Luceat: User’s Manual

    by Ernst J. Schumacher, University of Bern

Shortcut

Let's assume that you have unpacked luceat.zip into C:\luceat = fireflyDir, and read 'Installation' below

  1. In C:\luceat: Start with 'luceat.exe'. A template of the configuration file pops up. Look at it, then click 'Ok'.
    The configuration file is openend in the editor. Look for and edit External Editor, fireflydir, where you have installed luceat.exe, set Directory of firefly exec = fireflyBase to where you will be unpacking the firefly executable. Leave the rest for the moment. Save the file and exit the editor. Exit luceat by clicking 'File/Quit' on the MasterMenu.
  2. Get the newest firefly version 7.1.G, a Windows version, e.g. firefly_71g_windows_p4.zip, from firefly. Unzip the archive into fireflyBase using the password you obtained from A. A. Granovsky (link above or under References). Now unzip the samples.zip archive into a directory \Tests, which you have to create in the fireflybase directory (this is different from earlier releases of PC Gamess!)
  3. In c:\luceat: Start again by clicking 'luceat.exe'.
  4. Get an input file from 'Input/Tests' (MasterMenu) by clicking on its name
  5. On the main panel click 'View Input', then 'Run' that job
  6. After it has finished, 'Save', then 'View Output' file, look up some of the 'Properties' of interest. 'File/Quit' luceat.
  7. Congratulations! You now have a running luceat.exe and firefly.exe. Read some of the rest of this Manual and try more examples from \Tests or your own design. The \Tests directory has the expected, correct output files of every input file. Compare some of your outputs of test runs with those to validate your firefly installation.

Content

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

Introduction

           luceat is a 'Dialect'1 GUI to be used as a front- and back-end to firefly2. It allows one to build a molecule, save it, compose a firefly input file, run firefly with it, and view the structure and other properties 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. luceat has been written in the spirit of late Wayne P. Anderson's pcgRUN1.0, published in J. Chem. Educ. 2003, 80, 968. in July 2003. There is no guarantee that this version of the program will work properly on your system. USE AT YOUR OWN RISK. Please report any bugs to me.

There is (only) one piece of software I have used and included from the free pcgRUN1.0.zip archive at J.ChemEd. This is 'gamout2pdb.exe', a FORTRAN binary which needs two files as input ('natoms', a textfile with the number of atoms of the molecule, and 'gamess.coo', which are produced with [Save Job]). It produces three output files, 'molecule.pdb', 'molecule.ent' identical to the previous, and 'molecule.xyz'. The .pdb and .xyz files are copied to the \output directory, see Job Name.

If you are a user of PCgam: The last version (May 21, 2004) can be downloaded as PCgam.zip. While PCgam has been kept simple for didactical applications, luceat has extended functionality for some 'real' applications offering the same or even enhanced ease of usage.

If you are a user of pcgRUN1.0: Although most tasks possible with pcgRUN1.0 behave identically with luceat there are some differences in manipulation. Current firefly, version 7.1.G , is based on version 06 Jun 1999 of Gamess-US. Some differences are listed here:

  • 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 has changed. Carefully note in the template what information needs to be put into the configuration file if you plan to incorporate your own selection of 'Builder' and 'Viewer' tools. Please refer to the topics of Builders and Viewers and Configuration for special comments on installation.
  • The item 'OUT' in the 'Input Coordinate Type' has been replaced by 'COO'(rdinates), see Input Coordinate Type.
  • Generation and display of the vibrational spectrum have been merged into one button. The input data for it are handled differently, see IR/RAMAN SPECTRUM.
  • Density Functional Theory, DFT, has now been integrated. However, it is handled differently from Gamess-US! In firefly the $DFT group is not necessary. DFTTYP is declared in the $CONTRL group. 30 functionals are offered for use (B3LYP1 is identical to B3LYP in NWChem and Gaussian, B3LYP5 with the version in Gamess-US). In the recent Version 7.0 TDDFT code has been implemented for the determination of excited states in addition to the CIS method under Hartree-Fock.
  • Parallel runs are now enabled with the WMPI1.3 protocol (there are other options offered with firefly. But only WMPI1.3 is supported by luceat at this time). The script handles automatically any combination of SMP (Shared Memory Multiprocessor) and independent computers in the same LAN. For setting up the proper communication, see Configuration.

