| |
|
|
|
Jaguar has an X Window System (or "X") graphical interface in order to simplify the submission of jobs. You can run the interface and the actual Jaguar calculation on different machines. In addition, as with any X program, the machine running the interface (the X client) does not need to be the machine or terminal which displays the interface (the X server). Thus, from any X terminal or workstation running X, you can log onto a machine where the Jaguar interface is installed, and submit jobs on yet another machine on which the Jaguar main executables are installed.
Without the graphical interface, you would have to create input files with particular formats in order to run Jaguar. The graphical interface creates these input files for you, based on the information you give it, and submits the job, thus freeing you from learning the input format and program sequences and instead allowing you to concentrate on the science involved. The interface also provides a convenient method of incorporating other data, such as molecular geometries produced by modeling packages.
Try the sample calculation in Section 2.1 in order to get some experience with running Jaguar and to make sure your system is properly set up. If you have problems starting or using the interface or performing the calculation, you may be able to solve them using the troubleshooting suggestions in section 10.1. If any problems persist, please contact your system manager or Schrödinger, Inc.
The rest of this chapter describes the basics of using the interface, including inputting a geometry and submitting a job. The footnotes in this chapter describe Jaguar input file keywords and sections that correspond to particular interface settings. If you are working from the interface, you can ignore these footnotes, but you may later find them helpful if you decide to use input files to submit jobs without using the interface or if you want to edit keywords directly by using the Edit Job window described in Section 2.8 under Editing Input.
The brief sample calculation suggested in this section will only work if Jaguar has already been correctly installed. If the calculation does not work, try the suggestions in section 10.1, or see your system manager or the person who installed Jaguar at your site. Please contact Schrödinger if you cannot resolve the installation problems.
First, from a terminal or workstation running the X Window System, log into a machine where the Jaguar interface is installed. From a directory where you want the Jaguar input and output files for the sample job to appear, enter the command
The Jaguar main window and the Display window should appear. If the windows appear as outlines, or if you wish to alter them, you can use the mouse to position and size them. The Jaguar main window contains buttons that let you access various interface features. When you input a molecular structure, the Display window will show it. For now, if you want to, you can temporarily remove the Display window by dragging the mouse over its File menu and releasing it over the Close option.
Next, you should input a molecular geometry (structure). From the Jaguar main window, click on the button marked Edit near the Geometry heading. The Edit Geometry window should open. Move the mouse into the blank panel in the middle of the window, and enter the following lines, which will provide Jaguar with the geometry of a water molecule:
The labels begin with element symbols, `O' and `H.' Extra characters, a `1' and a `2,' have been added to the hydrogen labels to distinguish between the atoms. The next three numbers on each line give the x, y, and z Cartesian coordinates of the atoms in the geometry, in Angstroms. The number of spacing characters does not matter, as long as you use at least one to separate different items. Make sure to hit <return> at the end of each line, however. When you have finished entering the water geometry, click File in the upper left corner of the Edit Geometry window and select Save to save your changes, then click File again, selecting Close to close the Edit Geometry window.
The molecular structure should now be shown in the Display window. If you closed this window earlier, you can reopen it by clicking on the Display button, which appears near the Geometry heading in the main interface window. Section 2.5 discusses the Display feature in more detail.
Give your job a name by entering a single word in the Job Name box in the main Jaguar window. The names of the input, output, and log files for your job will depend on your entry: the Jaguar input file will be named jobname.in, the output file will be named jobname.out, and the log file will be named jobname.log, where jobname is your Job Name entry.
If you want to, you can now use the buttons in the bottom panel of the main Jaguar window to open other windows (the DFT window, for example), which you can use to set up the calculation you want to perform. These possible selections are described in Chapter 3 of this manual. If you don't make any non-default settings in these windows, Jaguar will run a single-point Hartree-Fock calculations ("single-point" means using only the molecular structure in the input, without optimizing that structure). Any time you want to retract any of the settings you have made since pulling up a window, you can hit the Cancel button at the bottom of the window. If, instead, you hit OK, the settings are registered in whatever way is appropriate for that window.
You could also now use the buttons near the Output heading to make selections requesting extra output for the job, but we suggest running this trial calculation without requesting any non-default output. Chapter 5 of this manual describes the output options.
When you have finished setting up your calculation, click on the Run button near the Jobs heading in the main interface window. The Run window will appear. The calculation host, the machine upon which the job will actually run, is listed at the top of the window. If Jaguar is installed on more than one machine at your site, you should be able to change the choice of calculation host by clicking on the host name shown and dragging the mouse to another name in the list. The Temp directory selection is a directory on the calculation host which will be used during the calculation to store temporary files. You should check from your X window to make sure the temp directory already exists on the calculation host; if it does not, you should create it.
The Run window settings should now be fine as they are, so you can start running the job by clicking on the RUN button at the bottom of the window. (If you do not want to perform the sample run using the selections shown, you can find more information on the Run window in Section 2.7. Section 6.1 explains how to change which options are presented in the Run window.)
After you have started running the job by clicking RUN in the Run window, another window will appear summarizing information about the job and where it is running. After you click the OK button in this window, it and the Run window will close and another window will open, possibly showing the Jaguar logo at first. This new window, the Job Status window, will automatically update to show your job's progress. As each separate program in the Jaguar code finishes running, its completion is noted in the window. When the program scf is running, the Job Status window also displays the energy and other data of each iteration. See section 5.8 on the log file if you wish to see more information on this data. You can close the Job Status window by clicking on the Close button at the upper right of the window; if you later want to reopen it, you can do so by clicking the Check button, which appears in the main window near the Jobs heading.
When the job finishes running, its output file will be copied to the directory where you started the interface. The output file's name always begins with the same characters as the job name you entered earlier, and ends with the extension ".out." For instance, if you entered the job name "h2o," the output file is called "h2o.out." You can look at the output file from your X window. If you want to exit the Jaguar interface, you can select the Quit button from near the top of the main interface window.
If you are satisfied with the results of this sample run, you should continue reading this chapter to learn more about using the interface. If you were unable to run the sample calculation, try following the troubleshooting suggestions in section 10.1. If you wish to change the options shown in the Run window, you can read section 6.1 for a description of how to do so, although you should probably wait until you have read the rest of this chapter and learned more about the interface.
