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Once you are familiar with the basics of running Jaguar, you may wish to use certain tricks to make it more pleasant or powerful to use. This chapter's contents include information on customizing the interface, restarting jobs, and using Jaguar's interface to help set up Gaussian jobs, as well as some extra suggestions for GVB calculations, geometry optimization, ESP fitting, and jobs involving transition metals.
Within the Jaguar home directory, there should be a file called jaguar.hosts. Jaguar uses the jaguar.hosts file to find out which other machines in your network can also run Jaguar. The file lists where the Jaguar home directories are on those machines, and what directory should be used for temporary files and directories that are created during a Jaguar job (and removed when the job is complete). The settings in the jaguar.hosts file used when you open the interface help determine the available options in the Run window. If you want to, you can make your own, personalized jaguar.hosts file (or files). You shouldn't need to update any jaguar.hosts files when you later install other versions of Jaguar.
The jaguar.hosts file used by the interface will be the jaguar.hosts file in the directory where you started the interface, if it exists; otherwise, it will be the jaguar.hosts file in your home directory, if that exists. If neither of these files exist, the configuration will be determined by the default jaguar.hosts file for the system. You can always figure out which jaguar.hosts configuration file the interface is using by clicking on the About button in the main interface window, then clicking on the Schrödinger button in the About window; the jaguar.hosts configuration file currently used by the interface will be listed near the bottom of the window.
If you would like to change entries in the jaguar.hosts file, it is usually best to make and edit your own jaguar.hosts file. If no jaguar.hosts file exists in your home directory or the directory from which you start the interface, you should identify the jaguar.hosts configuration file currently used by the interface (as described above), copy this jaguar.hosts file to your home directory or the directory where you are starting the interface, and edit it there.
The following short example of a jaguar.hosts file is used to discuss the format of the lines:
For each machine listed in the jaguar.hosts file, these three items should be listed in this order:
Here, machine is the name of a machine that can be used to run a Jaguar calculation, optional-comment is an optional comment that will show up in the Run window of the interface, homedir is the Jaguar home directory for that machine, and tempdir is a directory like /scr or /temp. For stand-alone workstations with multiple processors, set nprocs to the number of processors in the computer. For computer clusters, each node in the cluster should have an nprocs setting equal to the total number of processors in the entire cluster.
These entries in the jaguar.hosts file may be formatted with any combination of spaces and tabs, but the entire entry must be on one line. Any number of comments may also be included in the jaguar.hosts file; comments should start with an exclamation point (!).
A `*' at the beginning of a line designates the setting in that line as the default, for cases where you might want to specify more than one possible value. For instance, in the sample file, withi is the default host, and /exec/jaguar contains the Jaguar installation for this host. The other, non-default items will be accessible from the Run window, but if you do not specifically select them there, the Jaguar run will use the default hosts and directories.
The host name does not need to include the full Internet address (e.g. withi.schrodinger.com) unless the interface host is not on the same local network. If you have installed Jaguar on multiple machines, you may need to hand-edit each machine's jaguar.hosts file to add entries for the other machines.
The directory /tempdir/user/jobname is used during a job to store temporary files, where user is the user's account name on that machine and jobname is the name of the Jaguar job. For example, if the user erwin ran a job named "h2o" on the machine withi using the jaguar.hosts file above, the temporary directory used for the job would be /temp/erwin/h2o. (Jaguar will, by default, completely remove this subdirectory in the temporary space when the job is completed, after copying back all important files to the output directory.)
If you have different user names on the interface and calculation hosts and these machines are on separate area networks, you may need to create a jaguar.hosts file in your home directory to avoid getting an error message indicating that your login is not correct. The jaguar.hosts file should include a host line of the form
where the name of the machine in the "host:" field matches that of the output from the "uname -n" command for that machine. After you have created the jaguar.hosts file in your directory, substitute your user name on the calculation host for "schrod" and your calculation host name for "anny.schrodinger.com".
First, please note that if you use the window manager twm, you may be able to improve the appearance of the interface by adding the line
to your .twmrc file in your home directory. Without this line, the borders for the interface windows may not appear.
Some of the X resources used by the interface are determined by entries in the jaguar.style file. These X resources only affect the appearance the interface, not its functionality. If you want to change some or all of these resources for all users, copy the jaguar.style file from the Jaguar home directory to your home directory and edit the ones you want to change. Note that if a fixed-size font such as Courier is the default for a particular resource, you should probably only replace it with another fixed-size font, and that fonts which include the special ASCII characters above 127 (such as Å) are preferable.
