Creating oxygenated amorphous carbon

This tutorial will focus on using Grand-Canonical Monte-Carlo (GCMC) to determine equilibrium structures and properties of oxygenated amorphous carbon using TurboGAP.

The structure of this tutorial as as follows: 1. Create an amorphous carbon structure using molecular dynamics, via a melt-quench procedure. 2. Perform a standard GCMC calculation to populate the structure with oxygen. 3. Perform a hybrid Monte-Carlo/MD simulation, using the Hamiltonian MD approach, for an increased acceptance rate.

Create Amorphous Carbon

Here, we perform molecular dynamics simulations to form amorphous carbon from graphite. To do this, we use a simple melt-quench procedure.

1. We heat up the graphite to 9000K, thereby randomizing the structure. 2. We quench to 1000K. 3. We anneal the structure at 1000K, to allow the carbon bonds a chance to reform. 4. Cool to 300K, which is the temperature we want to do our GCMC simulations.

Perform Standard GCMC

There are many options for GCMC steps which one can perform. 1. Move: move any particle randomly, up to some maximum amount. 2.

NPT Monte-Carlo

A sample input file with a barostat (and without any vdW corrections yet!) looks like this:

! Species-specific info
atoms_file = 'melt.xyz'
pot_file = 'gap_files/carbon.gap'
n_species = 1
species = C
masses = 12.01

! MD options
md_nsteps = 100000
md_step = 1.
thermostat = berendsen
t_beg = 3500
t_end = 3500
tau_t = 100.
write_thermo = 1
write_xyz = 100
barostat = berendsen
barostat_sym = iso
p_beg = 1.
p_end = 1.
gamma_p = 10.
tau_p = 1000.
write_thermo = 1
write_xyz = 10
write_lv = .true.
neighbors_buffer = 0.5

Run this simulation with turbogap md. It will take a couple of hours with 4 CPU cores (mpirun -np 4 turbogap md).