Initinal commit /lps-lii-ps4-iodide-geometry
This commit is contained in:
佐久間 美波
+237
@@ -0,0 +1,237 @@
|
||||
#+TITLE: PS₄³⁻-Centered I⁻ Geometry Analysis in Li₂S–P₂S₅–LiI Glasses
|
||||
#+AUTHOR: Minami Sakuma
|
||||
#+OPTIONS: toc:2 num:nil
|
||||
|
||||
* Overview
|
||||
|
||||
This repository contains Python scripts for analyzing the local
|
||||
geometrical relationship between I⁻ ions and PS₄³⁻ tetrahedra in
|
||||
Li₂S–P₂S₅–LiI glass trajectories.
|
||||
|
||||
For each P atom, nearby I⁻ ions are classified according to the number
|
||||
of S atoms from the same PS₄³⁻ tetrahedron located within a specified
|
||||
I–S cutoff distance.
|
||||
|
||||
The resulting I⁻ spatial-density distributions are exported as Gaussian
|
||||
cube files and visualized as three-dimensional isosurfaces using Mayavi.
|
||||
|
||||
* Analysis Concept
|
||||
|
||||
For a given I⁻ ion and a given PS₄³⁻ tetrahedron, the number of nearby
|
||||
S atoms is defined as:
|
||||
|
||||
#+begin_example
|
||||
s_count = number of S atoms within 4.7 Å from I⁻
|
||||
#+end_example
|
||||
|
||||
The I⁻ configuration is classified as follows:
|
||||
|
||||
| Classification | s_count | Geometrical interpretation |
|
||||
|---+---:|---|
|
||||
| Zero-type | 0 | I⁻ is not close to any S atom of the reference PS₄³⁻ unit. |
|
||||
| Corner-type | 1 | I⁻ is located near one S vertex of the PS₄³⁻ tetrahedron. |
|
||||
| Edge-type | 2 | I⁻ is located near two S atoms forming one tetrahedral edge. |
|
||||
| Three-type | 3 | I⁻ is located near three S atoms of the same PS₄³⁻ unit. |
|
||||
|
||||
The terms corner-type and edge-type describe geometrical proximity only.
|
||||
They do not imply bond sharing or atom sharing between I⁻ and PS₄³⁻
|
||||
units.
|
||||
|
||||
* Workflow
|
||||
|
||||
#+begin_example
|
||||
LAMMPS trajectory
|
||||
|
|
||||
v
|
||||
dump2cube_edge_corner.py
|
||||
|
|
||||
+-- PS₄_I_All.cube
|
||||
+-- PS₄_I_zero.cube
|
||||
+-- PS₄_I_corner.cube
|
||||
+-- PS₄_I_edge.cube
|
||||
+-- PS₄_I_three.cube
|
||||
|
|
||||
v
|
||||
cube2mayavi_edge_corner.py
|
||||
|
|
||||
v
|
||||
Colored 3D isosurface visualization
|
||||
#+end_example
|
||||
|
||||
* Files
|
||||
|
||||
| File | Description |
|
||||
|--------------------------------------+------------------------------------------------------------------------------------------------------|
|
||||
| =dump2cube_edge_corner.py= | Reads a LAMMPS trajectory, aligns PS₄³⁻ units, classifies nearby I⁻ ions, and generates cube files. |
|
||||
| =cube2mayavi_edge_corner.py= | Visualizes multiple classified I⁻ cube files using different colors. |
|
||||
| =050Li3PS4-050LiI.lammpstrj= | Example LAMMPS trajectory for a Li₂S–P₂S₅–LiI glass. |
|
||||
| =050Li3PS4-050LiI_PS4_I_All.cube= | Spatial density of the four nearest I⁻ ions around each P atom. |
|
||||
| =050Li3PS4-050LiI_PS4_I_zero.cube= | Spatial density of zero-type I⁻ configurations. |
|
||||
| =050Li3PS4-050LiI_PS4_I_corner.cube= | Spatial density of corner-type I⁻ configurations. |
|
||||
| =050Li3PS4-050LiI_PS4_I_edge.cube= | Spatial density of edge-type I⁻ configurations. |
|
||||
| =050Li3PS4-050LiI_PS4_I_three.cube= | Spatial density of three-type I⁻ configurations. |
|
||||
|
||||
* Requirements
|
||||
|
||||
** Python packages
|
||||
|
||||
The scripts require Python 3 and the following packages:
|
||||
|
||||
- NumPy
|
||||
- Mayavi
|
||||
- VTK
|
||||
- Traits
|
||||
- PyQt5 or PySide6
|
||||
|
||||
Mayavi is generally easiest to install through conda-forge.
|
||||
|
||||
#+begin_src bash
|
||||
conda create -n ps4-iodide python=3.10
|
||||
conda activate ps4-iodide
|
||||
conda install -c conda-forge numpy mayavi pyqt
|
||||
#+end_src
|
||||
|
||||
Alternatively, NumPy can be installed with pip:
|
||||
|
||||
#+begin_src bash
|
||||
pip install numpy
|
||||
#+end_src
|
||||
|
||||
* Input Trajectory Format
|
||||
|
||||
=dump2cube_edge_corner.py= expects a LAMMPS trajectory containing the
|
||||
following atom columns:
|
||||
|
||||
#+begin_example
|
||||
ITEM: ATOMS id type element xu yu zu mol
|
||||
#+end_example
|
||||
|
||||
The trajectory must contain at least the following elements:
|
||||
|
||||
- Li
|
||||
- P
|
||||
- S
|
||||
- I
|
||||
|
||||
The script assumes that P and S atoms belonging to the same PS₄³⁻
|
||||
tetrahedron have the same molecule ID (=mol=).
