cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24435/materialscloud:qk-mn
title: A genetic optimization strategy with generality in asymmetric organocatalysis as primary target

description: A catalyst possessing a broad substrate scope, in terms of both turnover and enantioselectivity, is sometimes called "general". Despite their great utility in asymmetric synthesis, truly general catalysts are difficult or expensive to discover via traditional high-throughput screening and are, therefore, rare. Existing computational tools accelerate the evaluation of reaction conditions from a pre-defined set of experiments to identify the most general ones, but cannot generate entirely new catalysts with enhanced substrate breadth. For these reasons, we report an inverse design strategy based on the open-source genetic algorithm NaviCatGA and on the OSCAR database of organocatalysts to simultaneously probe the catalyst and substrate scope and optimize generality as primary target. We apply this strategy to the Pictet–Spengler condensation, for which we curate a database of 820 reactions, used to train statistical models of selectivity and activity. Starting from OSCAR, we define a combinatorial space of millions of catalyst possibilities, and perform evolutionary experiments on a diverse substrate scope that is representative of the whole chemical space of tetrahydro-β-carboline products. While privileged catalysts emerge, we show how genetic optimization can address the broader question of generality in asymmetric synthesis, extracting structure–performance relationships from the challenging areas of chemical space.
DOI: 10.24435/materialscloud:k2-e4
title: High throughput inverse design and Bayesian optimization of functionalities: spin splitting in two-dimensional compounds

description: The development of spintronic devices demands the existence of materials with some kind of spin splitting (SS). In this work, we have built a database of ab initio calculated SS in 2D materials. More than that, we propose a workflow for materials design integrating an inverse design approach and a Bayesian inference optimization.  We use the prediction of SS prototypes for spintronic applications as an illustrative example of the proposed workflow. The prediction process starts with the establishment of the design principles (the physical mechanism behind the target properties), that are used as filters for materials screening, and followed by density functional theory (DFT) calculations. Applying this process to the C2DB database, we identify and classify 315 2D materials according to SS type at the valence and/or conduction bands. The Bayesian optimization captures trends that are used for the rationalized design of 2D materials with the ideal conditions of band gap and SS for potential spintronics applications. This repository then contains the main source of data generated in this work, which encompasses full information regarding the materials structure and band structure calculations results, and a database of all the identified spin splittings for these compounds, available in multiple formats.
DOI: 10.24435/materialscloud:kr-7s
title: High throughput inverse design and Bayesian optimization of functionalities: spin splitting in two-dimensional compounds

description: The development of spintronic devices demands the existence of materials with some kind of spin splitting (SS). In this work, we have built a database of ab initio calculated SS in 2D materials. More than that, we propose a workflow for materials design integrating an inverse design approach and a Bayesian inference optimization.  We use the prediction of SS prototypes for spintronic applications as an illustrative example of the proposed workflow. The prediction process starts with the establishment of the design principles (the physical mechanism behind the target properties), that are used as filters for materials screening, and followed by density functional theory (DFT) calculations. Applying this process to the C2DB database, we identify and classify 315 2D materials according to SS type at the valence and/or conduction bands. The Bayesian optimization captures trends that are used for the rationalized design of 2D materials with the ideal conditions of band gap and SS for potential spintronics applications. This repository then contains the main source of data generated in this work, which encompasses full information regarding the materials structure and band structure calculations results, and a database of all the identified spin splittings for these compounds, available in multiple formats.
DOI: 10.24435/materialscloud:ze-58
title: High-throughput computation of Raman spectra from first principles

description: Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Raman spectra can be simulated using atomistic first-principles methods but these are computationally demanding and thus the existing databases of computational Raman spectra are fairly small. We developed an optimized workflow to efficiently calculate the Raman tensors, from which the Raman spectra can be straightforwardly simulated. The workflow was benchmarked and validated by comparison to experiments and previous computational methods for select technologically relevant material systems. Using the workflow, we performed high-throughput calculations for a large set of materials (5099) belonging to many different material classes, and collected the results to a database.
DOI: 10.24435/materialscloud:pg-h3
title: High-throughput computation of Raman spectra from first principles

