Giba is a script to simplify the process of studying an hydrogen bond
with GIMIC(1) by helping setting up the correct parameters for the gimic
calculation (bond distance, width and height of the integration window
and magnetic field orientation)
Usage:
In the command samples, parameters shown between [] are optional.
when two parameters are shown between {}, one of them must be given
*****Determining the distance:
The best distance along the bond to place the integration window must be
located. Giba can run the distance scan along the bond. First, all the
files needed for GIMIC to run must be in the current directory including
XDENS and gimic.inp with educated guessess for the integration window
size, palcement and magnetic field orientation.
$PATH/giba.py -D [-l bond_lenght -s step_lenght]
If the bond lenght defaults to 4 and the step lenght to 0.1 a.u..
giba will run a series of GIMIC calculations along the bond (as defined
in gimic.inp) starting from 0 and taking staps of step_lenght until
bond_lenght. The results will be written in folders inside the current
directory. The names are meant to be read by the giba analysis routines.
after these calculations are complete, the results can be analyzed with:
$PATH/giba.py [-t threshold -c ]
This will plot the negative and positive components of the current for
all the distance scan points. In the positive current plot, it will mark
the points for which the absolute value of both components differ in
more than threshold (default: 0.01 a.u). If -c option is given, giba
will analyze the "Induced current". By default, giba will analyze the
"Induced mod current".
To analyze distance scans is the default behavior of giba, so no option
is required. It can be made explicit with:
$PATH/giba.py -A --group "_d" [-t threshold -c ]
After the analysis, giba will write to the gimic.inp file in the main
directory the distance corresponding to the minimun value found for the
positive currents. Always check the plots to ensure the correctness of
the value written to the file!
****Determining the integration window size.
In order to scan for different plane sizes one must scan first width and
then heights of the plane:
$PATH/giba {-W or -H} [-s slice_size]
This sill run several GIMIC calculations in slices of slice_size
(default 0.1 a.u.) along the plane with to cover a maximun size of
10 a.u. (from -5.0 to 5.0 where 0 is the location of the bond. You can
scan larger or smaller planes with the --llimit and --rlimit options).
The -W option scans for width and the -H option for height.
After the width or height scan is complete, analyze with:
$PATH/giba.py --group "_w" [-t threshold -c ]
for width or:
$PATH/giba.py --group "_h" [-t threshold -c ]
for height.
It is important that width or height is scanned and analyzed before
starting with the other. Giba will produce graphs and write the points
for minimun positive current along the bond for with or height.
Again: looks at the graphs!
Finally, It might be desirable to scan the orientation of the magnetic
field. This is done with:
$PATH/giba -F [-s step] atom1 atom2 atom3
atom1-atom3 are atom indices. atom1 and atom2 must correspond to the
bond. atom1, atom2 and atom3 define the plane with respect to which the
field si normal when the angle is pi/2 radians. Giba will run GIMIC
calculations with B pointing to different angles between 0 (normal to
the bond, in the atom1, atom2, atom3 plane) and pi/2 (normal to the
atom1, atom2, atom3 plane) with a step of step radians.
To analyze the results form this scan run:
$PATH/giba.py --group "_a" [-t threshold -c ]
This will set the angle with less positive current and produce
graphs to analyze the results.
NOTE1: When performing distance, plane size or field analyses,
it is possible to plot the currents in nA/T instead of atomic units
by giving the --nA option. If the --total option is given, the total
currents are plotted in addition to the negative and positive
components.
Finally, giba can be used to set the magnetic field orientation to an
arbitrary angle between 0 and pi/2 as defined before.
$PATH/giba.py -o [-a angle] atom1 atom2 atom3
wheere angle is the desired angle (default 0)
NOTE2: There seem to be a disagreement between the GIMIC and the GIBA
definition of field angle. In consequence, the use of the field scan
and field orientation features is discouraged until the problem is
fixed.