MCF file

Hi Neda,

Rigid solid surfaces are not supported in Cassandra 1.0, but will be supported in Cassandra 1.1 -- to be released in the coming weeks.

Cheers,
Ryan

Hi Neda,

There are several examples of simulating various fluids within a rigid model of silicalite. You can find the examples in the Examples/GCMC directory. Each of these examples begins with an empty zeolite. During the course of the simulation, fluid phase molecules (e.g. methane, butane, nitrogen) are inserted according to the chemical potential set point.

See Ch 6 of the user guide for information on what files you will need to simulate water between sheets of graphene.

Do you have a configuration file listing your graphene atom coordinates?

I was able to get a test system of water between graphite sheets working. Have you made any progress yet?

Since you already have a configuration with graphene and water, you just need to convert your configuration file to the .xyz format.

Initial configuration
I made my configuration using VMD to create 4 layers of graphene 1nm x 1nm. The actual dimensions are 12.28 Angstroms x 12.762 Angstroms. This set up has 240 carbon atoms. I made the z-dimension of the box 50 Angstroms. I populated that box with 167 water molecules, and wrote out the whole configuration as an .xyz file. The .xyz created by vmd will have the number of atoms on line 1 and a comment on line 2:

741
generated by VMD
O -2.472000 3.701000 -2.396000
H -2.916000 4.070000 -3.198999
H -3.048000 3.998000 -1.673000
...
C 3.684000 6.381000 -19.975000

You can see that I listed the water molecules first. The .xyz file used to start a Cassandra simulation instead needs the number of molecules of each species on line 1. Here's my test.inp.xyz :

167 240
O -2.472000 3.701000 -2.396000
H -2.916000 4.070000 -3.198999
H -3.048000 3.998000 -1.673000
...
C 3.684000 6.381000 -19.975000

where you can see I specify that the xyz file contains 167 water molecules and 240 graphene "molecules". Since the graphene will be rigid, I opted to list each carbon atom as a different molecule.

Molecular Connectivity File (MCF)
You will also need an MCF for each species: water and carbon. MCFs for water are included with Cassandra in either the MCF or Examples directories. The MCF I created for carbon is pasted below. Note that there are no bonds defined. Here's my c.mcf :

!*******************************************************************************
!Molecular connectivity file for c.pdb
!*******************************************************************************
!Atom Format
!index type element mass charge type parameters
!type="LJ", parms=epsilon sigma

# Atom_Info
1
1 C C 12.011 0.0 LJ 18.611 3.602

# Bond_Info
0

# Angle_Info
0

# Dihedral_Info
0

# Improper_Info
0

!Fragment Format
!index number_of_atoms_in_fragment branch_point other_atoms

# Fragment_Info
1
1 1 1


# Fragment_Connectivity
0


END

Input File
In the input file, I included the following options. Note that the carbon atoms cannot be moved or rotated (dr.max = dtheta.max = 0). By contrast, water can be moved 1. Angstrom and rotate 10. degrees on each move. Also the box dimensions match that of the graphene crystal. This is not the full input file, just the sections that are specific to simulating with a rigid solid:

# Molecule_Files
spce.mcf 167
c.mcf 240
!

---

# Box_Info
1
ORTHOGONAL
12.280 12.762 50.000
!

---

# Move_Probability_Info

# Prob_Translation
0.5
1. 0.

# Prob_Rotation
0.5
10. 0.

# Done_Probability_Info
!

---

# Start_Type
read_old
test.inp.xyz
!

---