What is in the luceat Package luceat.zip

          The following parts are necessary for running firefly with luceat:

(1) luceat script
luceat.exe compiled script of the next four sources
luceat.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 MS, search of output file
Dialect.exe for recompiling this script after changes
gamout2pdb.exe produces pdb and xyz files from firefly output
keys.txt keys for which grep searches output, can be edited
keyvec.txt keys for searching CIS or TDDFT output
cvwmpi.dll library for parallel execution with the WMPI1.3 protocol

(2) luceat Manuals, examples, further information
PROG.DOC Programmer's references from Gamess-US
IRON.DOC Computer specifics from Gamess-US
TESTS.DOC description of >50 Gamess job files (Gamess-US)
DFT.htm Alex A.Granovsky's description of the DFT package
in firefly
cube.htm Alex A.Granovsky's description of the cube feature
in firefly
Manualp.htm this manual with auxiliary files
\WMPI1.3min minimum package for the implementation of the parallel
protocol WMPI1.3, including manual and automatic
installation software for wmpi_server.exe

(3) firefly, not included! Get it from firefly
Make sure you select the version appropriate to your CPU(s)
firefly.exe parallel and sequential (unified) binary
pcg2p.dll library
p4stuff.dll library
fastdiag.dll library for an improved diagonalization routine
mpibind.dll library to be copied and renamed from the BINDINGS directory
\tests create this subdirectory with 44 test examples ready for
running from the samples.zip archive of the firefly distro
INTRO.DOC Introduction manual from firefly in docs.zip
INPUT.DOC Input syntax manual from firefly in docs.zip
REFS.DOC 'Further Information' from firefly in docs.zip

Installation

          The script is supposed to be in the same directory with the auxiliary files, tables 1 and 2. Unzip the luceat.zip package into any suitable directory, e.g. c:\QC\luceat. Its location, named 'fireflydir', has to be edited in the Configuration file. Get the firefly distribution (table 3, above) and extract it into its own directory, here called 'fireflyBase'. Create a subdirectory 'tests' and unzip the samples.zip archive from the firefly distro into it. Two additional subdirectories are automatically created at startup of luceat, 'data', and 'output', managed by the script for input and output.

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 you are prompted to select and append a $HESS matrix to the input file.

 

Load $CISVEC or $TDVEC group

This offers the names of the stored \output\*.dat files for you to select the job from which you wish to extract a $CISVEC or $TDVEC group as starting vectors from previous $CIS or $TDDFT runs, e.g. to compute other excited states. The selected vectors are appended to your input file. Consult A.A.Granovsky's readme.cis and/or readme.tddft for instructions.

 

Load $CUBE groups

This offers the names of the stored \output\*.dat files for you to select the job from which you wish to extract $CUBE groups which subsequentially can be read in for rendering into 'Molekel', or 'gOpenMol'. Consult A.A.Granovsky's readme.cube for instructions.

 

Quit

Recommended termination of luceat. 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

\data\*.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 fireflydir\input and can be viewed and run (perhaps with your edits). Note: The input file may be in UNIX or PC style. If your input file stems from a current Gamess-US installation make sure to eliminate an entry for 'ISPHER' in the '$CONTRL' group when [View(ing) Input File] and, perhaps, move 'DFTtyp=XXX' from the $DFT group into $CONTRL.

 

'input' file

Opens a file 'input' in fireflydir or, if not found, in fireflybase. This file exists if a previous run has aborted because of e.g. syntax or point group error(s). It is then opened for corrections.

 

Tests

Opens the \tests directory for you to select one of the test files. This directory is located in the fireflyBase directory. After clicking on the desired name the file is transferred to fireflydir\input and can be viewed and run. The input file may be in PC or UNIX format. The \tests directory also contains the output generated by a correct run of firefly. You may want to compare your runs with those.

