Quantum 1 Modules

7       Zindo Interface

This section contains information on how to set up and run Zindo through the QUANTUM 1 module of the Cerius² interface.

This section includes:

Introduction

Additional definition of the model

Optional job control issues

Setting up and starting calculations

Analyzing Zindo results

Accessing Zindo in Cerius²

After starting Cerius², select the QUANTUM 1 card deck and then the ZINDO card. This gives you access to functionality for setting up and running your Zindo job and analyzing the results. The QUANTUM 1 card deck should now look something like:

Documentation

This section explains how to use the Cerius² Zindo interface and does not discuss the Zindo application in any detail. To learn more about Zindo, please refer to MSI's documentation of standalone Zindo, the most up-to-date version of which can be found at our website:

http://www.msi.com/doc/quantum9709/zindoC/

Introduction

Zindo can be used to perform these basic tasks:

Single-point energy

Single-point forces

Electronic excitations

Geometry optimization

Transition-state optimization

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 Zindo job

A typical Zindo 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 as 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 nearest point-group symmetry (and change the model's conformation to that 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 nondefault job type (task) or choose nondefault parameter values for defining the chosen task, click the Run menu item in the ZINDO card to open the Run Zindo control panel. The tasks are discussed in detail under Setting up and starting calculations.

2. Running and controlling the job--Once the model is set up correctly and if the default run-control parameters are satisfactory, all that is required is to click the Run menu item in the ZINDO card to open the Run Zindo 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 nondefault job-control or file-control parameters. These topics are discussed under Optional job control issues.

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

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:

Setting geometry constraints

Finding and setting the point-group symmetry

The Zindo program supports partial optimizations and transition-state searches. 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 are specified with the Atom Constraints control panel, which is accessed by selecting the Geometry/Constraints menu item on the ZINDO card.

Defining constraints

The Atom Constraints control panel contains controls that mark selected atoms as either fixed or free to move.

The set of atoms currently marked as fixed can be visualized in the model window by coloring them. Do do so, select the View/Colors... item from the menu bar near the top of the main Visualizer control panel to open the Color Selected Objects control panel. Then select Moveability in the Color by a Property list box.

(Internal coordinate constraints such as distance, bond angle, and dihedral angle constraints are not currently supported in the Cerius²·Zindo module.)

Finding and setting the point-group symmetry

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

The Zindo program can use symmetry to classify molecular orbitals and spectroscopic transitions. In addition, using symmetry in certain Zindo runs can significantly reduce the computational effort.

Finding symmetry

If you want only to find the nearest point-group symmetry group for your model but leave the model unchanged:

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

• 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.

If you also want to enforce exact symmetry by snapping the atoms to their exact symmetry positions and/or reorienting the model 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 action button.

Reorienting the structure may significantly displace your model from its starting position. To recenter 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 in the main Visualizer control panel) to manually adjust the geometry before using the Zindo Symmetry control panel.

Symmetry during the Zindo run

For some tasks, the symmetry found in this step may optionally be included in the Zindo run.

Optional job control issues

Who should read this section

By default, Zindo jobs are run on the same machine on which you are running Cerius². The job is run interactively and is monitored while it runs. If this is satisfactory, 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

Monitoring and controlling running jobs

Transferring files from one machine to another

Interactive

In interactive mode, Cerius² displays the Zindo 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 Analyzing Zindo results).

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 Zindo Job Control control panel to obtain a pulldown listing machines at your site to which you can send the Zindo 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. Click the Options... pushbutton to access the Zindo 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 in 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.

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 Zindo jobs can run for such long periods of time, the job list is maintained between Cerius² sessions via a status file (called .MSIzindostat 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

Setting up and starting calculations

The default Run Zindo control panel looks like:

For a given model, the most important options defining the Zindo run are the task and the method. Several other options are used for specifying the exact nature of the calculation, e.g., the charge and spin of the system.

Starting a run

If the default options are satisfactory, you need only click the RUN pushbutton in the Run Zindo control panel to start your run. Then proceed to Analyzing Zindo results.

Who should read this section

Read this section if you want information on:

Handling and naming Zindo input files

Choosing a task

Calculation methods

Specifying charge and spin

Molecular environment

Calculating properties

SCF options

Specifying output and run options

For additional information on the options in all the control panels mentioned in this section, please see the on-screen help.

Handling and naming Zindo input files

To change the default root name for files associated with your run, edit the contents of the File Prefix entry box in the Run Zindo control panel. Alternatively, you can select a root name from existing datafiles using controls on the Zindo Input File control panel (Saving, editing, and using input files). We refer to this root (or "seed") name as run_name in this documentation.

Run title

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

Saving, editing, and using input files

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

With the Zindo Input File control panel, you can:

• Save your input file.

Click the Save Zindo 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.inzindo.

• Edit an existing (saved) input file.

