Molecular dynamics calculation for equilibrium state of water
Case directory
$FOAM_TUTORIALS/discreteMethods/molecularDynamics/mdEquilibrationFoam/periodicCubeWater
Summary
Molecular Dynamics (MD) calculation is performed to calculate the equilibrium state of water.
The properties of the particles are defined in the files "moleculeProperties" and "idList" in the directory "constant". The external force and interparticle potential are defined in the file "potentialDict" in the directory "system", the initial conditions are defined in the file "mdInitialiseDict", and the temperature at equilibrium is defined in the file "mdEquilibrationDict".
The size of the model in the X, Y, and Z directions is 4.22 nm, respectively, and each face is set to a periodic boundary condition.
Model geometry
The initial position of the particles is defined based on the mesh. The mesh is as follows.
Meshes
The calculation result is as follows.
Particle distribution at 0 sec
Particle distribution at 5.0×10-12 sec
The energy and force of each potential at each distance are output to the file "O-O" and the file "electrostatic". In the file, the first column is the distance, the second column is the energy, and the third column is the force.
Results of distance-energy calculations are output to file "O-O"
Results of distance-force calculations are output to file "O-O"
Results of distance-energy calculations are output to file "electrostatic"
Results of distance-force calculations are output to file "electrostatic"
Visualization operations
To visualize discrete particles, load the data into ParaView by the paraFoam command, and then set the following in the Properties tab of the pipeline browser and click the Apply button.
- 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
Commands
cd periodicCubeWater
blockMesh
mdInitialise
mdEquilibrationFoam
paraFoam
gnuplot
gnuplot> plot "O-O" using 1:2
gnuplot> plot "O-O" using 1:3
gnuplot> plot "electrostatic" using 1:2
gnuplot> plot "electrostatic" using 1:3
Calculation time
43 minutes 37.74 seconds *Single, Inter(R) Core(TM) i7-2600 CPU @ 3.40GHz 3.40GHz