Quick Start Running Gaussian In This Quick Start: This chapter breaks into two branches:one for the Windows version(here Gaussian 94W),and one for all of the workstation and supercomputer versions.Although their Tutorial for UNIX capabilities are identical,their user interfaces are different enough to warrant separate and VMS Systems sections.The output produced by both of them is identical,and so we have Tutorial for recombined the two threads as we take our first look at Gaussian output in"A Quick Windows Systems Tour of Gaussian Output"on page xlix.At that point,and throughout the remainder of this book,the text will apply to all versions of Gaussian.The few interface A Quick Tour of differences between versions will be noted as appropriate. Gaussian Output The first subsection discusses running Gaussian on UNIX and VMS systems and uses Gaussian 94 as an example.The Gaussian 94W tutorial begins on page xxxviii. Tutorial for UNIX and VMS Systems This tutorial assumes that Gaussian 94 is already installed on your computer. Instructions for doing so are included with your program package. Executing a Gaussian job involves the following steps: Setting up the Gaussian environment (usually handled by your login initialization file). 翼 Preparing the input file. Running the program,either interactively or via a batch queue. ◆ Examining and interpreting the output. We'll discuss each of these steps in turn. 1.Execute the appropriate commands to set up the Gaussian environment on your systom. You must execute the Gaussian 94 initialization file included with the program in order to run it.This file sets the values of some environment variables(UNIX)or logical names(VMS)needed by the program.Usually,this file is executed from within your user initialization file (i.e.,.login,.profile,or LOGIN.COM,as appropriate), although you can also run the commands by hand. Exploring Chemistry with Electronic Structure Methods xxxiii
In This Quick Start: Tutorial for UNIX and VMS Systems Tutorial for Windows Systems AQuick Tour of Gaussian Output Running Gaussian This chapter breaks into two branches: one for the Windows version (here Gaussian 94W), and one for all ofthe workstation and supercomputer versions. Although their capabilities are identical, their user interfaces are different enough to warrant separate sections. The output produced by both of them is identical, and so we have recombined the two threads as we take our first look at Gaussian output in "A Quick Tour of Gaussian Output" on page xlix. At that point, and throughout the remainder of this book, the text will apply to all versions of Gaussian. The few interface differences between versions will be noted as appropriate. The first subsection discusses running Gaussian on UNIX and VMS systems and uses Gaussian 94 as an example. The Gaussian 94W tutorial begins on page xxxviii. Tutorial for UNIX and VMS Systems This tutorial assumes that Gaussian 94 is already installed on your computer. Instructions for doing so are included with your program package. Executing a Gaussian job involves the following steps: • Setting up the Gaussian environment (usually handled by your login initialization me). • Preparing the input file. • Running the program, either interactively or via a batch queue. • Examining and interpreting the output. We'll discuss each of these steps in turn. 1. Execute the appropriate commands to set up the Gaussian environment on your .y.tem. You must execute the Gaussian 94 initialization me included with the program in order to run it. This file sets the values of some environment variables (UNIX) or logical names (VMS) needed by the program. Usually, this file is executed from within your user initialization file (i.e., .login, .profile, or LOGIN.COM, as appropriate), although you can also run the commands by hand. Exploring Chemistry with Electronic Structure Methods xxxiii
Quick Running Gaussian Start These are the commands needed to prepare to run Gaussian 94: UNIX:C Shell 8 setenv g94root directory &source $g94root/g94/bsd/g94.login UNIX:Bourne Shell g94rootadirectory;export g94root s.Sg94root/g94/bsd/g94.protile VMS @disk:[G94.VMS.EDT]G94Login.Com UNIX users will need to specify the location of the Gaussian 94 tree on their system. VMS users will need to specify the disk location of the [G94]directory. You may want to add these commands to your user initialization file now if you haven't already done so.VMS users will also want to include a line like the following in their LOGIN.COM file,setting their working set to its maximum value: Set Work/NoAdjust/Quota=65536/Limit=65536 Next,we'll prepare a Gaussian input file for an energy calculation on water. 2.Start any text editor and enter the following into a new file: UNIX #T RHF/6-31G(d)Test VMS RunGauss #T RHF/6-31G(d)Test VMS users begin their input file by executing the command to run Gaussian;input to the program follows.UNIX users will redirect their input file to standard input of the Gaussian 94 command. The line beginning with is the route section for this job.The first line of the route section always begins with a pound sign in the first column(UNIX folks:this is not a comment marker).#T requests terse output from the program (only the essential results),alone requests normal(traditional)Gaussian output,and #P requests more detail in the output file. xxxiv Exploring Chemistry with Electronic Structure Methods
