This option becomes available in the main menu if the geometry is known, i.e. it has either been read in or constructed from scratch. The idea is this: starting from one atom, build up all or some its nearest neighbours, then nearest neighbours to latter atoms and so on. Finally, if desired, some or all boundary atoms of the cluster are terminated by hydrogen atoms positioned at a certain distance from them and along the directions of the actual bonds of the bulk system.
The Cl-menu initially looks like this:
>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<
... CURRENT lattice vectors for the supercell ARE...
AJ(1): 10.88160 0.00000 0.00000
AJ(2): 0.00000 10.88160 0.00000
AJ(3): 0.00000 0.00000 10.88160
>>>>>>>>>>>>>>>> Current species are: <<<<<<<<<<<<<<
Si O
========= CHOOSE AN OPTION:
/================================================\\
|| HELP: when using options N and H, you may not ||
|| be bothered about internal cluster atoms as ||
|| those will be ignored anyway ||
\\================================================/
R. Read existing cluster geometry
1. START HERE: choose the first cluster atom
------- g e n e r a l s e t t i n g s --------
XY. Produce <geom.xyz> file after every change for Xmol
Hs. H atoms to be added to <geom.xyz> file: NO
Co. Show lattice atomic positions
Hd. Distance between an atom and H is: 1.00000000000000
Nd. Spherical belt width when finding nn is: 0.100000001490116
W. Write <geom.xyz> file for the current cluster
Q. Proceed/Quit
-----> Choose an appropriate option:
At the top, lattice vectors of the unit cell are shown together with existing species. Start from option 1 that will prompt you to choose the very first atom of the cluster. After this is done, the menu grows into:
R. Read existing cluster geometry
1. Cluster has been started from atom = 1
Species = Si
Position = ( 0.05194, 0.05194, 0.03418)
N. Build all first neighbours around atom(s)
H. Terminate a range of atoms with hydrogens
mH. Move a range of H atoms along bonds
5. Rename a range of atoms: change species
----- operations with multiple lists of atoms ------
T. Tag atoms (specify multiple lists): currently OFF
----------- shift -----------------
O. General shift of the cluster (new origin)
Cm. Shift the cluster to the centre of mass
------------- final options -----------
Rt. Rotate the WHOLE cluster about the X,Y,Z axes
Mv. Move atom(s)
------- g e n e r a l s e t t i n g s --------
XY. Produce <geom.xyz> file after every change for Xmol
Hs. H atoms to be added to <geom.xyz> file: NO
Co. Show lattice atomic positions
Hd. Distance between an atom and H is: 1.00000000000000
Nd. Spherical belt width when finding nn is: 0.100000001490116
W. Write <geom.xyz> file for the current cluster
Cc. Show current atomic positions in Cartesian
S. Save geometry
Q. Proceed/Quit
-----> Choose an appropriate option:
Now it is possible to choose the first shell of nearest neighbours of the first atom by pressing N. All nearest neighbours of the first atom will be added. This is decided within a certain thickness specified in settings by Nd. Two new options appear in the Cl-menu:
/3. Remove a range of atoms from the cluster
\4. Keep a range of atoms in the cluster: remove the rest
At the end of the construction, by pressing option H, it is possible to terminate some or all atoms with hydrogens. Their distance from the boundary cluster atoms is determined by Hd in the settings. If the distance appeared wrong, you can either undo this step (option U), change the setting (option Nd) and then repeat the construction. Alternatively, the atom-H distances can be corrected using option mH.
Note that, when specifying a range of atoms (options N and H), it is possible to include internal atoms of the cluster as well in the lists; this is very convenient and does not have any effect at all as only external atoms will be considered anyway.
At each step, the current arrangement of the cluster atoms can be seen in Cc. If the option XY is on (either at Xmol or Ymol), then you can preview the cluster by invoking Xmol or similar software and reading in the file geom.xyz. This file is dumped automatically in the current directory every time a change is made.
Additionally to the above mentioned options, it is also possible to change species (or ``rename'') a set of atoms (option 5). The option T allows a different (and, in many cases, more convenient) way of choosing atoms ``by lists'' (Section 1.2). At any point the cluster can be shifted as a whole (options O and Cm).
At the end of the construction some or all atoms can be moved to new positions, option Mv, seen Section 2.6.11.2. Finally, the whole system can be rotated (option Rt, see Section 2.6.11.3). Note that either of the options Mv and Rt has been used, it will not longer be possible to add more atoms to the system and/or terminate boundary atoms with hydrogens, i.e. options N and H will be disabled (unvisible).
Finally, the cluster geometry can be saved in either an xyz or a mol file formats, the latter is an internal format of the Cl option. Files in the mol format can be read in by the option R of the Cl-menu (e.g. from the previous unfinished project).