I have a .xyz
file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well.
What software can I use to perform block analysis?
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Sign up to join this communityI have a .xyz
file for a trajectory and I want to perform block analysis on it, and to find the decorrelation time and to perform analysis on that as well.
What software can I use to perform block analysis?
This simple Python code does a Flyvbjerg-Petersen blocking analysis on column(s) of data. It is also used in some larger softwae packages, such as NECI.
You can run the code with the following command if you have just one column of data:
python blocking.py -f180000 -d5 -o/ file.out
where in this case 180000
is the line in file.out
at which you want to begin the blocking analysis, and -d5
tells the program that you want to apply the blocking analysis to column 5 of the data in file.out
.
If you want to do the blocking analysis on a ratio, then the command would be:
python blocking.py -f180000 -d1 -d5 -o/ file.out
where here we are doing column 1 divided by column 5.
I have several examples on my GitHub page, for example in this folder, you can see that I applied the above commands to the file RDMEstimates.uniform
and the result of the blocking analysis was printed to the file blockingResult.txt
.
See also: