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#Installation instructions#
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This package should include the following files:
atom.cc error.cc fxn.cc g03_out.h ic_out.cc molecule.cc
atom.h error.h fxn.h molecule.h test.cc ic_mod.cc
ic_ptb.cc test_class.h constants.h fvector.cc g03_out.cc Makefile
README
The following packages are neccessary for full functionality of this
program. Please ask your sysadmin to install them.
Necessary for even basic functionaly:
boost
Needed for molecular additions
lapack boost lapack bindings
These should be available from your unix distribution, excepting the
lapack bindings. These should have been packaged with this program.
They are also available at
http://news.tiker.net/software/boost-bindings, and should be installed
in the directory /usr/include/boost/numeric/bindings.
Next, modify the Makefile. "INSTALLDIR" should be a directory in your
path to allow you to use the program. "LDFLAGS" should point to the
location of the lapack library.
user@chem_computer> make install
should complete the installation.
The remainder of this README contains usage instructions. You can
also simply type:
user@chem_computer> ic_out
to get a detailed help message.
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#Standard help message#
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Help Information:
***** OVERVIEW *****
ic_out is intended to translate the output of Gaussian vibrational calculations into internal coordinates. The Gaussian output file must contain both a geometry optimization and frequency calculation. If it contains multiple frequency or geometry calculations, ic_out will only read the first of each.
By default, ic_out will translate the normal modes into a complete basis of internal coordinates (stretches, bends, and dihedrals). To choose the basis, you have three options: provide one, using the gaussian input z-matrix format, have ic_out choose the one used in the geometry calculation, or have ic_out derive a new one. By default, ic_out will find a basis by searching in that order. If you specify an unavailable option, ic_out will give you the option of quiting or using another option. It is imperative that the inputted z-matrix contains the atoms in the same order as the Gaussian output file - otherwise your results will be meaningless.
Note that each mode is output scaled to 1q (unitless). This means that the actual mass of each atom is crucial. ic_out will assume that each atom is its most common isotope; if you have used a different isotope for your Gaussian frequency calculation, you must notify ic_out.
By default, three files are written by this program, using a supplied output 'prefix'. 'prefix'.xyz holds a standard xyz format description of the molecule, 'prefix'.zmat holds a z-matrix description of the same. Note that this zmatrix file will also let you identify which internal coordinates coorespond to which movements. 'prefix'.modes holds the vibrational modes translated into internal coordinates. The first line of this file describes which ic each number cooresponds to. Each succeeding line describes one vibrational mode, in order of ascending frequency (the first line).
There is also an alternate functionality which is used to perturb a molecule along its vibrational modes, to an extent governed by the (experimentally determined dimensionless delta values of each mode.
***** OPERATION *****
syntax, including optional command line switches:
prompt> ic_out [-v...] inputfilename outputfilename [template]
files:
inputfilename : the name of the Gaussian output file
outputfilename : prefix for the ic_out output files
template : an optional filename. If included, ic_out
will use this file as an ic basis
switches:
Each switch should be preceded by the indicator '-'. Single letter
switches may concatenated thusly: -vta (in any order). The
switches should be before the files.
-v : produces verbose output while the program is running
-t : terse output: no .xyz or .zmat file written
-h : prints this help message and quits
-i=x,y : atom x is mass y. used for isotope calculations
-a : completely different! modifies atom position!
The following options are not yet fully implemented.
-s : saves/loads a binary file called outname.bin
-c=n : uses the nth frequency calculation for ic_out transformations.
-A : breaks modes into all ics - this is a redundant basis
-big : prints the names of the largest 10 ics, in
order. to determine ic order, dihedrals and angles have been
arbitrarily divided by 180. to change this, use '-big=new' where
'new' is the scaling factor to be used. this calculation does not
provide a complete basis. this option is typically coupled with
the -A option.
***** Examples *****
ic_out -b=1.6 H2O2.out H2O2 H2O2.com
will use the G03 input file to convert the frequency
calculation H202.out into internal coordinates. All bonds are
assumed to be 1.6 angstroms, and the output is written to
files called H202.xyz, H2O2.zmat, and H2O2.modes.
ic_out -At -big chomophore.out chromo
prints only the largest internal coordinates which contribute
to each mode in a file called chromo.modes. Does not write
any other files.
maintainer: Dan Wandschneider
dwandschneider@gmail.com
##########################################
#Description of mode addition file format#
##########################################
This format is laid out at the start of the ic_add subroutine in the
ic_out.cc file of this program. Feel free to modify this file, as
long as you send any modifications to me, as well.
Please adhere to the standards laid out here closely. No extra text
or comments are allowed. There is only a moderate amount of error-checking
of the format of these files, and so most syntax errors will simply
result in an 'abort, input file syntax error' type of error.
White space can be filled by any number of spaces, tabs or newlines
(carriage returns). I have divided them up into 'lines,' as that is
the format that makes sense to me personally.
The first line of the file describes the parameters of the calculation
that you wish to perform:
file.zmat file.modes output.xyz 500 25
file.zmat is a standard G03-type input file describing the initial
(ground-state) position of the molecule.
file.modes is the output of the standard ic_out program, describing
the vibrational modes of the same molecule in internal coordinates
output.xyz does not exist yet, and will contain the output
500 is the number of femtoseconds that the molecule will propogate
along hte requested trajectory.
25 is the time-step (femtoseconds)
Each additional line in the mode addition file should be as follows.
mode# frequency harmonic, dissociative, or impulse? delta
5 2024.15 h .73
The modes are counted starting from 0, and should match those
described in the *.modes file built by ic_out. The frequency is
assumed to be in wavenumbers. Harmonic modes are those that lie in a
harmonic potential well, and will return to the starting position.
Dissociative modes are those that will not return to the starting
point. Impulsively driven modes are those do not return to the start
position, but also feel no potential after the first infinitesimal
unit of time. Although this can be determined by damping time & other
factors, essentially, if the mode is on the reaction path, it is
dissociative, and if not, it is harmonic. Harmonic modes are
identified by the letter 'h,' dissociative by 'd,' and impulsive by
an 'i.' The delta should be experimentally determined.
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#Plausible modifications#
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For increased accuracy, and to specialize the program to fit your own needs:
See constansts.h for a couple of physical constants used.
The file atom.h contains a list of atom identities and masses.
g03.cc defines the expected input file format for gaussian03 .out
files
molecule.cc defines the read/write format of molecules.
The file ic_out.cc defines input format of mode addition files. It
also controls
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