| DMol |
DMol calculates variational self-consistent solutions to the density functional theory (DFT) equations, expressed in a numerical atomic orbital basis. The solutions to these equations provide the molecular wavefunctions and electron densities, which can be used to evaluate the energetics and the electronic and magnetic properties of the system. In addition, evaluation of the energy gradients provides a convenient method for determining the equilibrium geometry of the system. These results provide a reliable predictive method for theoretically exploring the properties of unknown compounds, as well as for explaining, on a microscopic scale, the known properties of existing compounds. The relatively low computational requirements of the method allow the study of larger molecular systems than would be possible with other ab initio methods.
The main DMol program solves the molecular DFT equations. Included in the DMol package is DAtom, a utility that generates atomic basis sets. In addition, the dmol_ master interface (the input preparation utility used in the standalone mode of DMol) aids in preparing and modifying input files and in creating and submitting jobs.
Typical uses for DMol include:
When used within the Insight interface, DMol is accessible as one of its application modules. (For more information on the basic operations, procedures, and functionality of the Insight program, please refer to the Insight documentation.) The functionality in DMol is accessed through pulldowns that contain the commands to set up the input control file for a DMol job. The parameter block for each command provides you with many useful defaults and preset strategies, all of which can be easily modified, if necessary, for your particular calculation. References to atoms or residues can be typed in or can be specified by picking the appropriate atom or residue in the displayed structure. You can then start the run while remaining in the Insight environment.
The parameter blocks in the Insight interface can also be used to prepare input files for running DMol in the standalone mode. These input files can be edited to develop more sophisticated computational strategies or for repetitive calculations better suited to the automatic control of batch queues.
When run as a standalone program outside the Insight environment, DMol uses a simple user interface in which you create a command input file that instructs DMol what to do.
When set up in the standalone mode, DMol has some capabilities that are not accessible through the Insight interface. For example, it allows:
You can also set up and run DMol independently of the Insight interface. The standalone user interface is activated as described under DMol input preparation utility: dmol_master. This interface prompts you as you set up the DMol calculation.
This guide contains instructions for preparing input files, running jobs, and interpreting output. In addition, it presents theoretical information on the DFT method. Introduction, Theory and Implementation, and General Methodology, References, Glossary. Files, and Utilities contain background information that is relevant to both the Insight and standalone modes of using DMol.
Using this guide
Theory and Implementation presents the theories upon which the functionalities of DMol are based. It is written mainly for the typical scientist-user of DMol. This section also presents some information on how the functionalities are implemented. General Methodology presents the general procedure for using DMol, either in the Insight environment or in the standalone mode.
References contains the scientific references cited in this documentation, and Glossary includes terms and symbols. The file formats are documented here for the files used by more than one program and under Files for files specific to DMol. Information on using the DAtom utility, running background jobs in the Insight environment, changing memory allocation, and recompiling DMol is contained in Utilities.
Using DMol via Insight interface
Command Summary--The Insight Environment, Methodology--Insight, and Tutorial--The Insight Environment contain information that is specific to using DMol in the Insight environment. Command Summary--The Insight Environment briefly summarizes the main functions of each command. Methodology--Insight explains how to use DMol in the Insight mode, while Tutorial--The Insight Environment describes several tutorial lessons that show you how to use it.
Command Summary--Standalone Mode, Methodology--Standalone Mode and Commands--Standalone Mode contain information that is specific to using DMol in the standalone mode. Command Summary--Standalone Mode briefly summarizes the main commands, and Methodology--Standalone Mode explains how to use DMol in the standalone mode. Commands--Standalone Mode explains the standalone keywords in detail.
In addition to the main Table of Contents and Index, a Cross-Index of Old and New Keywords is included.
In addition to this printed DMol documentation, on-line help is available and activated by clicking the help icon (which is the button containing a question mark, on the side of the main Insight window) or the Help pulldown. Printouts can be obtained through this help utility.
Additional information
In referring to commands that are used when running DMol interactively through the Insight interface, this guide uses the format Pulldown/Command, since you must use the mouse to first select the pulldown, before the command name appears. Note, however, that if you enter commands in the command area near the bottom of the Insight window, the command names must be entered in the format Command Pulldown or Command (whichever appears at the top of the equivalent parameter block).
Notes on command names