tutorial adf2007 the universal density functional package for chemists graphical user interface

Tutorial ADF2007The universal density functional

package for chemists

Graphical User Interface

16 April 2008ADF Workshop

What’s new in ADF2007? http://www.scm.com

ADFjobs ADFinput ADFview ADFmovie ADFlevels ADFspectar ADFtail BOB

ADF GUI modules



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.



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



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



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



This utility displays volume data, such as

electron densities, orbitals, electrostatic potentials

and more.

ADFView



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)



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)



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)



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)



Standard view commands

RESET VIEW

VIEW DIRECTION AXES

BACKGROUND

….

ADFInput (View)



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)



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



Calculation tasks

Fragment analysis Frequencies Geometry optimization IRC Linear Transit Poperties only Single Point Transition state search

ADFInput



All input options have default values. ADFInput uses presets which are a collection of input values to be usedtogether 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



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)



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)



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)



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)



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)4CO Ni



ADFSpectra shows the spectra calculated by ADF. Currently it can show:

IR Raman Excitation CD and VCD DOS plot

It handles .t21files.

ADFSpectra



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)



ADFSpectraTDDFT of C2H4 : the electronic excitation spectrum is plotted (f vs energy) Select energy units

Moving the mouse above a peak a pop-up gives all information



ADFSpectraTDDFT of C2H4 : the pop-up



ADFtail

ADFtail shows the logfileduring execution:

Useful to monitor convergence (in SCF, geo opt, TDDFT etc.)

detect in time possible errors



BOB (Output Browser) BOB shows the complete ADF output (can be large…) after execution

Useful to find specific output sections



Thanks to ADF developers!

Thank you for your attention!

Free 30-day trial available at www.scm.comQuestions outside presentation to: [email protected]

All the contents in detail can be found inADF-GUI Reference Manual

ADF Program System Release 2007.01

http://www.scm.com/

http://www.scm.com/

http://www.scm.com/

tutorial adf2007 the universal density functional package for chemists graphical user interface

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