6.3.12.1. ANALYSIS IN TEXT MODE, [A]

next, previous Section / Table of Contents / Index [A] This option allows you to obtain detailed information about the lattice section including all atom definitions and geometries based on text output. This analysis mode does not require graphics to work on your system. Selecting [A] in the BALSAC/CLUSTER main option menu shows the text mode analysis menu A which reads ========== ANALYSIS OPTIONS ======================================= [F]ull [S]ymmetry [A]nalyze [D]max( dc) [X]plot [?,]esc ============================================================= 46 == > [F] selected from submenu A gives the basic cluster definition together with the listing menu AF reading COMPLETE STRUCTURE OUTPUT : Title = ..title.. Cluster of nct atoms : nctv visible , (nct-nctv) invisible All atoms inside [ lx x ly x lz ] List atoms: [A]ll [V]isible [I]nvisible [?,]esc where "title" is the name given to the present cluster of nct atoms (nctv are visible, nct-nctv invisible). The atoms are enclosed in a rectangular block of lengths lx x ly x lz. > > [A] selected from submenu AF lists all atoms of the cluster (visible and invisible) in the format Atom listing (all atoms) : 1: Xyz,R,Id,V= x y z rad nuc vis 2: Xyz,R,Id,V= x y z rad nuc vis 3: ... ... ncoac of nac atom(s) coincide(s) within dc ** Press [C],L-click to continue; [,],R-click to escape ** where each atom is shown by its coordinates (x, y, z), atom radius rad, nuclear charge / element name nuc, and by its visibility flag vis (vis = "T" for visible, = "F" for invisible). After 20 atoms are listed the output stops with the above prompt where selecting [C] or L-click (DOS only) continues by listing (up to) 20 more atoms. After all atoms are listed or listing is cancelled by selecting [,] or R-click (DOS only) BALSAC returns to submenu A. After each block of (up to) 20 atoms is listed the number ncoac of coinciding atoms amongst the nac atoms listed so far is given. Further, all atoms which are found to coincide (with atoms listed before) are listed with a label by i: Xyz,R,Id,V= x y z rad nuc vis => ieq where "=> ieq" indicates that atoms no. i and ieq coincide with a given distance accuracy dc, see below. Note that coinciding atoms can be removed with the reduce option of the structure / symmetry menu, see Sec. 6.3.2.3. > > [V] selected from submenu AF lists all visible atoms of the cluster in the same format discussed before (option [A]) except that the statistics line about coinciding atoms is not included while coinciding visible atoms are labelled. After all atoms are listed or listing is cancelled by selecting [,] or R-click (DOS only) BALSAC returns to submenu A. > > [I] selected submenu AF prompt lists all invisible atoms of the cluster in the same format discussed before (option [A]) except that the statistics line about coinciding atoms is not included while coinciding visible atoms are labelled. After all atoms are listed or listing is cancelled by selecting [,] or R-click (DOS only) BALSAC returns to submenu A. > > [,] selected from submenu AF returns to the text mode analysis menu A without any atom listing. > [S] selected from submenu A analyzes the cluster symmetry and lists the symmetry center and point symmetry elements (inversion, mirror planes, rotations) by SYMMETRY ELEMENTS of the cltype cluster: Cluster center at Xyz= xcsy ycsy zcsy 1) [sy]: vx vy vz | 2) [sy]: vx vy vz ..... nsy) [sy]: vx vy vz | Total number of symmetry elements = nsy where cltype refers to the cluster shape ("1-atom, "linear", "planar", or "3-dim.") and the cluster symmetry center is given by cartesian coordinates (xcsy,ycsy,zcsy). Then all nsy point symmetry elements of the cluster are listed explicitly. For n-fold rotational axes (sy = "Cn") and improper rotation axes (sy = "Mn", Cn combined with inversion ) vector (vx,vy,vz) points along the axis. For mirror planes (sy = "M") vector (vx,vy,vz) points along the mirror plane normal while for the identity (sy = "1") and for inversion (sy = "I") the vector (vx,vy,vz)=(0,0,0) has no meaning. NOTE that for clusters with more than 10 atoms the analysis may take a long time. > [A] selected from submenu A allows you to analyze directions, distances, and angles of selected atoms of the cluster. This analysis requires internal numbers of respective atoms which are obtained from a preceding plot or listing. Atom numbers are shown in plots with the number labeling on (see Sec. 6.3.5.2) and in the numeric listing of all atoms (design option [L], see Secs. 6.3.5, 6.2.7). Atom numbers can also be directly obtained from graphics output using the graphic analysis option, see Sec. 6.3.12.2. The prompt Input atom numbers for analysis (N,NA,NB: 1-nct) : asks for three atom numbers n, na, nb within the range [1,nct]. These atoms are evaluated in their geometric properties and listed by Vectors for analysis : 1: Xyz,R,Id( n )= x y z rad nuc 2: Xyz,R,Id( na)= xa ya za rad nuc 3: Xyz,R,Id( nb)= xb yb zb rad nuc Difference vectors : V1(2-1): Xyz= ( x1 y1 z1 ) V2(3-1): Xyz= ( x2 y2 z2 ) |V1|= l1, |V2|= l2, Angle= ang12, |V1xV2|= ar12 ** Press [C], L-click to continue ** after which pressing [C] or L-click (DOS only) returns to the text mode analysis menu A. The above listing starts by coordinates and attributes of atoms n at r = (x, y, z), na at ra = (xa, ya, za), and nb at rrb = (xb, yb, zb) confirming the input. Then difference vectors between the atom centers are given in absolute cartesian coordinates v1 = ra - r = ( x1 y1 z1 ) v2 = rb - r = ( x2 y2 z2 ) together with their lengths l1, l2, the angle ang12 between them, and the area ar12 of the parallelogram spanned by v1, v2. If in the above analysis input atom numbers are used which lie outside the cluster range [1,nct] a message WARNING: input / n na nb / out of range [ 1,nct], NO analysis ** Press [C], L-click to continue ** will be issued listing the incorrect numbers n, na, nb and the available range [1,nct] and BALSAC returns to the text mode analysis menu A. > [D] selected from submenu A allows you to reset the coincidence distance determining the maximum distance between two atoms to be considered coinciding, see above. The prompt Atom coincidence distance ( dcold) : shows the present value of the coincidence distance dcold (also given in the text mode analysis menu, default = 1.D-5) and asks for a new value dc after which BALSAC returns to the text mode analysis menu A. > [X] selected from submenu A plots the lattice section (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 Secs. 6.3.5, 6.2.7. > [,] selected from submenu A returns to the BALSAC/CLUSTER main option menu, see Sec. 6.3.0. next, previous Section / Table of Contents / Index