From 3a8fe3bee27e1e7560dc467b40ddabc6d05ff646 Mon Sep 17 00:00:00 2001
From: Raimondas Galvelis <r.galvelis@acellera.com>
Date: Tue, 25 Oct 2022 13:56:21 +0200
Subject: [PATCH] More clean up

---
 tutorials/openmm-torch-nnpops.ipynb | 40 +++++------------------------
 1 file changed, 6 insertions(+), 34 deletions(-)

diff --git a/tutorials/openmm-torch-nnpops.ipynb b/tutorials/openmm-torch-nnpops.ipynb
index 0ac94be8..2f576611 100644
--- a/tutorials/openmm-torch-nnpops.ipynb
+++ b/tutorials/openmm-torch-nnpops.ipynb
@@ -104,21 +104,9 @@
     {
       "cell_type": "code",
       "metadata": {
-        "colab": {
-          "base_uri": "https://localhost:8080/"
-        },
-        "id": "zNng_d4mGKve",
-        "outputId": "218e0775-766b-4597-9d48-96e3d65df374"
+        "id": "zNng_d4mGKve"
       },
-      "outputs": [
-        {
-          "name": "stderr",
-          "output_type": "stream",
-          "text": [
-            "Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.\n"
-          ]
-        }
-      ],
+      "outputs": [],
       "source": [
         "import openmmtools\n",
         "\n",
@@ -152,32 +140,16 @@
       "cell_type": "code",
       "metadata": {
         "id": "ofemZo6sIbLU",
-        "outputId": "4181fcb6-db72-47e7-edb5-2a4bb0252de7"
+        "outputId": "9604e005-80ed-4553-eada-fc73f032b653"
       },
       "outputs": [
         {
-          "name": "stderr",
           "output_type": "stream",
-          "text": [
-            "/usr/local/lib/python3.7/site-packages/torchani/__init__.py:55: UserWarning: Dependency not satisfied, torchani.ase will not be available\n",
-            "  warnings.warn(\"Dependency not satisfied, torchani.ase will not be available\")\n"
-          ]
-        },
-        {
           "name": "stdout",
-          "output_type": "stream",
           "text": [
             "/usr/local/lib/python3.7/site-packages/torchani/resources/\n",
             "Downloading ANI model parameters ...\n"
           ]
-        },
-        {
-          "name": "stderr",
-          "output_type": "stream",
-          "text": [
-            "/usr/local/lib/python3.7/site-packages/torch/functional.py:1069: UserWarning: torch.meshgrid: in an upcoming release, it will be required to pass the indexing argument. (Triggered internally at  /home/conda/feedstock_root/build_artifacts/pytorch-recipe_1640851336451/work/aten/src/ATen/native/TensorShape.cpp:2156.)\n",
-            "  return _VF.cartesian_prod(tensors)  # type: ignore[attr-defined]\n"
-          ]
         }
       ],
       "source": [
@@ -204,7 +176,7 @@
         "\n",
         "    # Prepare the positions\n",
         "    positions = positions.unsqueeze(0).float() * 10 # nm --> Å\n",
-        "    \n",
+        "\n",
         "    # Run ANI-2x\n",
         "    result = self.model((self.atomic_numbers, positions))\n",
         "    \n",
@@ -230,12 +202,12 @@
       "cell_type": "code",
       "metadata": {
         "id": "D42I_L9r-Krj",
-        "outputId": "c1738d48-71e2-40ea-9965-d9dbd2147406"
+        "outputId": "0fb1e3f7-3042-401d-bca3-7ffb4b313739"
       },
       "outputs": [
         {
-          "name": "stdout",
           "output_type": "stream",
+          "name": "stdout",
           "text": [
             "-1301523.8702643516\n"
           ]