Diamond Function List

• 32 Bit MS Windows application with Multiple Document Interface (MDI), object-oriented menus, toolbars and local popup-menus. Allows 'simultaneous' handling of multiple structures.
  
  
  
  Input and Output:
  
  
• Proprietary binary Diamond 3/4 Document format (extension .diamdoc) :
  • Supports both crystal and molecular structures (i.e. with and without translational symmetry).
  • Storage of multiple structure data sets in a document, each with:
    • atomic parameters,
    • cell parameters and space-group (optional),
    • anisotropic displacement parameters,
    • connection parameters (bonds, H-bonds, non-bonding contacts)
    • chemical and bibliographic data (author, reference, database origin, etc.).
  • Supports multiple structure pictures for a structure data set. Saves your own built-up and designed frameworks of crystal structures.
  • Compatible with Diamond 2 format (DSF).
• Number of atoms, bonds, polyhedra etc. limited only by RAM.
• Manual input or update of chemical, crystallographic, and bibliographic data.
• Automatic import from data formats:
  • CRYSTIN download format created by ICSD or CRYSTMET
  • Cambridge Structural Database FDAT format.
  • Brookhaven Protein Data Bank format.
  • SHELX-93 format.
  • Crystallographic Information File (CIF).
  • XYZ format (free format with cartesian coordinates),
  • SYBYL MOL and MOL2 format,
  • Cerius2 (CSSR) format,
  • MDL MOL format.
• Export of structure data to:
  • CIF,
  • SCHAKAL,
  • XYZ format.
• POV-Ray assistant to create photo-realistic scenes with shadows, reflections, textures, background graphics, and more.
• Export of structure picture's 3D world to VRML.
• Export of structure picture's 2D graphics (for post-processing e.g. in a word processor or graphics application):
  • as Windows metafile (WMF, vector-oriented),
  • as bitmap (BMP; width, height and resolution user-defined),
  • as GIF, JPG, or PNG file, e.g. to link with an HTML document.
• Cut, Copy, or Paste of data sets between documents (together with associated structure pictures). Enables creation of small "databases".
• Search for chemical, crystallographic, or bibliographic data:
  • in files of selected types in selected directories,
  • in "Crystallography Open Database" (COD), including (amongst others) AMCSD ("American Mineralogist Crystal Structure Database") as well as CIF files from the IUCr journals, cf. "www.crystallography.net".
• Configurable list of structure data sets in a document:
  • as table ("structure list")
  • or in collapsed form as "structure info bar".
• Color coding to differentiate structure data sets in a document with multiple structures.
• Thumbnail overview of structure pictures of a selected data set or of the whole document.
• Recent picture list with thumbnails of last edited pictures/documents.
• Data sheet for comprehensive or compact textual representation of structure data.
• "Atom list": Hierarchical list of atoms in structure picture, groupes by atom sites and/or groups or by molecules.
• Printing of selected datasets, data sheet, tables, or structure pictures. Textual copy of datasets via Windows clipboard for post-processing.
• Export of data sheet and tables as HTML. 
  
  
  
  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").
• 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.
• 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.
• 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.
• 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).
  
  
  
  Animation:
  
  
• Movement of structure picture:
  • Modes:
    • Rotation along x-, y-, and/or z-axis,
    • horizontal and/or vertical shift within drawing area,
    • variation of enlargement factor (from Angstroems to centimeters),
    • variation of camera distance (perspective impression).
  • Controlled by:
    • Mouse (the faster the mouse the faster the rotation etc.),
    • keyboard (e.g. one degree rotation per keystroke),
    • numerically (input through dialog).
  • Optional "Spin" function, i.e. acceleration of movement.
  • Continuous movement, which can be interrupted and continued.
• "Grab mode": Arcball rotation of an atom under the mouse cursor. Shifting with the right mouse button pressed. Changing the enlargement factor with the mouse wheel.
• Walk-through mode, enabling the camera/viewer to navigate through the structure picture. 
• Recorder that helps to create video sequences, e.g. as AVI files.
  
  
  
  Exploration:
  
  
• Neighbourhood preview of atom under mouse cursor with radius of preview sphere variable with mouse wheel .
• Calculation of powder pattern:
  • Variation of diffraction parameters:
    • Radiation type: X-ray (laboratory, synchroton), neutron, electron,
    • wavelength,
    • LP correction,
    • 2theta range,
    • optional profile functions.
  • Diffraction diagram (styles, colors and line weights can be configured).
  • Table of reflection parameters with zoom in/zoom out and tracking through 2theta range.
• Calculation of distances and angles (incl. standard uncertainties):
  • in a configurable table, for selected atom types and a sizeable distances range,
  • around the atom(s) currently selected in structure picture.
  • Graphical representation of distances as histogram with color-coded distances.
• Measuring of distances, angles, and torsion angles interactively (incl. standard uncertainties).
• Measuring of extended geometric features (incl. standard uncertainties):
  • Angle between two planes (by hkl or (best) plane through 3 or more atoms),
  • angle between two lines,
  • angle between a normal of a plane and a line,
  • distances of atoms from a plane or a line,
  • centroid of a set of atoms,
  • planarity or linearity of a set of atoms (distances of constituent atoms from plane/line).
• New Properties pane, displays information about:
  • Contents of the structure picture (how many created atoms, bonds, polyhedra, etc.),
  • the current "formula sum", that means the number of created atoms associated to atom groups,
  • Info about the object that is selected in the structure picture or in the (optional) table above the properties pane, e.g. info about an atom of the parameter list,
  • Table of the currently selected objects,
  • Distances around the selected atom(s),
  • Distances between the selected atoms,
  • The center of the selected atoms (centroid),
  • The planarity or linearity of the selected atoms and the deviations of the atoms from that plane or line, rsp.,
  • Table of atoms assigned to the selected atom of parameter list or selected atom group,
  • Table of bonds assigned to the selected bond group (i.e. atom group pair),
  • Ligand, edges, and faces informations of the selected polyhedra.
  • Dirichlet domain of a selected atom site.
  • Neighbouring atoms and vertices of a selected Voronoi polyhedron.

System requirements

• Personal Computer with Microsoft Windows XP, Windows Vista, Windows 7, Windows 8/8.1 or Windows 10 operating system (note: does not run with Windows RT)
• Microsoft Internet Explorer 8 or higher
• Intel or AMD (or compatible) processor  with "x86" instruction set
• 1 GB of RAM
• 3.8 GB of free disk space (6 GB during installation procedure, for unpacking of Crystallography Open Database)
• Graphics resolution of 1024 x 768 pixels with 32,768 colors ("High Color") or higher (1280 x 800 pixels or more recommended)
• DVD-ROM drive (for installation from DVD)
• Microsoft-compatible mouse