MD functionality - 0K and finite temp elastic constants

hackathon/elastic_constants/MD_23-07-25.ipynb

@@ -0,0 +1,398 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4a26f12c-f1c4-4262-b978-8afec1537ae1",
+   "metadata": {},
+   "source": [
+    "# Temperature dependent elastic constants\n",
+    "\n",
+    "## Background\n",
+    "\n",
+    "$$C_{ijkl} = \\frac{1}{V} \\frac{\\partial^2 U}{\\partial \\varepsilon_{ij}\\partial \\varepsilon_{kl}}$$\n",
+    "\n",
+    "$$U(T) = \\frac{V}{2}C_{ijkl}(T)\\varepsilon_{ij}\\varepsilon_{kl}$$\n",
+    "\n",
+    "$$\\sigma_{ij} = C_{ijkl}{\\varepsilon_{kl}}$$\n",
+    "\n",
+    "### How to get $U$ or $\\sigma$\n",
+    "\n",
+    "- MD\n",
+    "- Quasi-Harmonic\n",
+    "\n",
+    "## Tasks\n",
+    "\n",
+    "- Get $a_0$ from potential\n",
+    "- Lattice parameter (as a function of T)\n",
+    "  - MD\n",
+    "    - NVT\n",
+    "    - NPT\n",
+    "  - QH\n",
+    "- Calculate $U$ or $\\sigma$ for various $\\varepsilon$\n",
+    "  - MD: Equilibriate and average with LAMMPS\n",
+    "  - QH: Get strains from Yuriy's tool and run phonopy\n",
+    "- Fit\n",
+    "\n",
+    "## Teams\n",
+    "\n",
+    "- MD: Erik, Han, (Raynol), Prabhath, Jan\n",
+    "- QH: Raynol, (Sam), Bharathi, Ahmed, Haitham\n",
+    "- Fit & Yuriy: Sam\n",
+    "- Literature"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "37118728",
+   "metadata": {},
+   "source": [
+    "# Implementation"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "e0b4e2eb",
+   "metadata": {},
+   "source": [
+    "* https://atomistics.readthedocs.io/en/latest/bulk_modulus_with_gpaw.html#elastic-matrix\n",
+    "* https://github.com/pyiron/atomistics/blob/main/tests/test_elastic_lammpslib_functional.py\n",
+    "* https://github.com/pyiron/pyiron_workflow_atomistics/blob/interstitials/pyiron_workflow_atomistics/dataclass_storage.py\n",
+    "* https://github.com/ligerzero-ai/pyiron_workflow_lammps/blob/main/pyiron_workflow_lammps/engine.py#L21"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "ab2a0224",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ase.build import bulk\n",
+    "from ase.atoms import Atoms"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "314284cf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from atomistics.calculators import evaluate_with_lammpslib, get_potential_by_name"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0640a5d2",
+   "metadata": {},
+   "source": [
+    "## Create bulk sample"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "4ce06b81",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "structure = bulk('Al', 'fcc', a=4.05, cubic=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "b07fbd51",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "potential_name = \"1999--Mishin-Y--Al--LAMMPS--ipr1\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "34e9442c",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/cmmc/ptmp/pyironhb/pyiron_latest_env/lib/python3.11/site-packages/atomistics/calculators/lammps/potential.py:324: SettingWithCopyWarning: \n",
+      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
+      "Try using .loc[row_indexer,col_indexer] = value instead\n",
+      "\n",
+      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
+      "  df_pot[\"Config\"] = config_lst\n"
+     ]
+    }
+   ],
+   "source": [
+    "df_pot_selected = get_potential_by_name(\n",
+    "    potential_name=potential_name\n",
+    ")\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b02f41d3",
+   "metadata": {},
+   "source": [
+    "## 0K Relaxed Structure"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "92ee7631",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_relaxed_structure(structure: Atoms, potential: str) -> Atoms:\n",
+    "    \n",
+    "    df_pot_selected = get_potential_by_name(\n",
+    "            potential_name=potential\n",
+    "        )\n",
+    "    \n",
+    "    result_dict = evaluate_with_lammpslib(\n",
+    "            task_dict={\"optimize_positions_and_volume\": structure},\n",
+    "            potential_dataframe=df_pot_selected,\n",
+    "        )\n",
+    "    \n",
+    "    structure_relaxed = result_dict['structure_with_optimized_positions_and_volume']\n",
+    "\n",
+    "    return structure_relaxed"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "2c46da55",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/cmmc/ptmp/pyironhb/pyiron_latest_env/lib/python3.11/site-packages/atomistics/calculators/lammps/potential.py:324: SettingWithCopyWarning: \n",
+      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
+      "Try using .loc[row_indexer,col_indexer] = value instead\n",
+      "\n",
+      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
