Small changes to Lobster classes #2434
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Mar 8, 2022
commit 3376f27a9c5a4cac1590169f2212361ab6c94388
Merge: 4b66ebc90 7b27d26b9
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Wed Mar 2 16:41:24 2022 -0800
Merge pull request #2450 from munrojm/master
Add monty `cached_class` to other compatibility schemes
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commit 2ad326e61ef19f62dd9f680e4e910ab023b8c1d9
Author: Jason <jmunro@lbl.gov>
Date: Wed Mar 2 15:34:37 2022 -0800
Add cached class to other compat. schemes
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Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Wed Mar 2 10:36:49 2022 -0800
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Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Mar 2 06:43:00 2022 -0800
Merge pull request #2449 from janosh/actions-checkout-v3
Bump `actions/checkout` in GitHub CI to v3
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Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Mon Feb 28 10:26:59 2022 -0800
Add additional logic to guard against .pmgrc.yml parsing issue
Thanks @BryantLi-BLI for reporting
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Date: Fri Feb 25 18:41:28 2022 -0800
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Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Fri Feb 25 17:37:30 2022 -0800
Set camera center to origin
Thanks @mattmcdermott
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Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Fri Feb 25 17:07:29 2022 -0800
Update changelog for v2022.2.25
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Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Fri Feb 25 10:56:11 2022 -0800
Merge pull request #2447 from mattmcdermott/cpd_fix
Fix bug in `ChemicalPotentialDiagram` initialization (interior point), improve default plots
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Date: Thu Feb 24 23:03:53 2022 -0800
re-run broken tests
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Author: Matthew McDermott <mcdermott@berkeley.edu>
Date: Thu Feb 24 22:43:47 2022 -0800
fix broken test caused by numerical precision
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Date: Thu Feb 24 15:52:08 2022 -0800
fix broken test due to sorting of array
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Date: Thu Feb 24 15:29:53 2022 -0800
add warning, clean up typing errors
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Author: Matthew McDermott <mcdermott@berkeley.edu>
Date: Thu Feb 24 14:53:53 2022 -0800
Clean up docstrings
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Add element padding to 2D plot
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Clean up formatting/layout
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adjust axis label sizes
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Date: Wed Feb 23 17:17:07 2022 -0800
add element padding for plots, change default min limit for stability
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Date: Wed Feb 23 13:54:43 2022 -0800
fix interior point issue
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Date: Wed Feb 23 13:34:27 2022 -0800
update chempot_diagram references
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Fix casting issues due to numpy.
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Add pydocstyle pre-commit hook
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Allow to switch off print of ChemEnv citation
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allow to switch off ChemEnv citation
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Merge pull request #2438 from janosh/fix-structure-from-yml
Fix Structure.from_file() for .yml ext
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Allow for float ENCUTs in Wavecar class
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check for both yml and yaml match in Structure.from_file()
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Small changes to Lobster classes
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Merge pull request #2430 from janosh/unpin-dev-reqs
Remove deprecated structure_2_lmpdata()
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Merge pull request #2432 from janosh/fix-type-annos
Fix and add some type annotations
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Merge pull request #2433 from janosh/fix-struct-apply_operation
Fix Structure.apply_operation() return val
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Use of Loewdin charges possible
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Small changes lobsterin
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Structure.apply_operation() says it returns structure but didn't
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fix Pourbaix casing
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more type hints for class SiteCollection
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UPdate CHanglog.
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Move cython to setup_requires
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Add --backup flag to pmg config
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Attempt to fix overwrite of pmgrc.yaml in MPRester. #2421
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Merge pull request #2420 from janosh/fix-get-crys-sys
Ensure SpacegroupAnalyzer.get_crystal_system() raises ValueError on neg space groups
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get_crystal_system() better value check
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test_get_crystal_system() assert raises on spg = 0
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Fix for parsing Vasprun with bad RANDOM SEED. Fixes #2418
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isort
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Update minimal basis
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Update minimal basis
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Make sure type is float for ENCUT in WAVECAR
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Add test for fractional ENCUT in WAVECAR
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Return None for complete_dos.spin_polarization if ISPIN=1
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Fix ENCUT type in Wavecar class (thanks @RyanNKHall)
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Allow for float ENCUTs in Wavecar class
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fix spin_polarization typing
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Return None for complete_dos.spin_polarization if ISPIN=1
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Black.
