chore: Remove .ipynb files from .gitignore and added example dftbplus…

… notebook
MolarVerse · May 14, 2024 · 3757cc7 · 3757cc7
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diff --git a/.gitignore b/.gitignore
@@ -77,7 +77,6 @@ target/
 
 # Jupyter Notebook
 .ipynb_checkpoints
-*.ipynb
 
 # IPython
 profile_default/

diff --git a/examples/Notebooks/dftbplus/ThermoScreening.ipynb b/examples/Notebooks/dftbplus/ThermoScreening.ipynb
@@ -0,0 +1,296 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Example 101 Thermochemistry using DFTB+"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Clone repo on GitHub: https://github.com/MolarVerse/ThermoScreening and install using `pip install .` in the root directory."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ThermoScreening.thermo.api import dftbplus_thermo\n",
+    "from ThermoScreening.calculator import Geoopt, Hessian, Modes\n",
+    "\n",
+    "from ase.io import read, write\n",
+    "\n",
+    "import os\n",
+    "skf_dir = 'skf-files/3ob-3-1'\n",
+    "\n",
+    "# set DFTB perfix and path \n",
+    "os.environ['DFTB_PREFIX'] = os.path.join(os.environ['HOME'], skf_dir)\n",
+    "os.environ['OMP_NUM_THREADS'] = '6'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "DFTB+ parameters for thermochemistry with COSMO solvation model"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dftb_parameters = dict(\n",
+    "    # SCC \n",
+    "    Hamiltonian_SCC=\"Yes\",\n",
+    "    Hamiltonian_MaxSCCIterations=250,\n",
+    "    Hamiltonian_SCCTolerance='1.0e-6',\n",
+    "    Hamiltonian_ReadInitialCharges=\"No\",\n",
+    "\n",
+    "    # Fermi smearing\n",
+    "    Hamiltonian_Filling=\"Fermi {\",\n",
+    "    Hamiltonian_Filling_empty=\"Temperature [Kelvin] = 300\",\n",
+    "\n",
+    "    # Convergence helper\n",
+    "    Hamiltonian_Mixer=\"DIIS{}\",\n",
+    "\n",
+    "    # Dispersion correction\n",
+    "    Hamiltonian_Dispersion=\"DftD4 {\",\n",
+    "    Hamiltonian_Dispersion_s6=1.0,\n",
+    "    Hamiltonian_Dispersion_s8=0.4727337,\n",
+    "    Hamiltonian_Dispersion_s9=0.0,\n",
+    "    Hamiltonian_Dispersion_a1=0.5467502,\n",
+    "    Hamiltonian_Dispersion_a2=4.4955068,\n",
+    "\n",
+    "    # H-Damping\n",
+    "    Hamiltonian_HCorrection=\"Damping {\",\n",
+    "    Hamiltonian_HCorrection_Exponent=4.00,\n",
+    "\n",
+    "    # Halogen correction\n",
+    "    Hamiltonian_HalogenXCorr=\"Yes\",\n",
+    "\n",
+    "    # Are guessed by ase\n",
+    "    Hamiltonian_MaxAngularMomentum_=\"\",\n",
+    "\n",
+    "    # Solvation model\n",
+    "    Hamiltonian_Solvation_ = \"Cosmo\",\n",
+    "    Hamiltonian_Solvation_Radii = \"VanDerWaalsRadiiD3 {}\",\n",
+    "    Hamiltonian_Solvation_RadiiScaling = 1.55,\n",
+    "    Hamiltonian_Solvation_AngularGrid = 110,\n",
+    "    Hamiltonian_Solvation_Solver = \"DomainDecomposition{\",\n",
+    "    Hamiltonian_Solvation_Solver_MaxMoment = 10,\n",
+    "    Hamiltonian_Solvation_Solver_Accuracy = 1.0e-8,\n",
+    "    Hamiltonian_Solvation_Solver_Regularisation = 0.2,\n",
+    "    Hamiltonian_Solvation_Solvent=\"\"\"FromConstants{\n",
+    "        Epsilon = 37.0,\n",
+    "        MolecularMass [amu] = 73.1,\n",
+    "        Density [kg/l] = 0.95\n",
+    "      }\"\"\",\n",
+    "    Hamiltonian_Solvation_empty = \"FreeEnergyShift [kcal/mol] = 0.0\",\n",
+    "\n",
+    "    # Hubbard derivatives\n",
+    "    Hamiltonian_ThirdOrderFull=\"Yes\",\n",
