Gameix for Linux: User's Manual

    by Ernst J. Schumacher, University of Bern

Shortcut 1: Compile Gamess-US and run Gameix on Knoppix live Linux

I have written gampix.csh which compiles and links Gamess-12 JAN 2009 (R1) and then installs the runscript Gameix, ready to be used, all automatically. On clicking [Help/Run all Tests] from the Gameix top panel, all 44 test examples are run in batchmode and finally compared to the correct results with Checktst from the Gamess distro.
A more complete script, gampixtvn.csh, compiles and links the Tinker, VB200017, and NEO modules into Gamess. gameix.exe has the additional [Help/Run ...] options to test these three modules separately.

On a Windows or Linux box start up Knoppix-V.5.xDVD live-Linux. Knoppix should have automatically established your Internet connection. Test this with typing firefox or clicking on iceweasel in the bottom-bar.

  1. Get gamess-current.tar.gz from Gamess-US.
  2. Get gampix.csh or gampixtvn.csh (get vb2000v18R3.tar.gz)
  3. Make the script executable with chmod a+x gampix.csh or gampixtvn.csh
  4. type gampix.csh or gampixtvn.csh<enter>
In about 10 to 14 min you have a gamess.00.x exec in the directory ~/gamess and an unpacked gameix system in ~/gameix, the wine emulator has been installed and you see an opened Dialect window, the script language, gameix has been written in. Close the Dialect window by clicking on the cross right, upper corner, or [File/Exit].
Now the configuration file is presented, click Ok. Next, close the editor window with the config file. There is no need to change this right now.
The panels of Gameix are now presented. Look at the tabs in the topmost menu and click on [Help/Run all Tests]. Now, the 44 Test examples are run. In about 4-6 min the computed results are automatically compared with the correct numbers stored in ~/gamess/tools/checktst. Checktst should tell you: 'All 44 test results are correct!'. If one of the tests should have failed, go into ~/gamess/tools/checktst and run checktst (not the calculations!) again. This time, everything should work out correctly.
If you have used gampixtvn.csh and downloaded VB2000 (you need an ID and password) you can also test the Tinker (automatically downloaded), VB, and NEO modules with the additional [Help/Run VB, Tinker, NEO, resp., Tests] items on the master menu of gameix.

Congratulations! You have a correctly working Gamess system.
If you are on a dual core machine, set 'Number of CPUs' in the Config file to 2, and enjoy about double speed for those Test examples which are parallel enabled (exam05, 23, 25, 27, 32, 39, and 42 are not).
Now read some of the rest of this Manual and try more examples of your own design.

Note: gampix.csh can do its automatic installation because Knoppix has a given and fixed environment and all the software necessary to compile Gamess and additional modules. You can export Gamess and Gameix to another Linux environment, consult with gamkpx, where scripts are downloadable to accomplish the transport.


Shortcut 2: Compile Gamess-US and run Gameix on Ubuntu live Desktop Linux

Use Ubuntu-7.04 to 8.10 desktop live-CD instead of the Knoppix-V5.xDVD as shown here for a completely automatic compilation of Gamess and installation of gameix.

Content

  1. Gameix script
  2. What is in the Gameix Package
  3. Installation
  4. The Master Menu
  5. The Configuration File
  6. Options in Gameix1.0
    1. BUILDER
    2. VIEWER
    3. JOB NAME
    4. BUILD
    5. GAMESS INPUT Options
    6. Advanced Options
  7. APPLY
  8. VIEW INPUT FILE
  9. RUN
  10. SUMMARY
  11. SAVE
  12. VIEW
  13. VIEW STRUCTURE
  14. IR/RAMAN SPECTRUM
  15. References

Introduction

           Gameix is a 'Dialect'1 GUI to be used in conjunction with GAMESS2. It allows one to build a molecule, save it, run Gamess, and view the structure directly from the output or as a .pdb or .xyz file using free software that can be downloaded off the Internet. By using the 'Configuration File', one can customize the interface to one’s own system. This program stands under the GPL (Gnu Public License). USE AT YOUR OWN RISK. Please report any bugs to me.

The Gameix panels and this Manual have been further developed from the layout of Wayne P. Anderson, J.Chem.Ed 80(2003)968, for PC Gamess, written in Tcl/Tk. However, only 'gamout2pdb.exe' has been copied from Anderson's free pcgRUN1.0.zip archive. It is a FORTRAN binary which produces three output files, 'molecule.pdb', 'molecule.ent' identical to the previous, and 'molecule.xyz'.

  • I have separated the more general tasks into a Master Menu, external to the main panel. It offers Input, Output and Configuration options in addition to Help and Quitting.
  • Configuration: The calls of external programs conforms to Linux. Carefully note in the template of the configuration file what information needs to be put into the configuration file if you plan to incorporate your own selection of 'Builder' and 'Viewer' tools. 'Molekel', version 4.3 for Linux, and the other builders and viewers should be installed as suggested in the respective packages.

What is in the Gameix Package gameix.zip

          The following parts are necessary for running Gamess with Gameix:

(1) Gameix script
gameix.exe compiled script of the next four sources
gameix.d Dialect source code of the main script
gaminp.d Dialect source code of the input script
advan.d Dialect source code of the advanced input script
raspec.d Dialect source code of the IR/Raman spectrum script
grep.exe from Microsoft's UnixTools, searches some of the temporary files
keys.txt keywords for which grep searches an output file (can be edited)
rungms.sh driver for setting up and running a Gamess job on 1 or several
nodes and CPU's (derived from rungms)
runtests.csh script for running and checking all Gamess testjobs in batch mode
Dialect.exe version 1.16 allows to recompile edited *.d scripts

(2) Auxiliary Linux setup
Wine Wine windows emulator of your Linux distro (not included)
molekel.sh driver for calling molekel (viewer not included, see refs.)
gopenmol.sh driver for calling gOpenMol (viewer not included, see refs.)
raswin32.exe RasWin molecule viewer
Jmol.sh driver for Jmol (viewer not included, see refs.)
/fonts content to be copied to ~/.wine/drive_c/windows/fonts

(3) Gamess-US and Gameix Manuals
INTRO.DOC 'Introduction' from Gamess-US
INPUT.DOC 'Input Description' from Gamess-US
REFS.DOC 'Further Information' from Gamess-US
PROG.DOC 'Programmer's References' from Gamess-US
IRON.DOC 'Hardware Specifics' from Gamess-US
TESTS.DOC 'Input Examples' from Gamess-US
Manualg.htm        this manual with auxiliary files

(4) gamess-current.tar.Z, not included! Get it from Gamess-US
the content of this table is all that gameix needs, once the compilations are done.
gamess.XX.exe executable with version number XX, compile from sources
ddikick.x driver for (multiprocessor) communication, compile from sources
ericfmt.dat auxiliary file from Gamess-US
/tests subdirectory with test examples ready for running
/mcpdata file with advanced basis sets

Installation

If you are using gampix.csh or ubuntugam you can skip this paragraph!

