Feature: support automated EOS test result analysis calculated by Quantum ESPRESSO

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Walkthrough

The recent changes enhance the APNS project by adding and updating various Python files to introduce new functionalities for handling, analyzing, and visualizing results from ABACUS and Quantum ESPRESSO simulations. Key updates include new utility functions, renaming functions and classes, fixing typographical errors, and updating data structures in example.json.

Changes

Files/Modules	Change Summary
`apns/.../apns2_ecut_abacus.py`	Introduces functions for ABACUS ecutwfc convergence tests, job repair, and plot generation.
`apns/.../apns2_ecut_qespresso.py`	Adds functions for collecting QESPRESSO results, processing data, and plot generation for ecutwfc tests.
`apns/.../apns2_ecut_utils.py`	Renames and redefines classes/functions for ecutwfc convergence tests, updates nested dictionary logic, and imports new utility functions.
`apns/.../apns2_eos_abacus.py`	Adds functions for analyzing APNS EOS test data, including job data collection, preparation, and plot generation.
`apns/.../apns2_eos_qespresso.py`	Introduces functions for analyzing QESPRESSO simulation results, data collection, preparation, and plot generation.
`apns/.../apns2_eos_utils.py`	Adds utility functions for EOS analysis, including reading data, calculating deltas, fitting EOS, and plotting.
`apns/.../apns2_utils.py`	Utility functions for reading APNS job descriptions and converting pseudopotential filenames.
`apns/.../driver_EOS_20240326.py`	Imports and updates utility functions for file concatenation and figure plotting.
`apns/.../external_frender/figure.py`	Corrects typos in function names and improves filename clarity.
`apns/.../eos.py`	Adds global constants, utility functions for EOS analysis, and refactors logic within key functions.
`apns/.../read_abacus_out.py`	Renames function for reading energy trajectory from a log file and improves energy conversion accuracy.
`apns/.../read_qespresso_out.py`	Introduces functions for reading and processing Quantum Espresso output data, including band structures and energy trajectories.
`apns/test/main.py`	Renames and updates Quantum ESPRESSO input file generation functions.
`example.json`	Updates values for ABACUS and QESPRESSO configurations, revises `atomsets` and `strusets` elements.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant APNS_System
    participant ABACUS_Module
    participant QESPRESSO_Module
    participant EOS_Module
    participant Utils

    User ->> APNS_System: Start simulation
    APNS_System ->> ABACUS_Module: Collect ABACUS results
    ABACUS_Module ->> APNS_System: ABACUS results collected
    APNS_System ->> QESPRESSO_Module: Collect QESPRESSO results
    QESPRESSO_Module ->> APNS_System: QESPRESSO results collected
    APNS_System ->> EOS_Module: Perform EOS analysis
    APNS_System ->> Utils: Read job descriptions and convert filenames
    EOS_Module ->> APNS_System: EOS analysis complete
    APNS_System ->> User: Return analysis and plots

Poem

In code so bright, a bunny’s delight,
ABACUS and Espresso took flight, 🐰
With functions anew, data they drew,
Convergence and EOS, a clearer view.
Utility tools, fixes to rules,
Together we cheer, these neat renewals. 🌟

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kirk0830 / ABACUS-Pseudopot-Nao-Square