After you have started the interface by typing "jaguar" or "jaguar &" at a UNIX prompt on an X terminal or workstation, the first thing you will probably want to do for any Jaguar calculation is to input a molecular structure (geometry).1 You can either use the interface to read in a file in one of several types of formats, as described in Section 2.4, or you can input and edit geometry coordinates yourself through the interface. This section describes how to create or edit a geometry and the input formats for Cartesian and Zmatrix geometries.
The geometry input also controls constraints of bond lengths or angles for geometry optimization and allows you to specify atoms for a counterpoise calculation. These aspects of geometry input are explained in this section as well.
To input or edit a geometry by hand (or to just look at the coordinates), select Edit from near the Geometry heading. The Edit window, a text window, will appear. If you have not yet used the interface to read in a geometry file, you may enter the geometry there, either by cutting and pasting from another text window, as described in your X documentation, or by simply typing in the geometry. You can also use the Edit window to change a geometry which you input earlier.
Your geometry can be in Cartesian (x,y,z) coordinates or in Zmatrix format. These formats are described below. The Cut, Copy, and Paste options in the Edit menu, which you can access by clicking on Edit (in the bar near the top of the window), may be useful to you for geometry input. To remove the entire geometry input at any point, click on Edit and select Clear.
You can also alter the geometry input by using the Zmatrix pull-down window. You can use the Convert to Zmatrix and Convert to Cartesians options to switch between Zmatrix format and Cartesian format. (These formats are described in more detail later in this section.) The option Assign standard atom labels converts all atom labels to the form El#, where El is the standard elemental symbol (Fe for iron, for instance) and # is a number indicating the line of the structure input on which the atom's coordinates are set (1 for the first atom, 2 for the second, and so on).
To save or remove your changes, or to close the Edit window, use the File pull-down menu. The Save option registers the changed geometry but leaves the window open. If you select Close, the window will close; if there are any unsaved changes, you will be asked if you want to save them or not. The Revert option lets you return to the original geometry (if any) in the window when you opened it, and Cancel closes the window without retaining any changes you have made from within it since you opened it.
The options in the Structure pull-down menu, and the Use initial geometry Zmatrix option in the Zmatrix pull-down menu, are useful for certain types of transition state optimization jobs, but not for other Jaguar jobs. Therefore, they will be described in section 4.3, which explains special options for transition state optimizations.
Please note that when you are editing a geometry and have not yet saved it, if you try to run a job or save an input file by hitting RUN in the Run window or OK in the Save window, you will get a warning about the open editing box. If you ignore the warning and proceed, the last geometry saved will be used, instead of the edited version.
The Cartesian geometry input format can simply consist of a list of atom labels and the atomic coordinates in Angstroms in Cartesian (x,y,z) form. For example, the input
describes a water molecule. Each atomic label must start with the one- or two-letter elemental symbol given in the periodic table and may be followed by additional alphanumeric characters, as long as the atomic label has four or fewer characters and the atomic symbol remains clear-for instance, "HE5" would be interpreted as helium atom "5", not hydrogen atom "E5". Either lowercase or uppercase characters are allowed in atom labels. The coordinates may be specified in any valid C format, but each line of the geometry input should contain 80 characters or fewer.
Coordinates can also be specified as variables whose values are set beneath the list of atomic coordinates. This feature makes it easier to input equal values and also makes it possible to keep several atoms within the same plane during a geometry optimization even while the coordinates change from their original values.
To use variables, type the variable name (zcoor, for instance) where you would normally type the corresponding numerical value for each relevant coordinate. You can put a + or - sign immediately before any variable, and you may use several variables if you want to. When you have entered the full geometry, add one or more lines setting the variables.
For instance, the Cartesian input
describes the same water coordinates as the previous Cartesian input example. If you performed a geometry optimization using this input structure, its ycoor and zcoor values might change, but their values for one hydrogen atom would always be the same as those for the other hydrogen atom, so the H atoms in the final geometry would be in the same xy plane as each other.
At times, the Edit window may list the variable settings on several lines, preceded by a line saying "Zvariables". This format is just another way the interface has of separating the variable settings from the atomic coordinates.
One final note: whenever Cartesian input with variables is used for an optimization, Jaguar performs the optimization using Cartesian coordinates rather than generating redundant internal coordinates, and the optimization does not make use of molecular symmetry.
As described in the subsection Variables in Cartesian Input, you can force certain Cartesian coordinates to remain the same as each other during an optimization by using variables. You can also constrain any geometry in Cartesian format so that some of the Cartesian coordinates you specify are held fixed during a geometry optimization by adding a `#' sign after the appropriate coordinate or coordinates. For example, if you added constraints to the zcoor variables in the water input example given above, as listed here:
and performed a geometry optimization on this molecule, the H atoms would only be allowed to move within the xy plane in which they started.
If frozen Cartesian coordinates are included in the input for an optimization, Jaguar uses Cartesian coordinates for the optimization rather than generating redundant internal coordinates, and the optimization does not make use of molecular symmetry.
Like Cartesian input geometries, Zmatrix-format geometries should specify atoms by atom labels that begin with the one- or two-letter elemental symbol given in the periodic table, in either uppercase or lowercase characters. The elemental symbol may be followed by additional characters, as long as the atom label has four or fewer characters and the elemental symbol is still clear. Geometry input files in Zmatrix form can also contain comment lines beginning with pound signs (#), although comments should not be included in input entered in the interface's Edit window.
The first line of the Zmatrix should contain only one item: the atom label for the first atom, which could be, for instance,
This atom (nitrogen, in this example) will be placed at the origin. The second line contains, in order, the atom label for atom 2, the identifier of atom 1, and the distance between atoms 1 and 2. Identifiers can either be atom labels or atom numbers, which correspond to the order the coordinates are listed (1 for the first atom, 5 for the fifth atom listed, and so on); for a second atom in this file, therefore, the identifier for the first atom could be either "N1" or "1". The second atom will be placed along the positive zaxis. For example,
places the carbon atom (C2) at (0.0, 0.0, 1.4589) in Cartesian coordinates. Distances between atoms must be positive.
