From dda393685508c973efb4b67bf240550ecfbb1ed4 Mon Sep 17 00:00:00 2001 From: Sangjoon Bob Lee Date: Tue, 9 Jul 2024 22:10:32 -0400 Subject: [PATCH] Deployed 62bd03e with MkDocs version: 1.6.0 --- index.html | 43 +++- notebooks/00_Intro/index.html | 62 ++++- notebooks/01_cif/index.html | 172 +++++++------- notebooks/02_cif_ensemble/index.html | 339 ++++++++++++++++++++++++--- search/search_index.json | 2 +- sitemap.xml.gz | Bin 127 -> 127 bytes 6 files changed, 485 insertions(+), 133 deletions(-) diff --git a/index.html b/index.html index fdc349a..62bb01a 100644 --- a/index.html +++ b/index.html @@ -561,8 +561,13 @@

Getting started

-

The purpose of this guide is to illustrate some of the main features that cifkit provides. It assumes a very basic knowledge of Python.

-

cifkit is an open source CIF library that supports supercell generation and provide tools for high-throuhgput analysis. It also provides various tools for determining coordination numbers, plotting polyhedrons from each site based on the coordination numbers, bond fractions, move and copy .cif files based on a set of attributes, and determine atomic mixing information in 2-3 lines of code.

+

The purpose of this guide is to illustrate some of the main features that +cifkit provides. It assumes a very basic knowledge of Python.

+

cifkit is an open source CIF library that supports supercell generation and +provide tools for high-throuhgput analysis. It also provides various tools for +determining coordination numbers, plotting polyhedrons from each site based on +the coordination numbers, bond fractions, move and copy .cif files based on a +set of attributes, and determine atomic mixing information in 2-3 lines of code.

Installation

Install cifkit via:

pip install cifkit
@@ -570,9 +575,12 @@ 
Installation

 
You may need to download other dependencies:

 
pip install cifkit pyvista gemmi
 

-
gemmi is used for parsing .cif files. pyvista is used for plotting polyhedrons.

+
gemmi is used for parsing .cif files. pyvista is used for plotting
+polyhedrons.

 
Start with CifEnsemble

-
cifkit offers a class called CifEnsemble which handles many .cif files in a high-throuhgput way. You can initialize the object using the folder path containing .cif files shown below.

+
cifkit offers a class called CifEnsemble which handles many .cif files in
+a high-throuhgput way. You can initialize the object using the folder path
+containing .cif files shown below.

 
from cifkit import CifEnsemble
 
 # Initialize
@@ -585,7 +593,8 @@ 
Start with CifEnsemble

 ensemble.cif_folder_path
 # "tests/data/cif/ensemble_test"
 

-
If you do not have .cif files for testing, cifkit also provides a set of .cif files accessible.

+
If you do not have .cif files for testing, cifkit also provides a set of
+.cif files accessible.

 
from cifkit import CifEnsemble, Example
 from cifkit import Example
 
@@ -593,7 +602,8 @@ 
Start with CifEnsemble

 ensemble = CifEnsemble(Example.ErCoIn_big_folder_path)
 

 
Get unique attributes

-
Use the ensemble object to get unique attributes such as elements, formulas, etc.

+
Use the ensemble object to get unique attributes such as elements, formulas,
+etc.

 
# Unique formulas
 ensemble.unique_formulas
 # {"EuIr2Ge2", "CeRu2Ge2", "LaRu2Ge2", "Mo"}
@@ -619,7 +629,8 @@ 
Get unique attributes

 # {"hex", "rt", "rt_hex", ""}
 

 
Get distances and supercell size per file

-
The following computes the size of each supercell and the minimum distance per file.

+
The following computes the size of each supercell and the minimum distance per
+file.

 
# Get min distance per file
 ensemble.minimum_distances
 # [("tests/data/cif/ensemble_test/250709.cif", 2.725),
@@ -649,7 +660,9 @@ 
Filter files by attributes

 ensemble_test.filter_by_space_group_numbers([139])
 

 
Move and copy files

-
Now you have a set of file paths with example below, you can copy and move files to a specific directroy. For high-throuhgout analysis, you might be interested in separating files based on tags, elements, coordination numbers, etc.

+
Now you have a set of file paths with example below, you can copy and move files
+to a specific directroy. For high-throuhgout analysis, you might be interested
+in separating files based on tags, elements, coordination numbers, etc.

 
file_paths = {
     "tests/data/cif/ensemble_test/300169.cif",
     "tests/data/cif/ensemble_test/300171.cif",
@@ -663,11 +676,19 @@ 
Move and copy files

 ensemble.copy_cif_files(file_paths, dest_dir_path)
 

 
Are you ready?

-
Now, if you are interested in working with individual .cif files and learn more about all features in cifkit, let's visit the Example notebooks section here!

+
Now, if you are interested in working with individual .cif files and learn
+more about all features in cifkit, let's visit the Example notebooks section
+here!

 
Research projects using cifkit

 
    
-
  • CIF Bond Analyzer (CBA) - extract and visualize bonding patterns - DOI | GitHub
    • 
-
  • Structure Analysis/Featurizer (SAF) - build geometric features for binary, ternary compounds - GitHub
    • 
+
  • CIF Bond Analyzer (CBA) - extract and visualize bonding patterns -
+  DOI |
+  GitHub
    • 
+
  • CIF Cleaner - move, copy .cif files based on attributes -
+  GitHub
    • 
+
  • Structure Analysis/Featurizer (SAF) - build geometric features for binary,
+  ternary compounds -
+  GitHub
    • 
 

 
 
diff --git a/notebooks/00_Intro/index.html b/notebooks/00_Intro/index.html
index 3309d97..084f24e 100644
--- a/notebooks/00_Intro/index.html
+++ b/notebooks/00_Intro/index.html
@@ -952,13 +952,13 @@ 
Installation
-