ML of excited states

There are several ways to learn and predict excited-state energies and forces with MLatom which are shown below. It is recommended that you get familiar with excited-state data format in MLatom which are required for training ML models. See the manuals for other cases such as application of ML for UV/vis one- and two-photon absorption calculations.

Multi-state ANI models

Multi-state learning model (MS-ANI) that has unrivaled accuracy for excited state properties (accuracy is often better than for models targeting only ground state!). We demonstrate that this model can be used for trajectory-surface hopping of multiple molecules (not just for a single molecule!) in:

  • Mikołaj Martyka, Lina Zhang, Fuchun Ge, Yi-Fan Hou, Joanna Jankowska, Mario Barbatti, Pavlo O. Dral. Charting electronic-state manifolds across molecules with multi-state learning and gap-driven dynamics via efficient and robust active learning. 2024. Preprint on ChemRxiv: https://doi.org/10.26434/chemrxiv-2024-dtc1w.

Zip with tutorial materials including Jupyter notebook:

msani

ML-NAMD with single-state models

In this tutorial, we show an example of running surface-hopping MD with single-state ML models. Please see a separate tutorial on machine learning potentials.

See our paper for more details (please also cite it if you use the corresponding features):

You can download the Jupyter notebook with the required initial conditions and ML models from this paper.

The tutorial calculations are very fast and you should be able to get the final population plot for 5 fs with 0.25 fs time step from 30 trajectories within a minute. Here is the Jupyter notebook code snippet:

import mlatom as ml
import os
import numpy as np

# Read initial conditions
init_cond_db = ml.data.molecular_database.load(filename='materials/init_cond_db_for_pyrazine.json', format='json')

# We need to create a class that accepts the specific arguments shown below and saves the calculated electronic state properties in the molecule object
class mlmodels():
    def __init__(self, nstates = 5):
        folder_with_models = 'materials/lz_models'
        self.models = [None for istate in range(nstates)]
        for istate in range(nstates):
            self.models[istate] = [ml.models.ani(model_file=f'{folder_with_models}/ensemble{ii+1}s{istate}.pt') for ii in range(2)]
            for ii in range(2): self.models[istate][ii].nthreads = 1

    def predict(self,
            molecule=None,
            nstates=5,
            current_state=0,
            calculate_energy=True,
            calculate_energy_gradients=True):

        molecule.electronic_states = [molecule.copy() for ii in range(nstates)]

        for istate in range(nstates):
            moltmp = molecule.electronic_states[istate]
            moltmpens = [moltmp.copy() for ii in range(2)]
            for ii in range(2):
                self.models[istate][ii].predict(molecule=moltmpens[ii], calculate_energy = True, calculate_energy_gradients = True)
            moltmp.energy = np.mean([moltmpens[ii].energy for ii in range(2)])
            moltmp.energy_gradients = np.mean([moltmpens[ii].energy_gradients for ii in range(2)], axis=0)

        molecule.energy = molecule.electronic_states[current_state].energy
        molecule.energy_gradients = molecule.electronic_states[current_state].energy_gradients

models = mlmodels()

# Arguments for running NAMD trajectories
timemax = 5 # fs
namd_kwargs = {
            'model': models,
            'time_step': 0.25, # fs
            'maximum_propagation_time': timemax,
            'dump_trajectory_interval': None,
            'hopping_algorithm': 'LZBL',
            'nstates': 5,
            'random_seed': 1, # making sure that the hopping probabilities are the same (should not be used in actual calculations!)
            'rescale_velocity_direction': 'along velocities',
            'reduce_kinetic_energy': False,
            }

# Run 30 trajectories
dyns = ml.simulations.run_in_parallel(molecular_database=init_cond_db[:30], task=ml.namd.surface_hopping_md, task_kwargs=namd_kwargs)
trajs = [d.molecular_trajectory for d in dyns]
ml.namd.analyze_trajs(trajectories=trajs, maximum_propagation_time=timemax)

# Dump the trajectories
for itraj in range(len(trajs)):
    trajs[itraj].dump(filename=f'traj{itraj+1}.json', format='json')

# Prepare the population plot
ml.namd.plot_population(trajectories=trajs, time_step=0.25,
                        max_propagation_time=timemax, nstates=5, filename=f'pop.png')

Since we used the fixed random seed, you should get the following final population:

_images/pyrazine_lznamd_ml_population.png