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Title: Pourbaix by xiaochendu · Pull Request #6 · learningmatter-mit/surface-sampling · GitHub

Open Graph Title: Pourbaix by xiaochendu · Pull Request #6 · learningmatter-mit/surface-sampling

X Title: Pourbaix by xiaochendu · Pull Request #6 · learningmatter-mit/surface-sampling

Description: MCMC-based algorithm for sampling surface reconstructions - Pourbaix by xiaochendu · Pull Request #6 · learningmatter-mit/surface-sampling

Open Graph Description: Add ability to sample under aqueous electrochemical conditions

X Description: Add ability to sample under aqueous electrochemical conditions

Opengraph URL: https://github.com/learningmatter-mit/surface-sampling/pull/6

X: @github

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MAINT: add back delete Pourbaix sampling fileshttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7eaa2e7c393f68ed4e36e6e358ddfc85cb2d65b9
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MAINT: update sample_pourbaix_surface.py to follow new MCMC initi…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7a4ead99887d8f3e8197afe87798fb98e0e31cc7
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MAINT: generate_pourbaix_atoms take in Path to phase_diagram and po…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/16f6da50195d4380f335f7e65eb4c72f942fa40b
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MAINT: SurfaceSystem fix fromdicthttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/5cca25678e8a9eb8aff4fc5141040958d9932084
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October 29, 2024 21:25https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6#commits-pushed-735936f
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MAINT: Refactor generate_pourbaix_atoms() to handle single and multi …https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/735936fcd40caab61cf62db457bae1d7a79caf78
735936fhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/735936fcd40caab61cf62db457bae1d7a79caf78
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MAINT: Add support for inputting job ID as the slab namehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/995ba1a17dc9ff546f528848f4194a132032b7e7
995ba1ahttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/995ba1a17dc9ff546f528848f4194a132032b7e7
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MAINT: Enhance Matplotlib settings with additional color configuratio…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/f1d6d4257989ead2b745beefd29e559bda463904
f1d6d42https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/f1d6d4257989ead2b745beefd29e559bda463904
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MAINT: Add GMM clustering support and extend clustering metric optionshttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/14734204ccab180cdd731d117febdcaf4ae6bc35
1473420https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/14734204ccab180cdd731d117febdcaf4ae6bc35
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MAINT: Update histogram plotting and filtering to handle missing atom…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/3d68f6a2f7a7095a491bae00f752cfa271d6fb4d
3d68f6ahttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/3d68f6a2f7a7095a491bae00f752cfa271d6fb4d
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MAINT: Add correction for H2O in formula calculations and update atom…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/4cf98f016408c0aa297766590bce0906690124f2
4cf98f0https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/4cf98f016408c0aa297766590bce0906690124f2
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MAINT: Refactor code for improved readability by formatting argument …https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/c6fa725903ae663268754f6a8d763b1f6e240010
c6fa725https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/c6fa725903ae663268754f6a8d763b1f6e240010
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MAINT: Update SurfaceOHCompatibility to include hydrogen bond correct…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7129fdf0ccda624e2e0214a5ae6c9406e9721b4f
7129fdfhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7129fdf0ccda624e2e0214a5ae6c9406e9721b4f
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MAINT: Add hydrogen bond energy correction and update argument parsin…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7294fdf7f5b03195fb6ec5969fc4c8ca144e5ddf
7294fdfhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/7294fdf7f5b03195fb6ec5969fc4c8ca144e5ddf
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MAINT: Update filter_stoichiometries to extract relaxed_atoms from Su…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/fc3b9657b6288b2fd4097378e1eded44f7470b82
fc3b965https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/fc3b9657b6288b2fd4097378e1eded44f7470b82
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MAINT: Enhance perturb_structures script with energy estimation and m…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/d00118c7c5f0feff4a772974c22cb5c6d482df0e
d00118chttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/d00118c7c5f0feff4a772974c22cb5c6d482df0e
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MAINT: Modify filter_stoichiometries to retain original structures wh…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/00fe5e68a8233f430601ff62f3d8a3d96ab14246
00fe5e6https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/00fe5e68a8233f430601ff62f3d8a3d96ab14246
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MAINT: Enhance plotting functions with optional titles and colormap s…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/e6f6f9c5f128e43bb735bbb1c67bc5b19d3a852c
e6f6f9chttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/e6f6f9c5f128e43bb735bbb1c67bc5b19d3a852c
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MAINT: Update perform_clustering to include colormap and title option…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/18e9cfaf899736f2afc09f222f6ee592be1256ef
18e9cfahttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/18e9cfaf899736f2afc09f222f6ee592be1256ef
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MAINT: Refactor plotting functions for improved layout, customization…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/2f551c05947c68ebe8e056dc42e37f87c36500bd
2f551c0https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/2f551c05947c68ebe8e056dc42e37f87c36500bd
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MAINT: Update create_surface_formation_entries to handle relaxed at…https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/677dbf25e69acc81ab5883a148e0802b513db8d4
677dbf2https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/677dbf25e69acc81ab5883a148e0802b513db8d4
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MAINT: Bump version to 0.3.0 and update pymatgen dependency to use forkhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/442e3a816c6776b61e01dcb61083ceb70e3fa612
442e3a8https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/442e3a816c6776b61e01dcb61083ceb70e3fa612
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MAINT: Update NeuralForceField dependency to use vssr_pourbaix branchhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/3c0c547f1c2107648ba9d21172cef14f97d6943d
3c0c547https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/3c0c547f1c2107648ba9d21172cef14f97d6943d
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MAINT: add data for pourbaix sampling examplehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/2f5bf8322d915d0272cc596b0bf1f3ef7f670376
2f5bf83https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/2f5bf8322d915d0272cc596b0bf1f3ef7f670376
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MAINT: update tutorials and testshttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/b3b5c8eb553bfdf4d4c84f86e63e6ff5af9536e9
b3b5c8ehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/b3b5c8eb553bfdf4d4c84f86e63e6ff5af9536e9
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MAINT: add uncertainty modulehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/ad2ab544fc4d7e4f3da21d4b2ddd69750a050e80
ad2ab54https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/ad2ab544fc4d7e4f3da21d4b2ddd69750a050e80
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MAINT: add customized LAMMPS calculator adapted from ASEhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/32ab93f4a75d2c652f97e20599f100d511a0f80d
32ab93fhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/32ab93f4a75d2c652f97e20599f100d511a0f80d
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MAINT: prepare for 0.3.0 releasehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/35150f78d231006d6de6d5501e4f250be0f7e99a
35150f7https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/35150f78d231006d6de6d5501e4f250be0f7e99a
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BUG: correct misformatting of importhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/be327de8bd309e2b56f224ccd9e485ad51448e6f
be327dehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/be327de8bd309e2b56f224ccd9e485ad51448e6f
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Update tests.ymlhttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/b0564c3881480f0186067bf53066f409642bf2fa
b0564c3https://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/pull/6/commits/b0564c3881480f0186067bf53066f409642bf2fa
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625129ehttps://patch-diff.githubusercontent.com/learningmatter-mit/surface-sampling/commit/625129e4956bfa9435ae28a139483065413731e6
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