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At least 235 records · Page 13

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

Scientific machine learning for modeling and simulating complex fluids

The formulation of rheological constitutive equations—models that relate internal stresses and deformations in complex fluids—is a critical step in the engineering of systems involving soft materials. While data-driven models provide accessible alternatives to expensive first-principles models and less accurate empirical models in many engineering disciplines, the development of similar models for complex fluids has lagged. The diversity of techniques for characterizing non-Newtonian fluid dynamics creates a challenge for classical machine learning approaches, which require uniformly structured training data. Consequently, early machine-learning based constitutive equations have not been portable between different deformation protocols or mechanical observables. Here, we present a data-driven framework that resolves such issues, allowing rheologists to construct learnable models that incorporate essential physical information, while remaining agnostic to details regarding particular experimental protocols or flow kinematics. These scientific machine learning models incorporate a universal approximator within a materially objective tensorial constitutive framework. By construction, these models respect physical constraints, such as frame-invariance and tensor symmetry, required by continuum mechanics. We demonstrate that this framework facilitates the rapid discovery of accurate constitutive equations from limited data and that the learned models may be used to describe more kinematically complex flows. This inherent flexibility admits the application of these “digital fluid twins” to a range of material systems and engineering problems. We illustrate this flexibility by deploying a trained model within a multidimensional computational fluid dynamics simulation—a task that is not achievable using any previously developed data-driven rheological equation of state.

Science & Technology - Other Topics↗

A machine-learning framework for the simulation of nuclear deflection of Planet-Killer-Asteroids

Here, as detection capabilities in astronomy have dramatically improved over the last two decades, concerns over Planet-Killer-Asteroids (PKAs) have become widespread, with nuclear weapons being proposed to destroy or deflect asteroids that are on a short-term projected collision course with Earth. Two main mitigation strategies have been proposed: • Case 1: Break up an incoming asteroid into smaller pieces that will disperse widely, resulting in smaller-scale, less detrimental, Earth-impacts or • Case 2: Deflect an incoming asteroid trajectory to avoid collision altogether. While the two strategies are not mutually exclusive, deflection is a safer strategy, ideally by harnessing all of the released energy from a nuclear device to move the asteroid as a rigid body. However, this case may not be always possible, since the strength of the energy release may break up the asteroid. In this work, the dynamical response of a PKA to a series of ultra-high energy impulses, such as those generated by nuclear devices, is formulated. A rapid iterative Discrete Element Method (DEM) method is developed to describe the deflection and potential breakup of the PKA as a function of a material bonding strength parameter within the asteroid and the magnitude of the applied impulse. The use of DEM allows for fragmentation of the PKA and the ability to compute the trajectories and distribution of the resulting debris field. Finally, a machine-learning algorithm is then developed and combined with the DEM approach to optimize the pulsation strategy for maximum possible safety and success.

42 ENGINEERING↗

Machine learning enabled discovery of superhard and ultrahard carbon polymorphs

The demand for multifunctional materials has motivated the move from near-equilibrium materials to metastable i.e. out-of-equilibrium phases that can meet several desired target properties. The search for such metastable phases with exotic properties is non-trivial and often serendipitous. Inverse design approaches based on evolutionary search have been powerful tools, but such traditional searches have focused on identifying primarily stable and metastable materials with the lowest enthalpy. The inverse design of materials, with a focus on a desired property such as, for example, hardness is a challenging task because of the expensive computational cost involved in sampling multiple structures. The recent advances in machine learning have brought new powerful AI techniques to the forefront which can potentially revolutionize the inverse design and discovery of materials, especially metastable phases capable of meeting multifunctionality. Here, in this work, we develop and apply an automated reinforcement learning workflow for inverse design that integrates first principles physics and atomistic simulations with machine learning (ML), and high-performance computing to allow rapid exploration of the superhard and ultrahard metastable phases of Carbon. We demonstrate an automatic machine learning based inverse design workflow to map new undiscovered metastable states ranging from near equilibrium to those far-from-equilibrium that satisfy multiple property objectives, specifically bulk moduli, shear moduli and hardness. We create a comprehensive library of carbon stable and metastable phases with varying hardness and subsequently shortlist 10 top performing candidate carbon structures, including two newly reported phases, based on their hardness and characterize their temperature dependent mechanical properties. A neural network model is built using featurization of allotropes of carbon to predict the quasi-harmonic Gibbs free energies. The Gibbs free energies of the top performing phases are analyzed to get an estimate of the experimental synthesizability of these superhard and ultrahard carbon phases. In general, we show using machine learning based inverse design approaches how hitherto inaccessible metastable states can be identified and potentially synthesized to meet the demand for multifunctional materials.

