Related papers: Accelerated molecular dynamics force evaluation on…
Molecular-scale computation is crucial for smart materials and nanoscale devices, yet creating single-molecule systems capable of complex computations remains challenging. We present a theoretical framework for a single-molecule computer…
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecular dynamics (MD) codes through a simple patching procedure.…
This study introduces a systematic approach for analyzing strongly correlated systems by adapting the conventional quantum cluster method to a quantum circuit model. We have developed a more concise formula for calculating the cluster's…
An improved implementation of an N-body code for simulating collisionless cosmological dynamics is presented. TPM (Tree-Particle-Mesh) combines the PM method on large scales with a tree code to handle particle-particle interactions at small…
This paper introduces open-source computational fluid dynamics software named open computational fluid dynamic code for scientific computation with graphics processing unit (GPU) system (OpenCFD-SCU), developed by the authors for direct…
The recent trend of using Graphics Processing Units (GPU's) for high performance computations is driven by the high ratio of price performance for these units, complemented by their cost effectiveness. At first glance, computational fluid…
We present the extension of the Tinker-HP package (Lagard\`ere et al., Chem. Sci., 2018,9, 956-972) to the use of Graphics Processing Unit (GPU) cards to accelerate molecular dynamics simulations using polarizable many-body force fields.…
The implementation of a new particle module describing the physics of dust grains coupled to the gas via drag forces is the subject of this work. The proposed particle-gas hybrid scheme has been designed to work in Cartesian as well as in…
Using molecular dynamics simulations, we study supercritical fluids near the gas-liquid critical point under heat flow in two dimensions. We calculate the steady-state temperature and density profiles. The resultant thermal conductivity…
We re-derive the expression for the heat current for a classical system subject to periodic boundary conditions and show that it can be written as a sum of two terms. The first term is a time derivative of the first moment of the system…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
The autocorrelation functions for the force on a particle, the velocity of a particle, and the transverse momentum flux are studied for the power law potential $v(r)=\epsilon (\sigma /r)^{\nu}$ (soft spheres). The latter two correlation…
This paper presents a fast, economical particle-multiple-mesh N-body code optimized for large-N modelling of collisionless dynamical processes, such as black-hole wandering or bar-halo interactions, occurring within isolated galaxies. The…
Molecular dynamics (MD) is an important research tool extensively applied in materials science. Running MD on a graphics processing unit (GPU) is an attractive new approach for accelerating MD simulations. Currently, GPU implementations of…
A computational procedure is developed for the efficient calculation of derivatives of integrals over non-separable Gaussian-type basis functions, used for the evaluation of gradients of the total energy in quantum-mechanical simulations.…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
An application based on graphical processing units (GPUs) applied to 3-D digital images is described for computing the linear anisotropic elastic properties of heterogeneous materials. The application can also retrieve the property…
Pairing the accuracy of Kohn-Sham density-functional framework with the efficiency of a stochastic algorithmic approach, mixed stochastic-deterministic Density Functional Theory (mDFT) achieves a favorable computational scaling with system…
With increasing interest in the use of glassy carbon (GC) for a wide variety of application areas, the need for developing fundamental understanding of its mechanical properties has come to the forefront. Further, recent theoretical and…
The calculation of thermal conductivity in insulating solids at temperatures below the Debye temperature is problematic, due to the breakdown of classical and semi-classical approaches. In this work, we present a fully quantum methodology…