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Tutorial ADF2007 The universal density functional package for chemists Graphical User Interface.

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Presentation on theme: "Tutorial ADF2007 The universal density functional package for chemists Graphical User Interface."— Presentation transcript:

1 Tutorial ADF2007 The universal density functional package for chemists Graphical User Interface

2 16 April 2008 ADF Workshop What’s new in ADF2007? ADFjobs ADFinput ADFview ADFmovie ADFlevels ADFspectar ADFtail BOB ADF GUI modules

3 16 April 2008 ADF Workshop What’s new in ADF2007? This utility manages your ADF jobs: run a job on your local machine or on remote machines. ADFJobs It also serves as interface to all files belonging to your job, and as a convenient launcher of the other ADF GUI modules.

4 16 April 2008 ADF Workshop What’s new in ADF2007? ADFJobs Job details (stored in.pid file from the job) Remote host Remote user Remore job directory Run command Kill command Job status command System status command Prolog command Epilog command Logfile extension

5 16 April 2008 ADF Workshop What’s new in ADF2007? A queue within ADFJobs is just a short-cut to set all job details for some selected job. There are default queues, but you can also define your own queues. Local queue: it is the simplest, called interactive in the supplied examples. When you run ADFJobs for the first time and it does not find any queue, it will automatically create such a queue for you. Remote interactive queue: it uses the same settings as for the interactive queue, except that you have to specify some remote machine (and optionally a remote user). Batch queue: a queue might be configured such that your job ends up in some batch queue using some submit commands. Details for these commands differ depending on your batch queue system and its configuration. ADFJobs comes with some examples for LSF, PBE and SGE. ADFJobs

6 16 April 2008 ADF Workshop What’s new in ADF2007? This utility enables ADF users to easily create ADF jobs: define your molecule (geometry), pre-optimize it and set your job's details. It will generate the complete job script for you. ADFInput

7 16 April 2008 ADF Workshop What’s new in ADF2007? This utility displays volume data, such as electron densities, orbitals, electrostatic potentials and more. ADFView

8 16 April 2008 ADF Workshop What’s new in ADF2007? NEW/OPEN IMPORT COORDINATES You can import coordinates from a.t21 file, from a.adf file, from text file (.mol,.xyz,.pdb). Z-matrix import is currently not available. EXPORT COORDINATES You can export the xyz coordinates of the current geometry. SAVE PICTURE You can save a picture of your molecule in different formats (.jpeg,.ps,.tiff,.png,.bmp). ADFInput (File)

9 16 April 2008 ADF Workshop What’s new in ADF2007? RUN This can be done also from ADFInput (and from ADFJobs). If you have made any changes in ADFInput, you will be asked to save the changes. When a run is finished, you will be asked if you wish to update the coordinates of your molecule with the most recent set of coordinates from the finished calculation. QUIT Stop ADFInput and asks to save changes if you made any. ADFInput (File)

10 16 April 2008 ADF Workshop What’s new in ADF2007? UNDO/REDO CUT/COPY/PASTE/CLEAR GROUP/UNGROUP The currently selected atoms and bonds will be grouped together (ungrouped). Groups may be nested. SET ORIGIN Translate all atoms such that the selected atom will be the new origin. If nothing is selected, the center of the atoms will be the new origin. When symmetry is used, the origin will be also the origin of symmetry. ADFInput (Edit)

11 16 April 2008 ADF Workshop What’s new in ADF2007? BOND LENGTHS CONSTRAINED When creating new atoms bonded to existing atoms, ADFInput will constrain the bond length to the textbook value. Select this menu command to toggle this behaviour. ADD BOND Create a bond (if possible) between two selected atoms. ADD HYDROGEN/REMOVE HYDROGEN Hydrogens will only be added to selected atoms or to the whole molecule if no atoms are selected. SELECT ALL/SELECT MOLECULE/SELECT CONNECTED ADFInput (Edit)

12 16 April 2008 ADF Workshop What’s new in ADF2007? Standard view commands RESET VIEW VIEW DIRECTION AXES BACKGROUND …. ADFInput (View)

13 16 April 2008 ADF Workshop What’s new in ADF2007? The Model menu gives access to the first group of input panels on your right-hand side. The Properties menu gives access to the second group of input panels on your right-hand side. ADFInput (Model) & ADFInput (Properties) ADFInput (Details) The Details menu gives access to the third group of input panels on your right-hand side. It is mainly for experts. ADFInput (Help)

