, 1.00e-03, 0 ! Cu2O
0.00e+00, 0.00e+00, 0 ! Cu
1.00e-06, 1.00e-02, 0 ! CuO2--
3 ! Number of terms
0 ! E_pzc (V)
0 ! a_0
0 ! a_1
0 ! a_2
0 ! a_3
0, -1, 1, 0, 0, 0.0e0, 0.0e0, 0.00e+00, 1.00e+01, 5.00e-01 !Charge Transfer : 1 P + 1 e <=> 1 Q
2, 1, -1, -1, 1, 3.89e+10, 1.00e-05, 0.0e0, 0.0e0, 0.50 !Chemical Reaction : 1 Q + 1 A <=> 1 P + 1 B


0, -1, 1, 0, 0.0e0, 0.0e0, -5.50e-01, 1.00e-01, 5.00e-01 !Charge Transfer : 1 Cu2O + 1 e <=> 1 Cu
0, 1, 0, -1, 0.0e0, 0.0e0, -1.20e-01, 1.00e+05, 5.00e-01 !Charge Transfer : 1 CuO2-- + 1 e <=> 1 Cu2O
23 changes: 10 additions & 13 deletions pymecsim/from_expt.inp
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@@ -1,10 +1,10 @@
2.98e+02 !T
0.00e+00 !Rh
5.00e-01 !E_start
-5.00e-01 !E_rev
5.10e-01 !E_start
-5.10e-01 !E_rev
1 !num_cycles
1.00e+00 !scan_rate
12 !points in time across n cycle
7.50e-02 !scan_rate
15 !points in time across n cycle
0 ! correct vscan and freq for DigiPot/FFT
1 ! output type: 0=E,i,t; 1=DigiPot compatible
0 ! EC type: 0 = Butler-Volmer, 1 = Marcus theory
Expand Down Expand Up @@ -35,18 +35,15 @@
1.00e-05 ! nu_RDE
1 ! number of AC sources to add (keep 1 with zero amplitude if want DC only)
0.00e+00, 1.80e+01 ! AC sin wave: amp (mV), freq(Hz) (REPEAT)
4 ! Number of species
1.00e-06, 1.00e-05, 0 ! P
0.00e+00, 1.00e-05, 0 ! Q
1.00e-05, 1.00e-05, 0 ! A
0.00e+00, 1.00e-05, 0 ! B
3 ! Number of species
1.00e-06, 1.00e-03, 0 ! Cu2O
0.00e+00, 0.00e+00, 0 ! Cu
1.00e-06, 1.00e-02, 0 ! CuO2--
3 ! Number of terms
0 ! E_pzc (V)
0 ! a_0
0 ! a_1
0 ! a_2
0 ! a_3
0, -1, 1, 0, 0, 0.0e0, 0.0e0, 0.00e+00, 1.00e+01, 5.00e-01 !Charge Transfer : 1 P + 1 e <=> 1 Q
2, 1, -1, -1, 1, 3.89e+10, 1.00e-05, 0.0e0, 0.0e0, 0.50 !Chemical Reaction : 1 Q + 1 A <=> 1 P + 1 B


0, -1, 1, 0, 0.0e0, 0.0e0, -5.50e-01, 1.00e-01, 5.00e-01 !Charge Transfer : 1 Cu2O + 1 e <=> 1 Cu
0, 1, 0, -1, 0.0e0, 0.0e0, -1.20e-01, 1.00e+05, 5.00e-01 !Charge Transfer : 1 CuO2-- + 1 e <=> 1 Cu2O
19 changes: 11 additions & 8 deletions pymecsim/input.py
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Expand Up @@ -129,9 +129,9 @@ def __init__(self, reactants, products, E0, ks=1e4, alpha=0.5):


def get_params_as_string(self):
params = ' ks= {:.2E}, '.format(self.ks)
params += 'E0 = {:.2E}, '.format(self.E0)
params += 'alpha = {:.2f}'.format(self.alpha)
params = ' ks= {}, '.format(process_parameter(self.ks))
params += 'E0 = {}, '.format(process_parameter(self.E0))
params += 'alpha = {}'.format(process_parameter(self.alpha))

return params

Expand Down Expand Up @@ -187,8 +187,8 @@ def __init__(self, reactants, products, kf=1e4, kb=1e4):


def get_params_as_string(self):
params = ' kf= {:.2E}, '.format(self.kf)
params += 'kb= {:.2E} '.format(self.kb)
params = ' kf= {}, '.format(process_parameter(self.kf))
params += 'kb= {} '.format(process_parameter(self.kb))

return params

Expand Down Expand Up @@ -329,13 +329,16 @@ class Voltammetry:
(This function has not been tested)
"""
def __init__(self, objs=None):
def __init__(self, objs=None, N=12):
"""
N : Number of spatial points as a power of two
"""
self.N = N
self.set_defaults()
self.objs = objs
self.ramp = 0
self._check_objs()


def from_file(self):
dirname = os.path.dirname(__file__)
fname = os.path.join(dirname, 'Einput.txt')
Expand All @@ -350,7 +353,7 @@ def get_input(self):
for key, value in self.dcvolt_params.items():
lines.append('{}\t!{}\n'.format(process_parameter(value), key))

lines.append('12\t!points in time across n cycle \n')
lines.append('{}\t!points in time across n cycle \n'.format(process_parameter(self.N)))
lines.append('0\t! correct vscan and freq for DigiPot/FFT \n')
lines.append('1\t! output type: 0=E,i,t; 1=DigiPot compatible \n')
lines.append('0\t! EC type: 0 = Butler-Volmer, 1 = Marcus theory \n')
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118 changes: 55 additions & 63 deletions pymecsim/log.txt
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Expand Up @@ -10,113 +10,105 @@
Uncompensated R = 0.0

