佐久間 美波
238 lines
6.7 KiB
Org Mode
238 lines
6.7 KiB
Org Mode
#+TITLE: PS₄³⁻-Centered Li⁺/I⁻ Spatial Density Analysis in Li₂S–P₂S₅–LiI Glasses
|
||
#+AUTHOR: Minami Sakuma
|
||
#+OPTIONS: toc:2 num:nil
|
||
|
||
* Overview
|
||
|
||
This repository provides Python scripts for analyzing the spatial
|
||
distributions of Li⁺ and I⁻ around PS₄³⁻ tetrahedra in
|
||
Li₂S–P₂S₅–LiI glass trajectories.
|
||
|
||
The workflow aligns individual PS₄³⁻ units into a common reference frame,
|
||
accumulates the positions of nearby Li⁺ ions and I⁻ ions, and exports
|
||
three-dimensional spatial-density fields in Gaussian cube format.
|
||
|
||
The generated cube files can be visualized as isosurfaces using Mayavi.
|
||
|
||
* Workflow
|
||
|
||
#+begin_example
|
||
LAMMPS trajectory
|
||
|
|
||
v
|
||
dump2cube.py
|
||
|
|
||
+-- PS₄_Li.cube : Li⁺ spatial-density field
|
||
|
|
||
+-- PS₄_I.cube : I⁻ spatial-density field
|
||
|
|
||
v
|
||
cube2mayavi.py
|
||
|
|
||
v
|
||
3D isosurface visualization
|
||
#+end_example
|
||
|
||
* Files
|
||
|
||
| File | Description |
|
||
|---+---|
|
||
| =dump2cube.py= | Reads a LAMMPS trajectory, aligns PS₄³⁻ units, and generates Li⁺/I⁻ cube files. |
|
||
| =cube2mayavi.py= | Reads a Gaussian cube file and visualizes the density field using Mayavi. |
|
||
| =050Li3PS4-050LiI.lammpstrj= | Example LAMMPS trajectory for a Li₂S–P₂S₅–LiI glass. |
|
||
| =050Li3PS4-050LiI_PS4_I.cube= | Example cube file containing the I⁻ spatial-density field. |
|
||
|
||
* Requirements
|
||
|
||
** Python packages
|
||
|
||
The scripts require Python 3 and the following packages:
|
||
|
||
- NumPy
|
||
- Mayavi
|
||
- VTK
|
||
- Traits
|
||
- PyQt5 or PySide6
|
||
|
||
Mayavi is most easily installed through conda-forge.
|
||
|
||
#+begin_src bash
|
||
conda create -n ps4-density python=3.10
|
||
conda activate ps4-density
|
||
conda install -c conda-forge numpy mayavi pyqt
|
||
#+end_src
|
||
|
||
If NumPy is not installed, it can also be installed with pip.
|
||
|
||
#+begin_src bash
|
||
pip install numpy
|
||
#+end_src
|
||
|
||
* Input Trajectory Format
|
||
|
||
=dump2cube.py= expects a LAMMPS trajectory containing the following atom
|
||
columns:
|
||
|
||
#+begin_example
|
||
ITEM: ATOMS id type element mol x y z
|
||
#+end_example
|
||
|
||
The trajectory must contain the following elements:
|
||
|
||
- Li
|
||
- P
|
||
- S
|
||
- I
|
||
|
||
The script assumes that P and S atoms belonging to the same PS₄³⁻ unit
|
||
share the same molecule ID (=mol=).
|
||
|
||
The current workflow has been tested primarily for orthorhombic
|
||
simulation cells. Periodic boundary conditions are applied when
|
||
calculating relative atomic positions.
|
||
|
||
* Analysis Method
|
||
|
||
For every frame in the trajectory, the following procedure is performed.
|
||
|
||
1. Each P atom is selected as the center of a reference PS₄³⁻ tetrahedron.
|
||
2. The four nearest I⁻ ions around the selected P atom are identified.
|
||
3. The nearest I⁻ ion is used to define the orientation of the PS₄³⁻ unit.
|
||
4. The four S atoms belonging to the PS₄³⁻ unit are rotated into a common
|
||
reference coordinate system.
|
||
5. Li⁺ ions within the specified cutoff distance from P are collected.
|
||
6. The four nearest I⁻ ions are collected.
|
||
7. The accumulated Li⁺ and I⁻ positions are converted into
|
||
three-dimensional histograms.
|
||
8. The histograms are exported in Gaussian cube format.
|
||
|
||
** Definition of the reference orientation
|
||
|
||
The PS₄³⁻ tetrahedron is aligned using the nearest I⁻ ion.
|
||
|
||
- The S atom farthest from the nearest I⁻ ion is aligned with the z axis.
|
||
- A second S atom is used to define the rotation around the z axis.
|
||
- The P atom is placed at the origin.
