| Quantum 1 Modules |
This section includes:
After starting Cerius2, select the QUANTUM 1 card deck and then the ADF card. This gives you access to functionality for setting up and running your ADF job and analyzing the results. The QUANTUM 1 card deck should now look something like:
This section explains how to use the Cerius2 ADF interface and does not discuss the ADF application in any detail. To learn more about ADF, please refer to the ADF 2.3 User's Guide published by the Vrije Universiteit Amsterdam, as well as their website (Other relevant websites).
Types of calculation tasks
Typical ADF calculations
This section describes how to perform the following basic tasks for which ADF is used:
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).
A typical ADF session involves several phases:
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 geometric constraints
What constraints are used for
The ADF program supports partial optimizations, transition-state searches, and potential scans. By partial, we mean that 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 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. The r#, a#, and t# labels are the names of each distance, angle, and torsion variable, respectively. You may change these names in the Variables entry boxes.
Tip
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If the table is blank or only a column of atom numbers is displayed in the Z-matrix list, then no Z-matrix information is available for the model. Z-matrix information can be obtained by using the Z-Matrix editor (see Editing Z-matrices), by saving a job input file for the model (the ADF interface calculates the Z-matrix when generating the file), or from an output file selected for analysis. |
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).
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 Variables 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).
When you click the Find All Symmetry action button, the program automatically assigns Z-matrix variable names to enforce symmetry during the calculation for bond (default), angle, torsion, or x, y, or z (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.
Note
When you click the Remove Symmetry Definitions action button, the symmetry definition(s) are removed from the selected Z-matrix line.
Finding and setting the point-group symmetry for your model
What symmetry is used for
With the ADF Symmetry control panel (which is accessed by selecting the Geometry/Symmetry menu item on the ADF 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 ADF calculation.
If you want only to find the point-group symmetry of all or part of your model:
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.
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 ADF Symmetry control panel.
The symmetry found in this step is automatically used by ADF if possible. Otherwise, the program automatically chooses the most appropriate related symmetry group. If you should want to use some other symmetry group in your calculation, choose an appropriate group from the Symmetry To Use In ADF Run pulldown.
Editing the Z-matrix for your model
Please see Editing Z-matrices, since this functionality is found in all the Quantum 1 applications.
Nondefault job-control conditions are set with the ADF Job Control control panel, which you access by clicking the Job Control menu item on the ADF card.
Optional job control issues
If you intend to run ADF 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
In interactive mode, Cerius2 displays the ADF 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.
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 ADF output).
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
By default, the ADF job runs on the machine on which you are running Cerius2. However, you may, for example, send it to a faster machine.
Click the Hosts arrow in the ADF Job Control control panel to obtain a pulldown listing machines at your site to which you can send the ADF 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).
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 ADF Job Control Options control panel, where you can input a User ID and Password before selecting your host machine.
Tip
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If in doubt about any of the options relating to machines and network configuration at your site, please see your system administrator. |
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
Setting Run Mode to NQS on the ADF Job Control control panel causes a More... pushbutton to appear. This button provides access to the NQS Control control panel, which allows you to set commonly used NQS flags (such as queue name and time and memory limits) and to set the names of the commands used to submit, monitor, and kill NQS jobs on the chosen host.
Choosing the executable and setting memory limits
Special executable for large problems
Click the Options... pushbutton in the ADF Job Control control panel to display the ADF Job Control Options control panel. This panel allows you to set a check box that enables you to run a version of ADF suitable for "large" computational problems.
Total nr. of points : 187645And the logfile contains a message such as:
Nr. of blocks : 62549
Block length : 3
Nr. of dummy points : 2
The Blocklength has become less than 10: the calculation may run very inefficiently. This can be solved by re-installing ADF with a larger Worksize for Reals.
1
<Nov04-97> <16:00:08> Block Length= 3
<Nov04-97> <16:00:08> **** WARNING : very small Blocksize
<Nov04-97> <16:00:08> Real Worksize too small: Increase and re-Install
Dynamic memory allocation
To specify the maximum amount of workspace to be dynamically allocated during the run, click the Run Options... pushbutton in the ADF Run control panel to open the ADF Run Options control panel. The enter a value in the Workspace Limit entry box.
Monitoring and controlling running jobs
The Cerius2 ADF Job Status list box in the ADF Job Control control panel shows the filenames and directories associated with your ADF runs. For each job, the list shows the host name, datafile prefix, status (started, running, or complete for interactive and background jobs, or NQS_SUB, NQS_RUN, or complete for NQS jobs), process or NQS-request ID, and working directory. Click the UPDATE pushbutton to update this list. To remove an item from the list (if that job has completed), click the REMOVE pushbutton.
