script to compute the dihedral distribution #2
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Script to compute either the dihedral or the improper distributions of a system. The computed angle is signed, i.e. the range is between -180 and 180 degrees.
compute the distribution of dihedral angles similar to bond and angle scripts. The dihedral angle is signed i.e. ranging from -180 to 180 degrees
script to compute the dihedral distribution
the data.py module is used without being imported. the added line of code is just the import command.
the data.py module is used without being imported. The added line takes care of that
The data.py module is used without being imported. The added line of code takes care of the import statement
The variable xprd (the length in the x-direction) was replaced with boxlength which is the length of the simulation box in the desired cartesian coordinate
replace the open and close statements of the output file with a "with" construct
removing the box variable since it was not really used in the code
remove the open and close statements of the output file and replace it with an "with" construct modified one printing statement to use the format option
large modifications to the code using numpy for the calculations - the goal is to speed up the computation
rewritting angle_distribute using numpy and in more pythonic style than c modifications are similar to those in bond_distribute.py script
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
compute the distribution of dihedral angles similar to bond and angle scripts. The dihedral angle is signed i.e. ranging from -180 to 180 degrees