TheGeomkeyword specifies the source of the molecule specification input, options related to coordinate definitions, and geometry related output. By default, it is read from the input stream, as described previously.Geommay be used to specify an alternate input source. It also controls what geometry-related information is printed and use of internal consistency checks on the Z-matrix. TheGeomkeyword is not meaningful without at least one item selection option.
Checkpoint
Causes the molecule specification (including variables) to be taken from the checkpoint file. Only the charge and multiplicity are read from the input stream. For example,Geom=Checkpointmay be used by a later job step to retrieve the geometry optimized during an earlier job step from the checkpoint file. This action is safe since Gaussian will abort the job if an optimization fails, and consequently subsequent job steps which expect to use the optimized geometry will not be executed.Checkpointmay be combined with theModRedundantoption if you want to retrieve and alter the molecule specification in a checkpoint file using redundant internal coordinate-style modifications.
AllCheck
Causes the molecule specification (including variables), the charge and multiplicity, and the title section to be taken from the checkpoint file. Thus, only the route section and any input required by keywords within it need be specified when using this option. This option is not valid withModifybut may be combined withModRedundant.
Step=N
Retrieves the structure produced by theNthstep of a failed or partial geometry optimization (it is not valid for a successful optimization).Step=Originalrecovers the initial starting geometry. This option is used for restarting geometry optimization from intermediate points. It must be combined with one ofCheckpoint,AllCheckorModify. Note that not all steps are always present in the checkpoint file; aHessian updatedmessage in the log file means that the corresponding step is available in the checkpoint file.NGeom=Nretrieves theNthgeometry from an optimization checkpoint file using the same record of points used for display in GaussView, whereN=1 corresponds to the input molecule specification.Geom=Step=Mis automatically converted toGeom=NGeom=M+1 if the previous optimization used redundant internal coordinates.
ModRedundant
Add, delete or modify redundant internal coordinate definitions (including scan and constraint information) before performing the calculation. This option requires a separate input section following the geometry specification. When used in conjunction withQST2orQST3, aModRedundantinput section must follow each geometry specification.AddRedundantis synonymous withModRedundant. This option may be used for job types other than optimizations. It may also be combined withNGeom,CheckorAllCheckto retrieve and modify an internal coordinate definition from a checkpoint file.
When used withCheckorNGeom, two input sections will be read: the first contains the charge and multiplicity, and the second contains alterations to the retrieved internal coordinate definition. When combined with theAllCheckoption, only the internal coordinate definition modifications input is needed.
Lines in aModRedundantinput section use the following syntax:
[Type]N1 [N2 [N3 [N4]]] [A|F] [[min]max]] [Type]N1 [N2 [N3 [N4]]]B[[min]max]] [Type]N1 [N2 [N3 [N4]]]K|R[[min]max]] [Type]N1 [N2 [N3 [N4]]]D[[min]max]] [Type]N1 [N2 [N3 [N4]]]Hdiag-elem[[min]max]] [Type]N1 [N2 [N3 [N4]]]Snsteps stepsize[[min]max]]
N1,N2,N3 andN4 are atom numbers or wildcards (discussed below). Atom numbering begins at 1, and any dummy atoms are not counted.
The atom numbers are followed by a one-character code letter indicating the coordinate modification to be performed; the action code is sometimes followed by additional required parameters as indicated above. If no action code is included, the default action is to add the specified coordinate. These are the available action codes:
| A | Activate the coordinate for optimization if it has been frozen. | |
| F | Freeze the coordinate in the optimization. | |
| B | Add the coordinate and build all related coordinates. | |
| K | Remove the coordinate and kill all related coordinates containing this coordinate. | |
| R | Remove the coordinate from the definition list (but not the related coordinates). | |
| D | Calculate numerical second derivatives for the row and column of the initial Hessian for this coordinate. | |
| H | Change the diagonal element for this coordinate in the initial Hessian todiag-elem. | |
| S | Perform a relaxed potential energy surface scan. Increment the coordinate bystepsizea total ofnstepstimes, performing an optimization from each resulting starting geometry. |
An asterisk (*) in the place of an atom number indicates a wildcard.Minandmaxonly apply to coordinate specifications containing wildcards. The action then specified by the action code is taken only if the value of the coordinate is in themin–maxrange (or below maximum value ifminis not given).