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Minor fix to changelog.
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Udpate change log
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Merge pull request #2407 from espottesmith/qchem_cc
Improve parsing of coupled-cluster calculations in Q-Chem
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black again
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black
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Add structure change data to parsing of PES Scan calculations
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Update row and group number for lanthanoids/actinoids
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Remove more deprecated stuff
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note recent deprecations and dropping py37 support in docs_rst/compatibility.rst
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Update zeo++ installation steps
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Revert breaking change in from_row_and_group
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Fix Zeo++ installation instructions
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Merge pull request #2357 from arosen93/rosen-ddec
Create a ChargemolAnalysis command line caller (for DDEC6, CM5 analysis)
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Merge pull request #2399 from arosen93/rosen-asemags
ASEAtomsAdaptor: magmom/charge site properties in Structure/Molecule become initial (rather than final) magmoms/charges in Atoms object
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Merge pull request #2397 from janosh/drop-deprecated
Delete overdue deprecations
commit 4753ce59e67f3d07e7a126b7cfbaf3c11259e1e9
Merge: 07794afb6 76088c3f1
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Mon Jan 31 08:36:11 2022 -0800
Merge pull request #2401 from janosh/gha-auto-pip-cache
Use setup-python automatic pip caching in CI
commit e578fca0d451231cf18cf92c9a17e0353b8b18ce
Author: Andrew <asrosen93@gmail.com>
Date: Mon Jan 31 00:05:13 2022 -0800
Fix spelling on some code comments
commit b2b23d228234b138ffa1e2445a9e4828f9b4c509
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Sun Jan 30 15:21:17 2022 -0800
Fix codecomment linting in ASEAtomsAdaptor
commit 4be3160113b59dd5580475485c9d9e0dc202e34d
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Sun Jan 30 15:15:56 2022 -0800
Update code comments for ASEAtomsAdaptor
commit 76088c3f1e8512f50f792b753a0ed65c237ac625
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sun Jan 30 13:14:43 2022 +0000
setup.py long_desc fix broken links
commit ebc4cd53b2f26669494c5d0f6259b90f7fc56b49
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sun Jan 30 13:06:20 2022 +0000
use correct cache-dependency-paths
commit eb1599f1ac2142052e53bb7d10f83eb1465aa36b
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sun Jan 30 10:16:57 2022 +0000
missed one
commit e060233439d9738fb5b9e51a8f0c79c2fc336b92
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sun Jan 30 10:09:12 2022 +0000
setup-python use auto pip caching
commit f7175b8baf09a7fb8ba423055804e1aea7d6e225
Merge: 51c3cb109 07794afb6
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Sun Jan 30 02:04:25 2022 -0800
Merge branch 'materialsproject:master' into rosen-zeo
commit 51c3cb109ab4974be18897864b6ceaa4c63aa730
Author: Andrew <asrosen93@gmail.com>
Date: Sun Jan 30 00:59:02 2022 -0800
Update zeo++ installation steps
commit ce3615803666b28726e56f1a1fd11c3676b06c60
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Sat Jan 29 18:05:20 2022 +0000
delete overdue deprecations
commit c5e4e24ceebc3491f0d554836e67d6c68ad6306c
Merge: ea11ee670 07794afb6
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Fri Jan 28 23:10:33 2022 -0800
Merge branch 'materialsproject:master' into rosen-asemags
commit ea11ee67096d0bb5ca02a1d6d144ac11fcb8a972
Author: Andrew <asrosen93@gmail.com>
Date: Fri Jan 28 22:43:14 2022 -0800
