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

[Eric Hermes]

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
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> > > > > > > > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-us
> > ers
> > > > > > > >
> > > > > > > >   
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> > s
> > > > > > >
> > > > > > >  
> > > > > >
> > > > > >  
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