TDEP

TDEP: Temperature Dependent Effective Potentials - Published in JOSS (2024)

https://github.com/tdep-developers/tdep

Scientific Fields

Earth and Environmental Sciences Physical Sciences - 34% confidence

Last synced: 4 months ago · JSON representation ·

Repository

The Temperature Dependent Effective Potentials (TDEP) code

Basic Info

Host: GitHub
Owner: tdep-developers
License: mit
Language: Fortran
Default Branch: main
Size: 18.8 MB

Statistics

Stars: 87
Watchers: 10
Forks: 33
Open Issues: 50
Releases: 3

Created over 2 years ago · Last pushed 4 months ago

Metadata Files

Readme Contributing License Citation

Temperature Dependent Effective Potentials (TDEP)

GitHub Release GitHub License

Briefly summarized, the package provides all the tools you need to build accurate model Hamiltonians for finite temperature lattice dynamics from first principles. TDEP includes several programs for different tasks:

generate_structure: Generate supercells of target size, with options to make them as cubic as possible to maximize the real-space cutoff for the force constants.
canonical_configuration: Create supercells with thermal displacements from an initial guess or existing force constants, using Monte Carlo sampling from a classical or quantum canonical distribution.
extract_forceconstants: Obtain (effective) harmonic force constants from a set of supercell snapshots with displaced positions and forces. Optionally fit higher-order force constants.
phonon_dispersion_relations: Calculate phonon dispersion relations and related harmonic thermodynamic properties from the second-order force constants.
thermal_conductivity: Compute thermal transport in the mode-coupling formalism including third- and fourth-order anharmonicity.
lineshape: Compute phonon spectral functions including lifetime broadening and shifts for single q-points, q-point meshes, or q-point paths in the Brillouin zone. The grid mode computes spectral thermal transport properties as well.
thermal_conductivity_2023: Compute thermal transport by solving the phonon Boltzmann transport equation with perturbative treatment of third-order anharmonicity. Legacy implementation, the significantly improved program thermal_conductivity should be used!

More details, examples, and theoretical background can be found in the online documentation. See below which references should be cited for which program.

Tutorials

You can find a range of tutorials for realistic research workflow using TDEP in a dedicated repository.

Installation

Please find installation instructions in the TDEP repository.

Report bugs and issues

Please use our github issue tracker to report any problems. Please make sure to include input/output and log files so that we can reproduce and investigate the question.

Contribute

Please find instructions in the repository.

Other things to look at

tdeptools a package to facilitate working with TDEP and perform additional postprocessing can be found here: https://github.com/flokno/tools.tdep

How to cite

This software is distributed under the MIT license. If you use it, please consider citing

F. Knoop et al., J. Open Source Softw 9(94), 6150 (2024)

and the respective publications for the algorithms that were used:

canonical_configuration

Classical statistics: D. West and S. K. Estreicher, Phys Rev Lett 96, 115504 (2006)
Quantum statistics: N. Shulumba, O. Hellman, and A. J. Minnich, Phys. Rev. Lett. 119, 185901 (2017)

extract_forceconstants

Second order: O. Hellman et al., Phys Rev B 87, 104111 (2013)
Third order: O. Hellman and I. A. Abrikosov, Phys Rev B 88, 144301 (2013)
Fourth order: A. H. Romero et al., Phys Rev B 91, 214310 (2015)

thermal_conductivity

Theory and implementation A. Castellano et al., Phys. Rev. B 111, 094306

lineshape

A. H. Romero et al., Phys Rev B 91, 214310 (2015)
N. Shulumba, O. Hellman, and A. J. Minnich, Phys. Rev. Lett. 119, 185901 (2017)
Grid mode for spectral transport: Đ. Dangić et al., Npj Comput Mater 7, 57 (2021)

thermal_conductivity_2023

Method: D. A. Broido et al., Appl Phys Lett 91, 231922 (2007)
Implementation: O. Hellman and D.A. Broido, Phys. Rev. B 90, 134309 (2014)
Fourth-order contributions: J. Klarbring et al., Phys Rev Lett 125, 045701 (2020)
Off-diagonal contributions:

Troubleshooting

Some common issues:

Symmetry errors

TDEP is very strict about crystal symmetries. In phonopy world, the symmetry precision is about 1e-10. If you see an error like

ERROR exit code 4: symmetry error

chances are high that your structure input files are not perfectly symmetric and consistent. Precise input structures are a prerequisite for using TDEP successfully.

