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Diamond Features: Manual building and designing of a picture

Go to Diamond Features Overview
Previous: Structure picture display
Next: Exploration view

Note: This article is about the bunch of functions for manual building and designing in Diamond and will be updated while the corresponding chapter in the Diamond 5 manual is updated. Provisionally we give you a list of functions.

Construction:
  • Optional assistant that helps to create a structure picture from scratch or to modify a picture.
  • "Auto Picture Creator" - available in a docking window side-by-side with the structure picture - to interactively change picture building as well as picture design and viewing direction.
  • "Building schemes" (in Diamond 3 called "Auto-Builder") that create pictures automatically or according to a user-defined strategy. Useful when visualizing a lot of similar structures.
  • Conversion between "crystal" and "molecular" structures, i.e. adding or removal of cell and symmetry information.
  • Filling of unit cell, multiple cells, any cell range, or boxes or spheres around selected central atoms.
  • Filling of user-defined rectangular areas within the screen.
  • Filling of slabs along a plane (hkl or least-squares) or between a plane and the walls of the coordinate system.
  • Selection of atoms to construct sublattices ("Filter").
  • Support for disorder parts when searching for neighbouring atoms and bonds as well as in "Filter" function.
  • Creation (and discussion) of atomic environments, optionally from Dirichlet domains of the atom sites.
  • Discussion of connectivity assisted by histograms showing the distribution of distances between selected atom types and from the bond parameters, together with automatic calculation and checking of distance ranges.
  • Creation of bonds automatically, basing on connecitivity, or manually by inserting bonds between two atoms each.
  • Adding all atoms (and optionally bonds, H-bonds, contacts) of atomic parameter lists as well as from connection parameter lists.
  • Generation of atoms from parameter list serving as initial atoms for building up complex frameworks.
  • Completion of coordination spheres around selected atoms.
  • "Pump up": Generation of multiple spheres around selected atoms and its reversal ("shrink").
  • Automatic generation of molecules or completion of fragments which have e.g. been clipped at cell edges.
  • Definition of molecular units (from atomic parameter list).
  • Generation of molecules from molecular units at symmetry-equivalent positions.
  • Search for molecules in the neighbourhood of selected atoms or molecules.
  • Creation of molecular packings (parallelepiped, sphere, slab, or layer).
  • "Grow" and "cut: Expansion and reduction of polymers or molecular fragments.
  • Creation of "broken-off" bonds to signal infinitesimal chains, layers, or 3D-frameworks. Conversion between "broken-off" and normal bonds.
  • Definition of H-bond and non-bonding contact connectivity. Creation of H-bonds and contacts.
  • Expansion to neighbouring atoms or molecules via H-bonds and/or contacts to build up molecule clusters and reversal ("reduce").
  • Discussion of contact spheres and expansion or reduction of molecule clusters with the mouse wheel.
  • Cut, copy and paste of structural parts between structure pictures:
    • A fragment of a structure picture (or the whole picture) can be copied.
    • The copied fragment can be pasted into a blank or another picture of the same data set.
  • User-controlled dismantling of built-up frameworks.
  • Multiple-step Undo and Redo function (with picture thumbnails) to enable safe experimentation with even high-complicated and unknown structural frameworks.

    Visualization:
  • "Design schemes" (a kind of style sheets) containing picture design and viewing settings for quick-and-easy application to other structure pictures.
  • Layout modes:
    • Regular/window,
    • for printout, e.g. A4 page size with white background,
    • for creation of a bitmap with given x and y dimension and a resolution in dpi.
  • Variable zoom factor (enhances "Page view" mode of Diamond 2).
  • Models, assigned globally or individually to single or groups of atoms (allows mixing of different models in one and the same picture):
    • Ball-and-stick (regular),
    • ellipsoid,
    • space-filling,
    • sticks or wires (depending on bond radius).
  • Definition of views along special axes or toward special planes.
  • Central or parallel projection, depth cueing, and stereo display.
  • Photorealistic rendered models with user-defined light source and material properties (OpenGL).
  • Variation of colors, styles and radii of atom groups and bonds. Individual design of each single atom is possible.
  • Variation of atom and bond radii with mouse wheel.
  • ORTEP-like atom styles (ellipses, octants) in both flat and rendering mode.
  • Optionally fragmentated and two-colored bonds.
  • Optionally adjustment of atoms' and bonds' transparencies to site occupation factors.
  • Optionally random distribution of mixed sites' components.
  • Labelling of atoms and bonds. User-defined text, can be placed at arbitrary position of picture.
  • Generation of coordination polyhedra:
    • Around central atoms of selected groups or around individually selected atoms,
    • built up from selected ligand atoms,
    • optionally with transparent or hatched surfaces.
  • Enhanced construction of coordination polyhedra:
    • Defining corners and edges by selecting (clicking on) atoms and bonds, rsp.
    • Removing of edges to increase triangles to higher polygons.
    • Copy and Paste of polyhedron buildings between atoms of same site each. 
  • Definition of (transparent) lattice planes and (best) planes or lines through selected atoms.
  • Adding of vectors to atoms to indicate e.g. a magnetic moment.
  • Alternative color differentation to visualize oxidation numbers, site occupation factors etc.
  • Full screen view (with window frame, menu, toolbars hidden).


  • Go to Diamond Features Overview
    Previous: Structure picture display
    Next: Exploration view