Using the ADF-GUI modules - release February 2005
Feedback
Since this is beta software we are very much interested in getting feedback. Both technical remarks (problems, bugs, etc.) and suggestions for improving the interface or feature set are very welcome. If some features are hard to understand, tell us!
Following is a short description of the main features of the programs. We hope you will not need to read it ... but if you get stuck it might help. But please let us know where you are getting stuck so we can improve the interface.
Starting the programs
To start the ADF-GUI modules, type the name of the executable on the commandline: adfinput, adfview, adfmovie, adfspectra, adftail or bob. For this to work properly, your $ADFBIN directory should be in your PATH environment variable. (Windows users can instead simply use the old shortcuts to start the new modules.)
The ADF-GUI modules work very well over the network using the X11 protocol. Thus you can start ADFview on the machine where your calculation results are (the .t41 or .t21 file), and have it use your local display to visualize those results. You do this as with any X11 program: by setting the DISPLAY environment variable properly.
Many of the ADF-GUI modules use OpenGL to get a good performance, and thus they need to use the graphics card of your local computer. To get this working properly:
- you must have an X11 installation including GLX on both computers (local and remote)
- if you normally route your X11 connection through ssh you might have trouble (failure to start up ADFview, or very slow performance). In that case set your DISPLAY variable to make a direct connection to your local display (and on your local machine, use xhost to allow this connection). Of course this connection will not be secure! Remote usage on a Windows machine is not possible.
Files
- .t21 (TAPE21) : binary result file from an ADF calculation that contains all relevant information (such as orbital coefficients)
- .t41 (TAPE41) : binary result file from the DENSF program containing field information (such as values of orbitals on a regular grid)
- .logfile (logfile): a short text summary of the progress of a calculation, updated while running
- .out (output): the text output of the main program
- .adf: the format used by ADFinput to store your input
- .amv: ADF movie file, used to display sequences of geometries using ADFmovie
The ADF-GUI programs require that files have the proper extensions. Thus, a TAPE21 result file must have a .t21 extension, otherwise the GUI modules cannot read it. The same is true for .t41 and other files.
Some GUI modules will not be fuly functional with older ADF versions, because required information is missing on TAPE21. For example, the CD and Raman spectra are not available with the 2004 version of ADF, but will work for (the upcoming) ADF2005 and later releases.
ADFinput beta tips
Opening and saving
ADFinput reads and writes .adf files. It can import some other formats. Use the "Edit:Import Molecule..." menu command to read .t21 files, or some text-based list of coordinates. This is very useful to avoid building large or complicated molecules from scratch!
Using the mouse
The mouse interaction has changed slightly with respect to the previous ADFinput version.
- left mouse button: rotate
- left mouse button AND control key: rotate in-plane
- middle mouse button, OR left AND alt key: translate
- right mouse button, OR left AND command key: zoom
If you perform these mouse operations on a selected object (atom or bond) it will operate on the selection only. If you click in empty space WITHOUT moving and using an atom tool, an atom will be created. Finally, zooming the selection moves the selection perpendicular to the screen (thus in or out the screen).
New Menu Commands
- Undo and Redo (for constructing your molecule)
- Cut, Copy and Paste (for constructing your molecule)
- Group and UnGroup (for constructing your molecule)
- Selection commands: select connected, select molecule or select everything
- Fuse atoms: merge atoms of the same type that are very close to each other into one atom
Other New Commands
- Structures: click and hold the button marked with a benzene structure.
- User Structures: extend the Structures menu using the SCM_STRUCTURES environment variable.
This will allow you to reuse structures from previous ADF calculations prepared with ADFinput. - Symmetry menu: read the pop-up help balloon for instructions how to use it to impose symmetry on your atomic coordinates.
- Smiley: the optimize command (running an extremely basic mm-type geometry optimization).
- Geometry Tuning: select 2, 3, or 4 atoms, and see or set the bond length, bond angle, or dihedral angle etc.
Shortcuts
The most important tools have keyboard shortcuts: Esc to go to pointer mode, C, N, H, O, F, P, and S to go to the corresponding atom tool, and a space to go to the last structure used.
ADFspectra beta tips
ADFspectra has been extended with new types of spectra, and some improvements in the user interface and graphical layout. As before, ADFspectra can read .t21 files only.
Use the Spectra menu to access the spectra available to you (depending on the kind of calculation that produced the .t21 you are reading). Moving the mouse over the spectra will pop up balloons showing information about the peaks close to the mouse.