The jaguar.style file used by the interface will be the jaguar.style file in the directory where you started the interface, if it exists; otherwise, it will be the jaguar.style file in your home directory, if that exists. If neither of these files exist, the configuration will be determined by the jaguar.style file in the Jaguar home directory.
On some machines, when you iconify the main Jaguar window, the Jaguar icon will not completely show. To improve the icon appearance, you can change the maximum size for icons by putting the appropriate line in a file called .Xdefaults in your home directory. For instance, for the mwm window manager, this line could read "Mwm*iconImageMaximum: 85x67."
This section contains information you may find useful for improving SCF convergence, running GVB jobs and optimizations, and fitting charges.
Generally, Hartree-Fock wavefunctions for simple organic molecules converge in fewer than 10 iterations, while complex calculations involving higher-level methods or open shells may take a few extra iterations. Molecules which include transition metals generally converge more slowly, however. Make sure your job has really converged and did not simply end because it reached the maximum number of SCF iterations, a number set in the Methods window.
If a job gives poor SCF convergence, you can try either modifying the convergence methods used or improving the initial guess. To modify the convergence methods, try any or all of the following settings:
· Try setting "iacscf" equal to 1, 2, 3, or 4 (see table 8.6.22 for descriptions of each number's function).
· Select GVB-DIIS from the Convergence scheme option menu in the Methods window. Generally, DIIS is the better choice, but the GVB-DIIS convergence scheme sometimes leads to convergence when DIIS does not.
· Set the SCF level shift in the Methods window to 0.5 or 1.0. The higher the setting, the more the virtual orbitals' energies are increased before diagonalization, and the more the mixing of the real and virtual orbitals is reduced. High SCF level shifts sometimes slow convergence by several iterations, but can often help otherwise intractable cases to converge. Because jobs with SCF level shifts are slightly more likely to converge to excited states, you may also wish to restart these jobs without any SCF level shift.
· Change the Accuracy level setting in the Methods window to ultrafine. This setting will cause the job to use denser pseudospectral grids and tighter cutoffs, and generally increases computational costs by a factor of two to three.
· If the calculation is a DFT job, use finer DFT grids. You can make this setting from the Grid density option menu in the DFT window. This setting will also increase the computational cost.
For transition-metal-containing systems, particularly organometallics, you can often obtain superior results by improving the initial guess wavefunction. Jaguar automatically generates high-quality initial guesses for transition-metal-containing compounds; if you supply the program with information about the charges and spins of the "fragments" in the compounds, it will use that information when generating the guess. Here, a fragment is defined as either a collection of one or more transition metals that are bonded together, or one or more non-transition-metal atoms bonded together. Put another way, each fragment is simply a group of atoms that would be bonded together even if all bonds between transition metal atoms and non-transition-metal atoms were broken. Typically, the system is broken into ligand fragments and transition metal fragments, or adsorbate fragments and cluster fragments. For example, for ferrocene, the iron atom is one fragment, and the two cyclopentadienyl ligands are two additional fragments.
To supply Jaguar with information on charges and spins for its high-quality initial guess for a transition-metal-containing system, you need to edit the input file, either from the Edit Job window in the Jaguar interface (which is accessible by clicking on the Edit Input button) or from a terminal window. First, add the line
between the "&gen" and the next "&" sign. Next, add these lines to the bottom of the input file:
(The exact number of spaces between words does not matter.)
Finally, fill in information for each fragment under the headings "atom," "formal," and "multip." You should add a single line for each fragment with a formal charge and/or non-singlet spin multiplicity. The first entry in the line (under the heading "atom") should be the atom label of any atom in the fragment. The next entry (under the heading "formal," and separated from the first entry by one or more spaces) should be the formal charge of the entire fragment. The third entry (under the heading "multip") should be the spin multiplicity of the fragment. If C1 is in one ring of ferrocene and C2 is in the other ring, then the following &atomic section could be used to help generate the initial guess:
Fragments with no formal charge and singlet spin (water, for example) do not need to be listed in the atomic section, because Jaguar will assume a default formal charge of 0 and multiplicity of 1 for each fragment. Note, however, that any charge or spin multiplicity settings in the atomic section must be compatible with any settings for overall charge and spin specified by the "molchg=" and "multip=" keywords in the gen section. For more information about the atomic section, please see section 8.9.
After saving the input file with the iguess setting and atomic section, you can run it in Jaguar in the usual manner.
For most molecules, Lewis dot structures give a reasonable idea of what GVB pairs you should consider setting. If you want to automatically assign pairs by Lewis dot structure for input files generated and submitted outside the interface, see the GVB and Lewis Dot Structure Keywords subsection of section 8.6. You do not have to assign all possible GVB pairs. You can set GVB pairs in any order.
