1. Fixed README.md 2. Modified Example

CederGroupHub · Apr 7, 2023 · 2d262e0 · 2d262e0
1 parent 1aea1fc
commit 2d262e0
Show file tree

Hide file tree

Showing 2 changed files with 45 additions and 34 deletions.
diff --git a/README.md b/README.md
@@ -47,7 +47,8 @@ pip install -e ./chgnet
 
 ### Direct Inference (Static Calculation)
 
-Pretrained `CHGNet` can predict the energy (eV/atom), force (eV/$\dot{\text A}$), stress (GPa) and magmom ($\mu_B$) of a given structure.
+Pretrained `CHGNet` can predict the energy (eV/atom), force (eV/$\AA$), stress (GPa) and
+magmom ($\mu_B$) of a given structure.
 
 ```python
 from chgnet.model.model import CHGNet

diff --git a/examples/CHGNet_examples.ipynb b/examples/CHGNet_examples.ipynb
@@ -1,7 +1,6 @@
 {
  "cells": [
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "f8c75a16",
    "metadata": {},
@@ -36,7 +35,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "16eeae1e",
    "metadata": {},
@@ -89,7 +87,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "abcc09b4",
    "metadata": {},
@@ -114,12 +111,11 @@
    "source": [
     "chgnet = CHGNet.load()\n",
     "\n",
-    "# Or you can read your own model\n",
-    "# model = CHGNet.from_file(model_path)"
+    "# Alternatively you can read your own model\n",
+    "# chgnet = CHGNet.from_file(model_path)"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "961d51fc",
    "metadata": {},
@@ -143,18 +139,18 @@
      "text": [
       "CHGNet-predicted energy=-7.371591567993164\n",
       "\n",
-      "CHGNet-predicted forces=[[ 4.4703484e-08 -2.7939677e-08  2.4071123e-02]\n",
-      " [ 1.4901161e-08 -2.9918738e-08 -2.4071217e-02]\n",
-      " [-1.1920929e-07  1.0244548e-08  2.5402993e-02]\n",
-      " [-0.0000000e+00 -2.3283064e-08 -2.5402665e-02]\n",
-      " [-1.7881393e-07  6.6356733e-08 -2.1660209e-02]\n",
-      " [ 2.4139881e-06 -7.9928432e-06  9.5508099e-03]\n",
-      " [-2.2053719e-06  7.9749152e-06 -9.5512867e-03]\n",
-      " [-5.9604645e-08 -0.0000000e+00  2.1660507e-02]]\n",
+      "CHGNet-predicted forces=[[ 4.4703484e-08 -4.2840838e-08  2.4071064e-02]\n",
+      " [-4.4703484e-08 -1.4551915e-08 -2.4071217e-02]\n",
+      " [-1.7881393e-07  1.0244548e-08  2.5402933e-02]\n",
+      " [ 5.9604645e-08 -2.3283064e-08 -2.5402665e-02]\n",
+      " [-1.1920929e-07  6.6356733e-08 -2.1660209e-02]\n",
+      " [ 2.3543835e-06 -8.0077443e-06  9.5508099e-03]\n",
+      " [-2.2947788e-06  7.9898164e-06 -9.5513463e-03]\n",
+      " [-5.9604645e-08 -0.0000000e+00  2.1660626e-02]]\n",
       "\n",
-      "CHGNet-predicted stress=[[ 3.3677614e-01 -1.9665707e-07 -5.6416429e-06]\n",
-      " [ 4.9939729e-07  2.4675032e-01  1.8549043e-05]\n",
-      " [-4.0414070e-06  1.9096897e-05  4.0323928e-02]]\n",
+      "CHGNet-predicted stress=[[ 3.3677638e-01 -3.7330341e-07 -5.1117036e-06]\n",
+      " [ 1.0701370e-06  2.4674933e-01  1.8477700e-05]\n",
+      " [-4.4460303e-06  1.9265182e-05  4.0324528e-02]]\n",
       "\n",
       "CHGNet-predicted magmom=[0.00521556 0.0052153  3.8572898  3.8572903  0.02538028 0.03706942\n",
       " 0.03706949 0.02538028]\n",
@@ -164,12 +160,13 @@
    ],
    "source": [
     "prediction = chgnet.predict_structure(structure)\n",
-    "for key in (\"energy\", \"forces\", \"stress\", \"magmom\"):\n",
+    "for key, _unit in zip(\n",
+    "    (\"energy\", \"forces\", \"stress\", \"magmom\"), (\"eV/atom\", \"eV/A\", \"GPa\", \"mu_B\")\n",
+    "):\n",
     "    print(f\"CHGNet-predicted {key}={prediction[key[0]]}\\n\")"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "2258f2f5",
    "metadata": {},
@@ -205,24 +202,38 @@
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "4"
-      ]
-     },
-     "execution_count": null,
-     "metadata": {},
-     "output_type": "execute_result"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n",
+      "CHGNet took 29 steps. Relaxed structure:\n",
+      "Full Formula (Li2 Mn2 O4)\n",
+      "Reduced Formula: LiMnO2\n",
+      "abc   :   2.865864   4.648716   5.827764\n",
+      "angles:  89.917211  90.239405  89.975425\n",
+      "pbc   :       True       True       True\n",
+      "Sites (8)\n",
+      "  #  SP            a          b         c      magmom\n",
+      "---  ----  ---------  ---------  --------  ----------\n",
+      "  0  Li+    0.494018   0.479737  0.387171  0.00498427\n",
+      "  1  Li+    0.008464   0.006131  0.625817  0.00512926\n",
+      "  2  Mn3+   0.50073    0.502478  0.869608  3.85374\n",
+      "  3  Mn3+   0.997815  -0.000319  0.139344  3.859\n",
+      "  4  O2-    0.502142   0.009453  0.363411  0.0253105\n",
+      "  5  O2-    1.00293    0.502592  0.104559  0.0366638\n",
+      "  6  O2-    0.493749   0.998092  0.903592  0.0365367\n",
+      "  7  O2-   -0.002278   0.495108  0.645655  0.0248522\n"
+     ]
     }
    ],
    "source": [
-    "result = relaxer.relax(structure)\n",
+    "structure.perturb(0.1)\n",
+    "result = relaxer.relax(structure, verbose=False)\n",
     "print(f\"\\nCHGNet took {len(result['trajectory'])} steps. Relaxed structure:\")\n",
     "print(result[\"final_structure\"])"
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "06f7e84c",
    "metadata": {},
@@ -271,7 +282,6 @@
    ]
   },
   {
-   "attachments": {},
    "cell_type": "markdown",
    "id": "c6a10ec8",
    "metadata": {},
@@ -1806,9 +1816,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py310",
+   "display_name": "Python (tf)",
    "language": "python",
-   "name": "python3"
+   "name": "myenv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1820,7 +1830,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,