Quantum 1 Modules

6       MOPAC Interface

Information on how to set up and run MOPAC through the Quantum 1 module of the Cerius² interface is contained in this section.

This section includes:

Typical MOPAC calculations

Additional definition of the model

Optional job control issues

Setting up and starting calculations

Studying MOPAC output

For information about	See
Configuring the MOPAC interface.	Quantum Chemistry Models..
Editing Z-matrices.	Quantum 1 Module Utilities.
Building or reading in models.	Cerius2 Modeling Environment and Cerius2 Builders.
Preparing representative conformers for flexible models.	Cerius2 Conformational Search and Analysis.

Accessing MOPAC in Cerius²

After starting Cerius², select the QUANTUM 1 card deck. The MOPAC card should already be at the front of the deck. If not, click its name. This card gives you access to functionality for setting up and running your MOPAC job and analyzing the results. The QUANTUM 1 card deck should look like:)

Documentation

This section explains how to use the Cerius² MOPAC interface and does not discuss the MOPAC application in any detail. To learn more about MOPAC, please refer to the MOPAC documentation set. If you have MOPAC93, refer to the documentation provided. Otherwise you can obtain a documentation set by ordering MOPAC7 from QCPE at Indiana University, Department of Chemistry, Bloomington, Indiana. Telephone: [+1] (812) 855-4784. Website: see Other relevant websites.

Typical MOPAC calculations

This section describes how to perform the following basic tasks for which MOPAC is used:

Single-point energy calculations

Geometry optimizations

Transition-state optimizations

Frequency calculations

Scanning the potential energy surface

Additional tasks are also available. For additional information, please see the on-screen help for the MOPAC Run and MOPAC Task Options control panels (see Setting up and starting calculations), as well as the MOPAC documentation set.

The current model

For all calculations, you of course first need to have a model present in Cerius². For information on building and reading in models, please see Cerius² Modeling Environment (published separately by MSI).

Phases of a typical MOPAC job

A typical MOPAC session involves several phases:

1. Setting up the job--Prepare the model and specify the calculations to be performed.

Your model may be satisfactory as built or read in from a file, or it may be necessary or helpful to further define the model before starting the run. For example, you may want to impose constraints or find the point-group symmetry before starting the run. You would use one or more of the Geometry control panels for these purposes (Additional definition of the model).

If you want to set a non-default job type (task) or choose non-default parameter values for defining the chosen task, click the Run menu item in the MOPAC card to open the MOPAC Run control panel. The tasks are discussed in detail under Setting up and starting calculations.

2. Running and controlling the job--If the default run-control parameters are satisfactory, the only step required next is to click the Run menu item in the MOPAC card to open the MOPAC Run control panel (if it is not already displayed on your screen) and then click the RUN pushbutton in that control panel.

However, you may want to define non-default job-control or file-control parameters. These topics are discussed under Optional job control issues.

3. Studying the output--Analyze the largely numeric data output from the MOPAC run. After your run is complete, you can examine and graphically analyze the results. Discussion of these procedures is in Studying MOPAC output.

Who should read this section

If your model structure is satisfactory, you do not need to read this section and may proceed to Optional job control issues.

Read this section if you want information on:

Defining dummy atoms

Setting geometric constraints

Finding and setting the point-group symmetry for your model

Editing the Z-matrix for your model

Setting geometric constraints

The MOPAC program supports partial optimizations, transition-state searches, and potential scans. That is, the coordinates of some atoms are allowed to vary, while the positions of other atoms remain fixed during a calculation. This can decrease computation time considerably.

The parts of the model to keep fixed or to allow to vary during optimization can be specified in either internal or Cartesian coordinates. You specify these geometric constraints with the MOPAC Geometry control panel, which is accessed by selecting the Geometry/Constraints menu item on the MOPAC card.

The MOPAC Geometry Constraints control panel looks something like:

The Z-matrix in this control panel

The list box in this control panel shows a Z-matrix specifying the model's geometry. By default, Vs are placed next to each coordinate value, indicating that all coordinates are free to vary.

