Merge pull request duartegroup#145 from duartegroup/v1.2.3

v1.2.3

Merge pull request duartegroup#134 from duartegroup/v1.2.2

v1.2.2

Merge pull request duartegroup#128 from duartegroup/v1.2.1

v1.2.1

Merge pull request duartegroup#123 from duartegroup/v1.2.0a

v1.2.0

Merge pull request duartegroup#95 from duartegroup/v1.1.3

v1.1.3

Merge pull request duartegroup#90 from duartegroup/v1.1.2

v1.1.2

Hotfix (duartegroup#83)

* Fixes comparison of similar energies

* Fix documentation typo

* Test comparisons

Merge v1.1dev (duartegroup#70)

* Values with units (duartegroup#49)

* Generalise values with units

* Species refactoring, typing init and repr

* Add keywords to energies

* Dihedral refactor

* Test equality

* Return values from EST wrappers

* Energy reset on atom change

* Documentation improvements

* RMSD check on atoms reset

* Improve QRC  (duartegroup#58)

* Improve QRC displacement

* Change value str

* Update changelog and backtrack

* Create pytest.yml

* Update and rename .github/ISSUE_TEMPLATE/workflows/pytest.yml to .github/workflows/pytest.yml

* Create deploy.yml

Adds documentation deployment to GitHub pages using template from t-young31/github_actions_cc

* Thermochemistry calculations  (duartegroup#51)

* Improve QRC displacement

* Change value str

* Update changelog and backtrack

* Create pytest.yml

* Improved decorators

* Typing and documentation

* ORCA Hessian extraction

* Add mass values

* Add coordinate value and hessian improvements

* Hessian projection and Atoms class

* Cached property for Python >3.2

* Fix Python 3.7 cached_property Hessian

* Linear projected hessian frequencies

* Remove set_lines for output

* More robust units for ValueArrays

* Gaussian Hessian extract

* Fix possible linear dependencies

* NWChem Hessian extraction

* Start otherm integration

* Remove backwards compatible keyword prefix

* More flexible thermochemistry calc and fix bug

* Deprecate get_free_energy and similar

* Refactor TS classes for Hessians

* Change Gradients to Gradient for consistency

* Remove Travis CI

* Zero gradients of chiral atoms and neighbours

* Add thermochemistry summary

* Remove calculation temperature

* Add atom test

* Tests and bug fixes

* Add quickstart video

* Add TS thermochemistry test

* Documentation and refactoring

* Add method string to thermo cont

* Add energies printing to a reaction

* Add energy to end of energies if present

* Bugfix in optimisation of displaced molecule

* Thermochemistry doc and allow .hess ORCA out

* Copy atoms in displacement

* Enum for LFM and improved exceptions

* Add max disp for mode checking

* Improved stochastic sampling (duartegroup#48)

* Uniform global minimisation

* nD PBC

* Add Catch2 tests

* Improve codecov

* Truncation bugfixes (duartegroup#61)

* Use minimal cycle basis

* Tweak tolerance on graph

* Remove find_complexes()

* Truncation threshold

* Alter truncated dir

* Update build badge

* Skip conformers with no atoms

* Bugfix in displacement enumeration

* Add tests

* Allow for XTB keywords

* Corrects benchmark. Grubbs example should be to be eta-2 reactant

* Enable smaller force constants in XTB

* Fix LGTM alert

* Update changelog

* Fixes possible zero distance constraints

* Allows get_active_atom_neighbour_lists with Species

* Improve peak checking

* Spin bugfix (duartegroup#64)

* Fix defined spin multiplicity

* Fix XTB calculations for non-singlet molecules

* Additional documentation and tests (duartegroup#65)

* Add additional benchmark tests

* Add comment for reactant and product complexes

* Update changelog for fixes

* Add another special case

* Update troubleshooting advice

* Bump version

* Delete co2 example

* Add catch2 tests to CI

* Update catch.yml

* Usability improvements (duartegroup#67)

* Typo in themochemistry doc

* Return None not an empty list from Speces.imaginary_frequencies

* Add Config.ORCA.other_input_block

* Reset the Config state

* Atoms refactor

* Raise exception if single point energy fails

* Minor doc improvements

* Add codecov satisfying tests

* JS changes

* Parallel conformer calculations (duartegroup#68)

* Fix yypo in themochemistry doc

* Return None not an empty list from Speces.imaginary_frequencies

* Add Config.ORCA.other_input_block

* Atoms refactor

* Raise exception if single point energy fails

* Minor doc improvements

* Changes looseopt to a maximum of 10 optimisation cycles

* Adds parallel conformer calculations

* Defines constraints for all species

* Remove superfluous get_conformer function

* Add benchmark

* Chagelog updates

* NWChem wrapper fix (duartegroup#69)

* Throw exception if no conformer energies or atoms

* Fix NWChem Hessian extraction

* NWChem wrapper improvements

* NWChem test data update

Bugfix in TS template saving

Update documentation (duartegroup#55)

* Update changelog and documentation