ADF View

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The ADF-GUI modules

ADFjobs - mangages ADF jobs.
ADFinput - builds the input for an ADF calculation.
ADFview - displays 3-D (volume) data, such as electron densities, orbitals, electrostatic potentials.
ADFspectra - shows spectra calculated by ADF, like IR and excitation spectra.
ADFmovie - follows geometry steps of geometry optimizations, IRC calculations, etc.
ADFlevels - shows energy diagram.
ADFtail - follows the progress of an ADF calculation.
BOB - browses the output generated by ADF.

The modules can be started from $ADFBIN or from a different module using the SCM menu.

module $ADFBIN file extension SCM menu.
ADFjobs adfjobs Jobs.
ADFinput adfinput .adf Input.
ADFview adfview .t21 .t41 View.
ADFspectra adfspectra .t21 Spectra.
ADFmovie adfmovie [-loop] .amv .logfile .t21 Movie.
ADFlevels adflevels .t21 Levels.
ADFtail adftail .logfile Logfile.
BOB bob .out Output.

Mouse Interaction

A one-button mouse button is the same as a Left mouse button.
Rotate Left.
Rotate in-plane Ctrl-Left.
Translate Middle, or Alt-Left.
Zoom Right, or Command-Left (drag up or down).
New selection Click on an object.
Clear selection Click in space.
Add or remove selection Shift-Click on object.
Add all objects within rectangle Shift-Drag in space.
Pop-up menus Press and hold the Right mouse button on the object (fast).
Pop-up menus Press and hold the Left mouse button on the object (slow).

Build the molecule

ADFinput drawing area
Import Coordinates: Select 'Import Coordinates ...' from the 'File' Menu.
Add atom: Select an atom-tool by clicking on the button with the 'C', 'O', 'N', 'H', 'Cl', or '>'.
Click somewhere in the drawing area to draw the atom.
Add hydrogens: Select 'Add Hydrogen' from the 'Edit' Menu.
http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_quickreference/print.html
Add structure: Select a structure from the Structures' Menu (the button with a benzene molecule). 
Click somewhere in the drawing area to place the structure. Double-click on an atom to replace it with the structure. Use the atom pop-up menu to replace all atoms in a selection by structures.
Predefined Structures can be found for: Alkyl Chains, Aromatic Molecules, Cyclic Hydrocarbons, Ligands, Polyhedra, Amino Acids, parts of DNA, Metal Complexes, Solvents.
Change atom (bond) type: Press and hold the Right mouse button on the atom (bond).
Select 'Change atom(s) type' ('Type') from the popup Menu.
Guess bonds: Select 'Guess bonds' from the 'Edit' Menu.
Delete atoms: Select the atoms. Press the backspace key.
Edit commands: Select 'Copy', 'Paste', 'Select ...', etc. from the 'Edit' Menu.
Undo: Select 'Undo' from the 'Edit' Menu to go back in time.
Pre-optimization of the geometry
ADFinput: Click on the MM optimizer button (the smiley button).

Run the ADF calculation

ADFinput: Build the molecule and select the desired options. Select 'Save' from the 'File' Menu. Enter a name in the File name field. Select 'Run' from the 'File' Menu.

Model Hamiltonians

XC energy functionals and potentials ADFinput: Select 'XC Functional' from the 'Model' Menu. Select the desired SCF potential from the 'xc potential in SCF' menu. Select for METAGGA or hybrid functional energies after SCF the corresponding box ADFUsersGuide: XC [1]. Relativistic effects (ZORA and spin-orbit coupling) ADFinput: Select 'Relativity' from the 'Model' Menu. Select 'None', 'Scalar, or 'Spin-Orbit' from 'Level of relativistic theory' menu. ADFUsersGuide: relativity [1]. Solvents and other environments ADFinput: COSMO: Select 'Solvation' from the 'Model' Menu. Select the checkbox 'Include solvation'. ADFinput: QM/MM: Select 'Protein' from the 'Model' Menu. Select the 'Select' from the menu 'PDB-file'. ADFinput: DRF and FDE: no direct GUI support. ADFUsersGuide: COSMO [1], QM/MM [1,2], DRF [1], FDE [1]. Homogeneous electric field and point charges ADFinput: Select 'Electric field' from the 'Model' Menu. Enter the values of the homogeneous electric field in the menu 'Electric field - '. Enter the coordinates and values of the point charges in the text box. ADFUsersGuide: EField [1]

