Broken with ASE 3.23.0b1

[HaoZeke]

• Question about usage? Please search your issue here first: Usage questions: Please ask here first [0] #589 and Usage questions about nglview: Please ask here first [1]  #785

• Version report

python -c 'import nglview; print(nglview.__version__)' # 3.0.3'
python -c 'import ipywidgets; print(ipywidgets.__version__)' #  '7.6.3'
python -c 'import ase; print(ase.__version__)' #  '3.23.0b1'

Consider the following snippet, which works with ase gui and other visualization methods:

import nglview as nv
from ase import Atoms
from ase.build import fcc111

atoms = fcc111('Au', size=(3,3,1))
atoms.symbols[4:10]='Ag'
nv.show_ase(atoms)

This errors out with:

Error output

---------------------------------------------------------------------------
LinAlgError                               Traceback (most recent call last)
/tmp/ipykernel_335/3578296922.py in <module>
----> 1 nv.show_ase(atoms)

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/show.py in show_ase(ase_atoms, **kwargs)
     83     """
     84     structure = ASEStructure(ase_atoms)
---> 85     return NGLWidget(structure, **kwargs)
     86 
     87 

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/widget.py in __init__(self, structure, representations, parameters, **kwargs)
    243         else:
    244             if structure is not None:
--> 245                 self.add_structure(structure, **kwargs)
    246 
    247         if representations:

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/widget.py in add_structure(self, structure, **kwargs)
   1111         if not isinstance(structure, Structure):
   1112             raise ValueError(f'{structure} is not an instance of Structure')
-> 1113         self._load_data(structure, **kwargs)
   1114         self._ngl_component_ids.append(structure.id)
   1115         if self.n_components > 1:

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/widget.py in _load_data(self, obj, **kwargs)
   1229         if not is_url:
   1230             if hasattr(obj, 'get_structure_string'):
-> 1231                 blob = obj.get_structure_string()
   1232                 kwargs2['ext'] = obj.ext
   1233                 passing_buffer = True

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/adaptor.py in get_structure_string(self)
    135 
    136     def get_structure_string(self):
--> 137         return _get_structure_string(self._ase_atoms.write)
    138 
    139 

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/nglview/adaptor.py in _get_structure_string(write_method, suffix)
     57 def _get_structure_string(write_method, suffix='.pdb'):
     58     with mkstemp_wrapper(suffix=suffix) as fname:
---> 59         write_method(fname)
     60         with open(fname) as fh:
     61             return fh.read()

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/atoms.py in write(self, filename, format, **kwargs)
   1962         """
   1963         from ase.io import write
-> 1964         write(filename, self, format, **kwargs)
   1965 
   1966     def iterimages(self):

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/io/formats.py in write(filename, images, format, parallel, append, **kwargs)
    626     io = get_ioformat(format)
    627 
--> 628     return _write(filename, fd, format, io, images,
    629                   parallel=parallel, append=append, **kwargs)
    630 

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/parallel.py in new_func(*args, **kwargs)
    242             not kwargs.pop('parallel', True)):
    243             # Disable:
--> 244             return func(*args, **kwargs)
    245 
    246         ex = None

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/io/formats.py in _write(filename, fd, format, io, images, parallel, append, **kwargs)
    662                 # XXX remember to re-enable compressed open
    663                 # fd = io.open(filename, mode)
--> 664             return io.write(fd, images, **kwargs)
    665         finally:
    666             if open_new and fd is not None:

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/io/formats.py in _write_wrapper(self, *args, **kwargs)
    189         if function is None:
    190             raise ValueError(f'Cannot write to {self.name}-format')
--> 191         return function(*args, **kwargs)
    192 
    193     @property

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/utils/__init__.py in iofunc(file, *args, **kwargs)
    484                 else:
    485                     fd = file
--> 486                 obj = func(fd, *args, **kwargs)
    487                 return obj
    488             finally:

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/ase/io/proteindatabank.py in write_proteindatabank(fileobj, images, write_arrays)
    192         cellpar = cell_to_cellpar(currentcell)
    193         exportedcell = cellpar_to_cell(cellpar)
--> 194         rotation = np.linalg.solve(currentcell, exportedcell)
    195         # ignoring Z-value, using P1 since we have all atoms defined explicitly
    196         format = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1\n'

<__array_function__ internals> in solve(*args, **kwargs)

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/numpy/linalg/linalg.py in solve(a, b)
    391     signature = 'DD->D' if isComplexType(t) else 'dd->d'
    392     extobj = get_linalg_error_extobj(_raise_linalgerror_singular)
--> 393     r = gufunc(a, b, signature=signature, extobj=extobj)
    394 
    395     return wrap(r.astype(result_t, copy=False))

~/Git/Github/lesHouches_greens21/tmp/lib/python3.8/site-packages/numpy/linalg/linalg.py in _raise_linalgerror_singular(err, flag)
     86 
     87 def _raise_linalgerror_singular(err, flag):
---> 88     raise LinAlgError("Singular matrix")
     89 
     90 def _raise_linalgerror_nonposdef(err, flag):

LinAlgError: Singular matrix

Although simpler basic snippets work:

import nglview as nv
from ase import Atoms
atoms = Atoms('N2', positions=[[0, 0, -1], [0, 1, 1]])
nv.show_ase(atoms)

Trajectories are also still working, just not the new Symbols approach to Atoms objects.

[hainm]

hi @HaoZeke

I think it's the problem with ASE, not nglview. Under the hood, nglview was trying to convert the Atoms object to pdb file.

    ...: from ase import Atoms
    ...: from ase.build import fcc111
    ...: 
    ...: atoms = fcc111('Au', size=(3,3,1))
    ...: atoms.symbols[4:10]='Ag'

In [15]: atoms.write("abc.pdb") # THIS CAUSES THE ISSUE

Please ping ASE team for the answer. Cheers.

[HaoZeke]

Thanks for the prompt response, I've reported it upstream:
https://gitlab.com/ase/ase/-/issues/964