From 4ff318501a9251e74ecef3f98ab06f99224a123b Mon Sep 17 00:00:00 2001
From: Sangjoon Bob Lee <bobleesj@gmail.com>
Date: Fri, 5 Jul 2024 14:45:22 -0400
Subject: [PATCH] Deployed 6ab3fc4 with MkDocs version: 1.6.0

---
 notebooks/00_Intro/index.html        |  63 +++++++++++++++++++++++++++
 notebooks/02_cif_ensemble/index.html |  38 ++++++++--------
 search/search_index.json             |   2 +-
 sitemap.xml.gz                       | Bin 127 -> 127 bytes
 4 files changed, 83 insertions(+), 20 deletions(-)

diff --git a/notebooks/00_Intro/index.html b/notebooks/00_Intro/index.html
index efa20de..3309d97 100644
--- a/notebooks/00_Intro/index.html
+++ b/notebooks/00_Intro/index.html
@@ -377,6 +377,17 @@
         
       
       
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    Installation
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
       <a href="./" class="md-nav__link md-nav__link--active">
         
   
@@ -387,6 +398,43 @@
 
       </a>
       
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#google-codelab" class="md-nav__link">
+    <span class="md-ellipsis">
+      Google Codelab
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#feedback-help" class="md-nav__link">
+    <span class="md-ellipsis">
+      Feedback &amp; help
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
     </li>
   
 
@@ -970,6 +1018,21 @@ <h1 id="installation">Installation<a class="anchor-link" href="#installation">¶
 </div>
 </div>
 </div>
+<div class="jp-Cell jp-MarkdownCell jp-Notebook-cell">
+<div class="jp-Cell-inputWrapper" tabindex="0">
+<div class="jp-Collapser jp-InputCollapser jp-Cell-inputCollapser">
+</div>
+<div class="jp-InputArea jp-Cell-inputArea"><div class="jp-InputPrompt jp-InputArea-prompt">
+</div><div class="jp-RenderedHTMLCommon jp-RenderedMarkdown jp-MarkdownOutput" data-mime-type="text/markdown">
+<h3 id="google-codelab">Google Codelab<a class="anchor-link" href="#google-codelab">¶</a></h3><p>You can also run the examples using Google Codelab by clicking the link below:</p>
+<a href="https://colab.research.google.com/drive/1mZLFWyYblc2gxRqjP7CejZcUNGbQBzwo#scrollTo=DlB6ZTVaOMpq" target="_blank">
+<img alt="Open In Colab" src="https://img.shields.io/badge/Google%20Colab-Open-blue.svg"/>
+</a>
+<h3 id="feedback-help">Feedback &amp; help<a class="anchor-link" href="#feedback-help">¶</a></h3><p>If you find <code>cifkit</code> beneficial for your research, or if you are considering its usage, please do not hesitate to contact me. You can reach out via the email provided on my GitHub profile.</p>
+</div>
+</div>
+</div>
+</div>
 </div> <!-- jp-Notebook -->
 </div> <!-- jupyter-wrapper -->
 
diff --git a/notebooks/02_cif_ensemble/index.html b/notebooks/02_cif_ensemble/index.html
index 00bd4a8..0317c0a 100644
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@@ -1036,7 +1036,7 @@ <h2 id="initialize-with-folder-path-and-preprocess-automatically">Initialize wit
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@@ -1225,7 +1225,7 @@ <h2 id="get-instant-properties">Get instant properties<a class="anchor-link" hre
 <pre>File count: 3
 Directory path: Example.ErCoIn_folder_path
 File paths: ['/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif']
-Cif objects: [&lt;cifkit.models.cif.Cif object at 0x16c818980&gt;, &lt;cifkit.models.cif.Cif object at 0x16c86a2d0&gt;, &lt;cifkit.models.cif.Cif object at 0x16c8cb0b0&gt;]
+Cif objects: [&lt;cifkit.models.cif.Cif object at 0x1554895e0&gt;, &lt;cifkit.models.cif.Cif object at 0x155320980&gt;, &lt;cifkit.models.cif.Cif object at 0x1569ef7a0&gt;]
 </pre>
 </div>
 </div>
@@ -1249,7 +1249,7 @@ <h2 id="get-individual-cif-properties">Get individual .cif properties<a class="a
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@@ -1293,19 +1293,19 @@ <h2 id="get-individual-cif-properties">Get individual .cif properties<a class="a
 Formula: Er10Co9In20
 Tag: 
 Mixing type: full_occupancy
-Unique bond pairs: {('Er', 'Er'), ('Co', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'In'), ('Co', 'Co')}
+Unique bond pairs: {('Co', 'In'), ('Er', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'Er'), ('Co', 'Co')}
 
 Er5In3.cif
 Formula: Er5In3
 Tag: 
 Mixing type: full_occupancy
-Unique bond pairs: {('Er', 'Er'), ('In', 'In'), ('Er', 'In')}
+Unique bond pairs: {('Er', 'In'), ('In', 'In'), ('Er', 'Er')}
 
 ErCoIn5.cif
 Formula: ErCoIn5
 Tag: rt
 Mixing type: full_occupancy
-Unique bond pairs: {('Er', 'Er'), ('Co', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'In'), ('Co', 'Co')}
+Unique bond pairs: {('Co', 'In'), ('Er', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'Er'), ('Co', 'Co')}
 </pre>
 </div>
 </div>
@@ -1329,7 +1329,7 @@ <h2 id="get-unique-properties">Get unique properties<a class="anchor-link" href=
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-<pre>Unique formulas: {'ErCoIn5', 'Er5In3', 'Er10Co9In20'}
+<pre>Unique formulas: {'Er5In3', 'ErCoIn5', 'Er10Co9In20'}
 Unique elements: {'In', 'Er', 'Co'}
 Unique structures: {'Ho10Ni9In20', 'HoCoGa5', 'Mn5Si3'}
 Unique atomic mixing types: {'full_occupancy'}
@@ -1438,7 +1438,7 @@ <h2 id="get-overall-stats-by-attribute">Get overall stats by attribute<a class="
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@@ -1539,7 +1539,7 @@ <h2 id="get-overall-stats-by-attribute">Get overall stats by attribute<a class="
 Space group number stats: {129: 1, 193: 1, 123: 1}
 Space group name stats: {'P4/nmm(originchoice2)': 1, 'P63/mcm': 1, 'P4/mmm': 1}
 Composition type stats: {3: 2, 2: 1}
-Unique elements stats: {'Er': 3, 'In': 3, 'Co': 2}
+Unique elements stats: {'Co': 2, 'In': 3, 'Er': 3}
 Site mixing type stats: {'full_occupancy': 3}
 Supercell size stats: {2654: 1, 558: 1, 255: 1}
 Min distance stats: {2.626: 1, 3.102: 1, 2.691: 1}
@@ -1568,7 +1568,7 @@ <h2 id="filter-cif-containing-specific-attributes">Filter .cif containing specif
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 <pre>{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif',
  '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif'}</pre>
@@ -1655,7 +1655,7 @@ <h2 id="filter-cif-by-specific-attributes">Filter .cif by specific attributes<a
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 <pre>
 File paths containing Er or Co or In:
-{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}
+{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}
 
 File paths containing Er and In:
 {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}
@@ -1744,7 +1744,7 @@ <h2 id="filter-by-range">Filter by range<a class="anchor-link" href="#filter-by-
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 <pre>File paths with min distance between 1.0 Å and 3.0 Å:
- {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}
+ {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif'}
 File paths with supercell atom count above 500 and below 3000:
- {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}
+ {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}
 </pre>
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diff --git a/search/search_index.json b/search/search_index.json
index 51a10e6..e9c4ed2 100644
--- a/search/search_index.json
+++ b/search/search_index.json
@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Getting started","text":"<p>The purpose of this guide is to illustrate some of the main features that <code>cifkit</code> provides. It assumes a very basic knowledge of Python.</p> <p><code>cifkit</code> 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 <code>.cif</code> files based on a set of attributes, and determine atomic mixing information in 2-3 lines of code.</p>"},{"location":"#installation","title":"Installation","text":"<p>Install <code>cifkit</code> via:</p> <pre><code>pip install cifkit\n</code></pre> <p>You may need to download other dependencies:</p> <pre><code>pip install cifkit pyvista gemmi\n</code></pre> <p><code>gemmi</code> is used for parsing <code>.cif</code> files. <code>pyvista</code> is used for plotting polyhedrons.</p>"},{"location":"#start-with-cifensemble","title":"Start with CifEnsemble","text":"<p><code>cifkit</code> offers a class called <code>CifEnsemble</code> which handles many <code>.cif</code> files in a high-throuhgput way. You can initialize the object using the folder path containing <code>.cif</code> files shown below.</p> <pre><code>from cifkit import CifEnsemble\n\n# Initialize\nensemble = CifEnsemble(\"tests/data/cif/ensemble_test\")\n\n# Initialize including nested files\nensemble = CifEnsemble(\"tests/data/cif/ensemble_test\", add_nested_files=True)\n\n# Folder path\nensemble.cif_folder_path\n# \"tests/data/cif/ensemble_test\"\n</code></pre> <p>If you do not have <code>.cif</code> files for testing, <code>cifkit</code> also provides a set of <code>.cif</code> files accessible.</p> <pre><code>from cifkit import CifEnsemble, Example\nfrom cifkit import Example\n\n# Initalize with the file path\nensemble = CifEnsemble(Example.ErCoIn_big_folder_path)\n</code></pre>"},{"location":"#get-unique-attributes","title":"Get unique attributes","text":"<p>Use the <code>ensemble</code> object to get unique attributes such as elements, formulas, etc.</p> <pre><code># Unique formulas\nensemble.unique_formulas\n# {\"EuIr2Ge2\", \"CeRu2Ge2\", \"LaRu2Ge2\", \"Mo\"}\n\n# Unique structures\nensemble.unique_structures\n# {\"CeAl2Ga2\", \"W\"}\n\n# Unique elements\nensemble.unique_elements\n# {\"La\", \"Ru\", \"Ge\", \"Ir\", \"Eu\", \"Ce\", \"Mo\"}\n\n# Unique space group names\nensemble.unique_space_group_names\n# {\"I4/mmm\", \"Im-3m\"}\n\n# Unique space group numbers\nensemble.unique_space_group_numbers\n# {139, 229}\n\n# Unique tags\nensemble.unique_tags\n# {\"hex\", \"rt\", \"rt_hex\", \"\"}\n</code></pre>"},{"location":"#get-distances-and-supercell-size-per-file","title":"Get distances and supercell size per file","text":"<p>The following computes the size of each supercell and the minimum distance per file.</p> <pre><code># Get min distance per file\nensemble.minimum_distances\n# [(\"tests/data/cif/ensemble_test/250709.cif\", 2.725),\n# (\"tests/data/cif/ensemble_test/300171.cif\", 2.383),\n# (\"tests/data/cif/ensemble_test/300170.cif\", 2.28)]\n\n# Get supercell size per file\nensemble_test.supercell_atom_counts\n# [(\"tests/data/cif/ensemble_test/250709.cif\", 54),\n# (\"tests/data/cif/ensemble_test/300171.cif\", 360),\n# (\"tests/data/cif/ensemble_test/300170.cif\", 360)]\n</code></pre>"},{"location":"#filter-files-by-attributes","title":"Filter files by attributes","text":"<p>The following returns a set of file paths to each <code>.cif</code> file.</p> <pre><code># By formulas\nensemble_test.filter_by_formulas([\"LaRu2Ge2\"])\nensemble_test.filter_by_formulas([\"LaRu2Ge2\", \"Mo\"])\n\n# By structures\nensemble_test.filter_by_structures([\"W\"])\nensemble_test.filter_by_structures(\"CeAl2Ga2\")\n\n# By space group\nensemble_test.filter_by_space_group_names(\"Im-3m\")\n\n# By space group numbers\nensemble_test.filter_by_space_group_numbers([139])\n</code></pre>"},{"location":"#move-and-copy-files","title":"Move and copy files","text":"<p>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.</p> <pre><code>file_paths = {\n    \"tests/data/cif/ensemble_test/300169.cif\",\n    \"tests/data/cif/ensemble_test/300171.cif\",\n    \"tests/data/cif/ensemble_test/300170.cif\",\n}\n\n# To move files\nensemble.move_cif_files(file_paths, dest_dir_path)\n\n# To copy files\nensemble.copy_cif_files(file_paths, dest_dir_path)\n</code></pre>"},{"location":"#are-you-ready","title":"Are you ready?","text":"<p>Now, if you are interested in working with individual <code>.cif</code> files and learn more about all features in <code>cifkit</code>, let's visit the <code>Example notebooks</code> section here!</p>"},{"location":"#research-projects-using-cifkit","title":"Research projects using <code>cifkit</code>","text":"<ul> <li>CIF Bond Analyzer (CBA) - extract and visualize bonding patterns - DOI | GitHub</li> <li>Structure Analysis/Featurizer (SAF) - build geometric features for binary, ternary compounds - GitHub</li> </ul>"},{"location":"notebooks/00_Intro/","title":"Installation","text":"In\u00a0[\u00a0]: Copied! <pre>pip install cifkit\n</pre> pip install cifkit <p>In Google Codelab, <code>pyvista</code> and <code>gemmi</code> need to be installed.</p> In\u00a0[\u00a0]: Copied! <pre>pip install cifkit pyvista gemmi\n</pre>  pip install cifkit pyvista gemmi"},{"location":"notebooks/00_Intro/#installation","title":"Installation\u00b6","text":"<p><code>cifkit</code> supports Python versions 3.10, 3.11, and 3.12.