Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session W25: Classical Monte Carlo and Molecular Dynamics: Methods and Applications |
Hide Abstracts |
Sponsoring Units: DCOMP Chair: Tim Germann, Los Alamos National Laboratory Room: 327 |
Thursday, March 21, 2013 2:30PM - 2:42PM |
W25.00001: Hard-Disk Equation of State: First-Order Liquid-Hexatic Transition in Two Dimensions with Three Simulation Methods Michael Engel, Joshua A. Anderson, Masaharu Isobe, Etienne P. Bernard, Werner Krauth, Sharon C. Glotzer We report large-scale computer simulations of the hard-disk system at high densities in the region of the melting transition~[1]. Our simulations reproduce the equation of state, previously obtained using the event-chain Monte Carlo algorithm, with a massively parallel implementation of the local Monte Carlo method~[2] and with event-driven molecular dynamics. We analyze the relative performance of these simulation methods to sample configuration space and approach equilibrium. Phase coexistence is visualized for individual configurations via the local orientations, and positional correlation functions are computed. Our results confirm the first-order nature of the liquid-hexatic phase transition in hard disks. \\[4pt] [1] J.A. Anderson, M. Engel, S.C. Glotzer, M. Isobe, E.P. Bernard, W. Krauth, arXiv:1211.1645. \newline [2] J.A. Anderson, E. Jankowski, T.L. Grubb, M. Engel, S.C. Glotzer, arXiv:1211.1646. [Preview Abstract] |
Thursday, March 21, 2013 2:42PM - 2:54PM |
W25.00002: Massively parallel Monte Carlo for many-particle simulations on GPUs Sharon Glotzer, Joshua Anderson, Eric Jankowski, Thomas Grubb, Michael Engel Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. We present a massively parallel method that obeys detailed balance and implement it for a system of hard disks on the GPU.[1] We reproduce results of serial high-precision Monte Carlo runs to verify the method.[2] This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a GeForce GTX 680, our GPU implementation executes 95 times faster than on a single Intel Xeon E5540 CPU core, enabling 17 times better performance per dollar and cutting energy usage by a factor of 10. [1] J.A. Anderson, E. Jankowski, T. Grubb, M. Engel and S.C. Glotzer, arXiv:1211.1646. [2] J.A. Anderson, M. Engel, S.C. Glotzer, M. Isobe, E.P. Bernard and W. Krauth, arXiv:1211.1645. [Preview Abstract] |
Thursday, March 21, 2013 2:54PM - 3:06PM |
W25.00003: Generalized Bond Order Parameters to Characterize Transient Crystals Masaharu Isobe, Berni Alder Higher order parameters in the hard disk fluid are computed to investigate the number, the life time and size of transient crystal nuclei in the pre-freezing phase. The methodology introduces further neighbor shells bond orientational order parameters and coarse-grains the correlation functions needed for the evaluation of the stress autocorrelation function for the viscosity. We successfully reproduce results by the previous collision method for the pair orientational correlation function, but some two orders of magnitude faster. This speed-up allows calculating the time dependent four body orientational correlation between two different pairs of particles as a function of their separation, needed to characterize the size of the transient crystals. The result is that the slow decay of the stress autocorrelation function near freezing is due to a large number of rather small crystal nuclei lasting long enough to lead to the molasses tail. [Preview Abstract] |
Thursday, March 21, 2013 3:06PM - 3:18PM |
W25.00004: Size-dependent Melting Behavior of Iron Nanoparticles by Replica Exchange Molecular Dynamics Qiang Shu, Yang Yang, Yingteng Zhai, Deyan Sun, Hongjun Xiang, Xingao Gong Due to the finite size effect, nanoparticles own unique physical, chemical, and magnetic properties. Comparing with the bulk materials, the large surface/volume ratio of nanoparticles could lead to more complicate atomic and electronic behavior, thus the thermodynamical properties can be also very rich. In the last a few decades, as one of the fundamental problems in the nano science, the melting behavior of nanoparticles had been widely investigated by numerous experimental and theoretical studies. Using replica-exchange molecular dynamics method (REMD), we have investigated the size dependence of the melting behavior of iron nanoparticles. Comparing to the conventional molecular dynamics (MD), the REMD method is found to be very efficient to determine the melting point, by avoiding the superheating and undercooling phenomena. With accurate determination of the melting point, we find that the melting temperature does not follow linearly with the inverse of size. By incorporating the size dependent thickness of surface liquid layer which is observed in our simulation, we propose a revised liquid skin melting model to describe the size dependent melting temperature. [Preview Abstract] |
