MacMolPlt Surfaces

The following surfaces are supported:


MacMolPlt supports several different surface types. You may have any number and any combination of surface types active at once, though having more than a couple of surfaces visible at once makes things hard to see. One useful feature is to have multiple sufaces defined, but only one visible at a time. You can then run through the surfaces one by one. This makes it easy to highlite important orbitals, etc when creating a presentation. To create surfaces open the Surfaces window and click the Add button in the lower right corner. All surfaces for a frame are listed in the menu near the top of the Surfaces window.

The surfaces are divided into three main types: 1D spectrum lines, 2D contour maps, and 3D isosurfaces. Common to all surfaces are the options to type in a label for the surface and an option to make the surface visible/invisible. The purpose for making a surface invisible is so that you can define the surface the way you want, and precalculate the grid and contour(s) and then work on a seperate surface. Then when you want to show off the surface to someone else simply make it visible.

1D spectrum lines allow for the spectrum of surface values on a line between two locations to be visualized. The endpoints of the line can be relocated through both the Surfaces dialog and with the mouse after the surface is created. To move with the mouse, click on the endpoint and drag it left and right. Both endpoints can be moved at the same time by holding down the Control/Command key while dragging. The endpoints can be moved in and out of the scene by tapping (holding is not required) the Shift key. The surface values can be visualized in one of two ways: a) as an embedded 2-D graph with the x-axis spanning between the two endpoints and the y-axis representing value intensity, or b) as a colored key ranging from blue at the minimum surface value to red at the clamped maximum value.

There are several options common to all 2D surfaces such as the ability to set contour colors and choose the plotting plane. The plotting plane can be fixed to the plane of the screen, in which case it is changed as the molecule is rotated, or the plane can be simply constant.

3D isosurfaces also have a few common features such as colors, number of grid points, grid size, and the contour value. The grid size referred to here is the size of the gridded volume (ie how far out from the molecule does the grid go). If your surface gets chopped off then try increasing this parameter.

The individual surface controls and options are listed below. For help with the controls common to all surfaces (ie update etc) see the Surfaces Window description.


CreatingSurfaces:

To create a new surface bring up the Surface window for the desired file. Then click the Add button in the lower right corner. This will bring up the followin dialog:

From this dialog click (or double click) on the desired surface type to create a surface of that type. Note that all of the surface types listed are not always available. The General 2D and 3D types are always available, 2D and 3D orbitals are available as long as the current file has an associated atomic basis set, and 2D and 3D TE densities and MEPMaps are available when a file has a basis set, eigenvectors (or MCSCF natural obitals) and thus has knowledge of the MO occupation numbers.


2D Orbitals:

The 2D orbital surface is a 2D contour map showing the changes in orbital density in the plotting plane. The 2D surface dialog and a sample contour map created with it are shown below:

The important controls are:


2D Total Electron Densities:

Creates a 2D contour map of the total electron density of a molecule. This requires that the original file read in by MacMolPlt contain basis set information and the natural orbitals (eigenvectors or MCSCF natural orbitals) or the wavefunction such that the orbital occupation information is also known. A sample dialog and its corresponding output are shown below:

The important controls are:


Molecular Electrostatic Potential Map (MEPMap):

Creates a 2D contour map of the Molecular Electrostatic Potential of a molecule. This requires that the original file read in by MacMolPlt contain basis set information and the natural orbitals (eigenvectors or MCSCF natural orbitals) or the wavefunction such that the orbital occupation information is also known. IMPORTANT: MEP's require calculating one-electron integrals which are much more computationally expensive than the other types of calculation in MacMolPlt. Thus don't expect to recalculate a surface in real time. A sample dialog and its corresponding output are shown below:

The important controls are:


General 2D Surface:

The general 2D surface is provided to allow users to read in any aribitrary grid data. MacMolPlt will then contour and plot the data. The file containing the grid data defines many parameters such as the plotting plane, the number of grid points and the grid data. The format for the 2D grid file is identical to the 2D surface export format. The dialog is:

The important controls are:


3D Orbital Isosurfaces:

3D orbital isosurfaces are a 3 dimensional surface of constant orbital density. Thus it can be thought of as a 3D representation of one of the 2D contours. To view 3D isosurfaces you must use QuickDraw 3D (and thus have a PPC). The dialog and a sample are:

The important controls are:


3D Total Electron Density:

Creates a 3D isosurface of the total electron density of a molecule. This requires that the original file read in by MacMolPlt contain basis set information and the natural orbitals (eigenvectors or MCSCF natural orbitals) or the wavefunction such that the orbital occupation information is also known. A sample dialog and its corresponding output are shown below:

The important controls are:


3D Molecular Electrostatic Potential Map (MEPMap):

Creates a 3D isosurface of the Molecular Electrostatic Potential of a molecule. This requires that the original file read in by MacMolPlt contain basis set information and the natural orbitals (eigenvectors or MCSCF natural orbitals) or the wavefunction such that the orbital occupation information is also known. A sample dialog and its corresponding output are shown below:

The important controls are:


General 3D Surface:

The general 3D surface is provided to allow users to read in any aribitrary grid data. MacMolPlt will then contour and plot the data. The file containing the grid data defines many parameters such as the number of grid points and the grid data. The format for the 3D grid file is identical to the 3D surface export format. The dialog is:

The important controls are:


1D Total Electron Densities:

Creates a linear sampling of total electron density between two locations.

The important controls are:


Density Differences:

Density differences are not as automated as other surface types in MacMolPlt. There are a series of steps to creating density difference surfaces of either total electron densities or orbital densities. Basically each part of the density difference must be created individually and export to seperate files. Then the difference density is created using either the General 2D or 3D surface and reading in the individual files. The key element in creating the individual surfaces is that they must all have the plane or 3D volume defined exactly the same. To make this possible each surface type has a Set Parameters button (some are abrieviated) to copy and paste the important parameters defining the plane or 3D cube.