The third line is made up of five items: the atom label for atom 3, the atom label of one of the previous atoms, the distance between atom 3 and this previous atom, the identifier of the other previous atom, and the angle defined by the three atoms. In this example:
the final line states that atoms C3 and C2 are separated by 1.5203 Å and that the C3-C2-N1 bond angle is 115.32 degrees. The bond angle must be between 0 and 180 degrees, inclusive. The third atom (C3 in this case) is placed in the xz plane (positive x). Clearly, three different atoms must be listed in this line.
Finally, the fourth line contains a third atom identifier of another previously defined atom, and a torsional angle. Consider this example:
The last line states that atoms O4 and C3 are 1.2036 units apart, that the O4-C3-C2 bond angle is 126.28 degrees, and that the torsional angle defined by O4-C3-C2-N1 is 150.0 degrees. This information is sufficient to uniquely determine a position for O4. If the first three atoms in the torsional angle definition were linear or very nearly linear, O4's position would be poorly defined, however. You should avoid defining torsional angles relative to three colinear (or nearly colinear) angles.
The torsional angle is best understood by "looking down" the "bond" between atoms C3 and C2 (looking from C3 towards C2). In the near field, the C3-O4 bond forms a ray in some direction perpendicular to the C3-C2 axis (ignore the component of C3-O4 along the C3-C2 direction). In the far field, the C2-N1 bond forms another ray perpendicular to the C2-C3 axis. The magnitude of the torsional angle is determined to be the angle between these rays (in either direction) chosen such that it is between 0 and 180 degrees. Its sign is positive if this angle is traced clockwise from the ray in the near field to the ray in the far field, and negative if the angle is traced counterclockwise from the ray in the near field to the ray in the far field.
Alternatively, the fourth atom's position can be specified using a second bond angle instead of a torsional angle, if ` 1' or ` -1' is added onto the end of the line. In these cases, the last angle specified is assumed to be between the first, second, and fourth atoms mentioned on the line (above, the O4-C3-N1 angle). Since there are two possible positions for the atom which meet the angle specifications, the position is defined by the vector product r12·(r23 x r24), where rij is defined as the vector pointing from the jth atom listed on that line to the ith atom listed. If this vector product is positive, the value at the end of the line should be ` 1'; otherwise, the value should be ` -1'. You should use torsional angles instead of second bond angles if you want to perform a constrained geometry optimization, however, since Jaguar cannot interpret any constraints on bond lengths or angles for geometries containing second bond angles.
All additional lines of the Zmatrix should have the same form as the fourth line. The complete Zmatrix for the example molecule (the 150° conformation of glycine) in Zmatrix form is
Bond lengths or angles can also be specified as variables which are set beneath the Zmatrix itself. This feature makes it easier to input equal values (such as C-H bond lengths or H-C-H bond angles for methane) and also makes it possible to keep several distances or angles the same as each other during an optimization even while they change from their original values.
To use variables, type the variable name (chbond, for instance) where you would normally type the corresponding number (such as a C-H bond length in Å) for each relevant occurrence of that number. You can put a + or - sign immediately before any variable, and you may use several variables if you want to. When you have entered the full Zmatrix, add a line at the bottom setting the variables, such as
At times, the Edit window may list the variable settings on several lines, preceded by a line saying "Zvariables". This format is just another way the interface has of separating the variable settings from the atomic coordinates.
Sometimes, defining dummy atoms can make the assignment of bond lengths and angles easier. Dummy atoms are simply a way of describing a point in space in the format used for an atomic coordinate while avoiding actually placing an atom at that point. Dummy atoms' "elements" are identified as `X', `x', or `Du'. An example of the use of a dummy atom for CH3OH input follows:
You can edit any geometry in Zmatrix format so that the bond lengths or angles you specify are held fixed during a geometry optimization by adding a `#' sign after the appropriate coordinate or coordinates. For example, to fix the HOH bond angle of water to be 106.0 degrees, you could input the following Zmatrix:
If you performed a geometry optimization on this input geometry, the bond angle would remain frozen at 106° throughout the optimization, although the bond lengths would vary. For more details, please see section 4.2, which describes how to set up constraints for optimizations.
If you want to constrain two quantities to be the same as each other during a geometry optimization, use variables in Zmatrix input. See Variables and Dummy Atoms in ZMatrix Input earlier in this section for help. To freeze any variables to remain unchanged during an optimization, add a `#' sign to the end of the variable setting in the line at the end of the geometry input that defines the variables, as in this example, where the C-H bond is frozen at 1.09 Å:
You should not make any constraint changes from the Edit or Optimization windows while both windows are open, because the Optimization settings could conflict with your hand-assigned constraints.
To perform counterpoise calculations, you can input a Cartesian or Zmatrix geometry that includes counterpoise atoms, which have the usual basis functions for that element but include no nuclei or electrons. These calculations can be useful for obtaining an estimate of basis set superposition error (BSSE). For LMP2 calculations (which are described in section 3.2), the LMP2 correction is already designed to avoid basis set superposition error, so we advise computing and adding on only the Hartree-Fock counterpoise correction term.
If you place an at sign (`@') after an atom's label, that atom will be treated as a counterpoise atom. For example, to place sodium basis functions at the Cartesian coordinates (0.0, 0.0, 1.0), you could include the following line in an input file:
Counterpoise atoms can also be included in Zmatrix format geometries by including at signs at the end of atom labels.
If you are optimizing a molecular structure to obtain a transition state, you may wish to refine the Hessian used for the job. section 4.3 explains the methods used for transition state optimizations, including Hessian refinement; this subsection explains only how to edit your input to specify particular coordinates for Hessian refinement. (Whether or not you refine particular coordinates, you can specify a certain number of the lowest eigenvectors of the Hessian for refinement, as described in section 4.3 in the subsection Refinement of the Initial Hessian-the Hessian can be refined in both ways in the same job.)
If you put an asterisk (`*') after a coordinate value, Jaguar will compute the gradient of the energy both at the original geometry and at a geometry for which the asterisk-marked coordinate has been changed slightly, and will use the results to refine the initial Hessian to be used for the optimization. To request refinement of a coordinate whose value is set using a variable, add an asterisk to the end of the variable setting in the line at the end of the geometry input that defines the variables. For instance, if you entered either of the following two input geometries in the Edit window:
they would have the same effect: a job from either input that included Hessian refinement would use both O-H bonds and the H-O-H angle in the refinement.