Outputdata

Load *.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 MasterMenu and [View Structure] in the main panel become active and let you extract molecular properties or visualize them in the chosen Viewer or generate an IR/Raman spectrum. An output file can be in PC or UNIX style, e.g. from a Gamess-US run.

 

Load *.dat

Opens the \output directory for you to choose a .dat file = firefly 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.

Properties

Show/Print

If a job has just been run and luceat 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' or 'gamess.equ', 'gamess.unq' in 'fireflydir'. 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, e.g. from 'serial' to 'parallel' runmode (with concomitant change of the number of CPU's to use). After closing the editor window the new configuration becomes active. For details, please consult the item 'Configuration File'.

Help

Manual

Opens this document in the Browser.

 

Intro.doc

Introduction to the scope of firefly and the history of its development.

 

Input.doc

Opens the Input documentation of Gamess-US to be consulted for the more specialized jobs, not provided for in the listboxes during configuration of an input file. You can search the text for less common keywords and get advice for the precise composition of the coordinates and their different formats.

 

Tests.doc

Opens the input files of the 37 test EXAMples in \tests from the documentation of Gamess-US. Since they contain a fair sample of the jobs firefly can do, they may be helpful for setting up your input. Some of the tests may not run under firefly since newer keywords are lacking. Look into the 13 BENCH files which work. For advanced functions and new keywords specific to firefly there are test input files in the many readme.topic files distributed by A.A.Granovsky with the firefly archive.

 

Refs.doc

Gives details about basis sets and their validity and many explanations about how to setup more sophisticated jobs, like CI, CASSCF, and MCSCF calculations and much more.

 

Prog.doc

Interesting for programming details.

 

Iron.doc

Hardware related informations, especially useful for setting up a multinode environment.

 

About

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



The Configuration file

           Many of the parameters in luceat can be set by the user in the configuration file luceat.ini. A template for this is presented when luceat 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 'fireflydir' where you have installed the luceat script, e.g. 'C:\AQC\luceat'
2) the path name of 'fireflybase' where you have installed the firefly distribution, e.g. 'C:\AQC\pcg71g', and
3) the correct name of the firefly binary to be used, currently 'firefly.exe' for the unified (serial and parallel) version (> 6.4).
If these three items are not given accurately, nothing runs!
Since new versions of firefly are running in serial and parallel mode you have to provide one of the DLL's reflecting your mode. Start with the sequential mode! Copy from fireflydir/BINDINGS mpibind.seq.dll to fireflydir and rename it to 'mpibind.dll'. This corresponds to 'serial' mode and 'Number of CPU's = 1 in the configuration file.
The configuration file is always read immediately when luceat starts up. It later can be edited by clicking on 'Configure/Conf File' in the MasterMenu.
Should you later move the luceat directory to another location in the directory tree (or to another computer), please remove the file luceat.ini before starting luceat.exe. This file will then be recreated, with your edits added to reflect the new location of at least 'fireflydir'.
If you have the new, unified (serial and parallel), firefly executable (versions > 6.4), you may switch between runmodes with 'Configure/Conf File': Change 'serial' to 'parallel', and give the number of CPU's appropriate for your setup. During the call of your next run luceat configures the parallel environment asking you for the paths to the various slaves. In addition you have to get a new mpibind.XX.dll from fireflydir/BINDINGS, e.g. mpibind.wmpi-1.3.dll, which you have to rename to mpibind.dll in fireflydir. Furthermore you have to install and activate the mpi-server 'wmpi_service.exe', see instructions below.
The management of distributed computation in a cluster of independent CPU's in any mix of SMP and external nodes on a LAN is done by WMPI1.3. The included WMPI1.3min package allows you to install this. You find all the necessary steps for this described in these instructions. They have been written for the earlier PCGam script but can be used equivalently for luceat.

           The directories of the file editor, the browser, the builders, and the structure viewers must be specified in luceat.ini. 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. You have to specify its input through the 'File/Open' dialogue. This is different for 'Molekel' and 'Molden'. Its calling specifications are automatically generated by the script once you have given the location of the executable in the conf file, see the template, and selected it as one of the viewers. 'Molekel' can read (all) information of firefly output files (structure, orbitals, dipole moments, vibrational frequencies and normal mode coordinates, for animation). From the orbitals and their occupations it generates 3D renderings, including total density, MEP and other properties. It can export images in various graphical formats (quality sufficient for scientific publications) and save structures in pdb and xyz file formats. 'Molden' is as versatile with a plethora of options a bit different. 'Molden' now shows an IR spectrum (with Lorentz line shapes, similar to this script's IR/Raman plots).

