6.3.2.2. MANIPULATING GROUPS OF ATOMS

next, previous Section / Table of Contents / Index Option [G] selected from the structure option menu S, see Sec. 6.3.2, 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. So this option can be used to rebuild parts of the cluster beyond manipulating single atoms in the atom modify option, see Sec. 6.3.2.1. The group modify menu SG reads =========================================================================== Group definition text Group: [G]def [L]ist [T]ransl [C]opy [U]n[H]ide [Z]defn [R]ot [A]rot+ [E]xpnd [F]xpnd+ m[I]rr m[J]rr+ c[P]fl m[V]fl [S]equ(rpt) [X]plot [?,]esc ===================================================================== 18 == where the group definition text reads Group of ng atom(s) defined (cluster total = nct) if a group of ng atoms is presently defined or No group defined and the value of the sequential repeat flag rpt reads "on" or "off" depending on the repeat state (see options [T], [C], [R], [A], [E], [F], [I], [J], [S] below). > [G] selected from submenu SG allows you to define a group of atoms or modify the present group definition by adding or removing atoms. The group definition menu SGG reads =============================================== Group of ng atom(s) defined : p1 p2 ... png [G]new [A]dd [R]emove [?,]esc ========================================= 19 == if a group of ng atoms is presently defined where p1 p2 ... png are pointers denoting respective atom numbers. A missing group definition is indicated by "No group defined" above. Note that the graphic analysis option offers also group (re)definition which is much more intuitive and faster, see Sec. 6.3.12. > > [G] selected from submenu SGG defines a group of atoms from scratch overriding the present group definition (if it exists). The prompt Define new group: size NGRP (-1=esc,-2=all) : asks for the number ng of atoms forming the group (dummy input ng = -1 will cancel the group definition, ng = -2 will define all cluster atoms as a group) and then Define ng atom(s) asks for ng atom numbers p1 ... png (where invalid and duplicate numbers are ignored). Values of atom numbers may be obtained from atom listings (see suboption [L] of the structure option menu S) or from a graphic analysis of the cluster, see Sec. 6.3.12. After the group definition BALSAC returns to submenu SG. > > [A] selected from submenu SGG adds atoms to an existing group. If no group is defined this option is identical to option [G] of submenu SGG. The prompt Add to group (NADD, NADD atom(s)) : asks for the number nadd of atoms to be added to the group and for nadd atom numbers p1 ... pnadd (where invalid numbers or numbers of the present group definition are ignored). Values of atom numbers may obtained from atom listings (see suboption [L] of the structure option menu S) or from a graphic analysis of the cluster, see Sec. 6.3.12. After adding atoms BALSAC returns to submenu SG. > > [R] selected from submenu SGG removes atoms from an existing group. If no group is defined this option has no effect. The prompt Remove from group (NREM, NREM atom(s)) : asks for the number nrem of atoms to be removed from the group and for nrem atom numbers p1 ... pnrem (where invalid numbers or numbers outside the present group definition are ignored). Values of atom numbers may obtained from atom listings (see suboption [L] of the structure option menu S) or from a graphic analysis of the cluster, see Sec. 6.3.12. After removing atoms BALSAC returns to submenu SG. > > [,] selected from submenu SGG leaves the present group definition unchanged and returns to submenu SG. > [L] selected from submenu SG allows you to list all or selected atoms of the present group definition. If no group is defined this option has no effect. The listing of ng atoms shows as 1) Xyz,R,Id( p1,V) : x y z , rad , nuc ... ng) Xyz,R,Id( png,V) : x y z , rad , nuc where p1 ... png gives the atom pointers, V denotes the visibility of each atom ("T" = visible, "F" = hidden), (x,y,z) denotes its position, rad its atom radius, and nuc its nuclear charge (element name). If the number of group atoms exceeds 20 the listing will be preceded by a prompt Group of ng atom(s) , List (NA,NE) : asking for two numbers na, ne with 0 < na <= ne <= ng after which the na-th to ne-th atom of the group definition will be listed as above. Large listings (exceeding 20 atoms) will be interrupted and the prompt ** Press [C], L-click to continue; [,], R-click to escape ** allows you to continue (select [C]) or finish listing (select [,]). After listing is finished BALSAC returns to submenu SG. > [T] selected from submenu SG translates all atoms of an existing group by a fixed shift vector s = (xs,ys,zs). The prompt Shift