Molecular symmetry or the use of variables, either of which may constrain several coordinate values to be equal to each other, can reduce the number of coordinates actually used for refinement. For example, for the second water input example shown above, only two coordinates will actually be refined (the O-H bond distance, which is the same for both bonds, and the H-O-H angle); the same would be true for the first example if molecular symmetry is used for the job.
The State window, whose button appears near the Geometry heading in the main interface window, contains the settings describing the molecular charge and the spin multiplicity of the input molecule. If the molecule you are studying is an anion or cation, you should set the net molecular charge, whose default is 0, by clicking in its box in the State window and editing the value.2 The spin multiplicity default is singlet, but you can change it to anything up to octet by clicking in the Spin Multiplicity box and making another selection from the option menu.3 The spin multiplicity is also shown numerically. If the molecular charge and spin multiplicity settings you make do not agree for your molecular input-for instance, if your molecule has an odd number of electrons and you leave the spin multiplicity set to singlet-Jaguar warns you to reset one or the other.
If you already have files containing geometries (either with or without a description of a calculation to perform), you can read them into the Jaguar interface's Read window, which is accessed from the Read button in the top row of the main Jaguar window. The interface can read Jaguar input files generated previously using the Save or Run options described in Section 2.7 or files generated from other programs.
This section describes the types of files which can be read in to the interface and explains how to read in these input files. Because files in many format types can be used only to provide geometries (not calculation settings), the first subsection below explains how to read in a geometry from a file without reading any calculation settings from that file. The next subsection explains how for some files (Jaguar input files in particular), you can also read in calculation settings.
From the Jaguar interface's Read window, you can read a geometry (molecular structure) from a Jaguar input file or from any file of an input type recognized by the program Babel [24]. After reading in the geometry, you can then use the interface to set up Jaguar calculation options for the geometry in question.
When you read in a geometry from a file, Jaguar will also try to obtain information on the molecular charge. Therefore, for any of the file reading techniques described here, the molecular charge may be updated from information in the input file. However, for all non-Jaguar input files, we recommend that you double-check the molecular charge setting in the State window after reading in the geometry.
To read in a file, the interface must know what type of file it is, what directory the file is in, and what the file is called. The default directory searched is the directory where you started the interface, so you may find it easiest to start the interface from the directory containing the relevant input file or files.
When you first select Read, a window appears. This Read window includes information on the current directory whose files are listed, and lists all Jaguar input files in that directory, if any. A Jaguar input file is the standard input for Jaguar jobs, and contains the various settings for the job. Jaguar input files are generated at the beginning and end of runs, or when you use the Save window to save the input without running a job.
If you want to read in the geometry from a file that is not a Jaguar input file, first click on the File Format option menu and select the appropriate file format from the list. Next, set the Read as option menu to Geometry (new job) if you want to make sure all calculation options are set to their defaults (until you change them in other windows of the interface), or set Read as to Initial geometry if you want to leave intact all calculation settings made from the interface or read into it from previous input files.
If you want to read in the geometry but not the calculation settings from a Jaguar input file, you do not need to alter the setting marked File Format immediately after opening the Read window for the first time, because it is set to Jaguar input by default. However, you must alter the setting marked Read as from its default, Geometry and settings (this default means the interface will read in calculation settings also, as discussed below in the subsection Reading In Both Geometries and Job Settings). Change the Read as setting to Geometry (new job) if you want to remove any calculation settings made earlier from the interface or by reading in a previous file's calculation settings. If, instead, you want to leave all calculation settings made from the interface or read into it intact, but change the geometry, change the Read as setting to Initial geometry.
At this point, if the file you wish to read in already appears in the list in the Files box on the right, you can select it by clicking on it. The file you have chosen will then be listed in the Selection bar, and when you click on OK, the interface will read in the geometry from the file.
If the file does not appear in the list, you need to tell the interface where to look for it. The Filter bar at the top of the window indicates what directory and what name type the interface has searched to generate the list of possibilities in the Files box. A `*' is a wild card character, meaning it can represent any text. The word after the last slash is the file name the interface will search for, while the rest of the entry is the directory in which it will search. You can edit the Filter bar by clicking in it and typing, or you can change it by selecting another directory from the Directories box. (If you want to go up one directory, you should select the <current directory>/.. option, where <current directory> indicates the appropriate directory name.)
Once you have altered the Filter bar properly, you can list files meeting that description by clicking on the Filter button at the bottom of the window. As described above, if the file you want to read in shows up in the Files box, simply select it by clicking on its name, then hit OK to read it in.
If you know from the start what directory and file name you wish to select, and do not need to see a list of options in the Files window, you can also bypass the Filter by editing the Selection bar by hand at any point, changing the File Format and Read as settings, if necessary, and hitting OK to read in the specified file.
After you read in a file, you can use other windows to change settings before actually running the job. Most of the rest of this manual concerns calculation options for Jaguar and how to set up Jaguar jobs.
The only file types for which Jaguar can read any calculation information besides the geometry and molecular charge are Jaguar input files, Gaussian [23] input files, and BIOGRAF [21] Hessian files. The procedure for reading in the geometry and calculation settings from a file of one of these types is exactly like that described above in the subsection Reading a Geometry, But No Calculation Settings, except that the Read as option menu in the Read window should be set to Geometry and settings.
When you read the geometry and settings in a Jaguar or Gaussian input file into the interface, the interface updates to show the geometry and all the calculation information in the input file. If you read in a Jaguar input file whose sections contain non-default settings not found in the interface, as described in Chapter 8, all calculation settings will still be read in.
In the Read window, two options in the Read as option menu, Geometry 2 and Geometry 3, are designed for input only for certain types of transition state optimizations. Therefore, they will be described in section 4.3, which explains special options for transition state optimizations.
Several different versions of the Jaguar interface exist in order to support different types of graphics hardware for viewing the molecular structure in the interface's Display window. Jaguar will automatically choose which version of the Jaguar interface to run, depending on the machine type and operating system on your interface host (X client) and display host (X server). The interface executables have the names and uses shown in Table 2.5.1.
