6.3.2. STRUCTURE OPTION, [S]

next, previous Section / Table of Contents / Index [S] This option allows you to modify, shift, add, hide, or remove atoms of the cluster studied in a BALSAC/CLUSTER session. If BALSAC/CLUSTER is started from scratch in an interactive session (without a structure input file) this option defines the initial cluster where ====== STRUCTURE OPTIONS ============== Build structure from scratch Title (A60) : asks for a title (up to 60 ASCII characters) describing the cluster and No. of atoms N (>0, 0=esc) : asks for the total number nct of atoms to define the cluster. (Dummy input nct = 0 returns to the BALSAC/CLUSTER startup menu.) This is followed by nt prompts 1 (X,Y,Z,R,NUC) : ... nct (X,Y,Z,R,NUC) : requesting five numbers each defining the cluster atoms by their positions (x,y,z) in absolute cartesian coordinates, atom radii rad and nuclear charges nuc. Atomic radii do not need to be known at this point and can be determined later, see option [R] below and Sec. 6.3.3. The initial cluster definition is confirmed by nct (nel) different atoms (elements) where nel gives the number of elements (= atoms of different nuclear charge) after which BALSAC moves to the structure option menu. This startup input is not required if the structure option is chosen from the main option menu of BALSAC/CLUSTER. Selecting [S] from the main option menu of BALSAC/CLUSTER shows the structure option menu, submenu S ====== STRUCTURE OPTIONS ============================================= [T]it [R]ad/nuc [A]toms [G]rp [F]ilrd [L]ist [S]ymm [D]ispla [X]plot [?,]esc ================================================================ 9 == from which atoms of the cluster can be (re)defined, listed, or plotted in many different ways. > [T] selected from submenu S shows the present title of the cluster by Title [ ... old title ... ] New (A60,"-"=esc) : asking for a new title (up to 60 characters, longer text will be truncated). Answering the prompt by a one character title "-" will leave the present title unchanged. After title (or dummy) input BALSAC returns to the structure option menu S. > [R] selected from submenu S moves to the radii/charge option menu allowing you to modify radii and nuclear charges of all atoms of the cluster. The options of this menu are explained in detail in Sec. 6.3.3. If the radii/charge option menu is closed by selecting [,] BALSAC returns to the structure option menu S. > [A] selected from submenu S allows you to add, hide, move, or delete cluster atoms. This option can be used to rebuild parts of the cluster. Details of the atom modify menu are described in Sec. 6.3.2.1. > [G] selected from submenu S allows you to define and modify groups of atoms of the cluster by changing their coordinates in simple geometric operations, store groups on external files for later use, and more. Details of the group modify menu are described in Sec. 6.3.2.2. > [F] selected from submenu S allows you to include additional atoms from an external (PLOT3D format) file in the present cluster. Examples are combinations of molecules and/or lattice sections built in separate BALSAC sessions and joined to form a compound system. The prompt File name for add ("-"=esc) : asks for the name (up to 72 characters) of a (PLOT3D format) file defining any cluster. Dummy input "-" will immediately return to submenu S while a valid file name fname containing a cluster of nn atoms shows submenu SF nn Atoms to add: [A]ddall [P]rompt [?,]esc asking for the include mode. > > [A] selected from submenu SF includes all cluster atoms of the external file in the present cluster (if possible) which is confirmed by nac ( nn ) atoms added from file name = [ fname ] giving the number nac of new atoms included and the number nn of atoms stored in the external file fname. The value nac will be smaller than nn if the total number of atoms after the include process exceeds the internal maximum namax ( = 2001 (DOS) or = 8000 (Unix)). After all atoms are included BALSAC returns to the structure option menu S, see Sec. 6.3.2. > > [P] selected from submenu SF allows you to include selected cluster atoms from the external file in the present cluster. Here for each atom stored in the file a line Xyz,R,Id= x y z rad nuc : [A]cc [I]gn [?,]esc shows the atom position (x,y,z), its radius rad and nuclear charge nuc. This atom can then be included in the present cluster by selecting [A] which is confirmed by Atom accepted as no. ni where ni denotes the last atom of the present cluster list. Alternatively, the atom can be ignored by selecting [I] which is confirmed by Atom ignored After the atom has been accepted/ignored the next atom of the file is shown. After all atoms of the external file have been prompted or [,] was selected in the atom prompt the message nac ( nn ) atoms added from file name = [ fname ] gives the number nac of new atoms included in the cluster and the total number nn of atoms stored in the external file fname after which BALSAC returns to the structure option menu S, see Sec. 6.3.2. > > [,] selected from submenu SF returns to the structure option menu S, see Sec. 6.3.2, without atoms included in the present cluster. Note that all new atoms included from an external file will be automatically considered a new group of atoms overriding the former group definition (if it exists). Therefore, the complete set of new atoms may be subject to group operations such as translation or copying, see Sec. 6.3.2.2. This becomes particularly important if new atoms coincide with or come very close to existing atoms and need to be "moved out of the way" (shift the whole group by a large vector, group translate option). > [L] selected from submenu S allows you to list all or selected atoms of a cluster. The line nct ( nel) different atoms (elements) , List (NA,NE) : shows the total number nct (nel) of atoms (different elements) of the cluster and prompts for a range of atoms [na,ne] (given as two integers) to be listed. For 0 < na <= ne <= nct the positions and attributes of atoms no. na to ne are listed in the form Atom X Y Z R El/Nuc Vis ---------------------------------------------------------- na) x y z r nuc visbl na+1) x y z r nuc visbl ... ne) x y z r nuc visbl ** Press [C], L-click to continue; [,], R-click to escape ** where (x,y,z) are coordinates of atom no. i (i=na...ne), r its radius, nuc its nuclear charges, and visbl its visibility flag ("T" for visible or "F" for invisible, see Sec. 6.3.2.1). After this BALSAC returns to the structure option menu S. Some lines of the above listing may read i ) x y z r nuc visbl => ieq which indicates that atoms i and ieq coincide. Coinciding atoms should be removed from the cluster, see options [H], [P] of the atom modify menu, Sec. 6.3.2.1. > [S] selected from submenu S allows you to impose point symmetries on the cluster where the cluster will be completed by adding atoms (if needed) to achieve the required symmetry. Details of the cluster symmetry menu are described in Sec. 6.3.2.3. > [D] selected from submenu S shows up to 10 lines of the most recent output generated by the graphic analysis option, see Sec. 6.3.12.2, by ============ Latest Graphics Output ================== 1: Xyz,R,Id( n1)= x y z rad nuc ... ====================================================== This allows you to look up and use numerical output from the analysis for input within submenu S. > [X] selected from submenu S plots the cluster (switching to graphics mode (DOS) or opening a graphics window (Unix)) or lists its atom coordinates depending on the plot/list mode defined in the graphics option, see Sec. 6.2.7. > [,] selected from submenu S moves to the view option menu, see Sec. 6.3.4, if the cluster is built from scratch or returns to the BALSAC/CLUSTER main option menu, see Sec. 6.3.0. next, previous Section / Table of Contents / Index