Structure and Reactivity

Geometry Optimizations, Transition State searches, Intrinsic Reaction Coordinates, Linear Transit ADFinput: Select 'Main Options' from the Menu on the right hand side. Select 'Geometry Optimization', http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_quickreference/print.html 'Transition State Search', 'IRC', or 'Linear Transit' in the 'Preset' menu. ADFmovie: follow the steps in the geometry . ADFUsersGuide: geometry optimization [1], TS [1,2], IRC [1], LT [1]. Optimizations in Cartesian, internal, and delocalized coordinates ADFinput: Select 'Coordinates' from the 'Model' Menu. Select 'Cartesian', 'Internal', or 'Delocalized' from the 'Use ... coordinates' menu. ADFUsersGuide: coordinates [1]. Constraints ADFinput: Select 'Coordinates' from the 'Model' Menu. To freeze a coordinate: check the corresponding box in the list of atoms. ADFinput: Select 'Geometry Restraints' from the 'Details' Menu. Select the checkbox 'Include restraints'. Select the atoms with the mouse. Select the 'Add' command to add a restraint. ADFUsersGuide: constraints [1,2,3].

Spectroscopic properties

If possible do a molecular property in a single point run.

BOB: Browse the output to find the values (scalars, vectors, tensors) of the calculated property.

Vibrational spectroscopy IR frequencies and intensities ADFinput: Select 'Main Options' from the Menu on the right hand side. Select the 'Frequencies' in the 'Preset' menu. ADFspectra: Select 'Vibration' from the 'Spectra' Menu. Move Mouse above the spectrum to get more information in a popup menu. Select mode for visualization with ADFmovie. ADFUsersGuide: IR [1]. (Resonance) Raman ADFinput: Select 'Main Options' from the Menu on the right hand side. Select the 'Frequencies' in the 'Preset' menu. Next select 'Task: Frequencies' from the 'Properties' Menu. Select the checkbox 'Raman intensities in range'. ADFspectra: Select 'Raman' from the 'Spectra' Menu. Move Mouse above the spectrum to get more information in a popup menu. ADFUsersGuide: Raman [1], Resonance Raman [1]. Vibrational Circular Dichroism (VCD) ADFinput: Select 'Main Options' from the Menu on the right hand side. Select the 'Frequencies' in the 'Preset' menu. Next select 'Task: Frequencies' from the 'Properties' Menu. Select the checkbox 'alculate VCD intensities ADFspectra: Select 'VCD' from the 'Spectra' Menu. Move Mouse above the spectrum to get more information in a popup menu. ADFUsersGuide: VCD [1]. Time-dependent DFT ADFUsersGuide: TDDFT [1]. UV/Vis spectra, oscillator strengths, open shell excitations, core excitations ADFinput: Select 'Excitations' from the 'Properties' Menu. Select, for example, the checkbox 'SingletAndTriplet'. http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_quickreference/print.html ADFspectra: Select 'Excitation' from the 'Spectra' Menu. Move Mouse above the spectrum to get more information in a popup menu. ADFUsersGuide: UV/Vis spectra, oscillator strengths [1], open shell excitations [1], core excitations [1]. frequency-dependent (hyper)polarizabilities ADFinput: Select 'Polarizability' from the 'Properties' Menu. Select the property 'Polarizability', 'StatHyperpol' or 'DynHyperpol' from the 'Property' popup Menu. ADFUsersGuide: polarizabilities [1]. van der Waals dispersion coefficients ADFinput: Select 'Polarizability' from the 'Properties' Menu. Select the property 'VanDerWaals' from the 'Property' popup Menu. ADFUsersGuide: dispersion [1,2]. Rotatory strengths (CD) and optical rotatory dispersion (ORD) ADFinput: CD spectrum: Select 'Excitations' from the 'Properties' Menu. Select the checkbox 'Calculate rotatory strengths (CD)'. Select, for example, the checkbox 'SingletAndTriplet'. ADFspectra: CD: Select 'CD' from the 'Spectra' Menu. Move Mouse above the spectrum to get more information in a popup menu. ADFinput: ORD: Select 'Polarizability' from the 'Properties' Menu. Select the property 'OpticalRotation' from the 'Property' popup Menu. ADFUsersGuide: CD [1], ORD [1]. NMR chemical shifts, spin-spin couplings ADFinput: Select 'NMR' from the 'Properties' Menu. Select the checkbox 'Isotropic Shielding Constants' or 'Shielding Tensor', or Select the checkbox 'Calculate spin-spin coupling constants'. ADFUsersGuide: chemical shifts [1,2], spin-spin couplings [1]. ESR (EPR) g-tensor, A-tensor ADFinput: Select 'ESR, EPR, EFG' from the 'Properties' Menu. Select the checkbox 'ESR g-tensor/A-tensor'. ADFUsersGuide: ESR [1,2]. Nuclear quadrupole coupling constants ADFinput: Select 'ESR, EPR, EFG' from the 'Properties' Menu. Select the checkbox 'EFG Q-tensor'. ADFUsersGuide: EFG [1].