If you are studying a dissociating bond, you should assign all reasonable GVB pairs for that bond. For some purposes, such as for dipole moment calculations, you may find that assigning only pairs for bonds between two different atoms will suffice. Bonds to hydrogen atoms can also be ignored for some cases.
You should not assign GVB lone pairs if you are using a minimal basis set, since the basis set will not have enough degrees of freedom to handle the lone pair. When assigning lone pairs, you should only put one GVB lone pair on atoms from the nitrogen group, two for those from the oxygen group, three for the fluorine group, and one for the carbon group. In the last case, assigning lone pairs is only reasonable when the atom is bonded to only two neighbors. If you assign one GVB lone pair for an atom, you should also assign any other possible GVB lone pairs on that atom.
If you are performing a geometry optimization and are not starting from a high-quality initial molecular structure, you may wish to do a "quick and dirty" calculation to obtain a somewhat better geometry, then perform a more accurate calculation by starting with the results you have generated already. For example, if you wanted to perform an LMP2 geometry optimization, you could start by performing a Hartree-Fock geometry optimization, then restart the calculation by using the HF results in an LMP2 geometry optimization. See Section 6.4 for a description of restarting calculations and incorporating previous results in a later run.
Whenever you are doing a geometry optimization, make sure that you really do obtain a converged structure; the run will end before converging if you reach the maximum number of iterations allowed (as set in the Optimization window). If it did not reach convergence, you can restart the run, as described in Section 6.4.
It is probably best not to constrain electrostatic potential charge fitting to reproduce multipole moments higher than the dipole moment, because the errors in fitting the Coulomb field outside the molecule are likely to be high. Fitting to the dipole moment is usually safe; in fact, even without this constraint, the dipole moment resulting from the fitted charges is generally similar to that calculated from the wavefunction.
Sometimes, you may find it useful to restart a job, either because you want to refine the results and do not want to start from the beginning of the calculation, because you want to alter the calculation slightly but want to use an initial guess or geometry from the previous run, or because you encountered some sort of problem that prevented the job from finishing. New input files, which are also called restart files, generated during each job can be used to restart the jobs. These files are automatically written to your local job directory at the end of a run; if the run did not complete, you can usually find the new input file by following the directions under Finding the Restart File in the Temp Directory below.
A new input file, or restart file, appears in the local job directory when any Jaguar job is completed. This file contains all the information needed for a new run incorporating the results from the first run. This file will contain the same job settings you made for the original input file for the job, but will also contain the results of the job-the final wavefunction, the final geometry, and the like. Thus, if you want to restart the calculation with the wavefunction and other data already calculated, you can just read in the new input file. The file's name is <job>.**.in, where the asterisks represent a two-digit number. This number is 01 if the name of the input file for the job during which it was generated is not in the form <job>.**.in, and is otherwise set to the number after that assigned to the current input file. These files will overwrite any other existing files of the same name.
As an example, if you run the job h2o, the restart file generated during the run will be called h2o.01.in. You could then read this file into the interface, as described in section 2.4, and use it to continue on with the calculation, possibly after making some changes to the calculation requested. The new input file generated during this second run would be called h2o.02.in.
If you want to start a new job where the previous job left off, you need only read the new input file in, then make any changes you think are necessary-for example, you could change the SCF energy convergence criterion from the Methods window, whose button appears in the main window. Similarly, if you wish to perform an additional calculation once a geometry has been optimized, you can read in the restart file as input for the second job and make any necessary changes to it, such as selecting a GVB calculation instead of Hartree-Fock. section 2.4 contains information on reading input files into the interface. Please see Chapter 8 if you would like more information on input files.
Please note that if you restart a run, you may not get exactly the same results as you would if you had simply performed a longer run in the first place, even if the calculation type is the same. The methods used in Jaguar sometimes use data from previous iterations, if this information is available, but the data may not be stored in the new input file. For example, the DIIS convergence scheme uses Fock matrices from all previous iterations for the run, and Fock matrices are not stored in new input files. However, calculations should ultimately converge to the same answer within a standard margin of error whether they are restarted or not.
If your run aborted or was killed before completion, and you want to restart the calculation or start another calculation where that one left off, you can look for a file called "restart.in" in the temporary space used for the job. The file will be located in a subdirectory whose name is the same as the job's, and which is found within the temp directory for the job, which was listed in the Run window.
By default, the restart.in file is written out at the end of the Jaguar programs for calculating the initial guess, performing the SCF iterations, and calculating a new geometry for geometry optimizations, as well as at the end of each SCF iteration. (To turn off restart.in file generation, the input file output keywords ip151 and/or ip152 in the gen section would need to be set to 0.) The restart.in file overwrites itself each time, so that the final version is written either at the end of the run or just prior to any problems encountered.