Tip

Detailed information on Z-matrices is contained in Quantum 1 Module Utilities.

Which atoms correspond to which line in the Z-matrix?

To identify the atoms in your model more easily, you may label them by selecting NUMBERS from the label-style popup (second control from the left in the tool bar of the man Visualizer control panel).

Defining constraints

To fix a bond, angle, or torsion, use the mouse to select (highlight) the line in the Z-matrix that contains the desired item. Then click the appropriate FIX pushbutton in the Constraint controls below the list box. The flag for that item in the Z-matrix changes to F, and the pushbutton is now labelled VARY (so that you can reset the flag to V if you want).

Find all symmetry.

When you click the Find all symmetry action button, the program automatically enforces symmetry during the calculation for bond (default), angle, or torsion (as determined by the popup) parameters in the current model. Use the associated entry box to specify a tolerance factor (in angstroms or degrees, as appropriate) within which parameters should be considered equal for the purpose of applying symmetry constraints.

You can also use the MOPAC Symmetry control panel (Finding and setting the point-group symmetry for your model) to find and set molecular symmetry.

Note

Remove symmetry definitions.

When you click the Remove symmetry definitions action button, the symmetry definition(s) are removed from the selected Z-matrix line.

Additional information

Please see the on-screen help for additional information on the controls in this panel.

Finding and setting the point-group symmetry for your model

With the MOPAC Symmetry control panel (which is accessed by selecting the Geometry/Symmetry menu item on the MOPAC card), you can find the symmetry group of all or some of the atoms in your model within a desired level of tolerance. You can also enforce exact symmetry upon the conformation of all or part of your model and specify that symmetry be used in your MOPAC calculation.

Note

What symmetry is used for

Using symmetry in an MOPAC run can significantly reduce the computational effort. The number of integrals that need to be evaluated and the number of degrees of freedom in geometry and transition-state calculations are reduced.

Finding symmetry

If you want only to find the point-group symmetry of all or part of your model:

• Make sure that the check boxes for snapping and reorienting atoms are not checked.

• Select ALL or SELECTED from the atoms popup, depending on whether you want the symmetry of the entire model or of only part of it.

• Choose a desired preset level of tolerance from the Tolerance popup or enter the tolerance value in angstroms. (If a symmetry determination fails, try decreasing or increasing the tolerance.)

• Click the Find symmetry action button.

Setting exact symmetry

If you also want to enforce exact symmetry by snapping the atoms to their exact symmetry positions and/or reorienting the structure to the symmetry axes, make sure that the check boxes for Snap atoms to exact symmetry and/or Re-orient atoms to symmetry axes are checked when you click the Find symmetry of action button.

Reorienting the structure may significantly displace your model from its starting position. To re-center the model, click the Reset View icon (on the tool bar of the main Visualizer control panel) or press <Home> on your keyboard.

Difficult models

If you find that you need to use very large tolerance values, you should probably use the Bond Geometry control panel (accessed by selecting the Move/Bond Geometry... item from the menu bar at the top of the main Visualizer control panel) to manually adjust the geometry before using the MOPAC Symmetry control panel.

Symmetry during the MOPAC run

The symmetry found in this step is automatically used by MOPAC if possible. Otherwise, the program automatically chooses the most appropriate related symmetry group.

Editing the Z-matrix for your model

Optional job control issues

Who should read this section

If you intend to run MOPAC on the same machine on which you are running Cerius² and do not care about monitoring the job while it runs or about transferring files, you do not need to read this section and may proceed to Setting up and starting calculations.

Read this section if you want information on:

Interactive vs. background or NQS run mode

Selecting a machine and base directory

Setting up NQS-mode jobs

Other output options

Monitoring and controlling running jobs

Transferring files from one machine to another

Creating hessian and coordinate files

Interactive

In interactive mode, Cerius² displays the MOPAC logfile output so you can monitor the progress of the jobs. However, you cannot do anything else in the Cerius² interface until the job is complete, so this is useful only for jobs that you expect to finish quickly.

