def do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY_old, theta, dtheta, \
L, thres_Z, interval, traj, M, twist, save = True):
write_line_own(mdlogf, '# Hysteresis simul begins \n', 'w')
#kink_vanis = False
y0 = atoms.positions[rend_b, 1]
i,m = 0, 0
time = 0.
while 0 < theta:
theta -= dtheta
twist.set_angle(theta)
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
deltaY = deltaY_old + atoms.positions[rend_b, 1] - y0
R = get_R(L, deltaY)
hmax = np.max(atoms.positions[:,2]) - 3.4 #subsract the height of the plane
data = [time, deltaY, R, theta, hmax, epot, ekin, epot + ekin]
#data = [i * dt, deltaY, R, theta, epot, ekin, epot + ekin]
if save:
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1 or k == 2:
stringi += '%.4f ' %d
else:
stringi += '%.12f ' %d
write_line_own(mdlogf, stringi + '\n', 'a')
print i/interval, theta / (2*np.pi) * 360, R
if np.max(atoms.positions[:,2]) < thres_Z and m == 0:
write_line_own(mdlogf, '# Kink vanish! ' + '\n', 'a')
print ' kink vanished! '
m += 1
#kink_vanis = True
if i % int(M/100) == 0: theta / (2 * np.pi) *360
#if kink_vanis: m += 1
i += 1
time += dt
def do_dynamics(mdlogf, atoms, dyn, rend_b, rend_t, v, dt, deltaY_old, theta, dtheta, \
L, thres_Z, interval, traj, M, twist, save = True):
write_line_own(mdlogf, '# Hysteresis simul begins \n', 'w')
#kink_vanis = False
y0 = atoms.positions[rend_b, 1]
i, m = 0, 0
time = 0.
while 0 < theta:
theta -= dtheta
twist.set_angle(theta)
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
deltaY = deltaY_old + atoms.positions[rend_b, 1] - y0
R = get_R(L, deltaY)
hmax = np.max(
atoms.positions[:, 2]) - 3.4 #subsract the height of the plane
data = [time, deltaY, R, theta, hmax, epot, ekin, epot + ekin]
#data = [i * dt, deltaY, R, theta, epot, ekin, epot + ekin]
if save:
stringi = ''
for k, d in enumerate(data):
if k == 0:
stringi += '%.2f ' % d
elif k == 1 or k == 2:
stringi += '%.4f ' % d
else:
stringi += '%.12f ' % d
write_line_own(mdlogf, stringi + '\n', 'a')
print i / interval, theta / (2 * np.pi) * 360, R
if np.max(atoms.positions[:, 2]) < thres_Z and m == 0:
write_line_own(mdlogf, '# Kink vanish! ' + '\n', 'a')
print ' kink vanished! '
m += 1
#kink_vanis = True
if i % int(M / 100) == 0: theta / (2 * np.pi) * 360
#if kink_vanis: m += 1
i += 1
time += dt
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)
def runAndStudy(params_set, pot_key, save = False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric= params_set['dt'], params_set['fric']
tau = params_set['tau']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
ncores = params_set['ncores']
Ld_i = params_set['Ldilde_i']
bend, straight, [matchL_idx, matchR_idx, vec], [L_bend, L_straight], [left_idxs, right_idxs]\
= create_bend_stucture(width, ratio, Ld_i, edge, bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_corrStick', width, \
L_bend, L_straight, int(T), taito, key = 'corrStick')
if relaxed:
bend = PickleTrajectory(mdrelax, 'r')[-1]
else:
relaxBend(bend, left_idxs, right_idxs, edge, bond, mdrelax)
bend.set_constraint([])
shift_v = -straight.positions[matchR_idx] + (bend.positions[matchL_idx] + vec)
straight.translate(shift_v)
atoms = bend + straight
cell = [1.5*(L_bend + L_straight), L_bend + L_straight, 20]
atoms.set_cell(cell)
atoms.positions[:,2] = 3.4
trans_vec = trans_atomsKC(straight.positions[matchR_idx], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
if edge == 'ac':
nx = int((cell[0]/5 - np.min(atoms.positions[:,0]))/(3*bond))
ny = int((cell[1]/5 - np.min(atoms.positions[:,1]))/(np.sqrt(3)*bond))
atoms.translate([nx*3.*bond, ny*np.sqrt(3)*bond, 0])
width_f = np.sqrt(3)/2.*bond*(width - 1)
elif edge == 'zz':
nx = int((cell[0]/5 - np.min(atoms.positions[:,0]))/(np.sqrt(3)*bond))
ny = int((cell[1]/5 - np.min(atoms.positions[:,1]))/(3*bond))
atoms.translate([nx*np.sqrt(3)*bond, ny*3*bond, 0])
width_f = (3./2.*width - 1)*bond
cminx, cmaxx = strip_Hend(atoms, 'right')
left_b = get_idxOfEnds(atoms, cminx, cmaxx)[0]
# CONSTRAINTS
constraints = []
constraints.append(FixAtoms(indices = left_b))
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = ncores
add_pot = KC_potential_p(params)
constraints.append(add_pot)
atoms.set_constraint(constraints)
##
# CALCULATOR
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
##
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
traj = PickleTrajectory(mdfile, 'w', atoms)
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
####
# SIMULATION PARAMS
nframes = 1000
M = int(20*tau/dt)
interval = int(M/nframes)
thres_cancel= 2*bond
stick = 'True'
xmax_idx = np.where(atoms.positions[:,0] == np.max(atoms.positions[:,0]))[0][0]
r_init = atoms.positions[xmax_idx].copy()
R = L_bend/np.pi*3.