The jaguar.mesa interface uses software rendering which is displayed via X11, a process which is significantly slower than the hardware rendering for OpenGL. The advantage of jaguar.mesa is that it works on most X terminals or workstations. If you use an 8-bit color console with this version, there may be colormap flashing as your input focus switches to or from the Display window. The flashing results because private colormap must be used for the rendering to insure a reasonable display. When flashing occurs, some of the buttons on the interface and possibly some of the atom labels may be difficult to read.
If your display supports an 8-bit TrueColor visual (but not 24-bit), the graphics may look better if you use an 8-bit color visual instead. (The available visuals may be listed using the xdpyinfo command.) In this case, try the command
from a display host window to see if it improves the image.
When you start the interface, or when you select the Display button near the Geometry heading, a display window will appear. You may need to resize the window using the mouse. If you have provided a molecular structure, a graphical display of it should be visible.
For the Display window, the positive z axis points out, the x axis runs from left (negative) to right (positive) in the window plane, and the y axis runs from the bottom (negative) to the top (positive) of the window.
The display is controlled by the mouse. Note that changing the view of the molecule shown on the display does not affect the geometry used by the rest of Jaguar. The mouse commands and their effects on the graphical display are shown in Table 2.5.2.
When you translate the molecule in the z direction, the display actually shows only a slice of the molecule containing a certain range of z values. This option may be useful if, for instance, you want to look at a set of atoms at the "back" of a molecule-by translating the molecule in the z direction, you could make the atoms at the front invisible to the display. Similarly, the last option in the table allows you to vary the thickness in the z direction of the layer of molecules visible.
If you hold down the Ctrl key before pressing a mouse button, you may end up accidentally resizing the window, depending on your window manager. If this problem occurs, try to make sure to press the mouse button first when entering the commands described.
You can display the molecule in several different styles by choosing the appropriate option under the Display pull-down menu in the Display window: Ball & Stick, GVB Pair, Lines, or Space-filling (spheres only). For the Display options involving spheres (that is, all of them except the Lines option), the atomic radii are chosen according to the Spheres selection under the Options pull-down menu, as described below.
The "sticks" in the ball and stick display are generally from the Jaguar interface's simple calculation of connectivity, where all "bonds" found are displayed as solid cylinders. If, however, the input file is a BIOGRAF .bgf or MacroModel .dat file that contains bonding information, the interface will use this information in the ball and stick display, representing single bonds as solid cylinders, double bonds as two-piece cylinders (with one thin band in the middle), and triple bonds as three-piece cylinders (with two thin bands).
For the GVB pair display, single GVB pairs are displayed as cylinders and multiple pairs as divided cylinders. Lone pairs are currently not displayed. Atoms which are close enough to be considered connected, yet are not GVB pairs, are connected by thin lines called bond lines. This display option can be helpful if you set GVB pairs from within the interface, as described in section 3.3. As pairs are added from the GVB window, they appear in the display.
You can choose to have atom labels appear in the display by making a selection other than none from the Display window's Labels pull-down menu. Counterpoise atoms are shown with an `@' symbol, as they are listed in the geometry. If you choose number, the atoms are labeled with the numbers representing the order they appear in the molecular geometry input, while element shows their periodic table labels. To see both at once, you can select element + number. To see the labels you provided in the geometry input, you can choose user label.
You may make additional adjustments to the display under the Display window's Options pull-down menu. First, you can set the size of the spheres used by several of the Display options.
The Resolution window lets you determine the appearance and smoothness of the spheres with the Sphere depth slide bar. This window also lets you determine the number of sides on any cylinder used to show bonds, with the Cylinder sides slide bar, and the quality of the display shown as you rotate the molecule with the mouse, which is set in the Rotation mode option menu. Generally, the higher the display quality, the more slowly the display will respond to your commands; the connectivity or quick render rotation mode options often lead to much faster rotations than the standard render option.
The Colors window under the display window's Options pull-down menu lets you set the lighting effect on the spheres, the Specular highlights, on or off. You can set the Atom label option menu to show atom labels in colors which are complementary to the color of the atoms they appear on, the same colors as the atoms they appear on, or in the text color, which is set later. The Bond line option menu lets you pick whether the bond lines, such as those appearing in connectivity displays, are portrayed using the atom colors of each atom in the bond or the line color set later. The Text slide bars allow you to determine the relative contributions of red, green, and blue to the text color mentioned above. If you set all three slide bars to .00, you will get black text; if you set them all to 1.00, you will get white text. Similarly, the line color, which appears in the bands on the cylinders representing multiple bonds and possibly in bond lines as well (see above), can be set with the Line slide bars. The color of the window background appearing behind the molecule can be set with the Background slide bars.
The final selections found under the Options pull-down menu in the display are Realign Geometry and Recenter Geometry. Realign Geometry reverses any rotations and returns the molecular coordinates to their original values, the coordinates used by the rest of Jaguar. Recenter Geometry moves the input structure back to the middle of the window, but leaves any rotations you have made intact.
As will be described later in section 4.3, for certain kinds of transition state optimization jobs, you need to input more than one structure. The Structure pull-down menu in the Display window lets you select which such structure is displayed. The structure will also be identified in the upper-left corner of the Display window.
The Close option, found in the File pull-down menu, allows you to exit the display window, saving any settings you have made there for any future displays of that geometry input, but leaving the molecular coordinates used by the rest of Jaguar intact.
When you click the "Clean up geometry" button on the Jaguar Cleanup panel, Jaguar first performs a quick charge-equilibration (Qeq) calculation to obtain partial charges for all atoms in the system, and then uses those charges in an energy minimization which is based on Goddard and Rappe's Universal Force Field (UFF). Because UFF includes parameters for all elements in the periodic table, it can be used for inorganic complexes as well as organic compounds.
During the UFF minimization, the label on the "Clean up geometry" button changes to "Halt cleanup." You can click this button at any time to cut short the minimization. After the cleanup is finished, Jaguar will reanalyze the symmetry of the molecule and display the point group of the minimized structure. If you're satisfied with the results of the cleanup procedure, you can click the "OK" button to accept the final geometry.
Clicking the "Cancel" button will throw away the cleaned-up geometry and revert to the geometry you had before opening the Cleanup panel.
The convergence criteria for the cleanup minimization are deliberately set fairly loose, so that even large systems can be optimized interactively. In addition, a time limit is imposed on the minimization to keep it from running excessively long. As a result, you may find that the geometry continues to change if you perform a second cleanup minimization on a "cleaned up" structure.