          Note: Presently 'Molden' depends on the program molden.csh in the c:\Molden directory' which calls the Xwindows server and then starts (g)molden.exe for a file mold.out sent to it by luceat from an open job when clicking 'View structure'. You have to install the X-Windows system (e.g. MI/X_4.2) yourself and find Howto's in molden's readme files. If you are using Ghemical as molecule builder you can make use of its inbuilt Xwindows server XWin.exe. 'Molden' has to be installed as second viewer and both, Ghemical's and Molden's paths are hardwired as c:\Ghemical and c:\Molden. Please, keep this in mind when installing those two programs. 'Molden's homepage gives instructions.

           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, such as 'Notepad.exe' for Windows 2000 and XP, another editor is needed for Windows 95, 98SE, and ME because the 'old' Notepad.exe included in those OS's can only read files smaller than 64kB. 'NoteTab.exe'3 is a free editor adequate for the purpose. In addition, Windows 9X and ME need the program 'hostname.exe' which is in the package. It may be removed from the luceat directory in Win2k & XP where it exists already.

Options in luceat

BUILDER


           The program used to draw and build the molecule is set in luceat.ini. Four builders may be set in the program.
With ArgusLab4 a molecule can be built and then converted into a reasonable 3D structure by the 'Clean Geometry' button or an MM or even SCF/Mopac optimization.
ChemSketch5 can be used to build a molecule in 2D and then convert the structure to 3D as long as a restricted subset of elements is present. One can use one of these elements to build a molecule initially, and then change to the desired element in the 3D structure. Only standard valences are supported by the 3D conversion utility in ChemSketch as well. The resulting structure can be saved in .mol format.
ISIS/Draw6 can also be used to generate a 2D structure and save it in .mol format. The resulting .mol file can be read into ViewerLite™® 7 and converted to 3D. If you use ViewerLite, be sure to turn on the 2D to 3D conversion option before importing the file from ISIS/Draw. If you also wish to use ViewerLite to view the final structure, be sure to turn the 2D to 3D conversion option off or your calculated structure will be altered upon import.
Ghemical15 is much more than a builder. After building and MM optimizing a molecule, it can compose a firefly input file, submit and run it. There is no backend, however. You can also copy the generated input file to the \data directory of luceat, edit and run it under the guidance of luceat and have all the backend options of this script.
Commercial programs such as HyperChem® 8 or PCModel® 9 can be used as well. The builder must be able to generate an initial set of 3D coordinates for the molecule and be able to save the file in .mol or in .pdb format.


VIEWER


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


JOB Name


           The name of the JOB must be entered here. The files ‘jobname’.out, ‘jobname’.pdb, ‘jobname’.dat, 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 at the start of the computation.- If you [Output/Read *.out] (MasterMenu) 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 firefly output file, named ‘jobname’.out, may also be used for coordinate input. In the MasterMenu click on [Properties, Show/Print], click on the output file desired and then choose 'Coordinates'. This generates a file 'gamess.coo', and with runtype = Optimize 'gamess.equ' (= equilibrium coordinates) and 'gamess.unq (= symmetry unique equilibrium coordinates, if they exist) which can be read in when composing the input file, choosing 'COO', 'EQU', or 'UNQ' as Coordinate Type.
In luceat input/output files are in separate directories called .\data and .\output.


firefly INPUT


           The firefly Input button allows one to set many of the input parameters for firefly, 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 'fireflydir'. Coordinates can also be entered manually, see below.

