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.
ModRedundant
Modify the current geometry (regardless of its coordinate system) using redundant internal coordinate modifications before performing the calculation. This option may be used to modify a geometry specified in the input file using these features even when some calculation type other than an optimization is to be performed. It may also be combined with Step, Check or AllCheck to retrieve and modify a geometry from a checkpoint file.
When used with Check or Step, two input sections will be read: the first contains the charge and multiplicity, and the second contains alterations to the retrieved geometry. When combined with the AllCheck option, only the geometry modifications input is needed.
Modification specifications for redundant coordinates have the same format as the input for the ModRedundant option of the Opt keyword (we summarize these formats only briefly here; see the discussion of the Opt keyword for a full description):
[type] N1 [N2 [N3 [N4]]] [[+=]value] [action [params]] [[min] max]]where N1, N2, N3 and N4 are atom numbers or wildcards. Numbering begins at 1 and any dummy atoms are not counted. Value gives a new value for the specified coordinate, and +=value increments the coordinate by value. Finally, action is an optional one-character code letter indicating the coordinate modification to be performed, sometimes followed by additional required parameters (the default action when the code letter is omitted is to add the specified coordinate):
| B | Add the coordinate and build all related coordinates. | |
| K | Remove the coordinate and kill all related coordinates containing this coordinate. | |
| A | Activate the coordinate for optimization if it has been frozen. | |
| F | Freeze the coordinate in the optimization. | |
| R | Remove the coordinate from the definition list (but not the related coordinates). | |
| S n stp | Perform a relaxed potential energy surface scan. Set the initial value to Value (or its current value), and increment the coordinate by stp a total of n times, performing an optimization from each resulting starting geometry. | |
| H dv | Change the diagonal element for this coordinate in the initial Hessian to dv. | |
| D | Calculate numerical second derivatives for the row and column of the initial Hessian for this coordinate. |
| X | Cartesian coordinates. In this case, Value, Min and Max are each triples of numbers, specifying the X,Y,Z coordinates. | |
| B | Bond length | |
| A | Valence angle | |
| D | Dihedral angle | |
| L | Linear bend specified by three or four atoms, where the optional fourth atom is used to determine the 2 orthogonal directions of the linear bend (N4 can be -1). In this case, Value, Min and Max are each pairs of numbers, specifying the two orthogonal bending components. | |
| O | Out-of-plane bending coordinate for a center (N1) and three connected atoms. |
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.
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 2.0This 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 -1This 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/1000 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/1000 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/1000 Hartree/Bohr2. RHarmonic is a synonym for this option.
ReadFreeze
Read an input section modifying which atoms are to be optimized or frozen. The atom list is specified in a separate input section (terminated by a blank line). The initial atom list contains those atoms which are frozen (i.e., would not be optimized) based on the settings within the molecule specification or structure read-in from the checkpoint file.
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, and the atom list is initially empty. 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/not include 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.
noatoms atoms=1-100 notatoms=HAtoms 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.
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.
Guess=Read, Opt=ModRedundant
Last updated on: 9 Jun 2009