update: use relaxation from made-tools

Exabyte-io · May 11, 2024 · 877d402 · 877d402
1 parent e15bd4a
commit 877d402
Showing 1 changed file with 51 additions and 6 deletions.
diff --git a/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb b/other/materials_designer/create_interface_with_relaxation_ase_emt.ipynb
@@ -97,11 +97,19 @@
    "source": [
     "RELAXATION_PARAMETERS = {\n",
     "    \"FMAX\": 0.018,\n",
-    "}"
+    "}\n",
+    "\n",
+    "from mat3ra.made.tools.modify import RelaxationSettings, CalculatorEnum, OptimizerEnum\n",
+    "relaxation_settings = RelaxationSettings()\n",
+    "\n",
+    "relaxation_settings.optimizer = OptimizerEnum.BFGS\n",
+    "relaxation_settings.calculator = CalculatorEnum.EMT\n",
+    "relaxation_settings.fmax = 0.05"
    ],
    "metadata": {
     "collapsed": false
-   }
+   },
+   "execution_count": null
   },
   {
    "cell_type": "markdown",
@@ -303,7 +311,7 @@
     "termination_or_its_index = selected_termination\n",
     "# select the first interface with the lowest strain and the smallest number of atoms\n",
     "interfaces_slice_range_or_index = 0\n",
-    "interface = interface_data_holder.get_interfaces_as_materials(termination_or_its_index, interfaces_slice_range_or_index)"
+    "interface = interface_data_holder.get_interfaces_as_materials(termination_or_its_index, interfaces_slice_range_or_index)[0]"
    ]
   },
   {
@@ -341,6 +349,29 @@
     "### 7.1. Apply relaxation to the selected interface"
    ]
   },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
+    "from utils.plot import create_realtime_plot, update_plot\n",
+    "\n",
+    "from mat3ra.made.tools.modify import relax_atoms\n",
+    "from mat3ra.made.tools.convert import to_ase\n",
+    "\n",
+    "final_interface = relax_atoms(Material(interface), relaxation_settings)\n",
+    "\n",
+    "f = create_realtime_plot()\n",
+    "steps = []\n",
+    "energies = []\n",
+    "update_plot(f, steps, energies)\n",
+    "\n",
+    "visualize(final_interface, repetitions=[1, 1, 1], rotation=\"0x\")"
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -354,14 +385,24 @@
     "from ase.optimize import BFGS\n",
     "from ase.calculators.emt import EMT\n",
     "\n",
+    "\n",
     "# Set up the calculator \n",
     "calculator = EMT()\n",
+    "print(calculator)\n",
     "\n",
     "# Set up the interface for relaxation\n",
-    "ase_interface = pymatgen_to_ase(interface)\n",
+    "ase_interface = to_ase(interface)\n",
+    "print(ase_interface)\n",
     "ase_interface.set_calculator(calculator)\n",
+    "print(ase_interface)\n",
     "dyn = BFGS(ase_interface)\n",
-    "\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "outputs": [],
+   "source": [
     "# Initialize empty lists to store steps and energies\n",
     "steps = []\n",
     "energies = []\n",
@@ -410,7 +451,11 @@
     "print('Original structure:\\n', ase_to_poscar(ase_original_interface))\n",
     "print('\\nRelaxed structure:\\n', ase_to_poscar(ase_final_interface))\n",
     "print(f\"The final energy is {float(relaxed_energy):.3f} eV.\")"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   },
+   "execution_count": null
   },
   {
    "cell_type": "markdown",