1) Get gamess-current.tar.Z or gamess-current.tar.gz from Gamess-US (contains items of table 4 and utilities) and extract it from your /home/$USER directory (with 'zcat gamess-current.tar.Z | tar xvf -' or 'tar xzvf gamess-current.tar.gz') into its default directory ~/gamess. Compile and link to the executable gamess.XX.x and ddikick.x using the fine scripts provided with the Gamess source: comp, compall, lked, and ddi/compddi. I am assuming that you use gfortran/gcc as Fortran and C-compilers. You have to specify gfortran in the scripts ddi/compddi, comp, and lked. For other compilers the scripts give the proper names to insert. These three scripts and compall have to be edited to reflect your system. Do not forget to edit and compile actvte.code in the /tools directory:
  • 'cp actvte.code actvte.f'.
  • 'vi actvte.f'. Replace all the strings '*UNX' which are at line beginnings of the fortran code by four spaces with the vi command: ':%s/^\*UNX/ /'. 20 replacements!
  • Save and get out of vi by typing: ':wq'.
  • Now compile: 'gfortran -o actvte.x actvte.f' which produces actvte.x
2) The script gameix.exe and auxiliary files, content of tables 1 to 3 (except wine emulator), are extracted from gameix.tar.gz (with 'tar xzvf gameix.tar.gz') into any directory.

3) rungms.sh is preset for one computer with one or two CPU's (separate sockets or dualcore). If you have a computer with more than 2 CPU's in an SMP enclosure or a multinode cluster, edit rungms.sh to reflect your setup. You'll find all necessary instructions in the comments of the script (from Gamess-US).

Two subdirectories (among others) '/tests' and '/mcpdata are installed during extraction of the gamess distribution. Three additional subdirectories are automatically created at the startup of Gameix: '/data', '/output', managed by the script for input and output, and '/scratch' used by the Gamess driver into ~/gamess.
Take note, that the '/tests' and '/mpcdata contents are supplied by the Gamess-US distribution and are not in gameix.tar.gz.

Installation of the Wine emulator: When you are done with the installations above, go into the directory where gameix.exe has been installed. Now type wine gameix.exe. It takes a couple of minutes for wine to install itself if it has never been used before. You might get several pop-ups which you can dismiss or close. Finally, the template for the configuration file, see below for editing, will be shown. Close it or Save/close it whereupon the panels of gameix are shown. Unfortunately, the font used by wine is usually not acceptable. This can be remedied as follows. Wine has created a directory .wine below your home directory. Now cd .wine/drive_c/windows/fonts. Copy the content (2 files) from 'gameix_directory'/fonts (table 2 above) into this directory. You now have a Courier and an Arial font which match the requirements of gameix. Go back to your gameix_directory and retype 'wine gameix.exe'. Now the panels should look properly. When your configuration file is correctly edited, you can now do all the things, the script is made for. See the rest of this document.

The Master Menu

File

Load $VEC group

This offers the names of the stored \output\*.dat files for you to select the job from which you wish to extract the $VEC group, i.e. the converged orbitals computed in a previous run of the target molecule.

 

Load $HESS group

This offers the names of the stored \output\*.dat files for you to select the job from which you wish to extract the $HESS group, i.e. the matrix of force constants computed in a previous Hessian run of the target molecule. If you set RUNTYP=RAMAN or RUNTYP=VSCF you are prompted to append the $HESS matrix to the input file.

 

Quit

Recommended termination of Gameix. Closes all windows opened during the run, except the display of an IR spectrum which has its own 'Close' button. Of course, you may close any window by clicking into the cross, top right.

Inputdata

Import *.inp

Opens the \data directory for you to choose an input file composed elsewhere and put into the \data directory or load an input file of an earlier run. After clicking on the desired name the file is transferred to gamessdir\input and can be viewed and run (perhaps with your edits). Note: The input file may be in UNIX or PC style. However, 'PC Gamess' input files from RUNpcg are not compatible with 'Gamess' input files. If you want to use PC Gamess input you have to eliminate the entry for 'DFTTYP' in the '$CONTRL' group when [View(ing) Input File].

 

Tests

Opens the \tests directory for you to select one of the test files. After clicking on the desired name the file is transferred to gamessdir\input and can be viewed and run. The input file may be in PC or UNIX format.

Outputdata

Read *.out

Opens the \output directory for you to choose an output file of an earlier run. After clicking on the desired name the file is opened in the editor. The buttons [Properties, Show/Print] in the Master Menu and [View Structure] in the main panel become active and let you extract molecular properties or visualize them in the chosen Viewer.

 

Read *.dat

Opens the \output directory for you to choose a .dat file = Gamess PUNCH, of an earlier run. After clicking on the desired name the file is opened in the editor. You can now select and copy $VEC, $HESS, and other groups for pasting into a new application requiring this data. However, in most cases where such an operation is necessary, you are prompted to select an \output\*.dat file. After clicking on the desired filename the extraction of a $VEC or $HESS group is automatically done and written into the input file being created.

 

Read *.log

Opens the ~/gamess/logs directory for you to choose a .log file = Gamess testjob, of a [Help/Run all Tests], see below under 'Help'. The selected testjob can now be investigated as if you had run it from Gameix, the same as [Read *.out], above.

Properties

Show/Print

If a job has just been run and Gameix is still active, [Properties, Show/Print] allows to extract a property from the (long!) output file. The property is chosen from a drop-down menu and shown in tabular form in an editor window.
If no job is active, the \output directory is first opened for you to choose an output file of an earlier run. After clicking on the desired name the property list, as above, is shown for you to choose from. If you select 'Coordinates' as the property, either the input or the optimized coordinates (depending on runtype) are shown and written into a file 'gamess.coo'. From there it can be read into the input of a new job, e.g. to compute the Hessian after an optimization.- The properties may be printed from the editor window in the usual way by clicking [File/Print].

Configure

Conf File

Opens the 'Configuration File' in the editor to make changes. After editing/saving/closing the editor window the new configuration becomes active. For details, please consult the item 'Configuration File', below.

Help

Manual

Opens this file in the Browser.

 

Six DOC files

Opens one of the chapters of the Gamess US documentation in the external editor. It can be searched for keywords etc.

 

Run all Tests

Calls runtests.csh which runs all examples in /Tests as a Gamess batchjob. After finishing the results are compared to the correct numbers stored in ~/gamess/tools/checktst. If all tests "PASSED" you have a pretty good check that Gamess runs correctly. The outputfiles are stored as *.log in ~/gamess/logs and can be studied with [Outputdata/Read *.log].

 

About

Shows an URL for checking whether a new version of the script is available.



