def makeatoms(self, *args):
self.update_element()
if self.legal_element is None:
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
symb = self.legal_element
length = int(self.length.value)
bl = self.bondlength.value
self.atoms = nanotube(n, m, length=length, bond=bl, symbol=symb)
# XXX can this be translated?
self.pybut.python = py_template % {'n': n, 'm':m, 'length':length,
'symb':symb, 'bl':bl}
h = np.zeros(3)
uc = self.atoms.get_cell()
for i in range(3):
norm = np.cross(uc[i-1], uc[i-2])
norm /= np.sqrt(np.dot(norm, norm))
h[i] = np.abs(np.dot(norm, uc[i]))
label = label_template % {'natoms' : self.atoms.get_number_of_atoms(),
'symbols' : formula(self.atoms.get_atomic_numbers()),
'volume' : self.atoms.get_volume(),
'diameter' : self.atoms.get_cell()[0][0]/2.0}
self.status.set_markup(label)
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None:
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
symb = self.legal_element
length = int(self.length.value)
bl = self.bondlength.value
self.atoms = nanotube(n, m, length=length, bond=bl, symbol=symb)
# XXX can this be translated?
self.pybut.python = py_template % {
'n': n,
'm': m,
'length': length,
'symb': symb,
'bl': bl
}
h = np.zeros(3)
uc = self.atoms.get_cell()
for i in range(3):
norm = np.cross(uc[i - 1], uc[i - 2])
norm /= np.sqrt(np.dot(norm, norm))
h[i] = np.abs(np.dot(norm, uc[i]))
label = label_template % {
'natoms': self.atoms.get_number_of_atoms(),
'symbols': formula(self.atoms.get_atomic_numbers()),
'volume': self.atoms.get_volume(),
'diameter': self.atoms.get_cell()[0][0] / 2.0
}
self.status.set_markup(label)
def test_Foutier_ASE_C_Ring():
pytest.importorskip("ase")
from ase.structure import nanotube
cnt = nanotube(3, 3, length=1, bond=1.4)
four = Fourier()
four.grid.bins = [6, 6, 2]
four.structure = cnt
four.grid.ll = [0.0, 0.0, 0.0]
four.grid.lr = [2.0, 0.0, 0.0]
four.grid.ul = [0.0, 2.0, 0.0]
four.grid.tl = [0.0, 0.0, 0.5]
results = four.calc()
expected_result = [[[6.36497605e+03, 3.18248802e+03],
[5.19826149e+03, 2.62430530e+03],
[2.62792897e+03, 1.44984089e+03],
[5.38964665e+02, 4.77287736e+02],
[1.77345692e+01, 5.96777257e+01],
[5.61330972e+02, 2.13240090e-01]],
[[5.19824634e+03, 2.58464390e+03],
[4.19804025e+03, 2.08045239e+03],
[2.02566353e+03, 1.13472923e+03],
[3.43108613e+02, 3.82910378e+02],
[4.89415344e+01, 6.29938344e+01],
[5.92919277e+02, 4.58410816e+00]],
[[2.62726847e+03, 1.23823945e+03],
[2.02670889e+03, 8.48260672e+02],
[7.91958690e+02, 3.42380372e+02],
[3.33463046e+01, 5.27598268e+01],
[2.30729880e+02, 5.28798893e-01],
[7.98830716e+02, 8.58598324e+00]],
[[5.35796499e+02, 1.75090475e+02],
[3.44314616e+02, 3.58530973e+01],
[3.54586483e+01, 1.01212665e+01],
[1.11489239e+02, 1.22750852e+02],
[6.43708514e+02, 2.21345300e+02],
[1.09996107e+03, 1.70969809e+02]],
[[2.07782589e+01, 8.83691575e+01],
[4.95216235e+01, 3.06779369e+02],
[2.12904292e+02, 6.20110076e+02],
[6.00173935e+02, 8.55468985e+02],
[1.07400507e+03, 8.34634162e+02],
[1.26315713e+03, 5.49870658e+02]],
[[6.17667297e+02, 7.27129729e+02],
[6.16759220e+02, 1.22358912e+03],
[7.37019649e+02, 1.60499636e+03],
[9.37950901e+02, 1.66971846e+03],
[1.09292588e+03, 1.35970016e+03],
[1.03004750e+03, 8.27690724e+02]]]
assert_array_almost_equal(results, expected_result, 5)
results = four.calc(fast=False)
assert_array_almost_equal(results, expected_result, 5)
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None:
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
symb = self.legal_element
length = int(self.length.value)
bl = self.bondlength.value
self.atoms = nanotube(n, m, length=length, bond=bl, symbol=symb)
