[ase-users] VASP+Hookean constraint

[Tristan Maxson]

Optionally, can we turn off this feature of shuffling?  Sometimes I would
like to preserve my atoms ordering.

Tristan Maxson

On Jan 24, 2017 9:46 AM, "Eric Hermes" <ehermes at chem.wisc.edu> wrote:

> On Mon, 2017-01-23 at 19:34 -0500, Tristan Maxson via ase-users wrote:
> > A second solution would be to attempt to use the interactive vasp
> > calculator.  I don't recall how far Eric Hermes got with this, but I
> > had my original version halfway working for this exact purpose.
> > Maybe he can clarify where this project is at currently and what work
> > still needs to be done.
> >
> > Last I recall though, this calculator was very rudimentary and
> > required you to set up the calculation except for the POSCAR by
> > hand.  While this is a pain to some degree,  the benefit of running
> > VASP interactively should be quite large as it does not have to
> > restart and can use the old wavefunctions etc.
>
> The VaspInteractive calculator is "complete" in the sense that it
> *should* work exactly like the original Vasp calculator, except that
> VASP keywords affecting dynamics are incompatible. I would appreciate
> it if people could try out the VaspInteractive calculator to see if it
> is useful in their workflow.
>
> That said, the VaspInteractive calculator will not fix this issue. This
> is an issue with the Hookean class. VaspInteractive shuffles atom
> indices in exactly the same way as the Vasp calculator -- in fact, it
> uses the exact same code to do so.
>
> Ultimately, I think we need some unit tests on index_shuffle. We
> consistently have issues with constraints breaking when used in VASP
> because of broken or missing index_shuffle methods.  I'll try to take a
> look at Andrew's MR some time today.
>
> Eric
>
> >
> > Thank you,
> > Tristan Maxson
> >
> > On Mon, Jan 23, 2017 at 5:42 PM, Peterson, Andrew via ase-users <ase-
> > users at listserv.fysik.dtu.dk> wrote:
> > > Looks like index_shuffle was not implemented correctly for the
> > > Hookean constraint. I think I just fixed it in MR !405. However, I
> > > don't have Vasp, so can't check your example. (Note this occurs
> > > because Vasp internally re-arranges the atom order.) I added a test
> > > to make sure indices were shuffling as I expect them too, but it
> > > would be nice if you are able to try the branch in the merge
> > > request to make sure it works for you...
> > >
> > > https://gitlab.com/ase/ase/merge_requests/405
> > > https://gitlab.com/andrew_peterson/ase/commits/hookean-shuffle
> > >
> > > On Mon, Jan 23, 2017 at 3:31 PM, Glen Jenness via ase-users <ase-us
> > > ers at listserv.fysik.dtu.dk> wrote:
> > > > Dear ASE Users,
> > > > I am attempting to use the Hookean constraint with VASP (with the
> > > > eventual goal of doing some minima hopping).
> > > >
> > > > However, I keep running into the following error:
> > > >
> > > > Traceback (most recent call last):
> > > >   File "mwe.py", line 27, in <module>
> > > >     opt.run(fmax=0.05)
> > > >   File "/home/1482/programs/ase/ase/optimize/optimize.py", line
> > > > 161, in run
> > > >     self.set_force_consistent()
> > > >   File "/home/1482/programs/ase/ase/optimize/optimize.py", line
> > > > 214, in set_force_consistent
> > > >     self.atoms.get_potential_energy(force_consistent=True)
> > > >   File "/home/1482/programs/ase/ase/atoms.py", line 680, in
> > > > get_potential_energy
> > > >     self, force_consistent=force_consistent)
> > > >   File "/home/1482/programs/ase/ase/calculators/vasp.py", line
> > > > 834, in get_potential_energy
> > > >     self.update(atoms)
> > > >   File "/home/1482/programs/ase/ase/calculators/vasp.py", line
> > > > 492, in update
> > > >     self.calculate(atoms)
> > > >   File "/home/1482/programs/ase/ase/calculators/vasp.py", line
> > > > 684, in calculate
> > > >     self.initialize(atoms)
> > > >   File "/home/1482/programs/ase/ase/calculators/vasp.py", line
> > > > 592, in initialize
> > > >     self.atoms_sorted = atoms[self.sort]
> > > >   File "/home/1482/programs/ase/ase/atoms.py", line 949, in
> > > > __getitem__
> > > >     con.index_shuffle(self, i)
> > > >   File "/home/1482/programs/ase/ase/constraints.py", line 946, in
> > > > index_shuffle
> > > >     self.indices = [ind.index(self.indices[0]),
> > > > AttributeError: 'numpy.ndarray' object has no attribute 'index'
> > > >
> > > > Can anyone provide any insight into this?
> > > >
> > > > Attached is a MWE that demonstrates the problem.
> > > >
> > > >
> > > > Thanks!
> > > > Dr. Glen Jenness
> > > > Catalysis Center for Energy Innovation (CCEI)
> > > > University of Delaware
> > > >
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> > > >
> > >
> > >
> > >
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