Tip
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The status of the job is updated only if you click the UPDATE pushbutton, not if you merely close the ADF Job Control control panel or exit the Cerius2 session. |
Transferring files from one machine to another
If it is necessary to move output files from a remote machine to the run directory on your local machine (in some situations they are automatically returned at the end of a job), select the job in the Job Status list in the ADF Job Control control panel and click the TRANSFER pushbutton.
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The remote file system may actually be the same as your local file system (if, for example, it is NFS mounted the same way on both systems). In this case, no transfer of files is necessary. |
To start your ADF run from within the Cerius2 interface, access the ADF Run control panel by selecting the Run menu item on the ADF card.
Setting up and starting calculations
If the default task (single-point energy calculation) and other options are satisfactory, you need only click the RUN pushbutton in the ADF Run control panel to start your run.
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 the job and then proceed to Studying ADF output.
Read this section if you want information on:
For complete lists and descriptions of available calculation tasks, approximation methods, and basis sets, see the ADF documentation.
Geometry optimizations
To optimize the geometry (minimize the energy) of your model, set the Task popup in the ADF Run control panel to Geometry Optimization.
An additional More... pushbutton appears in the ADF Run control panel, next to the Task popup. Clicking it brings up the ADF Geometry Optimization control panel, which you can use to control the optimization iterations.
Transition-state optimizations
To optimize a transition state for your model (i.e., to find a saddle point on the potential energy surface), set the Task popup in the ADF Run control panel to TS Optimization.
A More... pushbutton appears in the ADF Run control panel, next to the Task popup. Clicking it brings up the ADF TS Optimization control panel, which you can use to control the optimization procedure.
Frequency calculations
To calculate the vibrational modes and frequencies of your model, set the Task popup in the ADF Run control panel to Frequency.
A More... pushbutton appears in the ADF Run control panel, next to the Task popup. Clicking it brings up the ADF Frequency control panel, which you can use to control the frequency calculation.
Scanning the potential energy surface
To perform a sequence of related geometry optimizations for your model (e.g., to systematically vary one or more torsion angles and to optimize the geometry at each defined set of torsion angles), set the Task popup in the ADF Run control panel to Scan Potential Surface.
A More... pushbutton appears in the ADF Run control panel, next to the Task popup. Clicking it brings up the ADF Scan control panel, which you can use to control the calculation.
Although you can define many variables, scanning in ADF is one-dimensional. That is, all variables are changed simultaneously; the remaining variables can be optimized or fixed during the scan. Optimization controls are accessed by clicking the Optimization Controls... pushbutton in the ADF Scan control panel, which brings up the ADF Geometry Optimization control panel.
To define the values between which to change the varied coordinates during the scan, select the coordinate from the list box in the ADF Scan control panel and enter the desired start and stop values and the number of steps in the respective entry boxes below the list box.
To remove a definition from the list, select it and click the DELETE pushbutton.
Approximation methods
For any calculation task and whether you choose the nonlocal or local Method in the ADF Run control panel, you can select the associated More... pushbutton (next to the Method popup) to bring up the ADF Method Options control panel so you can examine the default values for related parameters and, if you want, change them.
Basis sets
If you want to use a nondefault basis set, select another one from the Basis Set popup in the ADF Run control panel. You can choose between large- and small-core versions for any of the available basis sets. Large core means that the inner- and outer-core electrons are frozen (i.e., only valence orbitals are allowed to relax); small core means that only the inner-core orbitals are frozen.
For all choices, you may in addition click the associated More... pushbutton (next to the Basis Set popup in the ADF Run control panel) to further refine your basis set assignments, considering each element individually.
Specifying charge and spin
Regardless of the type of calculation you want to perform, if your model is not neutral you need to inform ADF of its charge by entering a value in the Charge entry box in the ADF Run control panel. Enter 0 for a neutral molecule, 1 for a singly charged cation, etc.
SCF options
To change the default values for the parameters that control how SCF is achieved, click the SCF Options... pushbutton in the ADF Run control panel, which gives you access to the ADF SCF Options control panel.
The Integration Accuracy specifies the number of significant digits in which to evaluate the integrals. Recommended values are mentioned in the on-screen help. The accuracy must be in the range 0.5-10.0. The default integration accuracy is task dependent since, for example, higher accuracy is required for transition-state optimization than for single-point energies.
Handling and naming ADF input files
Filenames
To change the default root name for files associated with your run, edit the contents of the File Prefix entry box in the ADF Run control panel. Alternatively, you can select a root name from existing datafiles using controls on the ADF Input File control panel (Saving, editing, and using input files). We refer to this root (or "seed") name as run_name in this documentation.