Jaguar includes a basic command-line interface to the program MOPAC 6.0 [91]. The interface makes it easy to run MOPAC jobs from Jaguar input and to incorporate MOPAC results (such as optimized geometries or Hessians) into Jaguar input files.
For the Jaguar/MOPAC interface, all commands are in the format
where options indicates optional flags and input indicates the full name of either a MOPAC input file whose name ends in the suffix ".dat" or a Jaguar input file whose name ends in the suffix ".in".
Features of the Jaguar/MOPAC interface that can be accessed with commands of this sort are described below. You can also view some help for the Jaguar/MOPAC interface by entering the command
From the Jaguar/MOPAC interface, the command to run MOPAC using input from a Jaguar input file is
where jobname.in is a Jaguar input file. The MOPAC input file jobname.dat is generated and then submitted to MOPAC, which produces several files. The MOPAC output for the job is written to the file jobname.out.
If you have a MOPAC input file named jobname.dat, you can submit it to MOPAC through the Jaguar/MOPAC interface with the command
Once again, the main output for the MOPAC job is written to the file jobname.out.
You can use MOPAC keywords for MOPAC runs by adding the flag "-k" to the command, followed by the desired MOPAC keyword(s). If you are specifying more than one MOPAC keyword, the keywords should be within quotation marks, in this manner:
where keyword1 and keyword2 are MOPAC keywords and input is either a Jaguar input (.in) file or a MOPAC input (.dat) file.
If you want to obtain a MOPAC input file to run later in MOPAC, you can do so with the command
which creates a MOPAC input file jobname.dat from a Jaguar input file jobname.in.
You can use the Jaguar/MOPAC interface to replace the geometry in a Jaguar input file with a MOPAC-optimized one by using the "geom" option. For instance, the command
takes the Jaguar input jobname.in, generates from it the MOPAC input file jobname.dat, runs MOPAC with the input jobname.dat, extracts the resultant MOPAC-optimized geometry from the MOPAC output file jobname.out, and uses it when creating a new Jaguar input file jobname_mopac.in that is identical to the original input file jobname.in except for the geometry.
With the "hess" option to the Jaguar/MOPAC interface, you can add a MOPAC Hessian to a Jaguar input file, so that it will be used as the initial Hessian for a subsequent Jaguar optimization. Before using the "hess" option, however, you should decide whether you want the geometry in the resultant Jaguar input file to be the MOPAC-optimized geometry or the geometry in the original input file submitted to the "jaguar mopac" command.
To create a Jaguar input file with a MOPAC-optimized geometry and Hessian, enter a command in the format
where input is either a Jaguar input (.in) file or a MOPAC input (.dat) file. A new Jaguar input file jobname_mopac.in will be created, containing the MOPAC-optimized geometry and Hessian; if input was a Jaguar input file, jobname_mopac.in will also contain other job settings from the file input.
To add a MOPAC Hessian to a Jaguar input file without actually changing the geometry, enter a command in the format
where jobname.in is a Jaguar input file. A new Jaguar input file jobname_mopac.in will be created, containing the MOPAC-optimized Hessian and any other job settings from the file jobname.in. The "align" flag tells the Jaguar/MOPAC interface to orient the MOPAC Hessian and the initial geometry the same way.
As described above, if you run a MOPAC job from Jaguar input jobname.in, the MOPAC input file generated is called jobname.dat by default. You can specify a different name for the MOPAC input file by using the "m" option. For instance, the command
would create a MOPAC input file called mopjob.dat from the Jaguar input file jagjob.in, and run MOPAC using mopjob.dat as input.
Similarly, if you use the Jaguar/MOPAC interface to create a new Jaguar input file that incorporates a MOPAC geometry and/or Hessian, you can specify the name of the new Jaguar input file with the "j" option. For example, the command
takes the Jaguar input file jagjob.in, generates from it the MOPAC input file jagjob.dat, runs MOPAC with the input jagjob.dat, extracts the resultant MOPAC-optimized geometry from the MOPAC output file jagjob.out, and uses it when creating a new Jaguar input file newjagjob.in that is identical to the original input file jagjob.in except for the geometry.
We recognize that some Jaguar users also use Gaussian for calculations. Therefore, Jaguar can generate or read Gaussian input files. If you plan to perform GVB calculations with Gaussian, you will find this feature particularly useful, since you can use Jaguar to generate a high-quality GVB initial guess automatically.