vector X,Y,Z ("0,0,0"=esc) : asks for the cartesian components xs, ys, zs of the shift vector to be added to the original coordinates of all group atoms. Dummy input "0,0,0" cancels the action while other vectors translate the group which is confirmed by Group translated After this BALSAC returns to submenu SG if the sequential repeat flag (shown in submenu SG) is set to "off". If the repeat flag is set to "on" the prompt [R]epeat operation [?,]esc repeats the group translation sequentially using the same shift vector (select [R]) or returns to submenu SA (select [,]). Note that the repeated translation does not affect the group definition but the atom coordinates will be redefined with each translation. > [C] selected from submenu SG copies all atoms of the present group and translates all new atoms by a fixed shift vector s = (xs,ys,zs). The prompt Shift vector X,Y,Z ("0,0,0"=esc) : asks for the cartesian components xs, ys, zs of the shift vector to be added to the original coordinates of all new atoms. Dummy input "0,0,0" cancels the action while other vectors copy the group which is confirmed by Group copied (added and shifted) After this BALSAC returns to submenu SG if the sequential repeat flag (shown in submenu SG) is set to "off". If the repeat flag is set to "on" the set of new atoms produced by the operation forms a new group which replaces the previous definition and the prompt [R]epeat operation [?,]esc repeats the group copy applying the previous shift vector on the new group (select [R]) or returns to submenu SA (select [,]). Note that the repeated copy does affect the group definition while setting the repeat flag to "off" leaves the group definition unchanged. > [H]/[U] selected from submenu SG hides/unhides all atoms of the present group. Hidden atoms are treated as invisible by setting their internal visibility flag to "F" and they and will not appear in subsequent plots. However, their coordinates and attributes are still contained in the atom definition list and hidden atoms can be revived in the same BALSAC/CLUSTER session by the unhide option [U] of submenu SA described below. Hidden atoms will not be stored on structure output files and, thus, will be lost in subsequent BALSAC/CLUSTER sessions. Unhiding atoms sets their internal visibility flag to "T" and they and will appear again in subsequent plots. Note that the graphic analysis option offers atom hiding/ unhiding which is much more intuitive and faster, see Sec. 6.3.12.2. The prompt Confirm group hide: [H]ide [U]nhide [?,]esc asks to confirm hiding (select [H]) which shows Group hidden or to confirm unhiding (select [U]) which shows Group unhidden while selecting [,] cancels the hiding process after which BALSAC returns to submenu SG. > [Z] selected from submenu SG assigns the same (new) nuclear charge to all atoms of the present group. Since atom painting depends on the nuclear charge this option allows you to assign the same color to a group of atoms which can help to emphasize parts of a cluster visually. The prompt ng atom(s): new charge Z (0=esc) = asks for a nuclear charge value 0 < zn <= 100 to be assigned to all group atoms. The charge (re)assignment is confirmed by Z= zn assigned to group atoms after which BALSAC returns to submenu SG. > [P]/[V] selected from submenu SG stores all atoms of the present group in an external file. The file is of PLOT3D format containing all graphics definitions of the present BALSAC session. Thus, it can be used as input to a subsequent BALSAC/CLUSTER session dealing only with the atoms of the group. The group definition remains unchanged by the file saving. However, option [P] leaves the visibility flag of all cluster atoms unchanged whereas [V] hides all atoms of the group (visibility flag set to "F"). The prompt File name for group save/move ("-"=esc): asks for the name (up to 72 characters) of a file to be used for output. Dummy input "-" will immediately return to submenu SG while a valid file name starts saving which is concluded by ng atom(s) saved if option [P] was chosen and by ng atom(s) moved if option [V] was chosen after which BALSAC returns to submenu SG. > [R]/[A] selected from submenu SG rotates all atoms of the present group about a predefined axis (option [R]) or copies all atoms of the present group and rotates the new atoms about an axis (option [A]). The prompt Rotation origin NC,X,Y,Z ("-1,0,0,0"=esc) : asks for four numbers defining an origin of the rotation axis given either in absolute coordinates (0,x,y,z) or denoting the center of an existing atom n by (n,0,0,0). Dummy input "-1,0,0,0" returns immediately to submenu SG. After the origin is defined the prompt Rotation axis, angle (X,Y,Z,PHI) : asks for cartesian