Analysis Menu 1249

L-clicking the entry "Analysis menu …" opens the analysis window and allows performing many of the analyses available with the graphical analysis options inside the main graphics window. However, here the analysis input and corresponding results are shown in a separate analysis window. This can be useful if atoms to be used in an analysis are not visible with the present view parameters but their atom indices are known.


The analysis window contains two parts,

·      the upper part starts with the line “Composition = …” showing the element composition of the present particle in a pseudo-chemical format “ E1n1.E2n2. … ” where Ei denote the elements appearing in the particle and ni refers to the corresponding number of atoms of the element type. As an example, Ni1.O4.C4. means that the particle contains 1 nickel, 4 oxygen, and 4 hydrogen atoms. Further, “Ntot atoms” gives the total number of atoms Ntot of the particle where both visible and hidden atoms are included.

·      Next the part entitled “Atoms :” shows up to six atom centers A – F used in a previous analysis by their indices and atom definitions as

X = n   Eln (nl/ nb) / ( xn yn zn ), rn

(X = “A” to “F”), where n its internal number of the corresponding atom, Eln its element name nl its layer index, and nb its atom basis index (depending in the layer if reconstructed). The indices nl and nb refer to Balsac/Lattice sessions and are not shown in Balsac/Cluster sessions. Further, (xn, yn, zn) are Cartesian coordinates of the atom, and rn is its present atom radius (all lengths are given in units of the atom coordinates).
Depending on the previous analysis option not all or none of the atom entries A – F may have been used. Unused atom entries are labeled by an index value 0 with no further details.

Typing a valid atom index (e.g. obtained from a previous analysis inside the graphics window) in one of the active atom input boxes next to “A” – “F” allows defining an atom for the analysis where the definition is confirmed after pressing the Enter key (or moving to another input box) by giving the full atom definition next to the atom input box in the format described above.

If atoms resulting from a graphical analysis are saved on the vector stack their atom indices can be retrieved and used for input. R-clicking the enabled text labels “A =” to “F =” to the left of the index input boxes fills all enabled input boxes with the atom indices of the latest graphical analysis (group selection, or atom hiding/reviving operation). The indices appear in the same order as those of the previous graphical analysis and can be used for analysis.

Depending on the analysis option, those atom input boxes which are not required will be disabled shown by gray shading. The complete atom input can be deleted (start from scratch) by L-clicking the button “Scratch” to the right of the atom input part.

·      The lower part shows a frame entitled “Options :” containing all analysis options presently available. The options are described by a short-hand notation specifying the atoms A - F required for the analysis in the analysis window. They are completely analogous to those of the graphical analysis inside the graphics window (shown in parentheses below) with the results formatted identically.

Available analysis options are

Distances :     AB                   ( Atom - Atom),

                        AB/C                ( Atom - Line),

                        ABC/D              ( Atom - Plane).

Angles :          ABC                 ( Connected Atom Pairs),

                        AB/CD              ( Separate Atom Pairs),

                        ABC/DE            ( Plane with Vector),

                        ABC/ABD         ( Dihedral),

                        ABC/DEF          ( Plane with Plane).

Neighbor :      Shells              ( Neighbor Shell),

                        Planes             ( Neighbor Plane).

A graphics option is selected by L-clicking the radio button next to the option name.

L-clicking the “Previous | List open” entry at the top of the window opens the analysis box at the bottom showing the instruction line.

Previous analysis results, L-click button to inspect -->

L-clicking the arrow button to the right of the analysis box opens a drop down box (with a vertical scroll bar if needed) listing of up to 12 previous lines of a previous graphical analysis (including group selections and atom hiding/reviving operations). This list is identical with that of the Previous Analysis option of the graphics window. L-clicking inside this list retrieves the corresponding analysis line and moves it to the analysis box. This makes the line available for cut-and-paste operations. (Ctrl+c saves the line content, Ctrl+v inserts in a different application.) Note that this option is available only after at least one analysis has been performed. L-clicking the “Previous | List close” entry at the top of the window closes the analysis box.

L-clicking the button “Evaluate” to the right of the option frame performs the analysis with the atom centers selected in the atom input part above. The analysis result is shown below “Results :” using the same format as for the graphical analysis.

If the atoms selected for the analysis are not meaningful or the set of required atoms incomplete an error message wiil be shown below “Results :”.

L-clicking the button “Close” closes the analysis window and returns to the main graphics window.