Parrinello-Rahman Molecular Dynamics Research Articles

Effect of Nonspherical Encapsulated Guests on the Volumetric Behavior of Structure H Clathrate Hydrates

Since its first discovery, technologies utilizing the structure H (sH) clathrate hydrates have been proposed. To develop the technology, understanding the mechanism of thermophysical property manifestation would be of fundamental importance. It is reported in the literature that the molecular properties of guest molecules had a significant influence on the crystal structure and the resulting thermophysical properties of the sH hydrate. In the present study, the effect of linear N2 help-gas molecule on the crystal structure was experimentally and computationally investigated to focus on the shape of the guest molecule in the sH binary clathrate with neohexane. Powder X-ray diffraction (PXRD) measurements were performed in temperatures from 93 to 183 K. The lattice constant values on a and c axes, the cage occupancies of small 512 and 435663 cages, and guest distributions in the host cages were determined. Parrinello–Rahman molecular dynamics (MD) simulations were performed on the sH clathrate hydrate phase...

A multiscale molecular dynamics method for isothermal dynamic problems using the seamless heterogeneous multiscale method

Abstract Based on recent developments in Parrinello–Rahman molecular dynamics a hierarchical two-scale molecular dynamics framework is derived that couples a coarse scale local particle dynamics with a fine scale molecular dynamics. This multiscale structure provides a seamless transition from the atomistic to continuum scale for an isothermal problem. The molecular dynamics cells at the fine scale are constrained by the deformation and temperature of the coarse scale grid and supply the coarse scale with the constitutive behaviour of the material computed directly from atomistics. Furthermore, the seamless heterogeneous multiscale method is employed to efficiently perform the time integration by solving the coarse and fine scale equations of motion simultaneously with independent clocks. Numerical examples demonstrate the performance of the proposed multiscale scheme.

A multiscale molecular dynamics allowing macroscale mechanical loads

We proposed a novel multiscale molecular-dynamics model in order to apply macroscale boundary conditions to microscale molecular systems, which is difficult for classical molecular dynamics. Unlike in statistical mechanics, in which macroscale quantities such as temperature and pressure are collected from molecular information, the proposed approach is a reversed procedure to find optimal molecular states when macroscale conditions such as traction are enforced. The model is originated from Parrinello-Rahman molecular dynamics but extends it to solve finite-size, inhomogeneous molecular-dynamics problems by generalizing the representative volume element to a “material point” in continuum mechanics. An example of compressing a nickel nanowire is presented to demonstrate the capacity of the method to simulate localized phase transition in a finite-size molecular system, which validates the effectiveness of the method.

A concurrent multiscale micromorphic molecular dynamics

In this work, we have derived a multiscale micromorphic molecular dynamics (MMMD) from first principle to extend the (Andersen)-Parrinello-Rahman molecular dynamics to mesoscale and continuum scale. The multiscale micromorphic molecular dynamics is a con-current three-scale dynamics that couples a fine scale molecular dynamics, a mesoscale micromorphic dynamics, and a macroscale nonlocal particle dynamics together. By choosing proper statistical closure conditions, we have shown that the original Andersen-Parrinello-Rahman molecular dynamics is the homogeneous and equilibrium case of the proposed multiscale micromorphic molecular dynamics. In specific, we have shown that the Andersen-Parrinello-Rahman molecular dynamics can be rigorously formulated and justified from first principle, and its general inhomogeneous case, i.e., the three scale con-current multiscale micromorphic molecular dynamics can take into account of macroscale continuum mechanics boundary condition without the limitation of atomistic boundary condition or periodic boundary conditions. The discovered multiscale scale structure and the corresponding multiscale dynamics reveal a seamless transition from atomistic scale to continuum scale and the intrinsic coupling mechanism among them based on first principle formulation.

Effect of Guest Size and Conformation on Crystal Structure and Stability of Structure H Clathrate Hydrates: Experimental and Molecular Dynamics Simulation Studies

To better understand the effect of size and flexibility of large molecule guest substances (LMGSs) on crystal lattice structure and thermodynamic stability of structure H (sH) clathrate hydrates, we performed powder X-ray diffraction (PXRD) measurements and Parrinello–Rahman molecular dynamics (MD) simulations on six alkane and cycloalkane LMGS in the presence of methane help gas. We first quantitatively analyze the dependence of the experimental lattice constants and formation pressure on the average maximum length of the LMGS guests as determined by MD simulation. The PXRD results show that within a family of LMGSs with similar molecular structures molecules of optimum size give better stability of sH hydrate phase. The most stable hydrate in each class has larger lattice constants along the a-axis and smaller lattice constant along the c-axis. The lattice expansion/shrinkage is well reproduced in the MD simulations. From the MD simulations, we determine the changes in the conformation as a result of en...

