Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Classical molecular dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 739 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Molecular Dynamics Simulations of Supercritical Carbon Dioxide and Water using TraPPE and SWM4-NDP Force Fields

The increased levels of carbon dioxide (CO 2 ) emissions due to the combustion of fossil fuels and the consequential impact on global climate change have made CO 2 capture, storage, and utilization a significant area of focus for current research. In most electrochemical CO 2 applications, water is used as a proton donor due to its high availability and mobility and use as a polar solvent. Additionally, supercritical CO 2 is a promising avenue for electrochemical applications due to its unique chemical and physical properties. Consequently, understanding the interactions between water and supercritical CO 2 is of great importance for future electrochemical applications. Molecular dynamics (MD) simulation is a powerful tool that enables atomistic-resolution dynamics of molecular systems, which can complement and guide future experimental investigations. This study employed atomistic MD to study the cosolubilities, codiffusivities, and structure of supercritical CO 2 and water systems, with a polarizable water model (SWM4-NDP) and a nonpolarizable CO 2 model (TraPPE). Additionally, ab initio MD simulations were used to better understand how atomistic polarizable/nonpolarizable models compare to explicit modeling of electron densities. The polarizable water model exhibited substantial improvement in water-associated properties. In conclusion, we anticipate the development of a compatible polarizable CO 2 model to yield similar improvement, providing a pathway for realizing novel high-pressure electrochemical systems.

25 ENERGY STORAGE↗
DOE OSTI2021

Rotaxane rings promote oblique packing and extended lifetimes in DNA-templated molecular dye aggregates

Abstract Molecular excitons play a central role in natural and artificial light harvesting, organic electronics, and nanoscale computing. The structure and dynamics of molecular excitons, critical to each application, are sensitively governed by molecular packing. Deoxyribonucleic acid (DNA) templating is a powerful approach that enables controlled aggregation via sub-nanometer positioning of molecular dyes. However, finer sub-Angstrom control of dye packing is needed to tailor excitonic properties for specific applications. Here, we show that adding rotaxane rings to squaraine dyes templated with DNA promotes an elusive oblique packing arrangement with highly desirable optical properties. Specifically, dimers of these squaraine:rotaxanes exhibit an absorption spectrum with near-equal intensity excitonically split absorption bands. Theoretical analysis indicates that the transitions are mostly electronic in nature and only have similar intensities over a narrow range of packing angles. Compared with squaraine dimers, squaraine:rotaxane dimers also exhibit extended excited-state lifetimes and less structural heterogeneity. The approach proposed here may be generally useful for optimizing excitonic materials for a variety of applications ranging from solar energy conversion to quantum information science.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Molecular Rotations, Multiscale Order, Hyperuniformity, and Signatures of Metastability during the Compression/Decompression Cycles of Amorphous Ices

We model, via large-scale molecular dynamics simulations, the isothermal compression of low-density amorphous ice (LDA) to generate high-density amorphous ice (HDA) and the corresponding decompression extending to negative pressures to recover the low-density amorphous phase (LDA HDA ). Both LDA and HDA are nearly hyperuniform and are characterized by a dynamical HBN, showing that amorphous ices are nonstatic materials and implying that nearly hyperuniformity can be accommodated in dynamical networks. In correspondence with both the LDA-to-HDA and the HDA-to-LDA HDA phase transitions, the (partial) activation of rotational degrees of freedom activates a cascade effect that induces a drastic change in the connectivity and a pervasive reorganization of the HBN topology which, ultimately, break the samples’ hyperuniform character. Key to this effect is the rapid rate at which changes occur, and not their magnitude. The inspection of structural properties from the short- to the long-range shows that signatures of metastability are present at all length-scales, hence providing further solid evidence in support of the liquid–liquid critical point scenario. LDA and LDA HDA differ in terms of HBN and structural properties, implying that they are distinct low-density glasses. Our work unveils the role of molecular rotations in the phase transitions between amorphous ices and shows how the unfreezing of rotational degrees of freedom generates a cascade effect that propagates over multiple length-scales. Our findings greatly improve our basic understanding of water and amorphous ices and can potentially impact the field of molecular network-forming materials at large.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Targeted Adjusting Molecular Arrangement in Organic Solar Cells via a Universal Solid Additive