|
||
|
||
This alignment enables the spatial distributions of Li⁺ and I⁻ around
|
||
many PS₄³⁻ units and trajectory frames to be accumulated in a common
|
||
coordinate system.
|
||
|
||
* Usage
|
||
|
||
** Generate Cube Files
|
||
|
||
#+begin_src bash
|
||
python dump2cube.py \
|
||
-i 050Li3PS4-050LiI.lammpstrj \
|
||
-m 160 160 160 \
|
||
-cut 8
|
||
#+end_src
|
||
|
||
Arguments:
|
||
|
||
| Argument | Description |
|
||
|---+---|
|
||
| =-i=, =--trjfile= | Input LAMMPS trajectory file. |
|
||
| =-m=, =--mesh= | Number of grid points along the x, y, and z directions. |
|
||
| =-cut=, =--cutoff= | Cutoff distance around the reference P atom in Å. |
|
||
|
||
For the example above, the expected output files are:
|
||
|
||
#+begin_example
|
||
050Li3PS4-050LiI_PS4_Li.cube
|
||
050Li3PS4-050LiI_PS4_I.cube
|
||
#+end_example
|
||
|
||
** Visualize the I⁻ Spatial-Density Field
|
||
|
||
#+begin_src bash
|
||
python cube2mayavi.py \
|
||
-i 050Li3PS4-050LiI_PS4_I.cube \
|
||
-atom I \
|
||
-iso 1.26483e-09
|
||
#+end_src
|
||
|
||
** Visualize the Li⁺ Spatial-Density Field
|
||
|
||
#+begin_src bash
|
||
python cube2mayavi.py \
|
||
-i 050Li3PS4-050LiI_PS4_Li.cube \
|
||
-atom Li \
|
||
-iso 1.0e-09
|
||
#+end_src
|
||
|
||
The appropriate isovalue depends on the number of trajectory frames,
|
||
the number of PS₄³⁻ units, the mesh size, and the cutoff distance.
|
||
Therefore, the =-iso= value should be adjusted for each dataset.
|
||
|
||
* Output
|
||
|
||
Each generated cube file contains:
|
||
|
||
- A reference PS₄³⁻ tetrahedron
|
||
- One P atom located at the origin
|
||
- Four S atoms in the aligned coordinate system
|
||
- A three-dimensional spatial-density field for Li⁺ or I⁻
|
||
|
||
The cube files can also be viewed with software supporting Gaussian cube
|
||
format, including:
|
||
|
||
- Mayavi
|
||
- VMD
|
||
- ParaView
|
||
- PyMOL
|
||
|
||
* Visualization Settings
|
||
|
||
The default colors in =cube2mayavi.py= are:
|
||
|
||
| Object | Color |
|
||
|---+---|
|
||
| P atom | Purple |
|
||
| S atom | Yellow |
|
||
| P–S bond | Gray |
|
||
| Li⁺ density | Blue |
|
||
| I⁻ density | Red |
|
||
|
||
For Li⁺ visualization, the script separates the density field into
|
||
an inner region and an outer region:
|
||
|
||
- Inner region: within 5 Å of the P atom
|
||
- Outer region: between 5 Å and 9 Å from the P atom
|
||
|
||
* Example Interpretation
|
||
|
||
The I⁻ cube file can be used to examine whether I⁻ ions are distributed
|
||
uniformly around PS₄³⁻ tetrahedra or occupy preferred directions.
|
||
|
||
An anisotropic I⁻ density distribution indicates that I⁻ ions form
|
||
characteristic local geometries relative to PS₄³⁻ units rather than being
|
||
randomly distributed in the glass network.
|
||
|
||
* Notes and Limitations
|
||
|
||
- The input trajectory must include =id type element mol x y z= columns.
|
||
- The P and S atoms of a PS₄³⁻ tetrahedron must have the same molecule ID.
|
||
- The cube field is generated from accumulated histogram counts and is
|
||
intended for relative spatial-distribution analysis.
|
||
- The output file name is generated from the input trajectory name.
|
||
The current implementation expects a filename containing =LiI=.
|
||
- Large trajectory and cube files may exceed GitHub's 100 MB file-size
|
||
limit. Git LFS is recommended for large files.
|
||
- The visualization script opens an interactive Mayavi window. A GUI-capable
|
||
Python environment is required.
|
||
- Before use, confirm that the trajectory format and simulation-cell
|
||
definition are compatible with the parser implemented in =dump2cube.py=.
|
||
|
||
* Citation
|
||
|
||
If this repository contributes to published work, please cite the
|
||
corresponding paper, poster, presentation, or dataset describing the
|
||
Li₂S–P₂S₅–LiI glass simulations and PS₄³⁻-centered spatial-density
|
||
analysis.
|
||
|
||
* License
|
||
|
||
This repository is intended for academic and research use.
|