0.4.0

Release 0.4.0 version: SOMD engine Decoupling Support

What's Changed

• Decoupled SOMD engine from a3fe calculation and removed run_somd.sh and template_config.cfg, replacing them with a3fe.configuration.slurm_config.SlurmConfig and a3fe.configuration.engine_config.SomdConfig.
• SystemPreparationConfigs saved as readable yaml file, rather than as a pickle.
• Separated system preparation configuration from system preparation and configured SOMD with a3fe.configuration.system_prep_config.SomdSystemPreparationConfig.
• Streamlined the installation process with a Makefile.

Full Changelog: 0.3.5...0.4.0

0.3.5

Update defaults affecting adaptive simulations and automated lambda spacing to be internally consistent and consistent with the publication.

What's Changed

• Update defaults for runtime_constant and delta_er by @fjclark in #62

Full Changelog: 0.3.4...0.3.5

0.3.4

Issue fixed by making loguru explicit

0.3.3

What's Changed
Fixed bug in water analysis by @Roy-Haolin-Du in #43.

0.3.2

What's Changed

• Bugfix rename equil files by @fjclark in #36
• bugfix replace-output-directory by @Roy-Haolin-Du in #37
• Ensure all matplotlib resources get closed after analysis by @fjclark in #39

Full Changelog: 0.3.1...0.3.2

0.3.1

What's Changed

• Ensure SimulationRunnerIterator saves states when tearing down by @fjclark in #24

Full Changelog: 0.3.0...0.3.1

0.3.0 Improve CalcSet

What's Changed

• Feature Improved CalcSet by @fjclark in #22

This:

• Improved CalcSet so that 1) get_optimal_lam_vals can be called directly on the CalcSet object, and 2) analyse can be called directly without requiring experimental results (by specifying compare_to_exp=False).
• Documentation on PME vs RF slightly improved.

Full Changelog: 0.2.1...0.3.0

0.2.1

What's Changed

• Bugfix robust slurm queue read by @fjclark in #15

Full Changelog: 0.2.0...0.2.1

0.2.0 Support for Charged Ligands

What's Changed

• Added support for charged ligands using the co-alchemical ion approach (see https://a3fe.readthedocs.io/en/latest/guides.html#abfe-with-charged-ligands). By @fjclark in #10
• Added tests for parameterisation. By @fjclark in #10
• Made detection of username more robust (see #8). By @fjclark in #10
• Fixed bug arising from incorrect removal of “is_equilibrated” method (37de921). By @fjclark in #10

Full Changelog: https://a3fe.readthedocs.io/en/latest/CHANGELOG.html

0.1.3

What's Changed

• Bugfix write config option by @fjclark in #7

Full Changelog: 0.1.2...0.1.3