The Configuration file

           Many of the parameters in Gameix can be set by the user in the configuration file gameix.ini. A template for this is presented when Gameix is started for the first time. It is opened in the editor for you to adapt it to your system and save it. The most important items are
1) the path name of the directory where you have installed the Gamess distribution, e.g. '/home/$USER/gamess'.
2) the correct version of the gamess binary to be used, perhaps '01' or more informative '24MAR2007R1'.

The configuration file can later be edited by clicking on 'Configure/Conf File' in the Master Menu. Save changes. You might have to exit and restart gameix for the changes to take effect.

The directories of the file editor, the browser, the builders, and the structure viewers must be specified in the Configuration file. Four builders may be defined. Set their call specifications, and the name to be associated with those builders. Similarly, four structure viewers can be specified. The calls for them are to be set and their names specified. If the viewer is capable of reading an output file upon loading, the value of the file extension may be set to, e.g. “pdb” or “out” (for 'Molekel' and 'Molden'). If it is set to “”, no file will automatically be loaded when the viewer is opened. It has to be specified by the usual 'File/Open' dialogue.
           Some of the programs mentioned in this manual have licensing restrictions. Be sure to consult the license agreements before using the programs.
           Although any text file editor that reads large files can be used, I have chosen 'Kwrite' from the KDE desktop. You can choose another, e.g. 'gedit', and give the correct calling string. Only for the Configuration file 'Notepad.exe' from Windows has to be used. Wine shows it in a proportional font. That could be changed from the top menu of the opened editor. But, it probably is not necessary since edits in the configuration are usually small.

Options in gameix1.0

BUILDER

           The program used to draw and build the molecule is set in gameix.ini. Four builders may be set in the program. For now only one builder is actually installed: Ghemical16. The others shown in the drop-down menu are all Windows programs. The very versatile program Ghemical which exists in a Linux version can be installed automatically with 'apt-get install ghemical' (after an 'apt-get update') in a Knoppix derived or genuine Debian-Linux system. It is present on Knoppix-DVD 4.02 and later versions.

VIEWER

           Four viewers may be specified in gameix.ini. If the job is saved, the output structures will be converted to .pdb format with the name ‘jobname’.pdb and in .xyz format with the name ‘jobname’.xyz. gameix has been tested with gOpenMol10, RasWin12, Molekel13, Jmol15, and Molden16, but other viewers may be used as well. Electron densities and molecular vibrations can be generated in Molekel, gOpenMol, Jmol, and Molden. Files for creating high quality Pov-Ray™14 ray-traced images can be generated in VMD©11. One of the best and time-proven viewers is Molden16 (for Linux and Windows).

JOB Name

           The name of the JOB must be entered here. The files ‘jobname’.out, ‘jobname’.pdb, ‘jobname’.pun, and ‘jobname’.xyz will be generated in the output directory if the job is saved. The input coordinate file must also have the name ‘jobname’.xxx as specified below. In order to prevent unwanted overwriting of output files, ‘jobname’ here always means the given 'Job Name' plus a four digit number representing the time in hr:min of the start of the computation.- If you [Outputdata/Read *.out] (Master Menu) an earlier run its jobname is automatically placed into the 'Job Name' box.

BUILD

           The BUILD button calls up the builder specified above. The molecule must be converted to 3D and saved as ‘jobname’.mol, ‘jobname’.ent, ‘jobname’.pdb, or ‘jobname’.xyz in the input directory (specified automatically). A previous GAMESS output file, named ‘jobname’.out, may also be used for coordinate input. In the Master Menu click on [Properties, Show/Print], click on the output file desired and then choose 'Coordinates'. This generates a file 'gamess.coo' which can be read in when composing the input file, choosing 'COO' as Coordinate Type.
In gameix input/output files are in separate directories called ./data and ./output.

GAMESS INPUT

           The Gamess Input button allows one to set many of the input parameters for gamess, thus defining the nature of the quantumchemical calculation to be performed. The default parameters are set for a simple structure optimization job of a small to medium size, uncharged, singlet molecule. At a minimum the RUNTYP, BASIS, and COORDINATE TYPE will have to be set for each run. A coordinate input file must be in the ./data directory unless it is saved from a previous run in 'gamess.coo' or 'gamess.equ' in the gameix directory. Coordinates can also be entered manually, see below.


Some of the GAMESS options require additional input that cannot (yet) be entered through gameix. It is the responsibility of the user to review the input file generated by gameix and make any additions or changes that are necessary for a successful run. I cannot guarantee that the settings that are placed in the input file will necessarily give a meaningful run. Be sure to read the GAMESS documentation files, particularly INPUT.DOC. A copy of INPUT.DOC is placed in the gameix directory, and it can be accessed from HELP of the Master Menu. Note that this is the most recent INPUT.DOC from the Gamess-US distribution.


Summary of GAMESS INPUT Options

Items in bold - or a red bar on the panel - are the ones that are changed most often.
Gamess input orders the keywords into "groups", beginning with a "$" in the second position of a new line and ending with " $END". Groups may be given in any order (and even repeated on another line), keywords within groups, too. The following list of groups and their keywords is implemented in the listboxes of gameix. Keywords - parameters of the calculation - may be set by selecting appropriate values in those boxes. There are many more groups and keywords available for more sophisticated jobs, see INPUT.DOC. Names of groups and keywords are not case sensitive. Keywords within a group must be separated by space or newline.


$DATA

INPUT COORDINATE TYPE

This is by far the most important entry for any type of quantumchemical computation: The structure of a molecule, i.e. the spacial arrangement of its constituent atoms, determines its energy and most other properties. If not given carefully the whole effort may be meaningless.


 

NONE

The coordinates are to be entered manually by the user when 'View(ing) Input File'. This is especially necessary if you want to give internal coordinates as Gaussian Z-matrix 'ZMT' or Mopac Z-matrix 'ZMTMPC' format which the script is not able to provide, see 'Input Description' under [Help] in the Master Menu. Notice: I have not provided for the wide variety of Gamess-US input for the names of atoms. The script and its various file manipulations only understand IUPAC atomic symbols. With cartesian coordinates Gamess allows any name for the atoms because their identity is defined by the nuclear charge. gameix insists on using IUPAC symbols because these are used later for the .pdb and .xyz files to be produced at the end of a job. Furthermore, with ZMT or ZMTMPC coordinates Gamess allows to number the atoms, e.g. C1, C12 or Cu1, Cu19, etc. Please do not use this numbering. In ZMT(MPC) the numbers of the atoms are defined by the (implicit) number of the row in the matrix of structure data on which they appear. However, atomic symbols may be given as
'Se', 'sE', 'SE' or 'se', and ' C', 'C ', ' c', 'c ', 'C' or 'c'.


 

EQU

'Equilibrium' (Stationary State) Coordinates are to be read from a file named gamess.equ automatically created with the [SAVE] button or by clicking [Properties, Show/Print] 'Coordinates' in the Master Menu. This file, if it exists, is in the gamessdir directory. It is only created after a successful Optimize run and can be used for subsequent Hessian, and Raman runs. It has the full 10-digit precision of Gamess output. It is not overwritten by a subsequent run, unless this is a successful 'Optimize' run.