The incorporation of solid additive has been considered as an effective strategy for developing organic photovoltaics with multi-components, which is independent of dynamics, playing unique roles in morphology adjustment. However, their complex working mechanisms involving specific chemical structures are selective to material systems, hence limiting their university and flexibility in application. Herein, an inert small-molecular compound naphtho[1,2-c:5,6-c′]bis[1,2,5]thiadiazole (NT) is introduced into the bulk-heterojunction blend as the solid additive, which can function with various material systems and solvents, depending on its simple π-conjugated structure and S⋯N interaction for adjusting molecular alignment. It is interesting to note that the introduced NT can not only improve device performance, but also simplify complicated pre- or post-processing methods, reduce impact from batch-to-batch differences, construct sufficient energy transfer channel as well as improve device stability. The resulting devices based on PTzBI-dF:Y6-BO system show an impressive power conversion efficiency of 17.4% with obviously enhanced T 80 lifetime of >1200 h. These findings provide useful guidelines for exploring potential universal solid additives benefitting toward commercial application.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Toward Addressing the Challenge to Predict the Heat Capacities of RDX and HMX Energetic Materials

Availability of heat capacity as function of pressure and temperature is an essential prerequisite for development of a computational multiscale strategy capable to address the evolution of microstructure and energy release in advanced high energy density materials. In the case of 1,3,5-trinitro-1,3,5-triazinane (RDX) and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) systems as two of the most studied energetic materials, there are substantial gaps in experimental data, with available heat capacities values distributed only in a region close to standard ambient conditions. In this study we demonstrate how these major experimental limitations can be addressed in the case of the RDX and HMX systems based on the combined use of classical and quantum mechanical calculations. We show that by considering ideal gas properties evaluated using quantum mechanical methods, and residual properties obtained from molecular simulations using fully flexible atomistic force field models, excellent agreement can be obtained for the predicted heat capacities to the most recent experimental values. An important advantage of the current computational methodology is that it allows evaluation of both constant-volume and constant-pressure heat capacities for a broad interval of temperatures and pressures, which encompasses solid and liquid phases conditions. In the case of the solid α and γ phases of RDX and the β phase of HMX, the predicted results follow closely both the available experimental data at standard ambient conditions and the results obtained using density functional theory calculations at high pressures, a regime where experimental data are not available. A perspective to expand the current methodology is also discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structure of iso-density sets in supersonic isothermal turbulence

Context: The gas density structure of the cold molecular phase of the interstellar medium is the main controller of star formation. Aims: A theoretical framework is proposed to describe the structural content of the density field in isothermal supersonic turbulence. Methods: It makes use of correlation and structure functions of the phase indicator field defined for different iso-density values. The relations between these two-point statistics and the geometrical features of iso-density sets such as the volume fraction, the surface density, the curvature, and fractal characteristics are provided. An exact scale-by-scale budget equation is further derived revealing the role of the turbulent cascade and dilation on the structural evolution of the density field. Although applicable to many flow situations, this tool is here first invoked for characterising supersonic isothermal turbulence, using data from the currently best-resolved numerical simulation. Results: We show that iso-density sets are surface fractals rather than mass fractals, with dimensions that markedly differ between dilute, neutral, and dense regions. The surface–size relation is established for different iso-density values. We further find that the turbulent cascade of iso-density sets is directed from large towards smaller scales, in agreement with the classical picture that turbulence acts to concentrate more surface into smaller volumes. Intriguingly, there is no range of scales that complies with a constant transfer rate in the cascade, challenging our fundamental understanding of interstellar turbulence. Finally, we recast the virial theorem in a new formulation drawing an explicit relation between the aforementioned geometrical measures and the dynamics of iso-density sets.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The final piece of the Triangle of U: Evolution of the tetraploid Brassica carinata genome

Abstract Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. Brassica carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid species (AABB, AACC, and BBCC). Of the genomes of these species, that of B. carinata is the least understood. Here, we report a chromosome scale 1.31-Gbp genome assembly with 156.9-fold sequencing coverage for B. carinata, completing the reference genomes comprising the classic Triangle of U, a classical theory of the evolutionary relationships among these six species. Our assembly provides insights into the hybridization event that led to the current B. carinata genome and the genomic features that gave rise to the superior agronomic traits of B. carinata. Notably, we identified an expansion of transcription factor networks and agronomically important gene families. Completion of the Triangle of U comparative genomics platform has allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in the domestication and continuing agronomic improvement of B. carinata and other Brassica species.

