Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session T26: Classical Monte Carlo and Molecular Dynamics Methods |
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Sponsoring Units: DCOMP Chair: Timothy Germann, Los Alamos National Laboratory Room: 502 |
Thursday, March 6, 2014 11:15AM - 11:27AM |
T26.00001: Adapting phase-switch Monte Carlo method for flexible organic molecules Sally Bridgwater, David Quigley The role of cholesterol in lipid bilayers has been widely studied via molecular simulation, however, there has been relatively little work on crystalline cholesterol in biological environments. Recent work has linked the crystallisation of cholesterol in the body with heart attacks and strokes. Any attempt to model this process will require new models and advanced sampling methods to capture and quantify the subtle polymorphism of solid cholesterol, in which two crystalline phases are separated by a phase transition close to body temperature. To this end, we have adapted phase-switch Monte Carlo for use with flexible molecules, to calculate the free energy between crystal polymorphs to a high degree of accuracy. The method samples an order parameter $\mathcal{M}$, which divides a displacement space for the $N$ molecules, into regions energetically favourable for each polymorph; which is traversed using biased Monte Carlo. Results for a simple model of butane will be presented, demonstrating that conformational flexibility can be correctly incorporated within a phase-switching scheme. Extension to a coarse grained model of cholesterol and the resulting free energies will be discussed. [Preview Abstract] |
Thursday, March 6, 2014 11:27AM - 11:39AM |
T26.00002: Ab initio molecular dynamics with noisy and cheap quantum Monte Carlo forces: accurate calculation of vibrational frequencies Ye Luo, Sandro Sorella We introduce a general and efficient method for the calculation of vibrational frequencies of electronic systems, ranging from molecules to solids. By performing damped molecular dynamics with ab initio forces, we show that quantum vibrational frequencies can be evaluated by diagonalizing the time averaged position-position or force-force correlation matrices, although the ionic motion is treated on the classical level within the Born-Oppenheimer approximation. The novelty of our approach is to evaluate atomic forces with QMC by means of a highly accurate and correlated variational wave function which is optimized simultaneously during the dynamics. QMC is an accurate and promising many-body technique for electronic structure calculation thanks to massively parallel computers. However, since infinite statistics is not feasible, property evaluation may be affected by large noise that is difficult to harness. Our approach controls the QMC stochastic bias systematically and gives very accurate results with moderate computational effort, namely even with noisy forces. We prove the accuracy and efficiency of our method on the water monomer[A. Zen et al., JCTC 9 (2013) 4332] and dimer. We are currently working on the challenging problem of simulating liquid water at ambient conditions. [Preview Abstract] |
Thursday, March 6, 2014 11:39AM - 11:51AM |
T26.00003: Monte Carlo and Molecular Dynamics in the Multicanonical Ensemble: Connections between Wang-Landau Sampling and Metadynamics Thomas Vogel, Danny Perez, Christoph Junghans We show direct formal relationships between the Wang-Landau iteration [PRL 86, 2050 (2001)], metadynamics [PNAS 99, 12562 (2002)] and statistical temperature molecular dynamics [PRL 97, 050601 (2006)], the major Monte Carlo and molecular dynamics work horses for sampling from a generalized, multicanonical ensemble. We aim at helping to consolidate the developments in the different areas by indicating how methodological advancements can be transferred in a straightforward way, avoiding the parallel, largely independent, developments tracks observed in the past. [Preview Abstract] |
Thursday, March 6, 2014 11:51AM - 12:03PM |
T26.00004: OpenKIM - Building a Knowledgebase of Interatomic Models Matthew Bierbaum, Ellad Tadmor, Ryan Elliott, Trevor Wennblom, Alexander Alemi, Yan-Jiun Chen, Daniel Karls, Adam Ludvik, James Sethna The Knowledgebase of Interatomic Models (KIM) is an effort by the computational materials community to provide a standard interface for the development, characterization, and use of interatomic potentials. The KIM project has developed an API between simulation codes and interatomic models written in several different languages including C, Fortran, and Python. This interface is already supported in popular simulation environments such as LAMMPS and ASE, giving quick access to over a hundred compatible potentials that have been contributed so far. To compare and characterize models, we have developed a computational processing pipeline which automatically runs a series of tests for each model in the system, such as phonon dispersion relations and elastic constant calculations. To view the data from these tests, we created a rich set of interactive visualization tools located online. Finally, we created a Web repository to store and share these potentials, tests, and visualizations which can be found at https://openkim.org along with futher information. [Preview Abstract] |
