zsisa flow + thermal work (#342)

• Modification on test_qha_general_stress.

• Made some modifications to qha_general_stress.py.

• Add ScrFile plot_freqs_at_ggp method

• Fix AttributeError: ‘Arrow3D’ object has no attribute ‘do_3d_projection’ raised by structure.plot()

• scr.reader –> scr.r, minor improvements in docs

• Don’t deploy website on pull requests

• Cosmetic changes

• More Type hints, fix a couple of sphinx warnings

• update vars database

• Fix a couple of RST warnings

• app post-processing tools for QHA

• Saving work

• zsisa: add set_structure_stress_guess method + simplify if statements

• Use dataclasses instead of dictionaries

• Add Serializable mixin class

• More docs

• generate_deformations: return indices needed to insert PHDOSes in the 6d array

• Add .codespell.ignore

• Rename work.zsisa.cal_stress -> get_tstress and return ThermalData instance

• Activate elastic works

• model -> qha_model

• Use GPa_to_au from abinit_units

• if entry in phdos_6s is not None, path shall exist

• Finalize json format to support restart and post-processing

• Implement MultiRelaxTask

• Restore works.py to previous version

• Add register_multi_relax_task

• Finalize post-processing tools

• Use VzsisaResults

• Code cleanup

• Move prof_main to tools.cli_parsers

• Add support for tuna and snakeviz

• Add run_tests_on_changed.py

• Cosmetic changes

• Activate mypy

• Double relaxation only if optcell == 0

• Converge relaxation with thermal stress twice. Use dilatmx=1.0 in the second run

• Add with_piezo option. default: False

• Now structure_guess and stress_guess are removed from the init and passed to get_tstress

• Fix Deprecation Warning: Conversion of an array with ndim > 0 to a scalar

• Plot only indipendent constants

• Renaming

• Gibbs free energy is added to ZSISA.

• Continue to fix deprecation warnings

• fix a problem.

• plot_elastic_vs_t_and_p

• Move cmat_inds_names to qha_general_stress

• Add plot_gibbs

• Add tests for gibbs and elastic tensor

• Cosmetic changes

• Clarify that get_tstress receives pressure in GPa

• Cosmetic changes

• fix pv in gibbs units.

• cosmetic changes

• Continue to fix deprecation warnings

• get_tstress now receives elastic tensort in Gpa and Voigt notation instead of filename

• Postpone import of Element

• Cosmetic changes

• Cosmetic changes

• Cosmetic changes

• Add some documentation