相关论文: Second generation wave-function thermostat for ab-…
Advanced thermostats for molecular dynamics are proposed on the base of the rigorous Langevin dynamics. Because the latter accounts for the subsystem-bath interactions in details, the bath anisotropy and nonuniformity are described via the…
We present a new and improved method for simultaneous control of temperature and pressure in molecular dynamics simulations with periodic boundary conditions. The thermostat-barostat equations are build on our previously developed…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
We show a unified second-order scheme for constructing simple, robust and accurate algorithms for typical thermostats for configurational sampling for the canonical ensemble. When Langevin dynamics is used, the scheme leads to the BAOAB…
The origins of thermodynamics from the microscopic properties of matter have not been satisfactorily accounted for. This work presents a formulation that connects Lagrangian mechanics to thermodynamics. By using such a formulation and…
The equations of Lagrangian gas dynamics fall into the larger class of overdetermined hyperbolic and thermodynamically compatible (HTC) systems of partial differential equations. They satisfy an entropy inequality (second principle of…
A new configurational temperature thermostat suitable for molecules with holonomic constraints is derived. This thermostat has a simple set of motion equations, can generate the canonical ensemble in both position and momentum space, acts…
Thermostats are dynamical equations used to model thermodynamic variables such as temperature and pressure in molecular simulations. For computationally intensive problems such as the simulation of biomolecules, we propose to average over…
We present a robust reciprocal-space implementation of the temperature-dependent effective potential method. Our implementation can scale easily to large cell and long sampling time. It is interoperable with standard ab-initio molecular…
A systematic comparison was carried out to assess the influence of representative thermostat methods in constant-temperature molecular dynamics simulations. The thermostat schemes considered include the Nos\'e--Hoover thermostat and its…
Extended Lagrangian Born-Oppenheimer molecular dynamics [Niklasson, Phys. Rev. Lett. 100 123004 (2008)] has been generalized to the propagation of the electronic wavefunctions. The technique allows highly efficient first principles…
We study the problem of a potential interaction of a finite-dimensional Lagrangian system (an oscillator) with a linear infinite-dimensional one (a thermostat). In spite of the energy preservation and the Lagrangian (Hamiltonian) nature of…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
A dynamical formulation of the dimer method for the determination of transition states is presented. The method is suited for ab-initio molecular dynamics using the fictitious Lagrangian formulation. The method has been applied to the…
Nonequilibrium molecular dynamics simulations often use mechanisms called thermostats to regulate the temperature. A Hamiltonian is presented for the case of the isoenergetic (constant internal energy) thermostat corresponding to a tunable…
Molecular dynamics simulations of a three dimensional relativistic gas with a soft potential are conducted with different interactions and particle masses. For all cases the velocity distribution agrees numerically with the J\"uttner…
With this work we present two new methods for the generation of thermostated, manifestly Hamiltonian dynamics and provide corresponding illustrations. The basis for this new class of thermostats are the peculiar thermodynamics as exhibited…
We develop a thermodynamic framework for modeling innovation adoption and abandonment dynamics using statistical mechanics. Starting from a mathematical model for an adoption distribution that fits empirically obtained date, we construct a…
We present a new formulation of ab initio molecular dynamics which exploits the efficiency of plane waves in adaptive curvilinear coordinates, and thus provides an accurate treatment of first-row elements. The method is used to perform a…
A simple deterministic and time reversal invariant type of thermostat is proposed to be used for computer simulations of classical systems. It acts on collisions with the walls of the container exclusively. It maps the incoming and outgoing…