Pavlo O. Dral

Pavlo O. Dral, Fuchun Ge, Yi-Fan Hou et al.

Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows. This open-source package provides plenty of choice to the users who can run simulations with the command line options, input files, or with scripts using MLatom as a Python package, both on their computers and on the online XACS cloud computing at XACScloud.com. Computational chemists can calculate energies and thermochemical properties, optimize geometries, run molecular and quantum dynamics, and simulate (ro)vibrational, one-photon UV/vis absorption, and two-photon absorption spectra with ML, quantum mechanical, and combined models. The users can choose from an extensive library of methods containing pre-trained ML models and quantum mechanical approximations such as AIQM1 approaching coupled-cluster accuracy. The developers can build their own models using various ML algorithms. The great flexibility of MLatom is largely due to the extensive use of the interfaces to many state-of-the-art software packages and libraries.

Yuxinxin Chen, Pavlo O. Dral

Machine learning (ML) potentials typically target a single quantum chemical (QC) level while the ML models developed for multi-fidelity learning have not been shown to provide scalable solutions for foundational models. Here we introduce the all-in-one (AIO) ANI model architecture based on multimodal learning which can learn an arbitrary number of QC levels. Our all-in-one learning approach offers a more general and easier-to-use alternative to transfer learning. We use it to train the AIO-ANI-UIP foundational model with the generalization capability comparable to semi-empirical GFN2-xTB and DFT with a double-zeta basis set for organic molecules. We show that the AIO-ANI model can learn across different QC levels ranging from semi-empirical to density functional theory to coupled cluster. We also use AIO models to design the foundational model Δ-AIO-ANI based on Δ-learning with increased accuracy and robustness compared to AIO-ANI-UIP. The code and the foundational models are available at https://github.com/dralgroup/aio-ani; they will be integrated into the universal and updatable AI-enhanced QM (UAIQM) library and made available in the MLatom package so that they can be used online at the XACS cloud computing platform (see https://github.com/dralgroup/mlatom for updates).

Yi-Fan Hou, Lina Zhang, Quanhao Zhang et al.

Quantum chemical simulations can be greatly accelerated by constructing machine learning potentials, which is often done using active learning (AL). The usefulness of the constructed potentials is often limited by the high effort required and their insufficient robustness in the simulations. Here we introduce the end-to-end AL for constructing robust data-efficient potentials with affordable investment of time and resources and minimum human interference. Our AL protocol is based on the physics-informed sampling of training points, automatic selection of initial data, uncertainty quantification, and convergence monitoring. The versatility of this protocol is shown in our implementation of quasi-classical molecular dynamics for simulating vibrational spectra, conformer search of a key biochemical molecule, and time-resolved mechanism of the Diels-Alder reactions. These investigations took us days instead of weeks of pure quantum chemical calculations on a high-performance computing cluster. The code in MLatom and tutorials are available at https://github.com/dralgroup/mlatom.

Jakub Martinka, Lina Zhang, Yi-Fan Hou et al.

Nonadiabatic couplings (NACs) play a crucial role in modeling photochemical and photophysical processes with methods such as the widely used fewest-switches surface hopping (FSSH). There is therefore a strong incentive to machine learn NACs for accelerating simulations. However, this is challenging due to NACs' vectorial, double-valued character and the singularity near a conical intersection seam. For the first time, we design NAC-specific descriptors based on our domain expertise and show that they allow learning NACs with never-before-reported accuracy of $R^2$ exceeding 0.99. The key to success is also our new ML phase-correction procedure. We demonstrate the efficiency and robustness of our approach on a prototypical example of fully ML-driven FSSH simulations of fulvene targeting the SA-2-CASSCF(6,6) electronic structure level. This ML-FSSH dynamics leads to an accurate description of $S_1$ decay while reducing error bars by allowing the execution of a large ensemble of trajectories. Our implementations are available in open-source MLatom.

Jinming Hu, Hassan Nawaz, Yuting Rui et al.

We have developed Aitomia - a platform powered by AI to assist in performing AI-driven atomistic and quantum chemical (QC) simulations. This evolving intelligent assistant platform is equipped with chatbots and AI agents to help experts and guide non-experts in setting up and running atomistic simulations, monitoring their computational status, analyzing simulation results, and summarizing them for the user in both textual and graphical forms. We achieve these goals by exploiting large language models that leverage the versatility of our MLatom ecosystem, supporting AI-enhanced computational chemistry tasks ranging from ground-state to excited-state calculations, including geometry optimizations, thermochemistry, and spectral calculations. The multi-agent implementation enables autonomous executions of the complex computational workflows, such as the computation of the reaction enthalpies. Aitomia is the first intelligent assistant publicly accessible online on a cloud computing platform for atomistic simulations of broad scope (Aitomistic Hub at https://aitomistic.xyz). It may also be deployed locally as described at http://mlatom.com/aitomia. Aitomia is expected to lower the barrier to performing atomistic simulations, thereby democratizing simulations and accelerating research and development in relevant fields.

Fuchun Ge, Pavlo O. Dral

Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a pre-trained foundational model, MDtrajNet-1, that directly generates MD trajectories across chemical space, bypassing force calculations and integration. This approach accelerates simulations by up to two orders of magnitude compared to traditional MD, even those enhanced by machine-learning interatomic potentials. MDtrajNet combines equivariant neural networks with a transformer-based architecture to achieve strong accuracy and transferability in predicting long-time trajectories. Remarkably, the errors of the trajectories generated by MDtrajNet-1 for various known and unseen molecular systems are close to those of the conventional ab initio MD. The architecture's flexible design supports diverse application scenarios, including different statistical ensembles, boundary conditions, and interaction types. By overcoming the intrinsic speed barrier of conventional MD, MDtrajNet opens new frontiers in efficient and scalable atomistic simulations.