Gaussian 03 Online ManualLast update: 19 September 2003

Introduction o About Gaussian 03 o Gaussian 03 Citation o Additional Citation Recommendations Using the G03W Program Running Gaussian 03 o Configuring the Gaussian Environment o Setting Up the Default Route File o Efficient Use of Gaussian o Running Test Jobs o Program Limits Preparing Input Files o About Gaussian Input o Job Types o Model Chemistries o Basis Sets o The Title Section o Molecule Specifications o Multi-Step Jobs Gaussian 03 Keywords Gaussian 03 Utilities Additional Information About Z-Matrices References

Gaussian 03 Online ManualLast update: 4 April 2003

Gaussian 03 CapabilitiesGaussian has been designed with the needs of the user in mind. All of the standard input is free-format and mnemonic. Reasonable defaults for input data have been provided, and the output is intended to be self-explanatory. Mechanisms are available for the sophisticated user to override defaults or interface their own code to the Gaussian system. The authors hope that their efforts will allow users to concentrate their energies on the application of the methods to chemical problems and to the development of new methods, rather than on the mechanics of performing the calculations. The technical capabilities of the Gaussian 03 system are listed in the subsections below.

Fundamental Algorithms

Calculation of one- and two-electron integrals over any general contracted gaussian functions. The basis functions can either be cartesian gaussians or pure angular momentum functions, and a variety of basis sets are stored in the program and can be requested by name. Integrals may be stored in memory, stored externally, or be recomputed as needed [20,21,22,23,24,25,26,27,28]. The cost of computations can be linearized using fast multipole method (FMM) and sparse matrix techniques for certain kinds of calculations [29,30,31,32,33,34]. Transformation of the atomic orbital (AO) integrals to the molecular orbital basis by "in-core" means (storing the AO integrals in memory), "direct" means (no integral storage required), "semi-direct" means (using some disk storage of integrals), or "conventional" means (with all AO integrals on disk). Use of density fitting to speed up the Coulomb part of pure DFT calculations [35,36]. Numerical quadrature to compute DFT XC energies and their derivatives.

Energies

Molecular mechanics calculations using the AMBER [37], DREIDING [38] and UFF [39,40] force fields. Semi-empirical calculations using the CNDO [41], INDO [42], MINDO/3 [43,44], MNDO [43,45,46,47,48,49,50,51,52], AM1 [43,48,49,53,54], and PM3 [55,56] model Hamiltonians. Self-consistent field calculations using closed-shell (RHF) [57], unrestricted open-shell (UHF) [58], and restricted open-shell (ROHF) [59] Hartree-Fock wavefunctions. Correlation energy calculations using Mller-Plesset perturbation theory [60] carried to second, third [61], fourth [62,63], or fifth[64] order. MP2 calculations

use direct [21,65] and semi-direct methods [23] to use efficiently however much (or little) memory and disk are available. Correlation energy calculations using configuration interaction (CI), using either all double excitations (CID) or all single and double excitations (CISD) [66]. Coupled cluster theory with double substitutions (CCD)[67], coupled cluster theory with both single and double substitutions (CCSD) [68,69,70,71], Quadratic Configuration Interaction using single and double substitutions (QCISD) [72], and Brueckner Doubles Theory (BD) [73,74]. A non-iterative triples contribution may also be computed (as well as quadruples for QCISD and BD). Density functional theory [75,76,77,78,79], including general, user-configurable hybrid methods of Hartree-Fock and DFT. See this page for a complete list of available functionals. Automated, high accuracy energy methods: G1 theory [80,81], G2 theory [82], G2(MP2) [83] theory, G3 theory [84], G3(MP2) [85], and other variants [86]; Complete Basis Set (CBS) [87,88,89,90,91] methods: CBS-4 [91,92], CBS-q [91], CBS-Q [91], CBS-Q//B3 [92,93], and CBS-QCI/APNO [90], as well as general CBS extrapolation; the W1 method of Martin (with slight modifications) [94,95,96]. General MCSCF, including complete active space SCF (CASSCF) [97,98,99,100], and allowing for the optional inclusion of MP2 correlation [101]. Algorithmic improvements [102] allow up to 14 active orbitals in Gaussian 03. The RASSCF variation is also supported [103,104]. The Generalized Valence Bond-Perfect Pairing (GVB-PP) SCF method [105]. Testing the SCF wavefunctions for stability under release of constraints, for both Hartree-Fock and DFT methods [106,107]. Excited state energies using the single-excitation Configuration Interaction (CISingles) method [108], the time-dependent method for HF and DFT [109,110,111], the ZINDO semi-empirical method [112,113,114,115,116,117,118,119,120], and the Symmetry Adapted Cluster/Configuration Interaction (SAC-CI) method of Nakatsuji and coworkers [121,122,123,124,125,126,127,128,129,130,131,132,133,134,135].

Gradients and Geometry Optimizations

Analytic computation of the nuclear coordinate gradient of the RHF [136], UHF, ROHF, GVB-PP, CASSCF [137,138], MP2 [22,23,139,140], MP3, MP4(SDQ) [141,142], CID [143], CISD, CCD, CCSD, QCISD, Density Functional, and excited state CIS energies [108]. All of the post-SCF methods can take advantage of the frozen-core approximation. Automated geometry optimization to either minima or saddle points [136,144,145,146,147,148], using internal or cartesian coordinates or a mixture of coordinates. Optimizations are performed by default using redundant internal coordinates [149], regardless of the input coordinate system used. Automated transition state searching using synchronous transit-guided quasiNewton methods [150]. Reaction path following using the intrinsic reaction coordinate (IRC) [151,152].

Two- or three-layer ONIOM [153,154,155,156,157,158,159,160,161,162,163] calculations for energies and geometry optimizations. Simultaneous optimization of a transition state and a reaction path [164]. Conical intersection optimization using state-averaged CASSCF [165,166,167]. IRCMax calculation which locates the point of maximum energy for a transition structure along a specified reaction path [168,169,170,171,172,173,174,175,176]. Classical trajectory calculation in which the classical equations of motion are integrated using analytical second derivatives [177,178,179,180] using either: o Born Oppenheimer molecular dynamics (BOMD) [177,178,179,180,181,182] (see [183] for a review) [184,185,186,187,188]. This can be done using any method for which analytic gradients are available, and can optionally make use of Hessian information. o Propagation of the electronic degrees of freedom via the Atom Centered Density Matrix Propagation molecular dynamics model [188,189,190]. This method has similarity and differences to the related Car-Parrinello approach [191]. See the discussion of the ADMP keyword for details. This can be done using the AM1, HF, and DFT methods.

Frequencies and Second Derivatives

Analytic computation of force constants (nuclear coordinate second derivatives), polarizabilities, hyperpolarizabilities, and dipole derivatives analytically for the RHF, UHF, DFT, RMP2, UMP2, and CASSCF methods [25,139,192,193,194,195,196,197,198,199], and for excited states using CIS. Numerical differentiation of energies or gradients to produce force constants, polarizabilities, and dipole derivatives for the MP3, MP4(SDQ), CID, CISD, CCD, and QCISD methods [143,200,201,202]. Harmonic vibrational analysis and thermochemistry analysis using arbitrary isotopes, temperature, and pressure. Analysis of normal modes in internal coordinates. Determination of IR and Raman intensities for vibrational transitions [193,194,196,200,203]. Pre-resonance Raman intensities are also available. Harmonic vibration-rotation coupling [204,205,206,207]. Anharmonic vibration and vibration-rotation coupling [204,206,207,208,209,210,211,212,213,214]. Anharmonic vibrations are available for the methods for which analytic second derivatives are available.

Molecular Properties

Evaluation of various one-electron properties using the SCF, DFT, MP2, CI, CCD and QCISD methods, including Mulliken population analysis [215], multipole moments, natural population analysis, electrostatic potentials, and electrostatic potential-derived charges using the Merz-Kollman-Singh [216,217], CHelp [218], or CHelpG [219] schemes.

Static and frequency-dependent polarizabilities and hyperpolarizabilities for Hartree-Fock and DFT methods [220,221,222,223,224,225]. NMR shielding tensors and molecular susceptibilities using the SCF, DFT and MP2 methods [226,227,228,229,230,231,232,233,234,235]. Susceptibilities can now be computed using GIAOs [236,237]. Spin-spin coupling constants can also be computed [238,239,240,241] at the Hartree-Fock and DFT levels. Vibrational circular dichroism (VCD) intensities [242]. Propagator methods for electron affinities and ionization potentials [243,244,245,246,247,248,249]. Approximate spin orbit coupling between two spin states can be computed during CASSCF calculations [250,251,252,253,254]. Electronic circular dichroism [255,256,257,258,259] (see [260] for a review). Optical rotations and optical rotary dispersion via GIAOs [261,262,263,264,265,266,267,268,269,270,271]. Hyperfine spectra: g tensors, nuclear electric quadrupole constants, rotational constants, quartic centrifugal distortion terms, electronic spin rotation terms, nuclear spin rotation terms, dipolar hyperfine terms, and Fermi contact terms [272,273,274,275,276,277,278,279]. Input can be prepared for the widely used program of H. M. Pickett [280].