 

UNQ

Unique 'Equilibrium' (Stationary State) Coordinates are to be read from a file named gamess.unq automatically created with the [SAVE] button or by clicking [Properties, Show/Print] 'Coordinates' in the Master Menu. This file, if it exists, is in the gamessdir directory. It is only created after a successful Optimize run and can be used for subsequent runs of the same molecule with the same pointgroup symmetry. It has the full 10-digit precision of Gamess output. It is not overwritten by a subsequent run, unless this is a successful 'Optimize' run.


 

COO

Coordinates are to be read from a file named gamess.coo automatically created with the [SAVE] button from any run or by clicking [Properties, Show/Print] 'Coordinates' in the Master Menu. This file, if it exists, is in the gamessdir directory. The precision of coordinates is given in the 10-digit format of Gamess, if they are from an 'Optimize' run. In the case of Gamess runs other than 'Optimize' the atomic coordinates are taken from the input (in Bohr, but converted to Angstrom). The precision is given to 8-digits. They may be less precise than what the number of digits indicates, depending on the source of the input.


 

MOL

Coordinates are to be read from a file in “mol” format named ‘jobname’.mol and is usually produced by one of the molecule builders or read from a chemical databank and saved in the gamessdir\data directory.


 

PDB

Coordinates are to be read from a file in “pdb” format named ‘jobname’.pdb. PDB files may be exported from several molecule builder programs but also exist in vast numbers in chemical databanks (26319 structures by July 2004). Before using them they have to be deposited in the gamessdir\data directory. With the [SAVE] button the structural data of a successful Gamess run are saved as ‘jobname’.pdb in the .\output directory. If you request coordinates from a PDB file with the jobname given in the main panel of gameix and gameix does not find it in the \data directory, the \output directory is opened for you to choose a jobxxxx.pdb file, 'xxxx' being the time stamp of a previous run. Please note: PDB files are in a certain standard PDB format and contain coordinates only to 3-digit precision. Gamesss output coordinates have to be rounded to three digits while being written into a 'jobXXXX.pdb' file.


 

ENT

These structure files have the identical format of pdb files. They are produced and read by HyperChem named ‘jobname’.ent


 

XYZ

Coordinates are to be read from a file in “xyz” format named ‘jobname’.xyz. This is a format used by Rasmol (RasWin), Chime, and other viewers and is produced with [SAVE] at the end of a Gamess run and saved as ‘jobname’.xyz in the .\output directory. If you request coordinates from an XYZ file to read into an input file and gameix does not find it as 'jobname.xyz' in the \data directory, the \output directory is opened for you to choose a jobxxxx.xyz file, 'xxxx' being the time stamp of a previous run. The precision of coordinates is given to 8-digits, derived from the 10-digit format of Gamess. In the case of Gamess runs other than 'Optimize' the atomic coordinates are taken from the input (in Bohr, but converted to Angstrom). They may be less precise than what the number of digits indicates.
The format of XYZ files is not standardized (as is the case for MOL and PDB). The script can read XYZ files form Ghemical builder, too.


GROUP

 

Indicates the point group symbol that is to be used to build the molecule from symmetry unique coordinates. If the coordinates of all atoms are specified as input cart, choose C1 as the point group. This always works, even if the molecule has a higher symmetry. One disadvantage is, that an optimization run in the C1 group will not produce orbitals (SALC's) and (exact) coordinates reflecting the possibly existing higher symmetry. You may also enter the actual group with all cart coordinates if these accurately transform under the group's symmetry operations. However, a quirk of Gamess, the input generated by Gamess from your input coordinates may break the symmetry and e.g. produce IR/Raman lines violating the selection rules under the full symmetry group. If this should happen, use the equilibrium coordinates of the full group, but choose the group C1 and coord=cart when computing Raman transitions.
Do not forget to enter a blank line between the point group symbol and the first atom coordinates in the $DATA group unless the symbol is C1 when you must skip that blank line. Gameix does this correctly for you!


NAXIS

 

Indicates the order of the principal axis when the point group specification includes an “N”. E.g. for C3v NH3 molecule, select 'Cnv' for GROUP and '3' for NAXIS.




$CONTRL

EXETYP

CHECK

Indicates that the input file is to be checked for errors.

 

RUN

Indicates that a full GAMESS run is to be done.




RUNTYP

ENERGY

A single point calculation is to be done at the geometry specified in the input file.

 

OPTIMIZE

The geometry of the molecule is to be optimized. If you set HSSEND=.true. in the $STATPT group, see below, the Hessian is computed with the converged coordinates and a normal mode analysis performed as in the next case.

 

HESSIAN

The force constants and vibrational frequencies in the harmonic approximation are to be calculated at the equilibrium geometry specified in the input file. The intensities for infrared transitions are determined.

 

RAMAN

The force constants and vibrational frequencies in the harmonic approximation are to be calculated at the equilibrium geometry specified in the input file. IR- and Raman-intensities are computed. The inclusion of a $HESS group from a previous Hessian run into the input file is mandatory. If the 'RAMAN' keyword is set you are prompted to select a previous output .dat file for extraction of a $HESS group. In case there is none you are alerted. If there are several, the last one with (hopefully) converged force constants is chosen.

 

G3(MP2)

This new runtype (starting with Gamess 11 APR 2008 (R1)) offers a combination of calculations similar to the same method in Gaussian03 with the aim of obtaining accurate thermochemical quantities as described in L.A.Curtiss et al. JCP 110,4703-4709(1999). Gamess uses a step with CCSD(T), as in L.A.Curtiss et al. CPL 314,101-107(1999), whereas the same step in Gaussian has QCSID(T) model chemistry as in the first publication. Gamess carries the evaluation one step further and gives the expected final result as Std. Enthalpy of Formation ΔHf(0 and 298) in kcal/mol. Gameix extracts all relevant G3MP2 quantities from the output file and offers the runtype G3MP2 when composing the job such that the requirements of Gamess are fulfilled in the input file. Do not forget to provide adequate memddi by becoming root and typing /sbin/sysctl -w kernel.shmmax=100000000 or more, depending on the size of the job. If you are using WinGamess instead of Gamess-US do not declare memddi because that is not supported in WinGamess and you obtain an abort.

 

VSCF

The force constants and vibrational frequencies in an anharmonic approximation are to be calculated at the equilibrium geometry specified in the input file. IR intensities are computed and the coupling between oscillators is treated as well. The inclusion of a $HESS group from a previous Hessian run into the input file is mandatory. If the 'VSCF' keyword is set you are prompted to select a previous output .dat file for extraction of a $HESS group. In case there is none you are alerted. If there are several within the same .dat file, the last one with (hopefully) converged force constants is chosen.- There are more input options, see the keyword $VSCF in [Help/Input Description].

 

SADPOINT

A saddle point location calculation is to be done, see $STATPT for options and Master Menu [Help/Input Description] for details.

