DMol

4       Command Summary--The Insight Environment

DMol is accessed in the Insight environment by choosing DMol from the Module pulldown (which is accessed by clicking the MSI logo). The DMol module contains several pulldowns (in addition to the core pulldowns on the top menu bar), which appear on the lower menu bar. They are: Setup, Symmetry, Optimize, Environment, Background_Job, Run, and Analyze. Each pulldown gives access to several related commands. The Setup pulldown, for example, contains a set of commands used in setting up a DMol calculation: System, Parameters, and Setup_Grid_Output.

What the commands in these pulldowns do is summarized briefly below. For more detailed explanations of individual commands, refer to the on-line help facility (by clicking the help icon, which is the button containing a question mark, on the left side of the main Insight window). For information on how to use these commands, see Methodology--Insight.

Setup pulldown

The Setup/System command allows you to define the name of the model that you want to work with and to select the basic type of calculation, for example electronic energy, geometry optimization, harmonic frequencies.

The Setup/Parameters command is used to define all DMol parameters for a calculation. The predefined default values are appropriate for most calculations. You may, however, need to change specific parameters to refine your calculation. It allows you to:

• Specify the density functional method to be used in the calculation.

• Select the atomic basis functions used in the expansion of molecular orbitals.

• Freeze specific sets of orbitals.

• Control the selection of mesh points for the numerical integration process.

• Control the electronic state of the model--select spin-restricted or spin-unrestricted wavefunctions and set the molecular charge. You can specify occupations with a run_name.occup file.

• Define the electronic environment of the model--impose a static external electric field and read point charges from an external file.

• Invoke the COSMO solvation model by providing the name of a COSMO input file. This input is prepared with the Environment commands.

• Specify the file from which to restart a previous interrupted or unconverged SCF calculation.

• Define parameters for controlling a self-consistent field (SCF) calculation.

• Specify calculation of the dipole moment and of partial density-of-state information.

• Specify population analysis according to Mulliken or Hirshfeld charge partitioning (including atomic dipoles and quadrupoles).

• Specify calculation of the electric field gradients at nuclei.

• Specify calculation of the optical absorption spectra.

• Specify a bond order calculation.

• Request fitting of point charges to the ESP potential.

• Set up vibrational calculations and specify at atom number at which to restart an interrupted vibrational calculation.

• Specify what volumetric properties and grid data are to be calculated.

• Determine what is printed to the output file.

Symmetry pulldown

Optimize pulldown

The Optimize/Constraints command is used impose atom and geometry constraints on a model.

Environment pulldown

Background_Job pulldown

The Background_Job/Control_Bkgd_Job command allows you to coordinate running background jobs by detaching selected background jobs from or attaching them to the current Insight session. In addition, this command allows you to specify the interval for invoking a task specific to a particular background job for processing its output.

The Background_Job/Completion_Status command allows you to monitor and evaluate the completion status of one or all background jobs. In addition, this command can be used to look up the meaning of a return status code.

The Background_Job/Kill_Bkgd_Job command is used to terminate execution of a background job that was submitted during the current Insight session.

Run pulldown

Analyze pulldown

The Analyze/Orbital_Contour command allows you to display both the plus and minus phases of a molecular orbital in one step, at any grid level, and to customize their colors.

The Analyze/Charge_Display command allows you to display Mulliken, Hirshfeld, and ESP charges.

Analyze/Spectrum_Display command allows you to display optical absorption spectra.

Analyze/Isotope_Setup command allows you to choose isotope masses for atoms in the model.

The Analyze/Normal_Mode command is used to create a graph of your molecule's IR spectrum and to animate the molecule according to its normal modes of vibration.

Analyze/Stat_Mech command allows you to calculate thermodynamic properties for the model.

The Analyze/Density_of_States command is used to perform a total or partial density of state analysis.

The Analyze/Scan_DMol_Output command allows you to quickly examine the output file for a calculation that is still running or one that has already ended.