cmelab / cmelab/cmeutils

Add frame_to_CG_freud system

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#83 1 comment 0 reactions 2 assignees Claimed by @chrisjonesBSU View on GitHub
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Description

Add a function to cmeutils that takes in a gsd snapshot of an atomistic system and the CG mapping (obtained from grits), and it creates a freud system based on the CG beads. The resulting freud system is used in cmeutils functions that calculate structural properties such as rdf, order parameter, MSD, etc.

This function needs to calculate COM positions for the snapshot based on the mapping. We already have a similar function called `[frame_to_freud_system](https://github.com/cmelab/cmeutils/blob/master/cmeutils/gsd_utils.py#L13)`.

The benefit of having a function like that is that we can skip coarse graining the whole trajectory with grits and go straight to calculating our desired properties from the aa trajectories. Another benefit of this function is that it allows us to try on different mappings or smiles patterns for calculating properties.

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