afreqgen

afreqgen
	Appendix B. Utilities

Name

afreqgen — Generate vibrational frequency information from an AMPAC .vis file.

Description

Afreqgen reads the .vis file from an FORCE, LFORCE, NEWTON, or LTRD calcuation and outputs vibrational frequency analaysis at the final geometry. The format of the output is identical to a standard FORCE job. This utility uses Hessian information in the .vis file to avoid having to rerun the original job and so can't be used with other job types. Options allow the user to specify masses other than the used ones in the original job, so is particularly useful for isotopic substitution studies. Note, this utility can only be used with vis files generated with AMPAC-9.1.3 or later.

Usage:

afreqgen [-o outfile] [-i isofile] [-m:[string]] [-nproc=#|all|most|half] visfile

options

`-o` `outfile`	Specify Output File (default output to screen) .
`-i isofile`	Read Isotopic Masses from File. (Not compatable with -m.)
`-m:[string]`	Specify Isotopic Masses. (Not compatable with -i.)
`-nproc=n\|all\|most\|half`	Specifies the number of processors to use--equivalent to NPROC.

visfile

AMPAC Visualization file (input).

AFREQGEN_PARAMS shell variable controls

print	Increase print level (1..3).
time	Print the job time in the output.

Isotopic Specification:

By default, afreqgen will use the atomic masses from the original job in computing frequencies. There are two ways to override this behavior and specify the masses to be used in the analysis. This is very important in isotopic substition studies, since it allows one to generate output for many isotopologues from a single AMPAC run.

Using the -m:[string] command line option, sets the mass for each atom specified. All atoms not listed will be assigned the default atomic mass regardless of their mass in the orignal job. So, using just "-m" or "-m:" (i.e. no atoms specified) means that all atoms will have the default mass. The string is just a comma seperated lists of entries of the form n=m (m is an integer) or n=m.mmm (m.mmm is a real number), where n is an atom number. In the case of an integer, the mass is interpreted as a specific isotope. So, 3=14 where atom 3 is a carbon atom means use the mass of carbon-14. If the specified isotope is not recognized, then afreqgen will print a warning and stop. For real numbers, the value is taken as the mass for that atom.

The -i isofile option instructs afreqgen to read isotopic mass information from the specified file. The data may be seperated by commas, semi-colons, forward slashes, or spaces and be spread over as many lines as are needed. All text on a line after an exclamation point is considered to be a comment and will be ignored. The mass data may be specified in one of two formats. The first format is identical to the "-m:[string] option, where information is specified in the form n=m or n=m.mmm. Any atoms not listed are assigned the default atomic mass. When using this format, the first line of the file should begin with "Mass:" (case insensitive) to distinguish it from the second format. If the first line is blank or just contains the word "Mass:" then all of the atoms will be assigned the standard atomic masses.

The second format for use in an isofile is a list of mass-numbers for each non-dummy atom in the molecule. These values may be commas, semi-colons, forward slashes, or spaces and be listed on as many lines as needed. All comments (text after an exclamation point) will be ignored. The mass numbers may either be zero, an integer, or a real number. A zero is interpreted as the default atomic mass. An integer indicates the isotope number. (The job will fail if the isotope number is not a recognized value.) Finally, a real number is interpreted as a user-specified mass value.


acubegen		ampac