Balasubramanian, Karthik [Univ. of Illinois, Chica↗

Improving Detector Systematic Uncertainties Through Data-Driven Machine Learning

Detector simulation in liquid argon time projection chambers (LArTPCs) is a constant challenge. In particular the modeling of electrons response on wires is highly nontrivial. However, new machine learning techniques exist which can be leveraged to ameliorate these concerns. We present a novel methodology to attempt to learn from cosmic muon data in the ICARUS detector how reconstructed wire signals are influenced by features of the hits such as location, particle direction, angle relative to the wire plane, etc. A model can then be generated which can apply the learned mapping to Monte Carlo events to create a more data-like simulation sample. By creating such a sample we expect to reduce the systematic uncertainties at ICARUS due to our detector modeling.

Hausner, Harry [Fermilab] (ORCID:0000000188932280)↗

Improving Detector Systematic Uncertainties Through Data-Driven Machine Learning

Detector simulation in liquid argon time projection chambers (LArTPCs) is a constant challenge. In particular the modeling of electrons response on wires is highly nontrivial. However, new machine learning techniques exist which can be leveraged to ameliorate these concerns. We present a novel methodology to attempt to learn from cosmic muon data in the ICARUS detector how reconstructed wire signals are influenced by features of the hits such as location, particle direction, angle relative to the wire plane, etc. A model can then be generated which can apply the learned mapping to Monte Carlo events to create a more data-like simulation sample. By creating such a sample we expect to reduce the systematic uncertainties at ICARUS due to our detector modeling.

Hausner, Harry [Fermilab] (ORCID:0000000188932280)↗

Calomplification — the power of generative calorimeter models

Motivated by the high computational costs of classical simulations, machine-learned generative models can be extremely useful in particle physics and elsewhere. They become especially attractive when surrogate models can efficiently learn the underlying distribution, such that a generated sample outperforms a training sample of limited size. This kind of GANplification has been observed for simple Gaussian models. We show the same effect for a physics simulation, specifically photon showers in an electromagnetic calorimeter.

47 OTHER INSTRUMENTATION↗

EPiC-GAN: Equivariant point cloud generation for particle jets

With the vast data-collecting capabilities of current and future high-energy collider experiments, there is an increasing demand for computationally efficient simulations. Generative machine learning models enable fast event generation, yet so far these approaches are largely constrained to fixed data structures and rigid detector geometries. In this paper, we introduce EPiC-GAN - equivariant point cloud generative adversarial network - which can produce point clouds of variable multiplicity. This flexible framework is based on deep sets and is well suited for simulating sprays of particles called jets. The generator and discriminator utilize multiple EPiC layers with an interpretable global latent vector. Crucially, the EPiC layers do not rely on pairwise information sharing between particles, which leads to a significant speed-up over graph- and transformer-based approaches with more complex relation diagrams. We demonstrate that EPiC-GAN scales well to large particle multiplicities and achieves high generation fidelity on benchmark jet generation tasks.

Buhmann, Erik↗

Tuning water dissociation at oxide–electrolyte interfaces with electric fields

Understanding how electric fields influence water dissociation at heterogeneous interfaces is crucial for controlling interfacial chemical reactions and advancing next-generation energy technologies. Herein, ab initio–based machine learning simulations show that even small electric field changes can significantly alter the water dissociation fraction at planar TiO 2 –electrolyte interfaces. The resulting free energy difference between undissociated and dissociated interfacial water exhibits a linear dependence on the field change with a slope of 1.97 eÅ, which far exceeds the dissociation-induced dipole change of a water molecule. Employing a machine-learned collective variable to investigate the reaction statistics of thousands of water dissociation/recombination events, we find that small electric field changes exert minor effects on individual reaction energy barriers but significantly influence the populations of local configurations associated with initial states that are most favorable for reactions. These findings elucidate the pronounced impact of electric fields on interfacial water dissociation and reveal a mechanism for electric-field-controlled chemical reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Identifying Hydrometeorological Factors Influencing Reservoir Releases Using Machine Learning Methods