+    "    Hamiltonian_hubbardderivs_=\"\",\n",
+    "    Hamiltonian_hubbardderivs_C=-0.1492,\n",
+    "    Hamiltonian_hubbardderivs_N=-0.1535,\n",
+    "    Hamiltonian_hubbardderivs_O=-0.1575,\n",
+    "    Hamiltonian_hubbardderivs_H=-0.1857,\n",
+    "    Hamiltonian_hubbardderivs_S=-0.11,\n",
+    "    Hamiltonian_hubbardderivs_P=-0.14,\n",
+    "    Hamiltonian_hubbardderivs_F=-0.1623,\n",
+    "    Hamiltonian_hubbardderivs_Cl=-0.0697,\n",
+    "    Hamiltonian_hubbardderivs_Br=-0.0573,\n",
+    "    Hamiltonian_hubbardderivs_I=-0.0433,\n",
+    "    Hamiltonian_hubbardderivs_Zn=-0.03,\n",
+    "    Hamiltonian_hubbardderivs_Mg=-0.02,\n",
+    "    Hamiltonian_hubbardderivs_Ca=-0.0340,\n",
+    "    Hamiltonian_hubbardderivs_K=-0.0339,\n",
+    "    Hamiltonian_hubbardderivs_Na=-0.0454,\n",
+    "\n",
+    "    # Analysis\n",
+    "    Analysis_=\"\",\n",
+    "    Analysis_CalculateForces=\"Yes\",\n",
+    "    Analysis_MullikenAnalysis=\"Yes\",\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "----\n",
+    "\n",
+    "TODO:\n",
+    "- install `wfl` - not in pypi >:( - https://github.com/libAtoms/workflow\n",
+    "- rdkit NOT in dependencies of `wfl`\n",
+    "- restart kernel after installation\n",
+    "\n",
+    "Commands to install `wfl` and `rdkit`:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# pip install git+https://github.com/libAtoms/workflow.git"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# pip install rdkit"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Create `ase.Atoms` from SMILES"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:rdkit:Enabling RDKit 2023.09.6 jupyter extensions\n"
+     ]
+    }
+   ],
+   "source": [
+    "from wfl.generate import smiles\n",
+    "from ase.calculators.dftb import Dftb\n",
+    "\n",
+    "# quinone smile\n",
+    "smile = 'C1=CC(=O)C=CC1=O'\n",
+    "system = smiles.smi_to_atoms(smile)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "--------\n",
+    "\n",
+    "Run ThermoScreening with DFTB+:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "thermo = dftbplus_thermo(system, charge=0, **dftb_parameters)\n",
+    "zero = thermo.total_EeGtot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "thermo = dftbplus_thermo(system, charge=-1, **dftb_parameters)\n",
+    "neg1 = thermo.total_EeGtot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "thermo = dftbplus_thermo(system, charge=-2, **dftb_parameters)\n",
+    "neg2 = thermo.total_EeGtot()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "-18.304025003414917 -18.45846575894427 -18.580216476499253\n"
+     ]
+    }
+   ],
+   "source": [
+    "print(zero, neg1, neg2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Calculate redox potential:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "C1=CC(=O)C=CC1=O redox1: 4.20254791420707 V\n",
+      "C1=CC(=O)C=CC1=O redox2: 3.3130064817421263 V\n"
+     ]
+    }
+   ],
+   "source": [
+    "# faraday constant\n",
+    "F = 96485.3329\n",
+    "# hartree to j/mol\n",
+    "hartree = 2625500.2\n",
+    "\n",
+    "redox1 = - (neg1 - zero) * hartree / F\n",
+    "redox2 = - (neg2 - neg1) * hartree / F\n",
+    "\n",
+    "print(f'{smile} redox1: {redox1} V')\n",
+    "print(f'{smile} redox2: {redox2} V')"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "venv",
+   "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": "3.11.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}