# XXX can this be translated?
self.pybut.python = py_template % {'n': n, 'm':m, 'length':length,
'symb':symb, 'bl':bl}
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None:
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
symb = self.legal_element
length = int(self.length.value)
bl = self.bondlength.value
self.atoms = nanotube(n, m, length=length, bond=bl, symbol=symb)
self.pybut.python = py_template % {
'n': n,
'm': m,
'length': length,
'symb': symb,
'bl': bl
}
from ase.io import write
from ase.structure import bulk, nanotube, graphene_nanoribbon
import numpy as np
for i, a in enumerate([
bulk('Cu', 'fcc', a=3.6),
bulk('Cu', 'fcc', a=3.6, orthorhombic=True),
bulk('Cu', 'fcc', a=3.6, cubic=True)
]):
write('a%d.pov' % (i + 1),
a,
show_unit_cell=2,
display=False,
run_povray=True)
cnt1 = nanotube(6, 0, length=4)
cnt1.rotate('x', 'z', rotate_cell=True)
cnt2 = nanotube(3, 3, length=6, bond=1.4, symbol='Si')
cnt2.rotate('x', 'z', rotate_cell=True)
for i, a in enumerate([cnt1, cnt2]):
write('cnt%d.pov' % (i + 1),
a,
show_unit_cell=2,
display=False,
run_povray=True)
ind = [2, 0, 1]
gnr1 = graphene_nanoribbon(3, 4, type='armchair')
gnr1.set_cell(np.diag(gnr1.cell)[ind])
gnr1.positions = gnr1.positions[:, ind]
def constructTube():
cnt = nanotube(6, 6, length=l)
write('cnt.xyz', cnt)
return cnt
from ase.structure import molecule
from ase.structure import nanotube
from ase.optimize import BFGS, MDMin
from asap3 import BrennerPotential
from asap3.testtools import ReportTest
import numpy as np
atoms = nanotube(5, 5, length=10)
atoms.set_calculator(BrennerPotential())
uc = atoms.get_cell()
l0 = uc[2,2]
e = -1e100
for eps in np.linspace(0, 0.5, 201):
uc[2,2] = l0 * (1 + eps)
atoms.set_cell(uc, scale_atoms=True)
dyn = MDMin(atoms, logfile=None, dt=0.05)
dyn.run(fmax=0.01, steps=100)
epot = atoms.get_potential_energy()
if epot > e:
e = epot
print "%.3f %f" % (eps, epot)
print "Maximal energy:", e
ReportTest("Maximal energy", e, -969.0, 5.0)
if abs(e - -620.98) < 1.0:
print "Bug 42 is back!"
from ase.structure import nanotube
from gpaw import GPAW, Mixer, PoissonSolver, ConvergenceError
from gpaw.eigensolvers.rmm_diis import RMM_DIIS
from gpaw.mpi import size
from gpaw.mpi import rank
from gpaw.test import equal
from gpaw import use_mic
import time
tube = nanotube(6, 6, 10)
if rank == 0:
print "Starting solver..."
tstart = time.time()
if use_mic:
txt = 'out_nanotube_large_mic_p%d.txt' % size
else:
txt = 'out_nanotube_large_p%d.txt' % size
conv = {'eigenstates': 1e-4, 'density': 1e-2, 'energy': 1e-3}
calc = GPAW( # gpts=(96, 96, 128),
h=0.2,
nbands=-60,
width=0.1,
poissonsolver=PoissonSolver(eps=1e-12),
eigensolver=RMM_DIIS(keep_htpsit=False),
# eigensolver=RMM_DIIS(),
maxiter=6,
mixer=Mixer(0.1, 5, 50),
convergence=conv,
# creates: a1.png a2.png a3.png cnt1.png cnt2.png gnr1.png gnr2.png
from ase.io import write
from ase.lattice import bulk
from ase.structure import nanotube, graphene_nanoribbon
import numpy as np
for i, a in enumerate([
bulk('Cu', 'fcc', a=3.6),
bulk('Cu', 'fcc', a=3.6, orthorhombic=True),
bulk('Cu', 'fcc', a=3.6, cubic=True)]):
write('a%d.pov' % (i + 1), a,
show_unit_cell=2, display=False, run_povray=True)
cnt1 = nanotube(6, 0, length=4)
cnt1.rotate('x', 'z', rotate_cell=True)
cnt2 = nanotube(3, 3, length=6, bond=1.4, symbol='Si')
cnt2.rotate('x', 'z', rotate_cell=True)
for i, a in enumerate([cnt1, cnt2]):
write('cnt%d.pov' % (i + 1), a,
show_unit_cell=2, display=False, run_povray=True)
ind = [2, 0, 1]
gnr1 = graphene_nanoribbon(3, 4, type='armchair', saturated=True)
gnr1.set_cell(np.diag(gnr1.cell)[ind])
gnr1.positions = gnr1.positions[:, ind]
gnr2 = graphene_nanoribbon(2, 6, type='zigzag', saturated=True,
C_H=1.1, C_C=1.4, vacuum=3.0,
magnetic=True, initial_mag=1.12)
gnr2.set_cell(np.diag(gnr2.cell)[ind])
gnr2.positions = gnr2.positions[:, ind]
from ase.structure import nanotube
from gpaw import GPAW, Mixer, PoissonSolver
from gpaw.mpi import size
from gpaw.test import equal
from gpaw import use_mic
from gpaw.mpi import rank
import time
tube = nanotube(6,6,9)
if rank == 0:
print "Starting solver..."
