Geom Keyword
Last Update:
6/26/2001
DESCRIPTION
The Geom keyword specifies the source of the molecule specification input. 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 option.
ITEM SELECTION OPTIONS
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 98 will abort the job if an optimization fails, and
consequently subsequent job steps which expect to use the optimized geometry
will not be executed. May be combined with the ModRedundant option 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 ModRed.
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 [Opt]):
[Type] N1 [N2 [N3 [N4]]] [[+=]Value] [Action [Params]] [[Min] Max]]
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.
Action is an optional one-character code letter indicating the coordinate modification to be performed, sometimes followed by additional required parameters (the default action 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.
An asterisk (*) in the place of an atom number indicates a wildcard. Min and Max define a range (or maximum value if Min is not given) for coordinate specifications containing wildcards. The Action is taken only if the value of the coordinate is in the range.
Type can be used to designate a specific coordinate type (by default, the coordinate type is determined automatically from the number of atoms specified):
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 atoms (or 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, 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. Note that in
Gaussian 98, Modi is the shortest valid abbreviation for this
keyword.
Modification specifications for optimizations using redundant coordinates have the same format as the input for the ModRedundant option discussed previously.
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.
Connect
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 N¹s are atoms to which the current atom is bonded, and the Order¹s 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: 4 1.0 5 2.0
ModConnect
Modify the default connectivity of the atoms
in the molecule specification. 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 -1.0
OUTPUT-RELATED OPTIONS
Distance
Requests printing of the atomic distance
matrix (which is the default). NoDistance suppresses this output.
Angle
Requests printing of the interatomic angles,
using the Z-matrix to determine which atoms are bonded. The default is to print
unless some atoms are specified by Cartesian coordinates or an optimization in
redundant internal coordinates is being performed. NoAngle suppresses
this output.
CAngle
Requests printing of interatomic angles using
distance cutoffs to determine bonded atoms. The default is not to print unless
at least one atom is specified using Cartesian coordinates. Only one of
Angle, CAngle, and NoAngle may be specified.
Dihedral
Specifies printing of dihedral angles using
connectivity information from the Z-matrix to decide which atoms are bonded
(the default is not to print). NoDihedral suppresses this output.
CDihedral
Requests printing of dihedral angles using
distance cutoffs to determine connectivity. Only one of Dihedral,
CDihedral, and NoDihedral may be specified
GEOMETRY SPECIFICATION AND CHECKING OPTIONS
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).
KeepDefinition
Retains the definition of the redundant
internal coordinates (the default). Its opposite is NewDefinition.
NewDefinition
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
Activates and NoCrowd turns off a check
which aborts the job if atoms are closer than 0.5 Å. By default, the
check is done at the initial point, but not at later points of an optimization.
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).
MODEL BUILDER OPTIONS
ModelA
These options specify that model builder [240] connectivity information will be read
ModelB
and used to construct a symbolic Z-matrix. This
option is implemented only for H through Ne, and in some cases will not
generate a symbolic Z-matrix with the correct symmetry-constrained number of
variables. If geometry optimization has been requested and this problem occurs,
the job will be aborted. The input for the model builder is described in
Appendix B.
Print Turns on additional printing by the model builder facility.
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