Keyword ALIGNMENT

This keyword allows the control of the alignment procedure used either for the SADDLE interpolation method, or for pattern-geometry alignment (see 4.1.8). If no saddle interpolation (see 4.6.2) or similarity analysis (see 4.7.3) is requested, this keyword performs the alignment between the geometry and the pattern coordinates specified in the input.
Options:

	ENANTIOMER		Include enantiomers for the pattern-geometry alignment.
	EXCLUDE		Exclude the labels specified in the next line.
	OFF		Disable the alignment procedure (enabled by default).
	CONNECT		Try to preserve connectivity during the alignment procedure (always enabled for SADDLE interpolation).
	UNIFORM		Use non-weighted coordinates instead of mass-weighted coordinates.
	CUBE=$<$Integer$>$		Maximum grid density. The default is 6.
	TOL=$<$Integer$>$		Convergence threshold. The default is 50.

Description:
The automatic alignment of REACTANT and PRODUCT is enabled by default when performing a SADDLE interpolation for a transition state search. In this case molecular connectivity is preserved and it cannot be disabled unless the automatic alignment is disabled. Disabling of the automatic alignment means that the user has to define the input coordinates of the reactant and product in exactly the same order. The pattern-geometry alignment in an MD comparison analysis is enabled by default, molecular connectivity is not preserved by default but it can be enabled with the keyword option CONNECT. Inclusion of enantiomers of patterns can be enabled with the keyword option ENANTIOMER.

In all cases you can disable the automatic alignment of specific atoms using the EXCLUDE option or completely turn off the alignment procedure with the OFF option. The TOL option specifies the convergence threshold [78], a higher value is better to find the optimum alignment but it requires a denser grid and will take more time to complete. The CUBE option specifies the maximum grid density, each level makes the grid 8 times denser. A higher value is needed only when the superposition procedure does not converge. In such cases a warning message will be printed to the output file. The following is an example input for the ALIGNMENT keyword. Note the definition of two structures.

 Alignment ENANTIOMER
 #
 # Definition of reference structure
 #
 GEOMETRY
 C      0.00000      0.00000      0.00000
 H     -1.94688     -0.00000      0.89636
 C     -0.69473      1.05820      2.81736
 H      0.66851      0.48204     -0.72556
 O     -0.86210      1.65475      1.61542
 H     -1.63798      1.38692     -0.25767
 C     -1.19879      0.71251      0.49953
 H     -0.47414      1.84223      3.57858
 H      0.31112     -0.94053      0.47087
 O     -0.77370     -0.14111      3.05464
 PATTERN
 O      0.129600    1.190498   -0.168647
 C      1.134846    0.276024    0.115270
 O      0.649460   -1.029686    0.045734
 H     -1.273979   -1.662177    0.548734
 H     -1.031468   -1.191061   -1.188865
 H     -1.283657    0.657175    1.285269
 C     -0.787840   -0.942833   -0.135600
 C     -1.096353    0.518732    0.200367
 H     -1.916909    0.952610   -0.396583
 H      2.069202    0.455344   -0.442920