Josh Fass maxentile
maxentile
/ GlobalLocalReweightingOptimization.ipynb
Last active
September 21, 2023 14:05
fleshing out https://github.com/proteneer/timemachine/pull/654#discussion_r818092856
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maxentile
/ PermutationHREX.ipynb
Created
September 19, 2023 18:21
apply locally balanced MCMC to p(permutation | xs) step of {p(xs | permutation), p(permutation | xs)} HREX
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maxentile
/ restricted_permutations.py
Created
August 29, 2023 19:29
side exploration -- pre-enumerated neighborhoods for permutation MCMC
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| def enumerate_restricted_permutations(n_states=50, num_neighbor_swaps=1): | |
| """enumerate all permutations accessible within num_neighbor_swaps applications of a move that swaps (i,i+1)""" | |
| identity_permutation = tuple(range(n_states)) | |
| def neighbor_swap(perm, i): | |
| """return copy where (perm[i], perm[i+1]) are swapped""" | |
| assert (i + 1) < len(perm) | |
| new_perm = list(perm) |
maxentile
/ OptimalMuSigmaPath1D.ipynb
Last active
February 25, 2022 17:18
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maxentile
/ box_equilibration.ipynb
Created
March 19, 2021 13:37
effect of MC barostat proposal frequency on box equilibration speed
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maxentile
/ toolkit-dependent interpretation of two molecules in coverage dataset.ipynb
Created
October 22, 2020 13:57
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maxentile
/ Gradient-informed type refinement.ipynb
Last active
September 11, 2020 23:55
proof-of-concept for using per-particle gradients to inform discrete refinements of an atom-typing scheme, in the context of a simple charge-equilibration model
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maxentile
/ tk_dependent_chemical_environment_matches.txt
Created
August 25, 2020 22:52
molecules that are assigned different parameters in OpenFF1.1.0 depending on whether rdkit or openeye is used for chemical environment matches
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| [#6X4:1] | |
| c1c(OC)c(OC)C2C(=O)OCC2c1 (7 in RDKit, 6 in OpenEye) | |
| c1c(O)C2C(=O)C3cc(O)ccC3OC2cc1(OC) (7 in RDKit, 6 in OpenEye) | |
| [#1:1]-[#6X3] | |
| c1c(OC)c(OC)C2C(=O)OCC2c1 (1 in RDKit, 2 in OpenEye) | |
| c1c(O)C2C(=O)C3cc(O)ccC3OC2cc1(OC) (4 in RDKit, 5 in OpenEye) | |
| [#1:1]-[#6X4] | |
| c1c(OC)c(OC)C2C(=O)OCC2c1 (12 in RDKit, 11 in OpenEye) | |
| c1c(O)C2C(=O)C3cc(O)ccC3OC2cc1(OC) (9 in RDKit, 8 in OpenEye) | |
| [#6X3:1]-[#1:2] |
maxentile
/ Fitting to energies and forces in Gen.ipynb
Created
August 20, 2020 20:18
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maxentile
/ Linearized parameterization for springs.ipynb
Last active
August 13, 2020 16:50
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