+      "  df_pot[\"Config\"] = config_lst\n",
+      "--------------------------------------------------------------------------\n",
+      "WARNING: There was an error initializing an OpenFabrics device.\n",
+      "\n",
+      "  Local host:   cmti001\n",
+      "  Local device: hfi1_0\n",
+      "--------------------------------------------------------------------------\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "Atoms(symbols='Al4', pbc=True, cell=[4.050004662201837, 4.050004662201837, 4.050004662201837])"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "relaxed_structure = get_relaxed_structure(structure, potential_name)\n",
+    "relaxed_structure"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "115a15d0",
+   "metadata": {},
+   "source": [
+    "## 0K Lattice Constant"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "6ce6b4ba-ed90-4d53-a502-549e2980a481",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_minimum_lattice_constant(structure: Atoms, potential: str) -> float:\n",
+    "\n",
+    "    structure_relaxed = get_relaxed_structure(structure, potential)\n",
+    "    a_0 = structure_relaxed.get_volume()**(1/3) #Angstrom\n",
+    "\n",
+    "    return a_0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "e49c9a2b",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/cmmc/ptmp/pyironhb/pyiron_latest_env/lib/python3.11/site-packages/atomistics/calculators/lammps/potential.py:324: SettingWithCopyWarning: \n",
+      "A value is trying to be set on a copy of a slice from a DataFrame.\n",
+      "Try using .loc[row_indexer,col_indexer] = value instead\n",
+      "\n",
+      "See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy\n",
+      "  df_pot[\"Config\"] = config_lst\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "4.050004662201837"
+      ]
+     },
+     "execution_count": 9,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "a_0 = get_minimum_lattice_constant(structure, potential_name)\n",
+    "a_0"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "91518721",
+   "metadata": {},
+   "source": [
+    "# Skeleton for the workflow"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "347e96fd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_minimum_lattice_constant(structure: \"ase.atoms.Atoms\", engine) -> float:\n",
+    "    ...\n",
+    "    return a_0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "567a21f6-e0ab-46b1-970e-e780fd506e18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_lattice_constant_with_QH(\n",
+    "    structure: \"ase.atoms.Atoms\",\n",
+    "    temperature: list[float] | float,\n",
+    "    engine,\n",
+    "    **kwargs,\n",
+    ") -> list[float] | float:\n",
+    "    ...\n",
+    "    return a_0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "21d46f96-f98e-4162-851f-a394cad338cd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_lattice_constant_with_MD_NPT(\n",
+    "    structure: Atoms,\n",
+    "    temperature: list[float] | float,\n",
+    "    engine,\n",
+    "    **kwargs,\n",
+    ") -> list[float] | float:\n",
+    "    ...\n",
+    "    return a_0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f4746ba6-a30d-4185-991a-bd44ba18f345",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_lattice_constant_with_MD_NVT(\n",
+    "    structure: \"ase.atoms.Atoms\",\n",
+    "    temperature: list[float] | float,\n",
+    "    engine,\n",
+    "    **kwargs,\n",
+    ") -> list[float] | float:\n",
+    "    ...\n",
+    "    return a_0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c827ae3e-dfb2-4f01-ad77-0ffc849f5478",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_deformations(structure) -> list[list[float, float, float, float, float, float]]:\n",
+    "    ...\n",
+    "    return epsilon"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ccbad139-2a35-48a3-a40b-1807a78e2c8a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# distribute get_stress_with_MD\n",
+    "\n",
+    "def get_stress_with_MD(\n",
+    "    structure, temperature, strains: list[float, float, float, float, float, float], engine\n",
+    "):\n",
+    "    ...\n",
+    "    return sigma\n",
+    "\n",
+    "def get_energy_with_MD(structure, temperature, strains, engine):\n",
+    "    ...\n",
+    "    return energy\n",
+    "\n",
+    "def get_stress_with_QH(structure, temperature, strains, engine):\n",
+    "    ...\n",
+    "    return sigma\n",
+    "\n",
+    "def get_energy_with_QH(structure, temperature, strains, engine):\n",
+    "    ...\n",
+    "    return energy"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "pyiron-latest",
+   "language": "python",
+   "name": "pyiron-latest"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.6"
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