Dear everyone,
I want to use my extended XYZ files generated by OVITO to get the data-relationship of my interest.
These files look like:
4
Lattice=" 81.44899750 0.00000000 0.00000000 0.00000000 81.57330322 0.00000000 0.00000000 0.00000000 179.52000427" Properties=id:I:1:species:S:1:pos:R:3:Occupancy:I:1
33349 Type_1 -0.151932 -39.1362991 87.8544007 2
6491 Type_1 -2.01495 -37.0219994 92.0175018 2
33661 Type_1 -0.233858 -40.2531014 90.1147003 0
55309 Type_1 0.0 -40.7999993 89.7600022 0
This fragment represents one frame in the whole simulation and will repeat 100 to 200 times with variable length, which is due to the numbers of atoms selected and outputted at each frame are different.
There are two things I want to do:
1. If there are 100 frames, I want to calculate the sum of different ‘Occupancy’ number at each frame, which means I want to know, how many ‘0’s or ‘1’s or ‘2’s and so on, are there at each frame. The value of property ‘Occupancy’ is at the last column of the XYZ file.
2. Furthermore, I want to sort the results by some expression such as PositionX=5, which mean I want to know how many ‘0’s in a selected region or at a particular position.
I am relative new to Molecular Dynamics Simulation, and I am lack of knowledge of post-analysis. Could anybody give me some help on the basic idea of doing this? Or any suggestions on which programming language is more suitable?
Any help would be much appreciated!
With My Best Regards
Liu
To parse files (to extract the datas that interest you), I know that Perl or Python programming languages are often used. Perl is pretty good for parsing but I don't know if it's convenient for analysing the extracted datas afterward (like sorting by PositionX), so maybe Python would be more suitable to your situation
Hello!
I think the simplest way is to copy the strings with data in other file (you can use any programming language).
At the end of each string you can add an information about the frame.
Then you can import this new file (with csv-like structure) in any program for treating tabular data. (OOO Calc, MS Excel or any databases).
Dear Vasilets
Thanks very much for your advice!
I have a lot of XYZ files and each XYZ file has hundreds of frames. So I'd like to write a script in one programming language and maybe this can been done automatically. I am not familiar with OOO Calc. But it seems in MS Excel, I need to process each file manually.
Best Regards
Liu
Dear Letort,
I am learning Python now. It will take me some time to apply Python script to my situation. I am wondering that, could you please give me some advice on learning commands or some ideas against this particular purpose?
Best Regards
Liu
Hi Liu,
It would probably be easier to help if you added to your post your actual file for testing since It's hard to code a parser for something we are only seeing a part of. That said OVITO seems to be prepared to deal with Python:
http://www.ovito.org/manual/python/
, and I believe the format you are using is some association to the .xyz:
https://en.wikipedia.org/wiki/XYZ_file_format
If you look for a parser to .xyz you'll find plenty out there (look for ".xyz python" in google, for example):
http://molmod.github.io/molmod/tutorial/molecule.html
https://github.com/pele-python/pele/tree/master/pele/utils/tests
Now I'm not sure if the example you've put in the post is, strictly speaking, .xyz but if it is try to use those libraries or perhaps using a software to convert it to something more readable. For example OpenBabel:
http://openbabel.org/wiki/Main_Page
Hope it helps.
Hi Liu,
As Pedro said you can look at ovito python scripts integration or google examples.
Otherwise, here's an example of a python parser script that will count the number of '0' of occupencies in a file that contains datas similar to what you put in your example. Hope it will help you.
Dear Correia,
Thank you very much! You give me a lot of information.
The attachment of this message is a sample file which I need to process. What I want to get is described in my original message.
I am a freshman to Python, it seems I need to learn Python first. Otherwise, I cannot understand the docs you recommended to me.
Do you have any other suggestions about how to learning Python to solve my particular case? I mean how I can learn Python more efficiently to solve my problem.
Sorry for replying so late. I have been without Internet for last week.
And thanks for your help again!
Dear Letort,
Thank you very much for the Python script!
It is a bit hard for me to understand the parser.py file right now. I think maybe I need to learn Python thoroughly first. I am wondering do I need to modify the parser.py for my case or I can use it directly with no modification.
I am very sorry for replying late. I have been without Internet for one week.
And thank you very much for all your help!
Dear Letort,
I learned some basic knowledge of Python recently.
I used the parser.py today and also I tried to modify the file in order to fit my purpose.
The file parser.py is written to analyze the extended XYZ files for a similar purpose of mine. I think if I modify the file a bit, I can use it.
it is very helpful. Thank you very much!
Hi Liu,
Glad to hear that the file is hepfull. If you are going to use and modify it, I attached a new version of this file where I added comments so it will be easier for you to handle it.
Good luck
Dear Letort,
It is so nice of you to do this. Thank you very much indeed!
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