</p>"},{"location":"notebooks/01_cif/","title":"CIF","text":"<p>You can initialize <code>Cif</code> object using a file path to the <code>.cif</code> file. Or you can simply use the example <code>.cif</code> provided in <code>cifkit</code> below.</p> In\u00a0[1]: Copied! <pre>from cifkit import Example\nfrom cifkit import Cif\n\n# Initalize with the example file provided\ncif = Cif(Example.Er10Co9In20_file_path)\n\n# Print attributes\nprint(\"File name:\", cif.file_name)\nprint(\"Formula:\", cif.formula)\nprint(\"Unique element:\", cif.unique_elements)\n</pre> from cifkit import Example from cifkit import Cif  # Initalize with the example file provided cif = Cif(Example.Er10Co9In20_file_path)  # Print attributes print(\"File name:\", cif.file_name) print(\"Formula:\", cif.formula) print(\"Unique element:\", cif.unique_elements) <pre>File name: Er10Co9In20.cif\nFormula: Er10Co9In20\nUnique element: {'Co', 'In', 'Er'}\n</pre> In\u00a0[2]: Copied! <pre>from cifkit import Cif, Example\nimport json\n\n# Utility function for printing dictionary\ndef prettify_dict(dict_data):\n  return json.dumps(dict_data, indent=4)\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Print instantly available properties\nprint(\"Formula:\", cif.formula)\nprint(\"Structure:\", cif.structure)\nprint(\"Unique elements:\", cif.unique_elements)\nprint(\"Unitcell lenghts:\", cif.unitcell_lengths)\nprint(\"Unitcell angles:\", cif.unitcell_angles)\nprint(\"Site labels:\", cif.site_labels)\nprint(\"Weight:\", cif.weight)\nprint(\"Atomic mixing type:\", cif.site_mixing_type)\nprint(\"Space group number:\", cif.space_group_number)\nprint(\"Space group number:\", cif.space_group_name)\nprint(\"Composition type:\", cif.composition_type) # 3 -&gt; Ternary\nprint(\"Tag:\", cif.tag)\nprint(\"Atom_site_info:\", prettify_dict(cif.atom_site_info))\nprint(\"Wyckoff_symbol of Er1:\", cif.atom_site_info[\"Er\"][\"wyckoff_symbol\"])\n</pre> from cifkit import Cif, Example import json  # Utility function for printing dictionary def prettify_dict(dict_data):   return json.dumps(dict_data, indent=4)  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Print instantly available properties print(\"Formula:\", cif.formula) print(\"Structure:\", cif.structure) print(\"Unique elements:\", cif.unique_elements) print(\"Unitcell lenghts:\", cif.unitcell_lengths) print(\"Unitcell angles:\", cif.unitcell_angles) print(\"Site labels:\", cif.site_labels) print(\"Weight:\", cif.weight) print(\"Atomic mixing type:\", cif.site_mixing_type) print(\"Space group number:\", cif.space_group_number) print(\"Space group number:\", cif.space_group_name) print(\"Composition type:\", cif.composition_type) # 3 -&gt; Ternary print(\"Tag:\", cif.tag) print(\"Atom_site_info:\", prettify_dict(cif.atom_site_info)) print(\"Wyckoff_symbol of Er1:\", cif.atom_site_info[\"Er\"][\"wyckoff_symbol\"]) <pre>Formula: ErCoIn5\nStructure: HoCoGa5\nUnique elements: {'Co', 'In', 'Er'}\nUnitcell lenghts: [4.54, 4.54, 7.397]\nUnitcell angles: [1.5708, 1.5708, 1.5708]\nSite labels: ['In2', 'In1', 'Co', 'Er']\nWeight: 800.3\nAtomic mixing type: full_occupancy\nSpace group number: 123\nSpace group number: P4/mmm\nComposition type: 3\nTag: rt\nAtom_site_info: {\n    \"In2\": {\n        \"element\": \"In\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.5,\n        \"z_frac_coord\": 0.30474,\n        \"symmetry_multiplicity\": 4,\n        \"wyckoff_symbol\": \"i\"\n    },\n    \"In1\": {\n        \"element\": \"In\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.5,\n        \"y_frac_coord\": 0.5,\n        \"z_frac_coord\": 0.0,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"c\"\n    },\n    \"Co\": {\n        \"element\": \"Co\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.0,\n        \"z_frac_coord\": 0.5,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"b\"\n    },\n    \"Er\": {\n        \"element\": \"Er\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.0,\n        \"z_frac_coord\": 0.0,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"a\"\n    }\n}\nWyckoff_symbol of Er1: a\n</pre> In\u00a0[3]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Utility function for printing a set of tuples\ndef print_tuples(tuples):\n  for pair in tuples:\n    print(f\"({pair[0]}, {pair[1]})\")\n\n# All bond pairs\nprint(\"\\nAll possible bond pairs:\")\nprint_tuples(cif.bond_pairs)\n\nprint(\"\\nAll possible bond pairs sorted by Mendeleev:\")\nprint_tuples(cif.bond_pairs_sorted_by_mendeleev)\n\n# All label pairs\nprint(\"\\nAll possible label pairs from the formula:\")\nprint_tuples(cif.site_label_pairs)\n\nprint(\"\\nAll possible label pairs sorted by Mendeleev:\")\nprint_tuples(cif.site_label_pairs_sorted_by_mendeleev)\n\n# Atomic mixing per pair\nprint(\"\\nAtomic mixing per label pair:\")\nprint((cif.mixing_info_per_label_pair))\n\nprint(\"\\nAtomic mixing per label pair sorted by Mendeleev:\")\nprint(cif.mixing_info_per_label_pair_sorted_by_mendeleev)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Utility function for printing a set of tuples def print_tuples(tuples):   for pair in tuples:     print(f\"({pair[0]}, {pair[1]})\")  # All bond pairs print(\"\\nAll possible bond pairs:\") print_tuples(cif.bond_pairs)  print(\"\\nAll possible bond pairs sorted by Mendeleev:\") print_tuples(cif.bond_pairs_sorted_by_mendeleev)  # All label pairs print(\"\\nAll possible label pairs from the formula:\") print_tuples(cif.site_label_pairs)  print(\"\\nAll possible label pairs sorted by Mendeleev:\") print_tuples(cif.site_label_pairs_sorted_by_mendeleev)  # Atomic mixing per pair print(\"\\nAtomic mixing per label pair:\") print((cif.mixing_info_per_label_pair))  print(\"\\nAtomic mixing per label pair sorted by Mendeleev:\") print(cif.mixing_info_per_label_pair_sorted_by_mendeleev)  <pre>\nAll possible bond pairs:\n(Er, Er)\n(Co, Co)\n(Er, In)\n(Co, Er)\n(In, In)\n(Co, In)\n\nAll possible bond pairs sorted by Mendeleev:\n(Er, Er)\n(Co, Co)\n(Er, In)\n(In, In)\n(Co, In)\n(Er, Co)\n\nAll possible label pairs from the formula:\n(Er, Er)\n(Er, In2)\n(In1, In2)\n(Co, Co)\n(Co, Er)\n(Er, In1)\n(In1, In1)\n(Co, In2)\n(Co, In1)\n(In2, In2)\n\nAll possible label pairs sorted by Mendeleev:\n(Er, Er)\n(Co, Co)\n(Er, In2)\n(In1, In2)\n(Er, In1)\n(In1, In1)\n(Co, In2)\n(Co, In1)\n(Er, Co)\n(In2, In2)\n\nAtomic mixing per label pair:\n{('Er', 'Er'): 'full_occupancy', ('Er', 'In2'): 'full_occupancy', ('In1', 'In2'): 'full_occupancy', ('Co', 'Co'): 'full_occupancy', ('Co', 'Er'): 'full_occupancy', ('Er', 'In1'): 'full_occupancy', ('In1', 'In1'): 'full_occupancy', ('Co', 'In2'): 'full_occupancy', ('Co', 'In1'): 'full_occupancy', ('In2', 'In2'): 'full_occupancy'}\n\nAtomic mixing per label pair sorted by Mendeleev:\n{('Er', 'Er'): 'full_occupancy', ('Co', 'Co'): 'full_occupancy', ('Er', 'In2'): 'full_occupancy', ('In1', 'In2'): 'full_occupancy', ('Er', 'In1'): 'full_occupancy', ('In1', 'In1'): 'full_occupancy', ('Co', 'In2'): 'full_occupancy', ('Co', 'In1'): 'full_occupancy', ('Er', 'Co'): 'full_occupancy', ('In2', 'In2'): 'full_occupancy'}\n</pre> In\u00a0[4]: Copied! <pre>from cifkit import Cif, Example\n\ndef print_connected_points(all_labels_connections):\n    \"\"\"\n    Utility function for printing connections per site label\n    \"\"\"\n    for label, connections in all_labels_connections.items():\n        print(f\"\\nAtom site {label}:\")\n        for (\n            connected_label,\n            dist,\n            coords_1,\n            coords_2,\n        ) in connections:\n            print(f\"{connected_label} {dist} {coords_1}, {coords_2}\")\n\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Print CN Connections\nprint(\"\\nFind CN_connections_by_min_dist_method:\")\nprint_connected_points(cif.CN_connections_by_min_dist_method)\n\nprint(\"\\nFind CN_connections_by_best_methods:\")\nprint_connected_points(cif.CN_connections_by_best_methods)\n</pre>  from cifkit import Cif, Example  def print_connected_points(all_labels_connections):     \"\"\"     Utility function for printing connections per site label     \"\"\"     for label, connections in all_labels_connections.items():         print(f\"\\nAtom site {label}:\")         for (             connected_label,             dist,             coords_1,             coords_2,         ) in connections:             print(f\"{connected_label} {dist} {coords_1}, {coords_2}\")   # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Print CN Connections print(\"\\nFind CN_connections_by_min_dist_method:\") print_connected_points(cif.CN_connections_by_min_dist_method)  print(\"\\nFind CN_connections_by_best_methods:\") print_connected_points(cif.CN_connections_by_best_methods) <pre>\nFind CN_connections_by_min_dist_method:\n\nAtom site In2:\nCo 2.691 [0.0, -2.27, -2.254], [0.0, -4.54, -3.698]\nCo 2.691 [0.0, -2.27, -2.254], [0.0, 0.0, -3.698]\nIn2 2.889 [0.0, -2.27, -2.254], [0.0, -2.27, -5.143]\nIn1 3.199 [0.0, -2.27, -2.254], [-2.27, -2.27, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, 0.0, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, -4.54, 0.0]\nIn1 3.199 [0.0, -2.27, -2.254], [2.27, -2.27, 0.0]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, -4.54, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, -4.54, -2.254]\n\nAtom site In1:\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, 2.254]\nEr 3.21 [2.27, 2.27, 0.0], [-0.0, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [0.0, 0.0, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 0.0, 0.0]\n\nAtom site Co:\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, -2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [0.0, -2.27, 2.254]\n\nAtom site Er:\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, 2.254]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, 2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, 2.27, 0.0]\nCo 3.698 [0.0, 0.0, 0.0], [-0.0, -0.0, 3.698]\nCo 3.698 [0.0, 0.0, 0.0], [0.0, 0.0, -3.698]\nEr 4.54 [0.0, 0.0, 0.0], [-0.0, 4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [0.0, -4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [4.54, 0.0, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [-4.54, 0.0, 0.0]\n\nFind CN_connections_by_best_methods:\n\nAtom site In2:\nCo 2.691 [0.0, -2.27, -2.254], [0.0, -4.54, -3.698]\nCo 2.691 [0.0, -2.27, -2.254], [0.0, 0.0, -3.698]\nIn2 2.889 [0.0, -2.27, -2.254], [0.0, -2.27, -5.143]\nIn1 3.199 [0.0, -2.27, -2.254], [-2.27, -2.27, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, 0.0, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, -4.54, 0.0]\nIn1 3.199 [0.0, -2.27, -2.254], [2.27, -2.27, 0.0]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, -4.54, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, -4.54, -2.254]\n\nAtom site In1:\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, 2.254]\nEr 3.21 [2.27, 2.27, 0.0], [-0.0, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [0.0, 0.0, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 0.0, 0.0]\n\nAtom site Co:\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, -2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [0.0, -2.27, 2.254]\nEr 3.698 [-0.0, -0.0, 3.698], [0.0, 0.0, 0.0]\nEr 3.698 [-0.0, -0.0, 3.698], [-0.0, -0.0, 7.397]\nCo 4.54 [-0.0, -0.0, 3.698], [4.54, -0.0, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [-4.54, -0.0, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [-0.0, 4.54, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [0.0, -4.54, 3.698]\n\nAtom site Er:\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, 2.254]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, 2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, 2.27, 0.0]\nCo 3.698 [0.0, 0.0, 0.0], [-0.0, -0.0, 3.698]\nCo 3.698 [0.0, 0.0, 0.0], [0.0, 0.0, -3.698]\nEr 4.54 [0.0, 0.0, 0.0], [-0.0, 4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [0.0, -4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [4.54, 0.0, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [-4.54, 0.0, 0.0]\n</pre> In\u00a0[5]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\nprint(\"Shortest distance:\", cif.shortest_distance)\nprint(\"Shortest bond pair distances:\", cif.shortest_bond_pair_distance)\nprint(\"Shortest site pair distances:\", cif.shortest_site_pair_distance)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  print(\"Shortest distance:\", cif.shortest_distance) print(\"Shortest bond pair