Absolute atom positions can be frozen with the FIXED section. The section starts with the FIXED keyword as the first line and ends with the ENDFIXED keyword on the last. The format to fix a coordinate or coordinates of an atom is:
atom coordinate_reference
coordinate_reference can be any combination of up to three characters , and to specify the coordinate(s) to be fixed: , , , XY, XZ, YZ, XYZ. The fixing characters must be next to each other. e.g.,
FIXED 2 XY ENDFIXED
means the -coordinate and -coordinate of atom 2 are fixed, whereas
FIXED 2 X Y ENDFIXED
will yield erroneous results.
Note: When the FIXED section is specified within $opt, the optimization will proceed in Cartesian coordinates.
Note that frequency calculations for a system with frozen atom constraints will generally produce imaginary frequencies. These arise because the Hessian computed for the frequency calculation has different physics compared to the gradient computed during the fixed-atom optimization. One possible workaround is simply to zero out the elements of the Hessian associated with the frozen atoms. This removes the contribution of the frozen atoms to the normal modes and reduces the number of frequencies computed. For a system with atoms, where atoms are frozen, there will be normal modes, or if the system is linear. This “zeroing out” approach can be requested with a pair of $rem variables, FRZN_OPT and FRZ_ATOMS, as described below. A more elegant approach is to replace the strictly fixed atomic positions with soft harmonic confining potentials, which achieves effectively the same result but allows for relaxation (i.e., optimization) of all atomic coordinates, so that a proper vibrational frequency calculation can be performed. The use of harmonic confining potentials as a replacement for fixed atom constraints is described in Section 9.4.7.
FRZN_OPT
FRZN_OPT
Controls whether the job uses zeroed Hessian technique in the frequency calculations
TYPE:
LOGICAL
DEFAULT:
False
OPTIONS:
False
Do not use the zeroed out Hessian
True
Use the zeroed out Hessian
RECOMMENDATION:
False
FRZ_ATOMS
FRZ_ATOMS
Controls the number of frozen atoms
TYPE:
INTEGER
DEFAULT:
No default
OPTIONS:
User defined
RECOMMENDATION:
None
Note: The above two $rem variables are only relevant to frequency calculations; they are not required in geometry optimization with fixed atoms.
Example 9.12 Optimization of the water dimer structure with the structure of the first water frozen
$molecule 0 1 O -1.551007 -0.114520 0.000000 H -1.934259 0.762503 0.000000 H -0.599677 0.040712 0.000000 O 1.350625 0.111469 0.000000 H 1.680398 -0.373741 -0.758561 H 1.680398 -0.373741 0.758561 $end $rem JOBTYPE OPT METHOD B3LYP BASIS 6-31G(D) SCF_CONVERGENCE 8 $end $opt FIXED 1:3 XYZ ENDFIXED $end
Example 9.13 Frequency calculations using zeroed out Hessian technique. Note the frozen atom indices are specified in the $frozen_opt section.
$molecule 0 1 C -0.0014570824 1.4001468208 0.0000000000 H -0.0030029737 2.4867609686 0.0000000000 C -1.2093554750 0.6986986619 0.0000000000 H -2.1525287416 1.2392252926 0.0000000000 C -1.2094237515 -0.6985901650 0.0000000000 H -2.1508487680 -1.2427180000 0.0000000000 C -0.0003285453 -1.3965954363 0.0000000000 H -0.0006460438 -2.4839940415 0.0000000000 C 1.2098250013 -0.6978846084 0.0000000000 H 2.1493830451 -1.2446769146 0.0000000000 C 1.2133329176 0.6987868208 0.0000000000 H 2.1550504173 1.2408406009 0.0000000000 $end $rem JOBTYPE freq METHOD b3lyp BASIS 6-31G* FRZN_OPT 1 ! Turns on the freq calculation with frozen Hessians FRZ_ATOMS 2 ! No. of frozen atoms point_group_symmetry False integral_symmetry false $end $frozen_opt 1 11 $end