Update ASEAtomsAdaptor tests
commit 209db4b70cbb8b1e65bdd9efd9097c2bf949d9f7
Author: Andrew <asrosen93@gmail.com>
Date: Fri Jan 28 22:17:16 2022 -0800
Make magmom convention consistent with ASEAtomsAdaptor
commit 07794afb624f7613b3dbcebdf0034cab4c9ee7ea
Merge: 645a79bce 08ff11c43
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 27 12:17:27 2022 -0800
Merge pull request #2394 from JaGeo/master
Fix issue with gzipped DOSCAR files in Lobster module
commit 645a79bce73535a0da5fe30b5bfee02ee18b0988
Merge: 72849371a 9c3b416d6
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 27 12:17:06 2022 -0800
Merge pull request #2395 from samblau/qchem
Q-Chem Updates
commit 9c3b416d6dd77b94189a8cb4e3a3510375877a34
Author: samblau <samblau1@gmail.com>
Date: Thu Jan 27 11:40:35 2022 -0800
Run black
commit dde992dd0a68e3912e4dee076a003a3895678634
Merge: b4f43512f 72849371a
Author: samblau <samblau1@gmail.com>
Date: Thu Jan 27 11:19:49 2022 -0800
Merge branch 'master' into qchem
commit 08ff11c436018a2ffd8c8a81fdfd5d0865d83edc
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date: Thu Jan 27 19:43:22 2022 +0100
apply black
commit 32719b7aae340533b6541bcc3563d0d10f650202
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date: Thu Jan 27 19:22:27 2022 +0100
fix linting
commit 745c4f8c55f231610249bd81c05c0fcf2b2276a8
Merge: c4df24fd6 72849371a
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date: Thu Jan 27 19:10:56 2022 +0100
Merge branch 'master' of https://github.com/materialsproject/pymatgen
commit c4df24fd66a2f51c1c14c90ab54b15208db65eb0
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date: Thu Jan 27 18:44:59 2022 +0100
Fix problem zipped DOSCAR problem in Lobster module
commit 72849371a03ffda519e1f590776001b9076c9cd8
Merge: 85ea9dcc6 4f87d606b
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 27 08:05:58 2022 -0800
Merge pull request #2391 from janosh/compat.process_entry
Compat.process_entry
commit 85ea9dcc6fbb77cfe5d2fed1bdc365fd0856e8ee
Merge: f7525fce0 0498587d4
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 27 08:05:20 2022 -0800
Merge pull request #2392 from janosh/drop-ordered-dict
Drop OrderedDict
commit f7525fce039293a091374c890ea1ca1bf40aafa8
Merge: a13843919 7fd109a71
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 27 08:04:48 2022 -0800
Merge pull request #2393 from vorwerkc/qe_kpoints_output
Write k-point grids to QE input file
commit 7fd109a7143350b5dba492dfb4aa755b5a602d8a
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date: Thu Jan 27 08:56:36 2022 -0600
Remove debugging comment.
commit 8661eeda3952da112f158320955a6b0bb1b2753a
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date: Thu Jan 27 08:52:55 2022 -0600
Prevent workflows for forks again.
commit 0498587d46934de9d6ff20e99da624e5d9e82e57
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 27 14:32:46 2022 +0000
fix symbol_to_oxinum in pymatgen/io/cif.py
commit 278da04bf01316ce718ee70105fda21b0475de64
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 27 11:35:53 2022 +0000
fix mypy error in pymatgen/io/lobster/inputs.py
commit 0af8a0c66bd54a3dc83a3f33792d48ca0bf22632
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 27 11:22:37 2022 +0000
update doc strings mentioning OrderedDict
commit 4348e1de1162ceb9f923505d38a53e22c811fa6c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 27 11:18:40 2022 +0000
remove unused sort_dict in pymatgen/util/num.py
commit 7d6110f1c8d5a553010827bae9f6187bc1ed5598
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 27 11:17:47 2022 +0000
replace OrderedDict with dict which are insertion-ordered anyway in p37+
commit 67df7d627cd3ee9f3fe54cd0f4ae69dbb47c421f
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date: Wed Jan 26 18:18:18 2022 -0600
Re-activate linting and tests
commit b59380d49b808286462e65668b0a3d6cb7a65673
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date: Wed Jan 26 18:10:00 2022 -0600
Fix formatting of kpoints output and add corresponding test.
