6.3.2.1. MANIPULATING ATOMS

next, previous Section / Table of Contents / Index Option [A] selected from the structure option menu S, see Sec. 6.3.2, allows you to add, hide, move, or delete cluster atoms. So this option can be used to rebuild parts of the cluster. The atom modify menu SA reads ======================================================================== Atoms: [IA]dd [M]od [H]ide [U]nhide [P]urg [T]ransl [C]opy [R]cnt [S]equ(rpt) [X]plot [?,]esc ================================================================== 15 == where the value of the sequential repeat flag rpt reads "on" or "off" depending on the repeat state (see options [T], [C], [S] below). > [I] selected from submenu SA adds an atom to the cluster where internal coordinates are used for its position. The prompt na-th atom N0,N1,N2,DIST,THETA,PHI,RAD,NUC ("8*0"=esc) : (with na denoting the number of the new atom) asks for eight numbers defining an atom to be added as no. na (= nct+1) to the cluster of nct atoms. Here n0, n1, n2 are numbers of existing cluster atoms, dist is a distance, and theta, phi are respective rotation angles defining the atom position (x,y,z). The following conventions are used for the atom position: (a) n0 = n1 = n2 = 0 : atom position are in absolute spherical coordinates with respect to the origin of the basic coordinate system (X,Y,Z) x = dist * sin(theta) * cos(phi) y = dist * sin(theta) * sin(phi) z = dist * cos(theta) (b) n0 > 0, n1 = n2 = 0 : atom position are in spherical coordinates with respect to atom no. n0 at r0 = (x0,y0,z0) x = x0 + dist * sin(theta) * cos(phi) y = y0 + dist * sin(theta) * sin(phi) z = z0 + dist * cos(theta) where theta and phi are angles in the basic coordinate system (X,Y,Z). (c) n0 > 0, n1 >0, n2 = 0 : atom position are in spherical coordinates with respect to atom no. n0 at r0 = (x0,y0,z0) x = x0 + dist * sin(theta) * cos(phi) y = y0 + dist * sin(theta) * sin(phi) z = z0 + dist * cos(theta) where theta and phi are angles in a local cartesian coordinate system (X',Y',Z') with vector r1-r0 defining the Z'-axis. (d) n0 > 0, n1 >0, n2 > 0 : atom position are in spherical coordinates with respect to atom no. n0 at r0 = (x0,y0,z0) x = x0 + dist * sin(theta) * cos(phi) y = y0 + dist * sin(theta) * sin(phi) z = z0 + dist * cos(theta) where theta and phi are angles in a local cartesian coordinate system (X',Y',Z') with vector r1-r0 defining the Z'-axis. The plane through r0,r1,r2 contains the X'-axis such that vector r2 has a positive X' component. The above prompt requires in addition an atom radius rad and a nuclear charge nuc assigned to the new atom. Both values may be revised later. Correct input of the atom definition is confirmed by a message Xyz,R,Id,V( na)= x y z rad nuc T listing the (absolute cartesian) coordinates (x,y,z) of the new atom, its atom radius rad, its nuclear charge / element name, and its visibility flag value "T" ( = visible). Then BALSAC returns to submenu SA. Dummy input "8*0" in the above prompt returns immediately to submenu SA without an atom added. > [A] selected from submenu SA adds an atom to the cluster where absolute cartesian coordinates are used for its position. The prompt na-th atom X,Y,Z,RAD,NUC ("5*0"=esc) : (with na denoting the number of the new atom) asks for five numbers defining an atom to be added as no. na (= nct+1) to the cluster of nct atoms. Here (x,y,z) denotes the atom position in absolute cartesian coordinates, rad defines the atom radius, and nuc is the nuclear charge of the new atom. Correct input of the atom definition is confirmed by a message Xyz,R,Id,V( na)= x y z rad nuc T listing the (absolute cartesian) coordinates (x,y,z) of the new atom, its atom radius rad, its nuclear charge / element name, and its visibility flag value "T" ( = visible). Then BALSAC returns to submenu SA. Dummy input "5*0" in the above prompt returns immediately to submenu SA without an atom added. > [M] selected from submenu SA modifies an atom of the cluster. This allows you to change coordinates of an atoms as well as its atom radius and nuclear charge in one step. The option becomes particularly