coordinates (xr, yr, zr) giving the direction of the rotation axis and a value phi for the rotation angle (in degrees). The direction vector does not need to be normalized. For option [R] all atoms of the group will be rotated about the rotation axis in a clockwise direction. This option does not affect the group definition but all atom coordinates will be redefined. The process is concluded by Group rotated [A] a new group of atoms is defined by rotating the original group and its atoms are added to the cluster. The set of new atoms produced by the rotation forms a new group which replaces the previous definition. The process is concluded by Group added and rotated After this BALSAC returns to submenu SG or asks to repeat the operation depending on the state of the sequential repeat flag, see options [T], [C] above. > [E]/[F] selected from submenu SG expands (shrinks) the coordinates of all atoms of the present group homogeneously with respect to a given center (option [E]) or copies all atoms of the present group and expands (shrinks) the new atom coordinates (option [F]). The prompt Expansion origin NC,X,Y,Z ("-1,0,0,0"=esc) : asks for four numbers defining an origin of the expansion/shrinking given either in absolute coordinates (0,x,y,z) or denoting the center of an existing atom n by (n,0,0,0). Dummy input "-1,0,0,0" returns immediately to submenu SG. After the origin is defined the prompt Expansion factor : asks for a value fac defining the expansion factor. For values fac > 1 all atoms of the group are subject to a homogeneous expansion such that their distance with respect to the expansion origin is increased. For values fac < 1 their distance is decreased. Negative fac values result in an additional inversion about the expansion origin with fac = -1 defining inversion only. For option [E] all atoms of the group will be expanded/shrunk. This option does not affect the group definition but all atom coordinates will be redefined. The process is concluded by Group expanded [F] a new group of atoms is defined by expanding/shrinking the original group and its atoms are added to the cluster. The set of new atoms produced by the operation forms a new group which replaces the previous definition. The process is concluded by Group added and expanded After this BALSAC returns to submenu SG or asks to repeat the operation depending on the state of the sequential repeat flag, see options [T], [C] above. > [I]/[J] selected from submenu SG mirrors the coordinates of all atoms of the present group with respect to a predefined plane (option [I]) or copies all atoms of the present group and mirrors the new atom coordinates (option [J]). The prompt Mirror origin NC,X,Y,Z ("-1,0,0,0"=esc) : asks for four numbers defining an origin of the mirror plane given either in absolute coordinates (0,x,y,z) or denoting the center of an existing atom n by (n,0,0,0). Dummy input "-1,0,0,0" returns immediately to submenu SG. After the origin is defined the prompt Mirror plane normal (X,Y,Z) : asks for cartesian coordinates (xn, yn, zn) giving the direction of the mirror plane normal vector. This vector does not need to be normalized. For option [I] all atoms of the group will be mirrored. This option does not affect the group definition but all atom coordinates will be redefined. Note that repeating this operation reproduces the original coordinates. The process is concluded by Group mirrored [J] a new group of atoms is defined by the mirror operation acting on the original group and its atoms are added to the cluster. The set of new atoms produced by the operation forms a new group which replaces the previous definition. Note that repeating this operation may generate duplicate atoms of identical coordinates which have to be removed from the cluster, see Sec. 6.3.2.3. The process is concluded by Group added and mirrored After this BALSAC returns to submenu SG or asks to repeat the operation depending on the state of the sequential repeat flag, see options [T], [C] above. > [S] selected from submenu SG switches the sequential repeat flag between "on" and "off" (default) and returns to submenu SG. The present state of the flag is shown in the group modify menu SG. With the repeat flag set to "on" each of the atom group operations (translate, copy, rotate, expand, mirror) is followed by a prompt [R]epeat operation [?,]esc which allows you to repeat the operation on the group defined last using identical operation definitions (select [R]) or to return to submenu SG (select [,]). > [X] selected from submenu SG 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 SG returns immediately to the structure option menu S, see Sec. 6.3.2. next, previous Section / Table of Contents / Index