Glotzer:Lennard-Jones Fluid Module Basic
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Simulation Description
This simulation consists of a single-component system of particles that interact via the Lennard-Jones Potential. The system runs NVT Molecular Dynamics using the Berendsen Thermostat. The number of particles, number density, and temperature are all user-modifiable variables. The simulation outputs the radial distribution function ( RDF) at the end of the simulation, and the average temperature to the screen.
Simulation Model/Method
- Particle-particle interactions are modeled using the Lennard-Jones potential. Interactions are truncated and shifted at the standard 2.5σ, where σ, the particle diameter, is set to 1.
- This simulation uses Molecular Dynamics where the equations of motion are integrated using the Velocity Verlet integration scheme.
- Temperature is kept constant by the use of the Berendsen Thermostat.
- A brute force neighbor list routine is used to calculate particle-particle interactions, thus simulation is most suited for smaller system sizes < ~1000;
- periodic boundary conditionts are utilized.
Instructions
Installing
- Instructions for installing modules can be found on the Module Installation page.
Running
A variety of system parameters can be modified as shown in the schematic below.
- To run at this statepoint, simply press the Run Simulation button.
- After pressing Run Simulation a visualizer window with the simulation will appear, as shown below.
- Note that the number of timesteps completed are displaced in the bottom left corner.
- Note that the end of your simulation, the number of timesteps will report 5 less than the total you set (so if you set 10000 it will show 9995). This is just a minor glitch and does not mean the simulation has crashed.
- Name of run will correspond to the directory name where data will be saved. The code will crash if there are spaces or odd characters.
- The RDF is output as "r_vs_gr.txt" in the folder specified by "Name of run".
- Note that the radial distribution function is only output at the end of the simulation, so you must run the full length of time.
- The radial distribution function will not be output if the simulation is run for less than 2000 timesteps.
- The radial distribution function is continually averaged throughout the simulation; longer runs will produce smoother RDFs, as will systems with more particles.
The simulation can be terminated from within the visualizer window by pressing "escape", "q" or select "Quit" from the application menu. Additional functionality of the visualizer can be found on the Visualizer Controls page.
To copy an image of the system while running, you can select "copy" from the Edit menu, and paste to a Word document or other program.
Suggested Assignments
Phase Behavior
The phase behavior of this system will be a function of both temperature and number density. For example, at low number density and high temperature, we would expect a gas phase, where as low temperature and high number density we would expect a solid.
Structure
To see the differences in phase behavior, simulate this system at Number Density = 0.01, 0.4, and 0.7 and Temperature = 2.0, 1.0, and 0.25 respectively. You should be able to visually see a difference, and your observations should be reinforced by examination of the Radial Distribution Function (RDF or g(r) which will be output to the file r_vs_gr.txt inside the folder that was defined by the Name of Run field in the interface.
- Note: The Radial Distribution Function page contains several examples of the phase behavior for a Lennard-Jones system. You may additionally refer to the MATDL Examples given below, for more information regarding the conditions at specific statepoints.
Examples/Links
MATDL Examples
- Simulation snapshot and RDF of a single component Lennard-Jones gas, Full MatDL Record
- Simulation snapshot and RDF of a single component Lennard-Jones liquid, Full MatDL Record
- An example plot of RDF for a 2000 particle Lennard-Jones crystal simulated with Molecular dynamics at a number density = 1.0 and Temperature = 0.5.
Literature Examples
- SMIT B, PHASE-DIAGRAMS OF LENNARD-JONES FLUIDS , JOURNAL OF CHEMICAL PHYSICS 96 (11): 8639-8640 JUN 1 1992
- JOHNSON JK, ZOLLWEG JA, GUBBINS KE, THE LENNARD-JONES EQUATION OF STATE REVISITED, MOLECULAR PHYSICS 78 (3): 591-618 FEB 20 1993
Related Pages
- softmatter:Basic Dynamical Simulation Methodology
- softmatter:Molecular Dynamics Simulation (MD)
- softmatter:Berendsen Thermostat
- softmatter:Simulation Variables/Units
- softmatter:Periodic boundary conditions
- softmatter:Pair potential
- softmatter:The Lennard-Jones Potential
- softmatter:Radial Distribution Function
- Glotzer:modules
- Glotzer:Visualizer Controls
- Glotzer:Module_Installation
