[ase-users] Problem Restarting Constrained Relaxation with Vasp Calculator

Andrew Rosen rosen at u.northwestern.edu
Tue Jan 9 08:55:28 CET 2018 

Hi Eric,

Thank you for the incredibly informative reply (and apologies for
accidentally going off-list!). I was wondering why the SCF iterations were
higher with ASE/Vasp even if I wrote out the WAVECAR every step (obviously
that's significant file I/O). What you said makes sense. If I want to use
different optimizers than those in native VASP, I'll stick with the
VTSTools optimizers.

On Tue, Jan 9, 2018 at 1:45 AM Eric Hermes via ase-users <
ase-users at listserv.fysik.dtu.dk> wrote:

> The issue with the VaspInteractive calculator is that it is using an
> undocumented feature of VASP to update ion coordinates. Using ASE
> optimizers with the Vasp calculator has a different problem, specifically
> that it must start and stop VASP between every ionic step. The number of
> SCF iterations per ionic step will depend on your WAVECAR/CHGCAR settings
> (lwave, lcharg, istart, icharg), but it will generally take more SCF
> iterations than if you use built-in VASP optimizers (or Graeme Henkelman’s
> optimizers, which can be patched into VASP).
>
>
>
> That said, even if you fully write and read the WAVECAR at every step
> (lwave=True, istart=1, icharg=0) with an ASE optimizer, this will still
> take more SCF iterations per ionic step than using optimizers built into
> VASP. This is for two reasons: first, VASP uses the electron density from
> previous ionic iterations in its mixer history if maxmix is positive (the
> default is -45), and second, VASP **extrapolates** the wavefunction and
> charge density from the previous converged ionic step according to the new
> ion coordinates, which results in a better initial guess than simply using
> the previously converged wavefunction and charge density. Neither of these
> things are done if you use ASE optimizers with the Vasp calculator, and it
> would appear as though VASP doesn’t properly extrapolate (or maybe it
> doesn’t extrapolate at all) the wavefunction/charge density with
> interactive=True (VaspInteractive). If you set maxmix to a positive number,
> VaspInteractive should properly keep mixing across ionic steps though. I
> question whether this is a good idea in general (it’s not the default
> behavior, after all).
>
>
>
> In any case, I would advise most workflows to simply use the built-in
> optimizers (or Graeme Henkelman’s LBFGS and FIRE optimizers, they are
> better) with ASE by passing the appropriate geometry optimization flags to
> the Vasp calculator and then running my_atoms.get_potential_energy(). This
> is an abuse of syntax, and ASE won’t natively return the optimization
> trajectory (though you can still parse it from the OUTCAR or vasprun.xml
> file yourself), but it’s much more efficient for normal geometry
> minimizations. If you need atypical constraints that aren’t supported by
> VASP, such as fixing bond lengths or angles or doing a scan in internal
> coordinates, then you’re out of luck. Use the ASE optimizers with whichever
> seems more performant for your purposes, Vasp or VaspInteractive. If you
> need to do NEB, use Graeme Henkelman’s NEB patches rather than the ASE NEB
> routines.
>
>
>
> I wish VaspInteractive worked better than it did, but as it stands the
> most reliable way to use VASP in ASE is to leave all dynamics to VASP.
>
>
>
> (Re-added to list. I understand this is an old thread, but some people may
> still find this relevant.)
>
>
>
> Eric
>
>
>
> *From:* Andrew Rosen [mailto:rosen at u.northwestern.edu]
> *Sent:* Monday, January 8, 2018 4:26 PM
> *To:* Eric Hermes <ehermes at chem.wisc.edu>
> *Subject:* Re: [ase-users] Problem Restarting Constrained Relaxation with
> Vasp Calculator
>
>
>
> I know I'm reviving an old thread here, but have you noticed increased
> number of SCF iterations when using ASE's optimizers with Vasp (not just
> with VaspInteractive)? I have noticed this for a few test systems I'm