Analysis

If possible do the analysis in a single point run. BOB: Browse the output to find the complete analysis. Fragments ADFinput: Select 'Main Options' from the Menu on the right hand side. Select the 'Fragment Analysis' in the 'Preset' menu. Select all atoms that form a fragment. Press and hold the Right mouse button on one of the selected atoms and select from the popup menu 'New Fragment ...'. ADFUsersGuide: fragments [1]. Bond energy analysis ADFinput: No special input is needed. ADFUsersGuide: bond energy analysis [1]. http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_quickreference/print.html Advanced charge density and MO analysis ADFinput: No special input is needed. ADFlevels: Energy diagram. ADFview: Electron densities, potentials, MOs, ELF, etc. ADFspectra: Select 'DOS' from the 'Spectra' Menu. ADFUsersGuide: Mulliken [1], Hirshfeld and Voronoy deformation density [1], Bondorders [1], Bader [1], NBO [1]. Molecular symmetry ADFinput: Possibility to symmetrize the molecule with the 'Symmetry' Menu (the button which initially shows 'Nosym' on the top of the drawing area). ADFUsersGuide: symmetry [1,2].

Accuracy and Efficiency

Slater type basis sets, density fit and frozen core approximation
ADFinput: Select 'Main Options' from the Menu on the right hand side. Select the basis set from the 'Basis Set' Menu. Select the frozen core from the 'Core Type' Menu.
ADFUsersGuide: STO [1,2], density fit [1], frozen core approximation [1].
Integration scheme
ADFinput: Select 'Main Options' from the Menu on the right hand side. Enter the value for the accuracy of the integration grid in the menu 'Integration Accuracy'.
ADFUsersGuide: accuracy [1].

Parallelization

ADFinput: Not supported directly in the GUI.
ADFUsersGuide: parallelization [1].
Linear scaling / distance cut-offs
ADFinput: Select 'Technical' from the 'Details' Menu.
ADFUsersGuide: linear scaling [1].

