INPUT COORDINATE TYPE

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

NONE

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

EQU

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

UNQ

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

COO

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

MOL

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

PDB

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

ENT

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

XYZ

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

GROUP

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

NAXIS

Indicates the order of the principal axis when the point group specification includes an “N”. E.g. for C_3v NH₃ molecule, select 'Cnv' for GROUP and '3' for NAXIS.

EXETYP

CHECK

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

RUN

Indicates that a full GAMESS run is to be done.

RUNTYP

ENERGY

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

OPTIMIZE

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

HESSIAN

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

RAMAN

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

VSCF

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

G3(MP2)

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

SADPOINT

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

IRC

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

NMR

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

PROP

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

SCFTYP

RHF

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

UHF

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

ROHF

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

MPLEVL

0

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

2 [,3,4]

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

ISPHER

-1

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

0

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

1

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

ICHARG

Specifies the overall charge on the system.

MULT

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

ECP

NONE

Effective core potentials (pseudopotentials) are not being used.

SBKJC

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

HW

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

READ

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

MAXIT

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

COORD

CART

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

UNIQUE

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

ZMT

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

ZMTMPC

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

DFTTYP

NONE

No Density Functional Calculation is done (default)

B3LYP

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

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

TIMLIM

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

MWORDS

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

[ MEMDDI

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

GBASIS:

NGAUSS

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

NDFUNC

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

NFFUNC

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

NPFUNC

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

DIFFSP

.TRUE.

.FALSE.

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

DIFFS

checked

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

DAMP

.TRUE.

.FALSE.

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

SHIFT

.TRUE.

.FALSE.

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

DIRSCF

checked

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

CONV

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

OPTTOL

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

HESS

GUESS

Chooses a positive definite diagonal Hessian as an initial guess

READ

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

CALC

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

HSSEND

checked

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

NSTEP

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

METHOD

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

IFOLOW

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

MOLPLT

checked

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

PLTORB

checked

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

AIMPAC

checked

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

NOSYM

checked

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

INTTYP

POPLE

HONDO

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

IREST

0

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

2

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

LOCAL

NONE

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

BOYS

Do Foster-Boys localization.

RUEDNBRG

Do Edmiston-Ruedenberg localization.

POP

Do Pipek-Mezey population localization.

NRAD

96

number of radial grid points in Euler-Maclaurin quadrature.

NTHE

12

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

[ NPHI

24

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

GUESS

HUCKEL

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

MOREAD

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

NORB

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

HESS

GUESS

Chooses a positive definite diagonal Hessian as an initial guess

READ

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

CALC

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

IRC

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

PACE

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

SADDLE

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

FORWRD

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

NPOINT

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

STRIDE

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

MXOPT

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

CIS/TDDFT

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

NSTATE

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

IROOT

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

MULT

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

HAMTYP

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

RDVEC

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

NACORE

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

Lin (1/cm)

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

Lin (µ)

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

Half Intensity Width (1/cm)

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

Intensity Scale

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

Scale Frequencies

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