#Lee vmd calculator code#

The regulatable thermal conductivity and excellent mass transport performance demonstrate the promising potential of carbon nanotube as next-generation capillary wick of ultrathin heat pipe.Īccurate, fast, and flexible approaches for contact angle estimation in molecular dynamics simulations are of great importance for characterization of surface wettability, especially for machine learning approaches which would usually require thousands of computational contact angle evaluations for training and prediction purposes. Phonon spectral analysis and heat flow decomposition revealed that the decrease of water-filled carbon nanotube thermal conductivity originates from the low-energy coupling of van der Waals force between water molecules and carbon nanotube and the thermal motion of two water molecules layers. Importantly, the thermophoretic movement speed of water can reach up to 74 m/s and radial mass exchange occurs driven by temperature gradient. At overheating operation, the high thermal conductivity of empty carbon nanotube can reduce the temperature of the endothermic surface. Molecular dynamics simulation results found that the thermal conductivity of water-filled carbon nanotubes is reduced by 17.8%-23.8%, which is benefit to start-up operation. Here we propose the capillary wick of carbon nanotube array to regulate its heat transfer performance via the water filling ratio. However, achieving controllable thermal conductivity of the capillary wick materials to reduce the start-up time and total thermal resistance remains a challenge. Passive liquid cooling of ultrathin heat pipe has received considerable attention due to its excellent performance of removing heat from hot spot of electronic devices.

#Lee vmd calculator code#

The code can calculate both 1D and 2D density distributions in any specified local or global areas of the system. Solution method: The 1D or 2D density distribution is calculated through the following steps: slice the concerned area with specified resolutions in X, Y, and Z directions then the mass or atom number in each unit slice (or cuboid in 2D case) is calculated if there are multiple frames, average the mass or atom number by the frame number finally, density in each unit is divided by the slice volume to get the density.Īdditional comments including restrictions and unusual features: The code must be run with VMD as a platform, the current version only can only calculate mass or number density. Nature of problem: Calculate mass or number density distribution from trajectory files in VMD, and project the density along a specified 1D axis or onto a specified 2D plane. This work introduces the calculation method, code, and usages in detail to provide a quick start for users in their density analysis work. By using the built-in commands of VMD, the code can access and process trajectory files in any formats that are supported by VMD, as produced by mainstream simulation packages, i.e., LAMMPS, GROMACS, NAMD, and CHARMM, etc. This work presents a flexible and easy-to-use TCL code to be used in VMD, that can perform both 1D and 2D density calculations over any specified local areas of a given system. However, a density analysis is still not an in-built feature of VMD.

Visual Molecular Dynamics (VMD) is a widely used molecular visualization package that can not only visualize complex molecular systems but also perform analysis by integrating special plugins or by running in-house generated TCL scripts. Visualization of the density distribution is typically one of the most important properties in structural characterization. Characterization of structural information at the atomistic level in molecular dynamics (MD) simulations is a necessary task for researchers in the fields of materials modelling and simulation.