Python atoms2cmrの例

コード例 #1

ファイル: cmr_io.py プロジェクト: misdoro/python-ase

def write_db(filename, images, **kwargs):
    try:
        import cmr
        cmr.atoms2cmr(images, **kwargs).write(filename)
    except:
        raise
        raise NotAvailable('CMR version>0.3.2 is required')

コード例 #2

def write_db(filename, images, **kwargs):
    try:
        import cmr
        cmr.atoms2cmr(images, **kwargs).write(filename)
    except:
        raise
        raise NotAvailable('CMR version>0.3.2 is required')

コード例 #3

ファイル: cmr_rw.py プロジェクト: PHOTOX/fuase

import os
import warnings
# cmr calls all available methods in ase.atoms detected by the module inspect.
# Therefore also deprecated methods are called - and we choose to silence those warnings.
#warnings.filterwarnings('ignore', 'ase.atoms.*deprecated',)

import cmr

from ase.calculators.emt import EMT
from ase.structure import molecule

m1 = molecule('O2')
m1.set_calculator(EMT())
e1 = m1.get_potential_energy()

data = cmr.atoms2cmr(m1)
data.set_user_variable("molecule", "O2")
data.set_user_variable("potential", "EMT")
data.set_user_variable("db_keywords", ["O2", "EMT"])

data.write("O2.db")

reread = cmr.read("O2.db")
e2 = reread["ase_potential_energy"]
assert abs(e1-e2) < 1.e-6, str(e1) + ' ' + str(e2)

# clean
filename = "O2.db"
if os.path.exists(filename): os.unlink(filename)

コード例 #4

from ase.test import NotAvailable

try:
    import cmr
except ImportError:
    raise NotAvailable('CMR is required')

from ase.calculators.emt import EMT
from ase.structure import molecule

m1 = molecule('O2')
m1.set_calculator(EMT())
e1 = m1.get_potential_energy()

data = cmr.atoms2cmr(m1)
data.set_user_variable("molecule", "O2")
data.set_user_variable("potential", "EMT")
data.set_user_variable("db_keywords", ["O2", "EMT"])

data.write("O2.db")

reread = cmr.read("O2.db")
e2 = reread["ase_potential_energy"]
assert abs(e1 - e2) < 1.e-6, str(e1) + ' ' + str(e2)

# clean
filename = "O2.db"
if os.path.exists(filename):
    os.unlink(filename)