From 8af4507b06ba902b158d43faa34eddf6024d8752 Mon Sep 17 00:00:00 2001
From: BowenD-UCB <84425382+BowenD-UCB@users.noreply.github.com>
Date: Wed, 21 Feb 2024 14:31:17 -0800
Subject: [PATCH] update example with ase install

---
 examples/basics.ipynb | 58 ++++++++++++++++++++++++++-----------------
 1 file changed, 35 insertions(+), 23 deletions(-)

diff --git a/examples/basics.ipynb b/examples/basics.ipynb
index 030f091a..dc4a9dcf 100644
--- a/examples/basics.ipynb
+++ b/examples/basics.ipynb
@@ -19,7 +19,8 @@
     "    from chgnet.model import CHGNet\n",
     "except ImportError:\n",
     "    # install CHGNet (only needed on Google Colab or if you didn't install CHGNet yet)\n",
-    "    !pip install chgnet"
+    "    !pip install chgnet\n",
+    "    !pip install git+https://gitlab.com/ase/ase"
    ]
   },
   {
@@ -75,6 +76,14 @@
       "  6  O2-   0.5  0    0.901486\n",
       "  7  O2-   0    0.5  0.639176\n"
      ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/bowendeng/PackagesforReseach/pymatgen-private/pymatgen/io/cif.py:1186: UserWarning: The default value of primitive was changed from True to False in https://github.com/materialsproject/pymatgen/pull/3419. CifParser now returns the cell in the CIF file as is. If you want the primitive cell, please set primitive=True explicitly.\n",
+      "  warnings.warn(\n"
+     ]
     }
    ],
    "source": [
@@ -110,7 +119,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CHGNet v0.3.0 initialized with 412,525 parameters\n"
+      "CHGNet v0.3.0 initialized with 412,525 parameters\n",
+      "CHGNet will run on cpu\n"
      ]
     }
    ],
@@ -144,25 +154,25 @@
      "output_type": "stream",
      "text": [
       "CHGNet-predicted energy (eV/atom):\n",
-      "-7.371591567993164\n",
+      "-7.367691516876221\n",
       "\n",
       "CHGNet-predicted forces (eV/A):\n",
-      "[[ 0.     -0.      0.0241]\n",
-      " [ 0.     -0.     -0.0241]\n",
-      " [-0.      0.      0.0254]\n",
-      " [-0.     -0.     -0.0254]\n",
-      " [-0.      0.     -0.0217]\n",
-      " [ 0.     -0.      0.0096]\n",
-      " [-0.      0.     -0.0096]\n",
-      " [-0.     -0.      0.0217]]\n",
+      "[[ 0.     -0.      0.0238]\n",
+      " [ 0.      0.     -0.0238]\n",
+      " [ 0.     -0.      0.0926]\n",
+      " [-0.     -0.     -0.0926]\n",
+      " [ 0.      0.     -0.0024]\n",
+      " [-0.     -0.     -0.0131]\n",
+      " [ 0.      0.      0.0131]\n",
+      " [-0.      0.      0.0024]]\n",
       "\n",
       "CHGNet-predicted stress (GPa):\n",
-      "[[ 0.3368 -0.     -0.    ]\n",
-      " [ 0.      0.2468  0.    ]\n",
-      " [-0.      0.      0.0403]]\n",
+      "[[-0.3037 -0.      0.    ]\n",
+      " [-0.      0.2231 -0.    ]\n",
+      " [ 0.     -0.     -0.1074]]\n",
       "\n",
       "CHGNet-predicted magmom (mu_B):\n",
-      "[0.0052 0.0052 3.8573 3.8573 0.0254 0.0371 0.0371 0.0254]\n",
+      "[0.003  0.003  3.8694 3.8694 0.0441 0.0386 0.0386 0.0441]\n",
       "\n"
      ]
     }
@@ -260,12 +270,14 @@
     }
    ],
    "source": [
+    "# Perturb the structure\n",
     "structure.perturb(0.1)\n",
-    "for ase_filter in (\"FrechetCellFilter\", \"ExpCellFilter\"):\n",
-    "    result = relaxer.relax(structure, verbose=False, ase_filter=ase_filter)\n",
-    "    n_steps = len(result[\"trajectory\"])\n",
-    "    print(f\"\\n{ase_filter} took {n_steps} steps. Relaxed structure:\\n\")\n",
-    "    print(result[\"final_structure\"])"
+    "\n",
+    "# Relax the pur\n",
+    "result = relaxer.relax(structure, verbose=False, ase_filter=ase_filter)\n",
+    "n_steps = len(result[\"trajectory\"])\n",
+    "print(f\"\\n{ase_filter} took {n_steps} steps. Relaxed structure:\\n\")\n",
+    "print(result[\"final_structure\"])"
    ]
   },
   {
@@ -1848,9 +1860,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
+   "display_name": "Python (tf)",
    "language": "python",
-   "name": "python3"
+   "name": "myenv"
   },
   "language_info": {
    "codemirror_mode": {
@@ -1862,7 +1874,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.9.10"
   }
  },
  "nbformat": 4,