def makeatoms(self, *args):
self.update_element()
self.update_gui()
if self.legal_element is None or (self.struct.get_active() == 2 and
self.legal_element2 is None):
self.atoms = None
self.pybut.python = None
self.status.set_markup(_("Please specify a consistent set of atoms. "))
else:
n = int(self.n.value)
m = int(self.m.value)
CC = self.bondlength.value
vacuum = self.vacuum.value
orient = self.orient_text[self.orient.get_active()]
elem = self.legal_element
if self.struct.get_active() == 0:
# Extended sheet
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum, sheet=True,
main_element=elem)
elif self.struct.get_active() == 1:
# Unsaturated nanoribbon
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum,
main_element=elem)
elif self.struct.get_active() == 2:
# Saturated nanoribbon
elem2 = self.legal_element2
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
C_H=self.bondlength2.value,
vacuum=vacuum,
saturated=True,
main_element=elem,
saturate_element=elem2)
else:
raise RuntimeError("Unknown structure in SetupGraphene!")
# Now, rotate into the xy plane (ase.gui's default view plane)
pos = self.atoms.get_positions()
cell = self.atoms.get_cell()
pbc = self.atoms.get_pbc()
cell[1,1], cell[2,2] = cell[2,2], cell[1,1]
x = pos[:,1].copy()
z = pos[:,2].copy()
pos[:,1] = z
pos[:,2] = x
self.atoms.set_cell(cell)
self.atoms.set_positions(pos)
self.atoms.set_pbc([pbc[0], pbc[2], pbc[1]])
# Find the heights of the unit cell
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()}
self.status.set_markup(label)
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None or (self.struct.get_active() == 2
and self.legal_element2 is None):
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
CC = self.bondlength.value
vacuum = self.vacuum.value
orient = self.orient_text[self.orient.get_active()]
elem = self.legal_element
if self.struct.get_active() == 0:
# Extended sheet
self.atoms = graphene_nanoribbon(n,
m,
type=orient,
C_C=CC,
vacc=vacuum,
sheet=True,
main_element=elem)
elif self.struct.get_active() == 1:
# Unsaturated nanoribbon
self.atoms = graphene_nanoribbon(n,
m,
type=orient,
C_C=CC,
vacc=vacuum,
main_element=elem)
elif self.struct.get_active() == 2:
# Saturated nanoribbon
elem2 = self.legal_element2
self.atoms = graphene_nanoribbon(n,
m,
type=orient,
C_C=CC,
C_H=self.bondlength2.value,
vacuum=vacuum,
saturated=True,
main_element=elem,
saturate_element=elem2)
else:
raise RuntimeError("Unknown structure in SetupGraphene!")
# Now, rotate into the xy plane (ase.gui's default view plane)
pos = self.atoms.get_positions()
cell = self.atoms.get_cell()
pbc = self.atoms.get_pbc()
cell[1, 1], cell[2, 2] = cell[2, 2], cell[1, 1]
x = pos[:, 1].copy()
z = pos[:, 2].copy()
pos[:, 1] = z
pos[:, 2] = x
self.atoms.set_cell(cell)
self.atoms.set_positions(pos)
self.atoms.set_pbc([pbc[0], pbc[2], pbc[1]])
def make_neighSet(cutoff, edge, bond):
atoms = graphene_nanoribbon(50, 50, type='zigzag', C_C = bond)
atoms.rotate([1,0,0], np.pi/2, rotate_cell = True)
if edge == 'zz':
atoms.rotate([0,0,1], np.pi/2, rotate_cell = True)
if cutoff != 15:
print 'not implemented'
raise
if edge == 'ac':
if cutoff != 15:
print 'not implemented... cannot be sure of the alingmen for other cutoffs.'