Solvation ModelsAll of these models employ a self-consistent reaction field (SCRF) methodology for modeling systems in solution.

Onsager model (dipole and sphere) [281,282,283,284], including analytic first and second derivatives at the HF and DFT levels, and single-point energies at the MP2, MP3, MP4(SDQ), CI, CCD, and QCISD levels. Polarized Continuum (overlapping spheres) model (PCM) of Tomasi and coworkers [285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,30 3] for analytic HF, DFT, MP2, MP3, MP4(SDQ), QCISD, CCD, CCSD, CID, and CISD energies and HF and DFT gradients and frequencies. o Solvent effects can be computed for excited states [298,299,300]. o Many properties can be computed in the presence of a solvent [304,305,306]. o IPCM (static isodensity surface) model [307] for energies at the HF and DFT levels. o SCI-PCM (self-consistent isodensity surface) model [307] for analytic energies and gradients and numerical frequencies at the HF and DFT levels.

Technical Support InformationLast update: 24 March 2003

The current required citation for Gaussian 03 is the following (presented in two formats for convenient cutting and pasting):Normal Name Order Gaussian 03, Revision A.1, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA, 2003. Last Name First Gaussian 03, Revision A.1, Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian, Inc., Pittsburgh PA, 2003

Replace Revision A.1 with the identifier for the revision of the program that you actually use. A paper describing the scientific capabilities of Gaussian 03 is in preparation. Once it is published, this reference should be cited thereafter. The advances presented for the first time in Gaussian 03 are the work of M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin,

R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, A. D. Daniels, O. Farkas, A. D. Rabuck, K. Raghavachari and J. V. Ortiz.

Gaussian 03 Online ManualLast update: 19 September 2003

In general, we recommend citing the original references describing the theoretical methods used when reporting results obtained from Gaussian calculations, as well as giving the citation for the program itself. These references are given in the discussions of the relevant keywords. The only exceptions occur with long established methods such as Hartree-Fock theory which have advanced to the state of common practice and are essentially self-citing at this point. In some cases, Gaussian output will display the references relevant to the current calculation type. Gaussian also includes the NBO program as link 607. If this program is used, it should be cited separately as: NBO Version 3.1, E. D. Glendening, A. E. Reed, J. E. Carpenter, and F. Weinhold. The original literature references for NBO can also be cited [12,13,14,15,16,17,18,19].

Gaussian 03 Online ManualLast update: 4 April 2003

Using the G03W User Interface

Getting Started Menus and Toolbars Batch Processing of Gaussian Job Files Converting PDB and other Files Customizing the G03W Interface Setting G03W Execution Defaults Utility Programs Included with G03WLast update: 19 September 2003

Gaussian 03 Online Manual

This chapter explains the Windows approach to the Gaussian program, and gets you up and running with a simple example.

INPUT MADE EASYEvery complete set of instructions processed by Gaussian is called a job step. A file containing one or more jobs steps is called a job file. Gaussian job files have the 3 letter extension of GJF in the Windows environment. Job files that are composed of multiple jobs steps can have individual steps that are dependent on, or make reference to, previous job steps within the file. In addition, job files may have multiple job steps that have nothing to do with the other steps contained therein. Beyond multiple job step files, G03W can process batches of job files, through the use of a Batch Control & Batch Control File. While job steps may be stored in files, G03W allows simply entering your job step into an on screen form (called the Job Entry Form). From here you can begin processing the job step, and/or save what you've typed in to a GJF file.

PROCESSING OF JOB STEPS AT THE PRESS OF A BUTTON.Once you have a job step in memory, you can begin, pause, resume and/or kill the processing of that step (or group of steps) from buttons on the Toolbar or menu items. You can even use your favorite editor to edit the input and view the output right from inside of G03W.

VIEW GAUSSIAN OUTPUT TWO WAYSWhen processing jobs, G03W displays the current output in an on screen, scrollable area, while writing the output to a user defined file. Even if you minimize G03W down to an icon, the processing of the job steps is viewable, as the title of the icon continues to update the current status.

FILE CONVERSIONS INTEGRATEDThrough the use of the NewZMat utility, you can convert to and from numerous chemistry file formats, and automatically load the results into your favorite editor, or into Gaussian itself for processing.

CUSTOMIZE GAUSSIAN TO THE WAY YOU WORKTaking advantage of the full range of possibilities in the environment, G03W lets you setup your preferences about editors, directories, colors, fonts, warnings, questions and messages, and default behavior with normal and batch processing.

LIKE DRAG & DROP ?

G03W if a fully Drag & Drop-aware program. Select a GJF file in the file manager, drag it over the top of a non-processing Gaussian window or icon, and drop the file. Gaussian will load the file, and if you've customized it to do so, begin processing. Select several GJF files and drop them on Gaussian, and Gaussian builds a Batch Control File with your selections and loads it (and possibly starts processing them).

Gaussian 03 Online ManualLast update: 2 October 2003

Menus and ToolbarsMain Window

File Menu Process Menu Utilities Menu View Menu Main Window Toolbar

Job Edit Window

File Menu Edit Menu Set-Start Menu Check Route Menu Job Edit Window Toolbar

Additional Jobs Steps Window

Step Menu View Menu Check Route Menu Job Step Window Toolbar

Main Window: File MenuThe File menu allows you to create and access Gaussian 03W input files and to set program preferences. New: Create new Gaussian 03W input (residing only in memory until it is explicitly saved to disk). Open: Open an existing Gaussian 03W input file. The extension of a Gaussian 03W input file is .GJF. The Open menu item may also be used to load an existing batch control file.

The batch facility is described later in this section. Finally, it may be used to open a PDB file for conversion (this process is discussed later). Modify: Edit the current input, via the Existing File Job Edit window. Preferences: Set Gaussian 03W preferences. Preferences are described in a separate section later in this document. Exit: Exit from Gaussian 03W. You will be prompted whether to save any unsaved new or modified input files as well as any unsaved changes to the preferences.

Main Window: Process MenuThe Process menu allows you to manipulate executing jobs. All of its items have equivalent icons in the Job Processing window (described later in this section). Begin Processing: Begin executing the currently loaded input. Pause: Immediately suspend the currently executing job. Pause Next Link: Suspend execution of the currently executing job after it completes the current link. (The Gaussian 03 program is divided into a series of modules known as links. Different links perform different parts of the calculation, and the various links execute sequentially, making up the total job.) Resume: Restart execution of a paused job. Kill Job: Immediately abort the currently executing job. If a batch is running, the next job in the batch (batches are formally defined later in this section) will begin executing (unless the End Batch Run on Error preference is set). End Batch: Stop executing the current batch when the current job finishes. Kill Batch: Immediately abort the currently executing job and terminate batch processing without running any more jobs.

Main Window: Utilities MenuThe Utilities menu gives you access to the batch and file conversion facilities and other utilities provided with Gaussian 03W. Well consider them in detail later in this manual. Edit Batch List: Edit the currently loaded batch control file (extension .BCF), via the Edit Batch List window (described later). If no batch control file is loaded, then a new batch list is created and any currently loaded input is erased from memory.

NewZMat: Convert files using the NewZMat utility. After selecting this option, you designate the file to be converted from the Open File dialog box. The NewZMat File Conversion window then appears (described later in this document). CubeGen: Generate a cube file for use in a visualization program. You will be prompted for all necessary information. CubMan: Manipulate or transform one or more existing cube files. You will be prompted for all necessary information. FreqChk: Retrieve frequency and thermochemistry data from a checkpoint file. After selecting this option, you designate the checkpoint file to be used with the Open File dialog box. FormChk: Convert a binary checkpoint file to an formatted (ASCII) version. After selecting this option, you designate the checkpoint file to be used with the Open File dialog box. UnFchk: Convert a formatted checkpoint file back to its G03W binary format. After selecting this option, you designate the checkpoint file to be used with the Open File dialog box. ChkChk: Display information about the contents of a checkpoint file. After selecting this option, you designate the checkpoint file to be used with the Open File dialog box. ChkMove: Convert a binary checkpoint file to a form suitable for moving it to another kind of computer system. After selecting this option, you designate the checkpoint file to be used with the Open File dialog box. C8603: Convert a binary checkpoint file from a previous Gaussian version to the Gaussian 03 format. External PDB Viewer: View the current molecular structure with an external PDB viewing program. The program to use is specified in the preferences (described later in this document).