 

IRC

An Intrinsic Reaction Coordinate calculation is to be run, see $IRC in the 'Advanced Options' for fine tuning this calculation type and Master Menu [Help/Input Description] for details.

 

NMR

NMR shielding tensors (chemical shifts) for closed shell molecules by the GIAO method. The standard defaults are used. These can be finetuned with the help of a $NMR group. See [Help/Input Description] for details.

 

PROP

Certain specified properties of the molecule at the geometry specified in the input file are to be calculated. This requires some manual editing of the file.


SCFTYP

RHF

A restricted Hartree Fock calculation is to be carried out. This option is used for closed shell systems.

 

UHF

An unrestricted Hartree Fock calculation is to be carried out. This option is generally used for systems containing unpaired electrons and produces separated alpha- and beta-spin orbitals.

 

ROHF

A restricted open shell Hartree Fock calculation is to be carried out. This option is sometimes employed for systems containing unpaired electrons and produces orbitals with paired spins as much as possible.



MPLEVL

0

No Møller-Plesset perturbation calculation is to be carried out.

 

2 [,3,4]

Electron correlation is included through an MP2, [MP3, MP4] perturbation theory calculation following the Hartree Fock calculation. Please note: Gamess-US only offers MP2! If you need MP3, MP4 (up to the full set) you have to change to PC Gamess, V. 6.4 or later, script RUNpcg.

ISPHER

-1

Use Cartesian basis functions to construct symmetry-adapted linear combinations (SALC) of basis functions. The SALC space is the linear variation space used. (default)

 

0

Use spherical harmonic functions to create SALC functions, which are then expressed in terms of Cartesian functions. The contaminants are not dropped, hence this option has EXACTLY the same variational space as ISPHER = -1. The only benefit to obtain from this is a population analysis in terms of pure s,p,d,f,g functions which is valuable for teaching purposes.

 

1

Same as ISPHER=0, but the function space is truncated to eliminate all contaminant Cartesian functions [3S(D), 3P(F), 4S(G), and 3D(G)] before constructing the SALC functions. The computation corresponds to the use of a spherical harmonic basis.


ICHARG

Specifies the overall charge on the system.


MULT

Specifies the multiplicity of the system. This equals n+1, where n is the number of unpaired electrons.


ECP

NONE

Effective core potentials (pseudopotentials) are not being used.

 

SBKJC

Use the Stevens, Basch, Krauss, Jasien, Cundari ECP’s for the core electrons.

 

HW

Use the Hayes-Wadt ECP’s for the core electrons.

 

READ

The ECP’s are to be specified in the input file. This option requires manual editing of the input file.


MAXIT

The maximum number of iterations that are permitted to achieve SCF convergence, default = 30.


COORD

CART

The atom positions are expressed in Cartesian coordinates. This option must be used if the molecule is built with the BUILDERs in gameix.

 

UNIQUE

Give the coordinates of the symmetry unique atoms only when the point group is specified. The coordinate frame has to be defined in a certain way, see Input Description in the Master Menu [Help]. Cart = unique is Gamess default.

 

ZMT

The coordinates are expressed in the form of a Gaussian Z-matrix. The coordinates must be supplied manually if this option is selected. (Note that this option is not correctly implemented in pcgRUN1.0, since 'ZMAT' instead of 'ZMT' is used as keyword. 'ZMAT' is used as $ZMAT group to define internal coordinates if NZVAR > 0, see Input Description)

 

ZMTMPC

The coordinates are expressed in the form of MOPAC type internals. The coordinates must be supplied manually if this option is selected, see Input Description or any MOPAC manual.


DFTTYP

NONE

No Density Functional Calculation is done (default)

 

B3LYP

or 30 other DFT functionals may be selected. When right-clicking into the edit box, the list below with a short description of the available functionals pops up. Click on your favorite functional to get it written into the editbox. If you plan to often use DFT in your computations you probably should prefer PC Gamess over Gamess-US. A. A. Granovsky has optimized numerical integration and convergence such that DFT runs about four times faster than with Gamess-US, see the RUNpcg script.
DFT does not work with the semiempirical Hamiltonians MNDO, AM1, and PM3. If you select one of those, DFTtyp is automatically set to "NONE".
This is the list of available functionals for grid integration (default); we have not implemented the gridfree method here, see the Input Manual:

  exchange functionals: 
	SLATER	Slater exchange
	BECKE	Becke 1988 exchange
	GILL	Gill 1996 exchange
	OPTX	Handy-Cohen exchange
	PW91X	Perdew-Wang 1991 exchange
	PBEX	Perdew-Burke-Ernzerhof exchange
  pure correlation functionals:
	VWN	    Vosko-Wilk-Nusair correlation (VWN5)
	VWN1	Vosko-Wilke-Nusair correlation, RPA params.
	PZ81	Perdew-Zener 1981 correlation
	P86	    Perdew 1986 correlation
	LYP	    Lee-Yang-Parr correlation
	PW91	Perdew-Wang 1991 correlation
	PBEC	Perdew-Burke-Ernzerhof correlation
	OP	    One-parameter Progressive correlation
  exchange/correlation combination functionals:
	SVWN	SLATER exch. + VWN5 corr.= LDA/LSDA in physics
	BLYP	BECKE exchange + LYP correlation
	BOP	    BECKE exchange + OP correlation
	BP86	BECKE exchange + P86 correlation
	GVWN	GILL exchange + VWN5 correlation
	GPW91	GILL exchange + PW91 correlation
	PBEVWN	PBE exchange + VWN5 correlation
	PBEOP	PBE exchange + OP correlation
	PW91PBE	PW91 exchange + PBE correlation
	OLYP	OPTX exchange + LYP correlation
	PW91	PW91 exchange + PW91 correlation
	PBE	    PBE exchange + PBE correlation
  hybrid functionals:
	BHHLYP	HF and BECKE exchange + LYP correlation
	B3LYP	Becke + Slater + HF exch. and LYP + VWN5 corr.
	B3LYP1	use VWN1 in place of VWN5 (as in Gaussian)
	PBE0	a hybrid made from PBE
	X3LYP	HF+Slater+Becke88+PW91 exch., LYP+VWN1 corr.

$SYSTEM

TIMLIM

This gives the maximum time in minutes allowed for the run.


MWORDS

This selects the maximum number of megawords of memory allowed for the run. One word = 8 bytes. Large jobs will require a larger number than the default. Instead of MWORDS the keyword MEMORY may be given. The unit is word. MEMORY = 1000000 is equivalent to MWORDS = 1.