Biochemistry & Molecular Biology↗
DOE OSTI2020

A coarse-grain force field based on quantum mechanics (CGq FF) for molecular dynamics simulation of poly(ethylene glycol)- block -poly(ε-caprolactone) (PEG- b -PCL) micelles

In order to provide the means to predict from molecular dynamics (MD) simulations the structures of copolymer-based micelles in solution, we developed coarse grain force field (CGq FF) parameters for poly(ethylene glycol) (PEG) and for poly(ε-caprolactone) (PCL). A key advance here is the use of quantum mechanics to train the parameters describing the non-bonded (NB) interactions between the CG beads. The functional forms are the same as the MARTINI CG FF so standard MD codes can be used. Our CGq FF describes well the experimentally observed properties for the polymer–air and polymer–water interfaces, indicating the accuracy of the NB interactions. Additionally, the structural properties (density, radius of gyration ( R g ), and end-to-end distance ( h )) match both experiment and all atom (AA) simulations. We illustrate the application of this CGq FF by following the formation of a spherical micelle from 250 chains of PEG 23 - b -PCL 9 diblock copolymer, each block with molecular weight of 1000 Daltons (10 500 beads, corresponding to 123 250 atoms), in a water box with 119 139 water beads (426 553 water molecules).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An investigation of shock-induced phase transition in soda-lime glass

There exists a large body of evidence from experiments and molecular dynamics simulations to suggest the occurrence of phase transitions in soda-lime glass (SLG) and other silica glasses subject to shock compression to pressures above 3 GPa. In light of these findings, the current work investigated the existence of phase transition in SLG using shock and release experiments. The experiments employed symmetric SLG–SLG impact to achieve complete unloading to zero stress after shock compression to stresses in the range of 3–7 GPa. The stress–strain response and the Lagrangian release wave speed behavior of SLG obtained from these experiments are seen to reveal a mismatch between the loading and unloading paths of the pressure–strain curve for the material, which serves as compelling evidence for the occurrence of a shock-induced phase transition in the material at relatively low pressures. Furthermore, the release wave speed vs strain data obtained from experiments were used to construct a methodology for modeling the shock and release behavior of SLG. Lastly, this scheme implemented in numerical simulations was able to capture the release behavior of shock compressed SLG, for which a robust and satisfactory model was previously unavailable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Electrically controlling and optically observing the membrane potential of supported lipid bilayers

Supported lipid bilayers are a well-developed model system for the study of membranes and their associated proteins, such as membrane channels, enzymes, and receptors. These versatile model membranes can be made from various components, ranging from simple synthetic phospholipids to complex mixtures of constituents, mimicking the cell membrane with its relevant physiochemical and molecular phenomena. In addition, the high stability of supported lipid bilayers allows for their study via a wide array of experimental probes. In this work, we describe a platform for supported lipid bilayers that is accessible both electrically and optically, and demonstrate direct optical observation of the transmembrane potential of supported lipid bilayers. We show that the polarization of the supported membrane can be electrically controlled and optically probed using voltage-sensitive dyes. Membrane polarization dynamics is understood through electrochemical impedance spectroscopy and the analysis of an equivalent electrical circuit model. In addition, we describe the effect of the conducting electrode layer on the fluorescence of the optical probe through metal-induced energy transfer, and show that while this energy transfer has an adverse effect on the voltage sensitivity of the fluorescent probe, its strong distance dependency allows for axial localization of fluorescent emitters with ultrahigh accuracy. We conclude with a discussion on possible applications of this platform for the study of voltage-dependent membrane proteins and other processes in membrane biology and surface science.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Predicted Reaction Mechanisms, Product Speciation, Kinetics, and Detonation Properties of the Insensitive Explosive 2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105)

2,6-Diamino-3,5-dinitropyrazine-1-oxide (LLM-105) is a relatively new and promising insensitive high-explosive (IHE) material that remains only partially characterized. IHEs are of interest for a range of applications and from a fundamental science standpoint, as the root causes behind insensitivity are poorly understood. In this work, we adopt a multitheory approach based on reactive molecular dynamic simulations performed with density functional theory, density functional tight-binding, and reactive force fields to characterize the reaction pathways, product speciation, reaction kinetics, and detonation performance of LLM-105. We compare and contrast these predictions to 1,3,5-triamino-2,4,6-trinitrobenzene (TATB), a prototypical IHE, and 1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (HMX), a more sensitive and higher performance material. The combination of different predictive models allows access to processes operative on progressively longer timescales while providing benchmarks for assessing uncertainties in the predictions. We find that the early reaction pathways of LLM-105 decomposition are extremely similar to TATB; they involve intra- and intermolecular hydrogen transfer. Additionally, the detonation performance of LLM-105 falls between that of TATB and HMX. We find agreement between predictive models for first-step reaction pathways but significant differences in final product formations. Predictions of detonation performance result in a wide range of values, and one-step kinetic parameters show the similar reaction rates at high temperatures for three out of four models considered.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Thermal conductivity tensor of β -1,3,5,7-tetranitro-1,3,5,7-tetrazoctane ( β -HMX) as a function of pressure and temperature