distances:\", cif.shortest_bond_pair_distance) print(\"Shortest site pair distances:\", cif.shortest_site_pair_distance) <pre>Shortest distance: 2.691\nShortest bond pair distances: {('Co', 'In'): 2.691, ('In', 'In'): 2.889, ('Er', 'In'): 3.199, ('Co', 'Er'): 3.698, ('Co', 'Co'): 4.54, ('Er', 'Er'): 4.54}\nShortest site pair distances: {'In2': ('Co', 2.691), 'In1': ('In2', 3.199), 'Co': ('In2', 2.691), 'Er': ('In2', 3.199)}\n</pre> In\u00a0[6]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Bond counts\nprint(\"\\nCN_bond_count_by_min_dist_method:\")\nprint(cif.CN_bond_count_by_min_dist_method)\n\nprint(\"\\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\")\nprint(cif.CN_bond_count_by_min_dist_method_sorted_by_mendeleev)\n\nprint(\"\\nCN_bond_count_by_best_methods:\")\nprint(cif.CN_bond_count_by_best_methods)\n\nprint(\"\\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\")\nprint(cif.CN_bond_count_by_best_methods_sorted_by_mendeleev)\n\n# Bond fractions\nprint(\"\\nCN_bond_fractions_by_min_dist_method:\")\nprint(cif.CN_bond_fractions_by_min_dist_method)\n\nprint(\"\\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\")\nprint(cif.CN_bond_fractions_by_min_dist_method_sorted_by_mendeleev)\n\nprint(\"\\nCN_bond_fractions_by_best_methods:\")\nprint(cif.CN_bond_fractions_by_best_methods)\n\nprint(\"\\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\")\nprint(cif.CN_bond_fractions_by_best_methods_sorted_by_mendeleev)\n\n# Unique coordination numbers\nprint(\"\\nCN_unique_values_by_min_dist_method\")\nprint(cif.CN_unique_values_by_min_dist_method)\n\nprint(\"\\nCN_unique_values_by_best_methods\")\nprint(cif.CN_unique_values_by_best_methods)\n\n# Average coordination number\nprint(\"\\nCN_avg_by_min_dist_method:\")\nprint(cif.CN_avg_by_min_dist_method)\n\nprint(\"\\nCN_avg_by_best_methods: \")\nprint(cif.CN_avg_by_best_methods)\n\n# Min coordination number\nprint(\"\\nCN_max_by_min_dist_method:\")\nprint(cif.CN_max_by_min_dist_method)\n\nprint(\"\\nCN_max_by_best_methods:\")\nprint(cif.CN_max_by_best_methods)\n\n# Max coordination number\nprint(\"\\nCN_min_by_min_dist_method:\")\nprint(cif.CN_min_by_min_dist_method)\n\nprint(\"\\nCN_min_by_best_methods:\")\nprint(cif.CN_min_by_best_methods)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Bond counts print(\"\\nCN_bond_count_by_min_dist_method:\") print(cif.CN_bond_count_by_min_dist_method)  print(\"\\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\") print(cif.CN_bond_count_by_min_dist_method_sorted_by_mendeleev)  print(\"\\nCN_bond_count_by_best_methods:\") print(cif.CN_bond_count_by_best_methods)  print(\"\\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\") print(cif.CN_bond_count_by_best_methods_sorted_by_mendeleev)  # Bond fractions print(\"\\nCN_bond_fractions_by_min_dist_method:\") print(cif.CN_bond_fractions_by_min_dist_method)  print(\"\\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\") print(cif.CN_bond_fractions_by_min_dist_method_sorted_by_mendeleev)  print(\"\\nCN_bond_fractions_by_best_methods:\") print(cif.CN_bond_fractions_by_best_methods)  print(\"\\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\") print(cif.CN_bond_fractions_by_best_methods_sorted_by_mendeleev)  # Unique coordination numbers print(\"\\nCN_unique_values_by_min_dist_method\") print(cif.CN_unique_values_by_min_dist_method)  print(\"\\nCN_unique_values_by_best_methods\") print(cif.CN_unique_values_by_best_methods)  # Average coordination number print(\"\\nCN_avg_by_min_dist_method:\") print(cif.CN_avg_by_min_dist_method)  print(\"\\nCN_avg_by_best_methods: \") print(cif.CN_avg_by_best_methods)  # Min coordination number print(\"\\nCN_max_by_min_dist_method:\") print(cif.CN_max_by_min_dist_method)  print(\"\\nCN_max_by_best_methods:\") print(cif.CN_max_by_best_methods)  # Max coordination number print(\"\\nCN_min_by_min_dist_method:\") print(cif.CN_min_by_min_dist_method)  print(\"\\nCN_min_by_best_methods:\") print(cif.CN_min_by_best_methods) <pre>\nCN_bond_count_by_min_dist_method:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8}, 'Er': {('Er', 'In'): 12, ('Co', 'Er'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8}, 'Er': {('Er', 'In'): 12, ('Er', 'Co'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_best_methods:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8, ('Co', 'Er'): 2, ('Co', 'Co'): 4}, 'Er': {('Er', 'In'): 12, ('Co', 'Er'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8, ('Er', 'Co'): 2, ('Co', 'Co'): 4}, 'Er': {('Er', 'In'): 12, ('Er', 'Co'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_fractions_by_min_dist_method:\n{('Co', 'In'): 0.204, ('In', 'In'): 0.306, ('Er', 'In'): 0.367, ('Co', 'Er'): 0.041, ('Er', 'Er'): 0.082}\n\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\n{('Co', 'In'): 0.204, ('In', 'In'): 0.306, ('Er', 'In'): 0.367, ('Er', 'Co'): 0.041, ('Er', 'Er'): 0.082}\n\nCN_bond_fractions_by_best_methods:\n{('Co', 'In'): 0.182, ('In', 'In'): 0.273, ('Er', 'In'): 0.327, ('Co', 'Er'): 0.073, ('Co', 'Co'): 0.073, ('Er', 'Er'): 0.073}\n\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\n{('Co', 'In'): 0.182, ('In', 'In'): 0.273, ('Er', 'In'): 0.327, ('Er', 'Co'): 0.073, ('Co', 'Co'): 0.073, ('Er', 'Er'): 0.073}\n\nCN_unique_values_by_min_dist_method\n{8, 18, 11, 12}\n\nCN_unique_values_by_best_methods\n{18, 11, 12, 14}\n\nCN_avg_by_min_dist_method:\n12.25\n\nCN_avg_by_best_methods: \n13.75\n\nCN_max_by_min_dist_method:\n18\n\nCN_max_by_best_methods:\n18\n\nCN_min_by_min_dist_method:\n8\n\nCN_min_by_best_methods:\n11\n</pre> In\u00a0[7]: Copied! <pre>from cifkit import Cif, Example\nimport warnings\nwarnings.filterwarnings('ignore') # For Jupyter Notebook only\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Enter site labels. you can get site labels using cif.labels\nprint(\"Site labels:\", cif.site_labels)\n\n# Plot\ncif.plot_polyhedron(\"In1\", is_displayed=True)\n</pre> from cifkit import Cif, Example import warnings warnings.filterwarnings('ignore') # For Jupyter Notebook only  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Enter site labels. you can get site labels using cif.labels print(\"Site labels:\", cif.site_labels)  # Plot cif.plot_polyhedron(\"In1\", is_displayed=True) <pre>Site labels: ['In2', 'In1', 'Co', 'Er']\n</pre>"},{"location":"notebooks/01_cif/#cif","title":"CIF\u00b6","text":"<p>The <code>Cif</code> class generates an object for each <code>.cif</code> file. Each object can</p> <ul> <li>compute the coordination numbers for each site label using four methods</li> <li>compute bond fractions and bond counts at each site within the specified cutoff radius or based on -coordination number geometry</li> <li>categorize atomic mixing at bond-pair and file levels</li> <li>list all possible bond and label pairs derived from the formula</li> <li>generate a unit cell and a supercell by applying \u00b11 shifts</li> <li>parse formulas, structures, tags, space group names, supercell sizes, and elements</li> </ul>"},{"location":"notebooks/01_cif/#get-instant-properties-parsed-information","title":"Get instant properties - parsed information\u00b6","text":"<p>The <code>Cif</code> class provides a set of accessible properties that can be accessed. Each object is intialized with the <code>file_path</code> to the <code>.cif</code> file.</p>"},{"location":"notebooks/01_cif/#how-tag-is-parsed","title":"How tag is parsed\u00b6","text":"<p>Tag is parsed from the thrid line of each <code>.cif</code> file. Some databases such as Pearson's Crystal Data offers tags for each file.</p>"},{"location":"notebooks/01_cif/#get-instant-properties-bond-pairs","title":"Get instant properties - bond pairs\u00b6","text":"<ul> <li>The following code returns all possible element and site pairs from the formula in the .cif file.</li> <li>The <code>mixing_info_per_label_pair</code> and <code>mixing_info_per_label_pair_sorted_by_mendeleev</code> return site mixing information at the pair level.</li> </ul>"},{"location":"notebooks/01_cif/#how-atomic-mixing-type-is-defined","title":"How atomic mixing type is defined\u00b6","text":"<p>Each bonding pair or each file is defined with one of four atomic mixing categories:</p> <ul> <li>Full occupancy is assigned when a single atomic site occupies the fractional coordinate with an occupancy value of 1.</li> <li>Full occupancy with atomic mixing is assigned when multiple atomic sites collectively occupy the fractional coordinate to a sum of 1.</li> <li>Deficiency without atomic mixing is assigned when a single atomic site occupying the fractional coordinate with a sum less than 1.</li> <li>Deficiency with atomic mixing is assigned when multiple atomic sites occupy the fractional coordinate with a sum less than 1.</li> </ul>"},{"location":"notebooks/01_cif/#get-computed-properties-nearest-connections-per-site","title":"Get computed properties - nearest connections per site\u00b6","text":"<p>This section involves computing distances between atoms. Unlike instant properties, these properties may require extensive computation, typically ranging from 1-2 seconds for larger supercells containing more than 3,000 atoms.</p> <p>These properties are loaded lazily, meaning accessing any of the properties will execute <code>compute_connections()</code> internally. This function will then compute <code>connections</code>, providing all the nearest neighbors for each site.</p> <p>There are options in the <code>Cif</code> class to use either the <code>by_d_min_method</code> or <code>by_best_methods</code>. Please refer to the <code>README.md</code> for complete documentation.</p>"},{"location":"notebooks/01_cif/#get-computed-properties-distances","title":"Get computed properties - distances\u00b6","text":"<p>You can get the shortest distance from each site label or the shortest distance for each possible bond pair.</p>"},{"location":"notebooks/01_cif/#get-computed-properties-coordination-numbers","title":"Get computed properties - coordination numbers\u00b6","text":"<p>Compute <code>avg</code>, <code>min</code>, <code>max</code>, <code>unique</code> of coordination numbers determined by one of the best methods or min distance method.</p>"},{"location":"notebooks/01_cif/#draw-polyhedrons","title":"Draw polyhedrons\u00b6","text":"<p>You may use <code>Jupyter</code> notebook or a python script to execute the following to generate and save a polyhedron generated from each site and the nearest neighbor atoms are determined from the coordination number geometry.</p>"},{"location":"notebooks/02_cif_ensemble/","title":"CifEnsemble","text":"In\u00a0[10]: Copied! <pre>from cifkit import CifEnsemble, Example\n\n# Initialize\nensemble = CifEnsemble(Example.ErCoIn_folder_path)\n</pre> from cifkit import CifEnsemble, Example  # Initialize ensemble = CifEnsemble(Example.ErCoIn_folder_path) <pre>\nCIF Preprocessing in Example.ErCoIn_folder_path begun...\n\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif (1/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif (2/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif (3/3)\n\nSUMMARY\n# of files moved to 'error_operations' folder: 0\n# of files moved to 'error_duplicate_labels' folder: 0\n# of files moved to 'error_wrong_loop_value' folder: 0\n# of files moved to 'error_coords' folder: 0\n# of files moved to 'error_invalid_label' folder: 0\n# of files moved to 'error_others' folder: 0\n\n</pre> In\u00a0[11]: Copied! <pre># Initialize with nested .cif files in the folder\nensemble_nested = CifEnsemble(Example.ErCoIn_folder_path, add_nested_files=True)\n</pre>  # Initialize with nested .cif files in the folder ensemble_nested = CifEnsemble(Example.ErCoIn_folder_path, add_nested_files=True) <pre>\nCIF Preprocessing in Example.ErCoIn_folder_path begun...