UFF cleanup minimization is useful for quickly bringing a distorted molecule back into the neighborhood of the ab initio minimum-energy geometry, in preparation for full ab initio geometry optimization. However, it is no substitute for ab initio optimization because UFF is a relatively simple force field. It is probably a good idea to perform a cleanup minimization after creating a new molecule with the builder. On the other hand, performing a cleanup minimization on molecule that has already undergone ab initio minimization is likely to move the molecule away from the ab initio minimum. Also, you should be careful to avoid "cleaning up" a structure that has been prepared as an initial guess for a transition-state search.
By default, Jaguar takes advantage of molecular symmetry4 whenever possible, in order to obtain CPU savings. Both Abelian and non-Abelian point groups are recognized (a particular strength of Jaguar).
If you wish, you can turn the use of symmetry off5 by using the Symmetry pop-up menu in the Methods window of the interface. For some calculations, including GVB, LMP2, GVB-LMP2, and GVB-RCI calculations and calculations of IR intensities or hyperpolarizabilities, symmetry is not yet implemented and will be disabled automatically for the job.
Generally, you should symmetrize the geometry if you plan on using symmetry in the calculation itself. Otherwise, the input coordinates may not be accurate enough for all possible symmetry to be recognized.
The Symmetrize window allows you to apply a symmetrization procedure to an input geometry in order to assure that calculations take full advantage of molecular symmetry. You can access the Symmetrize window by clicking on the Symm. button in the main interface window near the Geometry heading.
Since an input geometry must have a certain orientation and sufficient precision in the coordinates before it can be symmetrized, the coordinates must be changed in several ways to generate a new, symmetrized geometry. First, the molecule is translated so that its center of mass is located at the origin of the coordinate system. Second, it is rotated so that it is aligned along the symmetry axes. Third, minor adjustments are made to the coordinates so that the molecule more precisely conforms to the point group.
Note that if you are comparing calculations from geometries which differ only slightly, you must use caution when symmetrizing coordinates. For example, a small symmetry-breaking change can be removed if its magnitude is smaller than the tolerance you have set, which establishes what changes are acceptable. In this case, you should inspect the symmetrized coordinates in the Edit window to insure that symmetrizing had the desired effect and did not wipe out any important information about the molecular geometry.
The tolerance is, roughly, the maximum distance any atom is allowed to be moved while the program searches for the highest possible symmetry for the molecule. Its units are the same as those of the input geometry. A large tolerance yields the highest symmetry but may cause the coordinates to be changed significantly. A small tolerance may yield a lower symmetry, since the coordinates cannot be moved as much. The main Jaguar programs use a small tolerance (1.0 x 106 bohr), which should result in molecular energy changes of 1 microHartree or less. You may wish to use a higher tolerance than that when symmetrizing the geometry.
Selecting Find point group will cause the program to find the molecule's point group for the tolerance indicated and display it near the heading Point Group. The geometry does not actually change until you select Symmetrize at the bottom of the window, as described below, so you can experiment with different tolerances to see what symmetry would be applied for each, if you are careful not to hit Symmetrize
Selecting Symmetrize will generally change the molecular geometry to a more symmetrical or differently oriented geometry. If you changed it by mistake, you will need to reenter the geometry as described in Section 2.2 and Section 2.4. If you are satisfied that the point group shown is the one you wish to apply to the molecule, you should select Symmetrize. If you are not sure, but wish to apply the point group, examine the resulting coordinates, and then decide whether to use them, you should make sure the original geometry is stored in a file so you can read it in again if necessary.
Select Cancel if you do not wish to change the geometry-for example, if you only wanted to know the symmetry within a certain tolerance, without actually changing the coordinates. Note that in this case the main programs may assume the geometry is of a lower symmetry than the one you saw in the Symmetrize window, and therefore may not take full advantage of molecular symmetry to speed up the calculation.
If you hit Symmetrize, the comment for the job, which is described in Section 2.7 and which appears in the input and output files for the job, will include the note, "Geometry symmetrized to point group," followed by the point group name.
You can submit a job either from within the interface or from a command-line prompt. Starting jobs from the interface is easier, but sometimes you might want to save the input files and submit the jobs by hand, in order to use batch queues, submit jobs remotely from a non-X terminal, use scripts for running multiple jobs, or hand-modify the input files. Information on submitting jobs by hand with the "jaguar run" command can be found in Chapter 8, particularly in section 8.1.
Once you have read in a geometry, you may start a Jaguar job from the interface by selecting Run from the Jobs row of buttons in the main interface window and entering the appropriate information. When you open the Run window, you should close any other open windows in order to save settings you may have changed.
The information you enter in the Run window is mainly used to tell Jaguar how and where to launch a job. The choices available in the Run window option depend on the jaguar.hosts configuration file. See section 6.1 for more information on this file. If you do not change the entries in the Run window, the settings shown will be used for the run.
If Jaguar is installed on more than one host at your location, you can select which host the calculation will actually be performed on from the option menu next to the Job Host heading. To make a non-default selection, click on the bar and then on one of the choices which appears.
A temporary directory on the calculation host is used to store intermediate files during the calculation. If there is more than one possible choice listed for the Temp directory setting, you should pick one. A subdirectory with the given job name ("h2o", for example) is created within the temporary directory, and the files from the calculation will be stored within this subdirectory. Note that the subdirectory and directory must have sufficient disk space for the job, or it will die.
If you are unsure about whether your temporary directory already exists, you should probably look for it from a terminal window. If it does not exist, you should create it or choose a directory which already exists. If none of the temporary directory choices already exist and you do not wish to create the necessary directories, you can change the jaguar.hosts file so that the interface will offer you different choices (see section 6.1).
The directory listed next to the heading Job directory is the local directory on the interface host where input and output files created by Jaguar will be written. The default local job directory is the directory from which you read the input file, if you read one; otherwise, the default is the directory where you started the interface. If you wish, you may change the default selection by clicking in the box and editing the text there.
If the job host is identified in the jaguar.hosts file as having more than one processor, that information will be indicated in the box marked # of Processors. If this number is greater than one, the job will run in parallel.
