add ase pwdft calculator file to pynta

zadorlab · Dec 13, 2024 · fe8c53a · fe8c53a
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diff --git a/ase_pwdft/README.md b/ase_pwdft/README.md
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+# PWDFT + ASE
+
+## About
+
+This module defines an ASE interface to PWDFT.
+PWDFT is a code of electronic structure that uses
+plane waves and pseudopotentials.
+
+PWDFT is available here: <https://github.com/ebylaska/PWDFT>
+
+## Acknowledgements
+This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357. Argonne National Laboratory’s work was supported by the U.S. Department of Energy, Office of Science, under contract DE-AC02-06CH11357.
+
+
+All rights reserved. Copyright Argonne National Laboratory UChicago LLC. Raymundo Hernandez-Esparza
diff --git a/ase_pwdft/__init__.py b/ase_pwdft/__init__.py
@@ -0,0 +1,3 @@
+from .pwdftio import *
+
+__all__ = ['PWDFT']
diff --git a/ase_pwdft/example/copper/Example_PWDFT_ASE.ipynb b/ase_pwdft/example/copper/Example_PWDFT_ASE.ipynb
@@ -0,0 +1,142 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "876244c1",
+   "metadata": {},
+   "source": [
+    "# Example of use PWDFT as a calculator"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "5a2e405d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ase import Atoms\n",
+    "from ase.visualize import view\n",
+    "from ase.build import bulk\n",
+    "from ase.io import write, Trajectory\n",
+    "from ase.cell import *\n",
+    "\n",
+    "import sys\n",
+    "import os\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import ase\n",
+    "sys.path.append(\"/home/rayhe/Github/utils_esp/ase_pwdft\")\n",
+    "from pwdft import PWDFT"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "bf9b2a77",
+   "metadata": {},
+   "source": [
+    "the line 'mpiexec -n 1 /home/rayhe/Github/PWDFT/build_new3/pwdft' indicates where binary is located, also I can increase the numper of mpiranks with -n $num"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "11a7218f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "Cu_pos = [[0.0, 0.0, 0.0],\n",
+    "        [0.0, 1, 1],\n",
+    "        [1, 0.0, 1],\n",
+    "        [1, 1, 0.0]]\n",
+    "Cu_cell = [\n",
+    "        [2.0, 0.0, 0.0],\n",
+    "        [0.0, 2.0, 0.0],\n",
+    "        [0.0, 0.0, 2.0]]\n",
+    "\n",
+    "command = 'mpiexec -n 1 /home/rayhe/Github/PWDFT/build_new3/pwdft < PREFIX.nwxi > PREFIX.nwxo'\n",
+    "cu = Atoms(\"Cu4\", \n",
+    "           positions=Cu_pos, \n",
+    "           cell=Cu_cell, pbc=(1,1,1),\n",
+    "           calculator=PWDFT(command=command,label='Cu',echo=True,charge=0\n",
+    "                             ,nwpw={'cutoff':60, 'xc':'PBE', 'loop':'10 250'}\n",
+    "                            )\n",
+    "          )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "c146b0cd",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "array([[-0.00011824, -0.00317398, -0.00014334],\n",
+       "       [-0.00059534,  0.00418138, -0.00011066],\n",
+       "       [-0.00026893, -0.00893213,  0.0002258 ],\n",
+       "       [ 0.00088577,  0.00788889,  0.00026748]])"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cu.get_forces()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "265e527f",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "-5391.361579138844"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "cu.get_potential_energy()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "eabda654",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/ase_pwdft/example/opt_freq_water/WaterOptFreq.ipynb b/ase_pwdft/example/opt_freq_water/WaterOptFreq.ipynb
@@ -0,0 +1,190 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "d55588a8",
+   "metadata": {},
+   "source": [
+    "# Example of Optimization + Freq using PWDFT as a calculator"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "4150d3de",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ase import Atoms\n",
+    "from ase.visualize import view\n",
+    "from ase.build import bulk\n",
+    "from ase.io import write, Trajectory\n",
+    "from ase.vibrations import Vibrations\n",
+    "from ase.cell import *\n",
+    "\n",
+    "import sys\n",
+    "import os\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import ase\n",
+    "sys.path.append(\"/home/rayhe/Github/utils_esp/ase_pwdft\")\n",
+    "from pwdft import PWDFT\n",
+    "from ase.optimize import BFGS                                                                       \n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "c1e40963",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "command = 'mpiexec -n 4 /home/rayhe/Github/PWDFT/build_new3/pwdft < PREFIX.nwxi > PREFIX.nwxo'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "20bcb8ba",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "water = Atoms(\"HOH\", positions=[[0,0,-1],[0,1,0],[0,0,1]],\n",
+    "             cell=[[10,0,0],[0,10,0],[0,0,10]], pbc=(1,1,1),\n",
+    "              calculator=PWDFT(command=command, label=\"Water\", echo=True, charge=0,\n",
+    "                              nwpw={\"cutoff\":60, \"xc\":\"PBE\", 'loog':'10 250'}\n",
+    "                              )\n",
+    "             )"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "4669535c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "opt1 = BFGS(water, trajectory=\"pwdft.opt.traj\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "f8ba8b14",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "      Step     Time          Energy         fmax\n",
+      "BFGS:    0 14:21:08     -464.084453        7.9911\n",
+      "BFGS:    1 14:21:52     -465.870441        7.2755\n",
+      "BFGS:    2 14:22:45     -468.142577        1.9503\n",
+      "BFGS:    3 14:23:22     -468.142592        2.8405\n",
+      "BFGS:    4 14:23:52     -468.229799        0.7549\n",
+      "BFGS:    5 14:24:16     -468.249741        0.6259\n",
+      "BFGS:    6 14:24:48     -468.277005        0.1669\n",
+      "BFGS:    7 14:25:04     -468.277253        0.0204\n",
+      "BFGS:    8 14:25:12     -468.277259        0.0088\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "opt1.run(fmax=0.01)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "342c319a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vib = Vibrations(water)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "b3603d9c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vib.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "a887419e",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "---------------------\n",
+      "  #    meV     cm^-1\n",
+      "---------------------\n",
+      "  0   18.5i    149.2i\n",
+      "  1    3.5i     28.5i\n",
+      "  2   16.3     131.3\n",
+      "  3   24.4     196.7\n",
+      "  4   27.9     224.9\n",
+      "  5   34.8     280.3\n",
+      "  6  202.5    1633.2\n",
+      "  7  446.4    3600.7\n",
+      "  8  459.2    3703.9\n",
+      "---------------------\n",
+      "Zero-point energy: 0.606 eV\n"
+     ]
+    }
+   ],
+   "source": [
+    "vib.summary()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "14224a25",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vib.write_mode(-1)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}