tqdm: A Fast, Extensible Progress Meter for Python and CLI

Costa-Luis, Casper da

doi:10.21105/joss.01277

Cited by 142 publications

(51 citation statements)

References 9 publications

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“… 59 All codes used to analyze the simulation trajectories and to generate the corresponding figures are available as a series of Jupyter notebooks 60 under the MIT license. Our analysis used the Matplotlib, 61 NumPy, 62 Pymatgen, 63 , 64 SciPy, 65 tqdm, 66 vasppy, 67 site-analysis, 68 polyhedral-analysis, 69 Kinisi, 70 and crystal-torture 71 Python packages.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Morgan

2021

Chem. Mater.

112

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The rational development of fast-ion-conducting solid electrolytes for all-solid-state lithium-ion batteries requires understanding the key structural and chemical principles that give some materials their exceptional ionic conductivities. For the lithium argyrodites Li 6 PS 5 X (X = Cl, Br, or I), the choice of the halide, X, strongly affects the ionic conductivity, giving room-temperature ionic conductivities for X = {Cl,Br} that are ×10 3 higher than for X = I. This variation has been attributed to differing degrees of S/X anion disorder. For X = {Cl,Br}, the S/X anions are substitutionally disordered, while for X = I, the anion substructure is fully ordered. To better understand the role of substitutional anion disorder in enabling fast lithium-ion transport, we have performed a first-principles molecular dynamics study of Li 6 PS 5 I and Li 6 PS 5 Cl with varying amounts of S/X anion-site disorder. By considering the S/X anions as a tetrahedrally close-packed substructure, we identify three partially occupied lithium sites that define a contiguous three-dimensional network of face-sharing tetrahedra. The active lithium-ion diffusion pathways within this network are found to depend on the S/X anion configuration. For anion-disordered systems, the active site–site pathways give a percolating three-dimensional diffusion network; whereas for anion-ordered systems, critical site–site pathways are inactive, giving a disconnected diffusion network with lithium motion restricted to local orbits around S positions. Analysis of the lithium substructure and dynamics in terms of the lithium coordination around each sulfur site highlights a mechanistic link between substitutional anion disorder and lithium disorder. In anion-ordered systems, the lithium ions are pseudo-ordered, with preferential 6-fold coordination of sulfur sites. Long-ranged lithium diffusion would disrupt this SLi 6 pseudo-ordering, and is, therefore, disfavored. In anion-disordered systems, the pseudo-ordered 6-fold S–Li coordination is frustrated because of Li–Li Coulombic repulsion. Lithium positions become disordered, giving a range of S–Li coordination environments. Long-ranged lithium diffusion is now possible with no net change in S–Li coordination numbers. This gives rise to superionic lithium transport in the anion-disordered systems, effected by a concerted string-like diffusion mechanism.

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Section: Methodsmentioning

confidence: 99%

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Morgan

2021

Chem. Mater.

112

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“…All code used to analyse the simulation trajectories and to generate the corresponding figures is available as a series of Jupyter notebooks [60] under the MIT licence. Our analysis used the matplotlib [61], numpy [62], pymatgen [63,64], scipy [65], tqdm [66], vasppy [67], site-analysis [68], polyhedralanalysis [69], kinisi [70], and crystal-torture [71] Python packages.…”