Simulation of reservoir releases plays a critical role in social-economic functioning and our nation's security. How-ever, it is challenging to predict the reservoir release accurately because of many influential factors from natural environments and engineering controls such as the reservoir inflow and storage. Moreover, climate change and hydrological intensification causing the extreme precipitation and temperature make the accurate prediction of reservoir releases even more challenging. Machine learning (ML) methods have shown some successful applications in simulating reservoir releases. However, previous studies mainly used inflow and storage data as inputs and only considered their short-term influences (e.g, previous one or two days). In this work, we use long short-term memory (LSTM) networks for reservoir release prediction based on four input variables including inflow, storage, precipitation, and temperature and consider their long-term influences. We apply the LSTM model to 30 reservoirs in Upper Colorado River Basin, United States. We analyze the prediction performance using six statistical metrics. More importantly, we investigate the influence of the input hydrometeorological factors, as well as their temporal effects on reservoir release decisions. Results indicate that inflow and storage are the most influential factors but the inclusion of precipitation and temperature can further improve the prediction of release especially in low flows. Additionally, the inflow and storage have a relatively long-term effect on the release. These findings can help optimize the water resources management in the reservoirs.

Fan, Ming↗

Molecular simulation and artificial intelligence for the circular economy of bioenergy and bioproducts

The concept of the circular bioeconomy is a carbon neutral, sustainable system with zero waste. One vision for such an economy is based upon lignocellulosic biomass. This lignocellulosic circular bioeconomy requires CO 2 absorption from biomass growth and the efficient deconstruction of recalcitrant biomass into solubilized and fractionated biopolymers, which are then used as precursors for the sustainable production of high-quality liquid fuels, chemical bioproducts, and bio-based materials. Here, in this study, we summarize the roles that molecular dynamics (MD) simulations and machine learning (ML) are playing in overcoming several fundamental challenges hindering the adoption of a circular bioeconomy. Specifically, we discuss the role of MD and ML/AI in overcoming lignocellulose recalcitrance by designing biomass pretreatment methods to efficiently produce solubilized cellulose/lignin/hemicellulose and of that in improving energy-intensive manufacturing of biomass-based materials and their structural and mechanical properties. Quantum mechanical methods and MD simulations, in addition to offering a mechanistic understanding of biomass deconstruction and biomaterials design, can provide meaningful structural, energetics, and physiochemical properties as inputs to train AI/ML models. The ML models can guide the experimental prioritization of materials/solvents and process parameters that significantly accelerate the development of biofuel and biomaterial components of the circular bioeconomy.

Smith, Jeremy C. [Oak Ridge National Laboratory (O↗

Smart Test Machines

Vern Wedeven, president of Wedeven Associates, developed the WAM4, a computer-aided "smart" test machine for simulating stress on equipment, based on his bearing lubrication expertise gained while working for Lewis Research Center. During his NASA years from the 1970s into the early 1980s, Wedeven initiated an "Interdisciplinary Collaboration in Tribology," an effort that involved NASA, six universities, and several university professors. The NASA-sponsored work provided foundation for Wedeven in 1983 to form his own company. Several versions of the smart test machine, the WAM1, WAM2, and WAM3, have proceeded the current version, WAM4. This computer-controlled device can provide detailed glimpses at gear and bearing points of contact. WAM4 can yield a three-dimensional view of machinery as an operator adds "what-if" thermal and lubrication conditions, contact stress, and surface motion. Along with NASA, a number of firms, including Pratt & Whitney, Caterpillar Tractor, Exxon, and Chevron have approached Wedeven for help on resolving lubrication problems.

Source record↗

Magnetic phases of spatially modulated spin-1 chains in Rydberg excitons: Classical and quantum simulations

Here, in this work, we study the magnetic phases of a spatially modulated chain of spin-1 Rydberg excitons. Using the Density Matrix Renormalization Group (DMRG) technique, we study various magnetic and topologically nontrivial phases using both single-particle properties, such as local magnetization and quantum entropy, and many-body ones, such as pair-wise Néel and long-range string correlations. In particular, we investigate the emergence and robustness of the Haldane phase, a topological phase of anti-ferromagnetic spin-1 chains. Furthermore, we devise a hybrid quantum algorithm employing restricted Boltzmann machine to simulate the ground state of such a system that shows very good agreement with the results of exact diagonalization and DMRG.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Investigation of the Effect of Framework Flexibility on Adsorption in SIFSIX-3-Cu using a Machine-Learned Force Field

