Overview - Basis Set Tool

The Basis Set Tool enables you to select predefined Gaussian Basis Sets or create new ones for use in ab initio electronic structure calculations within Ecce. This tool also allows you to access general information on the basis sets stored in the EMSL Gaussian Basis Set Library and to seek advice on which basis sets might be most appropriate for a given type of calculation.

Because the Basis Set Tool has many functions, for many situations it may be easiest to select a basis set directly from the Calculation Editor by clicking the arrow button on the Basis Set button (in the Calculation Editor). A short pop-up menu then displays the names of some frequently used basis sets that you can augment with your own favorites.

Key Concepts: The Basis Set Tool operates in either of two modes. Generally the tool enables you to select basis sets for a fixed chemical system: the chemical system is specified by the calculation selected in the Calculation Manager or in the Calculation Editor. A separate Browse Mode enables you to select basis sets for an arbitrary system instead.

• Calculations - If you are selecting a basis set for a calculation, then the basis set selection must be saved as part of a calculation. After you save a basis set selection, Ecce creates a default name based on the orbital basis set and any auxiliary functions. The basis set name will appear throughout the Ecce interface (for example, in the Calculation Manager) as a label associated with the corresponding calculation.
• Browse Mode - If you are selecting a basis set for a chemical system in Browse Mode, the basis set selection cannot be saved as part of a calculation. However you can save it as a user defined combination for re-use later or as an ASCII file for use outside Ecce.

Starting the Basis Set Tool

Ways to start the Basis Set Tool:

• In the Ecce Gateway - Click on the Basis Set Tool icon (above).
• In the Calculation Manager - Choose Basis Set Tool from the Tools menu.
• In the Calculation Editor - Click on the Basis Set button.

If the Basis Set Tool is already running, these actions bring the window to the front. To start a separate instance of the tool in a separate window, shift-click on the icon in the Gateway. If no calculation or chemical system is specified, the Basis Set Tool starts in Browse Mode.

The following items briefly describe elements of the Basis Set Tool window.

The Current Basis Set Library

The name of the current basis set library appears in the title bar of the Basis Set Tool window. The default library is the last one used in the previous session. Most people will want to use the standard EMSL Gaussian Basis Set Library. The basis set library has been updated to reflect the latest basis sets from the EMSL Gaussian Basis Set Web Order Form. For a list of the latest changes, see the update history of the basis set library.

Menu Bar

- Molecular Basis Menu

This menu enables you to perform operations on the entire collection of basis sets you have selected for use on the chemical system being studied.

Save	Save the basis sets you have selected to the Ecce database so that they can be used in the current calculation. If you attempt to quit the Basis Set Tool without first saving your selections, you will be warned and given a chance to save your work. Tip: As a shortcut way to save your basis set selections, click on the "Save Work" icon in the window footer .
Save to File...	Save the basis sets to an ASCII file. This option is useful if you want to generate basis sets for use outside of Ecce. You can put the Basis Set Tool into the Browse Mode (from the Browse Options menu), enter a chemical system, and select a format corresponding to the application you want to run.
View Exponents & Coefficients...	Open a window containing the Gaussian exponents and contraction coefficients in the proper format for the currently chosen application.
Quit	Close the Basis Set Tool. Tip: To end an Ecce session and close all tool windows at once, close the Gateway.

- Edit Menu

The Edit Menu enables you to clear (remove) items in the Molecular Basis table of selected basis sets.

- Atomic Bases Menu

The Atomic Bases menu enables you to view information about the database library.

- Browse Options Menu

The Basis Set Tool can operate in two modes. By default, when you start this tool from the Calculation Manager or Calculation Editor, the chemical system is fixed. You cannot switch to a different chemical system from within the Basis Set Tool. However, you can toggle the tool into the "Browse Mode," where you have the option of typing in any chemical formula you wish and selecting any code format.

Browse Mode

Toggle the Basis Set Tool into or out of the Browse Mode. In Browse Mode you can type in an arbitrary chemical system in the Chemical Formula field and select any one of the supported code formats. After selecting the basis sets, you can use the Save to File option in the Molecular Basis menu. When Browse Mode is enabled, the Import Structure option is also enabled.

Import Structure...

Open a file dialog window for importing a chemical system from a file. This option appears only when the Browse Mode is enabled. It enables you to import a variety of file formats, such as Alchemy (TRIPOS), MVM, PDB (Protein Data Bank), and XYZ. You must specify the format of the file to be imported. Other formats may become available. Note: At present only the chemical system (C2H4, for example) is imported from the file. Molecular coordinates are ignored, so it is not possible to select basis functions for individual atoms using the "By Atom" tab option in the Molecular Basis portion of the Basis Set Tool. Note: NWChem and Gaussian 98 imports will generally recognize basis set names. The name recognition capability is more robust for NWChem than Gaussian 98, but it should be possible to import substantially more input files than previously was the case. Gaussian 98 only calculations where the basis set name is specified in the route card are supported. Ecce will not be able to identify the basis set if you try to import Gaussian 98 files with a combination of basis set names and explicit coefficient lists or where the basis set names are used in the basis set field. For NWChem, only orbital basis sets will be imported. Fitting basis sets, such as XC and CD, and ECP functions will be ignored (ECP functions are also ignored for Gaussian imports). The orbital basis sets are sufficient to display molecular orbitals. How to... Import a Structure from a File

- Advanced Menu

The Basis Set Tool offers an "Advanced Mode" in support of the Amica code. This mode enables the inclusion of multiple orbital basis sets. The purpose of the Combine Multiple Basis Sets feature and the Edit Basis Set option (Contraction Editor) is to allow you to create your own custom basis sets by combining different contractions from heterogenous sources. The Contraction Editor also allows you to append tight and/or diffuse functions to fine-tune the endpoints of the electron distributions. These custom basis sets are required to obtain the higher accuracy required of the Amica code.