raise
atoms.center()
middle = [np.average(atoms.positions[:,0]), \
np.average(atoms.positions[:,1]), \
np.average(atoms.positions[:,2])]
rem = []
midMin = 100
for i, atom in enumerate(atoms):
if cutoff < np.linalg.norm(atom.position - middle): rem.append(i)
del atoms[rem]
for i, pos in enumerate(atoms.positions):
if np.linalg.norm(pos - middle) < midMin:
midMin = np.linalg.norm(pos - middle)
iCentre = i
return atoms.positions - atoms.positions[iCentre]
def make_neighSet(cutoff, edge, bond):
atoms = graphene_nanoribbon(50, 50, type='zigzag', C_C=bond)
atoms.rotate([1, 0, 0], np.pi / 2, rotate_cell=True)
if edge == 'zz':
atoms.rotate([0, 0, 1], np.pi / 2, rotate_cell=True)
if cutoff != 15:
print 'not implemented'
raise
if edge == 'ac':
if cutoff != 15:
print 'not implemented... cannot be sure of the alingmen for other cutoffs.'
raise
atoms.center()
middle = [np.average(atoms.positions[:,0]), \
np.average(atoms.positions[:,1]), \
np.average(atoms.positions[:,2])]
rem = []
midMin = 100
for i, atom in enumerate(atoms):
if cutoff < np.linalg.norm(atom.position - middle): rem.append(i)
del atoms[rem]
for i, pos in enumerate(atoms.positions):
if np.linalg.norm(pos - middle) < midMin:
midMin = np.linalg.norm(pos - middle)
iCentre = i
return atoms.positions - atoms.positions[iCentre]
def makeatoms(self, *args):
self.update_element()
if self.legal_element is None or (self.struct.get_active() == 2 and
self.legal_element2 is None):
self.atoms = None
self.pybut.python = None
else:
n = int(self.n.value)
m = int(self.m.value)
CC = self.bondlength.value
vacuum = self.vacuum.value
orient = self.orient_text[self.orient.get_active()]
elem = self.legal_element
if self.struct.get_active() == 0:
# Extended sheet
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum, sheet=True,
main_element=elem)
elif self.struct.get_active() == 1:
# Unsaturated nanoribbon
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
vacc=vacuum,
main_element=elem)
elif self.struct.get_active() == 2:
# Saturated nanoribbon
elem2 = self.legal_element2
self.atoms = graphene_nanoribbon(n, m, type=orient, C_C=CC,
C_H=self.bondlength2.value,
vacuum=vacuum,
saturated=True,
main_element=elem,
saturate_element=elem2)
else:
raise RuntimeError("Unknown structure in SetupGraphene!")
# Now, rotate into the xy plane (ase.gui's default view plane)
pos = self.atoms.get_positions()
cell = self.atoms.get_cell()
pbc = self.atoms.get_pbc()
cell[1,1], cell[2,2] = cell[2,2], cell[1,1]
x = pos[:,1].copy()
z = pos[:,2].copy()
pos[:,1] = z
pos[:,2] = x
self.atoms.set_cell(cell)
self.atoms.set_positions(pos)
self.atoms.set_pbc([pbc[0], pbc[2], pbc[1]])
def plot_fig1():
mdfile = '/space/tohekorh/ShearSlide/files/LJ_10/ac_twistTaito/w=7/md_L=24_v=0.20_00.traj'
#mdfile = '/space/tohekorh/ShearSlide/files/KC_10/ac_stickTaito/w=7/r=20/md_L=145_stL=27_00.traj'
traj = PickleTrajectory(mdfile)
z_init = np.average(traj[0].positions[:, 2])
xrange = [np.min(traj[0].positions[:, 0]), np.max(traj[0].positions[:, 0])]