Here are some examples of wildcard use:
| * | All atoms specified by Cartesian coordinates | |
| * * | All defined bonds | |
| 3 * | All defined bonds with atom 3 | |
| * * * | All defined valence angles | |
| * 4 * | All defined valence angles around atom 4 | |
| * * * * | All defined dihedral angles | |
| * 3 4 * | All defined dihedral angles around the bond connecting atoms 3 and 4 |
By default, the coordinate type is determined from the number of atoms specified: Cartesian coordinates for 1 atom, bond stretch for 2 atoms, valence angle for 3 atoms and dihedral angle for 4 atoms. Optionally,typecan be used to designate these and additional coordinate types:
| X | Cartesian coordinates. | |
| B | Bond length | |
| A | Valence angle | |
| D | Dihedral angle | |
| L | Linear bend specified by three atoms (ifN4 is-1) or by four atoms, where the fourth atom is used to determine the 2 orthogonal directions of the linear bend. In this case,minandmaxare each pairs of numbers, specifying the two orthogonal bending components. |
See the examples under theOptkeyword for illustrations of the use ofModRedundant.
Modify
Specifies that the geometry is to be taken from the checkpoint file and that modifications will be made to it. A total of two input sections will be read: the first contains the charge and multiplicity, and the second contains alterations to the retrieved geometry.
Modification specifications for geometry optimizations using Z-matrix coordinates have the following form:
variable[new-value] [A|F|D]
wherevariableis the name of a variable in the molecule specification,new-valueis an optional new value to be assigned to it, and the final item is a one-letter code indicating whether the variable is to be active (i.e., optimized) or frozen; the code letterDrequests numerical differentiation be performed with respect to that variable and activates the variable automatically. If the code letter is omitted, then the variable’s status remains the same as it was in the original molecule specification.
SkipAll
Suppresses automatic generation of any internal coordinates; all of them must be explicitly specified in theGeom=ModRedundantinput section.
SkipAng
Generates bonds but omits angles and dihedrals.
SkipDihedral
Suppresses the generation of dihedrals.
SkipHBond
Skips generation of hydrogen-bond coordinates.
Connectivity
Specify explicit atom bonding data via an additional input section (blank line-terminated) following the geometry specification and any modification to it. This option requires one line of input per atom, ordered the same as in the molecule specification, using the following syntax:
N1Order1 [N2Order2 …]
where theN’s are atoms to which the current atom is bonded, and theOrder’s are the bond order of the corresponding bond. For example, this input specifies that the current atom is bonded to atoms 4 and 5, with bond orders of1.0and2.0respectively:
8 4 1.0 5 2.0
A bond order of0.1indicates a bond which should be used in generating internal coordinates but which should not affect atom types or connectivity for molecular mechanics.
This input section is terminated by a blank line.
ModConnectivity
Modify the connectivity of the atoms in the molecule specification (or retrieved from the checkpoint file). This option requires an additional input section (blank line-terminated) following the geometry specification and any modification to it. Connectivity modifications use the following syntax:
MN1Order1 [N2Order2 …]
whereMis the atom number, theN’s are atoms to which that atom is bonded, and theOrder’s are the bond order of the corresponding bond. A bond order of -1.0 removes a bond. For example, this input specifies that atom 8 is bonded to atoms 4 and 5, with bond orders of 1.0 and 2.0 respectively, and removes any bond to atom 9:
8 4 1.0 5 2.0 9 -1
This input section is terminated by a blank line.
ZMConnectivity
Read connectivity using the atom numbering specified in the Z-matrix (including dummy atoms). Bond orders involving dummy atoms are discarded.
IHarmonic=n
Add harmonic constraints to the initial structure with force constantn/1000000 Hartree/Bohr2.InitialHarmonicis a synonym for this option.
ChkHarmonic=n
Add harmonic constraints to the initial structure saved on the checkpoint file with force constantn/1000000 Hartree/Bohr2.CHarmonicis a synonym for this option.
ReadHarmonic=n
Add harmonic constraints to an additional structure read in the input stream (in the input orientation), with force constantn/1000000 Hartree/Bohr2.RHarmonicis a synonym for this option.
