Molecular dynamics calculation of water in a nanoscale nozzle

Update: December 28, 2017
OpenFOAM 4.x

Case directory

$FOAM_TUTORIALS/discreteMethods/molecularDynamics/mdFoam/nanoNozzle

Summary

We will perform Molecular Dynamics (MD) calculations. The fluid is water, and the model sizes in the X, Y, and Z axes are 51.2 nm, 9.6 nm, and 12.8 nm, respectively. The boundary condition is a no-slip wall.

The properties of the particles are defined in the file "moleculeProperties" in the directory constant. The external force and interparticle potential are defined in the file "potentialDict" in the directory "system", and the temperature at equilibrium is defined in the file "mdEquilibrationDict".

In the file "blockMeshDict" in the directory "system", the regions "sectionA", "sectionB", and "sectionC" are defined, and the initial conditions for each region are defined in the file "mdInitialiseDict".

Model geometry Model geometry

The initial position of the particles is defined based on the mesh. The mesh is as follows.

Mesh Meshes

The calculation result is as follows.

Particle distribution at 1.5e-13 Particle distribution at 1.5×10-13
Particle distribution at 55e-13 Particle distribution at 5.0×10-14

Visualization operations

To visualize discrete particles, load the data into ParaView by the paraFoam command, and then perform the following operations.

  1. First, click the Apply button on the Properties tab of the pipeline browser to load the data as usual.

    Loading data Loading data
  2. In the toolbar, change to the time data in which the particle data exists.

    The time data in which the particle data exists The time data in which the particle data exists
  3. In the Properties tab, make the following settings and click the Apply button to display the particles in 3D.

    • Check only "moleculeCloud" in the Mesh Parts list
    • Uncheck all items in Volume Fields list
    • Check all items in Lagrangian Fields list
    Select display items Select display items

Commands

cp -r $FOAM_TUTORIALS/discreteMethods/molecularDynamics/mdFoam/nanoNozzle nanoNozzle
cd nanoNozzle

blockMesh
decomposePar
mpirun -np 4 mdInitialise -parallel
mpirun -np 4 mdFoam -parallel
reconstructPar

paraFoam

Calculation time

51 minutes 15.84 seconds *4 parallel, Inter(R) Core(TM) i7-2600 CPU @ 3.40GHz 3.40GHz