yrange = [np.min(traj[0].positions[:, 1]), np.max(traj[0].positions[:, 1])]
from ase.structure import graphene_nanoribbon
from ase.visualize import view
from ase import Atoms
base = graphene_nanoribbon(70,
50,
type='armchair',
saturated=False,
C_C=bond,
main_element='N')
base.rotate([1, 0, 0], np.pi / 2)
base.positions[:, 2] = z_init - 3.8
atoms_v = Atoms()
n = int(len(traj) / 1.3)
#n =
nsnap = 3
atoms_use = [traj[i] for i in np.array(range(nsnap)) * n / nsnap]
for i, atoms in enumerate(atoms_use):
atoms.positions[:, 1] = -atoms.positions[:, 1] - i * 20
#atoms.positions[:,0] = -atoms.positions[:,0]
atoms_v += atoms
cent_atoms = np.array([
np.average(atoms_v.positions[:, 0]),
np.average(atoms_v.positions[:, 1]), 0
])
cent_base = np.array([
np.average(base.positions[:, 0]),
np.average(base.positions[:, 1]), 0
])
base.translate(cent_atoms - cent_base)
#atoms_v += base
view(atoms_v, viewer='vmd')
def plot_fig1():
mdfile = '/space/tohekorh/ShearSlide/files/LJ_10/ac_twistTaito/w=7/md_L=24_v=0.20_00.traj'
#mdfile = '/space/tohekorh/ShearSlide/files/KC_10/ac_stickTaito/w=7/r=20/md_L=145_stL=27_00.traj'
traj = PickleTrajectory(mdfile)
z_init = np.average(traj[0].positions[:,2])
xrange = [np.min(traj[0].positions[:,0]), np.max(traj[0].positions[:,0])]
yrange = [np.min(traj[0].positions[:,1]), np.max(traj[0].positions[:,1])]
from ase.structure import graphene_nanoribbon
from ase.visualize import view
from ase import Atoms
base = graphene_nanoribbon(70, 50, type='armchair', saturated=False,
C_C=bond, main_element='N')
base.rotate([1,0,0], np.pi/2)
base.positions[:,2] = z_init - 3.8
atoms_v = Atoms()
n = int(len(traj)/1.3)
#n =
nsnap = 3
atoms_use = [traj[i] for i in np.array(range(nsnap))*n/nsnap]
for i, atoms in enumerate(atoms_use):
atoms.positions[:,1] = -atoms.positions[:,1] - i*20
#atoms.positions[:,0] = -atoms.positions[:,0]
atoms_v += atoms
cent_atoms = np.array([np.average(atoms_v.positions[:,0]), np.average(atoms_v.positions[:,1]), 0])
cent_base = np.array([np.average(base.positions[:,0]), np.average(base.positions[:,1]), 0])
base.translate(cent_atoms - cent_base)
#atoms_v += base
view(atoms_v, viewer = 'vmd')
'''
Created on 12.10.2015
@author: tohekorh
'''
from ase.structure import graphene_nanoribbon
from ase.visualize import view
import numpy as np
from scipy.optimize import fmin
from ase.calculators.lammpsrun import LAMMPS
from scipy.optimize import minimize
bond = 1.4
#atoms = graphene_nanoribbon(1, 1, C_C=bond, sheet=True)
atoms = graphene_nanoribbon(1, 1, type='armchair', C_C=bond, sheet=True)
atoms.rotate([1, 0, 0], -np.pi / 2, rotate_cell=True)
atoms.rotate([0, 0, 1], -np.pi / 2, rotate_cell=True)
del atoms[[0, 3]]
atoms.set_cell([[3. / 2 * bond, np.sqrt(3) / 2 * bond, 0],
[3. / 2 * bond, -np.sqrt(3) / 2 * bond, 0], [0, 0, 9]])
atoms.center()
atoms.set_pbc = [True, True, False]
def setCell(bond):
cell = np.array([[3. / 2 * bond, np.sqrt(3) / 2. * bond, 0],
[3. / 2 * bond, -np.sqrt(3) / 2. * bond, 0], [0, 0, 9.]])
