05-05-2009
error
Here is the list of errors, --probfile is correct, as I said this command works on its own, just not when in the script.
./assoc.sh: line 24: 31017 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31018 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31019 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31020 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31021 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31022 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31023 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31024 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31025 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31026 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31027 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31028 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31029 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31030 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31031 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31032 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31033 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31034 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31035 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31036 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31037 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31038 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
./assoc.sh: line 24: 31039 Segmentation fault mach2qtl -d PC_full.dat -p PC_full.ped -i $infofile --probfile $probfile >PC_full_$i.txt
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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)