description: Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Raman spectra can be simulated using atomistic first-principles methods but these are computationally demanding and thus the existing databases of computational Raman spectra are fairly small. We developed an optimized workflow to efficiently calculate the Raman tensors, from which the Raman spectra can be straightforwardly simulated. The workflow was benchmarked and validated by comparison to experiments and previous computational methods for select technologically relevant material systems. Using the workflow, we performed high-throughput calculations for a large set of materials (5099) belonging to many different material classes, and collected the results to a database.
DOI: 10.24435/materialscloud:js-pz
title: SPAᴴM: the spectrum of approximated hamiltonian matrices representations

description: Physics-inspired molecular representations are the cornerstone of similarity-based learning applied to solve chemical problems. Despite their conceptual and mathematical diversity, this class of descriptors shares a common underlying philosophy: they all rely on the molecular information that determines the form of the electronic Schrödinger equation. Existing representations take the most varied forms, from non-linear functions of atom types and positions to atom densities and potential, up to complex quantum chemical objects directly injected into the ML architecture. In this work, we present the Spectrum of Approximated Hamiltonian Matrices (SPAᴴM) as an alternative pathway to construct quantum machine learning representations through leveraging the foundation of the electronic Schrödinger equation itself: the electronic Hamiltonian. As the Hamiltonian encodes all quantum chemical information at once, SPAᴴM representations not only distinguish different molecules and conformations, but also different spin, charge, and electronic states. As a proof of concept, we focus here on efficient SPAᴴM representations built from the eigenvalues of a hierarchy of well-established and readily-evaluated "guess" Hamiltonians. These SPAᴴM representations are particularly compact and efficient for kernel evaluation and their complexity is independent of the number of different atom types in the database
DOI: 10.24435/materialscloud:nk-8g
title: High-throughput computation of Raman spectra from first principles

description: Raman spectroscopy is a widely-used non-destructive material characterization method, which provides information about the vibrational modes of the material and therefore of its atomic structure and chemical composition. Raman spectra can be simulated using atomistic first-principles methods but these are computationally demanding and thus the existing databases of computational Raman spectra are fairly small. We developed an optimized workflow to efficiently calculate the Raman tensors, from which the Raman spectra can be straightforwardly simulated. The workflow was benchmarked and validated by comparison to experiments and previous computational methods for select technologically relevant material systems. Using the workflow, we performed high-throughput calculations for a large set of materials (5099) belonging to many different material classes, and collected the results to a database.
DOI: 10.24435/materialscloud:8t-fv
title: SPAᴴM: the spectrum of approximated hamiltonian matrices representations

description: Physics-inspired molecular representations are the cornerstone of similarity-based learning applied to solve chemical problems. Despite their conceptual and mathematical diversity, this class of descriptors shares a common underlying philosophy: they all rely on the molecular information that determines the form of the electronic Schrödinger equation. Existing representations take the most varied forms, from non-linear functions of atom types and positions to atom densities and potential, up to complex quantum chemical objects directly injected into the ML architecture. In this work, we present the Spectrum of Approximated Hamiltonian Matrices (SPAᴴM) as an alternative pathway to construct quantum machine learning representations through leveraging the foundation of the electronic Schrödinger equation itself: the electronic Hamiltonian. As the Hamiltonian encodes all quantum chemical information at once, SPAᴴM representations not only distinguish different molecules and conformations, but also different spin, charge, and electronic states. As a proof of concept, we focus here on efficient SPAᴴM representations built from the eigenvalues of a hierarchy of well-established and readily-evaluated "guess" Hamiltonians. These SPAᴴM representations are particularly compact and efficient for kernel evaluation and their complexity is independent of the number of different atom types in the database
DOI: 10.24435/materialscloud:m2-09
title: A transferable force field for gallium nitride crystal growth from the melt using on-the-fly active learning

