arXiv subjects

Stephen Sanderson

Publications and source records attributed to Stephen Sanderson.

5 recordsLinked to original sources

arXiv2025

On the importance of numerical integration details for homogeneous flow simulation

The Sllod equations of motion enable modeling of homogeneous flow at the atomic scale, and are commonly used to predict fluid properties such as viscosity. However, few publicly available codes support such simulations, and those that do often do not implement a reversible numerical integration scheme or have other subtle problems. Here, we demonstrate a reversible and energy-conserving integration scheme for the Sllod equations of motion with error on the order of $\delta t^3$, in line with typical operator splitting integrators used in standard molecular dynamics simulations. We discuss various implementation details, and implement the scheme in LAMMPS where we find that our changes enable more accurate simulation of transient responses, mixed flows, and steady states, especially at high rates of flow. Importantly, we show that a lack of energy conservation can manifest as a systematic error in the direct ensemble average of the pressure tensor, leading to an error in the calculated viscosity which becomes significant at high flow rates.

cond-mat.soft↗

arXiv2025

Mechanical Degradation of Unentangled Polymer Melts under Uniaxial Extensional Flow

Complex flow fields govern the deformation of polymers in various manufacturing processes. However, high flow rates may trigger reaction events (i.e., bond breaking or undesirable reaction of mechanophores) in raw polymeric materials, leading to the mechanical or functional debasement of manufactured structures. Additionally, it is difficult to fully characterize such molecular-level flow in the laboratory due to time- and length-scale limits. In this study, we perform non-equilibrium molecular dynamics (NEMD) simulations to explore the rheological and mechanical degradation of unentangled polymer melts under uniaxial extensional flow (UEF), allowing for chain breaking. Our simulations demonstrate shear thickening-thinning-thickening stages with the increase of UEF extension rates, resulting from flow-induced changes of chain conformation. With further increasing UEF extension rates, a bond-breaking potential leads to another flow thinning stage. Interestingly, fracture kinetics is originally first-order owing to the need for highly stretched polymer chains before bond fracture. It is no longer first-order when bond fracture is instigated before chains are stretched. Our computational work provides insight into the optimal design of the manufacturing process for polymeric materials.

cond-mat.soft↗

arXiv2024

Local temperature measurement in molecular dynamics simulations with rigid constraints

Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g. from a set of atoms in a subvolume or from velocities in one Cartesian direction, the result can appear to unphysically violate equipartition of the kinetic energy if the local DoF are not correctly calculated. Here we determine how to correctly calculate local temperatures from arbitrary Cartesian component kinetic energies, accounting for general geometric constraints, by self-consistently evaluating the DoF of atoms subjected to those constraints. The method is validated on a variety of test systems, including systems subject to a temperature gradient and those confined between walls. It is also shown to provide a sensitive test for the breakdown of kinetic energy equipartition caused by the approximate nature of numerical integration or insufficient equilibration times. As a practical demonstration, we show that kinetic energy equipartition between C and H atoms connected by rigid bonds can be violated even at the commonly-used time step of 2 fs, and that this equipartition violation appears to usefully indicate configurational overheating.

cond-mat.stat-mech↗

arXiv2024

Fluctuation theorems and distribution functions for polar molecules in an electric field

In this perspective we consider how modern statistical mechanics and response theory can be applied to understand the response of polar molecules to an applied electric field and the fluctuations in these systems. Results that are consistent with thermodynamics and physical expectations are derived, as well as a new fluctuation relation that is tested in molecular simulations. It is demonstrated that a deterministic approach leads to distribution functions that continually evolve, even when system properties have relaxed, which has implications for treatment of nonequilibrium steady states.

cond-mat.stat-mech↗

arXiv2023

Machine learning a time-local fluctuation theorem for nonequilibrium steady states

Fluctuation theorems (FTs) quantify the thermodynamic reversibility of a system, and for deterministic systems they are defined in terms of the dissipation function. However, in a nonequilibrium steady state of deterministic dynamics, the phase space distribution is unknown, making the dissipation function difficult to evaluate without extra information. As such, steady state FTs for deterministic systems to date have required either that the trajectory segment of interest is relatively long, or that information is available about the entire trajectory surrounding that segment. In this work, it is shown that a simple machine learning model trained to predict whether a given steady state trajectory segment is being played forward or backward in time calculates a function that satisfies an FT and relies solely on information within the segment of interest. The FT is satisfied even for very short trajectory segments where the approximate relation derived from theory breaks down, for systems far from equilibrium, and for various nonequilibrium dynamics. It is further demonstrated that any function that is a well-calibrated predictor of time's arrow must satisfy a fluctuation theorem, and that a local FT can be derived which depends only on local dissipation and its correlations with the surrounding non-local dissipation.

cond-mat.stat-mech↗