It often happens that one wants to measure some geometric property (distance, angle or torsion) after running a simulation or geometry optimization. If this is known in advance of the simulation, it can be done by including the appropriate
distance,
angle or
torsion command in the input file. If this was not done, the quantity can be extracted from the output file using the
qbox_distance.py,
qbox_angle.py or
qbox_torsion.py scripts, for example
Code: Select all
$ qbox_distance.py N1 C3_222 file.r
5.0903
5.0908
5.0908
5.0908
5.0910
5.0911
5.0917
5.0926
5.0928
5.0932
Note that the scripts can also be used on a restart file, or a stripped version of a restart file created using the
get_atomset.sh script
Code: Select all
$ get_atomset.sh file.xml > file_atomset.xml
$ qbox_distance.py N1 C3_222 file_atomset.xml
5.0942
Note that the value saved in the restart file is not exactly the same as the last value found in the output file, which is computed from atomic positions before the last step was done.