Main Window: View MenuThe View menu controls the appearance of the window and enables you to invoke an external text editor. The default settings of the various display options may also be controlled via preferences. The editing options also have icon equivalents (described later in this section). Toolbar: Toggles the display of the toolbar portion of the window. When the toolbar is visible, this item is checked.

Processing Output: Toggles the display of the Output Display area of the window. When the Output Display area is visible, this item is checked. Status Bar: Toggles the display of the status bar portion of the window, which shows a brief description of the current menu item. When the status bar is visible, this item is checked. Editor: Invoke the external editor (which editor is used is defined in the preferences). Editor -> Output File: Invoke the external editor on the current output file. Note that an executing job must be paused before invoking an editor on its output file.

Main Window: Help MenuThe Help menu follows standard Windows conventions. Contents: Display the table of contents for the on-line help. About: Display an informational window about this version and copy of Gaussian 03W, including the program version and the serial number of this copy:

Start current job. Immediately pause job. Pause after the current link. Resume executing paused job. Terminate the current job. Edit the current Batch Control File (or create new one). End the current batch after the current job completes. Immediate kill current job and batch. Open external editor.

Edit G03W output file with external editor.

Job Edit Window: File MenuThe File menu allows you to load and save Gaussian 03 input files. Some of its options have equivalent icons (described later in this section). Load: Load an existing input file (extension .GJF), replacing any current input. If the filename field is filled in, this file will be loaded. If it is blank, then you will be prompted for the file to load. The loaded file replaces any current input (after prompting for needed saves). If you select the Load option without changing the contents of the filename field, then the current input will revert to the last-saved form on disk (provided that you answer No to the save prompt). Save Job: Save the current input to its original file (you will be prompted for a filename if it is newly created input). Save Job As: Save the current input to a file that you specify. External Editor: Invoke the external editor on the current input. The external editor is specified via the preferences. Abandon Data: Exit from this window, discarding all input and changes. Exit: Return to the Job Processing window. Current input is retained but is not automatically saved. Exit & Run: Return to the Job Processing window and begin executing the current input (not automatically saved to disk).

Job Edit Window: Edit MenuThe Edit menu includes the standard Windows Edit menu options: Undo, Cut, Copy, Paste, and Delete. It also has this additional option: Clear Form: Erase all information in all sections of the window. No warning is given about any unsaved changes. You can create a new input file from this form by selecting Clear Form, entering the desired input, and then saving it.

Job Edit Window: Check-Route Option

This item runs the Check Route utility on the current input (described later in this document). There is an equivalent icon for this option (described later).

Job Edit Window: Set-Start OptionThis option enables you to set the starting job step for this input file (additional job steps are discussed later in this section). The default is the main (first) step. Select the starting step by double clicking on the desired step. Exit from the window by choosing Close from the windows System menu (reached via the close bar in its upper left corner). There is an equivalent icon for this option (described later).

Return to main window and start job. Return to main window. Save all current input to disk. Discard all input and return to main window. Run the Check Route utility. Specify the starting job step. Load an input file (replacing current file).

Additional Jobs Steps Window: Step MenuThe Step menu is used to create, remove, and rearrange the order of job steps. Add Step: Create a new job step after the current one. The contents of the % Section, Title Section, and Charge & Multipl. areas from the main job are automatically copied to the new step. They may be edited as desired as the additional areas are filled in.

Delete Step: Remove the current step from the job. Reorder: Change the order of the job steps using the Re-Ordering Data window (described in a separate section later in this document). Load From File: Replace the current step with the job stored in an external file (you will be prompted for the filename). If the file contains more than one job step itself and the current step is the last job step, then all steps from the file will be loaded in their current order. If the file contains multiple job steps and the current step is not the last step in the job, then only the first step from the file will be loaded, as the current step, and an error message will be displayed. Exit: Return to the Job Edit window. There is an equivalent icon for this menu item (described later in this section).

Additional Jobs Steps Window: View MenuThe Additional Jobs Steps Window menu allows you to move among the additional jobs steps within the current job. Its items also have equivalent icons (described later in this section). Next Step: Move to the next step (higher numbered) in the job. Prev Step: Move to the previous step in this job. Choose Step: Move to the job step number that you specify.

Additional Jobs Steps Window: Check-Route ItemThis item runs the Check Route facility on the current input step (described in a separate section later in this document).

Go to next job step. Go to previous job step. Move to a specific job step.

Run the Check Route utility. Return to the Job Edit window.

Gaussian 03 Online ManualLast update: 19 September 2003

Batch processing in G03W is implemented through the use of the Batch Control system and BCF files. Multiple GJF files can be processed when in batch mode. This mode is entered automatically whenever a BCF file is loaded, or when batch data is entered directly. You access this feature via the Utilities=>Edit Batch menu item or via the corresponding toolbar icon: .

The built-in batch list editing features allow you to add, edit, delete, specify starting entry, and reorder entries in the batch list. You can also save, load and generate BCF files from this same editor. Any and all modifications you have made to the batch control system are saved in memory, and at exit, you are reminded if you have not saved them to a file. Batch processing can be paused, resumed, ended and killed through menu and toolbar process controls. BCF files are also automatically created if a group of files are dropped onto the G03W form or icon from an appropriate file manager. Lastly, you can control certain aspects of batch processing via Process Preferences selections.

The Edit Batch WindowDouble clicking on a filename in either the input or output list box allows editing of the individual elements in the list. Add Button: Adds an input/output file pair to the list. Delete Button: Removes the currently highlighted input/output file pair. Reorder Button: Allows the user to reorder the data in the list using the Reorder Data dialog (see below). Set-Start Button: Sets the starting file to process in the batch.

Reorder DataThis form allows for the reordering of list based data. The top list box contains those items (Batch Filename data or Additional Job Step names) that can be reordered, in their old order. Double-Clicking on an item in the top list box moves it to the bottom list box which holds the new order. Double-Clicking on an item in the bottom list box (New Order) moves it to the top list box (Old Order) and places it there in its original order. To move a group of items from one list box to another, hold down the Shift (select a range) or Control (select specific) key while clicking on your choices. Once your choices are highlighted, pressing the appropriate GROUP button will transfer the items. Only when all the items in the Old Order list box are in the New Order list box can you press OK, and implement the new orderin

Edit Batch Window: File MenuNew: This menu item clears the batch list and prepare memory for a new list typed in. Open: This menu item loads a BCF file. Save: This menu item saves changes to the already loaded file. Save As: This menu item saves the contents of the list to a new filename. Exit: This menu item exits the Edit Batch area. If there are any entries in the list, G94W stays in batch processing mode. If not, standard job processing mode is set.

Gaussian 03 Online ManualLast update: 19 September 2003

Use this command to translate from one chemistry file format to another, and load a converted file into memory or an external editor. After selecting an appropriate file, the dialog box appears for conversion. Preliminary conversion parameters are preset depending on the file extension of the filename selected. Use the FIND FILE button to quickly select a different conversion source file. Generate File Filename: The system attempts to build an appropriate filename for the selected source file. The generated file will be created in the same directory as the source file. The file extension will be adjusted as the user selects conversion parameters under output options.

Load Converted File as Job: Tells the system to load the newly generated file into memory for further processing by Gaussian. This will only happen if the file conversion was successful. Edit Generated File: Tells the system to load the newly generated file into memory, and display it for editing. Ext.Editor->Generated File: Tells the system to load the newly generated file into the user defined external editor for modification and display. The file is not loaded into Gaussian memory. Input Options: This button allows user control over the NewZMat Input Parameters. Output Options: This button allows user control over the NewZMat Output Parameters. Other Options: This button allows user control over the NewZMat Other Parameters. For more information about NewZMat, consult the Gaussian 03 User's Reference.

Gaussian 03 Online ManualLast update: 2 October 2003

Customizing the G03W InterfaceG03W allows you to configure to your tastes many aspects of the user interface, including visual aspects and operating procedures. VISUAL PREFERENCES: You can choose actively to display or not to display the toolbar, Processing Output Area and Status Bar via the View Menu on the main form. These menu items will change the size and shape of the main form, and you can make these choices permanent via the Display Preferences section of the Preferences form. On the display preferences form you can choose to see an hourglass when the a link has control of the CPU, whether or not to have a Motif-like look to Gaussian (raised or lowered 3D controls, gray background), how often to look into the run-time output file and display any new contents, the foreground and background colors to use for the output display area, and the fonts to use for both input and output. FILES AND MESSAGES: You can choose how you want to be prompted concerning over-writing existing files, and how to save complicated jobs (jobs which are a conglomeration of multiple files) from the Edit Preferences section of the Preferences form. In addition, each time you run, you may or may not want to be prompted for the name of the output file. The control for this is found under the Process Preferences section.

