Comments (2)
For reference, how long is it currently taking? I tested out a few larger systems (440,000 atoms) using the freud clustering approach in the polymer utils PR, and it takes about 0.2 - 0.5 seconds to go from an atomistic gsd to CG gsd for a single frame (depending on the degree of coarse graining). This is still technically using mbuild to generate the CG system, then saving to .gsd. I'm sure it would be quicker to use a gsd writer directly and skip mbuild.
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I think it's the smarts matching that is taking so long. I plan to use freud cluster module to break things up and then use smarts matching on only one section.
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Related Issues (16)
- Add CI/tests
- mappings to ring structures should not always share atoms
- Add a mapping save and load from mapping functions HOT 1
- Simulation example HOT 1
- clean up repo HOT 1
- Add bead mass
- Finegraining united atom to all-atom HOT 3
- Fix visualize method
- Idea: non chemistry based grammar
- CG_System not completely populating bonding informaiton in snapshots HOT 3
- switch from openbabel to rdkit HOT 2
- SMILES matching on UA need a better warning or different functionality
- Mapping of mass from atomistic to cg beads failing because of how pybel smarts matching works
- Improve the mapping operator HOT 1
- Update install instructions in the docs
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