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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# 14 - Using External ASE Objects (Calculators/Optimizers)\n", | ||
| "\n", | ||
| "### In this tutorial we will learn how to use external ASE calculators and optimizers within the architector framework.\n", | ||
| "\n", | ||
| "**(A)** Using arbitrary methods to perform energy/relaxations.\n", | ||
| "\n", | ||
| "**(B)** How to use example ASE calculator (MACE-MP-0) within Architector complex construction.\n", | ||
| "\n", | ||
| "**(C)** How to use arbirtrary ASE optimizers within Architector." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "To get started - make sure to install the MACE-MP-0 package and model:\n", | ||
| "\n", | ||
| "See: https://github.com/ACEsuit/mace" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Now, load in the correct functions and model\n", | ||
| "from architector import build_complex, view_structures, convert_io_molecule\n", | ||
| "from mace.calculators import mace_mp # Import Mace ASE calculator\n", | ||
| "calc = mace_mp(model=\"medium\", dispersion=True,\n", | ||
| " default_dtype=\"float32\") # Instantiate the MACE calculator\n", | ||
| "from architector.io_calc import CalcExecutor # Calculation executor interface.\n", | ||
| "import numpy as np" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now, Let's generate a structure (UFF) for an arbitary SMILES string and distort the coordinates by a random distance:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "arb_smiles = 'c1ccccc1CON'\n", | ||
| "mol = convert_io_molecule(arb_smiles)\n", | ||
| "mol.ase_atoms.set_positions(mol.ase_atoms.get_positions() + np.random.random(mol.ase_atoms.get_positions().shape) / 2)\n", | ||
| "view_structures(mol)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now, To relax this structure we can use the `CalcExeuctor` interface with MACE-MP-0:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "from ase.optimize import BFGS\n", | ||
| "out = CalcExecutor(mol,\n", | ||
| " relax=True, # Optimize the molecule\n", | ||
| " method='custom', # Use arbirtrary method.\n", | ||
| " calculator=calc, # Set the calc to be MACE-MP-0\n", | ||
| " ase_opt_method=BFGS, # Set ASE optimizer\n", | ||
| " save_trajectories=True, # Save the trajectories\n", | ||
| " debug=True) # Show the printout to verify it is using the methods asked for." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Now we can view the relaxation trajectory in its entirety\n", | ||
| "print('Relaxed')\n", | ||
| "view_structures(out.mol)\n", | ||
| "print('Trajectory')\n", | ||
| "view_structures(out.trajectory, trajectory=True, interval=600)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "# Also, the energy and initial energies, and any errors are stored in the output object\n", | ||
| "for key, val in out.__dict__.items():\n", | ||
| " if (key != 'parameters') and (key not in out.__dict__['parameters']):\n", | ||
| " print(key, ':', val)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## (B) Using arbirtrary ASE calculators to perform energy evaluations.\n", | ||
| "\n", | ||
| "Here, we can directly pluging calculators to the full architector search:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "inputDict = {'core':{'metal':'Fe','coreCN':6}, # Specify metal coordination number (CN)\n", | ||
| " 'ligands':['water']*6, # Specify what is filling the coordination environment\n", | ||
| " 'parameters':{'calculator':calc, # Assign ASE calculator \n", | ||
| " 'assemble_method':'UFF', # Use UFF for assembly\n", | ||
| " 'full_method':'custom'}} # Give 'custom' as a flag to use alternative calculator\n", | ||
| "fe_h2o_6_out = build_complex(inputDict); # Now just build using the dictionary!\n", | ||
| "view_structures(fe_h2o_6_out)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Note that Architector will assign the unpaired electrons to the ASE atoms object in the atoms\n", | ||
| "`initial magnetic moments` and the charges in the `initial charges` placeholders.\n", | ||
| "\n", | ||
| "Implementation of calculators may differ on whether this works or not." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## (C) Using arbirtrary ASE calculators to perform energy evaluations.\n", | ||
| "\n", | ||
| "Here, we can directly use other ASE optimizers as well, the default is LBFGSLineSearch. So Let's USE BFGS." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "inputDict = {'core':{'metal':'Fe','coreCN':1}, # Specify metal coordination number (CN)\n", | ||
| " 'ligands':['water'], # Specify what is filling the coordination environment\n", | ||
| " 'parameters':{'ase_opt_method':BFGS, # Directly pass the optimizer object\n", | ||
| " 'debug':True # Use debug to show that it is using BFGS instead of LBFGSLineSearch\n", | ||
| " }} \n", | ||
| "fe_h2o_out = build_complex(inputDict); # Now just build using the dictionary!" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "view_structures(fe_h2o_out)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "### Summary: In this tutorial we learned how to use external ASE calculators and optimizers within the architector framework. Including:\n", | ||
| "\n", | ||
| "**(A)** Using arbitrary methods to perform energy/relaxations.\n", | ||
| "\n", | ||
| "**(B)** How to use example ASE calculator (MACE-MP-0) within Architector complex construction.\n", | ||
| "\n", | ||
| "**(C)** How to use arbirtrary ASE optimizers within Architector." | ||
| ] | ||
| } | ||
| ], | ||
| "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": "3.10.12" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 4 | ||
| } |