You can stop an interactive job by using the Cerius² Interrupt window, which is displayed while the job is running to indicate that Cerius² is busy. If you click the INTERRUPT button and select the Stop current process ASAP option, Cerius² displays an additional dialog box from which you can confirm or cancel your request or send the job into the background.

Background

In background mode, the job runs without communicating with the Cerius² interface, and you can quit Cerius², allowing the job to run by itself. When you exit Cerius², a status file is automatically saved so that, if Cerius² is restarted, the job can be selected for monitoring or (if it has finished) the output files can be read in for analysis (see Studying MOPAC output).

NQS

In NQS mode, the job is submitted to the Network Queueing System, provided that this software has been installed, on the local or remote host. Once the job is queued, you can quit Cerius², allowing the job to run by itself. An NQS-mode job can be selected for monitoring or file transfer in a later Cerius² session.

Selecting a machine and base directory

Other machines

Click the Hosts arrow in the MOPAC Job Control control panel to obtain a pulldown listing machines at your site to which you can send the MOPAC job. The list contains all suitable hosts on your network (as defined in applcomm.db--for a description and example file entries, see the Cerius² Installation and Administration Guide).

Select a host by clicking its name in the list. This also closes the list. You can also close the list by clicking the triangular icon again. The host selected is displayed in the entry box. You can also enter a machine name by typing it in the entry box.

Permission and password

Depending on your site's setup, you might not have permission to run on all the machines listed in the pulldown, or you may need to specify a user ID and password to access some machines. Use the Options... pushbutton to access the MOPAC Job Control Options control panel, where you can input a User ID and Password before selecting your host machine.

Tip

Base directory

You also need to specify a working (base) directory on the host machine if the default specification is not correct. For more information on how to do this, as well as whether files need to be transferred between machines in consequence, please see the on-screen help (click the right mouse button while the cursor is over the Base Directory entry box).

Setting up NQS-mode jobs

Other controls enable you to display your NQS jobs and the supported limits on the chosen host. The More... pushbutton on the NQS Control control panel gives access to the NQS Options control panel, which allows you to change less commonly used NQS job submission flags.

Please see the on-screen help for information about all the controls in these control panels.

Other output options

Additional options governing the execution of your MOPAC job, such as SETUP file usage, time limit, and so on, can be set from the MOPAC Run Options control panel.

Open the MOPAC Run Options control panel by clicking the Options... pushbutton to the far right of the RUN pushbutton in the Run MOPAC control panel.

Refer to the on-line help text (available by right-clicking any control) and the MOPAC documentation to obtain more information about the controls in these control panels.

Monitoring and controlling running jobs

Tip

You can also monitor or kill a job that is running or import the files from a remote machine to the machine on which you are running Cerius² after your job has completed:

• Selecting a job from the Job Status list and clicking the Monitor Logfile action button opens a window showing the contents of the output file for that job. Because MOPAC jobs can run for such long periods of time, the job list is maintained between Cerius² sessions via a status file (called .MSImopacstat, and typically located in your home directory).

• To kill a queued or currently running job, select it in the Job Status list and click the Kill Job action button.

>	xhost remote_host_name 

Transferring files from one machine to another

Note

Creating hessian and coordinate files

your_path/mpcarhess.pl run_name.out

where run_name is the name you selected for the calculation, and your_path is the UNIX path to the perl script. Typically, this will be defined at install time as $C2DIR/mopac.

This procedure will always create a run_name.car file. To create a run_name.hessian file in addition, you must do the following when you run the MOPAC job:

• Select a Frequency or Geometry Opt.&Frequency calculation;

• Click the Task More... button to bring up the MOPAC Task Options panel and make sure Output Force Matrix is checked;

• Select the Output Options... button to bring up the MOPAC Output Options panel and make sure Initial Data and Cartesian Coordinates are both checked.

If you plan to use this hessian file in subsequent calculations (for example, for DMol³ optimizations) you must be aware of several features imposed by the design of the Cerius² interface to MOPAC. The order of the atoms in the MOPAC z-matrix is typically different from the order of atoms assigned in the Cerius² interface. The order of atoms in the run_name.car and run_name.hessian files corresponds to the order in the MOPAC output file, not to the order in the Cerius² interface. Whenever you run subsequent calculations using the hessian file, you must open the run_name.car file as your starting point, not the MOPAC run_name.out file.