commit 4f87d606bc831e3294ffa2fd0c0c0a93f80e3d35
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 20:49:23 2022 +0000
ignore type error, add mypy commit hook to catch these errors locally before PR
commit 803c97e4241aeaf00abb1b947820737fa36656d7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 20:30:49 2022 +0000
use try/except in Compatibility.process_entry() to avoid double work
commit a13843919e6fe57fad7e1056b2af260462bb76cb
Merge: 17ce53597 46e2b3f32
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Wed Jan 26 12:08:28 2022 -0800
Merge branch 'master' of github.com:materialsproject/pymatgen
commit 17ce5359759130a6e420024aa6a0ce3fa48e2f0d
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Wed Jan 26 10:41:09 2022 -0800
Fix tests.
commit 46e2b3f32a550be6432716a24ae27a630f6a25b8
Merge: d6dbe43bc 04d7a9918
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:28:34 2022 -0800
Merge pull request #2380 from janosh/flynt-aggressive
flynt --aggressive
commit d6dbe43bcd4aadf6c5505eaef454984c730e33ec
Merge: be0a675cb c4bd7150d
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:28:13 2022 -0800
Merge pull request #2385 from janosh/autoflake
Autoflake
commit be0a675cb38ba35251fcd8207271886a040c48c4
Merge: 420c77530 b706b6560
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:27:49 2022 -0800
Merge pull request #2388 from arosen93/rosen-charge
Store the actual charge and spin_mult in structure.as_dict()
commit c4bd7150de5203a7e3a4c53adda47745ab1f7b6d
Merge: c3592de6d 420c77530
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:27:27 2022 -0800
Merge branch 'master' into autoflake
commit 420c77530975ed6a36ab9f69b1313ba1befe377c
Merge: 4eca6adca dfd56f670
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:26:48 2022 -0800
Merge pull request #2387 from janosh/readme-badges
Fix readme badges
commit 4eca6adca23cc6f68140aea3b735b6be17ac9a73
Merge: 6c31f7e38 ff60e222a
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Wed Jan 26 10:26:10 2022 -0800
Merge pull request #2389 from janosh/pdentry-repr
override PDEntry.__repr__ to include name attr if not fallback value
commit ff60e222aa9df1d2a8dc6e6f740495306bbfc815
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 18:14:04 2022 +0000
override PDEntry.__repr__ to include name attr if not fallback value
commit b706b6560ea94f1444bb48d0cdb960b255ec850d
Author: Andrew <asrosen93@gmail.com>
Date: Wed Jan 26 10:00:08 2022 -0800
Fix as_dict() test assertions
commit 36d62f7d0e1598feaf833746a8b536504e1a7813
Author: Andrew <asrosen93@gmail.com>
Date: Wed Jan 26 09:51:28 2022 -0800
Add tests for default charge/spin mult
commit b872a046fa641a4633672e1fd39a542b033e14c8
Author: Andrew <asrosen93@gmail.com>
Date: Wed Jan 26 08:38:20 2022 -0800
Store the actual charge and spin_mult in as_dict()
commit dfd56f6706c44ef35716280786fe796b6fcbd025
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 14:40:26 2022 +0000
uniform shield.io readme badges brought onto 1 line, fix GH CI badge, add PyPI download badge
commit c3592de6d003fd0439af90d3ddf19bd5c0b81b4c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 10:41:26 2022 +0000
fix self.assertEqual(str(self.cellin), ans)
in FiestaInputTest.test_str_and_from_string()
commit 2c542054e1fb21b7a04379e0bbf5a7c3024f9f20
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 10:24:52 2022 +0000
remove annoying pylint commit hook, keeps complaining about missing types for standard lib modules like math
pymatgen/analysis/phase_diagram.py:2929:48: I1101: Module 'math' has no 'sqrt' member, but source is unavailable. Consider adding this module to extension-pkg-allow-list if you want to perform analysis based on run-time introspection of living objects. (c-extension-no-member)