Voltage ramp (V):
E_start = 0.5000
E_rev = -0.5000
E_end = 0.5000
E_start = 0.5100
E_rev = -0.5100
E_end = 0.5100
Cycles = 1
Total range = 2.0000
Total range = 2.0400

Scan rate (V/s) = 1.00000000E+00
Final time (s) = 2.00000000E+00
Scan rate (V/s) = 7.50000000E-02
Final time (s) = 2.72000000E+01

Found 1 AC signal(s). Max frequency = 0.0000 Hz
0.0000 mV at 18.0000 Hz
0.0000 mV at 18.0147 Hz

No capacitor requested

Need to enter ghost reaction of the form
C + 1e = D ; E0 = 0.922 , ks = 0.0000E+00 , alpha = 0.500
with E0= 0.92182831236606899
Linked CT reaction at CT reaction number 1
With species numbers: 3 0 0

Found a total of 4 species
Found a total of 3 species

No pre-equilibriation; use entered concentrations

Summary of solution reactions:
Charge transfer = 1
Charge transfer = 2
1st Order Chem = 0
2nd Order Chem = 1
2nd Order Chem = 0
Summary of surface confined reactions:
Charge transfer = 0
1st Order Chem = 0
2nd Order Chem = 0

Charge transfer reaction(s):
A + 1e = B ; E0 = 0.000 , ks = 1.0000E+01 cm/s , alpha = 0.50
; K_eqm = 2.8576E+08
Chemical reaction(s):
B + C = A + D ; kf,kb = 3.890000E+10 1.000000E-05 cm3/(mol.s)
; K_eqm = 3.8900E+15
A + 1e = B ; E0 = -0.550 , ks = 1.0000E-01 cm/s , alpha = 0.50
; K_eqm = 8.4471E+17
C + 1e = A ; E0 = -0.120 , ks = 1.0000E+05 cm/s , alpha = 0.50
; K_eqm = 4.5139E+10

Electrode geometry:
Planar with area = 1.00000000E+00 cm^2

Technical details of simulation
Using Butler-Volmer Theory
Points in time = 2^12 = 4096
delt = 4.8828E-04 and delE = 4.8828E-04
Exponential spatial grid with 180 points and delx(0) = 5.0104E-11
x = 2.4426E-11 7.7099E-11 1.3531E-10 1.9965E-10 | 2.9755E-02
Points in time = 2^15 = 32768
delt = 8.3008E-04 and delE = 6.2256E-05
Exponential spatial grid with 60 points and delx(0) = 9.1109E-03
x = 4.4416E-03 1.4020E-02 2.4605E-02 3.6303E-02 | 3.3158E+01

Solution phase:
Initial scaled concentrations and diffusion coeff (cm2/s)
[A] = 1.00000000E-06 ; D = 1.00000000E-05
(0.09090909)
[B] = 0.00000000E+00 ; D = 1.00000000E-05
(0.00000000)
[C] = 1.00000000E-05 ; D = 1.00000000E-05
(0.90909091)
[D] = 0.00000000E+00 ; D = 1.00000000E-05
[A] = 1.00000000E-06 ; D = 1.00000000E-03
(0.50000000)
[B] = 0.00000000E+00 ; D = 1.00000000E+00
(0.00000000)
Concentrations scaled by 1.10000000E-05 mol/cm3
1.10000000E+01 mM
[C] = 1.00000000E-06 ; D = 1.00000000E-02
(0.50000000)
Concentrations scaled by 2.00000000E-06 mol/cm3
2.00000000E+00 mM