print '# data_line: width, length bend, length tail, tail/bend, theta'
print width_f, L_bend, L_straight, L_straight/L_bend, width_f/(2*R)
# SIMULATION LOOP
for i in range(nframes):
print float(i)/nframes*100.
dyn.run(interval)
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
data = [i*interval*dt, epot, ekin, epot + ekin]
if save:
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1 or k == 2:
stringi += '%.4f ' %d
else:
stringi += '%.12f ' %d
write_line_own(mdlogfile, stringi + '\n', 'a')
#print np.linalg.norm(atoms.positions[xmax_idx] - r_init)
if thres_cancel < np.linalg.norm(atoms.positions[xmax_idx] - r_init):
stick = 'false'
break
make_stick_simul_param_file(simulfile, width, L_bend, L_straight, T, \
dt, fric, interval, M, edge, stick)
return stick == 'True'
#plot_posits(atoms, edge, bond)
#view(atoms)
def shearDyn(width, ratio, edge, save=False, force_dir_update=True):
atoms, L, W, length_int, b_idxs = create_stucture(ratio,
width,
edge,
key='rib+base')
view(atoms)
# FIXES
constraints, add_LJ, rend_b, rend_t = get_constraints(
atoms, edge, bond, b_idxs)
# END FIXES
# CALCULATOR LAMMPS
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
add = ''
if force_dir_update: add = '_ff'
mdfile, mdlogfile, mdrelax, simulfile = get_fileName('LJ', edge + add, width, \
length_int, int(T), taito)
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_LJ)
dyn = BFGS(atoms, trajectory=mdrelax)
dyn.run(fmax=0.05)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
n = 0
header = '#t [fs], shift y [Angstrom], Rad, epot_tot [eV], ekin_tot [eV], etot_tot [eV] \n'
write_line_own(mdlogfile, header, 'w')
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T * units.kB)
deltaY = 0.
eta = 1.1 # ratio between the lengths of the streched and compressed side of the ribbon.
r = L / W # length to width ratio.
deltaYMax = W / 2. * (eta + 1) / (eta - 1) * (1 - np.cos(2 * r *
(eta - 1) /
(eta + 1)))
# Estimate for the required shift
dy = v * dt
M = deltaYMax / dy
interval = int(M / 1000)
kink_formed = False
dir_vec = np.array([0., 1., 0.])