Comments on a Continuum-Related Parrinello-Rahman Molecular Dynamics Formulation

Phase transitions in solid mechanics are commonly studied employing Parrinello-Rahman molecular dynamics. This type of molecular dynamics may lead to a proper description of the atomistic scale in multi-scale analysis of engineering problems. However, the proposed Lagrangian is stated without derivation and lacks invariance under modular transformations. Recently, this type of dynamics was re-interpreted into a continuum-related Parrinello-Rahman molecular dynamics. The continuum-related formulation is derived in a consistent physical manner and becomes equal to the original formulation by employing two propositions. The propositions are stated without validation and the treatment shows no numerical example demonstrating the performance of the proposed formulation. Based on this recent continuum-related derivation, this paper investigates the validity of the two propositions in a numerical example, namely a phase transition in a nickel single crystal. Furthermore, the invariance of the continuum-related Lagrangian is investigated. This implies that the obtained dynamics is invariant to the chosen unit cell, which corroborates with results in solid state physics and which is a mandatory requirement for the suitability for multi-scale analysis.

On (Andersen–)Parrinello–Rahman Molecular Dynamics, the Related Metadynamics, and the Use of the Cauchy–Born Rule

It is shown that the Parrinello–Rahman Lagrangian is obtained by assuming that (i) the cell inertia tensor is spherical and constant in time, and that (ii) the cell fluctuation motions are irrotational. A slightly different Lagrangian is suggested, arrived at by dropping the sphericity assumption in (i). A related metadynamics is also proposed, based on replacing by (ii) the various no-cell-rotation assumptions that are customarily used. Finally, a zero-temperature, scale-bridging relation is proposed between the intermolecular potential and the macroscopic stored-energy mapping.

Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study

The sliding in a Ni symmetrical tilt grain boundary, $\ensuremath{\Sigma}5$ (012) [100], is investigated by modified Parrinello-Rahman molecular dynamics which deals with the thermodynamic ensemble characterized by the number of atoms $N$, temperature $T$, and the shear stress $\mathbf{t}$. It is found that the grain boundary can slide in the direction perpendicular to the tilt axis $[02\overline{1}]$ with the aid of shear stress in that direction. The sliding is coupled to the migration involving a collective motion of the third layer atoms hopping into the hollow site in between the first (GB) and second layers. Here, the critical stress necessary to move the grain boundary damps almost exponentially as the temperature is increased. At temperatures above about $820\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, random walk of GB migration occurs without the assistance of stress. On the other hand, it is only at much higher shear stress that the grain boundary can slide in the direction parallel to the tilt axis [001]. This may be because this sliding mechanism does not involve the coupling to the migration mode.

Molecular dynamics studies of titanylphthalocyanine crystals

Molecular dynamics calculations have been used to study the stability of a titanylphthalocyanine (TiOPc) crystal called Y-form. This crystal is of interest as a photoconductive material. A Parrinello–Rahman molecular dynamics calculation and a rigid-molecule intermolecular potential have been used in this study. The proposed TiOPc Y-form crystal structure was found from powder X-ray diffraction analysis to be stable from 300 to 600 K, indicating that the crystal structure proposed is reasonable.

Computer simulation of hydrogen embrittlement in metals

IT has been long known that hydrogen can substantially reduce the mechanical stability of transition metals under tensile stress1–3. This phenomenon of 'hydrogen embrittlement' has important consequences for the safety of fusion reactors and for space technology; but there remains considerable uncertainty about its microscopic origin2, 3. Here we report the results of a study of fracture of hydrogen-loaded palladium under tensile stress which uses Parrinello–Rahman molecular dynamics based on a many-body alloy hamiltonian. A rather unexpected result is that the apparent hydrogen embrittlement results from a local enhancement of ductility in hydrogen-saturated regions of the metal which causes a reduction of the critical tensile stress at which failure occurs.

Fluctuations and thermodynamic response functions in a Lennard-Jones solid.

Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid\char21{}heat capacity, thermal-expansion coefficient, compressibility, and elastic constants\char21{}are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results.

Ergodicity and Convergence of Fluctuations in Parrinello-Rahman Molecular Dynamics

ABSTRACTDistortion and rotation of a molecular dynamics cell used in Parrinello-Rahman molecular dynamics are found to lead to slow convergence, or nonconvergence of fluctuations from thermodynamic averages. The variations are shown to be related to nonconservation of the total angular momentum and translational symmetry variance of the dynamics. A modified equation of motion is presented which eliminates these variations. It is shown that the ergodicity is achieved in the MD ensemble generated by the new equations of motion. However, the rate of convergence is strongly affected by the choice of the MD cell mass W. Simulation results show that not all values of Wcan be used to give a desired convergence of fluctuations from thermodynamic averages in finite simulations. The fastest convergence is achieved by using the optimal cell mass.