Thursday, March 6, 2014 12:03PM - 12:15PM |
T26.00005: Density Functional Atom-In-Molecule Force Field for Charge Transfer Systems Susan R. Atlas, Steven M. Valone Given an arbitrary molecular structure and corresponding total electronic density, the Hohenberg-Kohn theorem of density functional theory induces an approximate but unique atom-in-molecule density decomposition [1]. The decomposition is expressed as an ensemble-of-ensembles, a weighted double sum over ionic and excited state densities, and yields effective atomic charges consistent with chemical intuition, and in remarkable accord with the topological AIM theory of Bader. We show that this decomposition further induces a corresponding ensemble energy expression and multiscale force field appropriate for open, charge-transfer dynamical systems simulation. [1] SR Atlas, J Dittman, V Janardhanam, G Amo-Kwao, and SM Valone, to be submitted (2013). [Preview Abstract] |
Thursday, March 6, 2014 12:15PM - 12:27PM |
T26.00006: Objectivity in Classical Molecular Dynamics: Objective Velocity, Temperature and Virial Stress Zidong Yang, James Lee, Azim Eskandarian In classical mechanics, axiom of objectivity requires that all balance laws and all constitutive equations must be form-invariant with respect to rigid motions of the spatial frame of reference. Any tensorial quantity is said to be objective if it is independent of the motion of the observer. Quantities such as temperature and stress should be objective. In Molecular Dynamics(MD), objectivity was rarely discussed. This paper addresses the objectivity of the governing equation and constitutive equations in MD. It can be shown that the interatomic potential and force are objective because they are based on relative position vectors of atoms, which are objective. Also, the governing equation in MD can be shown to satisfy objectivity too. On the other hand, velocity and relative velocity are not objective. Consequently, quantities such as temperature and Virial stress that are based on velocities of atoms are not objective. This becomes an issue if the simulation is conducted in a non-inertial reference frame. To resolve this deficiency, this paper adopts the formulation of thermal velocity that is proved to be objective. Thus the application of axiom of objectivity on MD will provide more credibility to the simulations of complex systems. [Preview Abstract] |
Thursday, March 6, 2014 12:27PM - 12:39PM |
T26.00007: Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory Keith Runge, Valentin Karasiev, Pierre Deymier The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances [A] in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. [A] V. V. Karasiev, D. Chakraborty, O. A. Shukruto, and S. B. Trickey, Phys. Rev. B 88, 161108(R) (2013). [Preview Abstract] |
Thursday, March 6, 2014 12:39PM - 12:51PM |
T26.00008: Towards a Discrete Element Method (DEM) for modeling anisotropic, nano- and colloidal scale particles in Molecular Dynamics (MD) Ryan Marson, Matthew Spellings, Joshua Anderson, Sharon Glotzer Faceted shapes, such as polyhedra, are commonly created in experimental systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystalline nucleation and growth, vacancy motion, and glassy dynamics, are challenging to model in these systems because they require detailed dynamical information at the individual particle level. Within the granular materials community the Discrete Element Method has been used extensively to model systems of anisotropic particles under gravity, with friction. We report the first implementation of DEM MD intended for thermodynamic nanoscale simulation. Our method is implemented in parallel on the GPU within the HOOMD-Blue framework. By decomposing the force calculation into its components, this implementation can take advantage of massive data parallelism, enabling optimal use of the GPU for even relatively small systems while achieving a speedup of 60 times over a single CPU core. This method is a natural extension of classical molecular dynamics into the realm of faceted particles, and allows simulation of disparate size scales ranging from the nanoscale to granular particulates, all within the same framework. [Preview Abstract] |