i, m = 0, 0
print 'width = %i, length = %i' % (width, length_int)
while m <= int(M / 30):
if tau < i * dt:
deltaY += dy * dir_vec[1]
for ind in rend_b:
atoms[ind].position[:] += dy * dir_vec
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
R = get_R(L, deltaY)
if force_dir_update: dir_vec = get_dir(atoms, rend_b, rend_t)
data = [i * dt, deltaY, R, epot, ekin, epot + ekin]
if save:
stringi = ''
for k, d in enumerate(data):
if k == 0:
stringi += '%.2f ' % d
elif k == 1 or k == 2:
stringi += '%.4f ' % d
else:
stringi += '%.12f ' % d
write_line_own(mdlogfile, stringi + '\n', 'a')
n += 1
if thres_Z < np.max(atoms.positions[:, 2]) and m == 0:
idxs = np.where(thres_Z < atoms.positions[:, 2])
write_line_own(mdlogfile,
'# Kink! at idxs %s' % str(idxs) + '\n', 'a')
print ' kink formed! '
kink_formed = True
if save and T != 0 and i * dt == tau:
write_line_own(mdlogfile, '# Thermalization complete. ' + '\n',
'a')
if i % int(M / 100) == 0: print str(i / int(M / 100)) + ' ~ % done'
if kink_formed: m += 1
i += 1
make_simul_param_file(simulfile, W, L, width, length_int, v, dy, T, \
dt, fric, thres_Z, interval, deltaY, M, edge)
def shearDyn(params_set, pot_key, save = False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric= params_set['dt'], params_set['fric']
tau = params_set['tau']
vmax = params_set['vmax']
vMAX = params_set['vMAX']
thres_Z = params_set['thresZ']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
atoms, L, W, length_int, b_idxs = \
create_stucture(ratio, width, edge, key = 'top', a = bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_twistRod', width, \
length_int, vmax * 1000, int(T), taito)
#view(atoms)
# FIXES
constraints, add_pot, twist, rend_b, rend_t = \
get_constraints(atoms, edge, bond, b_idxs, \
key = 'twist_p', pot = pot_key)
# END FIXES
if relaxed:
atoms = PickleTrajectory(mdrelax, 'r')[-1]
else:
trans = trans_atomsKC(atoms.positions[rend_b], edge, bond)
atoms.translate(trans)
#plot_posits(atoms, edge, bond)
# CALCULATOR LAMMPS
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_pot)
dyn = BFGS(atoms, trajectory = mdrelax)
dyn.run(fmax=0.05)
dist = np.linalg.norm(atoms.positions[rend_b] - atoms.positions[rend_t])
twist.set_dist(dist)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
y0 = atoms.positions[rend_b, 1]
kink_formed = False
kink_vanished = False
i = 0
print 'width = %i, length = %i, v=%.6f' %(width, length_int, vmax)
M_therm = int(tau / dt)
dyn.run(M_therm)
M = int(2 * L / (np.pi * dt * vmax))
M_min = int(2 * L / (np.pi * dt * vMAX))
dtheta = np.pi / 2 / M
dtheta_max = np.pi / 2 / M_min
interval = int( M / 1000 )
theta, time, m = 0., 0., 0
i_kink = 0
while 0. <= theta:
if not kink_formed:
if theta < np.pi/4:
theta += dtheta_max
else:
theta += dtheta
twist.set_angle(theta)
else:
if i_kink / 10 < m:
theta -= dtheta
twist.set_angle(theta)
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
deltaY = atoms.positions[rend_b, 1] - y0
hmax = np.max(atoms.positions[:,2]) #substract the height of the plane?
R = get_R(L, deltaY)
data = [time, deltaY, R, theta, hmax, epot, ekin, epot + ekin]
if save:
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1 or k == 2:
stringi += '%.4f ' %d
else:
stringi += '%.12f ' %d
write_line_own(mdlogfile, stringi + '\n', 'a')
if thres_Z < hmax and not kink_formed:
idxs = np.where(thres_Z < atoms.positions[:,2])
write_line_own(mdlogfile, '# Kink! at idxs %s' %str(idxs) + '\n', 'a')
print ' kink formed! ' + str(i / interval)
kink_formed = True
i_kink = i
if hmax < 3.6 and kink_formed and not kink_vanished:
write_line_own(mdlogfile, '# Kink vanished! \n', 'a')
print ' kink vanished '
kink_vanished = True
print i/interval, theta / (2*np.pi) * 360, R
if kink_formed: m += 1
i += 1
time += dt
make_simul_param_file(simulfile, W, L, width, length_int, dtheta/dt, dtheta, T, \
dt, fric, thres_Z, interval, deltaY, theta, i, edge)