commit f7171f4d753a035c432924d7d5ba5eaad0e74d60
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 10:23:55 2022 +0000
typos
commit 644df535de16868762f6d5a117bc095f249ba3ae
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 09:07:42 2022 +0000
fix UnboundLocalError: local variable 'coord' referenced before assignment in pymatgen/util/tests/test_coord.py
commit a3dda95ac600033ee466fd0714429dd777e1a233
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:58:14 2022 +0000
revert openbabel try-except imports
commit 5c1458b36ed82b9b8b62c7cd0c9ed96ad13583c7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:42:23 2022 +0000
convert os + warnings + numpy to own imports in test modules instead of from starred imports
commit 797d99e34ecf42390875d5463c9cb71844ad642c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:34:17 2022 +0000
reduce namespace pollution in pymatgen/util/tests/test_coord.py
commit f76bcd336b294afebf3d367cb522ba9a6aec234a
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:24:41 2022 +0000
autoflake -ri --remove-all-unused-imports --ignore-init-module-imports pymatgen
commit 41b1009224ca0b96f9046a9883aaa43dba41c8a9
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:17:50 2022 +0000
autoflake expand star imports
commit 6f7c428da87193946cd0b04f5052923b8dda0f14
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:14:34 2022 +0000
autoflake remove unused imports + useless pass statements
commit 04d7a99182cfea007e048b1e5700208bb4e721c3
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Wed Jan 26 08:07:42 2022 +0000
fix KpointsTest.test_init() failing due to change in Kpoints.__str__()
commit b4f43512fc7e9b88a8fcfab41dca2085e4b7374d
Author: samblau <samblau1@gmail.com>
Date: Tue Jan 25 16:26:30 2022 -0800
Turn non-NBO output tests back on
commit 20537e4819cc1a25329ff38efe18fa96045a5e98
Merge: b22aba284 6c31f7e38
Author: samblau <samblau1@gmail.com>
Date: Tue Jan 25 16:21:26 2022 -0800
Merge branch 'master' into qchem
commit a3b9c2b45705bbff4c025503fd55fb8aef3ca496
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Tue Jan 25 20:09:44 2022 +0000
fix self.assertEqual(gau.to_string(cart_coords=False), gau_str) due to charge_str = f"{self.charge}" in gau.to_string()
commit deb84ec8060926e217a8546d08d4e73ab6323fce
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Tue Jan 25 19:32:04 2022 +0000
more auto-conversions from flynt ./pymatgen --aggressive (checked these all more carefully)
commit 6c31f7e38268986bd23110c2fbd4f14a09042a2a
Merge: 5a05f662d 8b697ed4f
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Tue Jan 25 11:01:30 2022 -0800
Merge pull request #2379 from janosh/flynt
Flynt
commit 8b697ed4fa702bb2b7ddefb4d9fb9a60fa6a3657
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Tue Jan 25 15:28:30 2022 +0000
fix ValueError: Format specifier missing precision
commit d068c1e39b4168a93de04745ff8af1a5fe4117c0
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Tue Jan 25 15:02:16 2022 +0000
commit hook auto fixes in files changed by prev commit
commit 265a2a2b828e8f1cd3063df5571d72c200346769
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Tue Jan 25 15:00:32 2022 +0000
flynt ./pymatgen (automatic f-string conversion)
commit 5a05f662d35ab3c0d93f252f1c73e813e87c75f6
Merge: bc5af845c 5f09cfbe8
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Tue Jan 25 06:56:09 2022 -0800
Merge branch 'master' of github.com:materialsproject/pymatgen
commit bc5af845cca5953f7d7623a64341c5bb862839ed
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Tue Jan 25 06:54:31 2022 -0800
Fix.
