Quantum 1 Modules

1       Introduction

This documentation set describes the applications (ADF, DMol³, Gaussian, MOPAC, Zindo) that make up the Cerius^2[TM] Quantum 1 module, a suite of application modules that provide sophisticated quantum mechanical functionality in the Cerius² environment.

Who should use this guide

Prerequisites

You should already be familiar with:

• The windowing software on your workstation.

• Use of the mouse on your workstation.

• Basic UNIX^® commands.

• Basic use of the Cerius² interface.

• Quantum mechanical techniques.

Your workstation needs to have:

• Access to a licensed copy of Cerius².

• A home directory in which you can create subdirectories.

• Cerius² Modeling Environment--Basic use of the Cerius² interface and the C²·Visualizer module.

• Cerius² Builders--How to use the builders to create crystal, surface, interface, polymer, and amorphous models.

• Cerius² Tutorials--Several guides illustrating the use of Cerius².

• Forcefield-Based Simulations, CDiscover, and Cerius² Simulation Tools--Discuss forcefields and forcefield-based calculations; CDiscover in the Cerius² and standalone modes; and the Open Force Field, Force Field Editor, Charges, Minimizer, Dynamics Simulation, and Analysis modules.

• Cerius² Command Script Guide--How to capture and replay a script of Cerius² commands and enhance your command scripts with the features of the Tool Command Language (Tcl).

• Cerius² Installation and Administration Guide--Step-by-step instructions for installing and administering Cerius² in your operating environment.

On-screen help is available within the Cerius² environment. It is accessed by clicking the right mouse button while the cursor is over the item in the interface about which you want information. A brief identification of some items appears when you simply allow the cursor to linger over them. Additional help and some demos are accessed from the Help menu.

MSI's website

The URL for the documentation library at MSI's site on the World Wide Web is:

http://www.msi.com/doc/

http://www.msi.com/support/

Other relevant websites

Information on ADF can be obtained from the Scientific Computing & Modelling group in the Chemistry Department of the Vrije Universiteit, Amsterdam, at:

http://tc.chem.vu.nl/

http://www.gaussian.com/

http://www.osc.edu/ccl/qcpe/QCPE/index.html

http://www.qtp.ufl.edu/zindo.html

• Terms introduced for the first time are presented in italic type. For example:

Instructions are given to the software via control panels.

• Keywords in the interface are presented in bold type. In addition, slashes (/) are used to separate a menu item from a submenu item. For example:

Select the View/Colors... menu item means to click the View menu item, drag the cursor down the pulldown menu that appears, and release the mouse button over the Colors... item.

• Words you type or enter are presented in bold type. For example:

Enter 0.001 in the entry box.

• UNIX command dialog and example lines in files are represented in a typewriter font. For example, the following illustrates a line in a .grf file:

  
        CERIUS Grapher File
  
  

• Words in italics represent variables. For example:

  
  >	cerius2 -b outputfile scriptfile
  

In this example, the name of the file to which text output should be directed replaces the value outputfile, and scriptfile is the name of a file containing a command script.