Spartan 5.1 User's Guide

Chapter 9: The Display Menu

This section reviews functions available under the Display menu. These include display of output from ab initio, density functional, semi-empirical and molecular mechanics calculations, query of total and orbital energies, dipole moments and atomic charges, and "measurement" of property values mapped onto graphical surfaces. Functions under the Display menu also provide displays of isosurfaces and 2D slices, and animation of vibrational modes from frequency calculations. Text and graphical output resulting from Gaussian 94 are also accessible from the Display menu.

Clicking on Display results in display of the following menu:

Output
Properties
Surfaces
Slices
Isosurfaces
Vibrations


Section 9.1: Output

Clicking on Output under the Display menu results in the following dialog.

This contains the text output generated by the selected job, and can either be scrolled in the usual manner or "paged" using Page Up and Page Down at the bottom of the dialog. The "top" and "bottom" of the output file may quickly be reached by clicking on Top and Bottom, respectively. The dialog may be exited by clicking on OK. For jobs which are currently executing, this dialog contains all output generated up to the stage that the dialog was requested. The contents of the Output dialog are updated while it is displayed.

View Global (top right) is available only for jobs which are part of a list. In this case, the global display (View Global "on") may provide output pertaining to how the list was generated, e.g., from a conformational search, while the local display (View Global "off") provides text output for the selected "local" job.


Section 9.2: Properties

Clicking on Properties under the Display menu results in a sub-menu:

Output
Properties > Energy in hartrees
Surfaces Energy in kcal/mol
Slices
Isosurfaces Dipole
Vibrations E(HOMO/LUMO)
Molecular Weight
Charges

Surfaces


Section 9.2.1: Energy in hartrees


Section 9.2.2: Energy in kcal/mol


Section 9.2.3: Energy in kJ/mol

Selection results in display of a dialog which contains the total energy for an ab initio or density functional calculation, heat of formation for a semi-empirical calculation and strain energy for a molecular mechanics calculation, e.g., for a semi-empirical heat of formation in kcal/mol.

Available units are hartrees (the standard for ab initio and density functional calculations), kcal/mol (the standard for semi-empirical and molecular mechanics calculations) and kJ/mol (SI units). In case of calculations which produce multiple energies, e.g., MP2 calculations, all are displayed in the dialog.

Note, that this function is available for calculations performed using Gaussian 94 as well as Spartan.

If the selected molecule is a member of a list, a different dialog is presented, e.g., for a semi-empirical heat of formation in kcal/mol.

This is identical to the original dialog except that it incorporates a Post button. Clicking on Post enters the energy (heat of formation, strain energy) for each and every member of the list into the next available column in the associated spreadsheet.


Section 9.2.4: Dipole

Selection results in display of a dialog which contains the dipole moment (in debyes).

In addition, the dipole moment vector is drawn on screen with the usual sign convention.

Note, that this function is available for calculations performed using Gaussian 94 as well as Spartan.

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates a Post button. Clicking on Post enters the dipole moment for each and every member of the list into the next available column in the associated spreadsheet.


Section 9.2.5: E (HOMO/LUMO)

Selection results in display of a dialog which contains both the energy of the highest-occupied molecular orbital (HOMO) and the lowest-occupied molecular orbital (LUMO), as well as the difference between them ("band gap") (Note: Orbital energies and band gaps are given in eV (electron volts) for semi-empirical calculations and in hartrees for ab initio and density functional calculations.).

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates three Post buttons (one each associated with E(HOMO), E(LUMO) and the band gap). Clicking on any or all of these, enters the corresponding quantity for each and every member of the list into the next available spreadsheet column(s).


Section 9.2.6: Molecular Weight

Selection results in display of a dialog which contains the molecular weight (in atomic mass units).

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates a Post button. Clicking on Post enters the molecular weight for each and every member of the list into the next available column in the associated spreadsheet.


Section 9.2.7: Charges

This displays natural bond orbital (NBO), Mulliken and electrostatic fit charges (in electrons) for a selected atom. While Mulliken and natural bond orbital charges are generated automatically following completion of a semi-empirical or an ab initio molecular orbital calculation or of a density functional calculation (Mulliken and natural bond orbital charges are the same for semi-empirical calculations), electrostatic-fit charges need to be requested explicitly. Selection results in a message in the menu bar.

Charges: Select on atom.

Clicking on an atom results in display of a dialog.

Charges for another atom may be obtained by clicking on it. When completed, clicking on Done exits the dialog.

Note that this function is available from calculations performed using Gaussian 94 as well as Spartan.

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates three Post buttons (one each associated with electrostatic, Mulliken and natural charges). Clicking on any or all of these, enters the corresponding charge for each and every member of the list into the next available spreadsheet column(s).