************** Starting Time Loop ******************

Done 10%; t,Eapp,i = 2.00E-01 3.00E-01 -1.58E-06, C_err= 8.19E-09
0.0909 0.0000 0.9090 0.0001 0.0000 0.0000
Done 20%; t,Eapp,i = 4.00E-01 1.00E-01 -3.34E-03, C_err= 9.19E-09
0.0891 0.0018 0.7448 0.1643 0.0000 0.0000
Done 30%; t,Eapp,i = 6.00E-01 -9.96E-02 -4.79E-03, C_err= 1.19E-08
0.0019 0.0890 0.0000 0.9091 0.0000 0.0000
Done 40%; t,Eapp,i = 8.00E-01 -3.00E-01 -3.14E-03, C_err= 1.28E-08
0.0000 0.0909 0.0000 0.9091 0.0000 0.0000
Done 50%; t,Eapp,i = 1.00E+00 -5.00E-01 -2.52E-03, C_err= 1.54E-08
0.0000 0.0909 0.0000 0.9091 0.0000 0.0000
Done 60%; t,Eapp,i = 1.20E+00 -3.00E-01 -2.16E-03, C_err= 1.75E-08
0.0000 0.0909 0.0000 0.9091 0.0000 0.0000
Done 70%; t,Eapp,i = 1.40E+00 -1.00E-01 -1.89E-03, C_err= 1.78E-08
0.0018 0.0891 0.0000 0.9091 0.0000 0.0000
Done 80%; t,Eapp,i = 1.60E+00 9.96E-02 -6.28E-04, C_err= 1.99E-08
0.0891 0.0018 0.0242 0.8849 0.0000 0.0000
Done 90%; t,Eapp,i = 1.80E+00 3.00E-01 -7.34E-07, C_err= 2.08E-08
0.0909 0.0000 0.1878 0.7213 0.0000 0.0000
Done 100%; t,Eapp,i = 2.00E+00 5.00E-01 -3.62E-10, C_err= 2.03E-08
0.0909 0.0000 0.2689 0.6402 0.0000 0.0000
Done 10%; t,Eapp,i = 2.72E+00 3.06E-01 1.05E-03, C_err= -3.42E-01
0.0000 0.0000 0.6581 0.0000 0.0000 0.0000
Done 20%; t,Eapp,i = 5.44E+00 1.02E-01 7.38E-04, C_err= -3.42E-01
0.0001 0.0000 0.6581 0.0000 0.0000 0.0000
Done 30%; t,Eapp,i = 8.16E+00 -1.02E-01 -2.12E-03, C_err= -1.47E-01
0.2828 0.0000 0.5706 0.0000 0.0000 0.0000
Done 40%; t,Eapp,i = 1.09E+01 -3.06E-01 -4.71E-03, C_err= 1.07E+00
2.0722 0.0001 0.0015 0.0000 0.0000 0.0000
Done 50%; t,Eapp,i = 1.36E+01 -5.10E-01 -9.95E-03, C_err= 5.00E-03
0.9702 0.0348 0.0000 0.0000 0.0000 0.0000
Done 60%; t,Eapp,i = 1.63E+01 -3.06E-01 -8.73E-04, C_err= 1.06E+00
2.0540 0.0007 0.0015 0.0000 0.0000 0.0000
Done 70%; t,Eapp,i = 1.90E+01 -1.02E-01 7.73E-03, C_err= -1.51E-01
0.2817 0.0000 0.5671 0.0000 0.0000 0.0000
Done 80%; t,Eapp,i = 2.18E+01 1.02E-01 2.52E-03, C_err= -3.42E-01
0.0001 0.0000 0.6581 0.0000 0.0000 0.0000
Done 90%; t,Eapp,i = 2.45E+01 3.06E-01 1.56E-03, C_err= -3.42E-01
0.0000 0.0000 0.6581 0.0000 0.0000 0.0000
Done 100%; t,Eapp,i = 2.72E+01 5.10E-01 1.16E-03, C_err= -3.42E-01
0.0000 0.0000 0.6581 0.0000 0.0000 0.0000

Concentration min/max values:
0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000
0.0909 0.0909 0.9091 0.9091 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2.0722 0.0357 0.6582 0.0000 0.0000 0.0000

****************************************************

Current minimum = -1.13560220E-02 and maximum = 0.00000000E+00
Voltage minimum = 4.49218750E-02 and maximum = 0.00000000E+00
Current minimum = -9.95293401E-03 and maximum = 2.15123940E-02
Voltage minimum = -5.10000000E-01 and maximum = 5.09937744E-01

Average number of iterations at electrode surface = 1.000
Average number of iterations for chemical reactions = 1.683
Average number of iterations for chemical reactions = 1.000
Average ODE calculations for iterating surface conf = 0.000
Average ODE calculations for bounding surface conf = 0.000

Final scaled concentrations on spatial grid
[A] = 9.09090923E-02 9.09090923E-02 9.09090923E-02 | 9.09090909E-02
[B] = 3.18134265E-10 3.18133433E-10 3.18131638E-10 | 1.34485939E-23
[C] = 2.68896937E-01 2.68896937E-01 2.68896937E-01 | 9.09090386E-01
[D] = 6.40193990E-01 6.40193990E-01 6.40193990E-01 | 5.23150001E-07

Error in concentration sum (=0 if D_A = D_B etc)
2.03333324E-08 2.03333321E-08 2.03333319E-08 | 1.64535052E-13
[A] = 1.48432686E-11 2.31381557E-02 7.28518007E-02 | 5.00000000E-01
[B] = 4.24636210E-12 1.73343792E-06 5.47146989E-06 | 4.53996721E-10
[C] = 6.58114176E-01 6.55627017E-01 6.50265599E-01 | 5.00000000E-01


Output file written to MECSimOutput_Pot.txt
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