\n\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif (1/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif (2/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif (3/3)\n\nSUMMARY\n# of files moved to 'error_operations' folder: 0\n# of files moved to 'error_duplicate_labels' folder: 0\n# of files moved to 'error_wrong_loop_value' folder: 0\n# of files moved to 'error_coords' folder: 0\n# of files moved to 'error_invalid_label' folder: 0\n# of files moved to 'error_others' folder: 0\n\n</pre> In\u00a0[12]: Copied! <pre># Get .cif file count in the folder\nprint(\"File count:\", ensemble.file_count) # 6\n\n# Get the directory path\nprint(\"Directory path:\", ensemble.dir_path)\n\n# Get all file paths in the folder\nprint(\"File paths:\", ensemble.file_paths)\n\n# Get all Cif objects initialized\nprint(\"Cif objects:\", ensemble.cifs)\n</pre> # Get .cif file count in the folder print(\"File count:\", ensemble.file_count) # 6  # Get the directory path print(\"Directory path:\", ensemble.dir_path)  # Get all file paths in the folder print(\"File paths:\", ensemble.file_paths)  # Get all Cif objects initialized print(\"Cif objects:\", ensemble.cifs) <pre>File count: 3\nDirectory path: Example.ErCoIn_folder_path\nFile paths: ['/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif']\nCif objects: [&lt;cifkit.models.cif.Cif object at 0x16c818980&gt;, &lt;cifkit.models.cif.Cif object at 0x16c86a2d0&gt;, &lt;cifkit.models.cif.Cif object at 0x16c8cb0b0&gt;]\n</pre> In\u00a0[13]: Copied! <pre># Print each property for each .cif file\nfor cif in ensemble.cifs:\n  print(f\"\\n{cif.file_name}\")\n  print(\"Formula:\", cif.formula)\n  print(\"Tag:\", cif.tag)\n  print(\"Mixing type:\", cif.site_mixing_type)\n  print(\"Unique bond pairs:\", cif.bond_pairs)\n</pre> # Print each property for each .cif file for cif in ensemble.cifs:   print(f\"\\n{cif.file_name}\")   print(\"Formula:\", cif.formula)   print(\"Tag:\", cif.tag)   print(\"Mixing type:\", cif.site_mixing_type)   print(\"Unique bond pairs:\", cif.bond_pairs) <pre>\nEr10Co9In20.cif\nFormula: Er10Co9In20\nTag: \nMixing type: full_occupancy\nUnique bond pairs: {('Er', 'Er'), ('Co', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'In'), ('Co', 'Co')}\n\nEr5In3.cif\nFormula: Er5In3\nTag: \nMixing type: full_occupancy\nUnique bond pairs: {('Er', 'Er'), ('In', 'In'), ('Er', 'In')}\n\nErCoIn5.cif\nFormula: ErCoIn5\nTag: rt\nMixing type: full_occupancy\nUnique bond pairs: {('Er', 'Er'), ('Co', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'In'), ('Co', 'Co')}\n</pre> In\u00a0[14]: Copied! <pre># Get unique formulas\nprint(\"Unique formulas:\", ensemble.unique_formulas)\n\n# Get unique elements\nprint(\"Unique elements:\", ensemble.unique_elements)\n\n# Get unique structures\nprint(\"Unique structures:\", ensemble.unique_structures)\n\n# Get unique atomix mixing types\nprint(\"Unique atomic mixing types:\", ensemble.unique_site_mixing_types)\n\n# Get unique elements\nprint(\"Unique elements including nested:\", ensemble_nested.unique_elements)\n\n# Get unique space group names\nprint(\"Unique space group names:\", ensemble.unique_space_group_names)\n\n# Get unique space group numbers\nprint(\"Unique space group numbers:\",ensemble.unique_space_group_numbers)\n\n# Get unique tags\nprint(\"Unique tags:\", ensemble.unique_tags)\n\n# Get unique composition types\nprint(\"Unique composition types:\", ensemble.unique_composition_types)\n</pre> # Get unique formulas print(\"Unique formulas:\", ensemble.unique_formulas)  # Get unique elements print(\"Unique elements:\", ensemble.unique_elements)  # Get unique structures print(\"Unique structures:\", ensemble.unique_structures)  # Get unique atomix mixing types print(\"Unique atomic mixing types:\", ensemble.unique_site_mixing_types)  # Get unique elements print(\"Unique elements including nested:\", ensemble_nested.unique_elements)  # Get unique space group names print(\"Unique space group names:\", ensemble.unique_space_group_names)  # Get unique space group numbers print(\"Unique space group numbers:\",ensemble.unique_space_group_numbers)  # Get unique tags print(\"Unique tags:\", ensemble.unique_tags)  # Get unique composition types print(\"Unique composition types:\", ensemble.unique_composition_types) <pre>Unique formulas: {'ErCoIn5', 'Er5In3', 'Er10Co9In20'}\nUnique elements: {'In', 'Er', 'Co'}\nUnique structures: {'Ho10Ni9In20', 'HoCoGa5', 'Mn5Si3'}\nUnique atomic mixing types: {'full_occupancy'}\nUnique elements including nested: {'In', 'Er', 'Co'}\nUnique space group names: {'P4/nmm(originchoice2)', 'P63/mcm', 'P4/mmm'}\nUnique space group numbers: {129, 123, 193}\nUnique tags: {'', 'rt'}\nUnique composition types: {2, 3}\n</pre> In\u00a0[15]: Copied! <pre># Get file count per structure\nprint(\"Structure stats:\", ensemble.structure_stats)\n\n# Get file count per formula\nprint(\"Formula stats:\", ensemble.formula_stats)\n\n# Get file count per tag\nprint(\"Tag stats:\", ensemble.tag_stats)\n\n# Get file count per space group number\nprint(\"Space group number stats:\", ensemble.space_group_number_stats)\n\n# Get file count per space group name\nprint(\"Space group name stats:\", ensemble.space_group_name_stats)\n\n# Get file count per composition type\nprint(\"Composition type stats:\", ensemble.composition_type_stats)\n\n# Get file count per Element\nprint(\"Unique elements stats:\", ensemble.unique_elements_stats)\n\n# Get file count per site mixing type\nprint(\"Site mixing type stats:\", ensemble.site_mixing_type_stats)\n\n# Get file count per supercell atom count\nprint(\"Supercell size stats:\", ensemble.supercell_size_stats)\n\n# Get file count per min distance\nprint(\"Min distance stats:\", ensemble.min_distance_stats)\n\n# Get file count per CN value by min dist method\nprint(\"CN value using min dist method stats:\", ensemble.unique_CN_values_by_min_dist_method_stat)\n\n# Get file count per CN value by best methods\nprint(\"CN value using best methods stats:\", ensemble.unique_CN_values_by_method_methods_stat)\n</pre> # Get file count per structure print(\"Structure stats:\", ensemble.structure_stats)  # Get file count per formula print(\"Formula stats:\", ensemble.formula_stats)  # Get file count per tag print(\"Tag stats:\", ensemble.tag_stats)  # Get file count per space group number print(\"Space group number stats:\", ensemble.space_group_number_stats)  # Get file count per space group name print(\"Space group name stats:\", ensemble.space_group_name_stats)  # Get file count per composition type print(\"Composition type stats:\", ensemble.composition_type_stats)  # Get file count per Element print(\"Unique elements stats:\", ensemble.unique_elements_stats)  # Get file count per site mixing type print(\"Site mixing type stats:\", ensemble.site_mixing_type_stats)  # Get file count per supercell atom count print(\"Supercell size stats:\", ensemble.supercell_size_stats)  # Get file count per min distance print(\"Min distance stats:\", ensemble.min_distance_stats)  # Get file count per CN value by min dist method print(\"CN value using min dist method stats:\", ensemble.unique_CN_values_by_min_dist_method_stat)  # Get file count per CN value by best methods print(\"CN value using best methods stats:\", ensemble.unique_CN_values_by_method_methods_stat) <pre>Structure stats: {'Ho10Ni9In20': 1, 'Mn5Si3': 1, 'HoCoGa5': 1}\nFormula stats: {'Er10Co9In20': 1, 'Er5In3': 1, 'ErCoIn5': 1}\nTag stats: {'': 2, 'rt': 1}\nSpace group number stats: {129: 1, 193: 1, 123: 1}\nSpace group name stats: {'P4/nmm(originchoice2)': 1, 'P63/mcm': 1, 'P4/mmm': 1}\nComposition type stats: {3: 2, 2: 1}\nUnique elements stats: {'Er': 3, 'In': 3, 'Co': 2}\nSite mixing type stats: {'full_occupancy': 3}\nSupercell size stats: {2654: 1, 558: 1, 255: 1}\nMin distance stats: {2.626: 1, 3.102: 1, 2.691: 1}\nCN value using min dist method stats: {10: 1, 12: 2, 13: 1, 14: 2, 16: 1, 17: 1, 11: 2, 15: 1, 8: 1, 18: 1}\nCN value using best methods stats: {10: 1, 12: 2, 13: 1, 14: 3, 16: 1, 17: 1, 11: 2, 15: 1, 18: 1}\n</pre> In\u00a0[16]: Copied! <pre># Return file paths by formulas\nensemble.filter_by_formulas([\"ErCoIn\", \"Er10Co9In20\"]) \n\n# Return file paths by structures\nensemble.filter_by_structures([\"Mn5Si3\"])\n\n# Return file paths by space group names\nensemble.filter_by_space_group_names([\"P4/mmm\"])\n\n# Return file paths by space group numbers\nensemble.filter_by_space_group_numbers([123])\n\n# Return file paths by site mixing types\nensemble.filter_by_site_mixing_types([\"full_occupancy\"])\nensemble.filter_by_site_mixing_types([\"full_occupancy\", \"deficiency_without_atomic_mixing\"])\n\n# Return file paths by composition types (1-&gt; unary, 2-&gt; binary)\nensemble.filter_by_composition_types([3])\n</pre> # Return file paths by formulas ensemble.filter_by_formulas([\"ErCoIn\", \"Er10Co9In20\"])   # Return file paths by structures ensemble.filter_by_structures([\"Mn5Si3\"])  # Return file paths by space group names ensemble.filter_by_space_group_names([\"P4/mmm\"])  # Return file paths by space group numbers ensemble.filter_by_space_group_numbers([123])  # Return file paths by site mixing types ensemble.filter_by_site_mixing_types([\"full_occupancy\"]) ensemble.filter_by_site_mixing_types([\"full_occupancy\", \"deficiency_without_atomic_mixing\"])  # Return file paths by composition types (1-&gt; unary, 2-&gt; binary) ensemble.filter_by_composition_types([3])   Out[16]: <pre>{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif',\n '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif'}</pre> In\u00a0[51]: Copied! <pre>print(\"\\nFile paths containing Er or Co or In:\")\nprint(ensemble.filter_by_elements_containing([\"Er\", \"Co\", \"In\"])) # \n\nprint(\"\\nFile paths containing Er and In:\")\nprint(ensemble.filter_by_elements_exact_matching([\"Er\", \"In\"]))\n\nprint(\"\\nFile paths containing CN value of 15:\")\nprint(ensemble.filter_by_CN_min_dist_method_containing([15]))\nprint(ensemble.filter_by_CN_best_methods_containing([15]))\n\nprint(\"\\nFile paths containing CN value of 11, 14, and 15:\")\nprint(ensemble.filter_by_CN_min_dist_method_exact_matching([11, 14, 15]))\nprint(ensemble.filter_by_CN_best_methods_exact_matching([11, 14, 15]))\n</pre>  print(\"\\nFile paths containing Er or Co or In:\") print(ensemble.filter_by_elements_containing([\"Er\", \"Co\", \"In\"])) #   print(\"\\nFile paths containing Er and In:\") print(ensemble.filter_by_elements_exact_matching([\"Er\", \"In\"]))  print(\"\\nFile paths containing CN value of 15:\") print(ensemble.filter_by_CN_min_dist_method_containing([15])) print(ensemble.filter_by_CN_best_methods_containing([15]))  print(\"\\nFile paths containing CN value of 11, 14, and 15:\") print(ensemble.filter_by_CN_min_dist_method_exact_matching([11, 14, 15])) print(ensemble.filter_by_CN_best_methods_exact_matching([11, 14, 15])) <pre>\nFile paths containing Er or Co or In:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}\n\nFile paths containing Er and In:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n\nFile paths containing CN value of 15:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n\nFile paths containing CN value of 11, 14, and 15:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n</pre> In\u00a0[52]: Copied! <pre># Return a set of .cif file paths with min distance between 1.0 \u00c5 and 3.0 \u00c5\nprint(\"File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\\n\", ensemble.filter_by_min_distance(1.0, 3.0))\n\n# Return a set of .cif file paths with supercell atom count above 500 and below 3000.\nprint(\"File paths with supercell atom count above 500 and below 3000:\\n\",ensemble.filter_by_supercell_count(300, 3000))\n</pre> # Return a set of .cif file paths with min distance between 1.0 \u00c5 and 3.0 \u00c5 print(\"File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\\n\", ensemble.filter_by_min_distance(1.0, 3.0))  # Return a set of .cif file paths with supercell atom count above 500 and below 3000. print(\"File paths with supercell atom count above 500 and below 3000:\\n\",ensemble.filter_by_supercell_count(300, 3000)) <pre>File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\n {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}\nFile paths with supercell atom count above 500 and below 3000:\n {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif'}\n</pre>"},{"location":"notebooks/02_cif_ensemble/#cifensemble","title":"CifEnsemble\u00b6","text":"<p>For high-throuhgput analysis, you can initialize multiple <code>.cif</code> files using <code>CifEnsemble</code>.</p>"},{"location":"notebooks/02_cif_ensemble/#initialize-with-folder-path-and-preprocess-automatically","title":"Initialize with folder path and preprocess automatically\u00b6","text":"<ul> <li><p><code>CifEnsemble</code> standardizes the site labels in <code>atom_site_label</code>. Some site labels may contain a comma or a symbol such as M due to atomic mixing. CBA reformats each <code>atom_site_label</code> so it can be parsed into an element type that matches atom_site_type_symbol.</p> </li> <li><p><code>CifEnsemble</code> removes the content of <code>publ_author_address</code>. This section often has an incorrect format that otherwise requires manual modifications.