commit 5f09cfbe8b575090faaf5901ccab37e50fccf677
Merge: 1a46190f4 671fd7f6a
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Tue Jan 25 06:49:36 2022 -0800
Merge pull request #2356 from arosen93/rosen-bader
Minor cleanup of bader_caller.py + new get_partial_charge() convenience function
commit 1a46190f48020669bf34266c81eebf87b89373e1
Merge: cf0f4a327 776dabac8
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Tue Jan 25 06:47:47 2022 -0800
Merge pull request #2362 from janosh/qa
QA
commit cf0f4a327329ff31a0af2a5f5a29cbb7ca3ce874
Merge: d8810634d 31f9f33cd
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Tue Jan 25 06:47:27 2022 -0800
Merge pull request #2371 from arosen93/rosen-ase-props
Pass oxidation states between Pymatgen structure/molecule and ASE Atoms
commit d8810634ddebac6171b8833aadc87ca0e0dac461
Merge: 41e171b5a c5b8d495e
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Mon Jan 24 17:28:34 2022 -0800
Merge pull request #2369 from arosen93/rosen-energy
Return the correct Vasprun().final_energy for VASP 6+ and change the default Outcar().final_energy to be energy(sigma->0)
commit c5b8d495e400e49a66aad90ddbb2ca31c91ee8f9
Author: Andrew <asrosen93@gmail.com>
Date: Mon Jan 24 16:30:40 2022 -0800
Do 1e-7 check in final_energy
commit ee423599fe370547250cc281d7c7935afc67cbf9
Author: Andrew <asrosen93@gmail.com>
Date: Mon Jan 24 16:25:23 2022 -0800
Update vasprun.final_energy check to be version-independent
commit 41e171b5aeae63bf73c130f7ef451fd77aa46e0f
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Mon Jan 24 06:25:14 2022 -0800
Update docs
commit d3b37eb5fb04a919a81c45bed780ce4c4d60477a
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Mon Jan 24 06:23:34 2022 -0800
Minor update.
commit 8808f7198a49b8358267fc36a1ba7a09cc8484ac
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Mon Jan 24 06:22:28 2022 -0800
Update changelog.
commit 5b8f704904fff3097ff45c1d182582b553bde686
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Mon Jan 24 06:20:01 2022 -0800
fix deprecated default flow style in YAML.
Fixes #2373.
commit 31f9f33cd3ea19aec9196163b285f8fbe512aace
Author: Andrew <asrosen93@gmail.com>
Date: Sun Jan 23 21:08:34 2022 -0800
Pass oxi states between ASE and pymatgen
Now oxidation states are passed between ASE and Pymatgen structure objects. Several new tests have been added.
commit afe802b10f7907b22141e2154f323900a412e351
Merge: 3cf1b4206 4813709cb
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Sat Jan 22 22:42:36 2022 -0800
Merge branch 'materialsproject:master' into rosen-energy
commit 3cf1b42067209f8743f7512cc13976948b9cc32d
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 21:39:36 2022 -0800
Fix Outcar test
commit 844f185b41b9c9af9e1e6bd26515f7a74eb0ce32
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 21:39:16 2022 -0800
Update Outcar() docs
commit a9eff3f577fa7b2251f57173b4c054fc4a110e7a
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 21:22:13 2022 -0800
Fix vasprun energy parsing for vdW
commit e10abaaef87379349f0d064f1222c84a32a88681
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 20:14:20 2022 -0800
Add tests to address energy parsing issue with Vasprun
commit 18ee0cc8f8fec8d4a1664ec782e2368ed6028d78
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 19:16:06 2022 -0800
Fix dielect OUTCAR test
commit 4813709cbccd35543e192cef6b7cf78153624cd6
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Sat Jan 22 18:22:37 2022 -0800
Fix memory error
commit fe4af2dd3523b1b686c23176fb549a98403f25e1
Author: Andrew <asrosen93@gmail.com>
Date: Sat Jan 22 18:09:47 2022 -0800
Return the correct e_0_energy with Vasprun and Outcar .final_energy
commit 7ac21b710e68e723d8fb556410787965740cac04
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Sat Jan 22 17:01:37 2022 -0800
Comment out bad test.
commit c07cd2bebfec5f68a3fd29d5c01c4a5f0d1501a7
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Sat Jan 22 16:39:59 2022 -0800
Fix wannier.