Select a file by clicking its name in the list box, then click the Edit Zindo Input File action button to edit this file. This automatically calls up vi (or EMACS, if it is specified by 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 no jobs with the specified file prefix are currently 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 keywords that are available in standalone but not through the Cerius² interface (please see the documentation of standalone Zindo, published separately by MSI) 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 Zindo in standalone mode.

• Run an existing input file.

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

The available tasks are:

Single-point energy

Single-point forces

Electronic excitations

Geometry optimization

Transition-state optimization

A single-point energy task computes the SCF solution for the input geometry. By default, a spectroscopic parametrization is used, which is suitable for studying electronic structure (molecular orbitals, dipole moment, etc.).

You can also use a theoretical parameterization suitable for comparing the energies of different conformations. The parameterizations and other options can be changed with the Zindo Single Point Options control panel, which can be accessed by clicking the More... pushbutton next to the Task popup in the Run Zindo control panel (when the Task is set to Single Point Energy).

Single-point forces

A single-point forces task computes the atomic forces for the input geometry from the SCF solution.

Electronic excitations

An electronic excitations task calculates the UV/visible spectrum for the model. A configuration interaction (CI) calculation is done to obtain the electronic excitation energies and transition dipole moments.

The basic functionality for controlling the CI calculation is available on the Zindo Electronic Excitations control panel, which is accessed by clicking the More... pushbutton next to the Task popup in the Run Zindo control panel (when the Task popup is set to Electronic Excitations). These options are adequate for many applications.

However, if required, additional control over the calculation is available on the Zindo Electronic Excitations Options control panel, which is accessed by clicking the More... pushbutton on the Zindo Electronic Excitations control panel.

Geometry optimization

A geometry optimization task optimizes your model to a stable geometry, that is, it locates a minimum in the potential energy surface.

If required, control over the optimization procedure is available on the Zindo Geometry Optimization control panel, which is accessed by clicking the More... pushbutton next to the Task popup in the Run Zindo control panel (when the Task is set to Geometry Optimization).

For information about constraining atoms during geometry optimization, please see Setting geometry constraints.

Transition-state optimization

A transition-state optimization task optimizes your model to a transition state, that is, it locates a saddle point on the potential energy surface.

Control over the optimization procedure is available on the Zindo TS Optimization control panel, which is accessed by clicking the More... pushbutton next to the Task popup in the Run Zindo control panel (when the Task is set to TS Optimization).

For information about constraining atoms during transition-state optimization, please see Setting geometry constraints.

Calculation methods

For additional information on these options, please see MSI Quantum Mechanics: Theory & General Methodology (to be published).

Specifying charge and spin

Likewise, if you want to consider a particular spin multiplicity, you need to enter the appropriate value in the Spin Multiplicity entry box in the Zindo Electronic State control panel (which is accessed by clicking the Electronic State... pushbutton in the Run Zindo control panel).

The Zindo Electronic State control panel also allows you to choose between restricted and unrestricted Hartree-Fock calculations.

Molecular environment

You can also include the effects of point charges on the electronic structure of your model. Point charges can be included by adding Cerius² dummy atoms of type Qe to your model and setting their charge to the required value. Do this with the Add Atom control panel, which is accessed by selecting the Build/Add Atom... menu item from the menu bar of the main Visualizer control panel.

Calculating properties

For example, to include quadrupole effects in a solvation model calculation, check the Calculate Quadrupole Moment check box.

The Zindo Properties control panel also provides options for calculating the static and/or dynamic hyperpolarizability of your model (this option is relevant only for an electronic excitations calculation).

SCF options

Specifying output and run options

Several options for limiting the size of a Zindo run are found on the Zindo Run Options control panel, which is accessed by clicking the Options... pushbutton in the Run Zindo control panel.

Analyzing Zindo results

Choosing the Zindo output files to be analyzed

Analyzing charges, dipoles, and forces

Analyzing density of states

Analyzing UV/visible spectra

Analyzing orbitals and densities

Displaying orbitals and densities as surfaces

Mapping a property onto a surface

Editing and displaying slices

Choosing the Zindo output files to be analyzed

Output from the last Zindo job completed in interactive mode during this Cerius² session is automatically selected for analysis. Any graphs produced (UV/visible spectrum) are automatically displayed at the end of the run.

Otherwise, you need to specify which file you want to analyze. Do this with the Zindo File Analysis control panel, which is accessed by selecting the Analyze/Files menu item on the ZINDO card.

Finding your output files

The list box in the Zindo File Analysis control panel shows the Zindo output files (run_name.outzindo) in your current directory. You can browse other directories by using the popup above the list box. If a file named run_name.outzindo corresponding to the desired job is present, the run has ended and the results can be analyzed by selecting that filename from the list box.