Thursday, March 6, 2014 12:51PM - 1:03PM |
T26.00009: Simulating ionic thermal trasport by equilibrium ab-initio molecular dynamics Aris Marcolongo, Paolo Umari, Stefano Baroni The Green-Kubo approach to thermal transport is often considered to be incompatible with ab-initio molecular dynamics (AIMD) because a suitable quantum-mechanical definition of the heat current is not readily available, due to the ill-definedness of the microscopic energy density to which it is related by the continuity equation. We argue that a similar difficulty actually exists in classical mechanics as well, and we address the conditions that have to be fulfilled in order for the physically well defined transport coefficients to be independent of the ill defined microscopic energy density from which they derive. We then provide two alternative approaches to calculating thermal conductivites from equilibrium AIMD. The first is based on the Green-Kubo formula, supplemented with an expression for the energy current, which is a generalization of Thouless' expression for the adiabatic charge current. The second approach, which avoids the recourse to an energy current altogether, rests on an efficient and accurate extrapolation to infinite wavelengths of the energy-density time correlation functions. The two methods are compared on a simple classical test bed, and their implementation in AIMD is demonstrated with the calculation of the thermal conductivity of simple fluids. [Preview Abstract] |
Thursday, March 6, 2014 1:03PM - 1:15PM |
T26.00010: A slave cluster expansion for obtaining ab-initio interatomic potentials Xinyuan Ai, Chris Marianetti Here we propose a new approach for performing a Taylor series expansion of the first-principles computed energy of a crystal as a function of the nuclear displacements. We enlarge the dimensionality of the existing displacement space and form new variables (i.e. slave clusters) which transform like irreducible representations of the point group and satisfy homogeneity of free space. Standard group theoretical techniques can then be applied to deduce the non-zero expansion coefficients \emph{apriori} at a given order, and the translation group can be used to contract the products and eliminate terms which are not linearly independent. While the expansion coefficients could likely be computed in a variety of ways, we demonstrate that finite difference is effective up to fourth order. We demonstrate the power of the method in the strongly anharmonic system PbTe. All anharmonic terms within an octahedron are computed up to fourth order. A proper linear transform demonstrates that the vast majority of the anharmonicity can be attributed to just two terms, indicating that a minimal model of phonon interactions is achievable. The ability to straightforwardly generate polynomial potentials will allow precise simulations at length and time scales which were previously unrealizable. [Preview Abstract] |
Thursday, March 6, 2014 1:15PM - 1:27PM |
T26.00011: Nucleation pathways in partially disordered lattice models David Quigley, Yuri Lifanov, Bart Vorselaars Simple lattice models are attractive for the study of non-classical nucleation and growth from solution, a phenomenon still largely inaccessible to atomistic simulation. We have extended the Potts Lattice Gas (PLG) model of Duff and Peters to include a metastable partially ordered precursor phase, mimicking the common mineral calcium carbonate. Using a combination of multicanonical Monte Carlo and equilibrium path sampling, we demonstrate that thermodynamically favourable pathways between a metastable solution state and the fully ordered lattice proceed via formation of partially ordered nuclei. By comparing the activation energy associated with the ordering of these nuclei to that needed to nucleate the ordered phase directly, we demonstrate dissolution and re-precipitation as an emergent growth phenomenon of our model. [Preview Abstract] |
Thursday, March 6, 2014 1:27PM - 1:39PM |
T26.00012: NiTi shape memory via solid-state nudge-elastic band Nikolai A. Zarkevich, Duane D. Johnson We determine atomic mechanisms of the shape memory effect in NiTi from a generalized solid-state nudge elastic band (SSNEB) method. We consider transformation between the austenite B2 and the ground-state base-centered orthorhombic (BCO) structures. In these pathways we obtain the R-phase and discuss its structure. We confirm that BCO is the ground state, and determine the pathways to BCO martensite, which dictate transition barriers. While ideal B2 is unstable, we find a B2-like NiTi high-temperature solid phase with significant local displacement disorder, which is B2 on average. This B2-like phase appears to be entropically stabilized. [Preview Abstract] |
