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jkitchin / vasp

New ASE compliant Python interface to VASP
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jasp vs vaspy on gilgamesh #12

Closed devonwa closed 8 years ago

devonwa commented 8 years ago

Can vasp handle jobs previously run by jasp? If so, I think there's a server implementation issue on gilgamesh.

This works:

from ase import Atoms, Atom
from jasp import *

with jasp('~/dft-book/molecules/simple-co') as calc:
    atoms = calc.get_atoms()

This doesn't:

from ase import Atoms, Atom
from vasp import Vasp

print(Vasp.default_parameters) # this works.

calc = Vasp('~/dft-book/molecules/simple-co') # breaks here
atoms = calc.get_atoms()

Trace:

Traceback (most recent call last):
  File "<stdin>", line 6, in <module>
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 45, in inner
    return func(self, *args, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp_core.py", line 242, in __init__
    str(label), atoms)
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner
    return self.exception_handler(self, *sys.exc_info())
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner
    return func(self, *args, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/ase-s16/ase/calculators/calculator.py", line 513, in __init__
    atoms, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner
    return self.exception_handler(self, *sys.exc_info())
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner
    return func(self, *args, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/ase-s16/ase/calculators/calculator.py", line 184, in __init__
    self.read(restart)  # read parameters, atoms and results
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner
    return self.exception_handler(self, *sys.exc_info())
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner
    return func(self, *args, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/readers.py", line 322, in read
    atoms = self.read_atoms()
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner
    return self.exception_handler(self, *sys.exc_info())
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner
    return func(self, *args, **kwargs)
  File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/readers.py", line 249, in read_atoms
    atoms.positions = xatoms.positions[resort]
AttributeError: 'NoneType' object has no attribute 'positions'
jkitchin commented 8 years ago

no. it can't.

John

Professor John Kitchin Doherty Hall A207F Department of Chemical Engineering Carnegie Mellon University Pittsburgh, PA 15213 412-268-7803 @johnkitchin http://kitchingroup.cheme.cmu.edu

On Thu, Jun 16, 2016 at 11:32 AM, Devon Walker notifications@github.com wrote:

Can vasp handle jobs previously run by jasp? If so, I think there's a server implementation issue on gilgamesh.

This works:

from ase import Atoms, Atomfrom jasp import * with jasp('~/dft-book/molecules/simple-co') as calc: atoms = calc.get_atoms()

This doesn't:

from ase import Atoms, Atomfrom vasp import Vasp print(Vasp.default_parameters) # this works.

calc = Vasp('~/dft-book/molecules/simple-co') # breaks here atoms = calc.get_atoms()

Trace:

Traceback (most recent call last): File "", line 6, in File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 45, in inner return func(self, _args, _kwargs) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp_core.py", line 242, in init str(label), atoms) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner return self.exception_handler(self, _sys.exc_info()) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner return func(self, args, _kwargs) File "/opt/kitchingroup/vasp-5.3.5/ase-s16/ase/calculators/calculator.py", line 513, in init atoms, _kwargs) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner return self.exception_handler(self, sys.exc_info()) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner return func(self, args, _kwargs) File "/opt/kitchingroup/vasp-5.3.5/ase-s16/ase/calculators/calculator.py", line 184, in init self.read(restart) # read parameters, atoms and results File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner return self.exception_handler(self, _sys.exc_info()) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner return func(self, args, _kwargs) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/readers.py", line 322, in read atoms = self.read_atoms() File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 51, in inner return self.exception_handler(self, _sys.exc_info()) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/vasp.py", line 48, in inner return func(self, args, *_kwargs) File "/opt/kitchingroup/vasp-5.3.5/vaspy/vasp/readers.py", line 249, in read_atoms atoms.positions = xatoms.positions[resort] AttributeError: 'NoneType' object has no attribute 'positions'

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devonwa commented 8 years ago

Oh, that might be it. Closed.