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1. Introduction
This chapter is missing from the distribution... Below is a text dump of the corresponding content in the PDF documentation
1.1 OVERVIEW OF THIS USER'S GUIDE
The Jaguar User's Guide is intended to help you perform ab initio calculations for a variety of methods, parameters, and calculated properties. On-line help is also available within Jaguar s graphical interface, although the information in this User s Guide is generally more comprehensive.
Chapter 2 contains information you will need to run Jaguar, including information about using the graphical user interface, geometry input formats, specifying file names for input and output, displaying molec-ular geometries, symmetrizing geometries, and setting run-time parameters such as the machine the calculation will be performed upon. We suggest that you start by trying the sample calculation in section 2.1. If the calculation runs successfully, you can proceed to the rest of the chapter to learn how to input molecular structures and run jobs. If you have problems starting the interface or running the sample calculation, see the troubleshooting information in section 10.1.
Chapter 3 and Chapter 4 describe the available calculation options, allowing you to specify what properties you wish the program to calculate and what methods you wish it to use. Chapter 3 includes information on using generalized valence bond (GVB), restricted configuration interaction (RCI), Møller-Plesset second-order pertur-bation theory, and density functional theory (DFT) techniques; calcu-lating solvation energies, vibrational frequencies, hyperpolarizabilities, multipole moments, and other properties; fitting charges; specifying basis sets; and various other options. Chapter 4 adescribes optimizations of the molecular structure, transition state searches, and geometry scans.
Chapter 5 describes how to summarize Jaguar output and the output or printing options available from the interface. The output file containing the primary Jaguar output is first described for cases where no Output options have been selected. Next, the output given when various Output settings are turned on is explained. Finally, the log file, another output file, is described.
The next chapter contains tips and suggestions for using Jaguar. The information in Chapter 6 includes a description of how to customize the interface; some general tips for different sorts of calculations; a description of how to restart calculations, how to incorporate results from previous runs; and some tips for people who use both Jaguar and GAUSSIAN.
Chapter 7 contains a description of some of the theory behind the pseudospectral method and the electron correlation methods used in Jaguar. This chapter includes information on pseudospectral imple-mentations of GVB, GVB-RCI, and local MP2 techniques, and a brief description of density functional theory.
Chapter 8 describes the Jaguar input file in detail. You may find this chapter especially useful if you want to run some jobs without using the interface. Chapter 9 describes other Jaguar files which are neces-sary for calculations. Neither Chapter 8 nor Chapter 9 is necessary reading if you wish to run all jobs from the interface, but you may want to skim them anyway to find out more about Jaguar and the methods it uses.
Chapter 10 contains some troubleshooting hints concerning the various sorts of problems you may encounter, especially when first setting up Jaguar on your system.
Throughout the User's Guide, numbers in brackets, like this: [13], refer to sources you may want to consult. The full reference list appears at the end of this manual. Superscripts in the text correspond to footnotes that list the Jaguar input file entries which correspond to particular interface settings. You can ignore the footnotes if you like, but you may find them useful for setting up files to do runs without using the interface, or for interpreting the input file.
1.2. CITING JAGUAR IN PUBLICATIONS
Use of this program should be acknowledged in publications as: Jaguar 4.1, Schrödinger, Inc., Portland, OR, 1991-2000.
1.3. TECHNICAL SUPPORT
If you have questions or problems concerning Jaguar, please report them to:Schrödinger, Inc. 1500 SW First Avenue, Suite 1180 Portland, OR 97201 Telephone: (503) 299-1150 Fax: (503) 299-4532 E-mail: help@schrodinger.comWe recommend contacting us by e-mail. When corresponding, please include relevant input and output. This information will help us eval-uate problems more quickly.
Schrödinger, Inc.
http://www.schrodinger.com
Voice: (503) 299-1150
Fax: (503) 299-4532
help@schrodinger.com
Last updated: Thu Oct 11 19:10:16 2001