♻️ Initialization of the refactoring of the LAMMPS plugin#35

Merged

chrisjsewell merged 73 commits intoaiidaplugins:developfrom JPchico:refactoring

Apr 5, 2022

+22,672-2,259

Commits on Oct 21, 2020

Fixing the examples so that they correspond to the new potential setup.
Jonathan Chico
committed
Fixed formatting error which caused the pre-commit hooks to fail
Jonathan Chico
committed

Commits on Jun 16, 2021

Merge remote-tracking branch 'upstream/master'
Jonathan Chico
committed

Commits on Jun 17, 2021

Merge branch 'master' of git://github.com/aiidaplugins/aiida-lammps
Jonathan Chico
committed

Commits on Nov 8, 2021

Adding a new auxiliary file to auto-generate the lammps input file.
Jonathan Chico
committed
Added a pre-commit in the style of the one in aiida-core. Change many files to follow this format.
Jonathan Chico
committed
(WIP) Adding a new file for the automatic generation of the lammps input file.
Jonathan Chico
committed

Commits on Nov 9, 2021

(WIP) Improving the input file generation.
Jonathan Chico
committed

Commits on Nov 10, 2021

(WIP) Improving the input generation.
Jonathan Chico
committed
(WIP) Makign the input generation more flexible.
Jonathan Chico
committed
(WIP) make the input file generation more flexible.
Jonathan Chico
committed

Commits on Nov 15, 2021

(WIP) making the input more flexible.
Jonathan Chico
committed

Commits on Nov 17, 2021

(WIP) Make the input generation more flexible.
Jonathan Chico
committed

Commits on Nov 19, 2021

(WIP) Improving the potential storage by making it similar to the PseudoData
Jonathan Chico
committed

Commits on Nov 22, 2021

(WIP) Improving the potential.
Jonathan Chico
committed

Commits on Nov 23, 2021

(WIP) Improving the potential storage.
Jonathan Chico
committed
(WIP) improving the generation of the input file.
Jonathan Chico
committed
(WIP) Improving the potential.
Jonathan Chico
committed

Commits on Nov 25, 2021

(WIP) Improvements on the input generation. Changes to ensure that the velocity can be read and properly parsed.
Jonathan Chico
committed

Commits on Nov 26, 2021

(WIP) Improvement of the input generation.
Jonathan Chico
committed

Commits on Nov 29, 2021

(WIP) Improving the input file generation.
Jonathan Chico
committed

Commits on Nov 30, 2021

(WIP) Improvement of the dosctrings and format to make it compatible with the pre-commit style.
Jonathan Chico
committed

Commits on Dec 1, 2021

(WIP) Fixing the format and docstrings so that they follow the pylint standard.
Jonathan Chico
committed
(WIP) Updating the pre-commit packages
Jonathan Chico
committed
(WIP) setting so that the correct pre-commit runs
Jonathan Chico
committed

Commits on Dec 3, 2021

(WIP) Trying to fix the format to fit the pre-commit standard.
Jonathan Chico
committed
Setting the version of pylint to 2.5
Jonathan Chico
committed
(WIP) Fixing formatting issues with pylint.
Jonathan Chico
committed
(WIP) Fixing issues with pylint formatting.
Jonathan Chico
committed
(WIP) Trying to fix the issues with pylint checking for duplicate code
Jonathan Chico
committed
(WIP) Removing pre-commit from the installation of the tests
Jonathan Chico
committed
(WIP) Fixing an issue with github actions.
Jonathan Chico
committed
(WIP) Fixing an issue with github actions.
Jonathan Chico
committed
(WIP) Fixing the tests so that they correctly refer to potential_type instead of type.
Jonathan Chico
committed
(WIP) Fixing an issue with the kind_symbols not being properly replaced in the string.
Jonathan Chico
committed
(WIP) Fixing issues with the tests.
Jonathan Chico
committed
(WIP) Making the trajectory generation compatible with aiida-core 1.65
Jonathan Chico
committed
(WIP) Fixing trajectories to make them compatible to aiida-core 1.65
Jonathan Chico
committed

Commits on Dec 6, 2021

(WIP) Fixing an issue in which the trajectories could not be properly sotred in 1.65. Added a temporary exception to handle the 2.x cases
Jonathan Chico
committed
(WIP) Fixing a small issue with the formatting.
Jonathan Chico
committed
(WIP) Fixing an issue in which the trajectory_filename is not being properly referenced by the tests.
Jonathan Chico
committed
(WIP) Adding test files for the new potential data format.
Jonathan Chico
committed

Commits on Dec 7, 2021

Adding tests for the new potential type in aiida-lammps.
Jonathan Chico
committed
(WIP) Adding tests for the potential block for the new potential style.
Jonathan Chico
committed

Commits on Dec 8, 2021

(WIP) Making the input file more flexible.
Jonathan Chico
committed
Fixing mislablled potential test from eam -> eam/alloy
Jonathan Chico
committed
Fixing an issue resulting from the re-labelling of the eam/alloy test potentials.
Jonathan Chico
committed
(WIP) Improving the input file generation.
Jonathan Chico
committed
Fix an issue that could lead the tests to fail due to how the block headers are written.
Jonathan Chico
committed
(WIP) Adding tests for the generation input files.
Jonathan Chico
committed
(WIP) Adding tests for the input file generation
Jonathan Chico
committed

Commits on Dec 9, 2021

Adding tests for the input file generation.
Jonathan Chico
committed
(WIP) Improving the flexibility of the input file.
Jonathan Chico
committed
(WIP) Improving input file generation.
Jonathan Chico
committed

Commits on Dec 10, 2021

(WIP) Making the lammps calculations more flexible.
Jonathan Chico
committed
Adding tests for the new parser.
Jonathan Chico
committed
(WIP) Making the calculations more flexible. Adding a new base calculation for the LAMMPS plugin.
Jonathan Chico
committed

Commits on Dec 13, 2021

Commits on Dec 14, 2021

Fixed issues with respect to the parsing of for the new base calculation.
Jonathan Chico
committed
Fixing issues with potential tests after reverting behaviour of potential lines.
Jonathan Chico
committed

Commits on Jan 28, 2022

(WIP) Working in the documentation of the package.
Jonathan Chico
committed

Commits on Feb 9, 2022