CONTROL OVER EVENTS: You can define what happens when a file is loaded (i.e. do you jump into the internal editor or not), what happens when a file or set of files is dropped on G03W, and how to handle messages, output and errors during batch processing. All these options are controlled from the Process Preferences section. DEFAULT LOGIC: You can also deal with multiple operating paths by setting the default path information on the main Preferences dialog. The BIN PATH entry tells Gaussian where to find its links. The scratch path entry tells the system where you want temporary files to be created and re-created. The optional output path tells the system where the default should be to create output files. If left blank, the default for GJF files is the directory where the input file was found, for BCF files, the output filename defines where it goes. The input path tells the system where it should look first to find files. If left blank, the system looks in the directory where you last loaded a file from (in the current session).

ASCII Editor Fill in this edit area with the fully qualified path and filename of the text editor you prefer to you use. This editor will be available from the edit form menus and the View menu, or from the toolbar button. In addition, after a job has successfully run, the editor can be called from the View menu with the output file, or from the toolbar button. During the initial installation, the ASCII Editor is preset to NOTEPAD.EXE if no other editor has been defined. Find File: Use this button to quickly locate your preferred editor executable. This function will fill in the edit area with your selection. Bin Path: This edit area tells G03W where the link executables exist on your system. This information is filled in by the initial installation program and should normally not be altered. WARNING: Having incorrect information will cause all jobs to fail at the first link. Scratch Path: This edit area tells G03W where the scratch files should be created. If this edit is empty, the system will assume no scratch directory is present, and all temporary files will be created in the same directory as the input file (if there is one) or the current working directory (if there is no input file). It is highly recommended that you have a scratch directory, as this will reduce the impact of multiple Gaussian job runs, (which can take up lots of disk space), by overwriting the same files.

Output Path: This edit area tells Gaussian where you would like all output files to be created. If this is edit is empty, then the output file will be created either where you specify it, or in the same directory that the input file was found in. Input Path: This edit area tells Gaussian you have a preferred default input path to search for GJF files. If this edit is empty, then the current working directory is used until a file is loaded. After a file is loade, the directory where the loaded file was found, becomes the default. Display: The display button allows control over the visual elements of the interface. (See Display Preferences ). Edit: The edit button allows control over the file editing elements of the interface. (See Edit Preferences ). Process: The process button allows control over the Gaussian Job Step processing elements of the interface. (See Process Preferences ).

Use this command to adjust the visual elements of the G03W interface to your tastes: Cursor Indication of Processing: This switch toggles whether or not the cursor should be changed to an hourglass while a link has the CPU. (An indicator of both processing and multitasking). (Default OFF). Motif Look: Toggle whether to use a gray background and add height or depth to on screen controls. (Default ON). Show ToolBar at Startup: Toggle whether or not to view the toolbar when the program first opens. (Default ON). Show Output File Area at Startup: Toggle whether or not to view the output of jobs run when the program first opens. (Default ON). Show Status Bar at Startup: Toggle whether or not to view the Status Bar at the bottom of the window when the program first opens. (Default ON). Output File Scan Time: Set the time (in seconds) that the front-end should wait to scan the output file for new information, and display it in the output display area. Range 23600 seconds. (Default: 15secs). Use System Colors: Toggle whether or not to use the colors defined in the current Windows system color scheme, for aspects of screen display (edits, list boxes, text,

scrollbars,etc...) Note: Motif Look overrides the color control for window backgrounds, whether or not this toggle button is checked. (Default OFF). Output Background: This button displays the color selection screen to allow the user to set a color for the background of the output display area. Keep in mind that a color should also be selected for the text (see Output Font below) that will allow seeing the text. (Default - Dark Blue R:0 B:64 G:0). Output Font: This button displays the font selection box for the output display area. Since the information in the output assumes a fixed font (terminal like) display, only fixed width fonts are available in this area. In addition, you may select a text color if the Use System Colors switch (above) is off. Note: to see an example in the Sample window, you must fully select a font, (meaning Name, style and size) and the text color must be anything but white. Input Font: This button displays the font selection box for the input displays (any edit area on the input forms). Any normal font can be used. Colors may not be set for this text edit area.

Use this command to adjust the file I/O elements of the G03W interface to your tastes: File OverWrite Warnings: Select whether you want notification that you are about to write over an existing file.

The first option provides notification anytime this would occur. The second option provides notification only when a file in memory is being saved to a different filename, and that new filename already exists. The last option never bothers the user with notification, and over-writes any previous files (dangerous).

Multi-Step Job File Saves: When the contents of memory comprises multi-step jobs, whether the user loaded steps from multiple files or not, the steps may be saved in one of three combinations:

Save the steps back to their original files (DEFAULT). Save all the steps to a single file. Save each step to an individual file (filename is created with the step number). The first toggle button controls whether the interface queries the user for a choice when this condition exists.

Use this command to adjust the job processing elements of the G03W interface to your tastes: Query Output Name: Toggles whether or not to ask the user the name and directory of the output file to create. (Default ON). Show File On Load: Toggles whether or not to display the contents of a file after its loaded. (Default ON). End Batch Run on Error: Toggles whether to halt batch processing when an error occurs, or to skip to the next job in the batch and keep going. (Default ON). Note: If this feature is active and an error occurs while processing a batch, the batch start entry value is set to the file that caused the error. Scan Output During Batch: Toggles whether or not to display the output of the currently processing job in the output display area when processing batches of jobs. (Default ON). Minimize Until End / Error: Toggles whether Gaussian should become an ICON while processing batch jobs. If an error occurs or the end of the batch is reached, and this feature is active, then Gaussian will re-display itself in an open state. (Default OFF). Prompt Messages: Toggles whether or not ask questions of the user when processing batches, or to assume default behavior. Such questions include file overwrite warnings and non-fatal system errors. (Default OFF). Run Dropped Files: Toggles whether or not to immediately run a file or list of files dropped on Gaussian by a file manager. (See Drag & Drop in your Windows manual). (Default OFF).

Gaussian 03 Online ManualLast update: 6 October 2003

Depending on the characteristics of a particular computer system, it is sometimes necessary for performance reasons to override some of the defaults built into the program. This can be done by creating a site customization file. On Unix systems, this file is named Default.Route, residing in $g03root/g03. Under Windows, the Gaussian defaults file is Default.Rou, and it is located in the Gaussian 03W scratch subdirectory (e.g., C:\G03W\scratch). The format of the file is the same on all computer systems.

The following subsections describe the types of information which can be supplied in the defaults file.

Route DefaultsThese parameters are introduced by -#- and have the same form as normal route section commands. For example, this line will set the default SCF algorithm to the conventional (non-direct) algorithm:-#- SCF=Conventional

There may be more than one -#- line in the file. Commands listed in Default.Route change only the defaults; they are overridden by anything specified in the route section of an input file. Thus, if the Default.Route contains:-#- MP2=NoDirect

and the route section contains the MP2 keyword, then the conventional MP2 algorithm will be used. However, if the route section contains the MP2=Direct keyword, then the direct algorithm will be used. All sites will want to specify the amount of scratch disk space available via the MaxDisk keyword in the Default.Route file. For example, the following line sets MaxDisk to 800 MB:-#- MaxDisk=800MB

This line will have the effect of limiting disk usage in the semi-direct algorithms to the specified amount. Some suitable limit should be defined for your configuration. Keep in mind that the more disk space is available, the faster the evaluation, especially for MP2.

Default.Route LimitationsNot all route section keywords are honored in the Default.Route file. In general, the rule is that only options which do not affect the outcome of a calculation (i.e., do not change the values of any predicted quantities) are allowed in the file. Thus, SCF=Conven, which changes only the integral storage algorithm, will be honored, while Int(Grid=3), which affects the results of many kinds of calculations, will be ignored.

Memory DefaultsIt is often the case that Gaussian jobs which unwisely use excessive memory can cause severe difficulties on the system. The -M- directive enforces a default dynamic memory limit. For example, the following line sets default memory use to 32 MB:

-M- 4000000

Note that this limit can be bypassed with the %Mem Link 0 command. The value may also be followed by KB, MB, GB, KW, MW or GW to indicate units other than words. The default memory size is 6 MW.

Number of ProcessorsIf your computer system has multiple processors, and parallel processing is supported in your version of Gaussian, you may specify the default number of processors to use in the Default.Route file. For example, the following command sets the default number of processors to 4:-P- 4

Normally, the program defaults to execution on only a single processor. The %NProcShared Link 0 command can be used to override the default for a specific job. Clearly, the number of processors requested should not exceed the number of processors available, or a substantial decrease in performance will result.

Site NameThe site name may be specified by the directive, which sets -S- as the site name to be used in archive entries generated by Gaussian. The default site name is GINC. For example, the following line sets the site name to EXPCONS:-S- EXPCONS

Typical Default SettingsHere are reasonable default settings for various machine configurations:

For a small workstation with 64 MB memory and 1 GB of disk, the default algorithms and memory allocation are fine. MaxDisk is all that need be specified.-#- MaxDisk=400MB

On a powerful workstation with 8 processors and 1 GB of memory, being used for large jobs, all 8 processors should be used by default. Also, more memory should be given to each job:-M- 64MW -P- 8 -#- MaxDisk=10GB

User Defaults Files

Gaussian users may set their own defaults by creating their own Default.Route file. Gaussian checks the current working directory for a file of this name when a job is initiated. Settings in the local file take precedence over those in the site-wide file, and options specified in the route section of the job take precedence over both of them.