ReadOptimize
Read an input section modifying which atoms are to be optimized. The atom list is specified in a separate input section (terminated by a blank line). By default, the atom list contains all atoms in the molecule, unless any atoms are designated as frozen within the molecule specification, in which case the initial atom list excludes them. If the structure is being read in from the checkpoint file, then the list of atoms to be optimized matches that in the checkpoint file.ReadOptandRdOptare synonyms for this option.ReadFreezeis a deprecated synonym.
The input section uses the following format:
atoms=list[notatoms=list]
where eachlistis a comma or space-separated list of atom numbers, atom number ranges and/or atom types. Keywords are applied in succession. Here are some examples:
atoms=3-6,17 notatoms=5Adds atoms 3, 4, 6 and 17 to the atom list.atoms=3 C 18-30 notatoms=HAdds all C & non-H among atoms 3, 18-30.atoms=C N notatoms=5Adds all C and N atoms except atom 5.atoms=1-5 notatoms=H atoms=8-10Adds non-hydrogens among atoms 1-5,and atoms 8-10 regardless of element type.
Bare integers without a keyword are interpreted as atom numbers:
1,3,5 7Adds atoms 1, 3, 5 and 7.
For ONIOM optimizations only,blockandnotblockcan be similarly used to include/exclude rigid blocks defined in ONIOM molecule specifications. If there are contradictions between atoms specified as atoms and within blocks—e.g., an atom is included within a block but excluded by atom type—Gaussian 09 generates an error.
You can start from an empty atom list by placingnoatomsas the first item in the input section. For example, the following input optimizes all non-hydrogen atoms within atoms 1-100 and freezes all other atoms in the molecule:
noatoms atoms=1-100 notatoms=H
Atoms can also be specified by ONIOM layer via the [not]layerkeywords, which accept these values:realfor the real system,modelfor the model system in a 2-layer ONIOM,middlefor the middle layer in a 3-layer ONIOM, andsmallfor the model layer of a 3-layer ONIOM. Atoms may be similarly included/excluded by residue withresidueandnotresidue, which accept lists of residue names. Both keyword pairs function as shorthand forms for atom lists.
Micro
Set up redundant internal coordinates for ONIOM(MO:MM) microiterations, even if this is not an optimization.
Distance
Requests printing of the atomic distance matrix (which is the default for molecules with fewer than 50 atoms).NoDistancesuppresses this output.
CAngle
Requests printing of interatomic angles using distance cutoffs to determine “bonded atoms”. The default is not to print (NoAngle).Anglerequests printing of the interatomic angles forOpt=Z-matrix(using the Z-matrix to determine which atoms are bonded). Only one ofCAngle,Angle, andNoAnglemay be specified.
CDihedral
Requests printing of dihedral angles using distance cutoffs to determine “connectivity”. The default is not to print (NoDihedral).Dihedralspecifies printing of dihedral angles forOpt=Z-matrix(using connectivity information from the Z-matrix to decide which atoms are bonded). Only one ofCDihedral,Dihedral, andNoDihedralmay be specified.
PrintInputOrient
Include the table giving the Cartesian coordinates in the input orientation.
KeepConstants
KeepConstantsretains andNoKeepConstantsdiscards information about frozen variables. The default is to retain them in symbolic form for the Berny algorithm, and to discard them for older optimization algorithms (which don’t understand them anyway).
NewDefinition
Generate a new set of redundant internal coordinates, replacing any that were in the checkpoint file.
NewRedundant
Rebuilds the redundant internal coordinates from the current Cartesian coordinates. If used withGeom=Modify, the new modifications are appended to any earlierOpt=ModRedundantinput before the coordinate system is updated.
Crowd
Crowdactivates andNoCrowdturns off a check which aborts the job if atoms are closer than 0.5 Å. By default, the check is performed for every read-in geometry. It is not performed by default for later points of geometry optimizations, numerical frequencies, etc., when the geometry has been generated during the job.NoTestskips the test entirely.
Independent
Independentactivates andNoIndependentturns off a check on the linear independence of the variables specified in a Z-matrix. This is done by default only if a full optimization is requested using the Berny algorithm (Opt=Z-matrix).
Print
Turns on additional printing by the model builder facility.
Huge
Changes various defaults for huge (>20K atom) systems. Currently, this setsGeom=NoTestandSymm=None.
Last update: 6 May 2013