Try clicking in the pop-up box on contributions or orbitals: the corresponding normal modes or orbitals will be shown using ADFmovie or ADFview.
You can change the axes (orientation and units) using the Axes menu.
You can change the peak shape and width with the controls below the graph.
ADFview beta tips
Opening and saving
ADFview can read .t21 files as created by ADF, or .t41 files as created by DENSF. The file should have the matching .t21 or .t41 extension, and you can specify the file to read on the command line (as only argument of adfview), or you can use the File:Open menu command to select the file.
When saving a picture, you need to supply a filename with extension. The extension determines the format used to save the picture. Currently supported formats are: PNG, JPG, TIFF, BMP and PS.
Add visual items
If you go to the Add menu, you will find a couple of ways to add visual elements to your picture. The isosurfaces are just that, but you can also add Cut planes. These cut planes are either colored by some function value, or they show contour lines of some function.
After you added a visual item, a line appears below the picture with controls specifically for that item. Just try what the different controls do. With the first pull-down menu you can show even more controls (Show Details).
If you make an object transparent (Show Details, and then reduce the opacity), results might contain lots of artefacts. Especially when you are looking through several transparent surfaces at the same time.
Using the mouse
By clicking and dragging in the picture, you can rotate, translate and zoom your surfaces:
- left mouse button: rotate
- left mouse button AND control key: rotate in-plane
- middle mouse button, OR left AND alt key: translate
- right mouse button, OR left AND command key: zoom
When rotating the picture you have two different modes:
'Joystick' mode (View:Mouse As:Joystick). The picture will continuously rotate in the direction of the mouse (or in-plane when using the control key).
'Trackball' mode (View:Mouse As:Trackball). The picture will follow the mouse. This is the default mode.
Fields
When using a TAPE21 (.t21) file, the fields need to be generated on-the-fly. The check-boxes in front of the fields show you which fields are currently present. Once calculated, such a field will be available until you quit ADFview. When you use a .t41 file, all fields on that file are available, and no more.
Use the Fields menu to generate new fields from the fields already present on your input file.
One type of field is a 'calculated' field: it is constructed by combining the existing fields in some way. Once generated, you can use them as any other field.
Another type of field is an 'interpolated' field: it is constructed using interpolation from an existing field. You can use it to create a field with more points to get smoother lines and surfaces. Or you can use it to create a field with less data points to make the visualization faster.
View
By default, the visual items are lighted by a light fixed with respect to the viewer. By activating a scene light you can also add a light in a position fixed with respect to the visual objects. You can manipulate the position of the scene light by selecting 'Position light', and moving the little ball over the surface of the sphere that appears. You can also set the intensity of the scene light, and of course turn it on or off.
You can activate anti-aliasing to get pictures which look better, especially for smoother edges of objects. This is good if you want to save a high-quality picture. But it is also extremely time-consuming, so you should probably leave it off in most cases. Use it only to produce a high-quality picture for a publication.
Using the background menu you can select the background color for your picture. You can set the default background color using the Preferences panel in ADFinput.
ADFmovie beta tips
Opening and saving
As with the previous version, you can open .logfile files, .t21 files or .amv files.
When saving a picture, you need to supply a filename with extension. The extension determines the format used to save the picture. Currently supported formats are: PNG, JPG, TIFF, BMP and PS.
When saving all picture frames, you need to supply a filename with extension. Again, the extension determines the format used. Next ADFmovie will save each frame of the movie, and the file names will be derived from the name you specified, with a sequence number. Next, you should probably use some external program to combine these individual frames into a movie.
Using the mouse
By clicking and dragging in the picture you can rotate, translate and zoom your surfaces:
- left mouse button: rotate
- left mouse button AND control key: rotate in-plane
- middle mouse button, OR left AND alt key: translate
- right mouse button, OR left AND command key: zoom
When rotating the picture you have two different modes:
Press the 'j' key to get in 'joystick' mode. The picture will continuously rotate in the direction of the mouse (or in-plane when using the control key).
Press the 't' key to get in 'trackball' mode. The picture will follow the mouse. This is the default mode.
By clicking ON an atom you select it. By shift-clicking on atoms, you modify the selection by adding or removing the atom clicked on. Information about the selection (bond distances, atom type, angles) will be visible below the picture.
View
You can activate anti-aliasing to get pictures which look better, especially for smoother edges of objects. This is good if you want to save a high-quality picture. But it is also extremely time-consuming, so you should probably leave it off in most cases.
Using the background menu you can select the background color for your picture.
