Any errors let me know
Generate a slab
A slab of NaCl will be generated with the (310) surface expressed.
The approach is first to generate the surface using the usual stackgen approach.
On running this, modify the staco0001.out file
1. remove lines from bulk --> slab and remove anal --> start
2. add lines after slab (before start):
vscale1
4.0 0.0
0.0 1.0
print dlpoly 1
The completed file should look something like:
Once this file is submitted it should generate a CONFIG, FIELD and CONTROL file. The FIELD file is only an approximate representation and is likely to require modificaton.
In general, the slab should at least be 20x20x20A. The thickness of the slab is controlled by the region line, The 3rd line of the lattice vector is: 1.7654146110 0.0000000000 -5.2962438329, and the region size (first number on region line) = 12. The thickness of the slab = 12 x 1.7654146110. The CONFIG file estimates the slab vector = 43.0000000000 0.0000000000 7.0616584440, which is slab thickness + 20A. If you require a 3D perfect cell, an estimate of the cell dimension is written on line 1 (a title line). For optimum efficiency, it is recommended that the 3rd line in transfered to the top, so as to make an orthorhombic cell. As it is simply a stacking vector and a vacuum is added the 7.06165.. can be replaced by 0.0000.
The first 2 dimensions are created by vscale1. The two lines are the combination of vectors used to create the new cell dimensions. The first, 4.0 0.0, means that the first vector is replaced by a new vector comprised of 4xoriginal first vector and 0xoriginal second vector. This might be clearer considering the (111) surface, as . The original second vector, 0.0000000000 3.9475870786 6.8374213874 if scaled by 3 would multiply the y and z taking it further from being orthorhombic. But if the second vscale1 was -2. 4. Then adding -2 of the first to 4 of the second will make the y component of vector 0.0000.
Add layer of water
Adding a layer of material, need a solvent file containing solvent and number of atoms in each solvent molecule.
surf # surface rather than slab
print dlpoly 2 reg2 2
region 12.00000 0.0 12.0 50.00000 # must ensure that reg1 block2 =0
adsorb # adsorption
solvent depth 40. void 1.4 shif 1.8 # depth of water =40A, void between water and shift layer away from surface
ends
dipole # preventing program finding an error with polar arrangement
coord ow core h core 1.4 # ensuring water stays together
Requires a file called SOLVENT in the same directory. The SOLVENT file needs to be of the form, LATT (with 3 lattice vectors), BASI # (where # is number of species in solvent molecule) followed by coordinates of solvent molecules and terminates with ENDS.
Checking Structure
Once the CONFIG file has been generated, it is worth checking that the structure looks sensible by sending it through METADISE again, regenerating a picture file and looking at the structure. The same is also true for the REVCON file, which is generated at the end of a simulation. This can be achieved by simply putting "dlpoly" on a line in front of the file and ends, notpoten, check, stop, start, stop in sequence of lines afterwards. We normally achieve this by using a simple script in either Unix or DOS. The script for the latter is attached:
Once in a METADISE form it can be used to modify the file. For example:
sendto reg1 ## converts the coordinates into reg1 for 2D or 1D simulations, ignoring the last or last lattice vectors
shell ## if it has a potential model present it will add a shell coordinate to all ions that have them.
SC Parker