vibrationalAnalysis

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Purpose

The vibrationalAnalysis command is used to perform normal mode analysis on the molecules in the current system, to selectively obtain the mass-weighted normal modes of vibration and the corresponding zero-point vibrational frequencies and their intensities.

Syntax

vibrationalAnalysis ?path? ?keyword = value?...


Path/Keyword      Values    Default	    Meaning


normal_m*odes     Boolean   false    Define whether the calculated normal 
                                     modes (eigenvectors) are to be output.

mode_i*ntensities Boolean   true     Define whether the vibrational 
                                     frequency intensities are to be output.

output                               Path to output control parameters.

print             Boolean   false    Define whether output is to be directed 
                                     to the output stream. If no other output 
                                     mode is defined, this defaults to true.

hes*sian          Boolean   false    Define whether output is to be written to 
                                     a Hessian file.

file*name         string    --       Define the name of the Hessian file for 
                                     output. If no value is given, the default 
                                     is run_name.hessian.

modes             string    --       If supplied, the value is the name of a 
                                     BTCL vector variable to which the normal 
                                     modes are to be output.

freq*uencies      string    --       If supplied, the value is the name of a 
                                     BTCL vector variable to which the 
                                     vibrational frequencies are to be output.

inten*sities      string    --       If supplied, the value is the name of a 
                                     BTCL vector variable to which the 
                                     vibrational frequency intensities are to 
                                     be output.

Description

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The vibrationalAnalysis command is used to find the internal vibrational modes and frequencies of a molecule. The calculation is performed by diagonalizing the Hessian matrix generated from the second derivatives of the internal potential energy of the molecule.

The first six frequencies and modes (five for linear molecules) represent the translation and rotation of the molecule as a whole and should have frequencies of approximately zero. If they do not, then the original molecule was probably not properly minimized with respect to the current system forcefield, and all results will be dubious.

The basic output from the normal mode calculation is the vibrational frequencies and their intensities, although you can select to also output the normal modes or not to output the intensities.

The output can be written to the output stream (usually run_name.out), to a Hessian file, or directly to BTCL variables for subsequent analysis. If the output goes to the output stream, the vibrational free energy and its components are also generated and output.

Example 1

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vibrationalAnalysis

If the vibrationalAnalysis command is configured with its default parameter values (listed in the table above), this causes a normal mode analysis calculation to be performed on the currently selected molecule(s). Vibrational frequencies, their intensities, and free energy results are written to the output stream.

Example 2

vibrationalAnalysis +normal_modes output +print +hessian \
 	 filename = vib

This example causes a vibrational (normal mode) analysis to be performed with frequencies, intensities, and normal modes being written both to the output file and to a Hessian file called vib.hessian.

Example 3

vibrationalAnalysis +normal_modes -mode_int output \
 	 frequencies = freqs modes = modes

This example causes a vibrational analysis to be performed on the current system, with the results being written to BTCL variables named freqs for the vibrational frequencies and modes for the vibrational normal modes. Note that freqs is a vector and modes is a matrix composed of the normal mode vectors.

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