1,033 research outputs found
Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps
The Verlet method is still widely used to integrate the equations of motion
in ab initio molecular dynamics simulations. We show that the stability limit
of the Verlet method may be significantly increased by setting an upper limit
on the kinetic energy of each atom with only a small loss in accuracy. The
validity of this approach is demonstrated for molten lithium fluoride.Comment: 9 pages, 3 figure
Path-integral molecular dynamics simulation of 3C-SiC
Molecular dynamics simulations of 3C-SiC have been performed as a function of
pressure and temperature. These simulations treat both electrons and atomic
nuclei by quantum mechanical methods. While the electronic structure of the
solid is described by an efficient tight-binding Hamiltonian, the nuclei
dynamics is treated by the path integral formulation of statistical mechanics.
To assess the relevance of nuclear quantum effects, the results of quantum
simulations are compared to others where either the Si nuclei, the C nuclei or
both atomic nuclei are treated as classical particles. We find that the
experimental thermal expansion of 3C-SiC is realistically reproduced by our
simulations. The calculated bulk modulus of 3C-SiC and its pressure derivative
at room temperature show also good agreement with the available experimental
data. The effect of the electron-phonon interaction on the direct electronic
gap of 3C-SiC has been calculated as a function of temperature and related to
results obtained for bulk diamond and Si. Comparison to available experimental
data shows satisfactory agreement, although we observe that the employed
tight-binding model tends to overestimate the magnitude of the electron-phonon
interaction. The effect of treating the atomic nuclei as classical particles on
the direct gap of 3C-SiC has been assessed. We find that non-linear quantum
effects related to the atomic masses are particularly relevant at temperatures
below 250 K.Comment: 14 pages, 15 figure
Neural network based path collective variables for enhanced sampling of phase transformations
We propose a rigorous construction of a 1D path collective variable to sample
structural phase transformations in condensed matter. The path collective
variable is defined in a space spanned by global collective variables that
serve as classifiers derived from local structural units. A reliable
identification of local structural environments is achieved by employing a
neural network based classification. The 1D path collective variable is
subsequently used together with enhanced sampling techniques to explore the
complex migration of a phase boundary during a solid-solid phase transformation
in molybdenum
Kinetic energy of protons in ice Ih and water: a path integral study
The kinetic energy of H and O nuclei has been studied by path integral
molecular dynamics simulations of ice Ih and water at ambient pressure. The
simulations were performed by using the q-TIP4P/F model, a point charge
empirical potential that includes molecular flexibility and anharmonicity in
the OH stretch of the water molecule. Ice Ih was studied in a temperature range
between 210-290 K, and water between 230-320 K. Simulations of an isolated
water molecule were performed in the range 210-320 K to estimate the
contribution of the intramolecular vibrational modes to the kinetic energy. Our
results for the proton kinetic energy, K_H, in water and ice Ih show both
agreement and discrepancies with different published data based on deep
inelastic neutron scattering experiments. Agreement is found for water at the
experimental melting point and in the range 290-300 K. Discrepancies arise
because data derived from the scattering experiments predict in water two
maxima of K_H around 270 K and 277 K, and that K_H is lower in ice than in
water at 269 K. As a check of the validity of the employed water potential, we
show that our simulations are consistent with other experimental thermodynamic
properties related to K_H, as the temperature dependence of the liquid density,
the heat capacity of water and ice at constant pressure, and the isotopic shift
in the melting temperature of ice upon isotopic substitution of either H or O
atoms. Moreover, the temperature dependence of K_H predicted by the q-TIP4P/F
model for ice Ih is found to be in good agreement to results of path integral
simulations using ab initio density functional theory.Comment: 11 pages, 6 figures, 2 table
From Classical to Quantum and Back: Hamiltonian Adaptive Resolution Path Integral, Ring Polymer, and Centroid Molecular Dynamics
Path integral-based simulation methodologies play a crucial role for the
investigation of nuclear quantum effects by means of computer simulations.