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]
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]
for i, a in enumerate([gnr1, gnr2]):
@author: tohekorh
'''
from ase.structure import graphene_nanoribbon
from ase.visualize import view
import numpy as np
from scipy.optimize import fmin
from ase.calculators.lammpsrun import LAMMPS
from scipy.optimize import minimize
bond = 1.4
#atoms = graphene_nanoribbon(1, 1, C_C=bond, sheet=True)
atoms = graphene_nanoribbon(1,1, type = 'armchair', C_C=bond, sheet = True)
atoms.rotate([1,0,0], -np.pi/2, rotate_cell=True)
atoms.rotate([0,0,1], -np.pi/2, rotate_cell=True)
del atoms[[0,3]]
atoms.set_cell([[3./2*bond, np.sqrt(3)/2*bond, 0],
[3./2*bond, -np.sqrt(3)/2*bond, 0],
[0,0,9]])
atoms.center()
atoms.set_pbc = [True, True, False]
def setCell(bond):
def get_atoms(wi):
if wi % 2 == 0:
if edge == 'ac':
atoms = graphene_nanoribbon(wi / 2,
1,
type='armchair',
C_C=bond,
saturated=True)
elif edge == 'zz':
atoms = graphene_nanoribbon(wi,
1,
type='zigzag',
C_C=bond,
saturated=True)
atoms.rotate([1, 0, 0], -np.pi / 2, rotate_cell=True)
atoms.rotate([0, 0, 1], -np.pi / 2, rotate_cell=True)
else:
if edge == 'ac':
atoms = graphene_nanoribbon(wi / 2 + 1,
1,
type='armchair',
C_C=bond,
saturated=True)
elif edge == 'zz':
atoms = graphene_nanoribbon(wi + 1,
1,
type='zigzag',
C_C=bond,
saturated=True)
atoms.rotate([1, 0, 0], -np.pi / 2, rotate_cell=True)
atoms.rotate([0, 0, 1], -np.pi / 2, rotate_cell=True)
ymax = np.max(atoms.positions[:, 1])
delis, hs = [], []
for i in range(len(atoms)):
if ymax - 2 < atoms.positions[i, 1]: delis.append(i)
else:
if atoms[i].number == 1:
hs.append(i)
atoms_add = Atoms()
for h in hs:
if edge == 'ac':
add_h_vec = [0, (wi - 1) * np.sqrt(3) / 2 * bond + 2 * .943, 0]
elif edge == 'zz':
add_h_vec = [
-np.sqrt(3) / 2 * bond,
(wi * 3. / 2 - 1) * bond + 2 * 1.09, 0
]
atoms_add += Atom('H', position=atoms[h].position + add_h_vec)
del atoms[delis]
atoms += atoms_add
if edge == 'ac':
atoms.set_cell([3 * bond, np.sqrt(3) / 2 * (wi + 8) * bond, 8])
elif edge == 'zz':
atoms.set_cell([np.sqrt(3) * bond, 3 * bond * (wi * 2), 8])
ymax = np.max(atoms.positions[:, 1])
yav = np.average(atoms.positions[:, 1])
miny = 100
minyidx = 0
for i, a in enumerate(atoms):
if np.abs(a.position[1] - yav) < miny:
miny = np.abs(a.position[1] - yav)
minyidx = i
fixId = [np.where(atoms.positions == ymax)[0][0], minyidx]
atoms.set_pbc([True, False, False])
atoms.center()
#view(atoms)
return atoms, fixId
def corr_KC():
atoms = graphene_nanoribbon(1, 1, type= 'armchair', C_C=bond, saturated = False)
atoms.rotate([1,0,0], np.pi/2, rotate_cell = True)
if edge == 'ac':
atoms.rotate([0,0,1], -np.pi/2, rotate_cell = True)
del atoms[[0,3]]
trans_idx = 1
elif edge == 'zz':
del atoms[[1,0]]
trans_idx = 0
atoms.set_cell([20, 20, 10])
atoms.center()
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = 2
add_KC = KC_potential_p(params, True)
constraints = []
for i in range(len(atoms)):
fix_l = FixedLine(i, [0., 0., 1.])
