So I've been banging my head against this for a few hours () and I can't see whats wrong with it, each part seems to work fine on its own when entered at command line, but then it falls down when pulled together.
I'm writing a script to translate fractional atomic coordinates to cartesian coordinates, itself a simple mathematical thing, but the input format is giving me trouble. The code should read in a .xyz file, which has 2 comment lines and then so many lines of atom x y z like so
48
Optimisation video
H 1.0000 1.0000 1.0000
C 1.2000 1.3000 1.3333
.
.
.
48
Optimisation Video
H 1.2000 1.2000 1.2000
C 2.0000 2.0000 2.0000
.
.
.
before being repeated (two comment lines etc) in a number of frames ($NoFrames), building up an animation of how the atoms move.
Ultimately I need to pull out each atom line and disregard the comment lines. I thought what I'd written (below) should do that but for some reason my sed -n statement always pulls out the comment lines as well
Code:
# $NoFrames and $NoAtoms are defined earlier in the code and do not change
#
# Start of the systematic loop, outer deals with frames, inner with atoms
#
FrameNumber=0 # Used to know which line the sed statement should strip out
FrameCounter=1 # Keeps a track of which frame we're analysing
AtomCounter=1 # Keeps a track of which atom (within each frame) we're analysing
while [[ $FrameCounter -le $NoFrames ]]; do
while [[ $AtomCounter -le $NoAtoms ]]; do
let "AdjustedAtomCounter=(($FrameNumber*($NoAtoms+2))+($AtomCounter+2))" # This line should allow me to skip the first two lines per frame (the comment lines)
sed -n "${AdjustedAtomCounter}p" *.xyz
let "AtomCounter=$AtomCounter+1"
done
echo $NoAtoms >> Cartesian.xyz
echo "Cartesian GeomOpt Video" >> Cartesian.xyz
let FrameCounter=FrameCounter+1
let FrameNumber=FrameNumber+1
let AtomCounter=1
done
rm *.txt
exit
I've stripped all the code back to this, If i can get this part to work i can send the values off to be processed and then written into the output (Cartesian.xyz) file. Any help with this would be greatly appreciated and I hope I've made the problem as clear as I can, but please do tell me if I need to elaborate on something.
I want to combine 2 conditional statements by using -o in bash, but it won't work.
if ; then
echo "The number needs to be between 0 and $nr"
fi
Each time i execute the file it says:
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"--"|"--""-")
"--""-"")
while
do
echo "Current Argument is ${1}"
case "$1" in
"--"|"--""-")
echo "Argument is ${1}"
shift # Skip ahead one to the next argument.
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I have the below BASH code which does not works for upper case alphabets except Z (upper case Z).
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case $var in
)
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echo "iarg_rd = $iarg_rd"
iarg_rd="2"
if ; then
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fi
if ; then
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frmt="${gap}${!frmt_titl_bk}"
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i need a equivalent for the statement i run in bash, so it would also run in other shells. Specially i need it for ksh to run on AIX.
Here the statements:
exec > >(tee -a $log)
exec 2> >(tee -a $log >&2)
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Discussion started by: dev123
0 Replies
LEARN ABOUT MOJAVE
geom
geom(1)geom(1)NAME
geom - analyzes a molecular geometry input in Cartesian coordinates.
DESCRIPTION
The program geom reads a set of Cartesian coordinates and determines from them the bond distances (Bohr and angstrom), bond angles, tor-
sional angles, out-of-plane angles (optional), moments of inertia, and rotational constants.
FILES REQUIRED
input.dat - Input file
and one of the following:
geom.dat - geometry file
file11.dat - PSI-format geometry/gradient file
FILES GENERATED
geom.out - file containing the analysis
INPUT OPTIONS
The geom program has the following options:
-h Print help information (these options).
-aces [filename]
Read the input in an ACES output format, with each line consisting of atomic symbol, atomic number, and Cartesian coordinates (in
Bohr). The optional argument is the name of the geometry input file, which defaults to geom.dat.
-qchem [filename]
Read the input in an QCHEM output format, with each line consisting of the atom number, the atomic symbol, and Cartesian coordinates
(in Angstroms). The optional argument is the name of the geometry input file, which defaults to geom.dat.
-xyz [filename]
Read the input in an XYZ output format. The first line contains the number of atoms and the second line is a comment line. Subse-
quent lines each contain the atomic symbol and Cartesian X Y and Z coordinates (in Angstroms). The optional argument is the name of
the geometry input file, which defaults to geom.dat.
-oop Print out-of-plane angles, where the angle a-b-c-d is defined as the angle formed by the vector a-d and the plane defined by atoms
b, c, and d.
DO_OOP = boolean
Same as command-line switch -oop described above.
ISOTOPES = matrix of reals/strings
Used to specify masses to be used in the calculation of the center of mass and rotational constants. One array is provided for each
isotopomer to be calculated. The arrays can mix floating point numbers with strings which designate isotopes. If this array is not
given and file11.dat is present, then the masses will be obtained by converting the atomic numbers in file11. If masses are not
given by ISOTOPES or by file11, then no mass-related quantities will be calculated.
-g [filename]
Read Cartesian coordinates from a file other than file11.dat. If a filename is not given, the default is geom.dat. The alternative
file is assumed to be in a format similar to that of PSI's geom.dat. Since such files do not contain atomic numbers, the moments of
inertia and rotational constants are not calculated if this option is used.
READ_GEOM = boolean
This option in input.dat tells geom to read the geometry from geom.dat in the PSI geom.dat format.
-a Print parameters for all pair distances.
PRINT_ALL_DIST = boolean
Same as -a flag described above.
-d distance
Only print parameters involving pairs of atoms which are less than distance bohr apart (default value is 4.0 bohr).
PRINT_DISTANCE = value
Same as -d flag described above.
-angstrom
The input coordinates are in angstroms, not bohr.
ANGSTROM = boolean
If TRUE, the input coordinates are in angstroms instead of bohr. The default is FALSE.
The following example is for calculating the geometrical information for water with several different isotopes. The geometry is
read from geom.dat rather than from file11.dat.
geom: (
read_geom = true
isotopes = (
(O H H)
(O D D)
(O18 1.007825 1.007825)
) )
5 June, 1998 geom(1)
02-18-2012
) and I can't see whats wrong with it, each part seems to work fine on its own when entered at command line, but then it falls down when pulled together.