Here, we have used reverse non-equilibrium molecular dynamics (RNEMD) simulations to determine the full thermal conductivity tensor for the monoclinic high explosive crystal β-1,3,5,7-tetranitro-1,3,5,7-tetrazoctane (β-HMX). In order to do so for the monoclinic crystal, four directions for heat propagation are used. Effects of the temperature and pressure are investigated between 200 and 500 K and 0 and 5 GPa, respectively, which approximately covers the range where the β polymorph is stable. Simulations are carried out with the Smith–Bharadwaj non-reactive empirical potential [Smith and Bharadwaj, J. Phys. Chem. B 103, 3570 (1999)], which is known to reproduce well the thermo-elastic properties of HMX. Our results indicate that the thermal conductivity, κ, is highly anisotropic, with 36% difference between the two extreme values at 300 K and 0 GPa. A simple function is used to interpolate κ in the pressure-temperature regime considered in this study, which can be used in continuum models. The results from RNEMD simulations compare well with available experimental results from the literature and allow the determination of κ for any direction and temperature and pressure within or around the fitting interval.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

UV-induced dissociation of CH 2 BrI probed by intense femtosecond XUV pulses

The ultraviolet (UV)-induced dissociation and photofragmentation of gas-phase CH 2 BrI molecules induced by intense femtosecond extreme ultraviolet (XUV) pulses at three different photon energies are studied by multi-mass ion imaging. Using a UV-pump–XUV-probe scheme, charge transfer between highly charged iodine ions and neutral CH 2 Br radicals produced by C–I bond cleavage is investigated. In earlier charge-transfer studies, the center of mass of the molecules was located along the axis of the bond cleaved by the pump pulse. In the present case of CH 2 BrI, this is not the case, thus inducing a rotation of the fragment. We discuss the influence of the rotation on the charge transfer process using a classical over-the-barrier model. Our modeling suggests that, despite the fact that the dissociation is slower due to the rotational excitation, the critical interatomic distance for charge transfer is reached faster. Furthermore, we suggest that charge transfer during molecular fragmentation may be modulated in a complex way.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2022

Persistence of negative vacancy and self-interstitial formation energies in atomistic models of amorphous silicon

We use classical potential atomistic modeling to demonstrate that negative vacancy and selfinterstitial formation energies are inherently present in amorphous silicon (a-Si). Our conclusions are based on comprehensive calculations of vacancy and self-interstitial formation energies in nine different models, ranging in size from 1000 to 2744 atoms and formed by quenching liquid Si at rates between 10 10 and 10 12 K/s. We account for a range of possible reference energies corresponding to different choices of reservoirs for atoms inserted into or removed from our models. Moreover, we show that successive addition of either vacancies or self-interstitials does not deplete the number of negative formation energy sites. Instead, it further lowers defect formation energies. Furthermore, these findings lead us to conclude that a-Si is not a structure at or near a local enthalpy minimum nor can it be brought to a local enthalpy minimum through the introduction of constitutional defects.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck–Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck–Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck–Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

ORNL_AISD_NiPt_108atoms

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for crystal structures with 108 atoms with 1,900 configurations. The data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system 'MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001' [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in a compressed zipped folders atoms108.zip. The zipped folder contains the data structured in the following way: - Ni_ground_state.cfg --> atomic configuration for the pure nickel - Pt_ground_state.cfg --> atomic configuration for the pure platinum - Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder - Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms108.zip is 66,132. This dataset is an extension to the dataset ORNL_AISD_NiPt [5] that has been previously released with crystal structures of 256 atoms, 864 atoms, and 2,048 atoms, with the same methodology for data collection. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D [5] M. Karabin, M. Lupo Pasini, and M. Eisenbach. ORNL_AISD_NiPt. United States: N. p., 2023. Web. doi:10.13139/OLCF/1958172.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Intermediate time sub-diffusion and stress relaxation in ring polymer melts