Owner

Name: tdep-developers
Login: tdep-developers
Kind: organization

Repositories: 1
Profile: https://github.com/tdep-developers

JOSS Publication

TDEP: Temperature Dependent Effective Potentials

Published

February 01, 2024

DOI

10.21105/joss.06150

Volume 9, Issue 94, Page 6150

Authors

Florian Knoop

Theoretical Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden

Nina Shulumba

Theoretical Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden

Aloïs Castellano

Nanomat group, QMAT center, CESAM research unit and European Theoretical Spectroscopy Facility, Université de Liège, allée du 6 août, 19, B-4000 Liège, Belgium

J. P. Alvarinhas Batista

Nanomat group, QMAT center, CESAM research unit and European Theoretical Spectroscopy Facility, Université de Liège, allée du 6 août, 19, B-4000 Liège, Belgium

Roberta Farris

Catalan Institute of Nanoscience and Nanotechnology - ICN2 (BIST and CSIC), Campus UAB, 08193 Bellaterra (Barcelona), Spain

Matthieu J. Verstraete

Nanomat group, QMAT center, CESAM research unit and European Theoretical Spectroscopy Facility, Université de Liège, allée du 6 août, 19, B-4000 Liège, Belgium, ITP, Physics Department, University of Utrecht, 3584 CC Utrecht, the Netherlands

Matthew Heine

Department of Physics, Boston College, Chestnut Hill, MA 02467, USA

David Broido

Department of Physics, Boston College, Chestnut Hill, MA 02467, USA

Dennis S. Kim

College of Letters and Science, Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), California 90025, USA

Johan Klarbring

Theoretical Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden, Department of Materials, Imperial College London, South Kensington Campus, London SW7 2AZ, UK

Igor A. Abrikosov

Theoretical Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden

Sergei I. Simak

Theoretical Physics Division, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden, Department of Physics and Astronomy, Uppsala University, SE-75120 Uppsala, Sweden

Olle Hellman

Weizmann Institute of Science, Rehovot, Israel

Editor

Rachel Kurchin

Citation (CITATION.cff)

cff-version: "1.2.0"
authors:
- family-names: Knoop
  given-names: Florian
  orcid: "https://orcid.org/0000-0002-7132-039X"
- family-names: Shulumba
  given-names: Nina
  orcid: "https://orcid.org/0000-0002-2374-7487"
- family-names: Castellano
  given-names: Aloïs
  orcid: "https://orcid.org/0000-0002-8783-490X"
- family-names: Batista
  given-names: J. P. Alvarinhas
  orcid: "https://orcid.org/0000-0002-3314-249X"
- family-names: Farris
  given-names: Roberta
  orcid: "https://orcid.org/0000-0001-6710-0100"
- family-names: Verstraete
  given-names: Matthieu J.
  orcid: "https://orcid.org/0000-0001-6921-5163"
- family-names: Heine
  given-names: Matthew
  orcid: "https://orcid.org/0000-0002-4882-6712"
- family-names: Broido
  given-names: David
  orcid: "https://orcid.org/0000-0003-0182-4450"
- family-names: Kim
  given-names: Dennis S.
  orcid: "https://orcid.org/0000-0002-5707-2609"
- family-names: Klarbring
  given-names: Johan
  orcid: "https://orcid.org/0000-0002-6223-5812"
- family-names: Abrikosov
  given-names: Igor A.
  orcid: "https://orcid.org/0000-0001-7551-4717"
- family-names: Simak
  given-names: Sergei I.
  orcid: "https://orcid.org/0000-0002-1320-389X"
- family-names: Hellman
  given-names: Olle
  orcid: "https://orcid.org/0000-0002-3453-2975"
doi: 10.5281/zenodo.10589895
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Knoop
    given-names: Florian
    orcid: "https://orcid.org/0000-0002-7132-039X"
  - family-names: Shulumba
    given-names: Nina
    orcid: "https://orcid.org/0000-0002-2374-7487"
  - family-names: Castellano
    given-names: Aloïs
    orcid: "https://orcid.org/0000-0002-8783-490X"
  - family-names: Batista
    given-names: J. P. Alvarinhas
    orcid: "https://orcid.org/0000-0002-3314-249X"
  - family-names: Farris
    given-names: Roberta
    orcid: "https://orcid.org/0000-0001-6710-0100"
  - family-names: Verstraete
    given-names: Matthieu J.
    orcid: "https://orcid.org/0000-0001-6921-5163"
  - family-names: Heine
    given-names: Matthew
    orcid: "https://orcid.org/0000-0002-4882-6712"
  - family-names: Broido
    given-names: David
    orcid: "https://orcid.org/0000-0003-0182-4450"
  - family-names: Kim
    given-names: Dennis S.
    orcid: "https://orcid.org/0000-0002-5707-2609"
  - family-names: Klarbring
    given-names: Johan
    orcid: "https://orcid.org/0000-0002-6223-5812"
  - family-names: Abrikosov
    given-names: Igor A.
    orcid: "https://orcid.org/0000-0001-7551-4717"
  - family-names: Simak
    given-names: Sergei I.
    orcid: "https://orcid.org/0000-0002-1320-389X"
  - family-names: Hellman
    given-names: Olle
    orcid: "https://orcid.org/0000-0002-3453-2975"
  date-published: 2024-02-01
  doi: 10.21105/joss.06150
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6150
  title: "TDEP: Temperature Dependent Effective Potentials"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06150"
  volume: 9
title: "TDEP: Temperature Dependent Effective Potentials"

