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