useful if you have mistyped coordinates of a cluster in the initial input and want to change components. The prompt Modify n-th atom N (1- nct , 0=esc) : (with nct denoting the total number of cluster atoms) asks for the number n of an atom to be modified. Here dummy input n=0 returns immediately to submenu SA. For values n within the valid range [1, nct] coordinates and attributes of atom no. n are listed, see above, as Xyz,R,Id,V( n)= x y z rad nuc T together with a prompt Modified atom: X,Y,Z,R,NUC ("5*0"=esc) : requesting five numbers redefining the cluster atom by its position (x,y,z) in absolute cartesian coordinates, an atom radius, and a nuclear charge. The input is confirmed by Xyz,R,Id,V( n)= x y z rad nuc T showing the new atom definition after which BALSAC returns to submenu SA. > [H] selected from submenu SA hides an atom of the cluster. 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. Note that the graphic analysis option offers atom hiding which is much more intuitive and faster, see Sec. 6.3.12. The prompt Hide n-th atom N (1- nct , 0=esc) : (with nct denoting the total number of cluster atoms) asks for the number n of an atom to be hidden. Here dummy input n=0 returns immediately to submenu SA. For values n within the valid range [1, nct] coordinates and attributes of atom no. n are listed, see above, as Xyz,R,Id,V( n)= x y z rad nuc T together with a prompt =================================================== Confirm: [H]ide [?,]esc ========================================== 16 ===== to confirm hiding. Selecting [H] in this prompt hides atom no. n and shows Atom no. n hidden while [,] cancels the hiding process returning to submenu SA. > [U] selected from submenu SA shows the unhide submenu SAU ======================================================= Unhide atoms: [A]ll [S]el [L]ist [?,]esc ================================================= 71 == which allows you to revive all or selected cluster atoms which have been hidden in the present BALSAC/CLUSTER session. Note that the graphic analysis option offers atom unhiding which is much more intuitive and faster, see Sec. 6.3.12. > > [A] selected from submenu SAU revives all atoms that are hidden in the present BALSAC/CLUSTER session by using the graphical hide option (see Sec. 6.3.12), suboption [H] of menu SA (atom hide), or of menu SG (group hide). Here the visibility flags of all hidden atoms are set to "T" so that they become visible in plots and are stored in structure output files. The process is confirmed by a message nvis atom(s) unhidden where nvis denotes the number of atoms formerly hidden after which BALSAC/CLUSTER returns to submenu SA. > > [S] selected from submenu SAU revives selected atoms that are hidden in the present BALSAC/CLUSTER session by using the graphical hide option (see Sec. 6.3.12), suboption [H] of menu SA (atom hide), or of menu SG (group hide). The prompt Unhide n-th atom N (1- nct , 0=esc) : (with nct denoting the total number of cluster atoms) asks for the number n of an atom to be unhidden. Here dummy input n=0 returns immediately to submenu SA. For values n within the valid range [1, nct] coordinates and attributes of atom no. n are listed, see above, as Xyz,R,Id,V( n)= x y z rad nuc V and for a hidden atom (V = "F") a line Atom no. n unhidden confirms unhiding setting its visibility flag to "T" while for a visible atom (V = "T") the line Atom is not hidden shows that the atom does not need to be unhidden. After this BALSAC returns to submenu SA. > > [L] selected from submenu SAU lists all coordinates and attributes of all nvis atoms that are presently hidden (invisible) by 1) Xyz,R,Id( p1) : x y z , rad , nuc ... nvis) Xyz,R,Id( pnvis) : x y z , rad , nuc nvis atom(s) hidden where (x,y,z) denotes the position of each atom, rad its atom radius, and nuc its nuclear charge (element name). If the number of hidden atoms exceeds 20 listing 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 SA. > > [,] selected from submenu SAU returns to submenu SA. > [P] selected from submenu SA removes all hidden atoms from the present cluster which is