Thursday, March 21, 2013 3:18PM - 3:30PM |
W25.00005: Nanoindentation in Nanoporous Silica: Multimillion-Atom Molecular Dynamics Simulations Adarsh Shekhar, Camilla N. Kirkemo, Anders Malthe-S{\O}renssen, Rajiv K. Kalia, Aiichiro Nakano, Priya Vashishta Nanoporous silica is widely used in catalysis, chromatography, anticorrosion coatings, desalination membranes, and as drug delivery vehicles because it is easy to tune the size of pores and their morphologies and to functionalize pore surfaces with a variety of molecular moieties. We have performed multimillion-atom molecular dynamics simulations to examine the structural properties and mechanical behavior of nanoporous silica at various densities. The simulations are based on experimentally validated force field for silica. We have examined the pore size distribution, and calculated roughness exponents of pores to characterize pore morphologies. We have determined the scaling of elastic moduli, hardness and fracture toughness with porosity of nanoporous silica through nanoindentation simulations. Our calculated value of hardness (10.6 GPa) for amorphous silica at normal density agrees very well with the experimental value (10 GPa) [1].\\[4pt] [1] K. Nomura, Y. Chen, R. K. Kalia, A. Nakano and P. Vashishta, Appl Phys Lett \textbf{99} (11), 111906 (2011). [Preview Abstract] |
Thursday, March 21, 2013 3:30PM - 3:42PM |
W25.00006: Automated generation of quantum-accurate classical interatomic potentials for metals and semiconductors Aidan Thompson, Stephen Foiles, Peter Schultz, Laura Swiler, Christian Trott, Garritt Tucker Molecular dynamics (MD) is a powerful condensed matter simulation tool for bridging between macroscopic continuum models and quantum models (QM) treating a few hundred atoms, but is limited by the accuracy of available interatomic potentials. Sound physical and chemical understanding of these interactions have resulted in a variety of concise potentials for certain systems, but it is difficult to extend them to new materials and properties. The growing availability of large QM data sets has made it possible to use more automated machine-learning approaches. Bart\'{o}k \emph{et~al.} demonstrated that the bispectrum of the local neighbor density provides good regression surrogates for QM models. We adopt a similar bispectrum representation within a linear regression scheme. We have produced potentials for silicon and tantalum, and we are currently extending the method to III-V compounds. Results will be presented demonstrating the accuracy of these potentials relative to the training data, as well as their ability to accurately predict material properties not explicitly included in the training data. [Preview Abstract] |
Thursday, March 21, 2013 3:42PM - 3:54PM |
W25.00007: Database Optimization for interatomic potential model Pinchao Zhang, Dallas Trinkle We develop a new algorithm for database optimization of interatomic potential models with Bayesian statistics. Conventional classical potential fitting schemes generates a best fit parameter set, but do not show inadequacies of the potential model nor give insight into viability of the fitting database. Our algorithm generates an ensemble of potential fits with Markov Chain Monte Carlo and make predictions based on Bayesian error estimation according to the ensemble. We consider a fitting database to be optimal when the sum of relative errors for all entries of the database is minimized. A specific objective function is proposed and an optimized database of the interatomic potential model can be obtained by modifying the relative importance (weights) of different structures in the database. We test the algorithm with a Lennard-Jones potential fitting of Ti, which shows specific limitations of this simple potential model. We also show that the derivative of the objective function with respect to weight determines whether a structure should be added to or removed from the database. [Preview Abstract] |
Thursday, March 21, 2013 3:54PM - 4:06PM |
