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MD_Setup_Checkpoints
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MD_Setup_Checkpoints
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Reference Paper : https://pubs.acs.org/doi/full/10.1021/jp0268112
On the Water−Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes
T. Werder, J. H. Walther, R. L. Jaffe, T. Halicioglu, and P. Koumoutsakos
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# fftool to generate input files for carrying MD simulation in LAMMPS
1. xyz files of graphite and water
H2O.xyz downloaded from http://materia.fisica.unimi.it/manini/dida/structures.html
graphite.cif downloaded from Materials Project Website
2. Extend to appropriate size to neglet finite size effects. Remove Addtional layers if it does not effect the property of study.
The first method of extension and then cleaving is quiet confusing as the supercell size becomes large. So , I opted for a
personally easier choice og the second option.
- Convert to a orthorhbic unit cell using atomsk initial.cif -orthogonal-cell final.cif
- Cleave the edges such that no overlap occurs when PBC is applied
- Extend the unit cell using edit unit cell option in vesta and click transform and change the diagonal indices to stretch in z and y directions
as required
- Cleave the edges to make sure that when PBC is applied , there would not be any overlap !
3. Fetching and creaing .ff files
Check the fftool documentation for file format https://github.com/paduagroup/fftool#force-field-file-format
For graphite , there are CC , CO , OH and CH bonds
3 Atom Types ( C , H , O )
2 Bond Types ( C-C , H-O ) . We can add C-H , C-O bonds if we want but they are unlikely.
2 Angle Types ( C-C and O-H)
1 Dihedtal Type (C-C-C-C)
In the paper , most models are based on a pairwise additive Lennard-Jones potential between the oxygen atoms of the water and the carbon
and H atoms of water and the Carbon.
Some models also include an electrostatic interaction between the partial charge sites on the water molecules and point quadrupole moments on the carbons.
Some models for Carbon-Water potential is based on mixing rules.
Some models used a flexible graphite surface.
> The details of each model is explained in the folder allocated for each model
The force fields considered in paper will just have ATOMS section for both materials graphite and water and once fftool creates the inut file ,
we can modify it to provide the LJ parameters for CO and OO interaction which are the only considered LJ interactions.`
4. Creating the simulation set up with packmol
- Water ocupies 30 armstrong cube roughly , for 1000 water molecules and leaving enough space both sides of graphite , watter
lattice size was chosen to be 65*65*7 armstrong.
- 3 armstrong spacing between water layer and graphite.
5. Creating a sample input file which later need to be modifed anyways
According to the paper , the force fields are considered for water as well as water carbon interaction only.
fftool -b x,y,z -l -a -p xy 1 graphite.xyz 1000 H20-SPC.xyz
# LAMMPS input script