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The
Yup.fpf
program (sometimes referred to as simply fpf) is
used to compile a source file containing force
field constants into a number of unformatted files,
one for each term of the force field. The program
must be run in a directory containing the source
file which must be named
"source-of-constants".
It is a good idea to have no other file in this
directory. Type the program name by itself, i.e.,
Yup.fpf,
and if there are no errors in the source file a
number of smaller files is created.
The
output files are unformatted and so they cannot be
viewed. Each section of the source file is
converted into an independent file. Exclusion and
Inclusion Atom Types are combined into one list,
sorted alphabetically, each type is assigned a
numerical code and the names are written to one
file. The force constants are converted from the
external units of measurements into internal units.
Names of atom type groups (bond pairs, angle
triplets, torsion quads, etc) are converted to
numerical codes and sorted. The constants are also
checked and unphysical values are
flagged.
This
command has one variation. Typing
Yup.fpf
-check
will run a check of the source file and the data
read from the source file is printed on the
standard output. The listing will look a bit
different from the source because of data
conversion, hashing and sorting. No output file is
created with this option.
The
format of the force constants source file is
documented here
[in a separate window]. The format of the
source file is also documented in the standard
library 'TestTube'. The location of this library
can be found by typing the following Python
commands:
>>> from Yup.Tools.misc import datasource
>>> print datasource( 'TestTube' )
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Go
to the directory which should be in a path (listed
by the above command) that ends in
Yup/Data/TestTube.
In this directory, view the file
source-of-constants.
Note that the other files in the directory are not
readable.
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