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+#+TITLE: Nearest P/I Environment Analysis for Li₃PS₄–LiI Glasses
+#+AUTHOR: Minami Sakuma
+#+OPTIONS: toc:2 num:t
+
+* Overview
+
+This repository contains a Python program for analyzing the local
+environments of Li⁺ ions in Li₃PS₄–LiI glass trajectories.
+
+For each Li⁺ ion, the program calculates the distances to the nearest
+P atom and I⁻ ion under periodic boundary conditions. It then determines
+whether the Li⁺ ion is closer to P or I⁻.
+
+The following two quantities are calculated for each composition:
+
+- The P fraction in the entire system:
+  P / (P + I)
+- The fraction of Li⁺ ions whose nearest center is P:
+  N_{Li-near-P} / N_{Li}
+
+The second quantity is calculated for each molecular-dynamics step and
+then averaged over all steps.
+
+* Target System
+
+The target system is Li₃PS₄–LiI glass.
+
+The following compositions are included in this repository:
+
+- 80Li₃PS₄–20LiI
+- 70Li₃PS₄–30LiI
+- 60Li₃PS₄–40LiI
+- 50Li₃PS₄–50LiI
+
+* Analysis Procedure
+
+For each molecular-dynamics step, the program performs the following
+operations:
+
+1. Read the coordinates of Li⁺, P, S, and I⁻.
+2. Calculate all Li⁺–P distances under periodic boundary conditions.
+3. Calculate all Li⁺–I⁻ distances under periodic boundary conditions.
+4. Identify the nearest P atom and I⁻ ion for each Li⁺ ion.
+5. Classify each Li⁺ ion according to whether P or I⁻ is closer.
+6. Calculate the fraction of Li⁺ ions whose nearest center is P.
+7. Average the fraction over all simulation steps.
+
+The minimum-image convention is used to calculate distances under
+periodic boundary conditions.
+
+* Requirements
+
+- Python 3
+- NumPy
+- Matplotlib
+
+The required Python packages can be installed using:
+
+#+BEGIN_SRC shell
+pip install numpy matplotlib
+#+END_SRC
+
+* Repository Contents
+
+#+BEGIN_EXAMPLE
+.
+├── calc_share.py
+├── 050Li3PS4-050LiI_thin100.lammpstrj
+├── 060Li3PS4-040LiI_thin100.lammpstrj
+├── 070Li3PS4-030LiI_thin100.lammpstrj
+├── 080Li3PS4-020LiI_thin100.lammpstrj
+├── Readme.org
+└── .gitignore
+#+END_EXAMPLE
+
+* Usage
+
+Run the program by specifying one or more trajectory files with the
+=-i= option:
+
+#+BEGIN_SRC shell
+python calc_share.py -i \
+  080Li3PS4-020LiI_thin100.lammpstrj \
+  070Li3PS4-030LiI_thin100.lammpstrj \
+  060Li3PS4-040LiI_thin100.lammpstrj \
+  050Li3PS4-050LiI_thin100.lammpstrj
+#+END_SRC
+
+A wildcard can also be used:
+
+#+BEGIN_SRC shell
+python calc_share.py -i *.lammpstrj
+#+END_SRC
+
+* Output
+
+The program generates a plot containing the following quantities:
+
+- Blue line: P / (P + I) in the entire system
+- Green line: fraction of Li⁺ ions whose nearest center is P,
+  averaged over all simulation steps
+
+The plot is saved as:
+
+#+BEGIN_EXAMPLE
+voronoi_count_diff.pdf
+#+END_EXAMPLE
+
+* Expected Trajectory Format
+
+The current parser assumes a specific LAMMPS trajectory format:
+
+- Each atom record contains six columns.
+- The third column contains the element name:
+  Li, P, S, or I.
+- The fourth to sixth columns contain the atomic coordinates.
+- The simulation cell is orthorhombic.
+- The number and order of header fields are fixed for every frame.
+
+If the trajectory format differs from these assumptions, the data-loading
+section of =calc_share.py= must be modified.
+
+* Notes
+
+- Li⁺ ions for which the nearest P and I⁻ distances are exactly equal
+  are excluded from both counts in the current implementation.
+- This analysis is based on nearest-neighbor distances and is not a
+  rigorous Voronoi tessellation.
+- The local P fraction around Li⁺ should be interpreted by comparison
+  with the P / (P + I) fraction in the entire system.
+- The current code assumes that both P and I⁻ are present in every
+  trajectory.