skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.


Title: Transferability evaluation of the deep potential model for simulating water-graphene confined system
Machine learning potentials (MLPs) are poised to combine the accuracy of ab initio predictions with the computational efficiency of classical molecular dynamics (MD) simulation. While great progress has been made over the last two decades in developing MLPs, there is still much to be done to evaluate their model transferability and facilitate their development. In this work, we construct two deep potential (DP) models for liquid water near graphene surfaces, Model S and Model F, with the latter having more training data. A concurrent learning algorithm (DP-GEN) is adopted to explore the configurational space beyond the scope of conventional ab initio MD simulation. By examining the performance of Model S, we find that an accurate prediction of atomic force does not imply an accurate prediction of system energy. The deviation from the relative atomic force alone is insufficient to assess the accuracy of the DP models. Based on the performance of Model F, we propose that the relative magnitude of the model deviation and the corresponding root-mean-square error of the original test dataset, including energy and atomic force, can serve as an indicator for evaluating the accuracy of the model prediction for a given structure, which is particularly applicable for large systems where density functional theory calculations are infeasible. In addition to the prediction accuracy of the model described above, we also briefly discuss simulation stability and its relationship to the former. Both are important aspects in assessing the transferability of the MLP model.  more » « less
Award ID(s):
1940118
PAR ID:
10467933
Author(s) / Creator(s):
; ;
Publisher / Repository:
API Water
Date Published:
Journal Name:
The Journal of Chemical Physics
Volume:
159
Issue:
4
ISSN:
0021-9606
Page Range / eLocation ID:
Article number 044712
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. An exploration of the “on-the-fly” nonadiabatic couplings (NACs) for nonradiative relaxation and recombination of excited states in 2D Dion–Jacobson (DJ) lead halide perovskites (LHPs) is accelerated by a machine learning approach. Specifically, ab initio molecular dynamics (AIMD) of nanostructures composed of heavy elements is performed with the use of machine-learning force-fields (MLFFs), as implemented in the Vienna Ab initio Simulation Package (VASP). The force field parametrization is established using on-the-fly learning, which continuously builds a force field using AIMD data. At each time step of the molecular dynamics (MD) simulation, the total energy and forces are predicted based on the MLFF and if the Bayesian error estimate exceeds a threshold, an ab initio calculation is performed, which is used to construct a new force field. Model training of MLFF and evaluation were performed for a range of DJ-LHP models of different thicknesses and halide compositions. The MLFF-MD trajectories were evaluated against pure AIMD trajectories to assess the level of discrepancy and error accumulation. To examine the practical effectiveness of this approach, we have used the MLFF-based MD trajectories to compute NAC and excited-state dynamics. At each stage, results based on machine learning are compared to traditional ab initio based electronic dissipative dynamics. We find that MLFF-MD provides comparable results to AIMDs when MLFF is trained in an NPT ensemble. 
    more » « less
  2. Abstract We present PyXtal_FF—a package based on Python programming language—for developing machine learning potentials (MLPs). The aim of PyXtal_FF is to promote the application of atomistic simulations through providing several choices of atom-centered descriptors and machine learning regressions in one platform. Based on the given choice of descriptors (including the atom-centered symmetry functions, embedded atom density, SO4 bispectrum, and smooth SO3 power spectrum), PyXtal_FF can train MLPs with either generalized linear regression or neural network models, by simultaneously minimizing the errors of energy/forces/stress tensors in comparison with the data fromab-initiosimulations. The trained MLP model from PyXtal_FF is interfaced with the Atomic Simulation Environment (ASE) package, which allows different types of light-weight simulations such as geometry optimization, molecular dynamics simulation, and physical properties prediction. Finally, we will illustrate the performance of PyXtal_FF by applying it to investigate several material systems, including the bulk SiO2, high entropy alloy NbMoTaW, and elemental Pt for general purposes. Full documentation of PyXtal_FF is available athttps://pyxtal-ff.readthedocs.io. 
    more » « less
  3. Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of ab initio molecular dynamics simulation. Integrating both atomic force and energy in predictions was found to be more accurate than using energy alone, yet it requires O(( NM) 3 ) computational operations for computing the likelihood function and making predictions, where N is the number of atoms and M is the number of simulated configurations in the training sample due to the inversion of a large covariance matrix. The high computational cost limits its applications to the simulation of small molecules. The computational challenge of using both gradient information and function values in GPs was recently noticed in machine learning communities, whereas conventional approximation methods may not work well. Here, we introduce a new approach, the atomized force field model, that integrates both force and energy in the emulator with many fewer computational operations. The drastic reduction in computation is achieved by utilizing the naturally sparse covariance structure that satisfies the constraints of the energy conservation and permutation symmetry of atoms. The efficient machine learning algorithm extends the limits of its applications on larger molecules under the same computational budget, with nearly no loss of predictive accuracy. Furthermore, our approach contains an uncertainty assessment of predictions of atomic forces and energies, useful for developing a sequential design over the chemical input space. 
    more » « less
  4. Abstract Atomistic modeling of chemically reactive systems has so far relied on either expensive ab initio methods or bond-order force fields requiring arduous parametrization. Here, we describe a Bayesian active learning framework for autonomous “on-the-fly” training of fast and accurate reactive many-body force fields during molecular dynamics simulations. At each time-step, predictive uncertainties of a sparse Gaussian process are evaluated to automatically determine whether additional ab initio training data are needed. We introduce a general method for mapping trained kernel models onto equivalent polynomial models whose prediction cost is much lower and independent of the training set size. As a demonstration, we perform direct two-phase simulations of heterogeneous H2turnover on the Pt(111) catalyst surface at chemical accuracy. The model trains itself in three days and performs at twice the speed of a ReaxFF model, while maintaining much higher fidelity to DFT and excellent agreement with experiment. 
    more » « less
  5. Abstract A next‐generation protocol (Poltype 2) has been developed which automatically generates AMOEBA polarizable force field parameters for small molecules. Both features and computational efficiency have been drastically improved. Notable advances include improved database transferability using SMILES, robust torsion fitting, non‐aromatic ring torsion parameterization, coupled torsion‐torsion parameterization, Van der Waals parameter refinement using ab initio dimer data and an intelligent fragmentation scheme that produces parameters with dramatically reduced ab initio computational cost. Additional improvements include better local frame assignment for atomic multipoles, automated formal charge assignment, Zwitterion detection, smart memory resource defaults, parallelized fragment job submission, incorporation of Psi4 quantum package, ab initio error handling, ionization state enumeration, hydration free energy prediction and binding free energy prediction. For validation, we have applied Poltype 2 to ~1000 FDA approved drug molecules from DrugBank. The ab initio molecular dipole moments and electrostatic potential values were compared with Poltype 2 derived AMOEBA counterparts. Parameters were further substantiated by calculating hydration free energy (HFE) on 40 small organic molecules and were compared with experimental data, resulting in an RMSE error of 0.59 kcal/mol. The torsion database has expanded to include 3543 fragments derived from FDA approved drugs. Poltype 2 provides a convenient utility for applications including binding free energy prediction for computational drug discovery. Further improvement will focus on automated parameter refinement by experimental liquid properties, expansion of the Van der Waals parameter database and automated parametrization of modified bio‐fragments such as amino and nucleic acids. 
    more » « less