Tips

Tear off field pull-down menus in ADFview.
Tear off normal mode menus in ADFspectra.
Right click (or click and hold down) on a bond or atom for a useful pop-up menu.
Right click (or click and hold down) on a bond to show or hide bonds.
Right click (or click and hold down) on an atom to change its properties.
Right click (or click and hold down) on an atom to select all similar elements.
Right click (or click and hold down) on an atom or selection to add structures.
Structure Tool: Double click on atom to replace it with a structure.
Structure Tool: Click in empty space and connect the structure to an atom.
Structure Tool: The Spacebar sets the last used Structure too.
Your own structures: save the .adf file in the $SCM_STRUCTURES folder.
Make use of 'set origin' and dummy atoms when making your own structures.
The help menu offers a direct link to the online tutorial for ADF-GUI.
The help menu offers a direct link to the ADF reference manual  http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_quickreference/print.html
Toggle the tips in the View menu and in your preferences.
Change the default background color for all GUI-modules in your preferences.
Change the default atom colors using the pop-up menu on an atom.
Use the SCM menu (the logo).
Zoom: drag the mouse up or down holding the right button or command-left.
Translate: drag the mouse while holding the middle button or alt-left.
Rotate: drag the mouse while holding the left button.
Rotate in Plane:drag the mouse while holding the ctrl-key.
Rotate Selection: drag while holding the mouse button down on the selection.
Select using shift-drag in space will select all atoms within the rectangle.
Use Anti-Alias to save high quality pictures (slow ...).
Save your default calculation setup by using the templates.
Use the PropertiesOnly option to avoid re-calculation.
Use the None preset to save only yellof fields in a preset.
Use the atom toolbuttons and doubleclick to change the chosen atom.
The C-key sets the Carbon tool.
The H-key sets the Hydrogen tool.
The N-key sets the Nitrogen tool.
The O-key sets the Oxygen tool.
The F-key sets the Fluorine tool.
The P-key sets the Phosphorus tool.
The S-key sets the Sulfur tool.
The Esc-key sets the Pointer tool.
The 1-key sets the single-bond mode.
The 2-key sets the double-bond mode.
The 3-key sets the triple-bond mode.
The 4-key sets the aromatic-bond mode.
Add hydrogen works on all available sites if you have no atoms selected.
Constrain bond lengths while building? Toggle this option in the Edit menu.
Bond Length: Select two atoms and, if possible, change the bond length.
Bond Angle: Select three atoms and, if possible, change the angle.
Dihedral Angle: Select four atoms and, if possible, change the angle.
Plane angle: Select five atoms that define two planes and change the angle.
Change the order of the atoms in the coordinates panel.
Changing the order of the atoms will affect the internal coordinates.
Deleting or adding bonds will affect the internal coordinates.
Use the User Input field to add anything you like to the ADF input file.
Double click the .run file in ADFjobs to edit it.
Click on "..." in ADFinput to quickly go to the relevant detail panel.

Run It in Kimik

The licences for all the adfviews are in kimik001, so the only place where you can run it is there. So first thing to do is: ssh -X kimik001

 ADFVIEW2007 
export ADFHOME=/usr/local/adf2007.01/
export ADFBIN=$ADFHOME/bin
export ADFRESOURCES=$ADFHOME/atomicdata
export SCMLICENSE=$ADFHOME/license
export SCM_TMPDIR=$TMPDIR
export SCM_USETMPDIR=yes
/usr/local/adf2007.01/bin/adfview

 ADFVIEW2006 
export ADFHOME=/usr/local/adf2006.01/
export ADFBIN=$ADFHOME/bin
export ADFRESOURCES=$ADFHOME/atomicdata
export SCMLICENSE=$ADFHOME/license
export SCM_TMPDIR=$TMPDIR
export SCM_USETMPDIR=yes
/usr/local/adf2006.01/bin/adfview

 ADFVIEW2005 
export ADFHOME=/usr/local/adf2005.01/
export ADFBIN=$ADFHOME/bin
export ADFRESOURCES=$ADFHOME/atomicdata
export SCMLICENSE=$ADFHOME/license
export SCM_TMPDIR=$TMPDIR
export SCM_USETMPDIR=yes
/usr/local/adf2005.01/bin/adfview

 ADFVIEW2004 
export ADFHOME=/usr/local/adf2004.01/
export ADFBIN=$ADFHOME/bin
export ADFRESOURCES=$ADFHOME/atomicdata
export SCMLICENSE=$ADFHOME/license
export SCM_TMPDIR=$TMPDIR
export SCM_USETMPDIR=yes
/usr/local/adf2004.01/bin/adfview