Fix&Feature&Refactor: sort and enrich the structure auto-generation functions

[kirk0830]

What's new

• fix the inconsistency of using "scale" between bravais/model systems and cif, in APNS2.0 the earlier version, the EOS actually ranges from 0.94^3 V to 1.06^3 V rather than 0.94V to 1.06V.
• add three perturbation method on solid structures (shear, twist and scale). For the third, if use scale-xyz, is identical with EOS setting the volumn rescaling
• align the molecule structure generation with ABACUS-ORBGEN

Summary by CodeRabbit

• New Features

  • Enhanced output formatting for pseudopotential identifiers across multiple functions.
  • Introduced a new fit function to process equations of state based on collected data.
  • Added a CellTransformer class for advanced cell transformations in simulations.

• Bug Fixes

  • Improved handling of directory validation and data extraction processes.
  • Added error handling for potential calculation issues in output functions.

• Documentation

  • Expanded docstrings for clarity and detailed explanations of functions.

• Chores

  • Updated configuration settings in JSON for improved simulation parameters and material definitions.

[coderabbitai[bot]]

Walkthrough

This pull request introduces a series of modifications across multiple Python files, focusing on refining output handling, enhancing data structures, and improving function documentation. Key changes include updates to how pseudopotential identifiers are formatted, restructuring of data extraction processes, and the introduction of new functions for fitting equations of state. Additionally, adjustments to command execution in testing scripts aim to enhance stability and usability. Overall, these changes reflect a comprehensive enhancement of the codebase's functionality and clarity.

Changes

Files Grouped by Similar Changes	Change Summary
apns/analysis/apns1_eos_abacus.py, apns/analysis/apns2_ecut_abacus.py, apns/analysis/apns2_ecut_qespresso.py, apns/analysis/apns2_eos_abacus.py, apns/analysis/apns2_eos_qespresso.py, apns/analysis/apns2_eos_utils.py, apns/analysis/apns2_utils.py	Modifications primarily focus on how pseudopotential identifiers are constructed and formatted, enhancing output clarity and improving data extraction processes. New functions and expanded logic have been introduced to accommodate more complex data structures.
apns/orbgen/postdft_eos.py, apns/orbgen/postdft_eta.py	Changes involve restructuring how test results are stored and formatted, improving data organization and output clarity in the handling of pseudopotential test cases.
apns/test/abacustest.py, apns/test/atom_species_and_cell.py, apns/test/bravis_and_molecule.py, apns/test/main.py	Enhancements to command execution, parameter handling, and function logic, focusing on improving stability, flexibility, and usability in testing scenarios.
example.json	Significant modifications to configuration settings, including changes in output directory paths, energy cutoff settings, basis types, and atom definitions.

Possibly related PRs

• #66: Modifications to the plot function and handling of return values from convert_fpp_to_ppid, related to changes in apns2_ecut_abacus.py.
• #67: Introduced changes to the AtomSpecies class, which relates to energy cutoff handling similar to the updates in this PR.
• #70: Updates to apns1_eos_abacus.py, including the plot function, reflecting a focus on output processing.
• #78: Enhancements to the collect function in apns2_ecut_abacus.py, aligning with the focus on refining function outputs.

Poem

🐰 In the meadow where data flows,
Changes sprout like blooming rows.
Pseudopotentials dance with glee,
Clarity shines for all to see.
With every tweak, our code does sing,
A brighter future, let’s all bring! 🌼

[!TIP]

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