example_usage.py

from pathlib import Path
import argparse

from pdf_gr_conversion import convert_file_gr_to_small_gr
from pdf_coordination import analyze_file_first_shell


def main():
    parser = argparse.ArgumentParser(description="Convert G(r) to g(r) and integrate first shell.")
    parser.add_argument("--input", required=True, help="Input G(r) file, e.g. data/std_Si.gr")
    parser.add_argument("--rho0", type=float, required=True, help="Number density in atoms/Å^3")
    parser.add_argument("--output-g", default=None, help="Output g(r) file")
    parser.add_argument("--output-plot", default=None, help="Output integration plot")
    parser.add_argument("--output-data", default=None, help="Output txt file for the full integration plot data")
    parser.add_argument("--output-region-data", default=None, help="Output txt file for integration-region-only data")
    args = parser.parse_args()

    input_file = Path(args.input)

    output_g = Path(args.output_g) if args.output_g else input_file.with_name(input_file.stem + "_small_g.dat")
    output_plot = Path(args.output_plot) if args.output_plot else input_file.with_name(input_file.stem + "_first_shell.png")
    output_data = Path(args.output_data) if args.output_data else input_file.with_name(input_file.stem + "_first_shell_data.txt")
    output_region_data = Path(args.output_region_data) if args.output_region_data else input_file.with_name(input_file.stem + "_first_shell_region.txt")

    convert_file_gr_to_small_gr(input_file=input_file, output_file=output_g, rho0=args.rho0)

    result = analyze_file_first_shell(
        input_file=output_g,
        rho0=args.rho0,
        plot_file=output_plot,
        data_file=output_data,
        region_data_file=output_region_data,
    )

    print("First-shell analysis result:")
    for k, v in result.items():
        print(f"{k}: {v}")
    print(f"Saved g(r): {output_g}")
    print(f"Saved plot: {output_plot}")
    print(f"Saved plot data: {output_data}")
    print(f"Saved region data: {output_region_data}")


if __name__ == "__main__":
    main()