return folder
def shearDyn(params_set, pot_key, save=False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric = params_set['dt'], params_set['fric']
tau = params_set['tau']
vmax = params_set['vmax']
vMAX = params_set['vMAX']
thres_Z = params_set['thresZ']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
atoms, L, W, length_int, b_idxs = \
create_stucture(ratio, width, edge, key = 'top', a = bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_twistRod', width, \
length_int, vmax * 1000, int(T), taito)
#view(atoms)
# FIXES
constraints, add_pot, twist, rend_b, rend_t = \
get_constraints(atoms, edge, bond, b_idxs, \
key = 'twist_p', pot = pot_key)
# END FIXES
if relaxed:
atoms = PickleTrajectory(mdrelax, 'r')[-1]
else:
trans = trans_atomsKC(atoms.positions[rend_b], edge, bond)
atoms.translate(trans)
#plot_posits(atoms, edge, bond)
# CALCULATOR LAMMPS
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_pot)
dyn = BFGS(atoms, trajectory=mdrelax)
dyn.run(fmax=0.05)
dist = np.linalg.norm(atoms.positions[rend_b] - atoms.positions[rend_t])
twist.set_dist(dist)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T * units.kB)
y0 = atoms.positions[rend_b, 1]
kink_formed = False
kink_vanished = False
i = 0
print 'width = %i, length = %i, v=%.6f' % (width, length_int, vmax)
M_therm = int(tau / dt)
dyn.run(M_therm)
M = int(2 * L / (np.pi * dt * vmax))
M_min = int(2 * L / (np.pi * dt * vMAX))
dtheta = np.pi / 2 / M
dtheta_max = np.pi / 2 / M_min
interval = int(M / 1000)
theta, time, m = 0., 0., 0
i_kink = 0
while 0. <= theta:
if not kink_formed:
if theta < np.pi / 4:
theta += dtheta_max
else:
theta += dtheta
twist.set_angle(theta)
else:
if i_kink / 10 < m:
theta -= dtheta
twist.set_angle(theta)
dyn.run(1)
if i % interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
deltaY = atoms.positions[rend_b, 1] - y0
hmax = np.max(
atoms.positions[:, 2]) #substract the height of the plane?
R = get_R(L, deltaY)
data = [time, deltaY, R, theta, hmax, epot, ekin, epot + ekin]
if save:
stringi = ''
for k, d in enumerate(data):
if k == 0:
stringi += '%.2f ' % d
elif k == 1 or k == 2:
stringi += '%.4f ' % d
else:
stringi += '%.12f ' % d
write_line_own(mdlogfile, stringi + '\n', 'a')
if thres_Z < hmax and not kink_formed:
idxs = np.where(thres_Z < atoms.positions[:, 2])
write_line_own(mdlogfile,
'# Kink! at idxs %s' % str(idxs) + '\n', 'a')
print ' kink formed! ' + str(i / interval)
kink_formed = True
i_kink = i
if hmax < 3.6 and kink_formed and not kink_vanished:
write_line_own(mdlogfile, '# Kink vanished! \n', 'a')
print ' kink vanished '
kink_vanished = True
print i / interval, theta / (2 * np.pi) * 360, R
if kink_formed: m += 1
i += 1
time += dt
make_simul_param_file(simulfile, W, L, width, length_int, dtheta/dt, dtheta, T, \
dt, fric, thres_Z, interval, deltaY, theta, i, edge)
return folder
def shearDyn(width, ratio, edge, save=False):
atoms, L, W, length_int, b_idxs = create_stucture(ratio,
width,
edge,
key='top')
view(atoms)
# FIXES
constraints, add_LJ, twist, rend_b, rend_t = get_constraints(atoms,
edge,
bond,
b_idxs,
key='twist')
# END FIXES
# CALCULATOR LAMMPS
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
mdfile, mdlogfile, mdrelax, simulfile = get_fileName('LJ', edge + '_twist', width, \
length_int, int(T), taito)
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_LJ)
dyn = BFGS(atoms, trajectory=mdrelax)
dyn.run(fmax=0.05)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, epot_tot [eV], \
ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T * units.kB)
y0 = atoms.positions[rend_b, 1][0]
kink_formed = False
dir_vec = np.array([0., 1., 0.])
i, m = 0, 0
interval = 20
print 'width = %i, length = %i' % (width, length_int)
M_therm = int(tau / dt)
dyn.run(M_therm)
F = 0.
while not kink_formed:
pos_0 = atoms.positions[rend_b][0]
F_vec = F * np.array([dir_vec[1], -dir_vec[0], 0.])