You can use Jaguar's interface as a convenient tool to create Gaussian input files, if you wish. The output file produced from the Jaguar run, whose name will end in .g92, can be used as a Gaussian input file. The .g92 file will request an HF or ROHF (restricted open-shell Hartree-Fock) calculation, whichever is appropriate for the number of electrons in the system, unless you choose to specify another method. Details applying only to constructing an input file for a GVB calculation are discussed below.
To create a .g92 file, turn on the Gaussian-92 input deck (.g92) option, which is found in the Files window, whose button appears under the Output heading. If you are just creating a Gaussian input file and you do not want to use Jaguar to generate a converged wavefunction, you can save some time by using the Edit Job window to add the keyword setting igonly = 1 (initial guess only) to the gen section of the input file.
The information in the .g92 file will depend on the information you have provided to the interface. The file will always contain a molecular geometry (in Cartesian coordinates and Angstroms); instructions for how to input geometries into the Jaguar interface are available in section 2.2. The file will also specify the molecular charge and the spin multiplicity of the molecule. If you want either of these values to be non-zero, you can make the appropriate settings near the bottom of the interface. You can also set the name of the basis set you want to provide in the .g92 file (for example, STO3G) by using the Basis Set window, whose button is also in the main window. (The default basis set choice is 631G**.)
If you want, you can turn off symmetry by using the Symmetry button found in the main window.
To actually generate the .g92 file, you need to run the Jaguar job you have just specified. See section 2.7 for information on running jobs.
Additional Details for Making Input Files for GVB Calculations
To set up the .g92 file for a GVB calculation, you should use the default setting, Compute from HF initial guess, from the GVB initial guess option menu, which is in the Methods window accessed by the Methods button in the main window. You should specify the GVB pairs in the GVB window, as well. See section 3.3 for information on setting up GVB calculations.
If you have selected a GVB calculation, the interface will automatically turn off the use of symmetry, and the .g92 file will also specify `nosymm.' You may wish to delete this setting from the .g92 file after it is produced.
The .g92 file will also contain a Jaguar-generated initial guess if you have selected a GVB calculation, and will note that this trial wavefunction is to be used as an initial guess for the Gaussian run ("guess=cards"). If you have chosen to do an initial-guess-only calculation, as described above, the initial guess will generated from Jaguar's GVB initial guess routine. Otherwise, the initial guess provided in the .g92 file will be the final wavefunction resulting from the Jaguar SCF calculation performed starting from the GVB initial guess.
Other Non-Interface Jaguar Options for the .g92 File
You can use a Jaguar input file to run a Jaguar job which generates a .g92 file. See Chapter 8 for a description of input files. Selecting the Gaussian-92 input deck (.g92) interface output option described above corresponds to setting the output keyword ip160 to 2 in the gen section of the input file.
You can create or edit Jaguar input files by hand, making keyword settings corresponding to all of the relevant options described above; see Chapter 8 for details. If you wish, you can make some of the desired settings with the interface, use the Save window to save a Jaguar input file, and edit it by hand later to set other keywords.
You can generate additional information for the .g92 file by setting the output keyword ip160 in the gen section of the input file to 3, 4, or 5. Setting this keyword to 3 lets you provide an initial guess within the .g92 file (as described for GVB calculations above) even if you are doing a non-GVB calculation. Setting it to 5 allows you to explicitly provide the basis set itself, rather than just the basis set name, within the .g92 file. This option is useful for specifying basis sets which are included in Jaguar but not in Gaussian. Setting ip160 to 4 allows you to include both the initial guess and the basis set in the .g92 file. These options will also appear in the interface in the future.
The preceding subsection describes how to generate basis sets or orbitals for a Gaussian input file. You can also output a basis set in the format used by Gaussian by turning on the Gaussian-92 basis set (.gbs) option, which is found in the Files window, whose button is under the Output heading. The output will appear in a file whose name will end with .gbs.
You can output orbitals from Jaguar in the format used by Gaussian (for its `guess=cards' option) by choosing to output the appropriate orbitals from the Orbitals window, which is described in section 5.7. You must choose the f19.15 or f8.5 format from the How option menu.
Gaussian input files can be read in to the Jaguar interface, which will get the molecular geometry from them, and will also turn symmetry off for the calculation or turn on electrostatic potential fitting to atomic centers if the Gaussian input file requests either of those options. Any other Jaguar settings will take on their default values. For information on scanning in Gaussian input files as Jaguar input, see section 2.4.
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Schrödinger, Inc. http://www.schrodinger.com Voice: (503) 299-1150 Fax: (503) 299-4532 help@schrodinger.com Last updated: Thu Oct 11 19:10:36 2001 |
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