commit 362e26fd69a121f5855ffc413de361b0c8cd1a9e
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Sat Jan 22 16:04:30 2022 -0800
Fix numpy int deprecations. Fixes #2366.
commit ae3f1b77d75b397735ee7cf16fcd77d8f487d85e
Merge: 729a26f2f 6753761b1
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Fri Jan 21 12:14:48 2022 -0800
Merge branch 'master' of github.com:materialsproject/pymatgen
commit 729a26f2f0d9b6ca083dcaffb86402b5e0be96ee
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Fri Jan 21 12:14:35 2022 -0800
Fix release workflow.
commit 776dabac89585ad7b9a5274f53515aa09ecf39e3
Merge: 05fcc2797 6753761b1
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Fri Jan 21 06:17:56 2022 +0000
Merge branch 'master' into qa
commit 593a18872ba19735f9d8296998a0f45aa179b2c9
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 20:18:03 2022 -0800
Fix max_row kwarg in periodic table heatmap plotter
commit c6d38b11dadf4ed5ada3f98cb7bf58a34960eb62
Merge: 43d9fc768 6753761b1
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date: Thu Jan 20 19:51:40 2022 -0800
Merge branch 'materialsproject:master' into rosen-ddec
commit b06efb1205af52e2eed8547ef68a672ef1ca3b05
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 19:36:14 2022 -0800
Fix from_row_and_group test
commit 55bf07a9c24e363f7f8d8fb396575d49879cf3fd
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 19:16:59 2022 -0800
Fix from_row_and_group test
commit a5082776043f530c5f67303b53a0e9614306ae6a
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 19:09:25 2022 -0800
Fix row and group test
commit 235e1b5d39c7c33454393fe7383ad17c2d4ce422
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 18:58:08 2022 -0800
Add new for test from_row_and_group
commit 5353523c642b473e306927fd195052a58f9998c9
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 18:51:47 2022 -0800
Add test cases for new group/row convention
commit 5c29d1d4b917865055eb83894eab6b4f5854ae6f
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 18:00:49 2022 -0800
Fix ptable plotter
commit 0d8038a487bab90f26a0ef2577bf74823f53c35f
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 17:38:07 2022 -0800
Fiz el.z typo in ptable plotter
commit 19247c6060830b561f3c2e70ecb7030b7895e7ad
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 17:35:02 2022 -0800
Fix ptable plotter for new lanthanoid/actinoid group #
commit 43d9fc768396929310db3dde0745a2b613145f30
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 17:15:12 2022 -0800
Use fstring in ChargemolAnalysis
commit 3979c7410573f4e6e7bbe0176784691292ba5417
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 16:51:23 2022 -0800
Add code comment for ChargemolAnalysis.summary
commit 46415dab1cbf8c830434e21bf79e85da06a377ce
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 16:47:35 2022 -0800
Add test for get_charge() in ChargemolAnalysis
commit 4ce2389ea83d1cbc831970fd49ba37ad8317acdb
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 16:40:33 2022 -0800
Add tests for Chargemol
commit 6753761b1f332b70507b8e019114ac65c45b5c75
Merge: 9cc63cac1 5792dcb1a
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date: Thu Jan 20 14:08:06 2022 -0800
Merge pull request #2358 from arosen93/rosen-mags
Don't perform dict type-check on the MAGMOM flag in io.vasp.sets (fixes downstream Atomate issue)
commit 5792dcb1a66814c4390ad64b73dd2f899fa32cdd
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 13:10:07 2022 -0800
Fix MPStaticSet test
commit 9cc63cac182dcf219c2a1791d7e36d3fe3c2c3b5
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Thu Jan 20 12:46:24 2022 -0800
Update docs
commit 6ba78931fef96af12779a1221727ba0353a1ceb6
Author: Shyue Ping Ong <shyuep@gmail.com>
Date: Thu Jan 20 12:45:13 2022 -0800
Update changelog.
