Skip to content

Commit

Permalink
update with exceptions, kzd example and edits to readme
Browse files Browse the repository at this point in the history
  • Loading branch information
Kiran Vaddi committed Aug 13, 2020
1 parent 1da7443 commit 0fe0ad1
Show file tree
Hide file tree
Showing 12 changed files with 8,886 additions and 16,557 deletions.
23 changes: 13 additions & 10 deletions Readme.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,14 @@ pip install git+https://github.com/kiranvad/pyMECSim#egg=pyMECSIM.`
```
Dependencies will be checked and installed from the setup.py file.

A sample usage is as follows:
To install the package locally:
```bash
git clone https://github.com/kiranvad/pyMECSim.git
cd pyMECSim
pip install -e .
```
There are two modes of usages:

## Mode 1: Using pymecsim experiment interface
```python
Expand Down Expand Up @@ -50,6 +57,7 @@ sim.plot() # plot the simulated CV curve
```

## Mode 2: Using MECSim configuration file
If you are familiar with original MECSim software and its configuaraton files (.inp), you can also pass it as an input.
Import `pymecsim` using the following:
```python
from pymecsim import MECSIM, pysed
Expand All @@ -73,22 +81,17 @@ for i,e0 in enumerate(E0):
ax = model.plot(ax = ax)
ax.set_label("E0 = "+str(e0))
plt.legend([r'$E_0=0.5$',r'$E_0=0.1$',r'$E_0=1e-2$'],loc='lower right')
#plt.savefig('cvexample.png',dpi=500,bbox_inches='tight')
plt.show()
```
This will plot the following:
<img src="notebooks/cvexample.png" width="400">
Once you have the mechanism file in say `/path/to/folder/mechanism.sk` format, turn it in as an input to pyMECSim using the following:
```python
model = MECSIM('/path/to/folder/mechanism.sk')
model.plot()
plt.show()
```
One can also get concentration profiles by first indicating `MECSIM` to return concentration profiles in the configuration file by setting `1 ! show debug output files as well as MECSimOutput.txt (1=yes; 0=no)`. `pymecsim` will then be able to return concentration profiles as numpy arrays. see `notebooks/Cyclic Voltammetry Simulation Example for Single Electron Transfer Mechanism.ipynb` for an example use case.
## 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)
## Notes
Expand Down
158 changes: 158 additions & 0 deletions notebooks/Kinetic Zone Diagram.ipynb
View file

Large diffs are not rendered by default.

98 changes: 55 additions & 43 deletions notebooks/log.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@


General parameters:
Temperature = 298.2000
Temperature = 298.0000
Uncompensated R = 0.0

Voltage ramp (V):
Expand All @@ -16,95 +16,107 @@
Cycles = 1
Total range = 2.0000

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

Found 1 AC signal(s). Max frequency = 0.0000 Hz
0.0000 mV at 180.0000 Hz
0.0000 mV at 18.0000 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

Found a total of 2 species
Found a total of 4 species

No pre-equilibriation; use entered concentrations

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

Charge transfer reaction(s):
A + 1e = B ; E0 = 0.250 , ks = 1.0000E+04 cm/s , alpha = 0.50
; K_eqm = 1.6794E+04
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

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

Technical details of simulation
Using Butler-Volmer Theory
Points in time = 2^14 = 16384
delt = 1.2207E-05 and delE = 1.2207E-04
Exponential spatial grid with 57 points and delx(0) = 3.4939E-06
x = 1.7033E-06 5.3763E-06 9.4355E-06 1.3922E-05 | 9.4112E-03
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

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


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

Done 10%; t,Eapp,i = 2.00E-02 3.00E-01 -7.11E-04, C_err= -2.87E-12
0.8752 0.1248 0.0000 0.0000 0.0000 0.0000
Done 20%; t,Eapp,i = 4.00E-02 1.00E-01 -1.47E-03, C_err= -1.78E-12
0.0029 0.9971 0.0000 0.0000 0.0000 0.0000
Done 30%; t,Eapp,i = 6.00E-02 -1.00E-01 -9.27E-04, C_err= -1.26E-12
0.0000 1.0000 0.0000 0.0000 0.0000 0.0000
Done 40%; t,Eapp,i = 8.00E-02 -3.00E-01 -7.36E-04, C_err= -1.42E-12
0.0000 1.0000 0.0000 0.0000 0.0000 0.0000
Done 50%; t,Eapp,i = 1.00E-01 -5.00E-01 -6.29E-04, C_err= -1.62E-12
0.0000 1.0000 0.0000 0.0000 0.0000 0.0000
Done 60%; t,Eapp,i = 1.20E-01 -3.00E-01 -5.59E-04, C_err= -1.83E-12
0.0000 1.0000 0.0000 0.0000 0.0000 0.0000
Done 70%; t,Eapp,i = 1.40E-01 -1.00E-01 -5.08E-04, C_err= -2.06E-12
0.0000 1.0000 0.0000 0.0000 0.0000 0.0000
Done 80%; t,Eapp,i = 1.60E-01 1.00E-01 -4.51E-04, C_err= -3.06E-12
0.0029 0.9971 0.0000 0.0000 0.0000 0.0000
Done 90%; t,Eapp,i = 1.80E-01 3.00E-01 2.10E-03, C_err= -6.10E-13
0.8747 0.1253 0.0000 0.0000 0.0000 0.0000
Done 100%; t,Eapp,i = 2.00E-01 5.00E-01 6.93E-04, C_err= -2.34E-12
0.9999 0.0001 0.0000 0.0000 0.0000 0.0000
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

Concentration min/max values:
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
1.0000 1.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 -0.0000 0.0000 0.0000 0.0000
0.0909 0.0909 0.9091 0.9091 0.0000 0.0000

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

Current minimum = -2.68622429E-03 and maximum = 2.24577576E-03
Voltage minimum = 2.21557617E-01 and maximum = 2.78686523E-01
Current minimum = -1.13560220E-02 and maximum = 0.00000000E+00
Voltage minimum = 4.49218750E-02 and maximum = 0.00000000E+00

Average number of iterations at electrode surface = 1.000
Average number of iterations for chemical reactions = 1.000
Average number of iterations for chemical reactions = 1.683
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] = 9.99940454E-01 9.98716251E-01 9.96076410E-01 | 9.99998347E-01
[B] = 5.95460837E-05 1.28374882E-03 3.92359046E-03 | 1.65337954E-06
[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)
-2.34245956E-12 -2.34312569E-12 -2.34601227E-12 | 6.50146603E-13
2.03333324E-08 2.03333321E-08 2.03333319E-08 | 1.64535052E-13


Output file written to MECSimOutput_Pot.txt
Expand Down
Loading

0 comments on commit 0fe0ad1

Please sign in to comment.