For example, in the simple case of hydrogen peroxide (HOOH), you might build the molecule with the atoms in the order H, O, O, H, so this order would be assigned by Cerius². However, the MOPAC z-matrix might start with the O-O bond, in which case the order of atoms in the MOPAC output file would be O, O, H, H. The ordering of atoms in the .car and .hessian files will correspond to this order, not to the order assigned by the interface. In order to set up subsequent jobs using the .hessian file, you should open the HOOH .car file, and not the MOPAC .out file.

Setting up and starting calculations

The default MOPAC Run control panel looks like:

Starting a run

If the default task (single-point energy calculation) and other options are satisfactory, you need only click the RUN pushbutton in the MOPAC Run control panel to start your run.

Otherwise, see the following sections and set the desired options before clicking the RUN pushbutton.

Who should read this section

If you are sure that the default task is appropriate to your computational problem, you do not need to read this section and may run your job and then proceed to Studying MOPAC output.

Read this section if you want information on:

Choosing a task

Approximation methods

Specifying charge and spin

SCF options

Solvation effects

Property calculation

Handling and naming MOPAC input files

Restarting a previous run

For complete lists and descriptions of available calculation tasks, approximation methods, and basis sets, see the MOPAC documentation. The objectives of some typical tasks are:

• Single-point energy calculation.

• Geometry optimization to a local minimum or a transition state.

• Determination of vibrational frequencies.

Specifying tasks

Specify the MOPAC calculation task by selecting the appropriate task from the Task popup.

You can also select the required calculation task from the popup at the top of the MOPAC Tasks control panel. Click the triangular icon to the right of the text box to obtain the list of tasks; close the list by selecting a task (by clicking its name) or by clicking the triangular icon again. The task selected is displayed both in the text box in this control panel and on the Task popup in the Run MOPAC control panel.

Specify appropriate task-related options using the controls in the MOPAC Task Options control panel. The options displayed here are specific to the selected task.

Single-point energy calculations

Geometry optimizations

You may also want to set additional options before clicking the RUN pushbutton (below and Approximation methods).

Click the More... pushbutton in the MOPAC Run control panel next to the Task popup to open the MOPAC Task Options control panel. You can use this panel to control the convergence criterion and set other options.

For additional information on the controls in this control panel, please see the on-screen help or the MOPAC documentation.

Transition-state optimizations

You may also want to set additional options before clicking the RUN pushbutton (below and Approximation methods).

Click the More... pushbutton in the MOPAC Run control panel next to the Task popup to open the MOPAC Task Options control panel. You can use this panel to control the optimization procedure.

For additional information on the controls in this control panel, please see the on-screen help or the MOPAC documentation.

Frequency calculations

You may also want to set additional options before clicking the RUN pushbutton (below and Approximation methods).

Click the More... pushbutton in the MOPAC Run control panel next to the Task popup to open the MOPAC Task Options control panel. You can use this panel to control the frequency calculation and specify some output.

For additional information on the controls in this control panel, please see the on-screen help or the MOPAC documentation.

Scanning the potential energy surface

You may also want to set additional options before clicking the RUN pushbutton (below and Approximation methods).

Click the More... pushbutton in the MOPAC Run control panel next to the Task popup to open the MOPAC Task Options control panel. You can use this panel to control the calculation.

Specifying parameters to vary

To systematically vary one or two bond lengths, dihedral angles, and/or torsion angles, enter the Line Number of the appropriate line in the Z-matrix, which you can obtain from the MOPAC Geometry control panel (Setting geometric constraints).

Scanning strategy

You can specify whether scanning in MOPAC is one or two dimensional and whether a regular range of values or only certain specified values are scanned.

Scanning range

To define the values between which to change regularly varied coordinates, enter the desired start and stop values and the number of steps in the respective entry boxes.

For additional information on the controls in this control panel, please see the on-screen help or the MOPAC documentation.