14 16 April 2008 ADF Workshop What’s new in ADF2007? In addition… there are Pop-up menus, which are opened by the mouse right-clic. Button and tools, which are located on the toolbar below the screen. You can get information and modify the displayed geometry at the bottom of the screen by selecting: 2 atoms: distance 3 atoms: angle 4 atoms: dihedral angle 5 atoms: angle between two planes ADFInput

15 16 April 2008 ADF Workshop What’s new in ADF2007? Calculation tasks Fragment analysis Frequencies Geometry optimization IRC Linear Transit Poperties only Single Point Transition state search ADFInput

16 16 April 2008 ADF Workshop What’s new in ADF2007? All input options have default values. ADFInput uses presets which are a collection of input values to be used together as defaults. The input fields use a colour coding to warn you that they have been modified: No special colour: original default value Yellow: changed by the user (only) Green: changed by the preset (only) Red: changed by the preset and next by the user ADFInput

17 16 April 2008 ADF Workshop What’s new in ADF2007? NEW OPEN Open a.t21,.t41,.runkf,.cube file to use for visualization. Multiple files can be opened. SAVE PICTURE Save a picture of visualization area in file. EXPORT AS VRML Export the current scene as a VRML file. QUIT ADFview (File)

18 16 April 2008 ADF Workshop What’s new in ADF2007? ISOSURFACE Add an isosurface: a surface through a field connecting all points with the same value (the isovalue) ISOSURFACE: COLORED Add an isosurface: a surface through a field connecting all points with the same value (the isovalue). The isosurface will be colored by a second field. ISOSURFACE: DOUBLE (+/-) Add a double isosurface: two isosurfaces at the same time, of different colors, through the same field. One isosurface corresponds with the chosen isovalue, the other one with the negative of that value. ADFview (Add)

19 16 April 2008 ADF Workshop What’s new in ADF2007? CUT PLANE: COLORED Add a plane and color the plane with some field. CUT PLANE: CONTOURS Add a plane and on that plane show contour lines for the requested contour value of some field. The contours will be colored by the value of the field. CUT PLANE: CONTOURS (+/-) Add a plane and on that plane show contour lines for the requested contour value of some field. In this case the positive and negative contours are shown in a different way, determined by the controls. ADFview (Add)

20 16 April 2008 ADF Workshop What’s new in ADF2007? CALCULATED Create a control bar where you can define a new field as some mathematical function of one or two existing fields. INTERPOLATED Create a control bar where you can define a new field as an interpolated field of an existing field. ADFview (Fields) ADFview (View) & ADFView (Help)

21 16 April 2008 ADF Workshop What’s new in ADF2007? ADFlevels Ni(CO) 4 (from Ni atom and four CO fragments) Displays molecule MOs levels of the molecule and its fragments Correlations are also displayed Ni(CO) 4 CONi

22 16 April 2008 ADF Workshop What’s new in ADF2007? ADFSpectra shows the spectra calculated by ADF. Currently it can show: IR Raman Excitation CD and VCD DOS plot It handles.t21 files. ADFSpectra

23 16 April 2008 ADF Workshop What’s new in ADF2007? OPEN SAVE POSTSCRIPT EXPORT XY VALUES Export the current xy values to a text file so that you can use it in your preferred graphing application. QUIT ADFSpectra (File)

24 16 April 2008 ADF Workshop What’s new in ADF2007? ADFSpectra TDDFT of C 2 H 4 : the electronic excitation spectrum is plotted (f vs energy) Select energy units Moving the mouse above a peak a pop-up gives all information

25 16 April 2008 ADF Workshop What’s new in ADF2007? ADFSpectra TDDFT of C 2 H 4 : the pop-up

26 16 April 2008 ADF Workshop What’s new in ADF2007? ADFtail ADFtail shows the logfile during execution: Useful to monitor convergence (in SCF, geo opt, TDDFT etc.) detect in time possible errors

27 16 April 2008 ADF Workshop What’s new in ADF2007? BOB (Output Browser) BOB shows the complete ADF output (can be large…) after execution Useful to find specific output sections

28 16 April 2008 ADF Workshop What’s new in ADF2007? Thanks to ADF developers! Thank you for your attention! Free 30-day trial available at Questions outside presentation to: All the contents in detail can be found in ADF-GUI Reference Manual ADF Program System Release


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