The text in the box headed Job name determines the names of many of the files created by Jaguar, as well as the name of the subdirectory within the temporary directory, which is described above. The files whose names depend on the job name include the input file, the log file (which shows the job's progress), and the output file listing the calculation results. For instance, if the job name is "h2o", the results are stored in a file called "h2o.out" within the local job directory.
The default setting for the job name is the base of the input file name, if any, from which the molecular geometry was read. For example, if you told the interface to read the geometry from a file called "h2o1.in", the default job name setting would be "h2o1". You can change the job name by editing it from the Job name bar in the Run window or from the Job Name box in the main interface window, by clicking on the bar and typing in a name. If you did not read in the geometry from a file, you should enter a job name in either the Run window or the main interface window.
Any text entered in the box marked Comment will appear in the input and output files for the job. If you symmetrize the geometry, a procedure described in Section , the comment will contain text noting that the geometry was symmetrized to a certain point group. You can enter other text describing the job for your own convenience. The comment should not contain any $ or & characters. The comment appears in the input file immediately before any keyword settings corresponding to later interface selections, and in the output file under the heading "Input file comments".
By default, all temporary files and directories are deleted when the job finishes, after the output file, restart file (which is described in section 6.4), and other useful files are copied back to the local job directory. If you want to save the binary files generated in the temporary directory's job subdirectory and used during the run, you may do so by selecting that option from the menu in the bar next to the heading Scratch Files. Note, however, that these files are often large and should only be saved if necessary, and that any files in the temp directory may be deleted automatically if your site has "scratching."
When you are satisfied with the run-time settings, you can start the job by clicking on the RUN button at the bottom of the window. You can then check the current status of the job from the Job Status window, as described in Section 2.8. If you submit additional jobs, they will run concurrently. If you exit the Jaguar interface, any Jaguar jobs still running will continue to run to completion.
You can run multiple Jaguar jobs sequentially using the Batch window of the Jaguar interface, which is accessible from the Batch button near the Jobs heading in the main interface window. This window lets you launch many jobs at once on the machine upon which you started the interface, changing calculation options in many input files if you wish. For instance, you can
· run a series of Jaguar jobs without changing the input files, launching each job only after the preceding job has completed;
· run the same type of job for several input geometries, launching each job only after the preceding job has completed; and
· run series of jobs in which later jobs use input files generated during earlier jobs, which include the results from the earlier jobs.
Several Jaguar batch scripts are included with the program. You can also write your own Jaguar batch scripts. section 8.20 explains what you can do with Jaguar batch scripts and what sort of format they should have. If you write your own batch scripts, make sure their file names end in the suffix ".bat".
To run a Jaguar batch job from the Batch window, you first need to select a batch script. The batch script can be in any of three directories:
· the batch script directory installed with Jaguar (identified in the interface as BUILTIN_SCRIPTS), whose location is hardwired in the Jaguar installation directories;
· your own personal Jaguar batch script directory, which is set by the environment variable JAGUAR_SCRIPTS if you have set it, and is otherwise assumed to be ~yourname/jaguar_scripts, where yourname is your user name; or
· the current directory, which is the directory containing the last input file you read in or wrote out or, if you have not read or written any files from the interface, the directory where you started the interface.
To select a Jaguar batch file in any of these directories, first click on the Select button in the upper right corner of the Batch window. The Select Batch Script window will open. By default, this window will show that the script selected is the JOBS.bat script. The Notes window shows comments from the JOBS.bat script; as they indicate, this script simply runs a series of jobs from the input files it is passed.
To select another one of the built-in scripts included with Jaguar, just click on its name in the list labeled Scripts, then click OK. To select a script from your own Jaguar batch script directory or from the current directory (both defined above), change the option menu in the middle of the window to the setting User scripts or Local scripts (respectively), click on the name of the script you want to select, then click OK.
Jaguar batch scripts can either require that you specify an input file (or list of input files) to be run with the "recipe" in the batch file, or they can include a self-contained list of Jaguar input files. If the script you have selected processes input files, you next need to select an input file (or list of files) to be fed to the batch script after you have selected the batch script. (If you are not sure whether the script processes input files or is a self-contained script, reopen the Select Batch Script window and look at the text in the middle of the window.)
Select input files from the window marked Inputs, which will list Jaguar input files in the directory shown in the Path box. The input files will be passed to the batch script in the order in which they appear in the list. You can select the first input file by clicking on its name. You can add other input files to the list by pressing the Shift key on your keyboard and selecting another file, which will add the whole range of files between the two to the list, or by pressing the Control key on your keyboard, then clicking on each additional file name you want to select. As you select files, their names will be highlighted. You can also use the (Un)Select All button at the bottom of the window to select or unselect all the files in the list, or use the Current job button to select the input you last read in or edited from other interface windows.
By default, the restart files produced at the end of Jaguar jobs, which are named in the form jobname.xx.in, where xx is a two-digit number, will not be listed in the Inputs file list. If you want to list them, click the box marked Hide restart files to deselect it. You can turn this option back on by clicking on it again.
After you have finished selecting the Jaguar batch script and (if necessary) Jaguar input files, click the RUN button to launch the batch job. The Jaguar jobs run as part of this batch job will run sequentially-that is, no job will start running until the previous job in the list (if any) has finished running.
Immediately after you click RUN, the Job Status window will open. This window will show you the batch log file(s) (*.blog) for the batch job. The information will be automatically updated as the Jaguar jobs run. If you close this window, you can reopen it by clicking on the Check button near the Jobs heading in the main interface window.
You can use the Save window to store a Jaguar input file generated by the interface, or to save a geometry in an appropriate format for another program. You can later scan Jaguar input files back into the interface, as described in Section 2.4, and run jobs from the interface, as described earlier in this section. Alternatively, you can use a Jaguar input file as input for a job submitted from the command line-that is, not using the interface. You would need to start jobs by hand if you wanted to use batch queues or submit jobs remotely from a non-X terminal. Information on submitting jobs by hand can be found in Chapter 8, especially in section 8.1. Jaguar input files can be copied to other machines with Jaguar and used for runs there.
In the Save window, which you can access by clicking the Save button in the top row of the main interface window, the directory listed next to the heading Input file directory is the directory on the interface host where the file saved by Jaguar will be written. The default input file directory is the directory from which you most recently read a file into the interface, if you read one; otherwise, the default is the directory where you started the interface. If you wish, you may change the default selection by clicking in the box and editing the text there.
