Hi all
I'm trying to design a calculator for use with ASE (Atomic Simulation
Environment: https://wiki.fysik.dtu.dk/ase/) which uses openbabel to get
energies using UFF and ghemical (for now). For this, I have a couple of
questions.
Is it possible to automatically add bonds. In our code, we do not
represent bonds as we usually just perform DFT calculations. I know
that avogadro/openbabel adds bonds automatically when reading an .xyz
file with openbable, so this should be possible.
When I set up the force field, I can get the energy with FF.Energy(). Is
it possible to get the gradient with respect to nuclear/atomic
coordinates. Something like this must be available for use in
openbabels internal structure optimizers.
And lastly: When doing an optimization, how do I get the new
coordinates? My calculation is like:
"""
import openbabel as ob
FF = ob.OBForceField.FindForceField("UFF")
mol = ob.OBMol()
a = mol.NewAtom()
a.SetAtomicNum(1)
a.SetVector(0,0,0)
b = mol.NewAtom()
b.SetAtomicNum(1)
b.SetVector(0,0,1)
mol.AddBond(1, 2, 1) # atoms indexed from 1
FF.Setup(mol)
print FF.Energy(), FF.GetUnit()
FF.ConjugateGradients(1000)
print FF.Energy(), FF.GetUnit()
print FF.GetCoordinates(mol)
"""
The last line just returns "True"
Thanks for your time reading this.
Best regards
Troels Kofoed Jacobsen
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
OpenBabel-discuss mailing list
OpenBabel-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
