1,224 research outputs found
An object oriented Python interface for atomistic simulations
Programmable simulation environments allow one to monitor and control calculations efficiently and automatically before, during, and after runtime. Environments directly accessible in a programming environment can be interfaced with powerful external analysis tools and extensions to enhance the functionality of the core program, and by incorporating a flexible object based structure, the environments make building and analysing computational setups intuitive. In this work, we present a classical atomistic force field with an interface written in Python language. The program is an extension for an existing object based atomistic simulation environment. </p
AtomSim: web-deployed atomistic dynamics simulator
AtomSim, a collection of interfaces for computational crystallography simulations, has been developed. It uses forcefield-based dynamics through physics engines such as the General Utility Lattice Program, and can be integrated into larger computational frameworks such as the Virtual Neutron Facility for processing its dynamics into scattering functions, dynamical functions etc. It is also available as a Google App Engine-hosted web-deployed interface. Examples of a quartz molecular dynamics run and a hafnium dioxide phonon calculation are presented
ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
ProtoMD is a toolkit that facilitates the development of algorithms for
multiscale molecular dynamics (MD) simulations. It is designed for multiscale
methods which capture the dynamic transfer of information across multiple
spatial scales, such as the atomic to the mesoscopic scale, via coevolving
microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to
calibrate parameters needed in traditional CG-MD methods. The toolkit
integrates `GROMACS wrapper' to initiate MD simulations, and `MDAnalysis' to
analyze and manipulate trajectory files. It facilitates experimentation with a
spectrum of coarse-grained variables, prototyping rare events (such as chemical
reactions), or simulating nanocharacterization experiments such as terahertz
spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is
written in python and is freely available under the GNU General Public License
from github.com/CTCNano/proto_md
The 1999 Center for Simulation of Dynamic Response in Materials Annual Technical Report
Introduction:
This annual report describes research accomplishments for FY 99 of the Center
for Simulation of Dynamic Response of Materials. The Center is constructing a
virtual shock physics facility in which the full three dimensional response of a
variety of target materials can be computed for a wide range of compressive, ten-
sional, and shear loadings, including those produced by detonation of energetic
materials. The goals are to facilitate computation of a variety of experiments
in which strong shock and detonation waves are made to impinge on targets
consisting of various combinations of materials, compute the subsequent dy-
namic response of the target materials, and validate these computations against
experimental data
kmos: A lattice kinetic Monte Carlo framework
Kinetic Monte Carlo (kMC) simulations have emerged as a key tool for
microkinetic modeling in heterogeneous catalysis and other materials
applications. Systems, where site-specificity of all elementary reactions
allows a mapping onto a lattice of discrete active sites, can be addressed
within the particularly efficient lattice kMC approach. To this end we describe
the versatile kmos software package, which offers a most user-friendly
implementation, execution, and evaluation of lattice kMC models of arbitrary
complexity in one- to three-dimensional lattice systems, involving multiple
active sites in periodic or aperiodic arrangements, as well as site-resolved
pairwise and higher-order lateral interactions. Conceptually, kmos achieves a
maximum runtime performance which is essentially independent of lattice size by
generating code for the efficiency-determining local update of available events
that is optimized for a defined kMC model. For this model definition and the
control of all runtime and evaluation aspects kmos offers a high-level
application programming interface. Usage proceeds interactively, via scripts,
or a graphical user interface, which visualizes the model geometry, the lattice
occupations and rates of selected elementary reactions, while allowing
on-the-fly changes of simulation parameters. We demonstrate the performance and
scaling of kmos with the application to kMC models for surface catalytic
processes, where for given operation conditions (temperature and partial
pressures of all reactants) central simulation outcomes are catalytic activity
and selectivities, surface composition, and mechanistic insight into the
occurrence of individual elementary processes in the reaction network.Comment: 21 pages, 12 figure
QuantumATK: An integrated platform of electronic and atomic-scale modelling tools
QuantumATK is an integrated set of atomic-scale modelling tools developed
since 2003 by professional software engineers in collaboration with academic
researchers. While different aspects and individual modules of the platform
have been previously presented, the purpose of this paper is to give a general
overview of the platform. The QuantumATK simulation engines enable
electronic-structure calculations using density functional theory or
tight-binding model Hamiltonians, and also offers bonded or reactive empirical
force fields in many different parametrizations. Density functional theory is
implemented using either a plane-wave basis or expansion of electronic states
in a linear combination of atomic orbitals. The platform includes a long list
of advanced modules, including Green's-function methods for electron transport
simulations and surface calculations, first-principles electron-phonon and
electron-photon couplings, simulation of atomic-scale heat transport, ion
dynamics, spintronics, optical properties of materials, static polarization,
and more. Seamless integration of the different simulation engines into a
common platform allows for easy combination of different simulation methods
into complex workflows. Besides giving a general overview and presenting a
number of implementation details not previously published, we also present four
different application examples. These are calculations of the phonon-limited
mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model
simulation of lithium ion drift through a battery cathode in an external
electric field, and electronic-structure calculations of the
composition-dependent band gap of SiGe alloys.Comment: Submitted to Journal of Physics: Condensed Matte
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