The slow dynamics of non-concatenated ring melts remains a frontier problem in polymer science with implications for many soft material environments including cellular biophysics. Here, in this work, we report large-scale simulations of model ring melts that analyze the monomer and center-of-mass (CM) mean square displacements (MSD) and stress relaxation function on intermediate time and length scales. The degree of dynamical slowing down is characterized by the maximally sub-diffusive fractional time scaling exponents. The data span an exceptionally wide range of ring degrees of polymerization and stiffnesses and are not successfully organized based on the classic measure linear chain entanglement, N/N e . Rather, we find that the crossover degree of polymerization, N D , based on ring macromolecular caging that successfully allows master curves to be constructed for the long-time CM self-diffusion constant also collapses these temporal dynamic scaling exponents. Different properties display different exponents and exhibit one or two regimes of linear variation with the logarithm of N D / N . A distinct crossover of the CM-MSD and stress relaxation exponents emerges at sufficiently large N or stiffness that is not found for the monomer MSD, indicating a novel form of dynamic decoupling. This crossover aligns with the predicted critical degree of polymerization for transitioning from a weak to strong caging regime, indicative of activated transport. The latter may reflect the emergence of an intermolecular collective contribution to stress in analogy with dense soft colloidal matter. Suggestions are made for future theoretical work to address the rich patterns of behavior discovered.

Anomalous diffusion↗
DOE OSTI2023

ORNL_AISD_NiPt

This dataset describes the nickel-platinum (NiPt) solid solution binary alloy, where the two constituent elements nickel (Ni) and platinum (Pt) are randomly placed on the face centered cubic (FCC) crystal structure, with the lattice constant of 3.840 angstroms. The dataset comprises data for three different sizes of the crystal structure: 256 atoms, 864 atoms, and 2,048 atoms, each of which contains 1900 configurations. For each size of the crystal structure, the data set was generated for concentrations ranging from 0at% of Pt to 100at% of Pt in the NiPt binary system, with increasing the concentration of Pt in the system every 5at%. For each one of the chemical compositions, 100 random configurations were generated, each with a different random seed. Each of the output files contains the mass, type, atomic coordinates, energy per atom, and forces in x, y, and z directions respectively. For each atomic configuration, the output was collected every 150 steps during the minimization stage and every 1000 steps during the replica exchange stage. Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) [1], which is a molecular dynamics code, was used to generate data for NiPt alloy. The simulation used the interatomic potential for NiPt binary system MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [3] from the OpenKIM library (Open Knowledgebase of Interatomic Models) [2]. This potential was developed based on the second nearest-neighbor modified embedded-atom method (2NN MEAM). The simulation process begins with the generation of the random NiPt structure and follows with the short minimization and replica exchange simulation. The minimization procedure adjusts atomic coordinates and performs energy minimization, which typically leads to a local potential energy minimum. The method used for the minimization was the conjugate gradient algorithm. A short replica exchange (parallel tempering) simulation involves four replicas (ensembles) of a system and follows the minimization stage. Multiple snapshots of the configuration were collected during the minimization and replica exchange stages. NiPt alloy is interesting due to its magnetic and charge transfer properties [4]. The data is provided in three compressed zipped folders: atoms256.zip, atoms864.zip, atoms2048.zip Each zipped folder contains the data that describes crystals of size 256 atoms, 864 atoms, and 2,048 atoms respectively. Each one of the three zipped folders contains the data structured in the following way: -Ni_ground_state.cfg --> atomic configuration for the pure nickel -Pt_ground_state.cfg --> atomic configuration for the pure platinum -Pt#_filtered --> folders containing atomic configurations for #at% concentration of platinum. The folder contains 100 atomic configurations, each saved in a subfolder. Each subfolder named config* is associated with a specific atomic configuration. Each of these subfolders contains files with .cfg format, corresponding to outputs for each atomic configuration The total number of atomic configurations contained in atoms256.zip is 65,046. The total number of atomic configurations contained in atoms864.zip is 63,936. The total number of atomic configurations contained in atoms2048.zip is 61,997. The total number of atomic configurations spanned by the entire dataset is 190,979. References [1] https://www.lammps.org/ [2] https://openkim.org/ [3] https://openkim.org/id/MEAM_LAMMPS_KimSeolJi_2017_PtNi__MO_020840179467_001 [4] El-Gendy, Ahmed A. and Hampel, Silke and Büccchner, Bernd and Klingeler, Rüdiger, Tuneable magnetic properties of carbon-shielded NiPt-nanoalloys, RSC Adv., volume 6, issue 57, pages 52427-52433, 2016, The Royal Society of Chemistry, doi:10.1039/C6RA05910D

36 MATERIALS SCIENCE↗