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

[Eric Hermes]

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-users
> > > > > > 
> > > > > >   
> > > > > > _______________________________________________
> > > > > > ase-users mailing list
> > > > > > ase-users at listserv.fysik.dtu.dk
> > > > > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> > > > > 
> > > > >  
> > > > 
> > > >  
> > > > _______________________________________________
> > > > ase-users mailing list
> > > > ase-users at listserv.fysik.dtu.dk
> > > > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> > 
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
> 
>