3.3.4.2. BALSAC/CLUSTER SESSIONS

next, previous Section / Table of Contents / Index In order to learn about the numerical analysis of clusters using the graphics output of a BALSAC/CLUSTER session you restart BALSAC with input from the backup file 'balsac.plt' which you have created in Sec. 3.3.2. You start BALSAC from the command line with options as balsac -cr or balsac -c balsac.plt Both commands tell BALSAC to load the structure file 'balsac.plt' and move to the BALSAC/CLUSTER main option menu. Pressing [X] produces a plot of the Ni(CO)4 molecule as shown before. After plotting has been completed and the option menu shows at the bottom of the screen you enter the graphic analysis by pressing [Q] which displays a one-line menu Analyze[DVRAENB] build[L!_GRPTO_HU_CK_Y:] draw/view[Z_IJ_FSQ+] [?,]esc at the bottom and a graphical pointer (standard mouse graphics pointer, "arrow", or crossing lines, "+", if no mouse is available) shows at the center of the screen (maybe only after an analysis option has been selected below). Now you can analyze each visible atom on the screen, obtain distances between two atoms, or angles and planar directions defined by three atoms using the graphical pointer. Let us try it out. First you select the distance analysis requiring two different atoms by pressing [D]. This allows you to move the graphical pointer on the screen by moving the mouse up/down/left/right on the table or by pressing the cursor keys (arrow up/down/left/right or number keys 2/8/4/6, see Sec. 5.5). Pressing [+] or [-] increases/decreases the step size of the pointer movement in keyboard mode. When the pointer points at the surface of an atom sphere (not necessarily the atom center itself) this atom can be analyzed by clicking the left mouse button (L-click) or by pressing [enter]. You choose a carbon atom of the molecule (those closest to the central Ni atom) and L-click or press [enter]. This marks the location you selected by a white "+" and shows a line 1: Xyz,R,Id( i)= x.xxxx y.yyyy z.zzzz r.rrrr 6/ C at the bottom of the screen telling you that you have selected as a first atom the i-th atom of the molecule located at (x.xxxx, y.yyyy, z.zzzz) in cartesian coordinates, with a sphere radius = r.rrrr, element name C and a nuclear charge = 6. Now point at different C atoms and identify them by L-clicking or pressing [enter] until you have found the C atom # 2. If less than 4 C atoms show on the screen some may be hidden behind other atoms which makes them unreachable by the pointer. In this case you have to leave the analysis option (R-click or press [,] until the main option menu shows), plot the molecule with a different viewing geometry (press [X] from the main option menu changing views with the fast plot keys ([arrow up/down/left/right]), see above) and reenter the analysis option (press [Q]). The successful selection of atom 2 results in an analysis line 2: Xyz,R,Id( 2)= 2.1651000 2.1651000 2.1651000 1.016784 6/ C Next you point at the central Ni atom and L-click or press [enter] after which the top line reads 2: Xyz,R,Id( 1)= 0.0000000 0.0000000 0.0000000 1.934219 28/Ni Since by now you have selected two different atoms you can perform the distance analysis R-clicking or pressing [X]. This shows a line (X,Y,Z),LV = (-2.16510000 -2.16510000 -2.16510000) 3.75006320 telling you that atoms 1 and 2 are connected by a vector (-2.1651, -2.1651, -2.1651) in absolute cartesian coordinates and of length 3.75006320 (The above result is exact to all 8 digits! However, remember you gave the original atom coordinates only with 4 digits accuracy). You can repeat this analysis as many times as you like by selecting two other atoms. If you R-click or press [M] after an analysis step is finished BALSAC returns to the analysis menu offering other analysis types. Try as an exercise the distance/angle analysis (selecting [V] from the graphical analysis menu) which requires three atoms or the neighbor shell analysis (select [E]) which requires one atom. Try also to hide atoms (select [H], hiding will be visible only after you replot the molecule). Further, define a group (select [G]) to be used in the structure option menu later on. The group definition may be changed interactively by adding atoms to the group (select [R], point/click at an atom to be added) or removing atoms from the group (select [P], point/click at an atom to be removed). You can also determine the center of gravity of a number of atoms (select [A]) or the normal direction of the plane defined by three atoms (select [N]). For further details consult Sec. 6.3.12. R-clicking or pressing [,] in the graphical analysis menu finishes the graphic analysis and allows you to continue with plotting or return to the BALSAC/CLUSTER main option menu. next, previous Section / Table of Contents / Index