From a322acc74bcaf10684498c91af932ea0fae3a30a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=E4=BD=90=E4=B9=85=E9=96=93=20=E7=BE=8E=E6=B3=A2?= Date: Fri, 7 Aug 2026 12:37:20 +0900 Subject: [PATCH] Fix README.org --- README.org | 20 +++++--------------- 1 file changed, 5 insertions(+), 15 deletions(-) diff --git a/README.org b/README.org index 09d533c..4c0e414 100644 --- a/README.org +++ b/README.org @@ -74,7 +74,7 @@ pip install numpy columns: #+begin_example -ITEM: ATOMS id type element mol x y z +ITEM: ATOMS id type element xu yu zu mol #+end_example 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. 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 +5. Li⁺ and I⁻ ions within the specified cutoff distance from P are collected. +6. The accumulated Li⁺ and I⁻ positions are converted into 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 @@ -212,26 +211,17 @@ randomly distributed in the glass network. * 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 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.