China
Africa
Explore chapters and articles related to this topic
Molecular simulations of water and ion transport through nanoporous membranes
Published in Alberto Figoli, Jan Hoinkis, Sacide Alsoy Altinkaya, Jochen Bundschuh, Application of Nanotechnology in Membranes for Water Treatment, 2017
Richard Renou, Minxia Ding, Haochen Zhu, Aziz Ghoufi, Anthony Szymczyk
Because of the high computational cost of MD simulations, the sides of the simulation box inside which atoms move are typically limited to a few tens of Angströms in size. In order to avoid problems associated with boundary effects caused by the limited size of the simulation box and to make the system equivalent to an infinite medium, periodic boundary conditions are applied. This consist of replicating the original box (without walls at its boundaries) in the three spatial dimensions to form an infinite lattice. In this way, as an atom moves outside the original box, one of its periodic images simultaneously enters through the opposite face of the box.
Nanodrops on the Solid surface Contact Angle, Sticking Force
Published in Eli Ruckenstein, Gersh Berim, Wetting Theory, 2018
Some microscopic approaches are based on Monte Carlo (MC) or molecular dynamics (MD) simulations,22,23 which involve periodic boundary conditions. Another limitation is the size of the simulation box, which rarely exceeds several tens of molecular diameters. However, the results of MC and MD simulations are often the only source of “experimental” information at the nanoscale and therefore the theories have to be adjusted to the settings of MC and MD experiments.
A computational investigation of the thermodynamics of the Stillinger-Weber family of models at supercooled conditions
Published in Molecular Physics, 2019
Francesco Ricci, Jeremy C. Palmer, Yagyik Goswami, Srikanth Sastry, C. Austen Angell, Pablo G. Debenedetti
In our study, we performed several types of simulations in multiple ensembles. Standard molecular dynamics (MD) simulations were performed in the canonical (NVT) ensemble using the LAMMPS [35] simulation package, with a Nosé-Hoover thermostat and a 1fs time step. Standard single-particle move Metropolis Monte Carlo (MC) simulations were performed in the isothermal-isobaric (NPT) ensemble using an in-house code developed for the Stillinger-Weber family of models. This in-house NPT MC code was also employed to perform the umbrella sampling simulations. All MD and MC simulations were initiated from liquid configurations equilibrated at 4000 K. At the beginning of a simulation, the temperature was instantaneously quenched from 4000 K to the temperature of interest. This was followed by a re-equilibration period at the temperature of interest, and then a subsequent production phase during which statistics were collected. Additional details of this procedure are described below. Cubic simulation cells with periodic boundary conditions were employed in all simulations.
Recent Features and Industrial Applications of the Hybrid SPH-FE Method
Published in International Journal of Computational Fluid Dynamics, 2021
Paul Groenenboom, Bruce Cartwright, Damian McGuckin
Periodic boundary conditions are mathematical conditions that can be placed on the boundary of a computational domain to mimic the behaviour of a larger or infinite domain. For Eulerian types of CFD, this may be accomplished by equating the inflow at one boundary to the outflow at the opposing boundary. For SPH, an additional requirement is that particles that exit at one boundary are entering at the opposite boundary at the same conditions, and that the neighbourhood of particles near such boundaries is extended to include the opposite boundary as well. An enhancement is the translating periodic boundary condition (TPBC), where the upstream and downstream boundaries can be assigned to move according to some arbitrary function, or to a selected FE node. This enables the study of a structure as it moves with respect to the fluid without modelling the entire distance that would be covered during the entire simulation. An optional feature of the translating periodic boundary is that the upstream conditions are those of a fluid at-rest, and not the disturbed downstream conditions in the case where a structure has interacted with the fluid in some way. In this case, the conditions and locations of the SPH particles as they exit the translating downstream boundary are reset to their (original) at-rest conditions and locations on re-entering the upstream periodic boundary condition. This feature allows recycling of the particles from the spray in the downstream region for an object interacting with the free surface as particles in the undisturbed fluid in front of the object. Figures 2 and 3 below sketch the application of the TPBC in horizontal direction; the damping zone may be included to mitigate any disturbance due to the interaction between the fluid and an immersed structure.
Spontaneous formation of cubic phases: a molecular dynamics study for soft repulsive spherocylinders
Published in Liquid Crystals, 2023
Keiko M. Aoki, Yasuhisa Yamamura, Shoichi Kutsumizu, Kazuya Saito
Throughout this paper, we use reduced simulation units: the energy, length, and mass are, respectively, measured in units of ϵ, D, and m (mass of a single molecule). The unit of time is (mD2/ϵ)1/2. The Boltzmann constant kB is set equal to unity. In this work, the length of the hard segment representing the long axis is L = 3. The molecular core volume Vcore described by the spherocylinder (depicted in Figure 1 as the line surrounding the hard long axis) is determined by the excluded distance dc. At temperature T, the value of dc exerted by the repulsive intermolecular potential is given by ij(dc) = T. We use the stress control method, with two anisotropic factors representing the aspect ratios of the simulation cell [18]. The method ensures that the system is under hydrostatic pressure even when the system is dynamically evolving. For details of the simulation method, see references [19,20]. Periodic boundary conditions (PBC) are applied in all directions for a rectangular simulation cell. Thus, all the phases obtained are triply periodic. The system size is N = 1920. The masses for the barostat and the thermostat are M = K = 1.0 × 106. The time step is δt = 1.0 × 10−5. To prepare a common initial configuration for the set of simulations, eight layers of spherocylinders are well equilibrated at a given temperature T = 10 and pressure P = 200. The orientational order parameter becomes S2 = 0.81 at the end (time t = 4000). This final state is used as a common initial configuration for all the simulations with different pressures at T = 10.