> working on but haven't dug into whether this is merely something on the
> user side or not. I figured I'd ask. I imagine if you found that to be the
> case with VaspInteractive it probably would be the case for regular Vasp
> too, right?
>
> On Mon, Oct 16, 2017 at 11:50 AM Eric Hermes via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
> On Mon, 2017-10-16 at 16:35 +0000, Andrew Rosen wrote:
> > Eric,
> > Just chiming in here out of interest. Would you suggest using the
> > VaspInteractive calculator when using the ASE Vibrations module as
> > well? I've noticed the significant overhead associated with using the
> > regular VASP calculator and the ASE optimizers but never thought much
> > of it since I switched to using IBRION keywords for geometry
> > optimizations.
> > Andrew
>
> Yes, that would be a good use of VaspInteractive. Personally, I just
> use the integrated VASP vibrations routines (IBRION=5,6,7, or 8). I
> will note that in general, VaspInterative seems to take more SCF
> iterations to converge than internal VASP routines do. I'm still not
> entirely sure why this is, but I think it might have something to do
> with how VASP extrapolates the charge density when atoms move.
>
> Eric
>
> >
> > On Mon, Oct 16, 2017, 11:13 AM Eric Hermes via ase-users <ase-users at l
> > istserv.fysik.dtu.dk> wrote:
> > > On Mon, 2017-10-16 at 11:49 -0400, Dennis Trujillo wrote:
> > > > I tried to reproduce the error again myself and it seems to work
> > > now
> > > > strangely enough. Is it possible to have the restarted
> > > calculation
> > > > write to the original trajectory file?
> > >
> > > That depends on how you are creating the trajectory. If you are
> > > using
> > > Trajectory directly, you can pass "mode='a'", e.g. my_trajectory =
> > > Trajectory('existing.traj', mode='a'). If you are using an ASE
> > > optimizer, then I don't believe you can.
> > >
> > > I would strongly advise against using an ASE optimizer with the
> > > regular
> > > VASP calculator though, as there is a substantial overhead involved
> > > with constantly stopping/starting VASP (I/O overhead if you
> > > read/write
> > > CHGCAR/WAVECAR files, CPU time overhead if you don't). I would
> > > suggest
> > > either using the built-in VASP optimizers (the IBRION tag), or
> > > using
> > > the VaspInteractive calculator with the ASE optimizers. The
> > > VaspInteractive calculator works basically the same as the normal
> > > Vasp
> > > calculator, except it forbids the use of VASP keywords that cause
> > > VASP
> > > to move atoms internally (e.g. IBRION), and instead it gets updated
> > > positions from ASE.
> > >
> > > Eric
> > >
> > > >
> > > >
> > > > > On Oct 16, 2017, at 11:40 AM, Eric Hermes via ase-users <ase-
> > > users@
> > > > > listserv.fysik.dtu.dk> wrote:
> > > > >
> > > > > On Mon, 2017-10-16 at 15:37 +0000, Dennis Trujillo wrote:
> > > > > > Here is the ase-sort.dat,
> > > > > >
> > > > >
> > > > > Please keep replies on-list.
> > > > >
> > > > > As I suspected, these two files match, and should not lead to
> > > the
> > > > > error
> > > > > message you are seeing. Can you please verify that this error
> > > is
> > > > > reproducible with the exact CONTCAR and ase-sort.dat files you
> > > sent
> > > > > me
> > > > > in the directory? Also, please share your Python script that is
> > > > > running
> > > > > this calculation. If you are modifying the CONTCAR or ase-
> > > sort.dat
> > > > > files after your initial calculation but before your
> > > restart=True
> > > > > calculation, that could cause this issue.
> > > > >
> > > > > Eric
> > > > > >
> > > > > >
> > > > > > > On Oct 16, 2017, at 11:33 AM, Eric Hermes via ase-users
> > > <ase-
> > > > > > > users@
> > > > > >
> > > > > > listserv.fysik.dtu.dk> wrote:
> > > > > > >
> > > > > > > On Mon, 2017-10-16 at 15:17 +0000, Dennis Trujillo wrote:
> > > > > > > > I am using Vasp 5.4.1, attached is the CONTCAR,
> > > > > > > >
> > > > > > >