commit 91c7fb0642f8fc37a76bab491da2e3631aee1f83
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 12:36:39 2022 -0800
Remove typecheck from magmom test
Remove the typecheck for MAGMOM being a dict
commit d5370df167e92aa4293a1bd15cc49c327be46cbd
Merge: fd553a8e8 e181a7fb8
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date: Thu Jan 20 12:19:57 2022 -0800
Merge pull request #2365 from janosh/fix_get_potcar_symbols
Fix Lobsterin()._get_potcar_symbols()
commit 200bb9c882adac3786b1c126d9b7e74d17b5957f
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 12:14:44 2022 -0800
Lint fix
commit 2cfdc3cdc0fde394b86a670ca0714a3c49e88e9c
Merge: 42bcf08f9 7c550b987
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 11:46:50 2022 -0800
Merge remote-tracking branch 'origin/rosen-mags' into rosen-mags
commit 42bcf08f92bd7267824edd7d1dcfe79d23ca3769
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 11:46:45 2022 -0800
Remove TypeError when MAGMOM is not a dict
commit e181a7fb800d7dff1a1074bc0be25f10e8558034
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 19:18:06 2022 +0000
ensure POTCAR data has utf-8 encoding
commit 6c57902c8fa7834c30c40e6ccb4ac6066edf6dfb
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 11:02:21 2022 -0800
mypy fix
commit 05fcc2797fce6f5b01c0c3c4c993575f49f984c7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 15:15:49 2022 +0000
update hash for vdW_parameters.yaml in SetChangeCheckTest
commit 8b4fb15b32e1694438e39b636efdb46e009f1442
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 11:12:42 2022 +0000
add autoflake cmmit hook
commit d7b4fba0cb04a5b80829613674f936b1418f9b54
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 11:06:39 2022 +0000
add pyupgrade commit hook
commit 862bf7b4c36da03cd4fda3beb5b0394e66ff7f34
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 11:03:53 2022 +0000
pyupgrade --py38-plus **/*.py
commit 586bea41032781c8ccac1a6fdfc6ad3d96baa555
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 10:53:06 2022 +0000
apply end-of-file-fixer + trailing-whitespace
commit 9f13e8c2ea91baf692329b41487e7cf771437df5
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date: Thu Jan 20 10:52:08 2022 +0000
update pre-commit config, exclude (docs|test_files), use standalone flake8 hook
commit c8893438b69642122950547b7ff17a844c258c33
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 02:17:35 2022 -0800
mypy fix
commit ac26d556340a7fcdfe58ee53f02b432407418565
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 02:02:38 2022 -0800
Introduce test suite for ChargemolAnalysis
commit 671fd7f6a15261715c594694e4e3aad5e4b47d6f
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 01:18:04 2022 -0800
Add two more bader tests
commit b1dc48d41bec78cc8dd79b0a3dbfe717aadf2d42
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 01:14:41 2022 -0800
Finalize chargemol_caller.py
Creates chargemol_caller.py for DDEC/CM5 analysis
commit 646d13853acb5ae247954e82f5a77829d568f842
Author: Andrew <asrosen93@gmail.com>
Date: Thu Jan 20 01:12:48 2022 -0800
finalize bader_caller cleanup
Minor code clarifications for bader_caller. Also adds new get_partial_chage() convenience function
commit d33eb3138dfc0017b4de0ac40b9c79fecfbe6865
Merge: 32bda0f32 7b2757a80
Author: Andrew <asrosen93@gmail.com>
Date: Wed Jan 19 15:40:11 2022 -0800
Merge remote-tracking branch 'origin/rosen-ddec' into rosen-ddec
commit 32bda0f3207d7878bfcc5e6c38290a0ac5b87ce2
Author: Andrew <asrosen93@gmail.com>
Date: Wed Jan 19 15:40:…
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Summary
I have changed the energy range for the standard Lobster computation. This is partially related to a VASP 6.0 problem with Fermi levels at the bottom of the band gap.
Furthermore, I have enabled the use of Loewdin charges to determine cation and anions and respective coordination environments based on the assessment of cation and anion bonds.
I have also included and/or adapted the tests.