</p> </li> <li><p><code>CifEnsemble</code> relocates any ill-formatted files, such as those with duplicate labels in <code>atom_site_label</code>, missing fractional coordinates, or files that require supercell generation.</p> </li> </ul>"},{"location":"notebooks/02_cif_ensemble/#initialize-with-nested-files","title":"Initialize with nested files\u00b6","text":"<p>You can also use the <code>add_nested_files</code> flag to include <code>.cif</code> files that are located in folders within the folder path provided.</p>"},{"location":"notebooks/02_cif_ensemble/#get-instant-properties","title":"Get instant properties\u00b6","text":"<p>Once the object is created, you can get instant properties suhc as file count, folder path, etc.</p>"},{"location":"notebooks/02_cif_ensemble/#get-individual-cif-properties","title":"Get individual .cif properties\u00b6","text":"<p>The <code>CifEnsemble</code> object contains a property called <code>cifs</code> which contains a list of <code>Cif</code> objects. You may loop through each to access both instant and computed properties described in the previous <code>CIF</code> section.</p>"},{"location":"notebooks/02_cif_ensemble/#get-unique-properties","title":"Get unique properties\u00b6","text":"<p>You can get all unique attributres such as formulas, elements, etc in the folder.</p>"},{"location":"notebooks/02_cif_ensemble/#get-overall-stats-by-attribute","title":"Get overall stats by attribute\u00b6","text":"<p>Get the number of files for each unique properties.</p>"},{"location":"notebooks/02_cif_ensemble/#filter-cif-containing-specific-attributes","title":"Filter .cif containing specific attributes\u00b6","text":""},{"location":"notebooks/02_cif_ensemble/#filter-cif-by-specific-attributes","title":"Filter .cif by specific attributes\u00b6","text":"<p>Filter .cif files either containing a set of items or files that exactly contain the values passed. <code>cifkit</code> supports elements and coordination numbers.</p>"},{"location":"notebooks/02_cif_ensemble/#filter-by-range","title":"Filter by range\u00b6","text":""},{"location":"notebooks/02_cif_ensemble/#move-and-copy-files","title":"Move and copy files\u00b6","text":"<p>Assume you have a set of file paths filered using the functions described in the previous section. Since we are using Jupyter and with predefined examples, you need to provide <code>file_paths</code> and <code>dest_dir_path</code> for your system.</p> <pre>file_paths = {\n    \"tests/data/cif/ensemble_test/300169.cif\",\n    \"tests/data/cif/ensemble_test/300171.cif\",\n    \"tests/data/cif/ensemble_test/300170.cif\",\n}\n\n# To move files\nensemble.move_cif_files(file_paths, dest_dir_path)\n\n# To copy files\nensemble.copy_cif_files(file_paths, dest_dir_path)\n</pre>"}]}
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+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Getting started","text":"<p>The purpose of this guide is to illustrate some of the main features that <code>cifkit</code> provides. It assumes a very basic knowledge of Python.</p> <p><code>cifkit</code> 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 <code>.cif</code> files based on a set of attributes, and determine atomic mixing information in 2-3 lines of code.</p>"},{"location":"#installation","title":"Installation","text":"<p>Install <code>cifkit</code> via:</p> <pre><code>pip install cifkit\n</code></pre> <p>You may need to download other dependencies:</p> <pre><code>pip install cifkit pyvista gemmi\n</code></pre> <p><code>gemmi</code> is used for parsing <code>.cif</code> files. <code>pyvista</code> is used for plotting polyhedrons.</p>"},{"location":"#start-with-cifensemble","title":"Start with CifEnsemble","text":"<p><code>cifkit</code> offers a class called <code>CifEnsemble</code> which handles many <code>.cif</code> files in a high-throuhgput way. You can initialize the object using the folder path containing <code>.cif</code> files shown below.</p> <pre><code>from cifkit import CifEnsemble\n\n# Initialize\nensemble = CifEnsemble(\"tests/data/cif/ensemble_test\")\n\n# Initialize including nested files\nensemble = CifEnsemble(\"tests/data/cif/ensemble_test\", add_nested_files=True)\n\n# Folder path\nensemble.cif_folder_path\n# \"tests/data/cif/ensemble_test\"\n</code></pre> <p>If you do not have <code>.cif</code> files for testing, <code>cifkit</code> also provides a set of <code>.cif</code> files accessible.</p> <pre><code>from cifkit import CifEnsemble, Example\nfrom cifkit import Example\n\n# Initalize with the file path\nensemble = CifEnsemble(Example.ErCoIn_big_folder_path)\n</code></pre>"},{"location":"#get-unique-attributes","title":"Get unique attributes","text":"<p>Use the <code>ensemble</code> object to get unique attributes such as elements, formulas, etc.</p> <pre><code># Unique formulas\nensemble.unique_formulas\n# {\"EuIr2Ge2\", \"CeRu2Ge2\", \"LaRu2Ge2\", \"Mo\"}\n\n# Unique structures\nensemble.unique_structures\n# {\"CeAl2Ga2\", \"W\"}\n\n# Unique elements\nensemble.unique_elements\n# {\"La\", \"Ru\", \"Ge\", \"Ir\", \"Eu\", \"Ce\", \"Mo\"}\n\n# Unique space group names\nensemble.unique_space_group_names\n# {\"I4/mmm\", \"Im-3m\"}\n\n# Unique space group numbers\nensemble.unique_space_group_numbers\n# {139, 229}\n\n# Unique tags\nensemble.unique_tags\n# {\"hex\", \"rt\", \"rt_hex\", \"\"}\n</code></pre>"},{"location":"#get-distances-and-supercell-size-per-file","title":"Get distances and supercell size per file","text":"<p>The following computes the size of each supercell and the minimum distance per file.</p> <pre><code># Get min distance per file\nensemble.minimum_distances\n# [(\"tests/data/cif/ensemble_test/250709.cif\", 2.725),\n# (\"tests/data/cif/ensemble_test/300171.cif\", 2.383),\n# (\"tests/data/cif/ensemble_test/300170.cif\", 2.28)]\n\n# Get supercell size per file\nensemble_test.supercell_atom_counts\n# [(\"tests/data/cif/ensemble_test/250709.cif\", 54),\n# (\"tests/data/cif/ensemble_test/300171.cif\", 360),\n# (\"tests/data/cif/ensemble_test/300170.cif\", 360)]\n</code></pre>"},{"location":"#filter-files-by-attributes","title":"Filter files by attributes","text":"<p>The following returns a set of file paths to each <code>.cif</code> file.</p> <pre><code># By formulas\nensemble_test.filter_by_formulas([\"LaRu2Ge2\"])\nensemble_test.filter_by_formulas([\"LaRu2Ge2\", \"Mo\"])\n\n# By structures\nensemble_test.filter_by_structures([\"W\"])\nensemble_test.filter_by_structures(\"CeAl2Ga2\")\n\n# By space group\nensemble_test.filter_by_space_group_names(\"Im-3m\")\n\n# By space group numbers\nensemble_test.filter_by_space_group_numbers([139])\n</code></pre>"},{"location":"#move-and-copy-files","title":"Move and copy files","text":"<p>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.</p> <pre><code>file_paths = {\n    \"tests/data/cif/ensemble_test/300169.cif\",\n    \"tests/data/cif/ensemble_test/300171.cif\",\n    \"tests/data/cif/ensemble_test/300170.cif\",\n}\n\n# To move files\nensemble.move_cif_files(file_paths, dest_dir_path)\n\n# To copy files\nensemble.copy_cif_files(file_paths, dest_dir_path)\n</code></pre>"},{"location":"#are-you-ready","title":"Are you ready?","text":"<p>Now, if you are interested in working with individual <code>.cif</code> files and learn more about all features in <code>cifkit</code>, let's visit the <code>Example notebooks</code> section here!</p>"},{"location":"#research-projects-using-cifkit","title":"Research projects using <code>cifkit</code>","text":"<ul> <li>CIF Bond Analyzer (CBA) - extract and visualize bonding patterns - DOI | GitHub</li> <li>Structure Analysis/Featurizer (SAF) - build geometric features for binary, ternary compounds - GitHub</li> </ul>"},{"location":"notebooks/00_Intro/","title":"Installation","text":"In\u00a0[\u00a0]: Copied! <pre>pip install cifkit\n</pre> pip install cifkit <p>In Google Codelab, <code>pyvista</code> and <code>gemmi</code> need to be installed.</p> In\u00a0[\u00a0]: Copied! <pre>pip install cifkit pyvista gemmi\n</pre>  pip install cifkit pyvista gemmi"},{"location":"notebooks/00_Intro/#installation","title":"Installation\u00b6","text":"<p><code>cifkit</code> supports Python versions 3.10, 3.11, and 3.12.</p>"},{"location":"notebooks/00_Intro/#google-codelab","title":"Google Codelab\u00b6","text":"<p>You can also run the examples using Google Codelab by clicking the link below:</p>"},{"location":"notebooks/00_Intro/#feedback-help","title":"Feedback &amp; help\u00b6","text":"<p>If you find <code>cifkit</code> beneficial for your research, or if you are considering its usage, please do not hesitate to contact me. You can reach out via the email provided on my GitHub profile.</p>"},{"location":"notebooks/01_cif/","title":"CIF","text":"<p>You can initialize <code>Cif</code> object using a file path to the <code>.cif</code> file. Or you can simply use the example <code>.cif</code> provided in <code>cifkit</code> below.</p> In\u00a0[1]: Copied! <pre>from cifkit import Example\nfrom cifkit import Cif\n\n# Initalize with the example file provided\ncif = Cif(Example.Er10Co9In20_file_path)\n\n# Print attributes\nprint(\"File name:\", cif.file_name)\nprint(\"Formula:\", cif.formula)\nprint(\"Unique element:\", cif.unique_elements)\n</pre> from cifkit import Example from cifkit import Cif  # Initalize with the example file provided cif = Cif(Example.Er10Co9In20_file_path)  # Print attributes print(\"File name:\", cif.file_name) print(\"Formula:\", cif.formula) print(\"Unique element:\", cif.unique_elements) <pre>File name: Er10Co9In20.cif\nFormula: Er10Co9In20\nUnique element: {'Co', 'In', 'Er'}\n</pre> In\u00a0[2]: Copied! <pre>from cifkit import Cif, Example\nimport json\n\n# Utility function for printing dictionary\ndef prettify_dict(dict_data):\n  return json.dumps(dict_data, indent=4)\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Print instantly available properties\nprint(\"Formula:\", cif.formula)\nprint(\"Structure:\", cif.structure)\nprint(\"Unique elements:\", cif.unique_elements)\nprint(\"Unitcell lenghts:\", cif.unitcell_lengths)\nprint(\"Unitcell angles:\", cif.unitcell_angles)\nprint(\"Site labels:\", cif.site_labels)\nprint(\"Weight:\", cif.weight)\nprint(\"Atomic mixing type:\", cif.site_mixing_type)\nprint(\"Space group number:\", cif.space_group_number)\nprint(\"Space group number:\", cif.space_group_name)\nprint(\"Composition type:\", cif.composition_type) # 3 -&gt; Ternary\nprint(\"Tag:\", cif.tag)\nprint(\"Atom_site_info:\", prettify_dict(cif.atom_site_info))\nprint(\"Wyckoff_symbol of Er1:\", cif.atom_site_info[\"Er\"][\"wyckoff_symbol\"])\n</pre> from cifkit import Cif, Example import json  # Utility function for printing dictionary def prettify_dict(dict_data):   return json.dumps(dict_data, indent=4)  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Print instantly available properties print(\"Formula:\", cif.formula) print(\"Structure:\", cif.structure) print(\"Unique elements:\", cif.unique_elements) print(\"Unitcell lenghts:\", cif.unitcell_lengths) print(\"Unitcell angles:\", cif.unitcell_angles) print(\"Site labels:\", cif.site_labels) print(\"Weight:\", cif.weight) print(\"Atomic mixing type:\", cif.site_mixing_type) print(\"Space group number:\", cif.space_group_number) print(\"Space group number:\", cif.space_group_name) print(\"Composition type:\", cif.composition_type) # 3 -&gt; Ternary print(\"Tag:\", cif.tag) print(\"Atom_site_info:\", prettify_dict(cif.atom_site_info)) print(\"Wyckoff_symbol of Er1:\", cif.atom_site_info[\"Er\"][\"wyckoff_symbol\"]) <pre>Formula: ErCoIn5\nStructure: HoCoGa5\nUnique elements: {'Co', 'In', 'Er'}\nUnitcell lenghts: [4.54, 4.54, 7.397]\nUnitcell angles: [1.5708, 1.5708, 1.5708]\nSite labels: ['In2', 'In1', 'Co', 'Er']\nWeight: 800.3\nAtomic mixing type: full_occupancy\nSpace group number: 123\nSpace group number: P4/mmm\nComposition type: 3\nTag: rt\nAtom_site_info: {\n    \"In2\": {\n        \"element\": \"In\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.5,\n        \"z_frac_coord\": 0.30474,\n        \"symmetry_multiplicity\": 4,\n        \"wyckoff_symbol\": \"i\"\n    },\n    \"In1\": {\n        \"element\": \"In\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.5,\n        \"y_frac_coord\": 0.5,\n        \"z_frac_coord\": 0.0,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"c\"\n    },\n    \"Co\": {\n        \"element\": \"Co\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.0,\n        \"z_frac_coord\": 0.5,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"b\"\n    },\n    \"Er\": {\n        \"element\": \"Er\",\n        \"site_occupancy\": 1.0,\n        \"x_frac_coord\": 0.0,\n        \"y_frac_coord\": 0.0,\n        \"z_frac_coord\": 0.0,\n        \"symmetry_multiplicity\": 1,\n        \"wyckoff_symbol\": \"a\"\n    }\n}\nWyckoff_symbol of Er1: a\n</pre> In\u00a0[3]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Utility function for printing a set of tuples\ndef print_tuples(tuples):\n  for pair in tuples:\n    print(f\"({pair[0]}, {pair[1]})\")\n\n# All bond pairs\nprint(\"\\nAll possible bond pairs:\")\nprint_tuples(cif.bond_pairs)\n\nprint(\"\\nAll possible bond pairs sorted by Mendeleev:\")\nprint_tuples(cif.bond_pairs_sorted_by_mendeleev)\n\n# All label pairs\nprint(\"\\nAll possible label pairs from the formula:\")\nprint_tuples(cif.site_label_pairs)\n\nprint(\"\\nAll possible label pairs sorted by Mendeleev:\")\nprint_tuples(cif.site_label_pairs_sorted_by_mendeleev)\n\n# Atomic mixing per pair\nprint(\"\\nAtomic mixing per label pair:\")\nprint((cif.mixing_info_per_label_pair))\n\nprint(\"\\nAtomic mixing per label pair sorted by Mendeleev:\")\nprint(cif.mixing_info_per_label_pair_sorted_by_mendeleev)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Utility function for printing a set of tuples def print_tuples(tuples):   for pair in tuples:     print(f\"({pair[0]}, {pair[1]})\")  # All bond pairs print(\"\\nAll possible bond pairs:\") print_tuples(cif.bond_pairs)  print(\"\\nAll possible bond pairs sorted by Mendeleev:\") print_tuples(cif.bond_pairs_sorted_by_mendeleev)  # All label pairs print(\"\\nAll possible label pairs from the formula:\") print_tuples(cif.site_label_pairs)  print(\"\\nAll possible label pairs sorted by Mendeleev:\") print_tuples(cif.site_label_pairs_sorted_by_mendeleev)  # Atomic mixing per pair print(\"\\nAtomic mixing per label pair:\") print((cif.mixing_info_per_label_pair))  print(\"\\nAtomic mixing per label pair sorted by Mendeleev:\") print(cif.mixing_info_per_label_pair_sorted_by_mendeleev)  <pre>\nAll possible bond pairs:\n(Er, Er)\n(Co, Co)\n(Er, In)\n(Co, Er)\n(In, In)\n(Co, In)\n\nAll possible bond pairs sorted by Mendeleev:\n(Er, Er)\n(Co, Co)\n(Er, In)\n(In, In)\n(Co, In)\n(Er, Co)\n\nAll possible label pairs from the formula:\n(Er, Er)\n(Er, In2)\n(In1, In2)\n(Co, Co)\n(Co, Er)\n(Er, In1)\n(In1, In1)\n(Co, In2)\n(Co, In1)\n(In2, In2)\n\nAll possible label pairs sorted by Mendeleev:\n(Er, Er)\n(Co, Co)\n(Er, In2)\n(In1, In2)\n(Er, In1)\n(In1, In1)\n(Co, In2)\n(Co, In1)\n(Er, Co)\n(In2, In2)\n\nAtomic mixing per label pair:\n{('Er', 'Er'): 'full_occupancy', ('Er', 'In2'): 'full_occupancy', ('In1', 'In2'): 'full_occupancy', ('Co', 'Co'): 'full_occupancy', ('Co', 'Er'): 'full_occupancy', ('Er', 'In1'): 'full_occupancy', ('In1', 'In1'): 'full_occupancy', ('Co', 'In2'): 'full_occupancy', ('Co', 'In1'): 'full_occupancy', ('In2', 'In2'): 'full_occupancy'}\n\nAtomic mixing per label pair sorted by Mendeleev:\n{('Er', 'Er'): 'full_occupancy', ('Co', 'Co'): 'full_occupancy', ('Er', 'In2'): 'full_occupancy', ('In1', 'In2'): 'full_occupancy', ('Er', 'In1'): 'full_occupancy', ('In1', 'In1'): 'full_occupancy', ('Co', 'In2'): 'full_occupancy', ('Co', 'In1'): 'full_occupancy', ('Er', 'Co'): 'full_occupancy', ('In2', 'In2'): 'full_occupancy'}\n</pre> In\u00a0[4]: Copied! <pre>from cifkit import Cif, Example\n\ndef print_connected_points(all_labels_connections):\n    \"\"\"\n    Utility function for printing connections per site label\n    \"\"\"\n    for label, connections in all_labels_connections.items():\n        print(f\"\\nAtom site {label}:\")\n        for (\n            connected_label,\n            dist,\n            coords_1,\n            coords_2,\n        ) in connections:\n            print(f\"{connected_label} {dist} {coords_1}, {coords_2}\")\n\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Print CN Connections\nprint(\"\\nFind CN_connections_by_min_dist_method:\")\nprint_connected_points(cif.CN_connections_by_min_dist_method)\n\nprint(\"\\nFind CN_connections_by_best_methods:\")\nprint_connected_points(cif.CN_connections_by_best_methods)\n</pre>  from cifkit import Cif, Example  def print_connected_points(all_labels_connections):     \"\"\"     Utility function for printing connections per site label     \"\"\"     for label, connections in all_labels_connections.items():         print(f\"\\nAtom site {label}:\")         for (             connected_label,             dist,             coords_1,             coords_2,         ) in connections:             print(f\"{connected_label} {dist} {coords_1}, {coords_2}\")   # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Print CN Connections print(\"\\nFind CN_connections_by_min_dist_method:\") print_connected_points(cif.CN_connections_by_min_dist_method)  print(\"\\nFind CN_connections_by_best_methods:\") print_connected_points(cif.CN_connections_by_best_methods) <pre>\nFind CN_connections_by_min_dist_method:\n\nAtom site In2:\nCo 2.691 [0.0, -2.27, -2.254], [0.0, -4.54, -3.698]\nCo 2.691 [0.0, -2.27, -2.254], [0.0, 0.0, -3.698]\nIn2 2.889 [0.0, -2.27, -2.254], [0.0, -2.27, -5.143]\nIn1 3.199 [0.0, -2.27, -2.254], [-2.27, -2.27, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, 0.0, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, -4.54, 0.0]\nIn1 3.199 [0.0, -2.27, -2.254], [2.27, -2.27, 0.0]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, -4.54, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, -4.54, -2.254]\n\nAtom site In1:\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, 2.254]\nEr 3.21 [2.27, 2.27, 0.0], [-0.0, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [0.0, 0.0, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 0.0, 0.0]\n\nAtom site Co:\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, -2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [0.0, -2.27, 2.254]\n\nAtom site Er:\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, 2.254]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, 2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, 2.27, 0.0]\nCo 3.698 [0.0, 0.0, 0.0], [-0.0, -0.0, 3.698]\nCo 3.698 [0.0, 0.0, 0.0], [0.0, 0.0, -3.698]\nEr 4.54 [0.0, 0.0, 0.0], [-0.0, 4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [0.0, -4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [4.54, 0.0, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [-4.54, 0.0, 0.0]\n\nFind CN_connections_by_best_methods:\n\nAtom site In2:\nCo 2.691 [0.0, -2.27, -2.254], [0.0, -4.54, -3.698]\nCo 2.691 [0.0, -2.27, -2.254], [0.0, 0.0, -3.698]\nIn2 2.889 [0.0, -2.27, -2.254], [0.0, -2.27, -5.143]\nIn1 3.199 [0.0, -2.27, -2.254], [-2.27, -2.27, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, 0.0, 0.0]\nEr 3.199 [0.0, -2.27, -2.254], [0.0, -4.54, 0.0]\nIn1 3.199 [0.0, -2.27, -2.254], [2.27, -2.27, 0.0]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, -4.54, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [2.27, 0.0, -2.254]\nIn2 3.21 [0.0, -2.27, -2.254], [-2.27, -4.54, -2.254]\n\nAtom site In1:\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 4.54, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [2.27, 2.27, 0.0], [4.54, 2.27, 2.254]\nEr 3.21 [2.27, 2.27, 0.0], [-0.0, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [0.0, 0.0, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 4.54, 0.0]\nEr 3.21 [2.27, 2.27, 0.0], [4.54, 0.0, 0.0]\n\nAtom site Co:\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, -2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-0.0, 2.27, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [2.27, -0.0, 5.143]\nIn2 2.691 [-0.0, -0.0, 3.698], [-2.27, -0.0, 2.254]\nIn2 2.691 [-0.0, -0.0, 3.698], [0.0, -2.27, 2.254]\nEr 3.698 [-0.0, -0.0, 3.698], [0.0, 0.0, 0.0]\nEr 3.698 [-0.0, -0.0, 3.698], [-0.0, -0.0, 7.397]\nCo 4.54 [-0.0, -0.0, 3.698], [4.54, -0.0, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [-4.54, -0.0, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [-0.0, 4.54, 3.698]\nCo 4.54 [-0.0, -0.0, 3.698], [0.0, -4.54, 3.698]\n\nAtom site Er:\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [2.27, 0.0, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-0.0, 2.27, -2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [-2.27, -0.0, 2.254]\nIn2 3.199 [0.0, 0.0, 0.0], [0.0, -2.27, 2.254]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, 2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [2.27, -2.27, 0.0]\nIn1 3.21 [0.0, 0.0, 0.0], [-2.27, 2.27, 0.0]\nCo 3.698 [0.0, 0.0, 0.0], [-0.0, -0.0, 3.698]\nCo 3.698 [0.0, 0.0, 0.0], [0.0, 0.0, -3.698]\nEr 4.54 [0.0, 0.0, 0.0], [-0.0, 4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [0.0, -4.54, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [4.54, 0.0, 0.0]\nEr 4.54 [0.0, 0.0, 0.0], [-4.54, 0.0, 0.0]\n</pre> In\u00a0[5]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\nprint(\"Shortest distance:\", cif.shortest_distance)\nprint(\"Shortest bond pair distances:\", cif.shortest_bond_pair_distance)\nprint(\"Shortest site pair distances:\", cif.shortest_site_pair_distance)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  print(\"Shortest distance:\", cif.shortest_distance) print(\"Shortest bond pair distances:\", cif.shortest_bond_pair_distance) print(\"Shortest site pair distances:\", cif.shortest_site_pair_distance) <pre>Shortest distance: 2.691\nShortest bond pair distances: {('Co', 'In'): 2.691, ('In', 'In'): 2.889, ('Er', 'In'): 3.199, ('Co', 'Er'): 3.698, ('Co', 'Co'): 4.54, ('Er', 'Er'): 4.54}\nShortest site pair distances: {'In2': ('Co', 2.691), 'In1': ('In2', 3.199), 'Co': ('In2', 2.691), 'Er': ('In2', 3.199)}\n</pre> In\u00a0[6]: Copied! <pre>from cifkit import Cif, Example\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Bond counts\nprint(\"\\nCN_bond_count_by_min_dist_method:\")\nprint(cif.CN_bond_count_by_min_dist_method)\n\nprint(\"\\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\")\nprint(cif.CN_bond_count_by_min_dist_method_sorted_by_mendeleev)\n\nprint(\"\\nCN_bond_count_by_best_methods:\")\nprint(cif.CN_bond_count_by_best_methods)\n\nprint(\"\\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\")\nprint(cif.CN_bond_count_by_best_methods_sorted_by_mendeleev)\n\n# Bond fractions\nprint(\"\\nCN_bond_fractions_by_min_dist_method:\")\nprint(cif.CN_bond_fractions_by_min_dist_method)\n\nprint(\"\\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\")\nprint(cif.CN_bond_fractions_by_min_dist_method_sorted_by_mendeleev)\n\nprint(\"\\nCN_bond_fractions_by_best_methods:\")\nprint(cif.CN_bond_fractions_by_best_methods)\n\nprint(\"\\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\")\nprint(cif.CN_bond_fractions_by_best_methods_sorted_by_mendeleev)\n\n# Unique coordination numbers\nprint(\"\\nCN_unique_values_by_min_dist_method\")\nprint(cif.CN_unique_values_by_min_dist_method)\n\nprint(\"\\nCN_unique_values_by_best_methods\")\nprint(cif.CN_unique_values_by_best_methods)\n\n# Average coordination number\nprint(\"\\nCN_avg_by_min_dist_method:\")\nprint(cif.CN_avg_by_min_dist_method)\n\nprint(\"\\nCN_avg_by_best_methods: \")\nprint(cif.CN_avg_by_best_methods)\n\n# Min coordination number\nprint(\"\\nCN_max_by_min_dist_method:\")\nprint(cif.CN_max_by_min_dist_method)\n\nprint(\"\\nCN_max_by_best_methods:\")\nprint(cif.CN_max_by_best_methods)\n\n# Max coordination number\nprint(\"\\nCN_min_by_min_dist_method:\")\nprint(cif.CN_min_by_min_dist_method)\n\nprint(\"\\nCN_min_by_best_methods:\")\nprint(cif.CN_min_by_best_methods)\n</pre> from cifkit import Cif, Example  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Bond counts print(\"\\nCN_bond_count_by_min_dist_method:\") print(cif.CN_bond_count_by_min_dist_method)  print(\"\\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\") print(cif.CN_bond_count_by_min_dist_method_sorted_by_mendeleev)  print(\"\\nCN_bond_count_by_best_methods:\") print(cif.CN_bond_count_by_best_methods)  print(\"\\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\") print(cif.CN_bond_count_by_best_methods_sorted_by_mendeleev)  # Bond fractions print(\"\\nCN_bond_fractions_by_min_dist_method:\") print(cif.CN_bond_fractions_by_min_dist_method)  print(\"\\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\") print(cif.CN_bond_fractions_by_min_dist_method_sorted_by_mendeleev)  print(\"\\nCN_bond_fractions_by_best_methods:\") print(cif.CN_bond_fractions_by_best_methods)  print(\"\\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\") print(cif.CN_bond_fractions_by_best_methods_sorted_by_mendeleev)  # Unique