|
||||
|
||||
Periodic boundary conditions are applied when calculating relative
|
||||
atomic positions.
|
||||
|
||||
* Analysis Procedure
|
||||
|
||||
For every trajectory frame, the following procedure is performed.
|
||||
|
||||
1. Each P atom is selected as the center of a reference PS₄³⁻ tetrahedron.
|
||||
2. The nearest I⁻ ion is used to define the orientation of the PS₄³⁻ unit.
|
||||
3. The S atom farthest from the nearest I⁻ ion is aligned with the z axis.
|
||||
4. A second S atom is used to fix the rotation around the z axis.
|
||||
5. The closest I⁻ ions are rotated into the common PS₄³⁻ reference frame.
|
||||
6. I⁻ ions are classified using the number of S atoms within 4.7 Å.
|
||||
7. The classified I⁻ coordinates are accumulated over all P atoms and
|
||||
trajectory frames.
|
||||
8. Three-dimensional histograms are exported as Gaussian cube files.
|
||||
|
||||
* Normalization
|
||||
|
||||
The density fields for zero-type, corner-type, edge-type, and three-type
|
||||
I⁻ configurations are normalized by the total number of I⁻ coordinates
|
||||
used for the overall I⁻ distribution.
|
||||
|
||||
Therefore, the relative density of each classified field reflects both:
|
||||
|
||||
- the spatial distribution of the configuration, and
|
||||
- the relative occurrence of that configuration.
|
||||
|
||||
* Usage
|
||||
|
||||
** Generate Cube Files
|
||||
|
||||
#+begin_src bash
|
||||
python dump2cube_edge_corner.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= | Spatial cutoff distance around the reference P atom in Å. |
|
||||
|
||||
Expected output files:
|
||||
|
||||
#+begin_example
|
||||
050Li3PS4-050LiI_PS4_I_All.cube
|
||||
050Li3PS4-050LiI_PS4_I_zero.cube
|
||||
050Li3PS4-050LiI_PS4_I_corner.cube
|
||||
050Li3PS4-050LiI_PS4_I_edge.cube
|
||||
050Li3PS4-050LiI_PS4_I_three.cube
|
||||
#+end_example
|
||||
|
||||
** Visualize Classified I⁻ Density Fields
|
||||
|
||||
#+begin_src bash
|
||||
python cube2mayavi_edge_corner.py \
|
||||
-i 050Li3PS4-050LiI_PS4_I_zero.cube \
|
||||
050Li3PS4-050LiI_PS4_I_corner.cube \
|
||||
050Li3PS4-050LiI_PS4_I_edge.cube \
|
||||
050Li3PS4-050LiI_PS4_I_three.cube \
|
||||
-iso 1.2e-09
|
||||
#+end_src
|
||||
|
||||
The script assigns colors based on the file name:
|
||||
|
||||
| Classification | Color |
|
||||
|----------------+--------|
|
||||
| Zero-type | Blue |
|
||||
| Corner-type | Green |
|
||||
| Edge-type | Red |
|
||||
| Three-type | Yellow |
|
||||
|
||||
The reference PS₄³⁻ tetrahedron is shown with:
|
||||
|
||||
| Object | Color |
|
||||
|-----------+--------|
|
||||
| P atom | Purple |
|
||||
| S atoms | Yellow |
|
||||
| P–S bonds | Gray |
|
||||
|
||||
* Output
|
||||
|
||||
Each Gaussian cube file contains:
|
||||
|
||||
- A reference PS₄³⁻ tetrahedron
|
||||
- P atom at the origin
|
||||
- Four S atoms in the aligned coordinate system
|
||||
- A three-dimensional spatial-density field of the selected I⁻ category
|
||||
|
||||
The cube files can be visualized using:
|
||||
|
||||
- Mayavi
|
||||
- VMD
|
||||
- ParaView
|
||||
- PyMOL
|
||||
- Other software supporting Gaussian cube files
|
||||
|
||||
* Notes and Limitations
|
||||
|
||||
- The I–S cutoff for classification is fixed at 4.7 Å in the script.
|
||||
- The cube files represent accumulated spatial-density distributions.
|
||||
- The current analysis uses the nearest I⁻ ion to define the orientation
|
||||
of each PS₄³⁻ tetrahedron.
|
||||
- The script searches the 15 nearest I⁻ ions around each P atom when
|
||||
classifying zero-, corner-, edge-, and three-type configurations.
|
||||
- The output filename is generated from the input trajectory name.
|
||||
The current implementation expects an input filename containing =LiI=.
|
||||
- The current trajectory parser is primarily intended for orthorhombic
|
||||
simulation cells.
|
||||
- The Mayavi visualization requires a GUI-capable Python environment.
|
||||
|
||||
* License
|
||||
|
||||
This repository is intended for academic and research use.
|
||||
Reference in New Issue
Block a user