Remove translation and rotational modes, sample w/ replacement

notebooks/1_explore-sampling-methods/3_displace-along-vibrational-modes.ipynb

@@ -176,6 +176,27 @@
     "evalues, emodes = np.linalg.eigh(vib_data.get_hessian_2d())"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "31bada31-2ea3-47b0-80d4-5bc98a4115ae",
+   "metadata": {},
+   "source": [
+    "Remove the six smallest eignvalues, which should be zero"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7c3ca6eb-dca1-4bab-8f7d-6c42ce429400",
+   "metadata": {
+    "tags": []
+   },
+   "outputs": [],
+   "source": [
+    "evalues = evalues[6:]\n",
+    "emodes = emodes[6:, :]"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "78563dd5-c6da-46d8-9b99-4928187023da",
@@ -270,6 +291,24 @@
     "print(f'Need to run {to_compute} calculations for full accuracy.')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "ed1742cd-45a7-44e4-8a38-ebf3d0ed321d",
+   "metadata": {},
+   "source": [
+    "Reduce the number of perturbations if too large"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "09e27062-59c4-421c-9de5-f5457bf0ad32",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "perturbs_per_evaluation = min(scaled_modes.shape[0], perturbs_per_evaluation)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "ad4c5d8e-96d4-4bb6-9bf2-6474d7563448",
@@ -381,7 +420,7 @@
     "iterator = tqdm(range(to_compute - num_done))\n",
     "for i in iterator:\n",
     "    # Choose a number of perturbation vectors\n",
-    "    to_disp = rng.choice(scaled_modes.shape[0], size=(perturbs_per_evaluation,))\n",
+    "    to_disp = rng.choice(scaled_modes.shape[0], size=(perturbs_per_evaluation,), replace=False)\n",
     "    \n",
     "    # Pick a random magnitude for each\n",
     "    disp = (scaled_modes[to_disp, :] * rng.uniform(-1, 1, size=(perturbs_per_evaluation, 1))).sum(axis=0)\n",

notebooks/1_explore-sampling-methods/run-all-methods.sh

@@ -17,7 +17,7 @@ done
 # Test with the vibrational modes
 notebook=3_displace-along-vibrational-modes.ipynb
 for step_size in 0.001 0.002; do
-    for n in 8 16 32; do
+    for n in 16 32 64; do
         papermill -p starting_geometry $xyz -p perturbs_per_evaluation $n -p step_size $step_size $notebook last.ipynb
     done
 done