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# creates: ase-db.txt, ase-db-long.txt, known-keys.csv
import subprocess
import ase.db
from ase import Atoms
from ase.calculators.emt import EMT
from ase.db.core import get_key_descriptions
from ase.optimize import BFGS
c = ase.db.connect('abc.db', append=False)
h2 = Atoms('H2', [(0, 0, 0), (0, 0, 0.7)])
h2.calc = EMT()
h2.get_forces()
c.write(h2, relaxed=False)
BFGS(h2).run(fmax=0.01)
c.write(h2, relaxed=True, data={'abc': [1, 2, 3]})
for d in c.select('molecule'):
print(d.forces[0, 2], d.relaxed)
h = Atoms('H')
h.calc = EMT()
h.get_potential_energy()
c.write(h)
with open('ase-db.txt', 'w') as fd:
fd.write('$ ase db abc.db\n')
output = subprocess.check_output(['ase', 'db', 'abc.db'])
fd.write(output.decode())
with open('ase-db-long.txt', 'w') as fd:
fd.write('$ ase db abc.db relaxed=1 -l\n')
output = subprocess.check_output(['ase', 'db', 'abc.db', 'relaxed=1', '-l'])
fd.write(output.decode())
row = c.get(relaxed=1, calculator='emt')
for key in row:
print(f'{key:22}: {row[key]}')
print(row.data.abc)
e2 = row.energy
e1 = c.get(H=1).energy
ae = 2 * e1 - e2
print(ae)
id = c.get(relaxed=1).id
c.update(id, atomization_energy=ae)
del c[c.get(relaxed=0).id]
with open('known-keys.csv', 'w') as fd:
print('key,short description,long description,unit', file=fd)
for key, keydesc in get_key_descriptions().items():
unit = keydesc.unit
if unit == '|e|':
unit = r'\|e|'
print(
'{},{},{},{}'.format(
key, keydesc.shortdesc, keydesc.longdesc, unit
),
file=fd,
)
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