from ase.io import read, PickleTrajectory
from ase.lattice import bulk
from ase.calculators.emt import EMT
a0 = 3.52 / np.sqrt(2)
c0 = np.sqrt(8 / 3.0) * a0
print '%.4f %.3f' % (a0, c0 / a0)
for i in range(3):
traj = PickleTrajectory('Ni.traj', 'w')
eps = 0.01
for a in a0 * np.linspace(1 - eps, 1 + eps, 4):
for c in c0 * np.linspace(1 - eps, 1 + eps, 4):
ni = bulk('Ni', 'hcp', a=a, covera=c / a)
ni.set_calculator(EMT())
ni.get_potential_energy()
traj.write(ni)
traj.close()
configs = read('Ni.traj@:')
energies = [config.get_potential_energy() for config in configs]
ac = [(config.cell[0, 0], config.cell[2, 2]) for config in configs]
from ase.optimize import polyfit
p = polyfit(ac, energies, 2)
from scipy.optimize import fmin_bfgs
a0, c0 = fmin_bfgs(p, (a0, c0))
print '%.4f %.3f' % (a0, c0 / a0)
assert abs(a0 - 2.466) < 0.001
assert abs(c0 / a0 - 1.632) < 0.005
def sphereDynamics(R, T, params):
d = params['d'] #2.934
nk = params['nk'] #20
fmax = params['fmax'] #1E-2
fric = params['fric'] #0.002 # equilibration time tau = 10 fs/fric (= mdsteps*dt)
dt = params['dt'] #5.0
mdsteps = params['mdsteps'] #int(10/fric/dt)
path = params['path'] #'/space/tohekorh/Au_bend/files/'
uzsize = params['uz_size']
print 'radius',R
name = '%.1f' %R
# ATOMS
#atoms = fcc111('Au',size=uzsize,a=np.sqrt(2)*d)
atoms = get_opmAtomsFlat(T, params)
atoms.rotate((0,0,1), -np.pi/6, rotate_cell = True)
length1 = np.linalg.norm( atoms.get_cell()[0] )
length2 = np.linalg.norm( atoms.get_cell()[1] )
n1 = ( np.cos(np.pi/3), np.sin(np.pi/3), 0)
n2 = (-np.cos(np.pi/3), np.sin(np.pi/3), 0)
angle1 = length1/R
angle2 = length2/R
#view(atoms)
# Scale the atoms close to ball
Lx = np.linalg.norm(atoms.get_cell()[0] + atoms.get_cell()[1])
Ly = np.linalg.norm(atoms.get_cell()[0] - atoms.get_cell()[1])
phi_max = Ly/R
theta_max = Lx/R
for a in atoms:
r0 = a.position
phi = r0[1]/Ly*phi_max
theta = r0[0]/Lx*theta_max
a.position[0] = R*np.sin(theta) #*np.sin(theta)
a.position[1] = R*np.sin(phi) #a.position[1] #R*np.sin(phi) #*np.sin(theta)
a.position[2] = R*np.cos(theta)
#atoms.translate((0,0,R))
# End scaling
atoms = Atoms(atoms=atoms,container='Sphere')
atoms.set_container(angle1=angle1,angle2=angle2,n1=n1,n2=n2,mode=4)
#view(atoms.extended_copy((2,2,1)))
# FOLDERS
path_md = path + 'sphere/md_data/T=%.0f/' %T
path_opm= path + 'sphere/opm/T=%.0f/' %T
checkAndCreateFolder(path_md)
checkAndCreateFolder(path_opm)
# CALCULATOR
calc = Hotbit(SCC=False, kpts=(nk,nk,1),txt= path_opm + 'optimization_%s.cal' %name,)
atoms.set_calculator(calc)
# RELAX
opt = BFGS(atoms, trajectory= path_opm + 'optimization_%s.traj' %name)
opt.run(fmax=fmax,steps=1000)
#write(path_opm + 'opm_structure_R%.3f' %R, atoms, format='traj')
# DYNAMICS
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R, 'w', atoms)
dyn = Langevin(atoms, dt*units.fs, units.kB*T,fric)
dyn.attach(MDLogger(dyn, atoms, path_md + 'md_R%.3f.log' %R, header=True, stress=False,
peratom=True, mode="w"), interval = 1)
dyn.attach(traj.write)
dyn.run(mdsteps)
traj.close()
# load the dynamics back.. To write the extended trajectory
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R)
trajToExtTraj(traj, (2, 2, 1), R, T, angle1, angle2, n1, n2, path)
def cylinderDynamics(R, T, params):
nk = params['nk'] #20
fmax = params['fmax'] #1E-2
fric = params['fric'] #0.002
dt = params['dt'] #5.0
mdsteps = params['mdsteps'] #int(10/fric/dt)
path = params['path'] #'/space/tohekorh/Au_bend/files/'
print 'radius',R, '\n'
name = '%.1f' %R
# Get the optimal flat atoms , unit-cell config for this temperature:
atoms = get_opmAtomsFlat(T, params)
# Take the diagonal of the cell:
L = atoms.get_cell().diagonal()
atoms.set_cell(L)
# The wedge angle is:
angle = L[1]/R
# fiddle with atoms:
atoms.rotate('y', np.pi/2)
atoms.translate((-atoms[0].x, 0, 0) )
#view(atoms)
# Initial map for atoms, to get the on surface of cylinder:
phi_max = angle
for a in atoms:
r0 = a.position
phi = r0[1]/L[1]*phi_max
a.position[0] = R*np.cos(phi)
a.position[1] = R*np.sin(phi)
#view(atoms)
# proper number of kappa points in angle direction, if angle >= 2*pi/3 the use genuine
# physical boundary conditions and proper kappa-points. With 64 atoms in unit cell souhld not
# happen as the radius -> very small if angle = 2*pi/3 or larger.
# Check that the unit-cell angle is 2*pi/integer. This can be removed!
if (2*np.pi/angle)%1 > 0:
raise
# This does not have any effect unless angle >= 2*pi/3:
m = int(round(2*np.pi/angle))
physical = False
if m <= 3:
nk1 = m
physical = True
else:
nk1 = nk
# Set up the wedge container:
atoms = Atoms(atoms = atoms, container = 'Wedge')
atoms.set_container(angle = angle, height = L[0], physical = physical, pbcz = True)
# Check that everything looks good:
#view(atoms.extended_copy((2,1,2)))
# FOLDERS
path_opm = path + 'cylinder/opm/T=%.0f/' %T
path_md = path + 'cylinder/md_data/T=%.0f/' %T
checkAndCreateFolder(path_opm)
checkAndCreateFolder(path_md)
# CALCULATOR
calc = Hotbit(SCC=False, kpts=(nk1, 1, nk), physical_k = physical, \
txt= path_opm + 'optimization_%s.cal' %name)
atoms.set_calculator(calc)
# RELAX
opt = BFGS(atoms, trajectory= path_opm + 'optimization_%s.traj' %name)
opt.run(fmax=fmax, steps=1000)
# DYNAMICS
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R,'w',atoms)
# Perform dynamics
dyn = Langevin(atoms, dt*units.fs, units.kB*T, fric)
dyn.attach(MDLogger(dyn, atoms, path_md + 'md_R%.3f.log' %R, header=True, stress=False,
peratom=True, mode="w"), interval = 1)
dyn.attach(traj.write)
dyn.run(mdsteps)
traj.close()
# load the dynamics back, to make exteded trajectory:
traj = PickleTrajectory(path_md + 'md_R%.3f.traj' %R)
trajToExtTraj(traj, (2, 1, 2), R, T, angle, L[0], path)