Quick Start I Running Gaussian These are the commands needed to prepare to run Gaussian 94: UNIX: C Shell % .etenv g94root directory % .ource $g94root/g94/bad/g94.1ogin UNIX: Bourne Shell $ g94root~di~cwry; export g94root $ • $g94root/g94/bad/g94.profile VWIS $ fl.disk: [G94.VMS.BDT]G94Login.Com. UNIX users will need to specify the location of the Gaussian 94 tree on their system. VMS users will need to specify the disk location ofthe [G9A] directory. You may want to add these commands to your user initialization file now if you haven't already done so. VMS users will also want to include a line like the followm, in their LOGIN.COM file, setting their working set to its maximum value: $ Set Work/HoAdju8t/Quota-65536/Limit-65536 Next, we'll prepare a Gaussian input file for an energy calculation on water. 2. Start any text editor and enter the following into a new file: UNIX #T RHF/6-31G(d) Test VWIS $ RunGauss #T RHF/6-31G(d) Test VMS users begin their input file by executing the command to run Gaussian; input to the program follows. UNIX users will redirect their input file to standard input ofthe Gaussian 94 command. The line beginning with # is the route section for this job. The first line of the route section always begins with a pound sign in the first column (UNIX folks: this is nota comment marker). #T requests terse output from the program (only the essential results), # alone requests normal (traditional) Gaussian output, and., requests morr detail in the output file. xxxiv Exploring Chemistry with Electronic Structure Methods
Tutorial for UNIX and VMS Systems The route section specifies the procedure and basis set we want to use for this calculation: Keyword Meaning RHF Restricted Hartree-Fock(restricted means that there are no unpaired electrons in our molecule). 6-31Gd Use the 6-31G(d)basis set (which is a useful and often-recommended basis set). We've chosen a restricted(R)Hartree-Fock(HF)calculation using the 6-31G(d)basis set(6-31G(d)). All route sections must include a procedure keyword and a basis set keyword. Additional keywords further specify the type of calculation desired and additional options. We've included only one additional keyword,Test,which says this is a test calculation whose results should not be entered into the Gaussian archive (if used at your site). 3.Next,enter a blank line into the file,followed by a one-line description of the cakulation. Your file will now look something like this: #T RHF/6-31G(d)Test My first Gaussian job:water single point energy This new line forms the title section for the job,which provides a description of the calculation for the job output and archive entry.It is not otherwise used by the program. 4. Enter another blank line after the title section,followed by these four lines: 01 0-0.4640.1770.0 H-0.4641.1370.0 H0.441-0.1430.0 This information makes up the molecule specification section,in this case for water. The first line of the molecule specification gives the charge and spin multiplicity for the molecule as two free-format integers.In this case,our molecule is neutral(charge 0),and has spin multiplicity 1(a singlet).Spin multiplicity is discussed in Chapter 2, and molecule specifications in general are discussed in Appendix B. The remaining three lines specify the element type and Cartesian coordinates(in angstroms)for each of the atoms in the molecule. Exploring Chemistry with Electronic Structure Methods
Tutorial for UNIX and VMS Systems The route section specifies the procedure and basis set we want to use for this calculation: Keyword RHF 6-31Gld) Meaning Restricted Hartree-Fock (restricted means that there are no unpaired electrons in our molecule). Use the 6-31G(d) basis set (which is a useful and often-recommended basis set). We've chosen a restricted (R) Hartree-Fock (HF) calculation using the 6-31G(d) basis set (6-31G(d)). All route sections must include a procedure keyword and a basis set keyword. Additional keywords further specify the type of calculation desired and additional options. We've included only one additional keyword, Test, which says this is a test calculation whose results should not be entered into the Gaussian archive (ifused at your site). 3. Next, enter a blank line into the file, followed by a one-line description of the cakulation. Your file will now look something like this: #T RHF/6-31Gldl Test My first Gaussian job: water single point energy This new line forms the title section for the job, which provides a description of the calculation for the job output and archive entry. It is not otherwise used by the program. 4. Enter another blank line after the title section, followed by these four lines: o 1 o -0.464 H -0.464 H 0.441 0.177 1.137 -0.143 0.0 0.0 0.0 This information makes up the molecule specification section, in this case for water. The first line of the molecule specification gives the charge and spin multiplicity for the molecule as two free-format integers. In this case, our molecule is neutral (charge 0), and has spin multiplicity 1 (a singlet). Spin multiplicity is discussed in Chapter 2, and molecule specifications in general are discussed in Appendix B. The remaining three lines specify the element type and Cartesian coordinates (in angstroms) for each ofthe atoms in the molecule. Exploring Chemistry with Electronic Structure Methods XXXV