- Help Menu

Basis Set List

The EMSL Gaussian Basis Set database contains well over 100 basis set families, and more are constantly being added. To make it easier to find a particular type of basis set, this part of the Basis Set Tool window enables you to view selected subsets of the library. Select basis sets in this list by double-clicking on them (or by selecting them in this list and using the "Add to Table" button). Your selections are then applied to the chemical system (or element) selected in the Molecular Basis table in the bottom portion of the window.

The tabs across the top of this area define broad categories of basis sets and/or effective core potentials (ECP):

• Orbital - The Orbital tab displays a scrolling list of orbital basis sets with a set of vertical tabs on the left to further divide the basis sets according to their type. For example, the default vertical tab is "Pople Shared," which indicates that the list will contain all known basis sets designed to use shared (s,p) Gaussian exponents. Orbital sets are likely to be the ones you need most frequently.
• ECP - The ECP tab displays a list of known effective core potentials that you can then match up with any orbital basis set. Most of the time you can choose an orbital ECP basis set and simultaneously get the accompanying ECP. However, in some cases you may want to use another orbital basis set, and this tab enables you to make that selection. If the ECP tab appears to be disabled (grayed out), the currently selected code does not support ECPs.
• DFT Fit - The DFT Fitting tab displays two scrolling lists of DFT fitting basis sets : one contains charge fitting basis sets, and the other contains exchange correlation fitting functions. If the DFT Fit tab appears to be disabled (grayed out), the currently selected code does not support DFT fitting basis sets. Although the charge and exchange-correlation fitting sets are usually chosen in pairs, it is possible to choose only one of these, or to choose two fitting sets from different basis set families.

Basis Set Details

The Details button opens a separate window with detailed reference and graphic information about the basis set that is currently highlighted in the basis set list.

Periodic Table

This Periodic Table portion of the Basis Set Tool enables you to narrow the list of orbital basis sets by clicking on elements of interest. For example, if you select H, Sc, and Br, the basis set list shows only basis sets that simultaneously support all three elements. If the Basis Set Tool is in Browse mode, you can type in a chemical formula in the Chemical Formula field and specify basis sets for that chemical system.

As with all instances of the Periodic Table that appear in Ecce, you can change the appearance of the table by pressing the right mouse button in the table area (but not on top of an element). By pressing the right mouse button on top of an element you can access element-specific information stored in the Ecce database.

Molecular Basis Area

The Molecular Basis area in the bottom half of the Basis Set Tool displays information about the basis sets you have selected using the basis set list and Add to Table button.

Molecular Basis Tabs

These tabs in the Molecular Basis area display the currently selected basis sets in a table and enable you to specify how they are applied to the current chemical system.

• Simple - This is the default tab and is used when the same basis set family is to be applied on all atoms in the current chemical system. The table shows you what basis sets are selected and characterizes each basis set according to several categories: orbital, polarization, diffuse, etc.
• By Element - This tab shows a table of all unique elements in the current chemical system and the corresponding basis functions associated with each. You can construct composite basis sets with one basis set on a subset of the elements and another basis set on the others.
• By Atom - [Not Implemented] This tab shows a complete listing of the atoms and Cartesian coordinates for the current molecule. You can then select basis functions on an atom-by-atom basis. Because the atomic coordinates are required, this option is NOT available in Browse mode.

Tip: You can customize the table of selected basis sets by dragging the table column separators with the mouse to widen, narrow, or hide columns in the table.

Add to Table Button

This button enables enables you to add basis sets to the Molecular Basis Area. To add basis sets, highlight the sets in the Basis Set List, then click the button to add them to the Molecular Basis Area.

Basis Set Options Panel

This options panel displays current settings for several options associated with the currently selected basis functions:

Code: Shows the code format currently in effect. In Browse Mode only, this is a pull-down menu that enables you to choose a different code format. Polarization Components: Enables you to select between Spherical and Cartesian forms of the polarization functions. Optimize General Contractions: Marking this option performs a transformation of certain kinds of general contractions to allow them to run more efficiently with some programs.

Functions and Primitives (display only): With general contractions the "effective" number of Gaussian primitives may differ from one application to another. That's why the number of functions listed under "Primitives" and "Eff. Primitives" may differ.

Window Footer

At the bottom of the window is a footer that displays status information as well as a drop site for receiving calculation inputs that have been "dragged" from another tool:

• the project path and name of the current calculation
• a colored icon that indicates the current state of the calculation
• a scrolling message area for system prompts and messages
• "Save Work" Icon -
  If you see a star-shaped icon, this indicates that you have made a basis set or code selection for a calculation but have not yet saved your work. When you are ready to save your choices, just click on the star icon.
• Padlock Icon -
  If you see a padlock icon above and to the right of the message area, this indicates that the current calculation is locked in the database (probably because it has already been submitted) and that you will not be able to modify the basis set selections.

• Drop Site - The "in-tray" square at the right side of the footer is a drop site destination for "drag & drop" operations. For example, if you launch the Basis Set Tool and wish to use it to select basis functions for a calculation in the Calculation Manager, you can use the middle mouse button to "drag" the calculation from the Calculation Manager and "drop" it on the drop site in the Basis Set Tool. The Basis Set Tool then presents the chemical system and any prior basis set selections for that calculation.

More about...		Items in the Ecce Window Footer
How to...		Drag & Drop with the Mouse