Merge pull request #22 from dwhswenson/fix-openmm81

Fix NB 2 for OpenMM 8.1

Author: dwhswenson

.github/workflows/ci.yml

@@ -21,9 +21,10 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - 3.7
-          - 3.8
-          - 3.9
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          #- "3.11"
 
     steps:
       - uses: actions/checkout@v2
@@ -59,9 +60,10 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - 3.7
-          - 3.8
-          - 3.9
+          - "3.8"
+          - "3.9"
+          - "3.10"
+          #- "3.11"
 
     steps:
       - uses: actions/checkout@v2

2_tps_analysis_tutorial.ipynb

@@ -42,7 +42,8 @@
     "import openpathsampling.visualize as ops_vis\n",
     "from IPython.display import SVG\n",
     "\n",
-    "import nglview as nv"
+    "import nglview as nv\n",
+    "import openmm"
    ]
   },
   {
@@ -327,10 +328,13 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# with OpenMM 8.0 or earlier: timestep = engine.snapshot_timestep\n",
+    "# (also should work for data generated with OpenMM 8.1 or later)\n",
+    "timestep = 2.0 * openmm.unit.femtosecond\n",
     "path_lengths = [len(step.active[0].trajectory) for step in flexible.steps]\n",
     "plt.hist(path_lengths, bins=40, alpha=0.5);\n",
-    "print(\"Maximum:\", max(path_lengths), \"(\"+str(max(path_lengths)*engine.snapshot_timestep)+\")\")\n",
-    "print(\"Average:\", \"{0:.2f}\".format(np.mean(path_lengths)), \"(\"+(np.mean(path_lengths)*engine.snapshot_timestep).format(\"%.3f\")+\")\")\n",
+    "print(\"Maximum:\", max(path_lengths), \"(\"+str(max(path_lengths)*timestep)+\")\")\n",
+    "print(\"Average:\", \"{0:.2f}\".format(np.mean(path_lengths)), \"(\"+(np.mean(path_lengths)*timestep).format(\"%.3f\")+\")\")\n",
     "plt.ylabel(\"Count\")\n",
     "plt.xlabel(\"Path length (Frames)\");"
    ]
@@ -468,7 +472,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -482,7 +486,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.9.13"
   },
   "toc": {
    "base_numbering": 1,

4_mstis_sampling_tutorial.ipynb

@@ -222,7 +222,7 @@
     "    filename = \"./inputs/mstis_bootstrap_py2.nc\"\n",
     "elif (3, 6) <= sys.version_info < (3, 8):\n",
     "    filename = \"./inputs/mstis_bootstrap_py3.nc\"\n",
-    "elif (3, 8) <= sys.version_info < (3, 10):\n",
+    "elif (3, 8) <= sys.version_info < (3, 11):\n",
     "    filename = \"./inputs/mstis_bootstrap_py38.nc\"\n",
     "else:\n",
     "    raise RuntimeError(\n",
@@ -599,7 +599,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -613,7 +613,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.10"
+   "version": "3.9.13"
   },
   "toc": {
    "base_numbering": 1,