Loading the output files

By default, when you select a run_name.outzindo file, the associated Zindo model is automatically loaded into the model display window. If a UV/visible spectrum was produced, it is automatically displayed.

Output file identification and contents

Information about the selected output file is displayed in the Summary of Calculation list box in the Zindo File Analysis control panel after a file is selected.

To display the complete output file in a separate window, click the Examine File action button in the Zindo File Analysis control panel.

Zindo files in Cerius²

The files that are generated by Zindo in the Cerius² interface (and required for data analysis) are:

• run_name.outzindo--Standard output file detailing what happened during the run.

• run_name.inb--Contains details about electronic structure, including molecular orbitals.

• run_name.opt--Additional output from geometry-optimization runs.

By default, the atomic charges in the model are replaced by the Mulliken charges calculated by Zindo. The dipole moment calculated by Zindo is also displayed as a vector in the model window.

To control the loading of atomic charges and the display of the dipole moment vector, use the controls in the Zindo File Analysis Options control panel, which is accessed by clicking the Options... pushbutton on the Zindo File Analysis control panel.

Atomic force vectors

Functionality for controlling the display of atomic force vectors produced from a single-point forces run is also found on the Zindo File Analysis Options control panel.

Analyzing density of states

Total DOS

To calculate and display the total density of states, click the Calculate action button on the Zindo DOS Analysis control panel.

Alpha and beta contributions to DOS

If you are analyzing the results of an unrestricted (UHF) SCF calculation, you can also separately calculate the alpha and/or beta contributions to the density of states or the difference between them (i.e., the spin density of states). To do this, select the appropriate item from the Density of States popup on the Zindo DOS Analysis control panel before clicking the Calculate action button.

Partial DOS

You can also calculate partial densities of states. To do so, check the Calculate Partial DOS check box before clicking the Calculate action button.

To specify the type of projection and which atomic orbitals to include in the partial DOS calculation, use the Zindo Partial DOS Options control panel, which is accessed by clicking the More... pushbutton that appears when the Calculate Partial DOS check box is checked.

Display of graphs

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

Analyzing UV/visible spectra

The Zindo UV/Vis control panel, which is accessed by selecting the Analyze/UV/Vis menu item on the ZINDO card, displays a list of the transitions (i.e., excitations) with their energies and oscillator strengths. Symmetry labels are also shown if symmetry was included in the Zindo calculation.

Selecting and displaying transitions and dipoles

To select an individual transition, highlight it in the list box on the Zindo UV/Vis control panel or pick a point on the graph. To display the transition dipole moment for the selected transition in the model window, check the Display check box in the Zindo UV/Vis control panel (the associated popup should be set to TRANSITION).

Other controls allow you to display the final-state dipole moment and to control the display of these dipole vectors.

Identifying molecular orbitals

Details about the important molecular orbitals involved in the selected transition may be obtained by clicking the Print information on selected transition pushbutton at the bottom of the panel. The information is printed in the text window.

Display of graphs

The Zindo UV/Vis control panel also includes options to control the display of the UV/visible spectrum in the Cerius² graph window: You can set the peak broadening method to Lorentzian or delta and use either energy units (cm^-1 or eV) or wavelength units (nm).

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

Analyzing orbitals and densities

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 (if symmetry was used in the run) 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, use the Zindo Surfaces control panel (Displaying orbitals and densities 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 in the Zindo Orbitals control panel 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 densities

Types of calculations

You can calculate the total electron density or the density of alpha or beta spins or the difference (i.e., spin density) between them. For a restricted open-shell Zindo calculation, the alpha and beta spin densities are calculated assuming that the z component of the total spin is at its maximum.

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

Displaying orbitals and densities as surfaces

The calculated orbitals and densities are ordinarily automatically displayed as surfaces as you create them. However, you would need to use the Zindo 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 Zindo Surfacing Files control panel. Select the desired run_name_property.mbk file and click the LOAD button. You can use the browser popup 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 Zindo Surfaces control panel are satisfactory, you can click the Create New Surface action button (in the Zindo 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 action button 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 Zindo 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 Zindo Property Maps control panel, which is accessed by selecting the Analyze/Property Maps menu item on the ZINDO 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 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 Zindo Surfaces control panel (Displaying orbitals and densities as surfaces).

Click the Add Property action button in the Zindo Property Maps control panel 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 Zindo Property Maps Preferences control panel.

Editing and displaying slices

Finding your surfacing files

If necessary, choose the orbital or density file to be surfaced by clicking the Files... pushbutton to access the Zindo 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 to access directories other than the current one.

Slice specification and display

Once you have loaded an .mbk file and if the default settings in the Zindo Slices control panel are satisfactory, you can click the Create New Slice action button 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 Zindo 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 action button.

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 Zindo Slice Preferences control panel, which contains additional controls that affect slices.

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 Zindo Slices control panel.