GitHub Events

Total

Create event: 21
Release event: 1
Issues event: 49
Watch event: 28
Delete event: 7
Member event: 1
Issue comment event: 91
Push event: 84
Pull request review comment event: 40
Pull request review event: 45
Pull request event: 33
Fork event: 6

Last Year

Create event: 21
Release event: 1
Issues event: 49
Watch event: 28
Delete event: 7
Member event: 1
Issue comment event: 91
Push event: 84
Pull request review comment event: 40
Pull request review event: 45
Pull request event: 33
Fork event: 6

Committers

Last synced: 5 months ago

All Time

Total Commits: 143
Total Committers: 5
Avg Commits per committer: 28.6
Development Distribution Score (DDS): 0.434

Past Year

Commits: 69
Committers: 5
Avg Commits per committer: 13.8
Development Distribution Score (DDS): 0.58

Top Committers

Name	Email	Commits
Florian Knoop	f**p@l**e	81
Aloïs Castellano	a**l@g**m	23
ejmeitz	e**1@g**m	16
Olle Hellman	o**n@g**m	13
Matthieu Verstraete	m**e@g**m	10

Committer Domains (Top 20 + Academic)

liu.se: 1

Issues and Pull Requests

Last synced: 4 months ago

All Time

Total issues: 88
Total pull requests: 70
Average time to close issues: 18 days
Average time to close pull requests: 27 days
Total issue authors: 45
Total pull request authors: 8
Average comments per issue: 2.07
Average comments per pull request: 1.43
Merged pull requests: 44
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 43
Pull requests: 42
Average time to close issues: 17 days
Average time to close pull requests: 16 days
Issue authors: 20
Pull request authors: 7
Average comments per issue: 0.93
Average comments per pull request: 1.67
Merged pull requests: 22
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

flokno (17)
Guodonglin-cqust (9)
phyjz (6)
ejmeitz (6)
tingguangli (5)
WenjiangZhou (2)
delchere (2)
mayankaditya (2)
chejunwei2 (2)
RobertaFarris93 (2)
Ssingsen (2)
R3aptor (1)
YuWu-thermal (1)
ganesh028 (1)
lshannnnn (1)

Pull Request Authors

flokno (42)
OrbitalC (12)
ejmeitz (7)
ollehellman (6)
mjv500 (5)
RobertaFarris93 (2)
jyyao27 (1)
MaxMignolet (1)

TDEP

Science Score: 98.0%

Scientific Fields

Repository

Basic Info

Statistics

Metadata Files

README.md

Temperature Dependent Effective Potentials (TDEP)

Tutorials

Installation

Report bugs and issues

Contribute

Other things to look at

How to cite

Troubleshooting

Symmetry errors

Owner

JOSS Publication

TDEP: Temperature Dependent Effective Potentials

Authors

Editor

Tags

Citation (CITATION.cff)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies