Scale perturbations by number of atoms involved

notebooks/1_explore-sampling-methods/0_random-directions-same-distance.ipynb

@@ -239,7 +239,7 @@
     "    # Sample a perturbation\n",
     "    disp = np.random.normal(0, 1, size=(n_atoms * 3))\n",
     "    disp /= np.linalg.norm(disp)\n",
-    "    disp *= step_size\n",
+    "    disp *= step_size * len(atoms) \n",
     "    disp = disp.reshape((-1, 3))\n",
     "    \n",
     "    # Subtract off any translation\n",

notebooks/1_explore-sampling-methods/1_random-directions-variable-distance.ipynb

@@ -227,7 +227,7 @@
     "    disp = np.random.normal(0, 1, size=(n_atoms * 3))\n",
     "    disp /= np.linalg.norm(disp)\n",
     "    my_step_dist = np.random.exponential(scale=step_size)\n",
-    "    disp *= my_step_dist\n",
+    "    disp *= my_step_dist * len(atoms)\n",
     "    disp = disp.reshape((-1, 3))\n",
     "    \n",
     "    # Subtract off any translation\n",

notebooks/1_explore-sampling-methods/2_displace-along-axes.ipynb

@@ -344,7 +344,7 @@
     "    # Create the perturbation vector\n",
     "    disp = np.zeros((n_coords,))\n",
     "    for d in perturb:\n",
-    "        disp[abs(d) - 1] = (1 if abs(d) > 0 else -1) * step_size\n",
+    "        disp[abs(d) - 1] = (1 if abs(d) > 0 else -1) * step_size / perturbs_per_evaluation\n",
     "    disp = disp.reshape((-1, 3))\n",
     "    \n",
     "    # Make the new atoms\n",

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

@@ -1,15 +1,15 @@
 #! /bin/bash
 
 xyz=../data/exact/caffeine_pm7_None.xyz
-for step_size in 0.04 0.02 0.01 0.005; do
+for step_size in 0.02; do
     # Do the randomized methods
     for method in 0_random-directions-same-distance.ipynb 1_random-directions-variable-distance.ipynb; do
         papermill -p starting_geometry $xyz -p step_size $step_size $method last.ipynb
     done
 
     # Test with different reductions for "along axes"
     notebook=2_displace-along-axes.ipynb
-    for n in 1 2 4; do
+    for n in 2 4 8; do
         papermill -p starting_geometry $xyz -p perturbs_per_evaluation $n -p step_size $step_size $notebook last.ipynb
     done
 done