[ MEMDDI

Not provided on the panel, see e.g. the testinput exam36.inp: Some runtypes, especially MPLEVL = 2, require a larger block of memory for communication between the parallel processes than offered by default. This is handled by adding MEMDDI=1 (megaword) in the $SYSTEM group. If you do not include this when the program needs it, you get an abort. With [View Output File] the error is explained and you are advised of the size for MEMDDI to add. Just [View Input File], make the necessary change to the $SYSTEM group by adding a line 'MEMDDI = 1' (or a larger number) and restart the computation. It may be necessary to click on [SAVE] before, to empty the \scratch and \temp directories from intermediate files of the abortive run. ]



$BASIS

GBASIS:


NGAUSS

These options are used to specify the basis set. To indicate STO-3G, set GBASIS to STO and NGAUSS to 3. For 3-21G, set GBASIS to N21 and NGAUSS to 3. For 6-31G, set GBASIS to N31 and NGAUSS to 6. Several additional basis set options, including those for use with ECP’s, are given as well. See the 'Input Description'.

NDFUNC

Gives the number of sets of d polarization functions to be added to the heavy atoms. For 6-31G(d), which is often designated as 6-31G*, and for 6-31G(d,p), which is often called 6-31G**, NDFUNC=1 (max. 3).

NFFUNC

Gives the number of sets of f polarization functions to be added to the heavy atoms. NFFUNC=0 or 1.

NPFUNC

The number of sets of p polarization functions to be added to hydrogen atoms. For 6-31G(d,p), NDFUNC=1 and NPFUNC=1 (max. 3).


DIFFSP

.TRUE.

.FALSE.

A diffuse sp function is included on non-hydrogen atoms in the basis set. This is often used with anions and is designated with a + in the basis set specification. For 6-31+G(d,p), DIFFSP=.TRUE..

DIFFS

checked

A diffuse s function is included on hydrogen atoms in the basis set. This is often used with anions and is designated with a + in the basis set specification. For 6-31++G(d,p), DIFFSP=.TRUE. and DIFFS=.TRUE..


$SCF

DAMP

.TRUE.

.FALSE.

Check DAMP to damp oscillations in the energy during SCF iterations. This is often necessary with transition metal complexes.


SHIFT

.TRUE.

.FALSE.

Check SHIFT to shift the energies of the virtual orbitals to assist convergence during SCF iterations. This is often necessary with transition metal complexes.


DIRSCF

checked

Direct SCF calculation in RAM. The default (unchecked) is 'conventional' SCF with integrals stored on disk. DIRSCF uses much less disk space and is faster for large numbers of basis functions. For smaller systems conventional SCF is faster. The 'crossover' point is dependent on the kind of computer system and parallelization, if any.


CONV

Gives the SCF convergence limited as 10**(-conv).


$STATPT

OPTTOL

Gives the gradient convergence tolerance in Hartree/Bohr. If this value is changed, the value of NCONV will also have to be adjusted.


HESS

GUESS

Chooses a positive definite diagonal Hessian as an initial guess

 

READ

Reads the Hessian from $HESS. You are prompted to load a $HESS group from a previous Hessian run in a .dat file.

 

CALC

The initial Hessian is computed. See $FORCE. Additional input may be required.


HSSEND

checked

If checked, the force constants and vibrational frequencies are calculated at the end of a geometry optimization, if converged. You can then [Show/properties] with added 'Normal Coordinates' and 'Thermochemistry', and generate an [IR Spectrum], similar to a Hessian run.


NSTEP

Indicates the maximum number of cycles allowed in a geometry optimization, default = 20.


METHOD

Selects the optimization algorithm. The default is QA = Quadratic Approximation. You can select NR = straight Newton-Raphson iteration, RFO = Rational Function Optimization, or CONOPT = CONstrained OPTimization. The latter must start from an energy minimum and is used for locating transition states by trying to push the geometry uphill along the mode chosen with IFOLOW, see below. For details see Input Description under 'METHOD'.


IFOLOW

Mode selection switch for RUNTYPE = SADPOINT. The default is 1, meaning that the first, lowest, vibrational 'mode' (rotational and translational degrees removed!) is very likely the reaction coordinate along which the potential energy has a negative curvature. Check the result to be sure that the selection was correct. After a saddle point location run it is recommended to run a Hessian job with the saddle point coordinates. The chosen, and only the chosen mode, usually mode 1, should then possess an imaginary frequency.


Advanced Options


Generally these parameters do not have to be changed. Those indicated are set by default without the necessity to click the button for 'Advanced Options'. However, they permit additional control over the calculation, see 'Input Description'. If you set 'Advanced options' different from the default values shown in the boxes, they are made available to the input file after clicking 'Save' on the 'Advanced Options' panel. They do not survive to the input file of your next job, however.

$CONTRL

MOLPLT

 

checked

Specifies whether the final coordinates are to be saved in Molplot format in ‘jobname’.dat. This can be processed by the routines in the GRAPHICS directory of a Gamess Cygwin- or Linux-Installation.

PLTORB

 

checked

Specifies whether the final coordinates and wavefunction informations are to be saved in PlotOrb format in ‘jobname’.dat. This can be processed by the routines in the GRAPHICS directory of a Gamess Cygwin- or Linux-Installations.

AIMPAC

checked

Specifies whether information for a Bader Atoms in Molecules input file is saved.

NOSYM

checked

The default is unchecked and means that the symmetry specified in $DATA is to be used as much as possible in integrals, SCF, gradients etc. If checked, the symmetry in $DATA is only used to build the molecule from unique coordinates, then not used anymore.

INTTYP

POPLE

HONDO

Indicates whether Pople or Hondo integrals are used. See GAMESS documentation.


IREST

0

Restart control options. "0" defaults to no restart planned. At the end of a Gamess run all files are erased except job.out, job.dat (=Gamess PUNCH file), which are saved to \output, and the input file saved as job.inp to \data.

 

2

Setting restart to "2" prevents some data files to be erased. This allows for SCF restart with 1-, 2-e integrals and MO's saved. There are more options to IREST, see Input Description.


LOCAL

NONE

Controls orbital localization. The default is 'none', skipping localization. A large number of options for finetuning localization is offered when including a $LOCAL group. gameix does not write a $LOCAL group. You have to compose it along the details given in Input Description.

 

BOYS

Do Foster-Boys localization.

 

RUEDNBRG

Do Edmiston-Ruedenberg localization.

 

POP

Do Pipek-Mezey population localization.


$DFT


NRAD

96

number of radial grid points in Euler-Maclaurin quadrature.

NTHE

12

number of angle theta grid points in Gauss-Legendre quadrature.

[ NPHI

24

number of angle phi grid points in Gauss-Legendre quadrature. Automatically assigned as twice NTHE.]


$GUESS

GUESS

HUCKEL

an (extended) Huckel approximation is to be used to generate the initial MO wavefunctions

 

MOREAD

the MO’s are to be read from the $VEC group of a previous calculation. When you are settting 'GUESS=MOREAD' you are asked for an outputfile name from where to append a $VEC group to the input file. In case there is no $VEC group in the selected file you are alerted. If there are several $VEC groups, as usual for Optmize jobs, the last one with (hopefully) converged orbitals is read in. Generally, using the $VEC group from a previous run to start from, is to be preferred compared to the default option 'GUESS=HUCKEL' since the SCF orbitals are of better quality than those from an extended Huckel computation. However, a real gain in computertime is only observable with large jobs.- It is mandatory to give the number of orbitals in NORB, see next item.