description: Atomic-scale simulations of reactive processes have been stymied by two factors: the general lack of a suitable semi-empirical force field on the one hand, and the impractically large computational burden of using ab initio molecular dynamics on the other. In this paper, we use an "on-the-fly" active learning technique to develop a non-parameterized force field that, in essence, exhibits the accuracy of density functional theory and the speed of a classical molecular dynamics simulation. We developed a force field suitable to capture the crystallization of gallium nitride (GaN) using a novel additive manufacturing route and a combination of liquid Ga and ammonia gas precursors to grow GaN thin films. We show that this machine learning model is capable of producing a transferable force field that can model all three phases, solid, liquid and gas, involved in this additive manufacturing process. We verified our computational results against a range of experimental measurements and ab initio molecular dynamics simulation, showing that this non-parametric force field shows excellent accuracy as well as a computationally tractable efficiency. The development of this transferable force field opens the opportunity to simulate liquid phase epitaxial growth more accurately than before, analyze reaction and diffusion processes, and ultimately establish a growth model of the additive manufacturing process to create gallium nitride thin films.
In this archive, we included the mapped Gaussian Process force field parameters of gallium and gallium nitride for LAMMPS simulations. Users can download these force field parameters to test and recreate similar Molecular Dynamic simulation discussed in the paper.
DOI: 10.24435/materialscloud:6e-46
title: A transferable force field for gallium nitride crystal growth from the melt using on-the-fly active learning

description: Atomic-scale simulations of reactive processes have been stymied by two factors: the lack of a suitable semi-empirical force field on the one hand, and the impractically large computational burden of using ab initio molecular dynamics on the other. In this paper, we use an "on-the-fly" active learning technique to develop a non-parameterized force field that, in essence, exhibits the accuracy of density functional theory and the speed of a classical molecular dynamics simulation. We developed a force field capable of capturing the crystallization of gallium nitride (GaN) during a novel additive manufacturing process featuring the reaction of liquid Ga and gaseous nitrogen precursors to grow crystalline GaN thin films. We show that this machine learning model is capable of producing a single force field that can model solid, liquid and gas phases involved in the process. We verified our computational predictions against a range of experimental measurements relevant to each phase and against ab initio calculations, showing that this non-parametric force field produces properties with excellent accuracy as well as exhibiting a computationally tractable efficiency. The force field is capable of allowing us to simulate the solid/liquid coexistence interface and the crystallization of GaN from the melt. The development of this transferable force field opens the opportunity to simulate liquid phase epitaxial growth more accurately than before, to analyze reaction and diffusion processes, and ultimately establish a growth model of the additive manufacturing process to create gallium nitride thin films.
In this archive, we included the LAMMPS compatible force field parameters of gallium nitride developed with FLARE++. Users can download these force field parameters to test and recreate similar Molecular Dynamic simulation discussed in the paper.
DOI: 10.24435/materialscloud:57-cj
title: A transferable force field for gallium nitride crystal growth from the melt using on-the-fly active learning

description: Atomic-scale simulations of reactive processes have been stymied by two factors: the lack of a suitable semi-empirical force field on the one hand, and the impractically large computational burden of using ab initio molecular dynamics on the other. In this paper, we use an "on-the-fly" active learning technique to develop a non-parameterized force field that, in essence, exhibits the accuracy of density functional theory and the speed of a classical molecular dynamics simulation. We developed a force field capable of capturing the crystallization of gallium nitride (GaN) during a novel additive manufacturing process featuring the reaction of liquid Ga and gaseous nitrogen precursors to grow crystalline GaN thin films. We show that this machine learning model is capable of producing a single force field that can model solid, liquid and gas phases involved in the process. We verified our computational predictions against a range of experimental measurements relevant to each phase and against ab initio calculations, showing that this non-parametric force field produces properties with excellent accuracy as well as exhibiting a computationally tractable efficiency. The force field is capable of allowing us to simulate the solid/liquid coexistence interface and the crystallization of GaN from the melt. The development of this transferable force field opens the opportunity to simulate liquid phase epitaxial growth more accurately than before, to analyze reaction and diffusion processes, and ultimately establish a growth model of the additive manufacturing process to create gallium nitride thin films.
In this archive, we included the LAMMPS compatible force field parameters of gallium nitride developed with FLARE++. Users can download these force field parameters to test and recreate similar Molecular Dynamic simulation discussed in the paper.
DOI: 10.24435/materialscloud:j6-js
title: A transferable force field for gallium nitride crystal growth from the melt using on-the-fly active learning