Quick Running Gaussian Start End the file with another blank line. The completed input file looks like this: Exercise QS.1:Water #T RHP/6-31G(d)Test Single Point Energy file:qs.com My first Gaussian job:water single point energy 01 0-0.4640.1770.0 H-0.4641.1370.0 H0.441-0.1430.0 VMS users will have the RunGauss command preceding this input in their version of the file. 6.Save the file under the name h2o.com,and exit from the editor. Notice that we never stated what kind of computation to perform.By default, Gaussian performs an energy calculation,which is what we want. We're now ready to run this calculation. 7.Execute this Gaussian job,using the appropriate command: UNIX 8g94 <h2o.com >h20.log C shell s g94 <h2o.com 2>81 >h20.1og Bourne shell VMS @H20.Com/output=H20.Log This job should complete very quickly.You may run the job in the background if desired with commands like these: UNIX 号g94<h2o.com>&h20.10g。 C shell g94 <h2o.com 2>&1 >h20.log& Bourne shell VMS Spawn/NoWait/Notify/In=820.Com/Out-20.Log The job's output goes to the file h2o.log.We'll look at the output in more detail later. For now,we'll examine it only briefly. i Exploring Chemistry with Electronic Structure Methods
Quick Start 11 Running Gaussian 5. End the file with another blank line. The completed input file looks like this: Exerci.e QS.l: Water Single Point Energy file: q••com iT RHF/6-31G(d) Test My first Gaussian job: water single point energy 0 1 0 -0.464 0.177 0.0 H -0.464 1.137 0.0 H 0.441 -0.143 0.0 VMS users will have the RunGaU5S command preceding this input in their version of the file. 6. Save the file under the name h20.com, and exit from the editor. Notice that we never stated what kind of computation to perform. By default, Gaussian performs an energy calculation, which is what we want. We're now ready to run this calculation. 7. Execute this Gaussian iob, using the appropriate command: UNIX % g9' <h20.com >. h20.log $ g" <h20.com 2>.1 >h20.log VMS $ .H20.Com/OUtput-H20.Log C shell Bourne shell f I I This job should complete very quickly. You may run the job in the background if l desired with commands like these: VMS $ Spawn/HoWait/Notify/ID-H20.Com/OUt-B20.Log C shell Bourne shell f I The job's output goes to the file h2o.log. We'll look at the output in more detail later. I. For now, we'll examine it only briefly. , r I i ~; ___________l UNIX % g96 <h20.com >. h20.log • $ g96 <h20.com 2>.1 >h20.1og • Exploring Chemistry with Electronic Structure Methods
Tutorial for UNIX and VMS Systems 8. Display the contents of the log file on the terminal screen. Once all of it has been displayed,verify that the job completed normally.A line like the following will appear at or near the end of the file: Normal termination of Gaussian 94. Resource usage statistics are also included. Next,we'll look for the results of our computation:the energy of the system. 9. Search the output file for the string "SCF Done". Using the appropriate search utility for your system,you'll find the following line: SCF Done:E(RHF)=-76.0098706218 A.U.after 6 cycles This indicates that the energy of the system,computed at the Hartree-Fock level,is about-76.00987 hartrees. Converting a Structure from a Graphics Program Molecule specifications can be entered by hand or be converted from the output of a graphics program.We'll perform a simple conversion here,converting the water molecule structure saved in Brookhaven Protein Data Bank(PDB)format.The file water.pdb in the quick subdirectory contains a PDB format structure for water. Exercise QS.2:Converting a PDB File file:water.pdb The NewZMat utility is provided with Gaussian to perform conversions between different data file formats.We'll use it to convert this PDB file to Gaussian input. 10.Execute the following NewZMat command: UNIX 8 newzmat -ipdb $g94root/g94/tutor/quick/water.pdb water.com VMS NewZMat-IPDB disk:【G94.utor.Qu1ck】Water.PDB【】Wat●x.Com This command will create a new Gaussian input file.NewZMat may prompt you for the charge and multiplicity to use;accept the default values offered. Exploring Chemistry with Electronic Structure Methods
Tutorial for UNIX and VMS Systems B. Display the contents of the log file on the terminal screen. Once all of it has been displayed, verify that the job completed normally. A line like the following will appear at or near the end ofthe file: ______________ Normal termination of Gaussian 94. 1I Resource usage statistics are also included. Next, we'll look for the results of our computation: the energy of the system. 9. Search the output file for the string IISeF Done". Using the appropriate search utility for your system, you'll find the following line: SCF Done: E(RHF) = -76.0098706218 A.U. after 6 cycles This indicates that the energy of the system, computed at the Hartree-Fock level. is about -76.00987 hartrees. Converting a Structure from a Graphics Program Molecule specifications can be entered by hand or be converted from the output of a graphics program. We'll perform a simple conversion here, converting the water molecule structure saved in Brookhaven Protein Data Bank (POB) format. The file wa ter . pdb in the quick subdirectory contains a POB format structure for water. Exercise QS.2: Converting a PDB File RIe: water.pdb The NewZMa t utility is provided with Gaussian to perform conversions between different data me formats. We'll use it to convert this POB file to Gaussian input. 10. Execute the following NewZMat command: UNIX % newzmat -ipdb $g94root/g94/tutor/quiek/water.pdb water.ea. VMS $ ReWZMat -IPDB disk: [G94.Tutor.Quick]Water.PDB []water.Coa This command will create a new Gaussian input file. NewZMat may prompt you for the charge and multiplicity to use; accept the default values offered. Exploring Chemistry with Electronic Structure Methods xxxvii