 

NORB

the number of MO’s to be read from a $VEC group when GUESS=MOREAD. You can look at the appended $VEC group when [View(ing) Input File] and write the largest number leftmost of the $VEC table into the NORB variable. There are other choices depending on your job, see the GAMESS Input Description in [Help] in the Master Menu.



HESS

GUESS

Chooses a positive definite diagonal Hessian as an initial guess

 

READ

Reads the Hessian from $HESS. Additional data must be supplied manually.

 

CALC

The initial Hessian is computed. See $FORCE. Additional input may be required.


$IRC

IRC

If RUNTYP=IRC this group governs the location of the intrinsic reaction coordinate, a steepest descent path connecting a saddle point to reactants and products. Therefore the prerequisite is a successful saddlepoint location run with RUNTYP=SADPOINT.

 

PACE

There are five integration methods: The default is GS2, the Gonzalez-Schlegel second order method using BFGS for updating the Hessian. There are more keywords for finetuning GS2, see Input Description. The other four choices for PACE are 'LINEAR', 'QUAD', 'AMPC4', and 'RK4', see Input Description, again.

 

SADDLE

If checked the IRC assumes starting from a precise saddle point. In this case the $HESS group of a SADPOINT run has to be attached to the input file. If unchecked, IRC starts from some other point _on_ the IRC path. The safest way is to start IRC from a converged SADPOINT run, check SADDLE, and read the $HESS group by setting HESS='READ' in the $STATPT group.

 

FORWRD

This defines in which direction the IRC starts from a saddle point. Default is FORWRD=checked, meaning that the IRC starts in the direction where the largest magnitude component of the imaginary normal mode is positive. You can identify this, if you look up the vibrational amplitudes of the imaginary frequency (normal mode table of the preceding SADPOINT run). If you pick the wrong direction you can always correct this in a second run with the advantage of thus getting an overview of both reaction directions, back to the reactants and forward to the products!

 

NPOINT

The number of IRC points to be located in this run, separated by STRIDE.

 

STRIDE

Determines how far apart points on the reaction path will be. STRIDE is used to calculate the step taken, according to the PACE method you selected. If you choose the robust method GS2 it can be 0.30 sqrt(amu)-Bohr, for the other methods it should be smaller, 0.1 or even 0.05.

 

MXOPT

Maximum number of constrained optimization steps for each IRC point. The default=20 is similar to NSTEP (in $STATPT) pertaining to optimization runs. If an IRC point does not converge, select a larger MXOPT and repeat the run.

$CIS/TDDFT

CIS/TDDFT

If CITYP=CIS or CITYP=TDDFT this group defines the details. Please consult the instructions, CIS and TDDFT computations are not entirely black-box for significant results and there are more parameters to select differently from the defaults than those offered on the panel. Note that TDDFT (time dependent DFT) often gives better results than CIS with the same basis.

 

NSTATE

Number of states to be found (excluding the ground state, so '1' means one excited state). For this number of singly excited states excitation energy and oscillator strength is computed.

 

IROOT

State for which properties and/or gradient (only for CIS) will be calculated. Only one state can be chosen.

 

MULT

Multiplicity (1 or 3) of the singly excited SAPS (the reference is necessarily single RHF). Only relevant for SAPS based run. SAPS are spin-adapted antisymmetrized products of the desired MULT.

 

HAMTYP

For CIS only: Type of CI Hamiltonian to use:
SAPS: spin-adapted antisymmetrized product of the desired MULT will be used (default)
DETS: determinant based, so both singlets and triplets will be obtained

 

RDVEC

For CIS only: Read CIS vectors from a previous computation of the same system, if you want to get other states (default = .false.)

 

NACORE

For CIS only: Omits the first n occupied alpha and beta orbitals from the calculation. The default for n is the number of chemical core orbitals.


APPLY

          The input file is written with the specified parameters. Until this button is pushed, nothing is written to your hard disk. The file “input” of a previous run is overwritten, but that file has already been saved by 'SAVE' as jobname.inp (including a time stamp) into the \data directory, so nothing is lost (unless you forgot to click 'SAVE', see below)!

VIEW INPUT FILE

           The VIEW INPUT FILE button calls up the required Gamess input file “input” in the editor for checking and, if necessary, editing. The “title” of the run and any special parameters can then be set manually and the file saved before starting a computation.

RUN

           The RUN button calls rungms.sh which has all required parameters to call ddikick.x and gamess.XX.x. The 'input' file is presented to gamess for computation. A shell window shows the start and calling string of the run, and announces the termination of the program. If there is an error condition announced by ddIkick there is, usually a comment to guide you to the next steps. If all's well – normal termination – you are prompted to look into the summary.

Summary

           The SUMMARY button shows a summary of the run in the Dialect worksheet. It announces whether the run was successful or unsuccessful. If a structure optimization has been run, convergence to a stationary state or failure to do so is announced as well as the final total energy. The output is written to the file .\output\‘jobname’.out.

SAVE

           The SAVE button generates ‘gamess.coo’ and the two files ‘jobname’.pdb, and ‘jobname’.xyz from either the input coordinates (runtype 'Energy', 'Gradient', Hessian', 'Raman', or an unsuccessful 'Optimize') or the last set of coordinates (successful 'Optimize') of a gamess run. The last two files are saved in the output directory. The equilibrium coordinates of a successful 'Optimize' run are additionally written into a file 'gamess.equ'. If you want to reuse coordinates in a new job with the same name, you can get them from three locations: 'COO', 'PDB', and 'XYZ' see Input Coordinate Type or from 'EQU' and 'UNQ', if you have deposited them from a converged 'Optimize' run. Note that ‘jobname’ contains a four digit time stamp to prevent overwriting files when you use the same job name in a new run. In addition the GAMESS 'PUNCH' file is moved to the output directory as ‘jobname’.dat. In \data a copy of the inputfile is saved as ‘jobname’.inp.

           Essential: Click on [Summary] and [Save] to save the output and clean the system for a new run.

VIEW

           The VIEW button opens the output file in the editor to study the detailed results. If the run was unsuccessful you find hints on what went wrong. Correct your input accordingly for a new try.


VIEW STRUCTURE

           The VIEW STRUCTURE button calls up the specified viewer. If vfile is set to “pdb” for that viewer, the output structure ‘jobname’.pdb is read into the viewer immediately. If vfile is set to "" in gameix.ini, the viewer is called up, but the user must select the file to be rendered manually. Molekel and Molden are different: They read all the pertinent parts of the output file, render the structure in the opening window and then let you choose any of their features in control menus.