To change the default title for your run, edit the contents of the Title entry box in the ADF Run control panel. This descriptive text is included in the input and output files associated with your run, to aid in file identification.
For other aspects of file handling, access the ADF Input File control panel by clicking the Files... pushbutton in the ADF Run control panel.
Output from the last ADF 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.
The list box in the ADF 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 file named run_name.t21 is present, the run has ended and the results can be analyzed.
By default, when you SELECT a run_name.t21 file, the associated ADF model is automatically loaded into the model display window, and graphs of any relevant properties present in the file are automatically displayed. You may want to prevent this for some reason (see Loading models and structures for how to load models after loading the run_name.t21 file). To unset these automatic options (before you click the SELECT pushbutton), click the Options... pushbutton in the ADF File Analysis control panel to access the ADF File Analysis Options control panel.
Output file identification and contents
The job identification, run time, title (see Handling and naming ADF input files on setting a nondefault title), and other information are displayed in the Summary of Calculation list box in the ADF File Analysis control panel after you SELECT a file.
Clicking the Examine File action button displays the results of the calculation in text format (run_name.adfout) in a separate window.
The files that are generated and used by ADF in the Cerius2 interface are:
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
When you select the output file (Choosing the ADF output files to be analyzed) from a frequency run (Frequency calculations) for analysis, the IR spectrum is automatically displayed in a graph window, and the lowest normal mode is displayed on the model. Selecting a peak in the graph window automatically shows the corresponding normal mode in the model window.
The ADF Vibration control panel, which is accessed by selecting the Analyze/Vibrations menu item on the ADF card, displays a full list of normal modes and their symmetry labels, frequencies, and IR intensities. As modes are picked in the graph, the corresponding mode in the control panel is highlighted.
The Display Selected Mode section of the ADF Vibration control panel controls the Cerius2 model window.
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
Orbitals, densities, and potentials are scalar functions that are defined in the continuous 3D space surrounding the model. In practice, they are evaluated on a fine grid of points that completely encompass the model. This produces a large amount of information, which is typically visualized as an isosurface; that is, the constant-value points surrounding the model are connected so as to form a surface. The data can also be visualized as slices showing the values of the function on a 2D plane cutting through the model.
Calculating orbitals
You can calculate (and display, see also Displaying orbitals, densities, and potentials as surfaces) the molecular orbitals, appropriately oriented with respect to the displayed model. To do this, use the ADF Orbitals control panel, which is accessed by selecting the Analyze/Orbitals menu item on the ADF card.
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.
To display more than one calculated orbital simultaneously, use the ADF Surfaces control panel (Displaying orbitals, densities, and potentials as surfaces).
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.
Click the Preferences... pushbutton in the ADF 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 the electron density
You can calculate (and display, see also Displaying orbitals, densities, and potentials as surfaces) the electron density, appropriately oriented with respect to the displayed model. To do this, use the ADF Density control panel, which is accessed by selecting the Analyze/Density menu item on the ADF card.
You can calculate the electron density from:
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).
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 calculate (and display, see also Displaying orbitals, densities, and potentials as surfaces) a representation of the electrostatic potential, appropriately oriented with respect to the displayed model. To do this, use the ADF Potential control panel, which is accessed by selecting the Analyze/Potential menu item on the ADF card.
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).
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
When you need to use this control panel
Finding your surfacing files
If you want to display a currently undisplayed surface, use the Files... pushbutton to access the ADF Surfacing Files control panel. Select the desired run_name_property.t41 file and click the LOAD button. You can use the browser popup to access directories other than the current one.
Once you have a surfacing file loaded and if the default settings in the ADF Surfaces control panel are satisfactory, you can click the Create New Surface action button (in the ADF 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.
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.
Specify a property to be mapped by choosing the appropriate run_name_property.t41 file from the list box and clicking the LOAD pushbutton. You can use the browser popup to access directories other than the current one.
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 ADF Surfaces control panel (Displaying orbitals, densities, and potentials as surfaces).
Click the Add Property action button in the ADF Property Maps control panel to display the property map.
Editing and displaying slices
To edit and display a 2D slice through the 3D grid of orbitals, density, or potential for your model, use the ADF Slices control panel, which is accessed by selecting the Analyze/Slices menu item on the ADF card.
If necessary, choose the orbital, density, or potential file to be surfaced by clicking the Files... pushbutton to access the ADF Surfacing Files control panel (Finding your surfacing files). Select the appropriate run_name_property.t41 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 a .t41 file and if the default settings in the ADF Slices control panel are satisfactory, you can click the Create New Slice action button (in the ADF Slices control panel) to create and display a selected slice for your model.
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.
Clicking the More Editing Options... pushbutton gives you access to the ADF Slice Preferences control panel, which contains additional controls that affect slices.