On 11 March 2010 11:07, Troels Kofoed Jacobsen <tkjacob...@gmail.com> wrote: > 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.
OBMol.ConnectTheDots() followed by OBMol.PerceiveBondOrders(). See API at http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBMol.shtml > 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. I will leave this to the others. Also I think you have a separate email on this topic. > 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" True means success. This is always good. If you check the coordinates of the atoms, e.g. mol.GetAtom(1).GetVector() you will see new values. > > Thanks for your time reading this. You've made my day. After a quick google, I see that you are a fellow open source developer - who else can understand the effort required? :-) > 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 > ------------------------------------------------------------------------------ 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
