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import json
import numpy as np
import ase.units as units
from ase import Atoms
from ase.data import chemical_symbols
nomad_api_template = ('https://labdev-nomad.esc.rzg.mpg.de/'
'api/resolve/{hash}?format=recursiveJson')
def nmd2https(uri):
"""Get https URI corresponding to given nmd:// URI."""
assert uri.startswith('nmd://')
return nomad_api_template.format(hash=uri[6:])
def download(uri):
"""Download data at nmd:// URI as a NomadEntry object."""
try:
from urllib2 import urlopen
except ImportError:
from urllib.request import urlopen
httpsuri = nmd2https(uri)
response = urlopen(httpsuri)
txt = response.read().decode('utf8')
return json.loads(txt, object_hook=NomadEntry)
def read(fd, _includekeys=lambda key: True):
"""Read NomadEntry object from file."""
# _includekeys can be used to strip unnecessary keys out of a
# downloaded nomad file so its size is suitable for inclusion
# in the test suite.
def hook(dct):
d = {k: dct[k] for k in dct if _includekeys(k)}
return NomadEntry(d)
dct = json.load(fd, object_hook=hook)
return dct
def section_system_to_atoms(section):
"""Covnert section_system into an Atoms object."""
assert section['name'] == 'section_system'
numbers = section['atom_species']
numbers = np.array(numbers, int)
numbers[numbers < 0] = 0 # We don't support Z < 0
numbers[numbers >= len(chemical_symbols)] = 0
positions = section['atom_positions']['flatData']
positions = np.array(positions).reshape(-1, 3) * units.m
atoms = Atoms(numbers, positions=positions)
atoms.info['nomad_uri'] = section['uri']
pbc = section.get('configuration_periodic_dimensions')
if pbc is not None:
assert len(pbc) == 1
pbc = pbc[0] # it's a list??
pbc = pbc['flatData']
assert len(pbc) == 3
atoms.pbc = pbc
# celldisp?
cell = section.get('lattice_vectors')
if cell is not None:
cell = cell['flatData']
cell = np.array(cell).reshape(3, 3) * units.m
atoms.cell = cell
return atoms
def nomad_entry_to_images(section):
"""Yield the images from a Nomad entry.
The entry must contain a section_run.
One atoms object will be yielded for each section_system."""
class NomadEntry(dict):
"""An entry from the Nomad database.
The Nomad entry is represented as nested dictionaries and lists.
ASE converts each dictionary into a NomadEntry object which supports
different actions. Some actions are only available when the NomadEntry
represents a particular section."""
def __init__(self, dct):
# assert dct['type'] == 'nomad_calculation_2_0'
# assert dct['name'] == 'calculation_context'
# We could implement NomadEntries that represent sections.
dict.__init__(self, dct)
@property
def hash(self):
# The hash is a string, so not __hash__
assert self['uri'].startswith('nmd://')
return self['uri'][6:]
def toatoms(self):
"""Convert this NomadEntry into an Atoms object.
This NomadEntry must represent a section_system."""
return section_system_to_atoms(self)
def iterimages(self):
"""Yield Atoms object contained within this NomadEntry.
This NomadEntry must represent or contain a section_run."""
if 'section_run' in self:
run_sections = self['section_run']
else:
assert self['name'] == 'section_run'
run_sections = [self] # We assume that we are the section_run
for run in run_sections:
systems = run['section_system']
for system in systems:
atoms = section_system_to_atoms(system)
atoms.info['nomad_run_gIndex'] = run['gIndex']
atoms.info['nomad_system_gIndex'] = system['gIndex']
if self.get('name') == 'calculation_context':
atoms.info['nomad_calculation_uri'] = self['uri']
yield atoms
def main():
uri = "nmd://N9Jqc1y-Bzf7sI1R9qhyyyoIosJDs/C74RJltyQeM9_WFuJYO49AR4gKuJ2"
print(nmd2https(uri))
entry = download(uri)
from ase.visualize import view
view(list(entry.iterimages()))
if __name__ == '__main__':
main()
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