Thursday, March 6, 2014 1:39PM - 1:51PM |
T26.00013: Amorphization of silicon crystals under shear stress Gianpietro Moras, Andreas Klemenz, Hiroshi Uetsuka, Michael Moseler, Lars Pastewka Phase transformations, and in particular amorphization, of crystalline silicon occur under contact loading, e.g. during indentation and scratching experiments. Little is known about shear-induced amorphization of Si, but molecular dynamics (MD) simulations recently unveiled that amorphization of diamond/diamond sliding interfaces is a mechanically driven process that is crucial to the anisotropic wear of diamond. Here, we report the results of MD simulations of Si crystals upon sliding load and compare them to analogous results obtained for diamond. Although crystalline Si is a brittle material with a diamond cubic structure, the properties of Si and C amorphous phases are strikingly different. Our simulations show that shear-induced phase transitions are also remarkably different in the two materials. In diamond, an amorphous region forms at the sliding interface and its thickness grows in time, with a rate that depends on normal load, surface orientation and sliding direction. Also in Si, a thin material region located at the sliding interface undergoes sudden amorphization when the shear stress exceeds the stability limit of the crystal. However, the thickness of such region does not grow in time due to competing amorphization and recrystallization processes. Further growth of the amorphous phase, at temperatures lower than the melting point, can only be achieved with normal loads that exceed the stability limit of the crystalline phase. [Preview Abstract] |
Thursday, March 6, 2014 1:51PM - 2:03PM |
T26.00014: Non-equilibrium relaxation analysis in cluster algorithms Yoshihiko Nonomura In Monte Carlo study of phase transitions, the critical slowing down has been a serious problem. In order to overcome this difficulty, two kinds of approaches have been proposed. One is the cluster algorithms, where global update scheme based on a percolation theory is introduced in order to refrain from the power-law behavior at the critical point. Another is the non-equilibrium relaxation method, where the power-law critical relaxation process is analyzed by the dynamical scaling theory in order to refrain from time-consuming equilibration. Then, the next step is to fuse these two approaches --- to investigate phase transitions with early-stage relaxation process of cluster algorithms. Since the dynamical scaling theory does not hold in cluster algorithms in principle, such attempt had been considered impossible. In the present talk we show that such fusion is actually possible using an empirical scaling form obtained from the 2D Ising models instead of the dynamical scaling theory. Applications to the $q \ge 3$ Potts models, $\pm J$ Ising models {\it etc.} will also be explained in the presentation. [Preview Abstract] |
Thursday, March 6, 2014 2:03PM - 2:15PM |
T26.00015: The effect of kinetic degrees of freedom in the study of microcanonical phase transitions Sergio Davis, Joaquin Peralta The methodology for the study of phase transitions in macroscopic systems is well established, as the thermodynamical properties in these systems are ensemble-independent. However, for systems of hundreds of atoms or less, this does not hold, and phase transitions are most commonly studied in the microcanonical ensemble. Microcanonical Monte Carlo (MMC) simulations are not straightforward to perform with both coordinates and momenta, however marginalization of the kinetic degrees of freedom leads to a tractable distribution which can be sampled via MMC methods. Uses of these techniques had been presented in the literature for equilibrium properties but scarcely for the study of phase transitions. In this work, we present a study of microcanonical phase transitions without the use of kinetic degrees of freedom. We generate configurations according to the MMC procedure, which are processed in the framework of the Z-method in order to determine the transition point. We show that the results agree with the standard molecular dynamics implementation of the method for melting. This suggest that the kinetic degrees of freedom (and therefore the microscopic dynamics) are irrelevant for the determination of the transition point, being only dependent on the potential energy landscape. [Preview Abstract] |
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