Other tasks

Refer to the on-screen help text (available by right-clicking any control) and the MOPAC documentation for information about all the tasks and their options.

Approximation methods

• PM3.

• AM1.

• MNDO.

• MINDO/3.

The controls on the MOPAC Methods control panel are largely context sensitive. That is, only those options appropriate for your chosen selections are displayed.

Refer to the on-screen help text (available by right-clicking any control) and the MOPAC documentation for detailed information about all options in this control panel.

Specifying charge and spin

If your model has any spin-unpaired electrons, you need to specify the number of alpha electrons minus the number of beta electrons in the Spin entry box.

It is up to you to choose the correct values for Charge and Spin, although the entry boxes do not accept values that are unreasonable.

To calculate atomic charges fit to the electrostatic potential of the molecule, check the ESPD Charge check box.

SCF options

For additional information on the controls in this control panel, please see the on-screen help or the MOPAC documentation.

Also refer to the on-line help text and the MOPAC documentation for information about the controls on the MOPAC I.P. Correction Setup control panel (accessed by clicking the Setup... pushbutton in the MOPAC SCF Options control panel, which appears only when MOPAC93 is selected).

Solvation effects

For MOPAC7 and MOPAC93 jobs, you can set up a COnductor-like Screening MOdel (COSMO) calculation using the controls on the MOPAC Solvent Options control panel, which is accessed by clicking the Solvent... pushbutton on the MOPAC Run control panel.

The MOPAC Solvent Options control panel contains controls that allow you to set various options to be used for your solvation job.

Refer to the on-screen help text (available by right-clicking any control) and the MOPAC documentation to obtain more information about the controls in this control panel.

Property calculation

Categories of property calculations include:

• Charges and population analysis.

• Electrostatic potential-derived (ESPD) charges.

• Hyperpolarizability.

You can specify the properties to be calculated during the MOPAC run and their associated options using the controls on the MOPAC Properties control panel which is accessed by selecting the Properties menu item from the MOPAC menu card.

Refer to the on-line help text (available by right-clicking any control) and the MOPAC documentation to obtain more information about options set by these controls.

Handling and naming MOPAC input files

MOPAC input and output files generated by the Cerius² have several different file extensions. To change the default root name for files associated with your run, edit the contents of the File Prefix entry box in the MOPAC Run control panel. Alternatively, you can select a root name from existing datafiles using controls on the MOPAC Input File control panel (Saving, editing, and using input files). We will refer to this root (or "seed") name as run_name in this section.

Run title

To change the default title for your run, edit the contents of the Title entry box in the MOPAC Run control panel. This descriptive text is included in the input and output files associated with your run, to aid in identifying your run.

Reviewing the current input file

Before you run your job (passing the input file generated by the MOPAC interface to the MOPAC software), you can review the commands that reflect your defined options in the Keyword scrolling list box on the MOPAC Run control panel.

Saving, editing, and using input files

For other aspects of file handling, access the MOPAC Input File control panel by clicking the Files... pushbutton in the Run MOPAC control panel.

With the MOPAC Input File control panel, you can:

• Save your input file.

Click the Save MOPAC Input File action button to write the input file you have built up so far in your Cerius² session to disk. The filename will be run_name.dat.

• Edit an existing (saved) input file.

Select a file by clicking its name in the list box, then click the Edit MOPAC Input File action button to edit this file. This automatically calls up vi (or EMACS, if it is specified in the $EDITOR environment variable) to edit the file in a separate window. If you prefer some other editor, open your editor in the usual way, then edit and save the input file. Before using this functionality, you should of course ensure that there are no jobs with the current file prefix already running.

Cerius² allows you much flexibility in performing your studies. You could, for example, build your model and set up most of your input file via the Cerius² interface, save this file, then include extra datablocks or keywords that are available in standalone but not through the Cerius² interface (please see the MOPAC documentation) by editing this file and saving it from the editor, and finally start your run from that edited file via the Cerius² interface (see next paragraph) or by running MOPAC in standalone mode.

• Run an existing input file.