Metal-organic frameworks (MOFs) are a promising class of adsorbents. The performance of MOF sorbents relies on high selectivity and low regeneration energy. This work focuses on the use of machine learned force fields (MLFFs) to model adsorption in a flexible MOF, SIFSIX-3-Cu. A DeePMD-based MLFF was trained to reproduce DFT (PBE+D3) energies, forces, and stresses, using an iterative sampling scheme combining sampling based on molecular dynamics, Monte Carlo, and geometry optimization to capture both attractive and repulsive regions of the potential energy surface. Flexibility of the MOF was explicitly included in this model. Hybrid Monte Carlo/molecular dynamics (MC/MD) simulations using the MLFF predicted adsorption isotherms in good agreement with experimental data for a range of pressures (40 Pa – 104 Pa) in contrast to rigid models, which overpredict CO2 adsorption at low pressures. The improvement was the result of a description of the variability of fluorine-fluorine diagonal distances at adsorption sites. This detailed description of flexibility afforded by the MLFF resulted in more accurate predictions adsorption isotherms when compared to the experimentally measured values. These results underscore the importance of including framework flexibility when modeling adsorption phenomena in MOFs, particularly for low pressure applications and provide a robust procedure for training MLFF models for MOFs.

Atomistic Simulation↗

Extreme Longitudinal Compression of Optimized Beams for MEV Ultrafast Electron Diffraction (Final Technical Report)

We worked out the design of a high repetition rate MeV energy ultrafast electron diffraction instrument based on the existing Cornell photoinjector, which can readily be applied to the presented findings. This example is a blueprint of other similarly arranged UED setups. Using particle tracking simulations in conjunction with multiobjective genetic algorithm optimization, we explored the smallest bunch lengths, emittance, and probe spot sizes achievable. As two limits, we defined stroboscopic conditions (with single electrons per pulse) and operation with 10 5 electrons per bunch which may be suitable for single-shot diffraction images. In the stroboscopic case, the flexibility provided by the many cavity bunching and acceleration allows for longitudinal phase space linearization without a higher harmonic field, providing sub-fs bunch lengths at the sample. Given low emittance photoemission conditions, these small bunch lengths can be maintained with probe transverse sizes at the single micron (1 μm) scale and below. In the case of 10 5 electrons per pulse, we simulated state-of-the-art 5D brightness conditions: rms bunch lengths of 10 fs with 3-nm normalized emittances, while permitting repetition rates as high as 1.3 GHz. We showed that in conjunction with collimating apertures, a novel focusing scheme achieves very high-quality emittance compensation for the central core of the beam composing 40% of particles, for a resulting beam size of 5 μm (rms). Finally, to aid in the design of new SRF-based ultrafast electron diffraction machines, we simulated the trade-off between the number of cavities used and achievable bunch length and emittance. In the longitudinal dimension, we made use of the fact that MeV UED requires much lower energy than the 15-MeV maxi mum energy of Cornell’s CBETA injector, and we may therefore use several of the SRF cavities for bunch length compression. In practice, we used a genetic optimization algorithm to choose the phases and amplitudes of the cavities appropriately for optimal bunching. In the zero space charge case, we found that bunching and acceleration are distributed across the six cavities in a way that produces a linearizing effect. And we showed that the ultimate bunch length can be limited by time-of-flight differences arising from transverse size and transverse momentum spread. The space charge code developed and used for this development is now permanent part of the Bmad accelerator simulation code and has already contributed to other developments, e.g., for the EIC electron cooler design.

43 PARTICLE ACCELERATORS↗

Cloud Services Enable Efficient AI-Guided Simulation Workflows across Heterogeneous Resources

Applications which fuse machine learning and simulation are rarely best served by a single computing resource. Highly parallel simulation codes are best deployed on super- computers, while AI tasks used to decide which simulations to perform may be best suited to specialized accelerators. Here we present a Function-as-a-Service (FaaS) system for executing complex, distributed computational campaigns that achieves performance parity with conventional workflow systems without the complexities of secure network connections between compute providers. One innovation enabling high performance is a subsystem that directly moves task data between sites, separate from the cloud-hosted FaaS system used to distribute task instructions. We also introduce a flexible scheduling system that allows us access factor of 2 trade offs between the amount of resources required to solve a problem at each compute site. We anticipate that this system will upgrade multi-site applications from demonstration projects to routine practice in computational science.

Ward, Logan↗