IR/RAMAN SPECTRUM

           In order to simulate a spectrum of the fundamental vibrations, the vibrational frequencies and their intensities have to be extracted from the output: From a 'Hessian' run or an 'Optimize' run with HSSEND = true (both are called 'Hessian', here) the Infrared intensities, from a 'Raman' run the IR and Raman intensities (and the depolarization ratios for the latter) are exported. This is done with the help of the Master Menu. There are three cases:

  • If you have a Hessian or Raman run 'on-line', i.e. the job has just been terminated, and gameix not yet exited, click on [Properties, Show/Print]: You see the drop-down menu of selectable properties. Choose 'Normal Coordinate Analysis'.
  • If you want to look at the vibrations of a previous run [Outputdata/Load *.out] opens the \output directory to select a Hessian or Raman output file. This done click on [Properties, Show/Print]. The drop-down menu of properties opens. Choose 'Normal Coordinate Analysis'.
  • You can click on 'Vibration Spectrum' whereby a drop-down list of all jobname.res files in the \output directory is shown for choosing the Normal Coordinates of a previously saved Hessian or Raman run. The normal coordinates are not shown in this case but the spectrum panel opens and lets you proceed as follows.
In the first two cases the frequencies, IR-, and, possibly, Raman-intensities are shown in an editor window. This is automatically saved as output\jobname.res for later reuse. Click [Vibrational Spectrum] on the gameix panel. A list of saved IR/Raman spectra - including the most recent - is opened for you to select one. The spectrum panel opens for you to click on either one of the next two buttons:


Lin (1/cm)

this produces a lineplot with an overlay of Lorentzian line shapes on a linear wavenumber scale. It resembles a measured IR spectrum, probably from an FTIR machine, as change in 'transmittance' (blue trace). The Raman bands, if they have been computed, are shown in 'emission' (red trace). The spectral range goes linearly from about 20 to 4200 cm-1.

Lin (µ)

this produces a lineplot with an overlay of Lorentzian line shapes in a linear wavelength scale. It resembles a measured IR spectrum from a Rock Salt prism spectrometer as change in 'transmittance' (blue trace). The 'fingerprint' region is better visible than in the first plot but has less detail in the C-H stretch region and the 'skeletal' motions below 666/cm are missing. The Raman bands, from a Raman run, are shown in 'emission' (red trace). The spectral window shown goes from 2.4 - 15 µ (with constant transmission!). Vibrations below about 650 cm-1 are not shown!

Half Intensity Width (1/cm)

You may adjust the 'Linewidth' (width of the spectral 'line' at half intensity) to approximate an experiment with varying resolution. Furthermore, the rotational part of a vibration-rotation band is not explicitly simulated. This can be approximately taken care of by adjusting the linewidth.

Intensity Scale

This button allows to make weaker IR transitions or Raman emissions visible, or to scale overshooting transitions down. There is no simulation of the transmission behavior of your spectrometer. Assume, that the simulated spectrum has been corrected for experimental shortcomings!

Scale Frequencies

It is a sad fact that even the best 'ab initio' computations have problems with the vibrational frequencies in the harmonic approximation. Most calculated frequencies are up to 10% too large, depending on the model chemistry used. This error has been determined over a large sample of calculated versus observed frequencies. It is fairly constant, hence it has become customary to correct calculated spectra by this 'fudge factor'. You can check 'Scale Frequencies' and then select a factor corresponding to your model chemistry. The factors used are published in many locations, e.g. on page 64 of the book 'Exploring Chemistry with Electronic Structure Methods', 2nd ed., by James B. Forseman & Æleen Frisch, ISBN 0-9636768-3-8.
You can get a better prediction of vibrational frequencies, if you run an anharmonic vibrational analysis using RUNTYP = VSCF and the keyword $VSCF (search for 'VSCF' in Master Menu [Help/Input Description]). However, this takes much more computer time than the harmonic approximation (determining many structure points along each normal coordinate to SCF precision, computing the vibrational eigenfunctions, and taking account of coupling between them). You are prompted to add a $HESS group from a previous Hessian run for starting VSCF. It is recommended to run VSCF only with a good basis set, about 6-31g(d) or better, since minimal basis sets, like STO-3G, often do not produce results that make sense.
Note: Molekel (version 4.3), Molden can animate vibrational modes from the "View Structure" button and their own menus. However, Molekel cannot use output from Raman runs whereas Molden can use IR- and Raman data and also draw a spectrum of both.



References

1.        Dialect®

           http://www.downlinx.com/proghtml/104/10441.htm 

2.        Gamess

Citations:
GAMESS-US: Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 13471363.
MacGAMESS: Bode, B. M., Ames Laboratory, Iowa State University, Ames, IA 50011.
PC GAMESS: Alex A. Granovsky, PC GAMESS/Firefly version 7.1.E, http://classic.chem.msu.su/gran/
gamess/index.html

Gamess has been compiled with gcc-gfortran from the current version of GAMESS-US ( 24 MAR 2007 (R3)), an ab initio quantum mechanical package.- If you prefer PC GAMESS, an equivalent script RUNpcglin is available.

           http://www.msg.ameslab.gov/GAMESS/gamess.html

           http://www.chemsoft.ch/qc/binaries.htm

3.        NoteTab Lite®

           http://www.notetab.com 

4.        ArgusLab 4.01© Freeware

           http://www.planaria-software.com/ 

5.        ACD/ChemSketch© Freeware

           http://www.acdlabs.com/download/chemsk.html 

6.        ISIS/Draw

           http://www.mdli.com

7.        ViewerLite

           http://www.accelrys.com/download/ 

8.        HyperChem®

           http://www.hyper.com/

9.        PCModel®

           http://serenasoft.com/index.html

10.       gOpenMol

gOpenMol is maintained by Leif Laaksonen, Center for Scientific Computing, Espoo, Finland.

           http://www.csc.fi/gopenmol/

11.      VMD©

VMD was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign.

See Humphrey, W., Dalke, A. and Schulten, K., “VMD - Visual Molecular Dynamics”, J. Molec. Graphics 1996, 14.1, 33-38.

           http://www.ks.uiuc.edu

12.      RasWin 

           http://www.umass.edu/microbio/rasmol/getras.htm

13.      Molekel, version 4.3 

           http://www.cscs.ch/molekel

14.      Pov-Ray

           http://www.povray.org/

15.      (g)Molden, version 4.4

           http://www.cmbi.ru.nl/molden/molden.html

16.      Ghemical, version 1.02(stable) or 1.90 (dev)

           http://www.uku.fi/~thassine/ghemical/

17.      VB2000, Version 1.8 Rev. 3

VB2000 is developed by Jiabo Li, Brian Duke, and Roy McWeeny, Scinet Technologies, San Diego, CA, 92127, USA: Jiabo Li, and Roy McWeeny, "VB2000: Pushing Valence Bond Theory to New Limits", Int. J. Quantum Chem., 89(2002)208-216

           http://www.vb2000.net