Add massive neutrino support and improve CSV/CLI output

- Add neutrino mass parameter to SpectrumConfig and CLI interface
- Update PhaseSpace component to handle neutrino mass effects properly
- Update CSV headers to show basic endpoint and all transition types
- Add --csv-verbosity option to CLI with 'full' and 'concise' options
- Fix comparison plots to properly show linear scale variations
- Add comprehensive tests for neutrino mass functionality

create_comparison_plot.py

@@ -0,0 +1,144 @@
+#!/usr/bin/env python3
+"""
+Script to create a comparison plot of total beta spectra for edge neutrino masses (1.5 keV and 2.5 keV)
+"""
+
+import pandas as pd
+import matplotlib.pyplot as plt
+import numpy as np
+
+# Input files
+mass_1_5_csv = "/home/unzhakov/workspace/massive_nu_pr/pr144_nu_mass_1_50keV.csv"
+mass_2_45_csv = "/home/unzhakov/workspace/massive_nu_pr/pr144_nu_mass_2_45keV.csv"
+
+# Output file
+output_png = (
+    "/home/unzhakov/workspace/massive_nu_pr/pr144_comparison_1_5_vs_2_45_keV.png"
+)
+
+print(f"Reading data from {mass_1_5_csv} and {mass_2_45_csv}...")
+
+
+# Read CSV files, skipping metadata headers
+# The metadata headers start with '#'
+def read_csv_with_metadata(filepath):
+    with open(filepath, "r") as f:
+        lines = f.readlines()
+
+    # Find the line where data starts (not starting with '#')
+    data_start_line = 0
+    for i, line in enumerate(lines):
+        if not line.startswith("#"):
+            data_start_line = i
+            break
+
+    # Read the data
+    df = pd.read_csv(filepath, skiprows=data_start_line)
+    return df
+
+
+# Read the data
+df_1_5 = read_csv_with_metadata(mass_1_5_csv)
+df_2_45 = read_csv_with_metadata(mass_2_45_csv)
+
+print("Data loaded successfully.")
+
+# Extract energy and spectrum data
+energies_1_5 = df_1_5["energy_MeV"].values
+spectrum_1_5 = df_1_5["spectrum"].values
+
+energies_2_45 = df_2_45["energy_MeV"].values
+spectrum_2_45 = df_2_45["spectrum"].values
+
+print(
+    f"Energy range: {energies_1_5[0] * 1000:.1f} eV to {energies_1_5[-1] * 1000:.1f} eV"
+)
+
+# Create comparison plot
+fig, ax = plt.subplots(figsize=(12, 8))
+
+# Plot both spectra
+ax.plot(energies_1_5 * 1000, spectrum_1_5, "b-", lw=2, label="m_ν = 1.5 keV")
+ax.plot(energies_2_45 * 1000, spectrum_2_45, "r--", lw=2, label="m_ν = 2.45 keV")
+
+# Set labels and title
+ax.set_xlabel(r"Electron kinetic energy $E$ [keV]", fontsize=12)
+ax.set_ylabel("Normalized Spectrum", fontsize=12)
+ax.set_title(
+    "Pr144 -> Nd144 Beta Decay: Comparison of Neutrino Mass Effects\n"
+    "(1.5 keV vs 2.45 keV)",
+    fontsize=14,
+)
+
+# Set log scale for y-axis to see the endpoint region clearly
+ax.set_yscale("log")
+
+# Add grid
+ax.grid(True, alpha=0.3)
+
+# Add legend
+ax.legend(fontsize=12)
+
+# Focus on the endpoint region (last part of the spectrum)
+# Find the energy range near the endpoint
+max_energy_keV = max(energies_1_5) * 1000
+# Show last 10 keV of the spectrum
+start_energy_keV = max_energy_keV - 10.0
+ax.set_xlim(start_energy_keV, max_energy_keV)
+
+# Save the plot
+plt.tight_layout()
+plt.savefig(output_png, dpi=150, bbox_inches="tight")
+print(f"Comparison plot saved to {output_png}")
+
+# Also create a linear scale plot for the endpoint region
+fig_linear, ax_linear = plt.subplots(figsize=(12, 6))
+
+# Plot both spectra in linear scale
+ax_linear.plot(energies_1_5 * 1000, spectrum_1_5, "b-", lw=2, label="m_ν = 1.5 keV")
+ax_linear.plot(energies_2_45 * 1000, spectrum_2_45, "r--", lw=2, label="m_ν = 2.45 keV")
+
+# Set labels and title
+ax_linear.set_xlabel(r"Electron kinetic energy $E$ [keV]", fontsize=12)
+ax_linear.set_ylabel("Normalized Spectrum", fontsize=12)
+ax_linear.set_title(
+    "Pr144 -> Nd144 Beta Decay: Comparison of Neutrino Mass Effects (Endpoint Region)\n"
+    "(1.5 keV vs 2.45 keV) - Linear Scale",
+    fontsize=14,
+)
+
+# Set linear scale for y-axis
+ax_linear.set_yscale("linear")
+
+# Set y-axis limits to show the variation in the spectrum
+# Find the min and max values in the endpoint region to set appropriate limits
+min_spec_1_5 = np.min(spectrum_1_5[-100:])  # Last 100 points
+max_spec_1_5 = np.max(spectrum_1_5[-100:])
+min_spec_2_45 = np.min(spectrum_2_45[-100:])
+max_spec_2_45 = np.max(spectrum_2_45[-100:])
+
+overall_min = (
+    min(min_spec_1_5, min_spec_2_45) * 0.9
+    if min(min_spec_1_5, min_spec_2_45) > 0
+    else 0
+)
+overall_max = max(max_spec_1_5, max_spec_2_45) * 1.1
+
+ax_linear.set_ylim(overall_min, overall_max)
+
+# Add grid
+ax_linear.grid(True, alpha=0.3)
+
+# Add legend
+ax_linear.legend(fontsize=12)
+
+# Focus on the endpoint region (last part of the spectrum)
+ax_linear.set_xlim(start_energy_keV, max_energy_keV)
+
+# Save the linear plot
+plt.tight_layout()
+linear_output_png = (
+    "/home/unzhakov/workspace/massive_nu_pr/pr144_comparison_1_5_vs_2_45_keV_linear.png"
+)
+plt.savefig(linear_output_png, dpi=150, bbox_inches="tight")
+print(f"Linear comparison plot saved to {linear_output_png}")