Section 9.2.8: Surfaces

This function allows "measurement" of property values both on isosurfaces (see Sections 9.3 and 9.5) and on 2D slices (see Section 9.4). Additionally, it displays the surface area and volume (isosurfaces only). Selection results in message in the menu bar.

Properties: Select on surface.

Clicking on any portion of a displayed surface or slice results in a replica of the cursor being placed on the graphic to indicate the selected position, and a dialog.

For isosurfaces, surface area in Å2 (Area) and volume in Å3 (Volume) are displayed*, together with the value of the property (Value) if one is available. For slices, only the value of the property is displayed. Unavailable or ill-defined information is indicated by the symbol N/A.

    *Note: Surface area and volume of electron density surfaces will be similar but not identical to values obtained from Surface Area and Volume (Geometry menu; see Sections 6.10 and 6.11). The latter are based on space-filling models.

Other points on the same isosurface or slice, or on a different isosurface or slice on the same or on a different molecule, may be selected and surface values measured simply by clicking on these points. The dialog is removed by clicking on Done.

Note, that this function is available for calculations performed using Gaussian 94 as well as Spartan.

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates three Post buttons (one each associated with the value of the property, the surface area and the volume). Clicking on the Post buttons for either surface area or volume enters the surface area or volume for each and every member of the list into the next available spreadsheet column. Clicking on the Post to Surface button for property value enters only the value corresponding to the selected molecule into the appropriate cell of the next available spreadsheet column.


Section 9.3: Surfaces

As previously commented, isosurfaces can be formed either from surface data (see Section 8.8.1), or from data uniformly tabulated inside a predefined volume (see Section 8.8.2). The former, which is less general but is easier to use, is described below. Section 9.5 describes the construction of isosurfaces from volume data.

Clicking on Surfaces under the Display menu results in the following dialog.

At the top is a summary of all surfaces associated with the active molecule, including the status of each. Files marked "completed" have been successfully generated, while those marked "failed" have been attempted but not been generated. (The reason for the failure will in most cases appear in the output file, see Section 9.1.) Finally, entries marked "pending" have yet to be completed (they may not even have been submitted). Only surfaces marked "completed" are available for display.

Surfaces are selected for display by clicking on them. Buttons at the bottom of the dialog control various aspects of the display.

  1. Display Surface

    Toggles the surface display "on" and "off".

  2. Map Property

    Toggles the display of a property mapped onto a surface "on" and "off". Display Surface (above) must be "on" and a property must be available (see Section 8.8.1).

  3. Style

    Selects a display type from among: Dots, Mesh, Solid or Transparent (solid).

  4. Colors

    Controls whether the map is presented in terms of a continuous distribution of colors (Continuous) or as a discrete set of color bands (Discrete). Colors is available only when Map Property is "on".

  5. Range

    Sets the lower (From) and upper (To) bounds of the color scale. The default settings (the minimum and maximum values of the data, respectively) may be changed, and can be restored by clicking on Reset. Range is available only when Map Property is "on".

  6. Legend

    Displays a scale of color values. Once displayed on screen, the legend is treated as any other graphical object. It can be selected by clicking on it (a yellow frame will then enclose the scale), and then moved about the screen and scaled. It cannot be rotated. Legend is available only when Map Property is "on".

As many surfaces as desired can be displayed at one time. These can all be set up in a single access to the Surfaces dialog, or in multiple accesses to the dialog. In addition to the surfaces, any one of the available structural representations (wire, ball-and-wire, tube, ball-and-spoke and space-filling) may be displayed, accomplished by using the appropriate entries from the Model menu. Finally, contours and other 2D slices as well as isosurfaces generated from volume data may be simultaneously displayed (see Sections 9.4 and 9.5 following).

The Surfaces dialog is exited, and a surface (or surfaces) with or without a mapped property is displayed, by clicking on OK.


Section 9.4: Slices

Slices constitute the first of two general types of graphical representations which may be created and displayed from volume data in real time. (The second type, isosurfaces, will be discussed in Section 9.5.) There are several different types of slices, ranging from a single cutting plane, to cylindrical and spherical "planes", to sets of planes. These are all handled by Spartan and will be discussed below.

There are fundamental differences in the way in which Spartan handles surface and volume data. Volumes, unlike surfaces, are not themselves displayed. Rather,
they are used to generate one or more 2D slices, each of which may be independently manipulated relative to the molecular framework in real time. Because of this, separate functions for creating slices from volume data, for editing them once created and for deleting them are required. These functions are described in turn below.

Selection of Slices from the Display menu results in a sub-menu:

Output
Properties
Surfaces
Slices > Create
Isosurfaces Edit
Vibrations Delete


Section 9.4.1: Create

Selection of Create results in the display of an on-screen dialog.