confirmed by np atoms of nct survive where nct is the number of atoms before and np that after the purge process. Note that this option does NOT prompt to confirm purging so that all hidden atoms are definitely lost after the purge! If there are no hidden atoms the purge option has no effect. After purging BALSAC returns to submenu SA. > [T] selected from submenu SA translates selected atoms by applying a shift vector. The prompt Translate n-th atom N (1- nct , 0=esc) : (with nct denoting the total number of cluster atoms) asks for the number n of an atom to be translated. Here dummy input n=0 returns immediately to submenu SA. For values n within the valid range [1, nct] coordinates and attributes of atom no. n are listed, see above, as Xyz,R,Id,V( n)= x y z rad nuc V and Shift X,Y,Z : asks for absolute cartesian coordinates (xs,ys,zs) defining a shift vector which will be added to the original coordinates of atom no. n to determine its new position (x',y',z') = (x,y,z) + (xs,ys,zs) listed by Xyz,R,Id,V( n)= x' y' z' rad nuc V to confirm translation. After this BALSAC returns to submenu SA if the sequential repeat flag (shown in submenu SA) is set to "off". If the repeat flag is set to "on" the prompt [R]epeat operation [?,]esc repeats the translation of atom no. n sequentially using the same shift vector (select [R]) or returns to submenu SA (select [,]). > [C] selected from submenu SA copies selected atoms after applying a shift vector. The prompt Copy from n-th atom N (1- nct , 0=esc) : (with nct denoting the total number of cluster atoms) asks for the number n of an atom to be used for the copy. Here dummy input n=0 returns immediately to submenu SA. For values n within the valid range [1, nct] coordinates and attributes of atom no. n are listed, see above, as Xyz,R,Id,V( n)= x y z rad nuc V and (nct+1)-th atom shift X,Y,Z : asks for absolute cartesian coordinates (xs,ys,zs) defining a shift vector which is added to the coordinates of atom no. n to determine the position (xn,yn,zn) = (x,y,z) + (xs,ys,zs) of a new atom (no. nct+1) which is added to the cluster. The additional atom agrees in its attributes (atom radius, nuclear charge, visibility) with atom no. n as shown by the line Xyz,R,Id,V( nct+1)= xn yn zn rad nuc V to confirm the copy. After this BALSAC returns to submenu SA if the sequential repeat flag (shown in submenu SA) is set to "off". If the repeat flag is set to "on" the prompt [R]epeat operation [?,]esc repeats copying sequentially by applying the same shift vector on the atom copy generated last (select [R], resulting in chains of identical atoms if applied more than once) or returns to submenu SA (select [,]). > [R] selected from submenu SA recenters the cluster by shifting all cluster atoms by a fixed vector such that v = (vx,vy,vz) forms the new origin. Hence, the coordinates of all atom positions are transformed as (x,y,z) --> (x',y',z') = (x,y,z) - (vx,vy,vz) If v coincides with the position vector of an atom this atom center will form the origin (0,0,0) of the recentered cluster. The prompt New origin NC,X,Y,Z ("-1,0,0,0"=esc) : asks for four numbers defining the origin vector v given either in absolute coordinates (0,vx,vy,vz) or denoting the center of an existing atom nv by (nv,0,0,0). Dummy input "-1,0,0,0" returns immediately to submenu SA. Now all cluster atoms will be recentered which is confirmed by either Location ( vx vy vz ) will be new origin if the input was given as (0,vx,vy,vz) or by Atom no. nv will be new origin if the input was given as (nv,0,0,0). After this BALSAC returns to submenu SA. > [S] selected from submenu SA switches the sequential repeat flag between "off" and "on" after which BALSAC returns to submenu SA. With the repeat flag set to "on" each atom copy/translate action is followed by a prompt, see above, allowing you to repeat the copying or translating process with identical shift vectors. > [X] selected from submenu SA 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 SA returns immediately to the structure option menu S, see Sec. 6.3.2. next, previous Section / Table of Contents / Index