twist.set_F(F_vec)
dyn.run(interval)
i += interval
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
pos_1 = atoms.positions[rend_b][0]
deltaY = pos_1[1] - y0
v = np.sign(pos_1[1] - pos_0[1]) * np.linalg.norm(
(pos_1 - pos_0) / (interval * dt))
R = get_R(L, deltaY)
dir_vec = get_dir(atoms, rend_b, rend_t)
data = [
i * dt, deltaY, R, epot, ekin, epot + ekin, F_vec[0], F_vec[1],
F_vec[2]
]
#if vmax/5 < v: F -= .01
if v < vmax / 5 and not kink_formed: F += .01
print deltaY, v, F
if save:
stringi = ''
for k, d in enumerate(data):
if k == 0:
stringi += '%.2f ' % d
elif k == 1 or k == 2:
stringi += '%.4f ' % d
else:
stringi += '%.12f ' % d
write_line_own(mdlogfile, stringi + '\n', 'a')
if thres_Z < np.max(atoms.positions[:, 2]) and m == 0:
idxs = np.where(thres_Z < atoms.positions[:, 2])
write_line_own(mdlogfile, '# Kink! at idxs %s' % str(idxs) + '\n',
'a')
print ' kink formed! '
kink_formed = True
F = 0
if save and T != 0 and i * dt == tau:
write_line_own(mdlogfile, '# Thermalization complete. ' + '\n',
'a')
if i % 100 == 0: print i
if kink_formed: m += 1
make_simul_param_file(simulfile, W, L, width, length_int, v, deltaY/i, T, \
dt, fric, thres_Z, interval, deltaY, i, edge)
def shearDyn(width, edge, save = False):
ratio = 8
atoms = create_stucture(ratio, width, edge, key = 'top')
# FIXES
constraints = []
top, bot = get_topInds(atoms)
rend = get_rightInds(atoms, top)
fix_bot = FixAtoms(indices = bot)
view(atoms)
constraints.append(fix_bot)
for i in rend:
constraints.append(FixedLine(i, (1,0,0)))
# KC
params = get_params(atoms)
params['top_inds'] \
= top
add_kc = KC_potential_p(params)
constraints.append(add_kc)
# END FIXES
# CALCULATOR LAMMPS
parameters = {'pair_style':'rebo',
'pair_coeff':['* * CH.airebo C H'],
'mass' :['1 12.0', '2 1.0'],
'units' :'metal',
'boundary' :'p p f'}
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
# END CALCULATOR
# TRAJECTORY
mdfile, mdlogfile, mdrelax = get_fileName(edge, width, ratio, v, taito = False)
if save: traj = PickleTrajectory(mdfile, 'w', atoms)
else: traj = None
#data = np.zeros((M/interval, 5))
# RELAX
atoms.set_constraint(add_kc)
dyn = BFGS(atoms, trajectory = mdrelax)
dyn.run(fmax=0.05)
# FIX AFTER RELAXATION
atoms.set_constraint(constraints)
# DYNAMICS
dyn = Langevin(atoms, dt*units.fs, T*units.kB, fric)
n = 0
header = '#t [fs], d [Angstrom], epot_tot [eV], ekin_tot [eV], etot_tot [eV] \n'
log_f = open(mdlogfile, 'w')
log_f.write(header)
log_f.close()
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T*units.kB)
for i in range(0, M):
if tau < i*dt:
hw = i*dy
for ind in rend:
atoms[ind].position[1] += dy
dyn.run(1)
if i%interval == 0:
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
if T != 0:
if tau < i*dt: hw = i*dy - tau*v
else: hw = 0
else: hw = i*dy
data = [i*dt, hw, epot, ekin, epot + ekin]
if save:
log_f = open(mdlogfile, 'a')
stringi = ''
for k,d in enumerate(data):
if k == 0:
stringi += '%.2f ' %d
elif k == 1:
stringi += '%.6f ' %d
else:
stringi += '%.12f ' %d
log_f.write(stringi + '\n')
log_f.close()
n += 1
if save and T != 0 and i*dt == tau:
log_f = open(mdlogfile, 'a')
log_f.write('# Thermalization complete. ' + '\n')
log_f.close()
if 1e2 <= M:
if i%(int(M/100)) == 0: print 'ready = %.1f' %(i/(int(M/100))) + '%'
def runAndStudy(params_set, pot_key, save=False):
bond = params_set['bond']
T = params_set['T']
taito = params_set['taito']
dt, fric = params_set['dt'], params_set['fric']
tau = params_set['tau']