The Volume box provides a summary of all volumes associated with the active molecule including the status of each. Entries marked "failed" have been attempted but not been generated. (The reason for the failure will in most cases appear in the output file, see Section 9.1.) Entries marked "pending" have yet to be completed (they may not even have been submitted).

Upon entering the Create dialog, the first entry in the Volume box will be highlighted. A different entry may be selected by clicking on it. Buttons at the bottom of the dialog control various features of the display.

  1. Plot Type

    Sets the type of display desired, either a continuous color fringe (Continuous), or as a set of color bands (Discrete), or a set of contour lines (Contour).

  2. Background

    Sets the color fringe and the background for the contour lines to either opaque (Opaque) or transparent (Transparent).

  3. Frame

    Turns "on" (On) and turns "off" (Off) a solid frame around the fringe or contour.

  4. Legend

    Opens a scale of color values (corresponding to different contours or fringes). Once displayed on screen, the legend is treated as any other graphical object. It can be selected by clicking on it (a yellow frame will then enclose the scale), and then moved about the screen and scaled. It cannot be rotated.

  5. Surface

    Selects the type of slice from among: a plane or planes (Plane(s)), a sphere (Sphere) or a cylinder (Cylinder). Specification of the number of planes and the spacing between planes for multi-plane displays, and the ratio of height to radius for cylindrical slices will be made in the Edit dialog (see Section 9.4.2).

After the appropriate selections have been made, clicking on Create exits the dialog and displays the graphic. The composite graphic (molecular models, any slices and any isosurfaces) are now selected, and any manipulations (translation, rotation, scaling) apply to it. An individual slice may be selected by clicking on its frame (or if the frame is absent, by clicking on any portion of the slice). This accomplished, manipulations will apply only to the slice. Selection of the molecular skeleton follows from clicking on it, after which manipulations again apply to the composite graphic.

Clicking on Cancel exits the dialog without creating a new slice.

Expert Mode

At the top right of the dialog is an Expert switch. As with other "expert" buttons, this is only visible if Expert in the Preferences dialog under the Logo menu (see Section 3.3) has been turned "on". Clicking on Expert results in a new dialog.

This is identical to the original dialog, except that a "keypad" appears in the center of the dialog to the right of Volume. This allows the final graphic to be constructed from combinations of data from different volumes. The keypad acts as a calculator. For example, to specify a slice: "0.5*density + 0.5*elpot", perform the following sequence of operations (the leading "zeros" are required):

    click on C [clear display]
    click on 0
    click on .
    click on 5
    click on *
    click on "density" from Volume
    click on +
    click on 0
    click on .
    click on 5
    click on *
    click on "elpot" from Volume

This results in the following sequence displayed at the top of the dialog:

0.5*density + 0.5*elpot

The expert dialog is more involved if the molecule belongs to a list.

Specifically another file browser (Molecule) accessing the individual molecules in the list appears at the left center of the dialog. This allows slices to be constructed from combinations of volumes from more than a single molecule. For example, a slice representing the difference in electron density between a "standard" molecule (frame01 in the above dialog) and the rest of the molecules in the list may be specified using the following sequence of operations:

    click on C [clear display]
    click on "frame01" from Molecule
    click on "density" from Volume
    click on ­
    click on "density" from Volume

This results in the following sequence at the top of the dialog:

frame01: density - density


Section 9.4.2: Edit

To edit a 2D slice, click on its frame (it will turn yellow), and then select Edit from the Slices sub-menu (Display menu), or simply double click on the frame. This results in the display of an on-screen dialog.

This contains some of the same controls as the Create dialog (see Section 9.4.1), and in addition controls to select a range of values, specify the number of layers (for multi-plane displays), the spacing between layers (for multi-plane displays) or the ratio of height to diameter (for cylindrical displays.) Provision for a legend (numerical scale relating to color values) has also been made. The Edit dialog also provides the ability to change plot type and background but it does not allow alteration of the type of slice (plane, sphere or cylinder) or of the quantity being displayed. This requires graphics deletion (see Section 9.4.3 below) and regeneration (Section 9.4.1).

  1. Range

    Sets the lower (From) and upper (To) bounds of the color scale. The default settings (the minimum and maximum values of the data, respectively) may be changed, and can be restored by clicking on Reset.

  2. Settings

    Sets the number of contour levels (Contours), and, in the case of planes, the number of planes (Layers). The default settings may be changed. The spacing between planes (in a multi-plane display) or the ratio of height to diameter (in a cylindrical display) is controlled by slider bar to the right of Spacing.

  3. Plot Type

  4. Background

  5. Frame

  6. Legend

    These are the same functions already described in Section 9.4.1.

  7. Property

    This passive display indicates the quantity being edited.