constraints.append(fix_l)
constraints.append(add_KC)
lamp_parameters = get_lammps_params(H=False)
calc = LAMMPS(parameters = lamp_parameters) #, files=['lammps.data'])
atoms.set_calculator(calc)
atoms.set_constraint(constraints)
#dyn = BFGS(atoms, trajectory = 'test.traj')
#dyn.run(fmax=0.05)
#plot_posits(atoms, edge, bond)
trans_vec = trans_atomsKC(atoms.positions[trans_idx], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
init_pos = atoms.positions.copy()
r_around = init_pos[trans_idx]
#thetas = np.linspace(0, np.pi/3, 7) #, endpoint = False)
#thetas_deg = np.array([1,3,5,7,9,11,12,13,15,17,43,45,47,48,49,51,57,55,57,59])
thetas_deg = np.array([.5,1.5,2.5,3.5,4.5,5.5,6.5,7.5,8.5,9.5,10.5,11.5,12.5,13.5,14.5,15.5,16.5,17.5,18.5,19.5])
traj = PickleTrajectory(path + '%s_corr_twist_thetas_(%.1f-%.1f).traj' \
%(edge, np.min(thetas_deg),
np.max(thetas_deg)), 'w', atoms)
n = 100
for i, theta_deg in enumerate(thetas_deg):
fname = path + 'corr_%s_theta=%.2f.data' %(edge, theta_deg)
print 'Calculating theta = %.2f' %(theta_deg)
theta = theta_deg/360*np.pi*2
print 'time ' + str(datetime.now().time())
atoms.positions = init_pos
atoms.rotate([0,0,1], theta, center = r_around)
rot_init_pos = atoms.positions.copy()
lat_vec_theta1 = lat_vec1.copy()
lat_vec_theta2 = lat_vec2.copy()
trans_vec2 = lat_vec_theta2.copy()/n
data = np.zeros((n,n))
for k in range(n):
atoms.positions = rot_init_pos
atoms.translate(lat_vec_theta1*float(k)/n)
#plot_posits(atoms, edge, bond, vecs = [lat_vec_theta1, lat_vec_theta2])
print '%.1f percent done' %(100*float(k)/n)
for l in range(n):
atoms.translate(trans_vec2)
emin = get_optimal_h(atoms, len(atoms), dyn = False)[0]
data[k,l] = emin #atoms.get_potential_energy()/len(atoms) #emin #
saveAndPrint(atoms, traj, False)
header = '%s runs along x-dir, angle measured from x-axis, natoms = %i. x (Angs), e (eV/atom), hmin \n\
the lattice vectors are l1 = [%.5f, %.5f, %.5f] and l2 = [%.5f, %.5f, %.5f], they are divided in %i parts. data[i,j,:] \n\
-> atoms pos += l1/n*i + l2/n*j, initial position is such that atom1 is in middle if hexagon.' \
%(edge, len(atoms), lat_vec_theta1[0], lat_vec_theta1[1], lat_vec_theta1[2], \
lat_vec_theta2[0], lat_vec_theta2[1], lat_vec_theta2[2], n)
np.savetxt(fname, data, header = header)
from ase.optimize import QuasiNewton from ase.structure import graphene_nanoribbon from gpaw import GPAW GNR = graphene_nanoribbon(12, 1, type='zigzag', vacc=6) GNR.set_pbc((0, 0, 1)) kpts = (1, 1, 10) calc = GPAW(kpts=kpts, spinpol=True) GNR.set_calculator(calc) dyn = QuasiNewton(GNR, trajectory='ZGNR12.traj') dyn.run(fmax=0.05)
