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

[Eric Hermes]

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
> >> 
> > 
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