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 |
|
|
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. |
|
|
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, |
|
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 |
$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
|
|
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 |
$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. |
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. |
|
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. |
$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.
|
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. |