From 401eabcdfd4122d49625e792954e3d3ee5c90886 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Mon, 24 Jun 2024 22:45:17 -0400 Subject: [PATCH] Add images to README --- README.md | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 59 insertions(+) diff --git a/README.md b/README.md index c4467e0..4f99b14 100644 --- a/README.md +++ b/README.md @@ -8,6 +8,7 @@ CIF Bond Analyzer (CBA) is an interactive, command-line Python application designed for the high-throughput extraction of bonding information from CIF (Crystallographic Information File) file. + ### Overview 1. Choose the folder interactively and decided to inculde .cif files in nested folders. @@ -183,6 +184,33 @@ For each folder, CBA generates `.xlsx` and `.json` files containing the shortest } ``` +An Excel file containing the information and each sheet having the bond pair. + +[20240623_ErCoIn_nested_element_pairs.xlsx](https://github.com/user-attachments/files/15963693/20240623_ErCoIn_nested_element_pairs.xlsx) + +![Excel screenshot](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/d6bed0df-b9ea-4922-967b-4656bb3ab3e0) + + +``` +File Distance +1814810.cif 2.623 +1803318.cif 2.644 +1840445.cif 2.691 +1818414.cif 2.729 +1234747.cif 2.737 +1140826.cif 2.743 +1229705.cif 2.794 +1956508.cif 2.799 +1000761.cif 2.81 +1233938.cif 2.881 +1803512.cif 2.882 +1925389.cif 2.922 + +Average 2.771 +SD 0.094 +``` + + ### Option 2. System Analysis System Analyiss is applicable for a folder containing either 2 or 3 unique elements. Four types are possible. @@ -205,6 +233,7 @@ Available folders containing 2 or 3 unique elements: 5. 20240611_binary_2_unique_elements, 2 elements (Er, Co), 4 files```` ``` + #### Output 2.1 Binary/ternary figures By deafult, all of the nested folders containing .cif files are automatically added. @@ -213,11 +242,37 @@ For Type 1, the following is generated. For Type 2, 3, 4, the following is generated. +Customizaiton: You move the positino of the legend in the ternary diagram, you may modify the values of `X_SHIFT = 0.0` and `Y_SHIFT = 0.0` in `core/configs/ternary.py`. + +Individual hexagons are also produced. + +![composite_binary_2](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/b385fe6e-f17e-439d-99e8-694378c097a3) +![composite_ternary_1](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/1cb0b0f8-501e-4c53-86fb-190e304f11a6) + + +![color_map_Er-In](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/2da0a905-b247-43ac-bebf-4afc4c0b0608) + +![color_map_In-In](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/874b083f-1aa3-4bd0-aba3-eb63bf5229e7) + +![color_map_overall](https://github.com/bobleesj/cif-bond-analyzer/assets/14892262/1a450ee5-053c-471e-b092-e1731427c2a0) + #### Output 2.2 Color map Color map for each bond type and the overall is generated for Type 2, 3, 4 above. +#### Output 2.3 Excel + +`system_analysis_files.xlsx` + +SA_main + + +`system_analysis_main.xlsx` + +SA_file + + ### Option 3. Coordination Analysis @@ -270,12 +325,16 @@ You may provide your radii values by modifying the radii.xlsx file. "neighbor": 12 } ] + } +} ``` #### Output 3.2 Excel A screenshot is provided below. Each sheet contains the file name and the formula associated with the file. +CN_excel + ## Installation