However, these techniques are significantly more demanding than corresponding
classical simulations. To reduce this numerical effort, we recently proposed a
method, based on a rigorous Hamiltonian formulation, which restricts the
quantum modeling to a small but relevant spatial region within a larger
reservoir where particles are treated classically. In this work, we extend this
idea and show how it can be implemented along with state-of-the-art path
integral simulation techniques, such as ring polymer and centroid molecular
dynamics, which allow the approximate calculation of both quantum statistical
and quantum dynamical properties. To this end, we derive a new integration
algorithm which also makes use of multiple time-stepping. The scheme is
validated via adaptive classical--path-integral simulations of liquid water.
Potential applications of the proposed multiresolution method are diverse and
include efficient quantum simulations of interfaces as well as complex
biomolecular systems such as membranes and proteins
Classical-path integral adaptive resolution in molecular simulation: towards a smooth quantum-classical coupling
Simulations that couple different classical molecular models in an adaptive
way by changing the number of degrees of freedom on the fly, are available
within reasonably consistent theoretical frameworks. The same does not occur
when it comes to classical-quantum adaptivity. The main reason for this is the
difficulty in describing a continuous transition between the two different kind
of physical principles: probabilistic for the quantum and deterministic for the
classical. Here we report the basic principles of an algorithm that allows for
a continuous and smooth transition by employing the path integral description
of atoms.Comment: 8 pages 4 figure
Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water
Quantum effects due to the spatial delocalization of light atoms are treated
in molecular simulation via the path integral technique. Among several methods,
Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to
investigate properties induced by spatial delocalization of atoms; however
computationally this technique is very demanding. The abovementioned limitation
implies the restriction of PIMD applications to relatively small systems and
short time scales. One possible solution to overcome size and time limitation
is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme
(AdResS). AdResS requires a relatively small region treated at path integral
level and embeds it into a large molecular reservoir consisting of generic
spherical coarse grained molecules. It was previously shown that the
realization of the idea above, at a simple level, produced reasonable results
for toy systems or simple/test systems like liquid parahydrogen. Encouraged by
previous results, in this paper we show the simulation of liquid water at room
conditions where AdResS, in its latest and more accurate Grand-Canonical-like
version (GC-AdResS), is merged with two of the most relevant PIMD techniques
available in literature. The comparison of our results with those reported in
literature and/or with those obtained from full PIMD simulations shows a highly
satisfactory agreement
Extreme multiplicity in cylindrical Rayleigh-Benard convection: II. Bifurcation diagram and symmetry classification
A large number of flows with distinctive patterns have been observed in
experiments and simulations of Rayleigh-Benard convection in a water-filled
cylinder whose radius is twice the height. We have adapted a time-dependent
pseudospectral code, first, to carry out Newton's method and branch
continuation and, second, to carry out the exponential power method and Arnoldi
iteration to calculate leading eigenpairs and determine the stability of the
steady states. The resulting bifurcation diagram represents a compromise
between the tendency in the bulk towards parallel rolls, and the requirement
imposed by the boundary conditions that primary bifurcations be towards states
whose azimuthal dependence is trigonometric. The diagram contains 17 branches
of stable and unstable steady states. These can be classified geometrically as
roll states containing two, three, and four rolls; axisymmetric patterns with
one or two tori; three-fold symmetric patterns called mercedes, mitubishi,
marigold and cloverleaf; trigonometric patterns called dipole and pizza; and
less symmetric patterns called CO and asymmetric three-rolls. The convective
branches are connected to the conductive state and to each other by 16 primary
and secondary pitchfork bifurcations and turning points. In order to better
understand this complicated bifurcation diagram, we have partitioned it
according to azimuthal symmetry. We have been able to determine the
bifurcation-theoretic origin from the conductive state of all the branches
observed at high Rayleigh number
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