coordination numbers print(\"\\nCN_unique_values_by_min_dist_method\") print(cif.CN_unique_values_by_min_dist_method)  print(\"\\nCN_unique_values_by_best_methods\") print(cif.CN_unique_values_by_best_methods)  # Average coordination number print(\"\\nCN_avg_by_min_dist_method:\") print(cif.CN_avg_by_min_dist_method)  print(\"\\nCN_avg_by_best_methods: \") print(cif.CN_avg_by_best_methods)  # Min coordination number print(\"\\nCN_max_by_min_dist_method:\") print(cif.CN_max_by_min_dist_method)  print(\"\\nCN_max_by_best_methods:\") print(cif.CN_max_by_best_methods)  # Max coordination number print(\"\\nCN_min_by_min_dist_method:\") print(cif.CN_min_by_min_dist_method)  print(\"\\nCN_min_by_best_methods:\") print(cif.CN_min_by_best_methods) <pre>\nCN_bond_count_by_min_dist_method:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8}, 'Er': {('Er', 'In'): 12, ('Co', 'Er'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_min_dist_method_sorted_by_mendeleev:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8}, 'Er': {('Er', 'In'): 12, ('Er', 'Co'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_best_methods:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8, ('Co', 'Er'): 2, ('Co', 'Co'): 4}, 'Er': {('Er', 'In'): 12, ('Co', 'Er'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_count_by_best_methods_sorted_by_mendeleev:\n{'In2': {('Co', 'In'): 2, ('In', 'In'): 7, ('Er', 'In'): 2}, 'In1': {('In', 'In'): 8, ('Er', 'In'): 4}, 'Co': {('Co', 'In'): 8, ('Er', 'Co'): 2, ('Co', 'Co'): 4}, 'Er': {('Er', 'In'): 12, ('Er', 'Co'): 2, ('Er', 'Er'): 4}}\n\nCN_bond_fractions_by_min_dist_method:\n{('Co', 'In'): 0.204, ('In', 'In'): 0.306, ('Er', 'In'): 0.367, ('Co', 'Er'): 0.041, ('Er', 'Er'): 0.082}\n\nCN_bond_fractions_by_min_dist_method_sorted_by_mendeleev:\n{('Co', 'In'): 0.204, ('In', 'In'): 0.306, ('Er', 'In'): 0.367, ('Er', 'Co'): 0.041, ('Er', 'Er'): 0.082}\n\nCN_bond_fractions_by_best_methods:\n{('Co', 'In'): 0.182, ('In', 'In'): 0.273, ('Er', 'In'): 0.327, ('Co', 'Er'): 0.073, ('Co', 'Co'): 0.073, ('Er', 'Er'): 0.073}\n\nCN_bond_fractions_by_best_methods_sorted_by_mendeleev:\n{('Co', 'In'): 0.182, ('In', 'In'): 0.273, ('Er', 'In'): 0.327, ('Er', 'Co'): 0.073, ('Co', 'Co'): 0.073, ('Er', 'Er'): 0.073}\n\nCN_unique_values_by_min_dist_method\n{8, 18, 11, 12}\n\nCN_unique_values_by_best_methods\n{18, 11, 12, 14}\n\nCN_avg_by_min_dist_method:\n12.25\n\nCN_avg_by_best_methods: \n13.75\n\nCN_max_by_min_dist_method:\n18\n\nCN_max_by_best_methods:\n18\n\nCN_min_by_min_dist_method:\n8\n\nCN_min_by_best_methods:\n11\n</pre> In\u00a0[7]: Copied! <pre>from cifkit import Cif, Example\nimport warnings\nwarnings.filterwarnings('ignore') # For Jupyter Notebook only\n\n# Initialize\ncif = Cif(Example.ErCoIn5_file_path)\n\n# Enter site labels. you can get site labels using cif.labels\nprint(\"Site labels:\", cif.site_labels)\n\n# Plot\ncif.plot_polyhedron(\"In1\", is_displayed=True)\n</pre> from cifkit import Cif, Example import warnings warnings.filterwarnings('ignore') # For Jupyter Notebook only  # Initialize cif = Cif(Example.ErCoIn5_file_path)  # Enter site labels. you can get site labels using cif.labels print(\"Site labels:\", cif.site_labels)  # Plot cif.plot_polyhedron(\"In1\", is_displayed=True) <pre>Site labels: ['In2', 'In1', 'Co', 'Er']\n</pre>"},{"location":"notebooks/01_cif/#cif","title":"CIF\u00b6","text":"<p>The <code>Cif</code> class generates an object for each <code>.cif</code> file. Each object can</p> <ul> <li>compute the coordination numbers for each site label using four methods</li> <li>compute bond fractions and bond counts at each site within the specified cutoff radius or based on -coordination number geometry</li> <li>categorize atomic mixing at bond-pair and file levels</li> <li>list all possible bond and label pairs derived from the formula</li> <li>generate a unit cell and a supercell by applying \u00b11 shifts</li> <li>parse formulas, structures, tags, space group names, supercell sizes, and elements</li> </ul>"},{"location":"notebooks/01_cif/#get-instant-properties-parsed-information","title":"Get instant properties - parsed information\u00b6","text":"<p>The <code>Cif</code> class provides a set of accessible properties that can be accessed. Each object is intialized with the <code>file_path</code> to the <code>.cif</code> file.</p>"},{"location":"notebooks/01_cif/#how-tag-is-parsed","title":"How tag is parsed\u00b6","text":"<p>Tag is parsed from the thrid line of each <code>.cif</code> file. Some databases such as Pearson's Crystal Data offers tags for each file.</p>"},{"location":"notebooks/01_cif/#get-instant-properties-bond-pairs","title":"Get instant properties - bond pairs\u00b6","text":"<ul> <li>The following code returns all possible element and site pairs from the formula in the .cif file.</li> <li>The <code>mixing_info_per_label_pair</code> and <code>mixing_info_per_label_pair_sorted_by_mendeleev</code> return site mixing information at the pair level.</li> </ul>"},{"location":"notebooks/01_cif/#how-atomic-mixing-type-is-defined","title":"How atomic mixing type is defined\u00b6","text":"<p>Each bonding pair or each file is defined with one of four atomic mixing categories:</p> <ul> <li>Full occupancy is assigned when a single atomic site occupies the fractional coordinate with an occupancy value of 1.</li> <li>Full occupancy with atomic mixing is assigned when multiple atomic sites collectively occupy the fractional coordinate to a sum of 1.</li> <li>Deficiency without atomic mixing is assigned when a single atomic site occupying the fractional coordinate with a sum less than 1.</li> <li>Deficiency with atomic mixing is assigned when multiple atomic sites occupy the fractional coordinate with a sum less than 1.</li> </ul>"},{"location":"notebooks/01_cif/#get-computed-properties-nearest-connections-per-site","title":"Get computed properties - nearest connections per site\u00b6","text":"<p>This section involves computing distances between atoms. Unlike instant properties, these properties may require extensive computation, typically ranging from 1-2 seconds for larger supercells containing more than 3,000 atoms.</p> <p>These properties are loaded lazily, meaning accessing any of the properties will execute <code>compute_connections()</code> internally. This function will then compute <code>connections</code>, providing all the nearest neighbors for each site.</p> <p>There are options in the <code>Cif</code> class to use either the <code>by_d_min_method</code> or <code>by_best_methods</code>. Please refer to the <code>README.md</code> for complete documentation.</p>"},{"location":"notebooks/01_cif/#get-computed-properties-distances","title":"Get computed properties - distances\u00b6","text":"<p>You can get the shortest distance from each site label or the shortest distance for each possible bond pair.</p>"},{"location":"notebooks/01_cif/#get-computed-properties-coordination-numbers","title":"Get computed properties - coordination numbers\u00b6","text":"<p>Compute <code>avg</code>, <code>min</code>, <code>max</code>, <code>unique</code> of coordination numbers determined by one of the best methods or min distance method.</p>"},{"location":"notebooks/01_cif/#draw-polyhedrons","title":"Draw polyhedrons\u00b6","text":"<p>You may use <code>Jupyter</code> notebook or a python script to execute the following to generate and save a polyhedron generated from each site and the nearest neighbor atoms are determined from the coordination number geometry.</p>"},{"location":"notebooks/02_cif_ensemble/","title":"CifEnsemble","text":"In\u00a0[2]: Copied! <pre>from cifkit import CifEnsemble, Example\n\n# Initialize\nensemble = CifEnsemble(Example.ErCoIn_folder_path)\n</pre> from cifkit import CifEnsemble, Example  # Initialize ensemble = CifEnsemble(Example.ErCoIn_folder_path) <pre>\nCIF Preprocessing in Example.ErCoIn_folder_path begun...\n\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif (1/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif (2/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif (3/3)\n\nSUMMARY\n# of files moved to 'error_operations' folder: 0\n# of files moved to 'error_duplicate_labels' folder: 0\n# of files moved to 'error_wrong_loop_value' folder: 0\n# of files moved to 'error_coords' folder: 0\n# of files moved to 'error_invalid_label' folder: 0\n# of files moved to 'error_others' folder: 0\n\n</pre> In\u00a0[3]: Copied! <pre># Initialize with nested .cif files in the folder\nensemble_nested = CifEnsemble(Example.ErCoIn_folder_path, add_nested_files=True)\n</pre>  # Initialize with nested .cif files in the folder ensemble_nested = CifEnsemble(Example.ErCoIn_folder_path, add_nested_files=True) <pre>\nCIF Preprocessing in Example.ErCoIn_folder_path begun...\n\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif (1/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif (2/3)\nPreprocessing /Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif (3/3)\n\nSUMMARY\n# of files moved to 'error_operations' folder: 0\n# of files moved to 'error_duplicate_labels' folder: 0\n# of files moved to 'error_wrong_loop_value' folder: 0\n# of files moved to 'error_coords' folder: 0\n# of files moved to 'error_invalid_label' folder: 0\n# of files moved to 'error_others' folder: 0\n\n</pre> In\u00a0[4]: Copied! <pre># Get .cif file count in the folder\nprint(\"File count:\", ensemble.file_count) # 6\n\n# Get the directory path\nprint(\"Directory path:\", ensemble.dir_path)\n\n# Get all file paths in the folder\nprint(\"File paths:\", ensemble.file_paths)\n\n# Get all Cif objects initialized\nprint(\"Cif objects:\", ensemble.cifs)\n</pre> # Get .cif file count in the folder print(\"File count:\", ensemble.file_count) # 6  # Get the directory path print(\"Directory path:\", ensemble.dir_path)  # Get all file paths in the folder print(\"File paths:\", ensemble.file_paths)  # Get all Cif objects initialized print(\"Cif objects:\", ensemble.cifs) <pre>File count: 3\nDirectory path: Example.ErCoIn_folder_path\nFile paths: ['/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif']\nCif objects: [&lt;cifkit.models.cif.Cif object at 0x1554895e0&gt;, &lt;cifkit.models.cif.Cif object at 0x155320980&gt;, &lt;cifkit.models.cif.Cif object at 0x1569ef7a0&gt;]\n</pre> In\u00a0[5]: Copied! <pre># Print each property for each .cif file\nfor cif in ensemble.cifs:\n  print(f\"\\n{cif.file_name}\")\n  print(\"Formula:\", cif.formula)\n  print(\"Tag:\", cif.tag)\n  print(\"Mixing type:\", cif.site_mixing_type)\n  print(\"Unique bond pairs:\", cif.bond_pairs)\n</pre> # Print each property for each .cif file for cif in ensemble.cifs:   print(f\"\\n{cif.file_name}\")   print(\"Formula:\", cif.formula)   print(\"Tag:\", cif.tag)   print(\"Mixing type:\", cif.site_mixing_type)   print(\"Unique bond pairs:\", cif.bond_pairs) <pre>\nEr10Co9In20.cif\nFormula: Er10Co9In20\nTag: \nMixing type: full_occupancy\nUnique bond pairs: {('Co', 'In'), ('Er', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'Er'), ('Co', 'Co')}\n\nEr5In3.cif\nFormula: Er5In3\nTag: \nMixing type: full_occupancy\nUnique bond pairs: {('Er', 'In'), ('In', 'In'), ('Er', 'Er')}\n\nErCoIn5.cif\nFormula: ErCoIn5\nTag: rt\nMixing type: full_occupancy\nUnique bond pairs: {('Co', 'In'), ('Er', 'In'), ('In', 'In'), ('Co', 'Er'), ('Er', 'Er'), ('Co', 'Co')}\n</pre> In\u00a0[6]: Copied! <pre># Get unique formulas\nprint(\"Unique formulas:\", ensemble.unique_formulas)\n\n# Get unique elements\nprint(\"Unique elements:\", ensemble.unique_elements)\n\n# Get unique structures\nprint(\"Unique structures:\", ensemble.unique_structures)\n\n# Get unique atomix mixing types\nprint(\"Unique atomic mixing types:\", ensemble.unique_site_mixing_types)\n\n# Get unique elements\nprint(\"Unique elements including nested:\", ensemble_nested.unique_elements)\n\n# Get unique space group names\nprint(\"Unique space group names:\", ensemble.unique_space_group_names)\n\n# Get unique space group numbers\nprint(\"Unique space group numbers:\",ensemble.unique_space_group_numbers)\n\n# Get unique tags\nprint(\"Unique tags:\", ensemble.unique_tags)\n\n# Get unique composition types\nprint(\"Unique composition types:\", ensemble.unique_composition_types)\n</pre> # Get unique formulas print(\"Unique formulas:\", ensemble.unique_formulas)  # Get unique elements print(\"Unique elements:\", ensemble.unique_elements)  # Get unique structures print(\"Unique structures:\", ensemble.unique_structures)  # Get unique atomix mixing types