Problem Set

Due date: Ten days after Session #5

We will be using the ITAP IMD molecular dynamics code.

Please see: The ITAP Molecular Dynamics Program for instructions and a manual. Compiled versions of the code are provided.

When you compile the code please make sure that the IMDSYS variable is set correctly:

setenv IMDSYS ia32-gcc2

For the EAM potential:

imd_nve_eam4point_glok_homdef_stress
(EAM energy minimization version)
imd_nve_eam4point_homdef_stress (EAM NVE version, homdef)
imd_nve_eam4point_deform_stress (EAM NVE version, deform)

For the LJ potential:

imd_nve_pair_lj_glok_homdef_stress (LJ energy minimization version)
imd_nve_pair_lj_homdef_stress (LJ NVE version, homdef)
imd_nve_pair_lj_deform_stress (LJ NVE version, deform)

"deform" - displace regions of atoms, e.g. for application of load by means of displacement BCs
"homdef" - homogeneous deformation according to specified deformation matrix

Please email the instructor in case you have any questions regarding compilation or techniques issues.

Problem Set (PDF)

Visualization

You may use the program "vmd" (download at Visual Molecular Dynamics) to visualize the results.

The output of IMD can be converted as follows to generate an animation with multiple frames:

cat OutFile*.chkpt > out.chkpt
python chkpt2xyz.py out.chkpt x.xyz 1.0

Then you may use vmd:

vmd x.xyz

Alternatively, you may use the Gnuplot program for plotting results.

More information can be found here: Gnuplot Homepage.

A good program to visualize 2D and 3D graphs is MATLAB® or Python's Matplotlib.