usage: averageSterimol.py [-h] [-if {log,out,dat}] -s TARGETS -a AVOID
[-r {bondi,umn}] [-l] [-t TEMPERATURE] [-f] [-w0 W0]
[-v] [-o output destination]
input files [input files ...]
calculate Boltzmann-weighted Sterimol parameters - see doi 10.1021/acscatal.8b04043
positional arguments:
input files file containing coordinates and energy
optional arguments:
-h, --help show this help message and exit
-if {log,out,dat}, --input-format {log,out,dat}
file format of input
-s TARGETS, --substituent-atom TARGETS
substituent atom
1-indexed position of the starting position of the
substituent of which you are calculating sterimol
parameters
-a AVOID, --attached-to AVOID
non-substituent atom
1-indexed position of the starting position of the atom
connected to the substituent of which you are calculating
sterimol parameters
-r {bondi,umn}, --radii {bondi,umn}
VDW radii to use in calculation
umn: main group vdw radii from J. Phys. Chem. A 2009, 113, 19, 5806–5812
(DOI: 10.1021/jp8111556)
transition metals are crystal radii from Batsanov, S.S. Van der Waals
Radii of Elements. Inorganic Materials 37, 871–885 (2001).
(DOI: 10.1023/A:1011625728803)
bondi: radii from J. Phys. Chem. 1964, 68, 3, 441–451 (DOI: 10.1021/j100785a001)
Default: bondi
-l, --old-l approximate FORTRAN Sterimol method for determining L
This is 0.4 + the ideal bond length for a target-H bond
to outer VDW radii of atoms projected onto L-axis
Default: L value is from VDW radii of target atom to outer
VDW radii of atoms projected onto L-axis
-t TEMPERATURE, --temperature TEMPERATURE
temperature in K
Default: 298.15
-f, --frequency input files are frequency job output files
additional average values will be calculated for ZPE, H, G, etc.
-w0 W0, --frequency-cutoff W0
cutoff frequency for quasi free energy corrections (1/cm)
Default: 100 cm^-1
-v, --verbose also print population
-o output destination, --output output destination
output destination
Default: stdout