from ase.optimize import QuasiNewton from ase.structure import graphene_nanoribbon from gpaw import GPAW GNR = graphene_nanoribbon(12,1,type='zigzag', vacc=6) GNR.set_pbc((0,0,1)) kpts = (1,1,10) calc = GPAW(kpts=kpts,spinpol=True) GNR.set_calculator(calc) dyn = QuasiNewton(GNR, trajectory='ZGNR12.traj') dyn.run(fmax=0.05)
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]
for i, a in enumerate([gnr1, gnr2]):
write('gnr%d.pov' % (i + 1), a,
show_unit_cell=2, display=False, run_povray=True)
def get_atoms(wi):
if wi % 2 == 0:
if edge == 'ac':
atoms = graphene_nanoribbon(wi/2,1, type = 'armchair', C_C=bond, saturated = True)
elif edge == 'zz':
atoms = graphene_nanoribbon(wi,1, type = 'zigzag', C_C=bond, saturated = True)
atoms.rotate([1,0,0], -np.pi/2, rotate_cell=True)
atoms.rotate([0,0,1], -np.pi/2, rotate_cell=True)
else:
if edge == 'ac':
atoms = graphene_nanoribbon(wi/2 + 1, 1, type = 'armchair', C_C=bond, saturated = True)
elif edge == 'zz':
atoms = graphene_nanoribbon(wi + 1, 1, type = 'zigzag', C_C=bond, saturated = True)
atoms.rotate([1,0,0], -np.pi/2, rotate_cell=True)
atoms.rotate([0,0,1], -np.pi/2, rotate_cell=True)
ymax = np.max(atoms.positions[:,1])
delis, hs = [], []
for i in range(len(atoms)):
if ymax - 2 < atoms.positions[i,1]: delis.append(i)
else:
if atoms[i].number == 1:
hs.append(i)
atoms_add = Atoms()
for h in hs:
if edge == 'ac': add_h_vec = [0, (wi-1)*np.sqrt(3)/2*bond + 2*.943, 0]
elif edge == 'zz': add_h_vec = [-np.sqrt(3)/2*bond, (wi*3./2 - 1)*bond + 2*1.09, 0]
atoms_add += Atom('H', position=atoms[h].position + add_h_vec)
del atoms[delis]
atoms += atoms_add
if edge == 'ac':
atoms.set_cell([3*bond, np.sqrt(3)/2*(wi + 8)*bond, 8])
elif edge == 'zz':
atoms.set_cell([np.sqrt(3)*bond, 3*bond * (wi*2), 8])
ymax = np.max(atoms.positions[:,1])
yav = np.average(atoms.positions[:,1])
miny = 100
minyidx = 0
for i, a in enumerate(atoms):
if np.abs(a.position[1] - yav) < miny:
miny = np.abs(a.position[1] - yav)
minyidx = i
fixId = [np.where(atoms.positions == ymax)[0][0], minyidx]
atoms.set_pbc([True, False, False])
atoms.center()
#view(atoms)
return atoms, fixId
def corr_KC():
atoms = graphene_nanoribbon(1,
1,
type='armchair',
C_C=bond,
saturated=False)
atoms.rotate([1, 0, 0], np.pi / 2, rotate_cell=True)
if edge == 'ac':
atoms.rotate([0, 0, 1], -np.pi / 2, rotate_cell=True)
del atoms[[0, 3]]
trans_idx = 1
elif edge == 'zz':
del atoms[[1, 0]]
trans_idx = 0
atoms.set_cell([20, 20, 10])
atoms.center()
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = 2
add_KC = KC_potential_p(params, True)
constraints = []
for i in range(len(atoms)):
fix_l = FixedLine(i, [0., 0., 1.])