           More advanced jobs and some of the firefly options require additional input that cannot (yet) be entered through luceat. It is the responsibility of the user to review the input file generated by luceat 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 firefly documentation files, particularly Input.doc. A copy of Input.doc is placed in the luceat directory, and it can be accessed from HELP of the MasterMenu. Note that this is the most recent Input.doc from the gamess-US distribution. Some of the keywords are not yet available with firefly, and some new keywords of firefly are not discussed in Input.doc. Consult the firefly homepage of Alex A. Granovsky2


Summary of firefly INPUT Options

Items in bold - or a red bar on the panel - are the ones that are changed most often.
firefly 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, keywords within groups, too. The following list of groups and pertaining keywords is implemented in the listboxes of luceat. 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 one of the most important entries for any type of quantumchemical computation: The structure of a molecule, i.e. the spatial 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.doc' under [Help] in the MasterMenu. 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 firefly allows any name for the atoms because their identity is defined by the nuclear charge. luceat insists on using IUPAC symbols because these are used for the .pdb and .xyz files produced at the end of a job and for the viewer 'Molekel'. Furthermore, with ZMT or ZMTMPC coordinates firefly 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 Job] button or by clicking [Properties, Show/Print] 'Coordinates' in the MasterMenu. This file, if it exists, is in the fireflydir 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 firefly output. It is not overwritten by a subsequent run, unless this is another 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 fireflydir 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 firefly output. It is not overwritten by a subsequent run, unless this is another successful 'Optimize' run.

 

COO

Coordinates are to be read from a file named gamess.coo automatically created with the [Save Job] button from any run or by clicking [Properties, Show/Print] 'Coordinates' in the MasterMenu. This file, if it exists, is in the fireflydir directory.

 

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 fireflydir\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 fireflydir\data directory. With the [Save Job] button the structural data of a successful firefly 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 luceat and luceat 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. fireflys 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 Job] at the end of a firefly 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 luceat 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 firefly. In the case of firefly 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.


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 firefly, the input generated by firefly 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.


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 firefly 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.

 

SADPOINT

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

 

PROP

Certain specified properties of the molecule at the geometry defined 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.


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 luceat.

 

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.doc in the MasterMenu [Help/Input.doc]. Cart = unique is firefly 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 was not correctly implemented in pcgRUN1.0, since 'ZMAT' instead of 'ZMT' was entered as keyword. 'ZMAT' is used as $ZMAT group to define internal coordinates if NZVAR > 0, see Input.doc)

 

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.DOC or any MOPAC manual.


SPHER

d5

If checked d5=.true. This means a spherical harmonic basis with 5 d (7 f, and 9 g) functions is used instead of the usual set with 6 d, 10 f, and 14 g functions. d5=.true. is equivalent to ISPHER=1 in Gamess-US. You can finetune this new feature in firefly: Add a new group
$d5 d5=.t. f7=.t. g9=.t. $end
This is the default, when d5=.t. in the $CONTRL group. In the $d5 group you can be selective and set anyone of the spherical harmonics to false. This is then expressed in the usual redundant cartesian mode.


$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.


$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.doc'.


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

checked

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

checked

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


SHIFT

checked

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.


NCONV

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




$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.DOC 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.

$DFT

DFTTYP

None

No Density Functional Calculation is done by default

 

B3LYP1

or 30 other DFT functionals may be selected. When right clicking into the edit box, a menu opens with the available categories of functionals. Click on the category you want and select your favorite functional to get it written into the editbox. Refer to README.DFT for more info about functionals.
Notice: The selected functional is written as DFTTYP = functl into the $CONTRL group. The $DFT group is used for controlling integration.
DFT does not work with the semiempirical Hamiltonians MNDO, AM1, and PM3. If you select one of those, DFTtyp is automatically set to "NONE".

The list of available functionals:


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.doc'. If you set 'Advanced options' different from the default values shown in the boxes, they are made available to the input file after clicking 'APPLY' 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 firefly 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 firefly 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 firefly documentation.


IREST

0

Restart control options. "0" defaults to no restart planned. At the end of a firefly run all files are erased except job.out, job.dat (=firefly 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.DOC.


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. luceat does not write a $LOCAL group. You have to compose it along the details given in INPUT.DOC.

 

BOYS

Do Foster-Boys localization.

 

RUEDNBRG

Do Edmiston-Ruedenberg localization.

 

POP

Do Pipek-Mezey population localization.