W25.00008: A first-principles interatomic potential via perturbative theory Xinyuan Ai, Chris Marianetti Here we propose a new approach for constructing a first-principles interatomic potential based upon a Taylor series expansion in clusters of the atomic displacements. While the number of clusters is very large in general, group theory can be used to generate a tractable number of clusters in materials with sufficiently high symmetry. A large dataset of perturbed structures which randomly samples the irreducible cluster phase space is constructed and computed in density functional theory. The cross validation score is then used to determine which clusters should be retained in the expansion. This method is then benchmarked on a one-dimensional atomic chain. Excellent agreement is achieved within a large range of atomic displacements in addition to large lattice strains. Additionally, one can recover the phonons as a function of strain. Further application of the method to two and three dimensional materials are also presented. [Preview Abstract] |
Thursday, March 21, 2013 4:06PM - 4:18PM |
W25.00009: A new type of interatomic potential for oxides and its applications to BiFeO$_3$ and PbTiO$_3$ Shi Liu, Hiroyuki Takenaka, Tingting Qi, Ilya Grinberg, Andrew Rappe Conventional first-principles methods are limited due to their intense computational cost. There is therefore still a strong need to develop accurate and efficient atomistic potential that could reproduce the full dynamical behaviors of metal oxides for large-scale finite-temperature simulations. We will present a new type of interatomic potential based on principles of bond-valence conservation and bond-valence vector conservation. The physical basis is justified quantum mechanically in the framework of a tight-bonding model, demonstrating that our model is formally equivalent to the bond-order potential (BOP), but is dramatically more efficient computationally. We will present an interatomic potential for BiFeO$_3$ and PbTiO$_3$, respectively. The validity of those model potentials is tested for both constant-volume and constant-pressure molecular dynamics simulations. The ferroelectric-to-paraelectric phase transitions of BiFeO$_3$ and PbTiO$_3$ are successfully reproduced. The calculated domain-wall energies using classical potentials are in satisfying agreement with DFT values. We conclude that our model potential is a promising type of force field that can have a broad application to a wide range of inorganic materials. [Preview Abstract] |
Thursday, March 21, 2013 4:18PM - 4:30PM |
W25.00010: A New Charge Model in The Valence Force Field Model for Phonon Calculations Christopher Barrett, Lin-Wang Wang The classical ball and spring Valence Force Field model is useful to determine the elastic relaxation of thousand-atom nanosystems. We have also used it to calculate the phonon spectra of nanosystems. However, we found that the conventional point charge model in the Valence Force Field model can cause artificial instability in nanostructures. In this talk, we will present a new charge model which represents the electron cloud feature of the Born charge in a real crystal. More specifically, we have two opposite-signed point charges assigned to each atom, one at its real position, another at a position determined by its neighbor atoms. This innovation allows both electrostatic charges and Born charges to be accurately represented while retaining extreme efficiency. This customized VFF method is developed to be fittable to the results of density functional theory (DFT) calculation. We will present the results of CdSe bulk, surface, and nanowire calculations and compare them with the equivalent ab-initio calculations, for both in their accuracies and their costs. [Preview Abstract] |
Thursday, March 21, 2013 4:30PM - 4:42PM |
W25.00011: Temperature-dependent classical phonons from efficient non-dynamical simulations Jorge Iniguez, Mathias P. Ljungberg We describe a rigorous approach to the calculation of classic lattice-dynamical quantities from simulations that do not require an explicit consideration of the time evolution. We focus on the temperature-dependent vibrational spectrum. We start from the usual moment expansion of the relevant time correlation function (position-position or velocity-velocity) for a many-body system, and show that it can be conveniently split into one-body-like contributions by using a basis in which the low-order terms are diagonal. This allows us to compute the main spectral features (e.g., position {\em and} width of the phonon peaks) from thermal averages readily available from any statistical simulation. We demonstrate our method with an application to a model system that presents a structural transition and strongly temperature-dependent phonons. Our theory justifies and clarifies the status of previous heuristic schemes to estimate phonon frequencies in a computationally efficient way. [Preview Abstract] |
Thursday, March 21, 2013 4:42PM - 4:54PM |
