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CederGroupHub · Feb 8, 2024 · 025a46a · 025a46a
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Showing 5 changed files with 76 additions and 78 deletions.
diff --git a/chgnet/utils/common_utils.py b/chgnet/utils/common_utils.py
@@ -73,7 +73,7 @@ def read_json(filepath: str) -> dict:
         filepath (str): file name of json to read.
 
     Returns:
-        dictionary stored in fjson
+        dict: data stored in filepath
     """
     with open(filepath) as file:
         return json.load(file)

diff --git a/examples/basics.ipynb b/examples/basics.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "f8c75a16",
+   "id": "0",
    "metadata": {},
    "source": [
     "# This notebook shows example to load the CHGNet for prediction\n"
@@ -11,7 +11,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "87432e22",
+   "id": "1",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7ead933c",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "16eeae1e",
+   "id": "3",
    "metadata": {},
    "source": [
     "### Read structure from a json or cif file\n"
@@ -51,7 +51,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "208fa4aa",
+   "id": "4",
    "metadata": {},
    "outputs": [
     {
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "abcc09b4",
+   "id": "5",
    "metadata": {},
    "source": [
     "### Define Model\n"
@@ -103,7 +103,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c04a0993",
+   "id": "6",
    "metadata": {},
    "outputs": [
     {
@@ -123,7 +123,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "961d51fc",
+   "id": "7",
    "metadata": {},
    "source": [
     "# Predict energy, force, stress, magmom\n"
@@ -132,7 +132,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2c7c1997",
+   "id": "8",
    "metadata": {
     "pycharm": {
      "name": "#%%\n"
@@ -181,7 +181,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2258f2f5",
+   "id": "9",
    "metadata": {},
    "source": [
     "# Structure Optimization\n"
@@ -190,7 +190,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "27dac383",
+   "id": "10",
    "metadata": {},
    "outputs": [
     {
@@ -211,7 +211,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "04bc3159",
+   "id": "11",
    "metadata": {},
    "outputs": [
     {
@@ -270,7 +270,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "06f7e84c",
+   "id": "12",
    "metadata": {},
    "source": [
     "# Molecular Dynamics\n"
@@ -279,7 +279,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "1a59a5b5",
+   "id": "13",
    "metadata": {},
    "outputs": [
     {
@@ -316,7 +316,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c6a10ec8",
+   "id": "14",
    "metadata": {},
    "source": [
     "# Magmom Visualization\n"
@@ -325,7 +325,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2d5c2f93",
+   "id": "15",
    "metadata": {},
    "outputs": [
     {
@@ -344,7 +344,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "db4c9f16",
+   "id": "16",
    "metadata": {},
    "outputs": [
     {
@@ -368,7 +368,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "a0fe8e50",
+   "id": "17",
    "metadata": {},
    "outputs": [
     {
@@ -784,7 +784,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c96fb111",
+   "id": "18",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -797,7 +797,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "71ac47b1",
+   "id": "19",
    "metadata": {},
    "outputs": [
     {
@@ -1862,7 +1862,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

diff --git a/examples/crystaltoolkit_relax_viewer.ipynb b/examples/crystaltoolkit_relax_viewer.ipynb
@@ -3,7 +3,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "f8c75a16",
+   "id": "0",
    "metadata": {},
    "source": [
     "# Crystaltoolkit Relaxation Viewer\n",
@@ -14,7 +14,7 @@
   {
    "attachments": {},
    "cell_type": "markdown",
-   "id": "a51da8f4",
+   "id": "1",
    "metadata": {},
    "source": [
     "Running the last cell in this notebook should spin up a `dash` app that looks like this:\n",
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "156e8031",
+   "id": "2",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -42,7 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7ead933c",
+   "id": "3",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -53,7 +53,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e6792912",
+   "id": "4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -72,7 +72,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "208fa4aa",
+   "id": "5",
    "metadata": {},
    "outputs": [
     {
@@ -100,7 +100,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d6e9fcc",
+   "id": "6",
    "metadata": {},
    "outputs": [
     {
@@ -218,7 +218,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c04ebd43",
+   "id": "7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -235,7 +235,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e7a91576",
+   "id": "8",
    "metadata": {},
    "outputs": [
     {
@@ -256,7 +256,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "c9f16422",
+   "id": "9",
    "metadata": {},
    "outputs": [
     {