Add energy statistics printing

Author: nedtaylor

example/python_pkg/Al_learn/DRAFFLE/pca.ipynb

@@ -212,6 +212,22 @@
     "print(\"Relaxed min energy: \", np.min(energies_per_atom))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"Aluminium search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/C_learn/DRAFFLE/pca.ipynb

@@ -169,6 +169,22 @@
     "  print(\"Minimum energy per atom is not zero. Check the energy calculation.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"Diamond search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/C_learn/DRSS/pca.ipynb

@@ -434,14 +434,14 @@
     "    q2 = subset['Energy per atom'].quantile(0.5)\n",
     "    q3 = subset['Energy per atom'].quantile(0.75)\n",
     "    \n",
-    "    ax_kde.axvline(q1, color=colour, linestyle='--', linewidth=1.25, label=f'{source} Q1')\n",
-    "    ax_kde.axvline(q2, color=colour, linestyle=':', linewidth=1.25, label=f'{source} Q2')\n",
-    "    ax_kde.axvline(q3, color=colour, linestyle='-.', linewidth=1.25, label=f'{source} Q3')\n",
+    "    ax_kde.axvline(q1, color=colour, linestyle='--', linewidth=1.7, label=f'{source} Q1', dashes=(10, 3))\n",
+    "    ax_kde.axvline(q2, color=colour, linestyle='-.', linewidth=1.7, label=f'{source} Q2')\n",
+    "    ax_kde.axvline(q3, color=colour, linestyle=':',  linewidth=1.7, label=f'{source} Q3')\n",
     "    # plot these only to the height of the rug at that point\n",
     "\n",
     "plt.tight_layout()\n",
     "# Save the figure\n",
-    "plt.savefig('C_'+identifier+'_kde_rug_rlxd_seed'+str(seed)+'.pdf', bbox_inches='tight', pad_inches=0, facecolor=fig.get_facecolor(), edgecolor='none')\n",
+    "plt.savefig('C'+identifier+'_kde_rug_rlxd_seed'+str(seed)+'.pdf', bbox_inches='tight', pad_inches=0, facecolor=fig.get_facecolor(), edgecolor='none')\n",
     "\n",
     "plt.show()\n"
    ]

example/python_pkg/C_learn/Dgraphite_diamond/pca.ipynb

@@ -168,6 +168,22 @@
     "  print(\"Minimum energy per atom is not zero. Check the energy calculation.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"Carbon search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/MoS2_learn/DRAFFLE/pca.ipynb

@@ -42,7 +42,7 @@
    "source": [
     "## Set the plotting parameters\n",
     "seed = 0\n",
-    "identifier = \"_VASP\"\n",
+    "identifier = \"\"\n",
     "output_directory_prefix = \"DResponse\"\n",
     "# min_energy = -"
    ]
@@ -57,7 +57,7 @@
     "from agox.models.descriptors.fingerprint import Fingerprint\n",
     "# from agox.models.descriptors import Voronoi\n",
     "\n",
-    "template = read(output_directory_prefix+identifier+\"/unrlxd_structures_seed0.xyz\")\n",
+    "template = read(output_directory_prefix+identifier+\"/unrlxd_structures_seed0.traj\")\n",
     "# diamond = bulk(\"C\", \"diamond\", a=3.567)  # Lattice constant for diamond cubic carbon\n",
     "confinement_cell = template.cell.copy()\n",
     "confinement_corner = np.array([0, 0, 0])\n",
@@ -97,7 +97,7 @@
    "outputs": [],
    "source": [
     "## Load the unrelaxed structures\n",
-    "unrlxd_structures = read(output_directory_prefix+identifier+\"/unrlxd_structures_seed\"+str(seed)+\".xyz\", index=\":\")"
+    "unrlxd_structures = read(output_directory_prefix+identifier+\"/unrlxd_structures_seed\"+str(seed)+\".traj\", index=\":\")"
    ]
   },
   {
@@ -107,7 +107,7 @@
    "outputs": [],
    "source": [
     "## Load the relaxed structures\n",
-    "rlxd_structures = read(output_directory_prefix+identifier+\"/rlxd_structures_seed\"+str(seed)+\".xyz\", index=\":\")"
+    "rlxd_structures = read(output_directory_prefix+identifier+\"/rlxd_structures_seed\"+str(seed)+\".traj\", index=\":\")"
    ]
   },
   {
@@ -174,6 +174,22 @@
     "  print(\"Minimum energy per atom is not zero. Check the energy calculation.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"MoS$_2$ search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/ScS2-Li_learn/DRAFFLE/pca.ipynb

@@ -161,6 +161,22 @@
     "print(\"Relaxed min energy: \", np.min(energies_per_atom))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"ScS$_2$-Li search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/Si-Ge_learn/DRAFFLE/pca.ipynb

@@ -251,6 +251,22 @@
     "print(\"Relaxed min energy: \", np.min(rlxd_en_per_area))"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_en_per_area), np.max(rlxd_en_per_area), \n",
+    "    np.mean(rlxd_en_per_area), np.std(rlxd_en_per_area)))\n",
+    "# plot in latex table format\n",
+    "print(\"Si|Ge search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_en_per_area), np.max(rlxd_en_per_area), \n",
+    "    np.mean(rlxd_en_per_area), np.std(rlxd_en_per_area)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,

example/python_pkg/graphene_grain_boundary_learn/DRAFFLE/pca.ipynb

@@ -44,9 +44,9 @@
    "outputs": [],
    "source": [
     "## Set the plotting parameters\n",
-    "seed = 2\n",
+    "seed = 0\n",
     "identifier = \"\"\n",
-    "output_directory_prefix = \"DResponse\"\n",
+    "output_directory_prefix = \"DOutput\"\n",
     "# min_energy = -9.064090728759766"
    ]
   },
@@ -122,7 +122,7 @@
    "outputs": [],
    "source": [
     "# ## Load the unrelaxed structures\n",
-    "unrlxd_structures = read(output_directory_prefix+identifier+\"/DTMP/unrlxd_structures_seed\"+str(seed)+\"_combined.traj\", index=\":\")"
+    "unrlxd_structures = read(output_directory_prefix+identifier+\"/unrlxd_structures_seed\"+str(seed)+\".traj\", index=\":\")"
    ]
   },
   {
@@ -132,7 +132,7 @@
    "outputs": [],
    "source": [
     "# ## Load the relaxed structures\n",
-    "rlxd_structures = read(output_directory_prefix+identifier+\"/DTMP/rlxd_structures_seed\"+str(seed)+\"_combined.traj\", index=\":\")"
+    "rlxd_structures = read(output_directory_prefix+identifier+\"/rlxd_structures_seed\"+str(seed)+\".traj\", index=\":\")"
    ]
   },
   {
@@ -170,6 +170,22 @@
     "  print(\"Minimum energy per atom is not zero. Check the energy calculation.\")"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# print the min, max, mean, and std of the relaxed energies\n",
+    "print(\"Relaxed energies per atom: min = {:.2f}, max = {:.2f}, mean = {:.2f}, std = {:.2f}\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))\n",
+    "# plot in latex table format\n",
+    "print(\"Graphene grain boundary search & {:.2f} & {:.2f} & {:.2f} & {:.2f} \\\\\\\\\".format(\n",
+    "    np.min(rlxd_delta_en_per_atom), np.max(rlxd_delta_en_per_atom), \n",
+    "    np.mean(rlxd_delta_en_per_atom), np.std(rlxd_delta_en_per_atom)))"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,