Select a file by clicking its name in the list box, then click the Run Selected MOPAC Input File action button to start an MOPAC run from a previously saved input file. The job uses the current settings of the MOPAC Job Control panel (host machine, run mode, etc., see Optional job control issues).

Restart files are saved periodically during the MOPAC run. From the MOPAC Run Options control panel, you can specify the amount of elapsed CPU between restart file saves (Dump Frequency entry box) and, therefore, the maximum amount of unrecoverable run time.

Studying MOPAC output

You may be able to obtain manually or extrapolate all the information that you require from the data in the output file. However, the MOPAC interface provides a set of analysis tools that you can use to analyze information from the output file and readily visualize the results using the rich Cerius² graphical display functionality.

Important

Information that can be analyzed using the MOPAC analysis tools includes:

• Model structure--Recover and analyze geometry, charges, and dipoles.

• Vibrational frequencies--Calculate and study vibrational frequencies and normal modes and display infrared spectra.

• Molecular orbitals and localized orbitals-- Calculate orbitals, which can then be displayed as 3D surface maps or a color-contoured slice plane.

• Electron densities--Calculate electron density, which can then be displayed as a 3D surface map or a color-contoured slice.

• Charge potentials--Calculate the electrostatic potential, which can then be displayed as a 3D surface map or a color-contoured slice.

Output from the last MOPAC job completed in interactive mode during this Cerius² session is automatically selected for analysis. Any graphs produced (IR spectrum, energy vs. structure number) are automatically displayed at the end of the run.

Otherwise, you need to specify which files contain the results to be analyzed. Do this with the MOPAC File Analysis control panel, which is accessed by selecting the Analyze/Files menu item on the MOPAC card.

Finding your output files

The list box in the MOPAC File Analysis control panel shows the files in your current directory. You can browse other directories by using the popup menu above the list box. If a MOPAC file named run_name.out is present, the run has ended and the results can be analyzed.

Before you load the output files ...

By default, when you SELECT a run_name.out file, the associated MOPAC model is automatically loaded into the model display window, and graphs of any relevant properties present in the file are automatically generated. You may want to prevent this for some reason (see Loading models and structures for how to load models after loading the run_name.out file). To unset these automatic options (before you click the SELECT pushbutton), click the Options... pushbutton in the MOPAC File Analysis control panel to access the MOPAC File Analysis Options control panel.

Output file identification and contents

A summary of the calculation is displayed in the Summary of Calculation list box in the MOPAC File Analysis control panel after you SELECT a file.

Clicking the Examine File action button displays the results of the calculation in text format.

Analyzing coordinates, charges, and dipoles

Loading models and structures

If you did not automatically load the model when you specified which file to analyze (Before you load the output files ...), you may load models by clicking the Recover structure action button. If the output file contains more than one structure, you may select which structure(s) to load by using the entry box and/or the increment and decrement buttons also on the top line of the control panel.

Displaying the dipole moment vector

The check box for Show Dipole Vector, the Color popup, and the Display Scale entry box control the display of a vector indicating the dipole moment of the model.

Analyzing vibrational frequencies and normal modes

The MOPAC Vibration control panel, which is accessed by selecting the Analyze/Vibrations menu item on the MOPAC card, displays a full list of normal modes and their frequencies and IR intensities. As modes are picked in the graph, the corresponding mode in the control panel is highlighted.

Several ways of displaying frequency results

The Display Selected Mode section of the MOPAC Vibration control panel controls the Cerius² model window.

To animate a normal mode, click the ANIMATE control. The Mode Scale determines the maximum movement of any atom; the step number can be used to freeze the model at any given step of the animation; and the total number of steps controls the smoothness and relative speed of the animation.

To simply display a normal mode (as a set of arrows superimposed on the current model), select a different color if desired and check the Display check box.

The Infrared Spectrum section of the control panel controls the Cerius² graph window, which displays a plot of the infrared spectrum. The peak shape and width can be adjusted: select LORENTZIAN or DELTA to set the peak shape; enter a number in the Width entry box to adjust the peak width (in cm^-1).