Gaussian 03 Online ManualLast update: 4 April 2003

Utility ProgramsThis page discusses various utility programs included with Gaussian 03. The utilities are discussed in alphabetical order within this chapter. Most utilities are available for both UNIX and Windows versions of Gaussian. However, be sure to consult the release notes accompanying the program for information pertaining to specific operating systems. The following lists the available utilities and their functions (starred items are included on the Gaussian 03W Utilities menu): c8603 chkchk* cubegen* cubman* formchk* Converts checkpoint files from previous program versions to Gaussian 03 format. Displays the route and title sections from a checkpoint file. Standalone cube generation utility. Manipulates Gaussian-produced cubes of electron density and electrostatic potential (allowing them to be added, subtracted, and so on). Converts a binary checkpoint file into an ASCII form suitable for use with visualization programs and for moving checkpoint files between different types of computer systems. Prints frequency and thermochemistry data from a checkpoint file. Alternate isotopes, temperature, pressure and scale factor can be specified for the thermochemistry analysis. Determines memory requirements for frequency calculations. Performs optimizations of variables other than molecular coordinates. On-line help for Gaussian. Standalone molecular mechanics program. Conversion between a variety of molecular geometry specification formats. Route section syntax checker and non-standard route generation. Convert a formatted checkpoint file back to its binary form (e.g., after moving it from a different type of computer system).

freqchk* freqmem gauopt ghelp mm newzmat* testrt* unfchk*

GAUSS_MEMDEF Environment VariableThe GAUSS_MEMDEF environment variable may be used to increase the memory available to utilities which do not offer such an option themselves. Its value should be set to the desired amount of memory in words.

Gaussian 03 Online ManualLast update: 10 October 2003

Running GaussianThis page describes the operating system commands required to execute Gaussian on Unix-based computer systems. See the additional instructions accompanying the program for the equivalent information for other operating systems. This discussion assumes that the program has already been installed. The final section lists the component links of the Gaussian 03 program. Running Gaussian involves the following activities:

Creating Gaussian input describing the desired calculation. Specifying the locations of the various scratch files. Specifying resource requirements. Initiating program execution, in either interactive or batch mode.

In this page, we will assume that a basic Gaussian input file has been created, and our discussion will examine the remaining three items on the list.

Gaussian uses several scratch files in the course of its computation. They include:

The Checkpoint file: name.chk The Read-Write file: name.rwf The Two-Electron Integral file: name.int The Two-Electron Integral Derivative file: name.d2e

By default, these files are given a name generated from the process ID of the Gaussian process, and they are stored in the scratch directory, designated by the GAUSS_SCRDIR environment variable (UNIX). You may also see files of the form name.inp in this directory. These are the internal input files used by the program. If the environment variable is unset, the location defaults to the current working directory of the Gaussian process.

By default, these files are deleted at the end of a successful run. However, you may wish to save the checkpoint file for later use in another Gaussian job, for use by a visualization program, to restart a failed job, and so on. This may be accomplished by naming the checkpoint file, providing an explicit name and/or location for it, via a %Chk command within the Gaussian input file. Here is an example:%Chk=water

This command, which is placed at the beginning of the input file (before the route section-see chapter 3 for details), gives the checkpoint file the name water.chk, overriding the usual generated name and causing the file to be saved at job conclusion. In this case, the file will reside in the current directory. However, a command like this one will specify an alternate directory location as well as filename:%Chk=/chem/scratch2/water

If disk space in the scratch directory is limited, but space is available elsewhere on the system, you may want to split the scratch files among several disk locations. The following commands allow you to specify the names and locations of the other scratch files:%RWF=path %Int=path %D2E=path Read-Write file Integral file Integral Derivative file

In general, the read-write file is by far the largest, and so it is the one for which an alternate location is most often specified.

Splitting Scratch Files Across DisksAn alternate syntax is provided for splitting the Read-Write file, the Integral file, and/or the Integral Derivative file among two or more disks (or file systems). Here is the syntax for the %RWF command: %RWF=loc1,size1,loc2,size2, ... where each loc is a directory location or a file pathname, and each size is the maximum size for the file segment at that location. Gaussian will automatically generate unique filenames for any loc which specifies a directory only. On UNIX systems, directory specifications (without filenames) must include a terminal slash. By default, the sizes are in units of words; the value may be followed by KB, MB or GB (without intervening spaces) to designate KB, MB or GB, respectively, or by KW, MW or GW to indicate units of kilowords, megawords or gigawords, respectively. Note that 1 MB = 10242 bytes = 1,048,576 bytes (not 1,000,000 bytes).

A value of -1 for any size parameter indicates that any and all available space may be used, and a value of 0 says to use the current size of an existing segment. -1 is useful only for the last file specified, for which it is the default. For example, the following directive splits the Read-Write file across three disks:%RWF=/dalton/s0/,60MW,/scratch/,800MB,/temp/s0/my_job,-1

The maximum sizes for the file segments are 480 MB, 800 MB, and unlimited, respectively. Gaussian will generate names for the first two segments, and the third will be given the name my_job. Note that the directory specifications include terminal slashes. Due to limitations in current UNIX implementations, -1 should be used with caution, as it will attempt to extend a file segment beyond all remaining disk capacity on these systems; using it will also have the side effect of keeping any additional file segments included in the list from ever being used.

Saving and Deleting Scratch FilesBy default, unnamed scratch files are deleted at the end of the Gaussian run, and named files are saved. The %NoSave command may be used to change this default behavior. When this directive is included in an input file, named scratch files whose directives appear in the input file before %NoSave will be deleted at the end of a run (as well as all unnamed scratch files). However, if the % directive naming the file appears after the %NoSave directive, the file will be retained. For example, these commands specify a name for the checkpoint file, and an alternate name and directory location for the readwrite file, and cause only the checkpoint file to be saved at the conclusion of the Gaussian job:%RWF=/chem/scratch2/water %NoSave %Chk=water Files to be deleted go here. Files to be saved go here.

Initialization FilesThe Gaussian system includes initialization files to set up the user environment for running the program. These files are:$g03root/g03/bsd/g03.login $g03root/g03/bsd/g03.profile C shell Bourne shell

Note that the g03root environment variable must be set up by the user. Thus, it is customary to include lines like the following within the .login or .profile file for Gaussian users:.login files:

setenv g03root location source $g03root/g03/bsd/g03.login .profile files: g03root=location export g03root . $g03root/g03/bsd/g03.profile

Once things are set up correctly, the g03 command is used to execute Gaussian 03 (see below).

The %Mem command controls the amount of dynamic memory to be used by Gaussian. By default, 6 megawords are used. This can be changed to n double-precision words by specifying:%Mem=n

For example, the following command sets memory use to 64 million bytes:%Mem=8000000

The value given to %Mem may also be followed by KB, KW, MB, MW, GB or GW (no intervening spaces) to denote other units. For example, the following command also sets the amount of dynamic memory to 64 MB:%Mem=64MB

Even larger allocations may be needed for very large direct SCF calculations-at least 3N2 words, where N is the number of basis functions. Frequency and post-SCF calculations involving f functions should be given 6 MWords if possible. Using more than 6 million words for moderate-sized calculations (i.e., a direct SCF with less than 500 basis functions) does not improve performance on most systems. Warning: Requesting more memory than the amount of physical memory actually available on a computer system will lead to very poor performance. If Gaussian is being used on a machine with limited physical memory, so that the default of 48 MB is not available, the default algorithms as well as the default memory allocation should be set appropriately during installation. See this page for more details on using Gaussian efficiently.

Once all input and resource specifications are prepared, you are ready to run the program. Gaussian 03 may be run interactively using one of two command styles:

g03 job-name g03 output-file

In the first form, the program reads input from job-name.com and writes its output to jobname.log. When job-name is not specified, the program reads from standard input and writes to standard output, and these can be redirected or piped in the usual UNIX fashion. Either form of command can be forced in the background in the same manner as any shell command using &.