CITYP

NONE

No computation of excited states

CIS

CIS computation of excited states, see readme.cis. Select the parameters below at $CIS,$TDDFT

TDDFT

TDDFT computation of excited states, see readme.tddft. Select the parameters below at $CIS,$TDDFT


$DFT


NRAD

63

number of radial grid points per atom.

LMAX

29

order of Lebedev angular grid, corresponds to 302 points per radial shell.

 

Before editing these numbers, read Granovsky's README.DFT


$GUESS

GUESS

HUCKEL

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

 

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 firefly Input.doc in [Help/Input.doc] in the MasterMenu.


$CUBE [$ELDENS, $ELPOT]


CUBE

checked

firefly can produce cube files to be rendered e.g. in gOpenMol, or Molekel. If CUBE is checked cube files are generated if ELDENS and/or ELPOT are checked. The main options can be selected and are described below. More can be found in the Cube Documentation (with example input files) from Alex A. Granovsky.- Use 'Molekel' to see 3D densities being computed and rendered without the necessity of a cube file. However, the CUBE option goes beyond this, e.g. being able to make many types of superpositions of densities and creating Laplacians and gradients of densities.
After a run with CUBE=checked the cube files can be extracted from the \output\*.dat file using the option unter 'File/Load $CUBE group(s)' in the Master menu. The selected cubes are saved with the name 'CUBE, number, job.cube' in the subdirectory \cubes of fireflydir.

MESH

COARSE (50)

MEDIUM(80)

FINE (100)

ULTRA (200)

This gives the number of grid points along each coordinate used in the cube file. A COARSE grid is generally sufficient. MEDIUM, FINE and especially ULTRA grids will generate very large cube files. COARSE cubes are 825kB those for ULTRA 64 times larger!

$ELDENS

ELDENS

checked

Sets IEDEN to 1 and allows several types of densities to be generated, depending on the next options. If none of them is checked, the total Electron density is computed


MORB

0

> 0

Indicates the MO whose electron density is to be computed. If this is left at 0, the total electron density is computed. Otherwise, the MO number must be entered.


spind

checked

Computes the total spin density of radicals.


diffd

checked

Produces several density differences, depending on the details of the job and the choice of the deriv(ative)s. options. E.g. look at Example1 in Cube Documentation, which uses this option and creates 8 different cubes!


skiphf

checked

Skips the cube production of the initial HF density.


derivs

0,0,0

any combination of up to three numbers 0, 1 & 2. Define the level of density derivatives to be used: 0 means density, 1 density gradient (or its norm), 2 density Laplacian. E.g. 0,0,2 produces two cubes: Density and its Laplacian; 0,1,2 the same plus the cube of the gradient of the density.


icorbs

checked

Reads the numbers of the orbitals given in the two boxes named 'orbitals' and 'beta orbitals (if UHF)' and produces cubes of the orbitals (not their density). Suppose you want to know the 3D shape of the orbitals of H2O. The molecule has 10 electrons, i.e. 5 doubly occupied orbitals. Hence orbital 5 is the HOMO. You have done an scftyp = "RHF" run and want to see the shapes of HOMO-2 to LUMO+1: Enter the numbers 3,4,5,6,7 in the upper box. The lower rests empty.
Let's assume now, that you repeat the computation with H2O+ (icharg=1, 9 electrons) with scftype = "UHF", multiplicity = 2. You will get alpha orbitals, singly occupied to number 5, and beta orbitals singly occupied to number 4. In order to compare with the previous run with neutral H2O you enter the numbers 3,4,5,6,7 in the upper box and e.g. 3,4,5 in the lower 'beta'-orbital box. In the inputfile you will see ICORBS(1)=3,4,5,6,7,-3,-4,-5. firefly needs a minus sign to distinguish between alpha and beta orbitals. This is automatically attached to the numbers entered into the beta orbital box. An orbital cube will be formed with these 8 orbitals. This cannot be properly rendered with Molekel, which presently only takes a cube with one 'object' at a time. However, 'gOpenMol' as viewer can read the output .dat (=PUNCH) file and correctly announces 8 orbitals. Follow gOpenMol's tutorial to learn how these have to be rendered. 'Facio', a backend for firefly (and other QC packages), can do this, too, and even in a much simpler way.
Finally, if you run an scftype = "ROHF" for H2O+, you get four doubly occupied orbitals, and a singly occupied HOMO. You do not need to change the input for ICORBS(1) from scftyp = "RHF".