print(\"Unique atomic mixing types:\", ensemble.unique_site_mixing_types)  # Get unique elements print(\"Unique elements including nested:\", ensemble_nested.unique_elements)  # Get unique space group names print(\"Unique space group names:\", ensemble.unique_space_group_names)  # Get unique space group numbers print(\"Unique space group numbers:\",ensemble.unique_space_group_numbers)  # Get unique tags print(\"Unique tags:\", ensemble.unique_tags)  # Get unique composition types print(\"Unique composition types:\", ensemble.unique_composition_types) <pre>Unique formulas: {'Er5In3', 'ErCoIn5', 'Er10Co9In20'}\nUnique elements: {'In', 'Er', 'Co'}\nUnique structures: {'Ho10Ni9In20', 'HoCoGa5', 'Mn5Si3'}\nUnique atomic mixing types: {'full_occupancy'}\nUnique elements including nested: {'In', 'Er', 'Co'}\nUnique space group names: {'P4/nmm(originchoice2)', 'P63/mcm', 'P4/mmm'}\nUnique space group numbers: {129, 123, 193}\nUnique tags: {'', 'rt'}\nUnique composition types: {2, 3}\n</pre> In\u00a0[7]: Copied! <pre># Get file count per structure\nprint(\"Structure stats:\", ensemble.structure_stats)\n\n# Get file count per formula\nprint(\"Formula stats:\", ensemble.formula_stats)\n\n# Get file count per tag\nprint(\"Tag stats:\", ensemble.tag_stats)\n\n# Get file count per space group number\nprint(\"Space group number stats:\", ensemble.space_group_number_stats)\n\n# Get file count per space group name\nprint(\"Space group name stats:\", ensemble.space_group_name_stats)\n\n# Get file count per composition type\nprint(\"Composition type stats:\", ensemble.composition_type_stats)\n\n# Get file count per Element\nprint(\"Unique elements stats:\", ensemble.unique_elements_stats)\n\n# Get file count per site mixing type\nprint(\"Site mixing type stats:\", ensemble.site_mixing_type_stats)\n\n# Get file count per supercell atom count\nprint(\"Supercell size stats:\", ensemble.supercell_size_stats)\n\n# Get file count per min distance\nprint(\"Min distance stats:\", ensemble.min_distance_stats)\n\n# Get file count per CN value by min dist method\nprint(\"CN value using min dist method stats:\", ensemble.unique_CN_values_by_min_dist_method_stat)\n\n# Get file count per CN value by best methods\nprint(\"CN value using best methods stats:\", ensemble.unique_CN_values_by_method_methods_stat)\n</pre> # Get file count per structure print(\"Structure stats:\", ensemble.structure_stats)  # Get file count per formula print(\"Formula stats:\", ensemble.formula_stats)  # Get file count per tag print(\"Tag stats:\", ensemble.tag_stats)  # Get file count per space group number print(\"Space group number stats:\", ensemble.space_group_number_stats)  # Get file count per space group name print(\"Space group name stats:\", ensemble.space_group_name_stats)  # Get file count per composition type print(\"Composition type stats:\", ensemble.composition_type_stats)  # Get file count per Element print(\"Unique elements stats:\", ensemble.unique_elements_stats)  # Get file count per site mixing type print(\"Site mixing type stats:\", ensemble.site_mixing_type_stats)  # Get file count per supercell atom count print(\"Supercell size stats:\", ensemble.supercell_size_stats)  # Get file count per min distance print(\"Min distance stats:\", ensemble.min_distance_stats)  # Get file count per CN value by min dist method print(\"CN value using min dist method stats:\", ensemble.unique_CN_values_by_min_dist_method_stat)  # Get file count per CN value by best methods print(\"CN value using best methods stats:\", ensemble.unique_CN_values_by_method_methods_stat) <pre>Structure stats: {'Ho10Ni9In20': 1, 'Mn5Si3': 1, 'HoCoGa5': 1}\nFormula stats: {'Er10Co9In20': 1, 'Er5In3': 1, 'ErCoIn5': 1}\nTag stats: {'': 2, 'rt': 1}\nSpace group number stats: {129: 1, 193: 1, 123: 1}\nSpace group name stats: {'P4/nmm(originchoice2)': 1, 'P63/mcm': 1, 'P4/mmm': 1}\nComposition type stats: {3: 2, 2: 1}\nUnique elements stats: {'Co': 2, 'In': 3, 'Er': 3}\nSite mixing type stats: {'full_occupancy': 3}\nSupercell size stats: {2654: 1, 558: 1, 255: 1}\nMin distance stats: {2.626: 1, 3.102: 1, 2.691: 1}\nCN value using min dist method stats: {10: 1, 12: 2, 13: 1, 14: 2, 16: 1, 17: 1, 11: 2, 15: 1, 8: 1, 18: 1}\nCN value using best methods stats: {10: 1, 12: 2, 13: 1, 14: 3, 16: 1, 17: 1, 11: 2, 15: 1, 18: 1}\n</pre> In\u00a0[8]: Copied! <pre># Return file paths by formulas\nensemble.filter_by_formulas([\"ErCoIn\", \"Er10Co9In20\"]) \n\n# Return file paths by structures\nensemble.filter_by_structures([\"Mn5Si3\"])\n\n# Return file paths by space group names\nensemble.filter_by_space_group_names([\"P4/mmm\"])\n\n# Return file paths by space group numbers\nensemble.filter_by_space_group_numbers([123])\n\n# Return file paths by site mixing types\nensemble.filter_by_site_mixing_types([\"full_occupancy\"])\nensemble.filter_by_site_mixing_types([\"full_occupancy\", \"deficiency_without_atomic_mixing\"])\n\n# Return file paths by composition types (1-&gt; unary, 2-&gt; binary)\nensemble.filter_by_composition_types([3])\n</pre> # Return file paths by formulas ensemble.filter_by_formulas([\"ErCoIn\", \"Er10Co9In20\"])   # Return file paths by structures ensemble.filter_by_structures([\"Mn5Si3\"])  # Return file paths by space group names ensemble.filter_by_space_group_names([\"P4/mmm\"])  # Return file paths by space group numbers ensemble.filter_by_space_group_numbers([123])  # Return file paths by site mixing types ensemble.filter_by_site_mixing_types([\"full_occupancy\"]) ensemble.filter_by_site_mixing_types([\"full_occupancy\", \"deficiency_without_atomic_mixing\"])  # Return file paths by composition types (1-&gt; unary, 2-&gt; binary) ensemble.filter_by_composition_types([3])   Out[8]: <pre>{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif',\n '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif'}</pre> In\u00a0[9]: Copied! <pre>print(\"\\nFile paths containing Er or Co or In:\")\nprint(ensemble.filter_by_elements_containing([\"Er\", \"Co\", \"In\"])) # \n\nprint(\"\\nFile paths containing Er and In:\")\nprint(ensemble.filter_by_elements_exact_matching([\"Er\", \"In\"]))\n\nprint(\"\\nFile paths containing CN value of 15:\")\nprint(ensemble.filter_by_CN_min_dist_method_containing([15]))\nprint(ensemble.filter_by_CN_best_methods_containing([15]))\n\nprint(\"\\nFile paths containing CN value of 11, 14, and 15:\")\nprint(ensemble.filter_by_CN_min_dist_method_exact_matching([11, 14, 15]))\nprint(ensemble.filter_by_CN_best_methods_exact_matching([11, 14, 15]))\n</pre>  print(\"\\nFile paths containing Er or Co or In:\") print(ensemble.filter_by_elements_containing([\"Er\", \"Co\", \"In\"])) #   print(\"\\nFile paths containing Er and In:\") print(ensemble.filter_by_elements_exact_matching([\"Er\", \"In\"]))  print(\"\\nFile paths containing CN value of 15:\") print(ensemble.filter_by_CN_min_dist_method_containing([15])) print(ensemble.filter_by_CN_best_methods_containing([15]))  print(\"\\nFile paths containing CN value of 11, 14, and 15:\") print(ensemble.filter_by_CN_min_dist_method_exact_matching([11, 14, 15])) print(ensemble.filter_by_CN_best_methods_exact_matching([11, 14, 15])) <pre>\nFile paths containing Er or Co or In:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n\nFile paths containing Er and In:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n\nFile paths containing CN value of 15:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n\nFile paths containing CN value of 11, 14, and 15:\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n{'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n</pre> In\u00a0[10]: Copied! <pre># Return a set of .cif file paths with min distance between 1.0 \u00c5 and 3.0 \u00c5\nprint(\"File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\\n\", ensemble.filter_by_min_distance(1.0, 3.0))\n\n# Return a set of .cif file paths with supercell atom count above 500 and below 3000.\nprint(\"File paths with supercell atom count above 500 and below 3000:\\n\",ensemble.filter_by_supercell_count(300, 3000))\n</pre> # Return a set of .cif file paths with min distance between 1.0 \u00c5 and 3.0 \u00c5 print(\"File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\\n\", ensemble.filter_by_min_distance(1.0, 3.0))  # Return a set of .cif file paths with supercell atom count above 500 and below 3000. print(\"File paths with supercell atom count above 500 and below 3000:\\n\",ensemble.filter_by_supercell_count(300, 3000)) <pre>File paths with min distance between 1.0 \u00c5 and 3.0 \u00c5:\n {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/ErCoIn5.cif'}\nFile paths with supercell atom count above 500 and below 3000:\n {'/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er10Co9In20.cif', '/Users/imac/Downloads/cifkit/src/cifkit/data/ErCoIn/Er5In3.cif'}\n</pre>"},{"location":"notebooks/02_cif_ensemble/#cifensemble","title":"CifEnsemble\u00b6","text":"<p>For high-throuhgput analysis, you can initialize multiple <code>.cif</code> files using <code>CifEnsemble</code>.</p>"},{"location":"notebooks/02_cif_ensemble/#initialize-with-folder-path-and-preprocess-automatically","title":"Initialize with folder path and preprocess automatically\u00b6","text":"<ul> <li><p><code>CifEnsemble</code> standardizes the site labels in <code>atom_site_label</code>. Some site labels may contain a comma or a symbol such as M due to atomic mixing. CBA reformats each <code>atom_site_label</code> so it can be parsed into an element type that matches atom_site_type_symbol.</p> </li> <li><p><code>CifEnsemble</code> removes the content of <code>publ_author_address</code>. This section often has an incorrect format that otherwise requires manual modifications.</p> </li> <li><p><code>CifEnsemble</code> relocates any ill-formatted files, such as those with duplicate labels in <code>atom_site_label</code>, missing fractional coordinates, or files that require supercell generation.</p> </li> </ul>"},{"location":"notebooks/02_cif_ensemble/#initialize-with-nested-files","title":"Initialize with nested files\u00b6","text":"<p>You can also use the <code>add_nested_files</code> flag to include <code>.cif</code> files that are located in folders within the folder path provided.</p>"},{"location":"notebooks/02_cif_ensemble/#get-instant-properties","title":"Get instant properties\u00b6","text":"<p>Once the object is created, you can get instant properties suhc as file count, folder path, etc.</p>"},{"location":"notebooks/02_cif_ensemble/#get-individual-cif-properties","title":"Get individual .cif properties\u00b6","text":"<p>The <code>CifEnsemble</code> object contains a property called <code>cifs</code> which contains a list of <code>Cif</code> objects. You may loop through each to access both instant and computed properties described in the previous <code>CIF</code> section.</p>"},{"location":"notebooks/02_cif_ensemble/#get-unique-properties","title":"Get unique properties\u00b6","text":"<p>You can get all unique attributres such as formulas, elements, etc in the folder.</p>"},{"location":"notebooks/02_cif_ensemble/#get-overall-stats-by-attribute","title":"Get overall stats by attribute\u00b6","text":"<p>Get the number of files for each unique properties.</p>"},{"location":"notebooks/02_cif_ensemble/#filter-cif-containing-specific-attributes","title":"Filter .cif containing specific attributes\u00b6","text":""},{"location":"notebooks/02_cif_ensemble/#filter-cif-by-specific-attributes","title":"Filter .cif by specific attributes\u00b6","text":"<p>Filter .cif files either containing a set of items or files that exactly contain the values passed. <code>cifkit</code> supports elements and coordination numbers.</p>"},{"location":"notebooks/02_cif_ensemble/#filter-by-range","title":"Filter by range\u00b6","text":""},{"location":"notebooks/02_cif_ensemble/#move-and-copy-files","title":"Move and copy files\u00b6","text":"<p>Assume you have a set of file paths filered using the functions described in the previous section. Since we are using Jupyter and with predefined examples, you need to provide <code>file_paths</code> and <code>dest_dir_path</code> for your system.</p> <pre>file_paths = {\n    \"tests/data/cif/ensemble_test/300169.cif\",\n    \"tests/data/cif/ensemble_test/300171.cif\",\n    \"tests/data/cif/ensemble_test/300170.cif\",\n}\n\n# To move files\nensemble.move_cif_files(file_paths, dest_dir_path)\n\n# To copy files\nensemble.copy_cif_files(file_paths, dest_dir_path)\n</pre>"}]}
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