Scripts and GaussianScripts designed to run Gaussian 03 may also be created in several ways (we will use the C shell in these examples). First, g03 commands like those above may be included in a shell script. Secondly, actual Gaussian input may be included in the script using the Status g03 < $file > $file:r.log echo "$file Done with status $status" >> Status end echo "All Done." >> Status

The following more complex script creates Gaussian input files on-the-fly from the partial input in the files given as the script's command line arguments. The latter are lacking full route sections; their route sections consist of simply a # sign or a # line

containing special keywords needed for that molecular system, but no method, basis set, or calculation type. The script creates a two-step job for each partial input file-a Hartree-Fock optimization followed by an MP2 single point energy calculation-consisting of both the literal commands included in the script and the contents of each file specified at script execution time. It includes the latter by exploiting the Gaussian 03 @ include file mechanism:#!/bin/csh echo "Current Job Status:" > Status foreach file ($argv) echo "Starting file $file at `date`" >> Status g03 > Status end # end of foreach echo "All Done." >> Status

Batch Execution with NQSGaussian may be run using the NQS batch facility on those UNIX systems that support it. The subg03 command, defined in the initialization files, submits an input file to a batch queue. It has the following syntax:subg03 queue-name job-name [-scrdir dir1] [-exedir dir2] [-p n]

The two required parameters are the queue and job names. Input is taken from jobname.com and output goes to job-name.log, just as for interactive runs. The NQS log file is sent to job-name.batch-log. The optional parameters -scrdir and -exedir are used to override the default scratch and executable directories, respectively. Any other parameters are taken to be NQS options. In particular, -p n can be used to set the priority within the queue to n. This is priority for initiation (1 being lowest), and does not affect the run-time priority. To submit an NQS job from an interactive session, a file like the following should be created (with filename name.job):# QSUB -r name -o name.out -eo # QSUB -lt 2000 -lT 2100 # QSUB -lm 7mw -lM 7mw g03 The default in Gaussian is a semi-direct algorithm. The AO integrals may be written out for use in the SCF phase of the calculation or the SCF may be done directly or in-core. The transformation recomputes the AO integrals as needed and leaves only the minimum number of MO integrals on disk (see below). The remaining terms are computed by recomputing AO integrals. A full transformation is performed if MaxDisk supplies sufficient disk for doing so. This will be faster than other approaches unless the computer system's I/O is very slow. The conventional algorithm, which was the default in Gaussian 90, involves storing the AO integrals on disk, reading them back during the transformation, and forming all of the MO two-electron integrals except those involving four

virtual orbitals. The four virtual terms were computed by reading the AO integrals. This procedure can be requested in Gaussian by specifying Tran=Conven in the route section. However, it is appropriate only on very slow machines like legacy PCs. If a post-SCF calculation can be done using a full integral transformation while keeping disk usage under MaxDisk, this is done; if not, a partial transformation is done and some terms are computed in the AO basis. Thus, it is crucial for a value for MaxDisk to be specified explicitly for these types of jobs, either within the route section or via a system wide setting in the Default.Route file. If MaxDisk is left unset, the program assumes that disk is abundant and performs a full transformation by default. If MaxDisk is not set and sufficient disk space is not available for a full transformation, the job will fail. The following points summarize the effect of MaxDisk for post-SCF methods:

CID, CISD, CCD, BD, and QCISD energies also have a fixed storage requirement proportional to O2N2, with a large factor, but obey MaxDisk in avoiding larger storage requirements. CCSD, CCSD(T), QCISD(T), and BD(T) energies have fixed disk requirements proportional to ON3 which cannot be limited by MaxDisk. CID, CISD, CCD, QCISD densities and CCSD gradients have fixed disk requirements of about N4/2 for closed-shell and 3N4/4 for open-shell.

Excited State Energies and GradientsIn addition to integral storage selection, the judicious use of the restart facilities can improve the economy of CIS and TD calculations.

Integral StorageExcited states using CI with single excitations can be done using five methods (labeled by their corresponding option to the CIS keyword). Note that only the first two options are available for the TD method: Direct Solve for the specified number of states using iterative diagonalization, forming the product vectors from two-electron integrals computed as needed. This algorithm reduces memory and disk requirements to O(N2). InCore Requests that the AO Raffenetti combinations be held in memory. In-core is quite efficient, but is only practical for small molecular systems or large memory computers as N4/4 words of memory are required. This approach is used automatically if there is sufficient memory available.

MO Solve for the specified number of states using iterative (Davidson) diagonalization, forming the product vectors using MO integrals. This is the fastest method and is the default. This algorithm is an efficient choice up to about 150 basis functions, depending on the number of occupied orbitals. The more occupied orbitals, the sooner the direct algorithm should be used. Since only integrals involving two virtuals are needed (even for gradients) an attempt is made to obey MaxDisk. The minimum disk required is about 4O2N2 (6O2N2 for open-shell). AO Solve for the specified number of states using iterative diagonalization, forming the product vectors from written-out AO integrals. This is a slow method and is never the best choice. ICDiag The entire CIS Hamiltonian matrix is loaded into core and diagonalized. This produces all possible states, but requires O2V2 memory and O3V3 CPU time. Accordingly, it is practical only for very small molecular systems and for debugging purposes.

Restarting Jobs and Reuse of WavefunctionsCIS and TD jobs can be restarted from a Gaussian checkpoint file. This is of limited use for smaller calculations, which may be performed in the MO basis, as new integrals and transformation must be done, but is invaluable for direct CIS. If a direct CIS job is aborted during the CIS phase, then SCF=Restart should be specified in addition to CIS=Restart or TD=Restart, as the final SCF wavefunction is not moved to its permanent location (suitable for Guess=Read) until the entire job step (or optimization step) completes.

CIS Excited State DensitiesIf only density analysis is desired, and the excited states have already been found, the CIS density can be recovered from the checkpoint file, using Density=(Check,Current) Guess=Only, which recovers whatever generalized density was stored for the current method (presumably CIS) and repeats the population analysis. Note that the one-particle (unrelaxed) density as well as the generalized (relaxed) density can be examined, but that dipole moments and other properties at the CIS level are known to be much less accurate if the one-particle density is used (i.e., if the orbital relaxation terms are neglected) [108,447]. Consequently, the use of the CIS one-particle density is strongly discouraged, except for comparison with the correct density and with other programs that cannot compute the generalized density. Separate calculations are required to produce the generalized density for several states, since a CPHF calculation must be performed for each state. To do this, first solve for all the states and the density for the first excited state:

# CIS=(Root=1,NStates=N) Density=Current

if N states are of interest. Then do N-1 additional runs, using a route section of the form:CIS=(Read,Root=M,NStates=N) Density=Current

for states M=2 through N.

Pitfalls for Open-Shell Excited StatesSince the UHF reference state is not an eigenfunction of S2, neither are the excited states produced by CIS or TD [573].

Stability CalculationsTests of Triplet and Singlet instabilities of RHF and UHF and restricted and unrestricted DFT wavefunctions can be requested using the Stable keyword. The MO, AO, Direct, and InCore options are available, which request the corresponding algorithm. The default is Direct. Direct stability calculations can be restarted as described above for CIS.

CASSCF EfficiencyThe primary challenge in using the CASSCF method is selecting appropriate active space orbitals. There are several possible tactics:

Use the standard delocalized initial guess orbitals. This is sometimes sufficient, e.g. if the active space consists of all p electrons. Use Guess=Only to inspect the orbitals and determine whether any alterations are required before running the actual calculation. Use localized initial guess orbitals. This is useful if specific bond pairs are to be included, since localization separates electron pairs. Use the natural orbitals from the total density from a UHF calculation (CASUNO) [415,416]. For singlets, this requires that one has coaxed the UHF run into converging to a broken symmetry wavefunction (normally with Guess=Mix). It is most useful for complex systems in which it is not clear which electrons are most poorly described by doubly-occupied orbitals.

In all cases, a single-point calculation should be performed before any optimization, so that the converged active space can be checked to ensure that the desired electrons have been correlated before proceeding. There are additional considerations in solving for CASSCF wavefunctions for excited states (see the discussion of the CASSCF keyword for details).

CASSCF Frequencies

CASSCF frequencies require large amounts of memory. Increasing the amount of available memory will always improve performance for CASSCF frequency jobs (the same is not true of frequency calculations performed with other methods). These calculations also require O2N2 disk space.

Running Gaussian Test JobsAn extensive set of test jobs for Gaussian are provided, along with their corresponding output files. The input files are found in directory $g03root/g03/tests/com. Output files are in a separate subdirectory under $g03root/g03/tests for each machine, such as tests/rs6k for the RS/6000 files. A command file is provided which runs ranges of test jobs automatically (described below). If you build the program from source code, we recommend that you run a few of the test jobs to verify that the program has been built correctly. However, it is not usually necessary to run the entire test suite. You do not need to run test jobs for binary distributions. Test job input files have names of the form testnnn.com. Tests 1, 28, 94, 155, 194, 296, and 302 cover a range of Gaussian capabilities. Note that some test jobs are intended for fast hardware and are quite expensive on smaller, slower computer systems. The file $g03root/g03/tests/tests.idx lists what each test job does, and the reference output files provided with Gaussian indicate how long the jobs can be expected to take. You can extract this information using the following commands:$ cd $g03root/g03/tests/`gau-machine` $ grep "cpu time" *.log

The utility gau-machine returns the system name on all UNIX platforms (i.e., a keyword corresponding to the type of computer on which you are running).