W25.00012: Density and Spectral-Density Matrices in Atomistic-Scale Models Steven Valone Density matrices for the states of atoms appear from the construction of a model referred to as the Fragment Hamiltonian (FH) model. The FH model is not dependent on construction of one-electron as a prelude to the atomistic level. Rather a density matrix of occupation numbers of the integer charge states is composed directly from a many-electron point of view to represent the state of each atom or fragment in a molecule or material. The properties of these density matrices comply with those general density matrices. Two particular properties are explored. One property that is unique to the FH model is that the coefficients of the occupancy density matrix can be transformed into functions of more familiar variables, such as net charge and ionicity that play a central role in regulating charge flow in a molecule or material. The second property is that the concept of a spectral density matrix can be defined as an extension of the occupancy density matrix and again is utilized in a manner that is analogous to the role of that concept in one-electron theories of electronic structure. The construction and functionalities of both density matrix concepts are illustrated through examples from idealized systems such as one-dimensional chains. [Preview Abstract] |
Thursday, March 21, 2013 4:54PM - 5:06PM |
W25.00013: Atomistic Simulation Studies of the Bulk Lithiated TiO$_2 $ Phuti Ngoepe, Malili Matshaba, Dean Sayle TiO$_2$ has been confirmed as a safe anode material in lithium ion batteries due to its higher Li-insertion potential, (1.5V) in comparison with commercialised carbon anode materials. In the current study, amorphisation recrystallization method is used to produce bulk TiO$_2$ with a brookite structure and lithium is inserted at different concentrations. In accordance with pair distribution function experiments [1], it is found that lithiation tends to amorphise the structures. Simulated X-ray diffraction patterns are produced from such structures and compared with the experimental XRDs. Microstructures of TiO$_2$ are generated and are found to be highly twinned hence forming straight and zigzag tunnels. The microstructures of lithiated TiO$_2$ display limited twinning and tunnels with less pathways available for lithium transport. The microstructures are compared with those of nanostructural TiO$_2$ and suggestions for the preference of the latter in anodes are put forward. \\[4pt] [1] D. Dambournet, K. W. Chapman, M.V. Koudriachova, P.J. Chupas, I. Belharouak, and K. Amine, Inorg. Chem. 2011, 50, 5855--5857. [Preview Abstract] |
Thursday, March 21, 2013 5:06PM - 5:18PM |
W25.00014: Atomistic simulations studies of the bulk cobalt pentlandite (Co$_9$S$_8)$: Validation of the potential model Mofuti Mehlape, Steve Parker, Phuti Ngoepe We investigate various forms of the cobalt pentlandite, Co$_{9}$S$_{8}$, at different temperatures, using classical atomistic simulation methods with the support of electronic structure calculations. The first interatomic potentials of Co$_{9}$S$_{8}$ based on the Born model, were derived with input data such as structure and elastic properties from experiments and electronic structure calculations respectively. The interatomic potentials were validated by running energy minimization and molecular dynamics calculations. The structure, elastic properties and phonon spectra corresponded well with those determined by electronic structure methods. The calculations further reproduced the complex high temperature transformation to high form pentlandite and the melting of Co$_{9}$S$_{8}$; as deduced from the crystal structure and radial distribution functions. The interatomic potentials can be used for studies of surfaces and nanostructures. [Preview Abstract] |
Thursday, March 21, 2013 5:18PM - 5:30PM |
W25.00015: Stable Algorithms for Modeling Thin-Film Epitaxial Growth Greg Seyfarth, Benjamin Vollmayr-Lee We search for stable time-stepping schemes for a phase-field model of thin film epitaxial growth. In particular, we consider a class of linear semi-implicit schemes which ensure the free energy decreases with time, a property called gradient stability. System dynamics slow at late times, so gradient stable schemes which allow adaptive time stepping are highly desirable. We perform a linear stability analysis and support it with numerical testing, revealing a region in parameter space of gradient stable semi-implicit schemes. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2019 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
1 Research Road, Ridge, NY 11961-2701
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700