> > > > > > >
> > > > > > > I can't reproduce this error. It is not related to
> > > constraints,
> > > > > > > but
> > > > > > > rather the atomic reordering the the VASP calculator does
> > > > > >
> > > > > > internally to
> > > > > > > make all atoms of the same kind contiguous. The error
> > > message
> > > > > >
> > > > > > indicates
> > > > > > > that the geometry file being read has fewer than 41 atoms,
> > > but
> > > > > > > the
> > > > > >
> > > > > > file
> > > > > > > you have attached indeed has 42 atoms. Are you sure you
> > > have
> > > > > > > sent
> > > > > >
> > > > > > the
> > > > > > > correct CONTCAR file? Could you attach the ase-sort.dat
> > > file
> > > > > > > found
> > > > > >
> > > > > > in
> > > > > > > the same directory? Those two files seem to be mismatched.
> > > > > > >
> > > > > > > Eric
> > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > > On Oct 16, 2017, at 11:07 AM, Eric Hermes via ase-users
> > > > > > > > > <ase-
> > > > > >
> > > > > > users@
> > > > > > > > listserv.fysik.dtu.dk> wrote:
> > > > > > > > >
> > > > > > > > > On Mon, 2017-10-16 at 10:59 -0400, Dennis Trujillo via
> > > ase-
> > > > > > > > > users
> > > > > > > >
> > > > > > > > wrote:
> > > > > > > > > > Hello *,
> > > > > > > > > >
> > > > > > > > > > I am having trouble restarting a Vasp relaxation with
> > > > > >
> > > > > > constrained
> > > > > > > > > > atoms; I am not sure if ase.io is designed to read in
> > > a
> > > > > > > >
> > > > > > > > constrained
> > > > > > > > > > POSCAR (i.e. with TTT, or etc. appended to the atomic
> > > > > > > > > > position).
> > > > > >
> > > > > > I
> > > > > > > > am
> > > > > > > > > > using ASE version 3.15.0, on python 3.5.2. ASE gives
> > > me
> > > > > > > > > > the
> > > > > > > >
> > > > > > > > following
> > > > > > > > > > error,
> > > > > > > > > >
> > > > > > > > > > > > > calc=Vasp(restart=True)
> > > > > > > > > >
> > > > > > > > > > Traceback (most recent call last):
> > > > > > > > > >     File "<stdin>", line 1, in <module>
> > > > > > > > > >     File "/users/dptru/.local/lib/python3.5/site-
> > > > > > > > > > packages/ase/calculators/vasp/vasp.py", line 53, in
> > > > > > > > > > __init__
> > > > > > > > > >       self.restart_load()
> > > > > > > > > >     File "/users/dptru/.local/lib/python3.5/site-
> > > > > > > > > > packages/ase/calculators/vasp/vasp.py", line 190, in
> > > > > >
> > > > > > restart_load
> > > > > > > > > >       atoms = ase.io.read('CONTCAR',
> > > > > > > > > > format='vasp')[self.resort]
> > > > > > > > > >     File "/users/dptru/.local/lib/python3.5/site-
> > > > > > > > > > packages/ase/atoms.py", line 954, in __getitem__
> > > > > > > > > >       atoms.arrays[name] = a[i].copy()
> > > > > > > > > > IndexError: index 40 is out of bounds for axis 1 with
> > > > > > > > > > size 40
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > We will need more information to help debug this issue.
> > > ASE
> > > > > > > > > does
> > > > > > > > > support reading/writing constraints from/to VASP
> > > geometry
> > > > > > > > > files
> > > > > > > > > (POSCAR, CONTCAR). Can you please attach the CONTCAR
> > > file
> > > > > > > > > that is
> > > > > > > >
> > > > > > > > being
> > > > > > > > > read here? Also, what version of VASP are you using?
> > > > > > > > >
> > > > > > > > > Eric
> > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > Any help is appreciated,
> > > > > > > > > >
> > > > > > > > > > -Dennis
> > > > > > > > > > _______________________________________________
> > > > > > > > > > ase-users mailing list
> > > > > > > > > > ase-users at listserv.fysik.dtu.dk
> > > > > > > > > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-us
> > > ers
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > _______________________________________________
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> > > > > > > >
> > > > > > > >
> > > > > > >
> > > > > > >
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