width = params_set['width']
ratio = params_set['ratio']
edge = params_set['edge']
ncores = params_set['ncores']
Ld_i = params_set['Ldilde_i']
bend, straight, [matchL_idx, matchR_idx, vec], [L_bend, L_straight], [left_idxs, right_idxs]\
= create_bend_stucture(width, ratio, Ld_i, edge, bond)
mdfile, mdlogfile, mdrelax, simulfile, folder, relaxed \
= get_fileName(pot_key, edge + '_corrStick', width, \
L_bend, L_straight, int(T), taito, key = 'corrStick')
if relaxed:
bend = PickleTrajectory(mdrelax, 'r')[-1]
else:
relaxBend(bend, left_idxs, right_idxs, edge, bond, mdrelax)
bend.set_constraint([])
shift_v = -straight.positions[matchR_idx] + (bend.positions[matchL_idx] +
vec)
straight.translate(shift_v)
atoms = bend + straight
cell = [1.5 * (L_bend + L_straight), L_bend + L_straight, 20]
atoms.set_cell(cell)
atoms.positions[:, 2] = 3.4
trans_vec = trans_atomsKC(straight.positions[matchR_idx], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
if edge == 'ac':
nx = int((cell[0] / 5 - np.min(atoms.positions[:, 0])) / (3 * bond))
ny = int((cell[1] / 5 - np.min(atoms.positions[:, 1])) /
(np.sqrt(3) * bond))
atoms.translate([nx * 3. * bond, ny * np.sqrt(3) * bond, 0])
width_f = np.sqrt(3) / 2. * bond * (width - 1)
elif edge == 'zz':
nx = int((cell[0] / 5 - np.min(atoms.positions[:, 0])) /
(np.sqrt(3) * bond))
ny = int((cell[1] / 5 - np.min(atoms.positions[:, 1])) / (3 * bond))
atoms.translate([nx * np.sqrt(3) * bond, ny * 3 * bond, 0])
width_f = (3. / 2. * width - 1) * bond
cminx, cmaxx = strip_Hend(atoms, 'right')
left_b = get_idxOfEnds(atoms, cminx, cmaxx)[0]
# CONSTRAINTS
constraints = []
constraints.append(FixAtoms(indices=left_b))
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = ncores
add_pot = KC_potential_p(params)
constraints.append(add_pot)
atoms.set_constraint(constraints)
##
# CALCULATOR
calc = LAMMPS(parameters=get_lammps_params())
atoms.set_calculator(calc)
##
# DYNAMICS
dyn = Langevin(atoms, dt * units.fs, T * units.kB, fric)
header = '#t [fs], shift y [Angstrom], Rad, theta [rad], hmax [A], epot_tot [eV], ekin_tot [eV], etot_tot [eV], F [eV/angst] \n'
write_line_own(mdlogfile, header, 'w')
traj = PickleTrajectory(mdfile, 'w', atoms)
if T != 0:
# put initial MaxwellBoltzmann velocity distribution
mbd(atoms, T * units.kB)
####
# SIMULATION PARAMS
nframes = 1000
M = int(20 * tau / dt)
interval = int(M / nframes)
thres_cancel = 2 * bond
stick = 'True'
xmax_idx = np.where(atoms.positions[:,
0] == np.max(atoms.positions[:,
0]))[0][0]
r_init = atoms.positions[xmax_idx].copy()
R = L_bend / np.pi * 3.
print '# data_line: width, length bend, length tail, tail/bend, theta'
print width_f, L_bend, L_straight, L_straight / L_bend, width_f / (2 * R)
# SIMULATION LOOP
for i in range(nframes):
print float(i) / nframes * 100.
dyn.run(interval)
epot, ekin = saveAndPrint(atoms, traj, False)[:2]
data = [i * interval * dt, epot, ekin, epot + ekin]
if save:
stringi = ''
for k, d in enumerate(data):
if k == 0:
stringi += '%.2f ' % d
elif k == 1 or k == 2:
stringi += '%.4f ' % d
else:
stringi += '%.12f ' % d
write_line_own(mdlogfile, stringi + '\n', 'a')
#print np.linalg.norm(atoms.positions[xmax_idx] - r_init)
if thres_cancel < np.linalg.norm(atoms.positions[xmax_idx] - r_init):
stick = 'false'
break
make_stick_simul_param_file(simulfile, width, L_bend, L_straight, T, \
dt, fric, interval, M, edge, stick)
return stick == 'True'
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)