Rename Existing Default.Route File Before Running Test JobsIf you choose to run some or all of the Gaussian test jobs, you will need to make sure that they run with the program's built-in default settings. Therefore, you'll need to rename both the site-wide Default.Route file (located in the $g03root/g03 directory) as well as any individual version of the defaults file that you may have prior to running any test job. Note that certain settings in this file can cause some test jobs to fail.

Examples

The script submit.csh can be used to run test jobs. It accepts two parameters: the numbers of the first and last jobs to run (by default, all of the tests are run). Note that you should run the test jobs from a separate directory to prevent them from clobbering the reference output.

The following commands illustrate the recommended procedure for running a test job, using the directory /chem/newtests as the test job executor area and test job 28 as an example:

$ mkdir /chem/newtests; cd /chem/newtests $ ln -s $g03root/g03/tests/com . $ mkdir `gau-machine` $ $g03root/g03/tests/submit.csh m n &

The final command runs test m through n. After each test job finishes, verify that it completed successfully. Then, compare its current output with the reference output using the d1 script. For example:$ $g03root/g03/tests/d1 m n

The d1 script filters out insignificant differences from the output files for test jobs m through n and pipes the remaining output through more. The differences that appear should be limited to non-substantive items.

This page outlines the various size limitations that exist within Gaussian 03. These limitations occur in the form of fixed dimension statements and algorithm design limitations, and their overall effect is to limit the size and types of calculation that can be performed.

Z-matrix LimitationsThere are restrictions on the size of a Z-matrix, the maximum number of variables and the maximum number of atoms within a calculation. These are set consistently for a maximum of 20000 real atoms (including ghost but not dummy atoms), and a maximum of 20000 Z-matrix centers (atoms, ghost atoms, and dummy atoms). In addition, the maximum number of variables that can be specified in an optimization is unlimited for Berny optimizations but must not exceed 50 for Murtaugh-Sargent or Opt=EF optimizations (30 for Fletcher-Powell optimizations).

Basis Set LimitationsThroughout the Gaussian 03 system, basis set limitations manifest themselves in two ways. The main restriction is imposed within the integral evaluation programs and limits the number of primitive gaussian functions and how they are combined into atomic orbital basis functions. Secondly, dimensioning requirements limit the total number of basis functions that can be used in a few of the older of the energy evaluation procedures.

Integral Program LimitationsTo understand fully the limitations in the integral programs, the reader must have some understanding of the concepts presented in discussion of the Gen keyword (input of nonstandard bases). In the terminology introduced there, the limitations are as follows: the maximum total number of primitive shells is 60000; the maximum number of primitive d-shells is 20000; the maximum number of primitive f-shells and higher is 20000; the maximum number of contracted shells is 20000. The maximum degree-of-contraction allowed is 100. The other major restriction that appears in the integral programs is in the manner in which integral labels are packed. These limits apply only when two-electron integrals are written out and can be avoided entirely by using SCF=Direct (which is the default in Gaussian 03). Normally, disk space limitations force the use of direct methods before the following limits are reached. When the conventional integral storage procedure is selected (in contrast to the Raffenetti ("PK") storage modes [574]), the suffixes , , , and of the two-electron integral (| ) are packed into a computer word as 8-bit quantities in the UNIX version, and as 16bit quantities in the UniCOS version. This in effect limits the number of basis functions to 255 under UNIX for conventional calculations in this mode. When the Raffenetti modes are selected (for SCF=Conventional except when Tran=Conventional, Stable=Complex, or CASSCF is also specified), the two linearized suffixes () and () (where (=((-1)/2)+) are packed into a word. This imposes a theoretical limit of 361 basis functions for conventional calculations on the 32-bit computer systems. These limits do not apply to direct calculations.

SCF and Post-SCF LimitationsThere are only a few other links which have additional dimensioning limits. There is no further restriction for RHF, UHF, ROHF, DFT, MP, CI, QCISD, CC, or BD calculations using the default algorithms. Complex HF calculations are limited to 180 basis functions, and complex MP2 calculations are effectively limited by a requirement of O(N3) words of main memory, and are also limited to f functions. The GVB program is limited to 100 paired orbitals, which is not a restriction in practice. The remaining restrictions are in some of alternative programs which must be specifically requested. SCF=DM is limited to 255 basis functions, although the preferred SCF=QC can be used with direct SCF and imposes no dimensioning limits. Link 903 (in-core MP2) requires O(N3) words of main memory.

NBO DimensionsNBO is dimensioned for 200 atoms and 10000 basis functions.

Gaussian 03 input consists of a series of lines in an ASCII text file. The basic structure of a Gaussian input file includes several different sections:

Link 0 Commands: Locate and name scratch files (not blank line terminated). Route section (# lines): Specify desired calculation type, model chemistry and other options (blank line terminated). Title section: Brief description of the calculation (blank line terminated). Molecule specification: Specify molecular system to be studied (blank line terminated). Optional additional sections: Additional input needed for specific job types (usually blank line terminated).

Many Gaussian 03 jobs will include only the second, third, and fourth sections. Here is an example of such a file, which requests a single point energy calculation on water:# HF/6-31G(d) water energy 0 1 O -0.464 0.177 H -0.464 1.137 H 0.441 -0.143 Route section Title section Molecule specification 0.0 0.0 0.0

In this job, the route and title sections each consist of a single line. The molecule specification section begins with a line giving the charge and spin multiplicity for the molecule: 0 charge (neutral molecule) and spin multiplicity 1 (singlet) in this case. The charge and spin multiplicity line is followed by lines describing the location of each atom in the molecule; this example uses Cartesian coordinates to do so. Molecule specifications are discussed in more detail later in this chapter. The following input file illustrates the use of Link 0 commands and an additional input section:%Chk=heavy #HF/6-31G(d) Opt=ModRedundant Opt job 0 1 atomic coordinates 3 8 2 1 3 opt. Link 0 section Route section Title section Molecule Specification section Add a bond and an angle to the internal coordinates used during the geom.

This job requests a geometry optimization. The input section following the molecule specification is used by the Opt=ModRedundant keyword, and it serves to add an

additional bond and angle in the internal coordinates used in the geometry optimization. The job also specifies a name for the checkpoint file. Link 0 commands were introduced in the last chapter and are discussed individually in the penultimate section of this chapter. The remaining input sections are discussed in the subsequent subsections of this introductory section. For convenience, the table below lists all possible sections that might appear within a Gaussian 03 input file, along with the keywords associated with each one.

In general, Gaussian input is subject to the following syntax rules:

Input is free-format and case-insensitive. Spaces, tabs, commas, or forward slashes can be used in any combination to separate items within a line. Multiple spaces are treated as a single delimiter. Options to keywords may be specified in any of the following forms:keyword = option keyword(option) keyword=(option1, option2, ...) keyword(option1, option2, ...)

Multiple options are enclosed in parentheses and separated by any valid delimiter (commas are conventional and are shown above). The equals sign before the opening parenthesis may be omitted, or spaces may optionally be included before and/or after it. Note that some options also take values; in this case, the option name is followed by an equals sign: for example, CBSExtrap(NMin=6). All keywords and options may be shortened to their shortest unique abbreviation within the entire Gaussian 03 system. Thus, the Conventional option to the SCF keyword may be abbreviated to Conven, but not to Conv (due to the presence of the Convergence option). This holds true whether or not both Conventional and Convergence happen to be valid options for any given keyword. The contents of an external file may be included within a Gaussian 03 input file using the following syntax: @filename. This causes the entire file to be placed at the current location in the input stream. Appending /N to such commands will prevent the included file's contents from being echoed at the start of the output file. Comments begin with an exclamation point (!), which may appear anywhere on a line. Separate comment lines may appear anywhere within the input file.

Gaussian 03 Input Section OrderingSection Keywords Final blank line?