description: Atomic-scale simulations of reactive processes have been stymied by two factors: the lack of a suitable semi-empirical force field on the one hand, and the impractically large computational burden of using ab initio molecular dynamics on the other. In this paper, we use an "on-the-fly" active learning technique to develop a non-parameterized force field that, in essence, exhibits the accuracy of density functional theory and the speed of a classical molecular dynamics simulation. We developed a force field capable of capturing the crystallization of gallium nitride (GaN) during a novel additive manufacturing process featuring the reaction of liquid Ga and gaseous nitrogen precursors to grow crystalline GaN thin films. We show that this machine learning model is capable of producing a single force field that can model solid, liquid and gas phases involved in the process. We verified our computational predictions against a range of experimental measurements relevant to each phase and against ab initio calculations, showing that this non-parametric force field produces properties with excellent accuracy as well as exhibiting a computationally tractable efficiency. The force field is capable of allowing us to simulate the solid/liquid coexistence interface and the crystallization of GaN from the melt. The development of this transferable force field opens the opportunity to simulate liquid phase epitaxial growth more accurately than before, to analyze reaction and diffusion processes, and ultimately establish a growth model of the additive manufacturing process to create gallium nitride thin films.
In this archive, we included the LAMMPS compatible force field parameters of gallium nitride developed with FLARE++. Users can download these force field parameters to test and recreate similar Molecular Dynamic simulation discussed in the paper.
DOI: 10.24435/materialscloud:r0-84
title: Active learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt

description: 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 H2 turnover 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.
DOI: 10.24435/materialscloud:g0-64
title: Active learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt

description: 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 H2 turnover 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.
DOI: 10.24435/materialscloud:jy-tw
title: Investigating finite-size effects in computer simulations of superionic materials

description: The effects of the finite size of the simulation box in equilibrium molecular dynamics simulations are investigated for prototypical superionic conductors of different types, namely the fluorite-structure materials PbF2, CaF2, and UO2 (type II), and the alpha phase of AgI (type I). Largely validated empirical force-fields are employed to run ns-long simulations and extract general trends for several properties, at increasing size and in a wide temperature range.
This work shows that, for the considered type-II superionic conductors, the diffusivity dramatically depend on the system size and that the superionic regime is shifted to larger temperatures in smaller cells. Furthermore, only simulations of several hundred atoms are able to capture the experimentally-observed, characteristic change in the activation energy of the diffusion process, occurring at the order-disorder transition to the superionic regime. Finite-size effects on ion diffusion are instead much weaker in alpha-AgI. The thermal conductivity is found generally smaller for smaller cells, where the temperature-independent (Allen-Feldman) regime is also reached at significantly lower temperatures. The finite-size effects on the thermal motion of the non-mobile ions composing the solid matrix follow the simple law which holds for solids.
In this record, I collect the input files employed to run the simulations, the data obtained from the latter and the Jupiter Notebook used to analyze the data.
DOI: 10.24435/materialscloud:bf-3h
title: Investigating finite-size effects in computer simulations of superionic materials

description: The effects of the finite size of the simulation box in equilibrium molecular dynamics simulations are investigated for prototypical superionic conductors of different types, namely the fluorite-structure materials PbF2, CaF2, and UO2 (type II), and the alpha phase of AgI (type I). Largely validated empirical force-fields are employed to run ns-long simulations and extract general trends for several properties, at increasing size and in a wide temperature range.
This work shows that, for the considered type-II superionic conductors, the diffusivity dramatically depend on the system size and that the superionic regime is shifted to larger temperatures in smaller cells. Furthermore, only simulations of several hundred atoms are able to capture the experimentally-observed, characteristic change in the activation energy of the diffusion process, occurring at the order-disorder transition to the superionic regime. Finite-size effects on ion diffusion are instead much weaker in alpha-AgI. The thermal conductivity is found generally smaller for smaller cells, where the temperature-independent (Allen-Feldman) regime is also reached at significantly lower temperatures. The finite-size effects on the thermal motion of the non-mobile ions composing the solid matrix follow the simple law which holds for solids.
In this record, I collect the input files employed to run the simulations, the data obtained from the latter and the Jupiter Notebook used to analyze the data.