本文整理汇总了Python中ase.optimize.BFGS.attach方法的典型用法代码示例。如果您正苦于以下问题：Python BFGS.attach方法的具体用法？Python BFGS.attach怎么用？Python BFGS.attach使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ase.optimize.BFGS的用法示例。
在下文中一共展示了BFGS.attach方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: range
# 需要导入模块: from ase.optimize import BFGS [as 别名]
# 或者: from ase.optimize.BFGS import attach [as 别名]
for i in range(3):
ranks = range(i * n, (i + 1) * n)
image = initial.copy()
if rank in ranks:
calc = GPAW(h=0.3,
kpts=(2, 2, 1),
txt='neb%d.txt' % j,
communicator=ranks)
image.set_calculator(calc)
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images, parallel=True)
neb.interpolate()
qn = BFGS(neb, logfile='qn.log')
traj = PickleTrajectory('neb%d.traj' % j, 'w', images[j],
master=(rank % n == 0))
qn.attach(traj)
qn.run(fmax=0.05)
示例2: Atoms
# 需要导入模块: from ase.optimize import BFGS [as 别名]
# 或者: from ase.optimize.BFGS import attach [as 别名]
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixBondLength
from ase.io import Trajectory
from ase.optimize import BFGS
a = 3.6
b = a / 2
cu = Atoms('Cu2Ag',
positions=[(0, 0, 0),
(b, b, 0),
(a, a, b)],
calculator=EMT())
e0 = cu.get_potential_energy()
print(e0)
d0 = cu.get_distance(0, 1)
cu.set_constraint(FixBondLength(0, 1))
t = Trajectory('cu2ag.traj', 'w', cu)
qn = BFGS(cu)
qn.attach(t.write)
def f(): print(cu.get_distance(0,1))
qn.attach(f)
qn.run(fmax=0.01)
assert abs(cu.get_distance(0, 1) - d0) < 1e-14
示例3: print
# 需要导入模块: from ase.optimize import BFGS [as 别名]
# 或者: from ase.optimize.BFGS import attach [as 别名]
from ase.optimize import BFGS
from ase.io import read, write
from ase.calculators.emt import EMT
from ase.ga.relax_attaches import VariansBreak
import sys
fname = sys.argv[1]
print("Now relaxing {0}".format(fname))
a = read(fname)
a.set_calculator(EMT())
dyn = BFGS(a, trajectory=None, logfile=None)
vb = VariansBreak(a, dyn)
dyn.attach(vb.write)
dyn.run(fmax=0.05)
a.info["key_value_pairs"]["raw_score"] = -a.get_potential_energy()
write(fname[:-5] + "_done.traj", a)
print("Done relaxing {0}".format(fname))
示例4: NEB
# 需要导入模块: from ase.optimize import BFGS [as 别名]
# 或者: from ase.optimize.BFGS import attach [as 别名]
if i == j:
image.set_calculator(calc)
image.set_constraint(constraint)
images.append(image)
images.append(final)
neb = NEB(images, climb=True, parallel=True)
neb.interpolate()
dyn = BFGS(neb, logfile="logFile")
#if rank % (size // ) == 0:
# traj = PickleTrajectory('neb%d.traj' % j, 'w', images[j], master=True)
# qn.attach(traj)
for i in range(0, numOfImages):
dyn.attach(PickleTrajectory('neb-%d.traj' % i, 'w', images[i]), master=True)
dyn.run(fmax=0.014)
#writes the coordinates for each image in NEB path in .xyz format
string = 'structure'
path = os.getcwd()
path = path + '/neb-scratch'
if not os.path.exists(path): os.makedirs(path)
outFileName = 'NEB-trajectory.xyz'
if os.path.exists(outFileName):
os.remove(outFileName)
for i in range(0, neb.nimages):
string = 'structure%03d' % (i,) +'.xyz'