$ELPOT


ELPOT

checked

Sets IEPOT to 1. The molecular electrostatic potential is computed and cubed. If IEDEN=1, too, both cubes will be produced, the electron density and the ESP. This allows one to plot the ESP on the total electron density surface using gOpenMol or Molekel. Again, Molekel offers the same functionality without a cube file.


$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.DOC. The other four choices for PACE are 'LINEAR', 'QUAD', 'AMPC4', and 'RK4', see INPUT.DOC, 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). For this number of singly excited states excitation energy and oscillator strength is computed.

 

ISTATE

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

 

ISTSYM

symmetry of states of interest. Default is zero, i.e., does not use any symmetry during calculations. Setting this to the desired index of irrep (according to firefly numbering) will solve only for the states of the desired symmetry, exploiting full (including non-abelian) symmetry of the molecule, thus significantly reducing computation time.

 

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.

 

RDVEC

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

 

NCORE

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 harddisk. The file “input” of a previous run is overwritten, but that file has already been saved by 'SAVE JOB' as jobname.inp (including a time stamp) into the \data directory, so nothing is lost (unless you forgot to click 'SAVE JOB', see below)!


VIEW INPUT FILE


           The VIEW INPUT FILE button calls up the required firefly 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 firefly with the 'input' file. A DOS Command window opens and shows the run attributes including runmode and number of CPU's in use. Termination of the firefly job is announced with the attribute 'NORMALLY' or 'ABNORMALLY' depending on 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 first and final total energy. The output is written to the file .\output\‘jobname’.out.


SAVE JOB


           The SAVE JOB 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 firefly 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' and 'gamess.unq' (for symmetry unique atoms). 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' or '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 firefly '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 [Save Job] to clean the system before a new run.

VIEW OUTPUT FILE


           The VIEW OUTPUT FILE button opens the current 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 luceat.ini, the viewer is called up, but the user must select the file to be rendered manually. The call to Molekel is different: Molekel always reads all the pertinent parts of the output file, renders the structure in the opening window and then lets you choose any of its features in a drop down menu activated with a right click into the window. The same is true for Molden with slightly different choices in their menus.


IR/RAMAN SPECTRUM


           In order to simulate a spectrum of the fundamental vibrations, the vibrational frequences 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 MasterMenu. There are three cases:

  • If you have a Hessian or Raman run 'on-line', i.e. the job has just been terminated, and luceat 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 are 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 luceat 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 lineshapes 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 lineshapes 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 absorptions 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 modelchemistry. 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.
Note: Molekel (version 4.3), and Molden can animate vibrational modes from the "View Structure" button and their own menus. However, neither 'Molekel' nor 'Molden' can use output from Raman runs.



References

1.        Dialect®

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

2.        Firefly®

            Citations:

Firefly QC package [1], which is partially based on the GAMESS (US) [2] source code.

[1] Alex A. Granovsky, Firefly version 7.1.G, www http://classic.chem.msu.su/gran/firefly/index.html

[2] M.W.Schmidt, K.K.Baldridge, J.A.Boatz, S.T.Elbert, M.S.Gordon, J.H.Jensen, S.Koseki, N.Matsunaga, K.A.Nguyen, S.Su, T.L.Windus, M.Dupuis, J.A.Montgomery J.Comput.Chem. 14, 1347-1363 (1993)

           http://classic.chem.msu.su/gran/firefly/index.html

           http://www.msg.ameslab.gov/gamess/gamess.shtml

Firefly, Version 7.1.G has additional functionalities compared to the current version of Gamess(US) (12 JAN 2009) but lacks several others developed between 1999 and the current release.

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.      Ghemical, version 2.01

           ghemical-2.01-win-noob.zip


16.      (g)Molden, version 4.7

           for Windows 95,NT,2000,XP