113 research outputs found
Non-Uniform FFT and Its Applications in Particle Simulations
Ewald summation method, based on Non-Uniform FFTs (ENUF) to compute the electrostatic interactions and forces, is implemented in two different particle simulation schemes to model molecular and soft matter, in classical all-atom Molecular Dynamics and in Dissipative Particle Dynamics for coarse-grained particles. The method combines the traditional Ewald method with a non-uniform fast Fourier transform library (NFFT), making it highly efficient. It scales linearly with the number of particles as , while being both robust and accurate. It conserves both energy and the momentum to float point accuracy. As demonstrated here, it is straight- forward to implement the method in existing computer simulation codes to treat the electrostatic interactions either between point-charges or charge distributions. It should be an attractive alternative to mesh-based Ewald methods
Spectral Ewald Acceleration of Stokesian Dynamics for polydisperse suspensions
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics
(SEASD), a novel computational method for dynamic simulations of polydisperse
colloidal suspensions with full hydrodynamic interactions. SEASD is based on
the framework of Stokesian Dynamics (SD) with extension to compressible
solvents, and uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J.
Comput. Phys. 229 (2010) 8994] for the wave-space mobility computation. To meet
the performance requirement of dynamic simulations, we use Graphic Processing
Units (GPU) to evaluate the suspension mobility, and achieve an order of
magnitude speedup compared to a CPU implementation. For further speedup, we
develop a novel far-field block-diagonal preconditioner to reduce the far-field
evaluations in the iterative solver, and SEASD-nf, a polydisperse extension of
the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118
(2003) 10323]. We extensively discuss implementation and parameter selection
strategies in SEASD, and demonstrate the spectral accuracy in the mobility
evaluation and the overall computation scaling. We
present three computational examples to further validate SEASD and SEASD-nf in
monodisperse and bidisperse suspensions: the short-time transport properties,
the equilibrium osmotic pressure and viscoelastic moduli, and the steady shear
Brownian rheology. Our validation results show that the agreement between SEASD
and SEASD-nf is satisfactory over a wide range of parameters, and also provide
significant insight into the dynamics of polydisperse colloidal suspensions.Comment: 39 pages, 21 figure
Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica
M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary
mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is
diffused in a large simulation community and it is worth to keep it efficient and updated.
With this goal in mind, a major revision of the package has been performed, leading to a version
where several enhancements have been added: two efficient grid-based algorithm for long range
interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi
graphics boards has been produced. With the new features, the program exhibits a remarkable
increase of computational efficiency and an improvement in global performance.
The new version of M.DynaMix has been applied for studying some selected high charged particle
system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and
counterions has been investigated, searching for sequence dependent features. For ionic liquids, we
focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its
description. In both cases, the problem of validation of MD simulations has been treated, testing a
new technique based upon the determination of quadrupolar decay parameters, for direct
comparison between simulation and experiments
Modelling in chimica computazionale: ottimizzazione di codici MD ed applicazioni allo studio di sistemi ad elevata carica
M.DynaMix is a modular general purpose Molecular Dynamics code for simulations of arbitrary
mixtures of either rigid or flexible molecules. For its features and capabilities, M.DynaMix is
diffused in a large simulation community and it is worth to keep it efficient and updated.
With this goal in mind, a major revision of the package has been performed, leading to a version
where several enhancements have been added: two efficient grid-based algorithm for long range
interactions, SPME and ENUF, are now available; besides, a version of the code runnable on multi
graphics boards has been produced. With the new features, the program exhibits a remarkable
increase of computational efficiency and an improvement in global performance.
The new version of M.DynaMix has been applied for studying some selected high charged particle
system: DNA oligomers and ionic liquids. For oligomers, interactions between DNA and
counterions has been investigated, searching for sequence dependent features. For ionic liquids, we
focused on 1-decyl-3-methil-imidazolium chloride, to find a proper Force Field parameter set for its
description. In both cases, the problem of validation of MD simulations has been treated, testing a
new technique based upon the determination of quadrupolar decay parameters, for direct
comparison between simulation and experiments
Inertial Coupling Method for particles in an incompressible fluctuating fluid
We develop an inertial coupling method for modeling the dynamics of
point-like 'blob' particles immersed in an incompressible fluid, generalizing
previous work for compressible fluids. The coupling consistently includes
excess (positive or negative) inertia of the particles relative to the
displaced fluid, and accounts for thermal fluctuations in the fluid momentum
equation. The coupling between the fluid and the blob is based on a no-slip
constraint equating the particle velocity with the local average of the fluid
velocity, and conserves momentum and energy. We demonstrate that the
formulation obeys a fluctuation-dissipation balance, owing to the
non-dissipative nature of the no-slip coupling. We develop a spatio-temporal
discretization that preserves, as best as possible, these properties of the
continuum formulation. In the spatial discretization, the local averaging and
spreading operations are accomplished using compact kernels commonly used in
immersed boundary methods. We find that the special properties of these kernels
make the discrete blob a particle with surprisingly physically-consistent
volume, mass, and hydrodynamic properties. We develop a second-order
semi-implicit temporal integrator that maintains discrete
fluctuation-dissipation balance, and is not limited in stability by viscosity.
Furthermore, the temporal scheme requires only constant-coefficient Poisson and
Helmholtz linear solvers, enabling a very efficient and simple FFT-based
implementation on GPUs. We numerically investigate the performance of the
method on several standard test problems...Comment: Contains a number of corrections and an additional Figure 7 (and
associated discussion) relative to published versio
Stochastic Eulerian Lagrangian Methods for Fluid-Structure Interactions with Thermal Fluctuations
We present approaches for the study of fluid-structure interactions subject
to thermal fluctuations. A mixed mechanical description is utilized combining
Eulerian and Lagrangian reference frames. We establish general conditions for
operators coupling these descriptions. Stochastic driving fields for the
formalism are derived using principles from statistical mechanics. The
stochastic differential equations of the formalism are found to exhibit
significant stiffness in some physical regimes. To cope with this issue, we
derive reduced stochastic differential equations for several physical regimes.
We also present stochastic numerical methods for each regime to approximate the
fluid-structure dynamics and to generate efficiently the required stochastic
driving fields. To validate the methodology in each regime, we perform analysis
of the invariant probability distribution of the stochastic dynamics of the
fluid-structure formalism. We compare this analysis with results from
statistical mechanics. To further demonstrate the applicability of the
methodology, we perform computational studies for spherical particles having
translational and rotational degrees of freedom. We compare these studies with
results from fluid mechanics. The presented approach provides for
fluid-structure systems a set of rather general computational methods for
treating consistently structure mechanics, hydrodynamic coupling, and thermal
fluctuations.Comment: 24 pages, 3 figure
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