You can also adjust the graph in the graph window using the usual Cerius² procedures, for example, to adjust the scale or view only a portion of the graph. (Please see Cerius² Modeling Environment for information on viewing and managing graphs.)

Scaling frequency values

Finally, you may scale the calculated frequencies by a Frequency Scale Factor, so that they agree better with experimental frequencies.

Analyzing orbitals, densities, and potentials

Calculating orbitals

Which orbitals to calculate and display

You may calculate orbitals for electrons with alpha or beta spin by choosing Alpha or Beta from a popup menu. The alpha or beta orbitals are shown in the list box, as well as their symmetry labels and energies. Select an orbital from the list or choose HOMO or LUMO to quickly select the highest occupied molecular orbital or lowest unoccupied molecular orbital.

If the default grid-control parameters are suitable (see Grid specification), simply click the Calculate action button. If not, adjust these parameters before clicking the Calculate action button.

To display more than one calculated orbital simultaneously, you can use the MOPAC Surfaces control panel (Displaying orbitals, densities, and potentials as surfaces).

Grid specification

You can control the resolution with which the grid is calculated, through a popup. LOW-resolution grids are faster to calculate and display, HIGH-resolution grids give the highest-quality graphic output, and MEDIUM-resolution grids represent a compromise between these considerations.

You can adjust additional grid-control parameters or control the resolution more precisely by clicking the Grid... pushbutton to access the Define Grid control panel.

Please see the on-screen help for information about the controls in this control panel.

Other controls

Click the Preferences... pushbutton if you want to turn off automatic (re)creation of orbital surfaces or change the default name of the file in which to save the calculated orbital grid.

Calculating localized orbitals

Which localized orbitals to calculate and display

To generate data for localized orbitals, click the LOCALIZE pushbutton in the MOPAC Localized Orbitals control panel.

You may calculate surfaces for localized orbitals for electrons with alpha or beta spin by choosing Alpha or Beta from a popup menu. The alpha or beta localized orbitals are shown in the list box, as well as other information. Select an orbital from the list to calculate it as a surface.

If the default grid-control parameters are suitable (see Grid specification), simply click the Calculate action button. If not, adjust these parameters before clicking the Calculate action button.

To display more than one calculated localized orbital simultaneously, you can use the MOPAC Surfaces control panel (Displaying orbitals, densities, and potentials as surfaces).

Grid specification

You can control the resolution with which the grid is calculated, through a popup. LOW-resolution grids are faster to calculate and display, HIGH-resolution grids give the highest-quality graphic output, and MEDIUM-resolution grids represent a compromise between these considerations.

You can adjust additional grid-control parameters or control the resolution more precisely by clicking the Grid... pushbutton to access the Define Grid control panel.

Please see the on-screen help for information about the controls in this control panel.

Other controls

Click the Preferences... pushbutton if you want to turn off automatic (re)creation of orbital surfaces, change the cutoff for display, or change the default name of the file in which to save the calculated orbital grid.

Calculating the electron density

You can control the resolution with which the grid is calculated, through a popup.

You can adjust additional grid-control parameters or control the resolution more precisely by clicking the Grid... pushbutton to access the Define Grid control panel (Grid specification).

Other controls

Click the Preferences... pushbutton if you want to turn off automatic (re)creation of electron density surfaces or change the default name of the file in which to save the calculated density grid:

Calculating the electrostatic potential

You can control the resolution with which the grid is calculated, through a popup.

You can adjust additional grid-control parameters or control the resolution more precisely by clicking the Grid... pushbutton to access the Define Grid control panel (Grid specification).

Other controls

Click the Preferences... pushbutton if you want to turn on or off automatic (re)creation of electrostatic potential surfaces or change the default name of the file in which to save the calculated potential grid.

Displaying orbitals, densities, and potentials as surfaces

The calculated orbitals and densities are ordinarily automatically displayed as surfaces as you create them. However, you would need to use the MOPAC Surfaces control panel if you want to:

• Change the transparency or color for an existing surface.

• Choose which of several calculated surfaces to display.

• Display several surfaces simultaneously.