Link 0 commands Route Section (# lines) Extra Overlays Title section Molecule specification Modifications to coordinates Connectivity specifications 2nd title and molecule specification Modifications to 2nd set of coordinates Connectivity specifications for 2nd set of coordinates 3rd title and initial TS structure Modifications to 3rd set of coordinates Connectivity specifications for 3rd set of coordinates Atomic masses Frequency of interest Initial force constants (Cartesian) Accuracy of energy & forces BOMD/ADMP input (1 or more sections) Basis set specification Basis set alterations

% commands all ExtraOverlays all all Opt=ModRedundant Geom=Connect or ModConnect Opt=QST2 or QST3 Opt=ModRedun and QST2 or QST3 Geom=Connect or ModConnect and Opt=ModRedun and QST2 or QST3 Opt=QST3 Opt=(ModRedun, QST3) Geom=Connect or ModConnect Opt=(ModRedun, QST3) IRC=ReadIsotopes CPHF=RdFreq Opt=FCCards Opt=ReadError ADMP and BOMD

no yes yes yes yes yes yes yes yes

yes yes for both yes

yes yes yes yes no yes yes yes yes yes yes yes no yes yes

Gen, GenECP, ExtraBasis Massage ExtraBasis, Pseudo=Cards, ECP specification GenECP Density fitting basis set specification Extra Density Basis Background charge distribution Charge Finite field coefficients Field=Read Symmetry types to combine Guess=LowSymm Orbital specifications (separate & Guess=Cards ) Orbital alterations (separate & ) Guess=Alter

Orbital reordering (separate & ) PCM solvation model input Filename for COSMO/RS Weights for CAS state averaging States of interest for spin orbit coupling # Orbitals/GVB pair Alternate atomic radii Data for electrostatic properties Cube filename (& Cards input) NBO input Orbital freezing information OVGF orbitals to refine Temperature, pressure, atomic masses PROAIMS/Pickett output filename

Guess=Permute SCRF=Read SCRF=COSMORS CASSCF=StateAverage CASSCF=Spin GVB Pop=ReadRadii or ReadAtRadii Prop=Read or Opt Cube Pop=NBORead ReadWindow options OVGF=ReadOrbitals Freq=ReadIsotopes Output=WFN or Pickett

no yes no no no no yes yes yes no yes yes no no

The route section of a Gaussian 03 input file specifies the type of calculation to be performed. There are three key components to this specification:

The job type The method The basis set

The following table lists the job types available in Gaussian 03:

SP Single point energy. Opt Geometry optimization. Freq Frequency and thermochemical analysis. IRC Reaction path following. IRCMax Find the maximum energy along a specific reaction path. Scan Potential energy surface scan. Polar Polarizabilities and hyperpolarizabilities. ADMP and BOMD Direct dynamics trajectory calculation. Force Compute forces on the nuclei. Stable Test wavefunction stability. Volume Compute molecular volume. Density=Checkpoint Recompute population analysis only. Guess=Only Print initial guess only; recompute population analysis. ReArchive Extract archive entry from checkpoint file only.

In general, only one job type keyword should be specified. The exceptions to this rule are:

Polar and Opt may be combined with Freq (although SCRF may not be combined with Opt Freq). In the latter case, the geometry optimization is automatically followed by a frequency calculation at the optimized structure. Opt may be combined with IRCMax in order to specify options for the optimization portion of the calculation.

When no job type keyword is specified within the route section, the default calculation type is usually a single point energy calculation (SP). However, a route section of the form: method2/basis2 // method1/basis1 may be used to request an optimization calculation (at method1/basis1) followed by a single point energy calculation (at method2/basis2) at the optimized geometry. For example, the following route section requests a HF/6-31G(d) geometry optimization followed by a single point energy calculation using the QCISD/6-31G(d) model chemistry:# QCISD/6-31G(d)//HF/6-31G(d) Test

In this case, the Opt keyword is optional and is the default. Note that Opt Freq calculations may not use this syntax. Predicting Molecular Properties The following table provides a mapping between commonly-desired predicted quantities and the Gaussian 03 keywords that will produce them:

Atomic charges: Pop Dipole moment: Pop Electron affinities via propagator methods: OVGF Electron density: cubegen Electronic circular dichroism: TD Electrostatic potential: cubegen, Prop Electrostatic-potential derived charges: Pop=Chelp, ChelpG or MK Frequency-dependent polarizabilities/hyperpolarizabilities: Polar CPHF=RdFreq High accuracy energies: CBS-QB3, G2, G3, W1U Hyperfine coupling constants (anisotropic): Prop Hyperfine spectra tensors (incl. g tensors): Freq=(VCD, VibRot[, Anharmonic]) Hyperpolarizabilities: Freq, Polar Ionization potentials via propagator methods: OVGF IR and Raman spectra: Freq Pre-resonance Raman spectra: Freq CPHF=RdFreq Molecular orbitals: Pop=Regular Multipole moments: Pop NMR shielding and chemical shifts: NMR NMR spin-spin coupling constants: NMR=SpinSpin Optical rotations: Polar=OptRot CPHF=RdFreq

Polarizabilities: Freq, Polar Thermochemical analysis: Freq UV/Visible spectra: CIS, Zindo, TD Vibration-rotation coupling: Freq=VibRot Vibrational circular dichroism: Freq=VCD

The combination of method and basis set specifies a model chemistry to Gaussian, specifying the level of theory. Every Gaussian job must specify both a method and basis set. This is usually accomplished via two separate keywords within the route section of the input file, although a few method keywords imply a choice of basis set. The following table lists methods which are available in Gaussian, along with the job types for which each one may be used. Note that the table lists only analytic optimizations, frequencies, and polarizability calculations; numerical calculations are often available for unchecked methods (see the discussion of the specific keyword in question for details).

If no method keyword is specified, HF is assumed. Most method keywords may be prefaced by R for closed-shell restricted wavefunctions, U for unrestricted open-shell wavefunctions, or RO for restricted open-shell wavefunctions: for example, ROHF, UMP2, or RQCISD. RO is available only for Hartree-Fock, all Density Functional methods, AM1, MINDO3 and MNDO and PM3 semi-empirical energies and gradients, and MP2 energies; note that analytic ROMP2 gradients are not yet available. In general, only a single method keyword should be specified, and including more than one of them will produce bizarre results. However, there are exceptions:

CASSCF may be specified along with MP2 to request a CASSCF calculation including electron correlation. ONIOM and IRCMax jobs require multiple method specifications. However, they are given as options to the corresponding keyword. The form model2 // model1 described previously may be used to generate an automatic optimization followed by a single point calculation at the optimized geometry.

Most methods require a basis set be specified; if no basis set keyword is included in the route section, then the STO-3G basis will be used. The exceptions consist of a few methods for which the basis set is defined as an integral part of the method; they are listed below:

All semi-empirical methods, including ZINDO for excited states. All molecular mechanics methods. Compound model chemistries: all Gn, CBS and W1 methods.

The following basis sets are stored internally in the Gaussian 03 program (see references cited for full descriptions), listed below by their corresponding Gaussian 03 keyword (with two exceptions):

STO-3G [309,310] 3-21G [311,312,313,314,315,316] 6-21G [311,312] 4-31G [317,318,319,320] 6-31G [317,318,319,320,321,322,323,324,325,326] 6-31G: Gaussian 03 also includes the 6-31G and 6-31G basis sets of George Petersson and coworkers, defined as part of the Complete Basis Set methods [88,327]. These are accessed via the 6-31G(d') and 6-31G(d',p') keywords, to which single or double diffuse functions may also be added; f functions may also be added: e.g., 6-31H(d'f), and so on. 6-311G: Specifies the 6-311G basis for first-row atoms and the McLean-Chandler (12s,9p) (621111,52111) basis sets for second-row atoms [328,329] (note that the basis sets for P, S, and Cl are those called "negative ion" basis sets by McLean

and Chandler; these were deemed to give better results for neutral molecules as well), the basis set of Blaudeau and coworkers for Ca and K [322], the WachtersHay [330,331] all electron basis set for the first transition row, using the scaling factors of Raghavachari and Trucks [332], and the 6-311G basis set of McGrath, Curtiss and coworkers for the other elements in the third row [324,333,334]. Note that Raghavachari and Trucks recommend both scaling and including diffuse functions when using the Wachters-Hay basis set for first transition row elements; the 6-311+G form must be specified to include the diffuse functions. MC-311G is a synonym for 6-311G. D95V: Dunning/Huzinaga valence double-zeta [335]. D95: Dunning/Huzinaga full double zeta [335]. SHC: D95V on first row, Goddard/Smedley ECP on second row [335,336]. Also known as SEC. CEP-4G: Stevens/Basch/Krauss ECP minimal basis [337,338,339]. CEP-31G: Stevens/Basch/Krauss ECP split valance [337,338,339]. CEP-121G: Stevens/Basch/Krauss ECP triple-split basis [337,338,339]. Note that there is only one CEP basis set defined beyond the second row, and all three keywords are equivalent for these atoms. LanL2MB: STO-3G [309,310] on first row, Los Alamos ECP plus MBS on NaBi [340,341,342]. LanL2DZ: D95V on first row [335], Los Alamos ECP plus DZ on Na-Bi [340,341,342]. SDD: D95V up to Ar [335] and Stuttgart/Dresden ECPs on the remainder of the periodic table [343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,36 1,362,363,364,365,366,367]. The SDD, SHF, SDF, MHF, MDF, MWB forms may be used to specify these basis sets/potentials within Gen basis input. Note that the number of core electrons must be specified following the form (e.g., MDF28 for the MDF potential replacing 28 core electrons). SDDAll: Sele