lamp_mac/ATOMS/
Fragment_AuAg.pro
top FRAGMENT_AuAg
FRAGMENT_AuAg, cluster, nc, cshell, ncsh, frag, nf, marco_out, shell_out, Dmin, Dmax
** ************* ** User callable ** Routine to read a structure file for a cluster of atoms ('cluster' variable) ** Add to surface atoms defined by clustershell fragments described by 'frag' file ** fragment is aligned along X ** Good file format for cluster and fragment models ** CAR format has header, block 9 columns by n rows, where n is number of atoms ** ** METHOD ** generate array of cluster atom coords: ClusterArr ** e.g. read from file ** check that cluster is centred on (0,0,0) ** identify outermost atoms ** initially on radius criteria only ** *** loop thro atoms in list ** use R2X.pro to find the matrix that rotates surface atom, normalised vector onto X axis ** rotate fragment onto the radial direction using inverse matrix ** translate fragment to target atom ** write fragment coords in array ** *** loop ** output a structure file for MS ** ** further developments: ** use a file of atoms to define shell ** structure made from vertex sites with Au and FC sites with Ag ** attach to Au sites ** look for Ag sites more than d (e.g. 4.5A) from Au for additional sites ** ** call requires structure files and corresponding atom numbers, an output file ** and the extra Ag sites where attachments are to be made, defined by Dmin, Dmax ** now add output file for modified shell ** ** M.R.J. Apr 2011 (ILL)
Parameters
- cluster
- nc
- cshell
- ncsh
- frag
- nf
- marco_out
- shell_out
- Dmin
- Dmax
File attributes
Modification date: | Tue Oct 1 14:45:53 2013 |
Lines: | 243 |