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HOOMD-TF CG Example#31

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RainierBarrett wants to merge 40 commits intocmelab:mastercmelab/polybinder:masterfrom RainierBarrett:htf-cgRainierBarrett/polybinder:htf-cgCopy head branch name to clipboard

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Commits on Jan 20, 2021

• Initial structure.

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• Initial bead count correct

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Commits on Jan 26, 2021

• Kernel dying when trying to find CG RDFs

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Commits on Jan 28, 2021

• Position tracking of CG beads working

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Commits on Feb 8, 2021

• First copy of CG demo .py file. Failing

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• Fix cg_num arg

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Commits on Feb 17, 2021

• Able to calculate CG bonds/angles/dihedrals

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Commits on Feb 18, 2021

• Can save out and load mapping indices from .npy files

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Commits on Feb 24, 2021

• Model compiles but doesn't train (dict key error)

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Commits on Mar 4, 2021

• Update uli-init to use hoomd-tf

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Commits on Mar 8, 2021

• Add online demo file. Offline demo broken

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Commits on Mar 10, 2021

• Fixed model input structure, need to test full run

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Commits on Mar 11, 2021

• Add script for plotting CG params and writing gsd of CG positions

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Commits on Mar 18, 2021

• Merge branch 'master' of github.com:cmelab/uli-init into htf-cg

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Commits on Apr 22, 2021

• Remove old matplotlib import

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• remove old matplotlib import

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• Merge branch 'master' into htf-cg

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Commits on May 4, 2021

• Update with some needed htf packages

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• Merge branch 'htf-cg' of https://github.com/RainierBarrett/uli-init into htf-cg

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• Remove json oops

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Commits on May 5, 2021

• fix Online example script after upstream HTF update

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Commits on May 6, 2021

• Add saving of CG params/energy/positions/forces

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• Fix outputs indexing

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• Update plotting from np.genfromtxt to np.load

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• Merge branch 'htf-cg' of https://github.com/RainierBarrett/uli-init into htf-cg

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Commits on Jun 10, 2021

• Add command line args for plotting CG results. Onlilne demo now picks one-molecule file dynamically by n_monomers, too

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Commits on Jun 30, 2021

• Update online demo file for tf.gather math

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• put several file types generated by online example file in gitignore

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Commits on Jul 7, 2021

• Add plotting of simulation potential energy vs time

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Commits on Jul 13, 2021

• Merge branch 'master' into htf-cg

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• Make TF nlist check period a Simulation param

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• Remove outdated environment include

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• Update environment mbuild address

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• Forgot nohoomd env file too

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Commits on Jul 16, 2021

• Update demo file for upstream changes. rename Initialize class.

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Commits on Aug 10, 2021

• HTF running, running out of CUDA memory

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Commits on Aug 26, 2021

• Try smaller nlists to save memory?

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Commits on Aug 30, 2021

• Add TF batch size arg to Simulate class

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Commits on Nov 29, 2021

• Add make_fg_traj script

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Commits on Mar 2, 2022

• Fix argument error in trajmodel

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