The Edit dialog is exited with the changes made by clicking on Done. Clicking on Cancel exits the dialog without changes made to the graphic. In either case, the graphic is no longer selected.


Section 9.4.3: Delete

Selection requires that a slice be the active graphical object, and results in removal of that object from the screen.


Section 9.4.4: Color Schemes for Display of Slices

Spartan's color controls (Colors under the Wavefunction Logo menu, see Section 3.2) can be employed to provide clearer images for the display of slices. For example, both the background color and the color inside the bounding frame can be set to the limiting color used to display the property (usually red).


Section 9.5: Isosurfaces

Isosurfaces constitute the second general type of graphical representation which can be produced from volume data. Isosurfaces may also be produced using explicit surface information (see Sections 8.8.1 and 9.3).

Selection of Isosurfaces from the Display menu results in a sub-menu:

Output
Properties
Surfaces
Slices
Isosurfaces > Create
Vibrations Edit
Delete


Section 9.5.1: Create

Selection of Create results in the display of a dialog.

The Volume box provides a summary of all volumes associated with the active molecule including the status of each. Entries marked "failed" have been attempted but not generated. (The reason for the failure will in most cases appear in the output file, see Section 9.1.) Entries marked "pending" have yet to be completed (they may not even have been submitted).

Upon entering the Create dialog, Specify Surface will be "on" and the first entry in the Specify Surface box will be highlighted. A different entry may be selected by clicking on it.

To map a property onto an isosurface click on Specify Property (Specify Surface will be turned "off"), and then click on the appropriate entry in the Specify Property box. Buttons at the bottom of the box control other aspects of the display.

  1. Style

    Selects a display type from among the possibilities Dots, Mesh, Solid or Transparent (solid).

  2. Colors

    Controls whether the map is presented in terms of a continuous distribution of colors (Continuous) or as a discrete set of color bands (Discrete). Colors is available only when a property has been requested.

  3. Legend

    Displays a scale of color values. Once displayed on screen, the legend is treated as any other graphical object. It can be selected by clicking on it (a yellow frame will then enclose the scale), and then moved about the screen and scaled. It cannot be rotated. Legend is available only when Map Property is "on".

After the appropriate selections have been made, clicking on Create exits the dialog and displays the graphic. The composite graphic (molecular models, the isosurface just specified with or without a mapped property displayed as a solid, and any slices or contours previously requested) are now selected, and any manipulations (translation, rotation, scaling) apply to the total image.

Clicking on Cancel exits the dialog without creating a new isosurface.

Expert Mode

This parallels the functionality already described in Section 9.4.1. Expert mode is reached by clicking on Expert at the top right of the dialog. As with the other "expert" buttons, this one is visible only if Expert in the Preferences dialog under the Logo menu (see Section 3.3) has been turned "on".


Section 9.5.2: Edit

To edit an isosurface, click on it (it will be surrounded by a yellow circle), and select Edit from the Isosurfaces sub-menu (Display menu), or simply double click on the isosurface. The dialog which appears contains controls for setting the isosurface value, for changing the type of display and for altering the range of the mapped property.

  1. Isovalue

    Contains the current value of the isosurface. Its contents can be changed either by altering the contents of the box or by using the s and t keys.

  2. Style

  3. Colors

  4. Range

  5. Legend

    These are the same functions already described in Section 9.5.1.

  6. Surface

    This passive display indicates the isosurface being edited.

  7. Property

    This passive display indicates the property mapped on the isosurface being edited.

The Edit dialog is exited and the changes made by clicking on Done. The isosurface is no longer selected.


Section 9.5.3: Delete

Selection requires that an isosurface be the active graphical object, and results in removal of that object from the screen.


Section 9.6: Vibrations

Spartan provides for animated display of normal modes of vibration. (This can also be done using Vibration Sequence under the Build menu; see Section 7.4). Clicking on Vibrations under the Display menu leads to the following dialog.

Frequencies are listed in ascending order at the top of the dialog, together with their symmetry labels. Imaginary frequencies, e.g., corresponding to the reaction coordinate for a transition state, appear at the head of the list and will have the word "imaginary" to the right of the symmetry label. Animated display follows by clicking on the desired frequency, and then clicking on Display. Clicking on Cancel exits the dialog without change.

Amplitude and Frames are available to modify the display. Amplitude controls the amplitude (extent) of the vibration while Frames controls the number of frames in the animation.

If the selected molecule is a member of a list, a different dialog is presented.

This is identical to the original dialog except that it incorporates a Post to Frequency button. Clicking on Post to Frequency enters the value of the selected frequency into a single cell of the next available column in the associated spreadsheet corresponding to the selected molecule.

Only one vibrational mode at a time may be animated for a given molecule, although vibrations for different molecules may be shown at once.


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