sakuma/lps-lii-ps4-density-analysis
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Fix README.org

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佐久間 美波
2026-08-07 12:37:20 +09:00
parent fe67036ccd
commit a322acc74b
1 changed files with 5 additions and 15 deletions
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@@ -74,7 +74,7 @@ pip install numpy
columns: columns:
#+begin_example #+begin_example
ITEM: ATOMS id type element mol x y z ITEM: ATOMS id type element xu yu zu mol
#+end_example #+end_example
The trajectory must contain the following elements: The trajectory must contain the following elements:
@@ -100,11 +100,10 @@ For every frame in the trajectory, the following procedure is performed.
3. The nearest I⁻ ion is used to define the orientation of the PS₄³⁻ unit. 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 4. The four S atoms belonging to the PS₄³⁻ unit are rotated into a common
reference coordinate system. reference coordinate system.
5. Li⁺ ions within the specified cutoff distance from P are collected. 5. Li⁺ and I⁻ ions within the specified cutoff distance from P are collected.
6. The four nearest I⁻ ions are collected. 6. The accumulated Li⁺ and I⁻ positions are converted into
7. The accumulated Li⁺ and I⁻ positions are converted into
three-dimensional histograms. three-dimensional histograms.
8. The histograms are exported in Gaussian cube format. 7. The histograms are exported in Gaussian cube format.
** Definition of the reference orientation ** Definition of the reference orientation
@@ -212,26 +211,17 @@ randomly distributed in the glass network.
* Notes and Limitations * Notes and Limitations
- The input trajectory must include =id type element mol x y z= columns. - The input trajectory must include =id type element xu yu zu mol= columns.
- The P and S atoms of a PS₄³⁻ tetrahedron must have the same molecule ID. - 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 - The cube field is generated from accumulated histogram counts and is
intended for relative spatial-distribution analysis. intended for relative spatial-distribution analysis.
- The output file name is generated from the input trajectory name. - The output file name is generated from the input trajectory name.
The current implementation expects a filename containing =LiI=. 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 - The visualization script opens an interactive Mayavi window. A GUI-capable
Python environment is required. Python environment is required.
- Before use, confirm that the trajectory format and simulation-cell - Before use, confirm that the trajectory format and simulation-cell
definition are compatible with the parser implemented in =dump2cube.py=. 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 * License
This repository is intended for academic and research use. This repository is intended for academic and research use.