constraints.append(fix_l)
constraints.append(add_KC)
lamp_parameters = get_lammps_params(H=False)
calc = LAMMPS(parameters=lamp_parameters) #, files=['lammps.data'])
atoms.set_calculator(calc)
atoms.set_constraint(constraints)
#dyn = BFGS(atoms, trajectory = 'test.traj')
#dyn.run(fmax=0.05)
#plot_posits(atoms, edge, bond)
trans_vec = trans_atomsKC(atoms.positions[trans_idx], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
init_pos = atoms.positions.copy()
r_around = init_pos[trans_idx]
#thetas = np.linspace(0, np.pi/3, 7) #, endpoint = False)
#thetas_deg = np.array([1,3,5,7,9,11,12,13,15,17,43,45,47,48,49,51,57,55,57,59])
thetas_deg = np.array([
.5, 1.5, 2.5, 3.5, 4.5, 5.5, 6.5, 7.5, 8.5, 9.5, 10.5, 11.5, 12.5,
13.5, 14.5, 15.5, 16.5, 17.5, 18.5, 19.5
])
traj = PickleTrajectory(path + '%s_corr_twist_thetas_(%.1f-%.1f).traj' \
%(edge, np.min(thetas_deg),
np.max(thetas_deg)), 'w', atoms)
n = 100
for i, theta_deg in enumerate(thetas_deg):
fname = path + 'corr_%s_theta=%.2f.data' % (edge, theta_deg)
print 'Calculating theta = %.2f' % (theta_deg)
theta = theta_deg / 360 * np.pi * 2
print 'time ' + str(datetime.now().time())
atoms.positions = init_pos
atoms.rotate([0, 0, 1], theta, center=r_around)
rot_init_pos = atoms.positions.copy()
lat_vec_theta1 = lat_vec1.copy()
lat_vec_theta2 = lat_vec2.copy()
trans_vec2 = lat_vec_theta2.copy() / n
data = np.zeros((n, n))
for k in range(n):
atoms.positions = rot_init_pos
atoms.translate(lat_vec_theta1 * float(k) / n)
#plot_posits(atoms, edge, bond, vecs = [lat_vec_theta1, lat_vec_theta2])
print '%.1f percent done' % (100 * float(k) / n)
for l in range(n):
atoms.translate(trans_vec2)
emin = get_optimal_h(atoms, len(atoms), dyn=False)[0]
data[
k,
l] = emin #atoms.get_potential_energy()/len(atoms) #emin #
saveAndPrint(atoms, traj, False)
header = '%s runs along x-dir, angle measured from x-axis, natoms = %i. x (Angs), e (eV/atom), hmin \n\
the lattice vectors are l1 = [%.5f, %.5f, %.5f] and l2 = [%.5f, %.5f, %.5f], they are divided in %i parts. data[i,j,:] \n\
-> atoms pos += l1/n*i + l2/n*j, initial position is such that atom1 is in middle if hexagon.' \
%(edge, len(atoms), lat_vec_theta1[0], lat_vec_theta1[1], lat_vec_theta1[2], \
lat_vec_theta2[0], lat_vec_theta2[1], lat_vec_theta2[2], n)
np.savetxt(fname, data, header=header)
if __name__ == '__main__':
from ase import Atoms
from ase.cluster.cubic import FaceCenteredCubic
from ase.structure import graphene_nanoribbon
from ase.visualize import view
surfaces = [(1,0,0), (1,1,0)]
layers = [3,2]
nano = Atoms(FaceCenteredCubic('Pt', surfaces, layers, 4.0))
symbols = nano.get_chemical_symbols()
symbols[0] = 'Cu'
symbols[12] = 'Cu'
nano.set_chemical_symbols(symbols)
nano.pop(6)
support = graphene_nanoribbon(8, 6, type='armchair', saturated=False)
support.translate([-8,-2,-8])
nano.extend(support)
support.translate([0,-3.0,0])
nano.extend(support)
nano.center(vacuum=10)
#~ view(nano)
calc = Hybrid()
nano.set_calculator(calc)
# check subsystems selection
from ase.io import write
write('nanoparticle.pdb', calc.np_atoms)
write('support.pdb', calc.sp_atoms)
print ("Energy %f eV"% nano.get_potential_energy())