The Geom keyword 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. Geom may 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. The Geom keyword 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=Checkpoint may 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. Checkpoint may be combined with the ModRedundant option 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 with Modify but may be combined with ModRedundant.
Step=N
Retrieves the structure produced by the Nth step of a failed or partial geometry optimization (it is not valid for a successful optimization). Step=Original recovers the initial starting geometry. This option is used for restarting geometry optimization from intermediate points. It must be combined with one of Checkpoint, AllCheck or Modify. Note that not all steps are always present in the checkpoint file; a Hessian updated message in the log file means that the corresponding step is available in the checkpoint file. NGeom=N retrieves the Nth geometry from an optimization checkpoint file using the same record of points used for display in GaussView, where N=1 corresponds to the input molecule specification. Geom=Step=M is automatically converted to Geom=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 with QST2 or QST3, a ModRedundant input section must follow each geometry specification. AddRedundant is synonymous with ModRedundant. This option may be used for job types other than optimizations. It may also be combined with NGeom, Check or AllCheck to retrieve and modify an internal coordinate definition from a checkpoint file.
When used with Check or NGeom, 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 the AllCheck option, only the internal coordinate definition modifications input is needed.
Lines in a ModRedundant input 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]]] H diag-elem [[min] max]] [Type] N1 [N2 [N3 [N4]]] S nsteps stepsize [[min] max]]
N1, N2, N3 and N4 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 to diag-elem. | |
| S | Perform a relaxed potential energy surface scan. Increment the coordinate by stepsize a total of nsteps times, performing an optimization from each resulting starting geometry. |
An asterisk (*) in the place of an atom number indicates a wildcard. Min and max only 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 the min–max range (or below maximum value if min is 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, type can 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 (if N4 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, min and max are each pairs of numbers, specifying the two orthogonal bending components. |
See the examples under the Opt keyword for illustrations of the use of ModRedundant.
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]
where variable is the name of a variable in the molecule specification, new-value is 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 letter D requests 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 the Geom=ModRedundant input 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:
N1 Order1 [N2 Order2 …]
where the N’s are atoms to which the current atom is bonded, and the Order’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 of 1.0 and 2.0 respectively:
8 4 1.0 5 2.0
A bond order of 0.1 indicates 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:
M N1 Order1 [N2 Order2 …]
where M is the atom number, the N’s are atoms to which that atom is bonded, and the Order’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 constant n/1000000 Hartree/Bohr2. InitialHarmonic is a synonym for this option.
ChkHarmonic=n
Add harmonic constraints to the initial structure saved on the checkpoint file with force constant n/1000000 Hartree/Bohr2. CHarmonic is 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 constant n/1000000 Hartree/Bohr2. RHarmonic is 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. ReadOpt and RdOpt are synonyms for this option. ReadFreeze is a deprecated synonym.
The input section uses the following format:
atoms=list [notatoms=list]
where each list is 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=5 Adds atoms 3, 4, 6 and 17 to the atom list. atoms=3 C 18-30 notatoms=H Adds all C & non-H among atoms 3, 18-30. atoms=C N notatoms=5 Adds all C and N atoms except atom 5. atoms=1-5 notatoms=H atoms=8-10 Adds 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 7 Adds atoms 1, 3, 5 and 7.
For ONIOM optimizations only, block and notblock can 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 placing noatoms as 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]layer keywords, which accept these values: real for the real system, model for the model system in a 2-layer ONIOM, middle for the middle layer in a 3-layer ONIOM, and small for the model layer of a 3-layer ONIOM. Atoms may be similarly included/excluded by residue with residue and notresidue, 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). NoDistance suppresses this output.
CAngle
Requests printing of interatomic angles using distance cutoffs to determine “bonded atoms”. The default is not to print (NoAngle). Angle requests printing of the interatomic angles for Opt=Z-matrix (using the Z-matrix to determine which atoms are bonded). Only one of CAngle, Angle, and NoAngle may be specified.
CDihedral
Requests printing of dihedral angles using distance cutoffs to determine “connectivity”. The default is not to print (NoDihedral). Dihedral specifies printing of dihedral angles for Opt=Z-matrix (using connectivity information from the Z-matrix to decide which atoms are bonded). Only one of CDihedral, Dihedral, and NoDihedral may be specified.
PrintInputOrient
Include the table giving the Cartesian coordinates in the input orientation.
KeepConstants
KeepConstants retains and NoKeepConstants discards 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 with Geom=Modify, the new modifications are appended to any earlier Opt=ModRedundant input before the coordinate system is updated.
Crowd
Crowd activates and NoCrowd turns 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. NoTest skips the test entirely.
Independent
Independent activates and NoIndependent turns 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 sets Geom=NoTest and Symm=None.
Last update: 6 May 2013