The text in the box headed Job name determines the name of the input file created by Jaguar. For instance, if the job name is "h2o" and you save a Jaguar input file, the input file saved will be called "h2o.in". The default setting for the job name is the base of the input file name, if any, from which the molecular geometry was read. You can change the job name by editing it from the Job name bar in the Save window or from the Job Name box in the main interface window, by clicking on the bar and typing in a name. If you did not read in the geometry from a file, you should enter a job name in either the Save window or the main interface window.
You can save files in a variety of formats for other programs by making the appropriate selection from the Save as menu bar. For any file formats other than the Jaguar input (*.in) file, only the geometry will be included in the file. The file's name will be determined by appending the extension indicated in the file type list to the job name.
Any text entered in the box marked Comment will appear in the input file for the job. If you symmetrize the geometry, a procedure described in Section , the comment will contain text noting that the geometry was symmetrized to a certain point group. You can enter other text describing the job for your own convenience. The comment should not contain any $ or & characters. The comment will appear in the Jaguar input file immediately before any keyword settings corresponding to later interface selections.
A Jaguar log file contains comments on the progress of a job. If the job was started from the interface, the log file is written to the local job directory selected in the Run window. The log file notes when each section of Jaguar is complete, as well as noting data from each iteration in an SCF calculation as it is calculated. You can look at this file by using the Job Status file viewer window, which comes up when a job is launched or when you click the Check button from the main window. When a job is running, the log file is displayed in the Job Status window. See section 5.8 for more information on this file.
The primary Jaguar output is contained in the output file, which is initially created on the temporary directory of the host where the calculation is performed, but is also copied back to the interface host when the job is complete. The output file is described in Chapter 5. From the file viewer window, once the log file shown for a job indicates that the job has completed, you can look at the corresponding output file by clicking the View File button at the top of the window, selecting the appropriate output file from the resulting list by clicking on it, and hitting OK.
Some other features of the interface which are not covered elsewhere are briefly described here. Note that sometimes a menu item is dimmed (meaning that its name appears in a different, usually less intense color), which means that this option is currently unavailable. For example, the Run button is dimmed until a geometry is entered.
The Job Status window allows you to examine Jaguar log files, output files, or any other text files. It opens automatically when you start a job. If you close the Job Status window, you can reopen it again later by clicking the Check button from the main window.
The log file for the last job you run (h2o.log for the job "h2o", for example) will be displayed automatically in the Job Status window. The log file indicates when each Jaguar program has finished running. section 5.8 contains more information about this file.
The View File button allows you to display the output file for the job, or any other text file, in the Job Status window. This window allows you to specify which file you want to display, in much the same way as you pick a file name when you want to read the geometry from a file. (See Section 2.4 for more information.) Note that by default, only output files are listed, but you can alter this search pattern by editing the Filter bar and hitting the Filter button at the bottom of the window.
Once you have chosen to display a file, its path and name will appear as an option when you select View File. You can use the New File option to display other files. Up to ten files can be listed under the View File option menu.
The Reset option, which near the Jobs heading in the main interface window, clears many of the settings, returning them to the defaults. Selecting Reset wipes out the geometry and any other files read in, as well as all settings describing the wavefunction and properties to be calculated and any settings you may have made with the Geometry or Output buttons. It also sets the Job name value in the Run or Save window to whatever is appropriate when you input the next geometry. However, the other selections you have made in the Run or Save window will remain the same. Reset usually prompts you to make sure you are willing to wipe out any changes. This question, like all those asked in Warning windows, must be answered before the interface will let you do anything else.
Selecting Quit closes the interface. If you have started a job, it will continue to run unless you kill it from your terminal window.
The About button displays information about Jaguar and Schrödinger. You must close it before using other parts of the interface.
The Help button in the upper right corner of the main interface window brings up the Help window. You can see on-line help on a variety of subjects by clicking on them as they are listed under the Help items heading so that they show up in the Selection bar, then hitting Select. You can also obtain help from the windows you use by pressing the Help buttons found within them. Pressing Help then brings up the Help window with the appropriate topic already selected. All of the information in the on-line help is also included in this manual.
The Edit Input button near the Job Name box in the main window of the interface brings up the Edit Job window, which allows you to make settings using the input file keywords for the gen section of the Jaguar input file, which are described in section 8.6, or alter any other input file settings. Formatting cannot be altered from the Edit Job window, however.
The options available for editing jobs from the Edit Job window appear under the pull-down menus File and Edit. These options function exactly like the corresponding options in the Edit window for editing geometries. See Inputting or Editing a Geometry Within the Interface in Section 2.2 for more details. Changes you make from the Edit Job window will not be saved outside of the interface until you select OK in the Run or Save window.
You do not need to use the Edit Job window to do anything described in Chapters 2 through 5; you can use the rest of the interface to set up calculations in all the ways described in these chapters. However, if you prefer to set up jobs with keywords, or if you want to use any options described in Chapter 8 that are not included in the interface, the Edit Job window provides you with a convenient way to do so. If you would like to use keyword settings instead of interface windows to set options that appear in the interface, please refer to the footnotes in Chapters 3 and 5 to find out which keyword settings are appropriate. If you make and save a setting in the Edit Job window that corresponds to something shown in an interface window, the interface selection will show the change.
From the Edit Job window, if you select a keyword with the mouse by double-clicking on it or dragging over the keyword, the keyword will often be described briefly at the bottom of the window. To see a fuller description of the option, you can then access the online help relevant to that option by clicking Help near the top of the Edit Job window.
If the input file contains input the interface does not understand (such as a keyword it does not recognize), you will get a warning that the keyword is unrecognized when you run the job or save the input file. If you hit OK in answer to this the warning, the unrecognized information will be retained in the input for the job.
Most of the scientific settings available are described in the next chapter. The Output buttons, which can be used to request additional information in output files, are described in Chapter 5.
1If you were working directly from an input file without using the interface, the geometry input would be in the zmat and zvar sections of the input file.
|
Schrödinger, Inc. http://www.schrodinger.com Voice: (503) 299-1150 Fax: (503) 299-4532 help@schrodinger.com Last updated: Thu Oct 11 19:10:16 2001 |
| |
|
|
|