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| from ase.build import molecule | |
| from ase.optimize import FIRE | |
| from ase.vibrations import Vibrations | |
| import time | |
| def run_vibrational_analysis(atoms, calculator, calc_name, box_size=20.0, fmax=0.01, steps=500): | |
| """ | |
| Function to perform optimization, vibrational analysis, and print the summary. | |
| Parameters: | |
| atoms - The ASE Atoms object (e.g., a molecule) | |
| calculator - The calculator to be used for optimization and vibrations | |
| calc_name - Name of the calculator (used in the output files) | |
| box_size - Size of the simulation box (default 20.0 Å) | |
| fmax - Maximum force for optimization (default 0.01 eV/Å) | |
| steps - Maximum steps for optimization (default 500) | |
| """ | |
| # Get timestamp for file names | |
| timestamp = time.strftime("%Y%m%d_%H%M%S") | |
| # Center molecule inside the box and set cell dimensions | |
| #atoms = molecule('H2O') | |
| atoms.center(vacuum=box_size / 2) | |
| atoms.set_cell([box_size, box_size, box_size]) | |
| atoms.set_pbc([True, True, True]) # No periodic boundary conditions | |
| # Step 2: Set the calculator | |
| atoms.set_calculator(calculator) | |
| # Step 3: Perform optimization | |
| opt = FIRE(atoms) | |
| opt.run(fmax=fmax, steps=steps) | |
| # Step 4: Perform vibrational analysis | |
| vib = Vibrations(atoms) | |
| vib.run() | |
| # Step 5: Save vibrational analysis summary to a log file | |
| summary_file = f'{timestamp}_{calc_name}_vib_summary.txt' | |
| vib.summary(log=summary_file) | |
| vib.clean() | |
| # Print vibrational summary | |
| with open(summary_file, 'r') as file: | |
| print(f"Vibrational analysis summary for {calc_name}:") | |
| print(file.read()) | |
| # Example usage with ORBCalculator and SevenNetCalculator | |
| if __name__ == "__main__": | |
| from orb_models.forcefield import pretrained | |
| from orb_models.forcefield.calculator import ORBCalculator | |
| from sevenn.sevennet_calculator import SevenNetCalculator | |
| # Prepare ORB Forcefield for calculation | |
| orbff = pretrained.orb_d3_v1(device='cuda') | |
| orbcalc = ORBCalculator(orbff, device="cuda") | |
| atoms = molecule('H2O') | |
| # Run vibrational analysis for ORBCalculator | |
| run_vibrational_analysis(atoms, orbcalc, 'ORBCalculator') | |
| # Prepare SevenNetCalculator for calculation | |
| scalc = SevenNetCalculator(device="cuda") | |
| run_vibrational_analysis(atoms, scalc, 'SevenNetCalculator') |
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