Exercise 3: Bulk Systems
In this section we will look into more complex systems like bulk materials.
After we have (hopefully) become acquainted with running CPMD jobs and Car-Parrinello MD runs for some systems, that are easy to follow and set up, we can now look into bulk systems, where using a plane wave basis set becomes a big advantage. Again we start with a rather simple system, bulk silicon, to explore the various options and look into some idiosyncrasies of CPMD calculations.
..this part should be complemented with theory/explanation.
Hydronium ion in Bulk Water
Requirements: Memory: 320 MB, CPU time: 15-30min WF OP, up to a few days MD.
The next step is a more typical application of the CPMD code: a Car-Parrinello MD simulation of a bulk system with water. In this specific example, we try to look at the Grotthuss mechanism for proton transport in water. Our system will consist of 32 water molecules and one hydronium ion (note the CHARGE keyword in the &SYSTEM section). To speed up the equilibration phase, we start from a restart configuration (32spce-h3op-1ns.xyz) that has been equilibrated with classical MD for about 1 ns using the SPC/E water potential and an accordingly parameterized hydronium ion potential
As usual, we start with a wavefunction optimization (see 1-proton-wfopt.inp).
We want to run the MD at 400 Kelvin, so we now run a short MD with temperature rescaling for the atoms and not thermostat for the electrons (2-proton-equilib.inp).
Now we are ready to start the production run with (at least) 2000 steps. (3-proton-md.inp). Be sure to move the outputs from the equilibration out of the way before you start production.
To illustrate the structural diffusion mechanism, you can load the VMD visualization script 32h2o-h3oplus-cpmd.vmd, which will read in the TRAJEC.xyz file. The yellow line traces the position of the hydronium ion (highlighted by a transparent yellow sphere) during the trajectory. The other colored lines follow the positions of (some) of the individual protons involved in the structural diffusion process.
See elsewhere on this homepage for a more detailed version of this example.