• Display surfaces that were calculated and saved in a previous Cerius² session.

• Display a surface that was not created automatically (if you unchecked the Automatically Create Surface check box in one or more of the Preferences control panels).

Finding your surfacing files

If you want to display a currently undisplayed surface, use the Files... pushbutton to access the MOPAC Surfacing Files control panel. Select the desired run_name_property.mbk file and click the LOAD button. You can use the browser popup menu to access directories other than the current one.

Surface specification and display

Once you have a surfacing file loaded and if the default settings in the MOPAC Surfaces control panel are satisfactory, you can click the Create New Surface action button (in the MOPAC Surfaces control panel) to create and display that surface on your model. Make sure that none of the surfaces in the list box is selected if you want to create and display a new surface in addition to those already displayed.

You can edit surfaces in several ways:

• Change the value in the Isosurface Value Range entry box to change which iso-value points within the grid are displayed when the Create New Surface pushbutton is clicked again.

• Check or uncheck the Show Surface check box to display selected surface(s) or not.

• Click the Delete Surface action button to delete selected surface(s) from the display and the Edit Surface list.

• Change the transparency and color of surfaces with the relevant controls at the bottom of the MOPAC Surfaces control panel.

An isosurface connects points in space that have the same value of some parameter. However, you can add an additional dimension to a surface, by making a property map, which displays the values of another property as different colors on an existing displayed surface.

To do this, use the MOPAC Property Maps control panel, which is accessed by selecting the Analyze/Property Maps menu item on the MOPAC card.

Finding your property files

Specify a property to be mapped by choosing the appropriate run_name_property.mbk file from the list box and clicking the LOAD pushbutton. You can use the browser popup menu to access directories other than the current one.

Map specification and display

If more than one surface is displayed or has been loaded, you may need to select the one on which to map the property, using the list box in the MOPAC Surfaces control panel (Displaying orbitals, densities, and potentials as surfaces).

Click the Add Property action button to display the property map.

You can vary the transparency of the displayed property map with the Transparency entry box.

You can change the range and color spectrum with which to display the property map by clicking the Preferences... pushbutton to access the MOPAC Property Maps Preferences control panel.

Editing and displaying slices

Finding your surfacing files

If necessary, choose the orbital, density, or potential file to be surfaced by clicking the Files... pushbutton to access the MOPAC Surfacing Files control panel (Finding your surfacing files). Select the appropriate run_name_property.mbk file from the list box and click the LOAD pushbutton. You can use the browser popup menu to access directories other than the current one.

Slice specification and display

Once you have loaded a .mbk file and if the default settings in the MOPAC Slices control panel are satisfactory, you can click the Create New Slice action button (in the MOPAC Slices control panel) to create and display a selected slice for your model.

However, you may want to edit the slice before displaying (or redisplaying) it.

The Edit Slice list box shows the slice(s) that are currently displayed. You can select one by clicking its name in the list box. Make sure that none of them is selected if you want to create and display a new slice in addition to those already displayed.

Check or uncheck the Show Slice check box to indicate whether to display the selected slice. Click the Delete Slice action button to delete the selected slice from the display and the list.

You can change the transparency in the Transparency entry box near the bottom of the MOPAC Slices control panel.

Positioning the slice plane

A slice is defined by its position and direction. The default position and direction are chosen so that the slice passes through the best-fit plane to the whole model or any selected atoms. A slice is created with a default position and direction and can be returned to the default position or direction by clicking the appropriate reset buttons.

To change the position through which the slice plane slices the grid, use the Position arrows to move the slice up or down the perpendicular to the slice plane. The numbers show the position that the slice plane passes through. They change as you click the arrows, or you can edit them directly.

To change the direction of the line perpendicular to the slice plane (up and down which the plane can be moved), edit the numbers in the Direction entry box.

Other controls

Clicking the More Editing Options... pushbutton gives you access to the MOPAC Slice Preferences control panel.

Plot the plane's values

To create a 2D contour graph corresponding to a selected slice plane, click the Create Slice Plot in Graph Window action button (in the MOPAC Slices control panel).