6.26. Surface Setup / Cubgen window

Adjust the display of volume data such as molecular orbit, electrostatic potential, various cube files.

File ‣ Open menu

Select the cube file you want to draw.

File ‣ Export VRML menu

Output in VRML format.

File ‣ Export VRML & Open VRML Viewer menu

Output in VRML format and open the file in a VRML viewer, which can be configured in the preferences.

File ‣ Open VRML Viewer menu

Displays the current file in the VRML viewer.

File ‣ Open Winmostar Viewer menu

View the current file in Winmostar Viewer.

File ‣ Close menu

Close this window.

Quantity pulldown menu

Specify the value of the isosurface to draw.

  • MO

    3D distribution of molecular orbitals selected by Selected MO.

  • Surface

    Molecular surface drawn at a distance of VDW radius (not exact)

  • ESP(Population Charge)

    ESP(Population Charge) is a three-dimensional distribution of electrostatic potential calculated from the point charge after Population analysis. It works faster than ESP. If more than one type of charge exists, ESP charge (high priority) > Lowdin charge > NBO charge > User charge > Mulliken charge (low priority) is used in that order.

  • ESP(Population Charge)/Surface

    Display ESP(Population Charge) information on the molecular surface. When multiple types of charges are present, it behaves like ESP (Population Charge).

  • MO/Surface

    Display MO information on the molecular surface.

  • Density

    It is a three-dimensional distribution of electron density.

  • ESP

    Three-dimensional distribution of electrostatic potential calculated directly by electronic state calculation.

Hint

You can display the ESP on the surface of the molecule corresponding to ESP/Surface by following the steps below. (Not supported for MOPAC.)

  1. Check Dump cube file and select Density with Quantity.

  2. Pressing the Draw button creates a file called *_den.cube.

  3. Select ESP with Quantity.

  4. When the Draw button is pressed, a file called *_esp.cube is created. This processor may take several minutes.

  5. If you open *_den.cube in the main window of Winmostar, a window called Cube Plot will open.

  6. Click the … button next to File 2 to open *_esp.cube.

  7. Click Draw button

Hint

If you have the Cubegen program included with Gaussian for Windows, you can speed up the display of ESP. In the Cubegen window that appears when you open a Cube file, check the Use Gaussian’s cubegen checkbox.

The following items can only be selected for the Cubegen window.

  • Spin

    This is the three-dimensional distribution of the spin density (density difference between alpha and beta spins).

  • Alpha

    This is the three-dimensional distribution of the alpha spin density.

  • Beta

    This is the three-dimensional distribution of the beta spin density.

  • CurrentDensity=X

    3D distribution of current density induced by a magnetic field, where X is the direction in which the magnetic field is applied, rewrite and run Y or Z as needed.

  • ShieldingDensity=XX1

    This is the three-dimensional distribution of the magnetic shielding density. The first X after = is the direction in which the magnetic field is applied, the second X is the direction of the induced field, and the third number is the number of the atom for which the shielding density is calculated; rewrite and execute as needed.

Selected MO

Specify the number of the molecular orbit to be drawn. Selecting a molecular orbital with Energy Level Diagram window will set the value in this location.

Show Diagram button

Energy Level Diagram window is displayed.

alpha/beta button

Select a spin.

Draw Style pulldown menu

Display the isosurface in grid (Mesh) or solid (Solid) model.

Transparency

Specify transparency. (0: opaque, 1: transparent)

Isosurface Value

Specify the value of the isosurface to draw.

Points

Specify the number of grid points on each side.

Scale

Specify the scaling factor that specifies the range to be drawn.

Draw boundary check box

Draw a line on the boundary of the cube file. It is mainly used for band calculation such as Quantum ESPRESSO, OpenMX.

Draw contour Map check box

Draw a contour line on the specified section.

Dump cube file check box

When you press the Draw button, cube file is output at the same time as drawing.

Draw button

Draw the volume data using Winmostar Viewer.

Close button

Close this window.