[ADF-LIST] ADF GUI help :ReaxFF molecular fractions

Gayani Nadeera Pallewela (Dr) gayani at ntu.edu.sg
Fri Oct 13 09:07:14 CEST 2017

Dear Laurens,

Thank you and I will try this

Best regards,
Gayani



From: ADFlist [mailto:adflist-bounces at scm.com] On Behalf Of Laurens Groot
Sent: Friday, October 13, 2017 3:02 PM
To: ADF discussion list
Subject: Re: [ADF-LIST] ADF GUI help :ReaxFF molecular fractions

Dear Gayani,

This is not possible yet with the GUI. A script would be required to parse the .rxmolfra file.
A quick python implementation is as follows:

#!/usr/bin/python

import sys

if (len(sys.argv) < 4):
    print("Incorrect number of arguments.")
    print("Usage: file.rxmolfra nstartmolecules mol1 [mol2 ...]")
    sys.exit()

filename = sys.argv[1]
nstartmolecules = sys.argv[2]
molecules = sys.argv[3:]
print("Iteration,"+",".join(molecules))
with open(filename) as f:
    for line in f:
        if "Iteration" in line:
            count = ['0'] * len(molecules)
            iteration = '0'
        if "Total number of molecules" in line:
            print(iteration+","+",".join(count))
        for imol, mol in enumerate(molecules):
            if " "+mol+" " in line:
                words = line.split()
                iteration = words[0]
                count[imol] = str(float(words[1])/float(nstartmolecules))

To run it on the example from the tutorial:
python script.py Methane.rxmolfra 350 CH4 H2O CO2 > result.csv
You can import this in your favourite plotting program. We will probably have a way to plot this directly in our GUI with the next release...
I hope this answers your question.

Kind regards,
Laurens

Op 9-10-2017 om 11:19 schreef Gayani Nadeera Pallewela (Dr):
Dear All,

As shown in the ADF tutorial I was able to obtain the molecular fractions of the simulated system.
I want to plot the ratio of Number of particular molecular type/Initial number of molecules with the time.

As I understood Max option give the absolute number of molecules.
Is there any way that I can get Number of particular molecular type/Initial number of molecules plot.
Do I have to use a separate script to do this using  .rxmolfra file as an input?

Thanks and regards,
Gayani

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