Gareth Kennedy

data scientist and mathematical modeller

 

MECSim Archive


MECSim Archive

To run MECSim requires the executable MECSim file and a text input file called "Master.inp".

Previous versions of MECSim are stored here. They use the 10/11/2015 version of the code and should only be used for consistency checks, or if the windows 10 compiled version does not work on your windows operating system. The current versions are found here.

Templates for the input text file can be downloaded below and the associated paper for MECSim will be available soon. Alternatively you can download the package for each operating system, which includes the MECSim program, a sample of input files and two documentation PDF files.

Windows 7 Download Package
Windows 10 Download Package
Win7/cygwin Download Package
Mac OS X version 10.11 "El Capitan" Download Package
ubuntu 14.04 Download Package

Notes:
(1) Windows 8 users should also use the Windows 7 versions.
(2) You may need to disable your firewall to download the executable files directly.
(3) Also you may need to to set windows to allow MECSim.exe to run (will ask when you double-click).

Input files

A list of "Master.inp" templates for the MECSim package are given in the zip file here. In addition to the templates themselves there is also a PDF file which explains the mechanism for each template. Both of these files come with the package downloads below. You will need to copy/rename one of these files to "Master.inp" for MECsim to use it - MECSim always takes it's input from this file.

The input files found in the templates zip file differ from previous versions in that the units have changed for surface confined reactions; so old input files will need to be checked or unphysical/unexpected results will occur.

Installation

All installations can now be run directly in each operating system. So all the installation required is to copy the executable file (MECSim or MECSim.exe) and the Master.inp text file into a directory.

Running MECSim

To run MECSim in windows: double-click on the MECSim.exe file in your file manager/windows explorer.

For Mac and Linux users: open a terminal and run the code using "./MECSim". The code will output some information to screen or to a file if you capture the output, e.g. "./MECSim > log.txt".

All versions will output the results to "MECSimOutput_Pot.txt" which is a text file in the DigiPot format (as default) which can be used in the same way as experimental data output from many machines.

The "MECSimOutput_Pot.txt" consists of a long header followed by data in order of applied voltage (V), current (A) and time (s). If additional details are specified in the "Master.inp" file then there will also be "EC_Model.tvc" which consists of the time, voltage, current, concentrations (all species at electrode surface) and "EC_Model.fin" which gives the final concentration profile of each chemical species as a function of distance from the electrode (first column).

For some analysis and basic plotting programs see the MECSim tools section here.

Using MECSim with cygwin

This is not recommended! For windows users please download the "Windows 7" version of MECSim directly. Cygwin has been increasingly difficult to use with gfortran and the installation process has been getting more complex.

If the need for cygwin is desperate then the installation for cygwin can be found here. During the installation make sure that you install the packages gfortran and dos2unix or the code will not run.

Assuming you have copied MECSim.exe and Master.inp to c:/MECSim and are using cygwin then you run MECSim by the following steps:

(1) Open up the cygwin terminal

(2) Change directory to where MECSim is kept, e.g. cd /cygdrive/c/MECSim/

(3) Make sure that all parameters in Master.inp are correctly set and the file has been saved. Now run MECSim from the cygwin terminal using the command ./MECSim.exe

(4) Check the output to screen that the correct mechanism and parameters have been simulated

(5) The end of the output to screen will also say what filename contains the simulated data, typically MECSimOutput.txt

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