Section: Methodsmentioning

confidence: 99%

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites

Morgan

2021

Preprint

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The rational development of fast–ion-conducting solid electrolytes for all-solid-state lithium-ion batteries requires understanding the key structural and chemical principles that give some materials their exceptional ionic conductivities. For the lithium argyrodites Li6PS5X (X = Cl,Br,I), the choice of the halide, X, strongly affects the ionic conductivity, with room-temperature ionic conductivities for X = {Cl, Br} ×103 higher than for X = I. This variation has been attributed to differing degrees of S/X anion disorder. For X = {Cl, Br} the S/X anions are substitutionally disordered, while for X = I the anion sublattice is fully ordered. To better understand the role of substitutional anion disorder in enabling fast lithium-ion transport, we have performed a first-principles molecular dynamics study of Li6PS5I and Li6PS5Cl, with varying amounts of S/X anion-site disorder. Considering the S/X substructure as a tetrahedrally close-packed lattice, we identify three partially occupied lithium sites that form a contiguous three-dimensional network of face-sharing tetrahedra. The active lithium-ion diffusion pathways within this network, however, depend on the S/X anion configuration. For anion-disordered systems, the active site–site pathways give a percolating three-dimensional diffusion network; whereas for anion-ordered systems, critical site–site pathways are inactive, giving a disconnected diffusion network with lithium motion restricted to local orbits around S positions. Analysis of the lithium substructure and dynamics in terms of the lithium coordination around each sulfur site shows a mechanistic link between substitutional anion disorder and lithium disorder, which enables fast lithium diffusion. In anion-ordered systems the Li-ions are pseudo-ordered, with preferential 6-fold coordination of sulfur sites. Long-ranged lithium diffusion disrupts this SLi6 pseudo-ordering, and is therefore disfavoured. In anion-disordered systems, a uniform 6-fold S–Li coordination is frustrated due to Li–Li Coulombic repulsion. Lithium positions become disordered, giving a range of S–Li coordination environments. Long-ranged Li diffusion is now possible with no net change in S–Li coordination numbers. This gives rise to superionic lithium transport in the anion-disordered systems, which is effected by a concerted string-like diffusion mechanism.

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“…1, 2, 4, 5, and 6 are available under the MIT licence. 71 Our analysis codes use the matplotlib, 72 numpy, 73 pandas, 74 pymatgen, 75 scipy, 76 tqdm, 77 and vasppy 78 Python packages, and SC-Fermi and Frozen SC-Fermi 45,46 for calculating self-consistent defect concentrations.…”

Section: Methodsmentioning

confidence: 99%

Native Defects and Their Doping Response in the Lithium Solid Electrolyte Li₇La₃Zr₂O₁₂

2019

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The Li-stuffed garnets LixM2M 3 O12 are promising Li-ion solid electrolytes with potential use in solid-state batteries. One strategy for optimising ionic conductivities in these materials is to tune lithium stoichiometries through aliovalent doping, which is often assumed to produce proportionate numbers of charge-compensating Li vacancies. The native defect chemistry of the Li-stuffed garnets, and their response to doping, however, are not well understood, and it is unknown to what degree a simple vacancy-compensation model is valid. Here, we report hybrid density-functional-theory calculations of a broad range of native defects in the prototypical Li-garnet Li7La3Zr2O12. We calculate equilibrium defect concentrations as a function of synthesis conditions, and model the response of these defect populations to extrinsic doping. We predict a rich defect chemistry that includes Li and O vacancies and interstitials, and significant numbers of cation-antisite defects. Under reducing conditions, O vacancies act as colour-centres by trapping electrons. We find that supervalent (donor) doping does not produce charge compensating Li vacancies under all synthesis conditions; under Li-rich / Zr-poor conditions the dominant compensating defects are LiZr antisites, and Li stoichiometries strongly deviate from those predicted by simple "vacancy compensation" models.

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tqdm: A Fast, Extensible Progress Meter for Python and CLI

Cited by 142 publications

References 9 publications

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites

Native Defects and Their Doping Response in the Lithium Solid Electrolyte Li₇La₃Zr₂O₁₂

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tqdm: A Fast, Extensible Progress Meter for Python and CLI

Cited by 142 publications

References 9 publications

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li6PS5X Argyrodites

Native Defects and Their Doping Response in the Lithium Solid Electrolyte Li7La3Zr2O12

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Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Mechanistic Origin of Superionic Lithium Diffusion in Anion-Disordered Li₆PS₅X Argyrodites

Native Defects and Their Doping Response in the Lithium Solid Electrolyte Li₇La₃Zr₂O₁₂