tstart = time.time()
if use_mic:
txt = 'out_nanotube2_mic_p%d.txt' % size
else:
txt = 'out_nanotube2_p%d.txt' % size
conv = {'eigenstates' : 1e-4, 'density' : 1e-2, 'energy' : 1e-3}
calc = GPAW(gpts=(96, 96, 128), nbands=-20, width=0.1,
poissonsolver=PoissonSolver(eps=1e-12),
mixer=Mixer(0.1, 5, 50),
convergence=conv, txt=txt)
tube.set_calculator(calc)
e = tube.get_potential_energy()
tend = time.time()
if rank == 0:
print "time for calculation: {0:.2f}sec".format(tend-tstart)
equal(e, -2159.016150, 1e-2)
tube[i + 2].symbol = 'N'
i += 3
return tube
def convert_BN(tube):
i = 0
while i < len(tube):
tube[i + 0].symbol = 'B'
tube[i + 1].symbol = 'N'
i += 2
return tube
tube = nanotube(n_inner, m_inner, length=6, bond=cbond, symbol='C')
lx, ly, lz = tube.get_cell()[0][0], tube.get_cell()[1][1], tube.get_cell(
)[2][2]
print 'Set lx and ly to ', lxoverride
tube.set_cell([lxoverride, lxoverride, lz], scale_atoms=False)
if BCN == True: convert_BCN(tube)
if BN == True: convert_BN(tube)
tube.center()
io.write('POSCAR.1', tube, sort=True)
tube2 = nanotube(n_outer, m_outer, length=6, bond=cbond, symbol='C')
from ase.structure import nanotube
from gpaw import GPAW, RMM_DIIS
from gpaw.mpi import size
from gpaw.test import equal
from gpaw import use_mic
from gpaw.mpi import rank
import time
tube = nanotube(8,8,8)
if rank == 0:
print "Starting solver..."
tstart = time.time()
if use_mic:
txt = 'out_nanotube1_mic_p%d.txt' % size
else:
txt = 'out_nanotube1_p%d.txt' % size
conv = {'eigenstates' : 1e-4, 'density' : 1e-2, 'energy' : 1e-2}
calc = GPAW(h=0.2, nbands=-20, width=0.1, kpts=(1,1,2),
eigensolver=RMM_DIIS(keep_htpsit=False),
#convergence=conv, txt=txt)
convergence=conv)
tube.set_calculator(calc)
e = tube.get_potential_energy()
tend = time.time()
if rank == 0:
print "time for calculation: {0:.2f}sec".format(tend-tstart)
equal(e, -628.838671, 1e-2)
from ase.structure import nanotube
from gpaw import GPAW, RMM_DIIS
from gpaw.mpi import size
from gpaw.test import equal
from gpaw import use_mic
from gpaw.mpi import rank
import time
tube = nanotube(8, 8, 8)
if rank == 0:
print "Starting solver..."
tstart = time.time()
if use_mic:
txt = 'out_nanotube1_mic_p%d.txt' % size
else:
txt = 'out_nanotube1_p%d.txt' % size
conv = {'eigenstates': 1e-4, 'density': 1e-2, 'energy': 1e-2}
calc = GPAW(
h=0.2,
nbands=-20,
width=0.1,
kpts=(1, 1, 2),
eigensolver=RMM_DIIS(keep_htpsit=False),
#convergence=conv, txt=txt)
convergence=conv)
tube.set_calculator(calc)
e = tube.get_potential_energy()
tend = time.time()
if rank == 0:
txt = 'output.txt'
maxiter = 16
conv = {'eigenstates' : 1e-4, 'density' : 1e-2, 'energy' : 1e-3}
# output benchmark parameters
if rank == 0:
print("#"*60)
print("GPAW benchmark: Carbon Nanotube")
print(" nanotube dimensions: n=%d, m=%d, length=%d" % (n, m, length))
print(" MPI task: %d out of %d" % (rank, size))
print(" using MICs: " + str(use_mic))
print("#"*60)
print("")
# setup the system
atoms = nanotube(n, m, length)
calc = GPAW(h=0.2, nbands=-60, width=0.1,
poissonsolver=PoissonSolver(eps=1e-12),
eigensolver=RMM_DIIS(keep_htpsit=True),
maxiter=maxiter,
mixer=Mixer(0.1, 5, 50),
convergence=conv, txt=txt)
atoms.set_calculator(calc)
# execute the run
try:
atoms.get_potential_energy()
except ConvergenceError:
pass