Feature: Support more options and features in the new script for RT-TDDFT absorption spectrum

[AsTonyshment]

Great thanks to @ESROAMER for trying out the new script and providing highly practical suggestions!

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What's changed?

1. Core Physics & Numerical Rigor Enhancements

• Updated the FFT processing to follow standard physics conventions ($e^{i\omega t}$) by properly applying complex conjugation (np.conj) to the Fourier-transformed arrays.
• Replaced implicit array divisions with explicit boolean masks to completely bypass NumPy complex ufunc masking bugs and prevent accidental NaN/Inf crashes during response function calculations.
• Implemented a Fermi-Dirac-like tapering window function in the frequency domain to smoothly suppress high-energy optical responses to a designated vacuum baseline, eliminating edge divergences.
• Expanded the Hilbert transform window with a $10\times$ padding factor to entirely eliminate periodic boundary wrap-around artifacts.

2. Robustness, Data Validation & Elastic Padding

• Enforced a pre-execution length check on signal files. The script now early-halts with clean error messages if the available simulation steps are fewer than the requested --step_end, avoiding partial out-of-bound errors.
• Added an automated elastic zero-padding mechanism for electric field profiles, accommodating minor line-count mismatches at the tail of the data cleanly.

3. CLI Architecture & Usability Overhaul

• Separated the mixed choices into two orthogonal, highly flexible parameters: --response_source (dipole / current) and --spectrum_type (epsilon / sigma).
• Programmed dynamic defaults for --signal_path based on the chosen --response_source (./OUT.ABACUS/dipole_s1.txt for dipole and ./OUT.ABACUS/current_tot.txt for current), minimizing user-end verbosity.
• Added explicit argument overrides for visual boundary clipping via --ylim_energy and --ylim_wavelength.

4. Advanced Plotting & Structured Export

• Designed a percentile-filtering logic (calculate_y_limits) coupled with a low-energy cutoff threshold ($0.2\text{ eV}$) to automatically ignore unphysical low-frequency divergences and produce clean plot scaling.
• The script now automatically generates and saves individual specialized graphs—including time-series signals, full spectrum profiles (Mixed, Real-only, and Imaginary-only components for both Energy and Wavelength domains), and incident field Fourier mappings.
• Data dumps are now properly segregated into distinct, cleanly headers-labeled real and imaginary coordinate text matrices ({type}_dat_real.txt and {type}_dat_imag.txt).

[Copilot]

Pull request overview

This PR modernizes the RT‑TDDFT absorption-spectrum plotting workflow by expanding the CLI and making the absorption/response calculations more flexible (dipole vs current; epsilon vs sigma), while adding additional plotting/export features and more defensive data handling.

Changes:

• Reworked the CLI to separate --response_source and --spectrum_type, with dynamic defaults for --signal_path and new plot viewport controls (--ylim_*, --*_range).
• Updated response-function/KK processing logic (FFT convention handling, safer complex division strategy, Hilbert padding/tapering) and expanded the set of generated plots and exported datasets.
• Removed the legacy dipole.py tool in favor of the consolidated script flow.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 5 comments.

File	Description
tools/rt-tddft-tools/plot_absorption.py	Major refactor: new CLI, revised spectrum computation, more robust I/O, expanded plotting and structured exports.
tools/rt-tddft-tools/dipole.py	Deleted legacy implementation (functionality now covered by the updated plotting script).

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[mohanchen]

LGTM, thanks for your contribution.