def test_Pt_stress_cellopt():
import numpy as np
from numpy.testing import assert_allclose
from ase.calculators.lammpsrun import LAMMPS
from ase.build import bulk
from ase.test.eam_pot import Pt_u3
from ase.constraints import ExpCellFilter
from ase.optimize import BFGS
# (For now) reuse eam file stuff from other lammps test:
pot_fn = 'Pt_u3.eam'
f = open(pot_fn, 'w')
f.write(Pt_u3)
f.close()
params = {}
params['pair_style'] = 'eam'
params['pair_coeff'] = ['1 1 {}'.format(pot_fn)]
with LAMMPS(specorder=['Pt'], files=[pot_fn], **params) as calc:
rng = np.random.RandomState(17)
atoms = bulk('Pt') * (2, 2, 2)
atoms.rattle(stdev=0.1)
atoms.cell += 2 * rng.rand(3, 3)
atoms.calc = calc
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
opt = BFGS(ExpCellFilter(atoms), trajectory='opt.traj')
for i, _ in enumerate(opt.irun(fmax=0.05)):
pass
cell1_ref = np.array([[0.16298762, 3.89912471, 3.92825365],
[4.21007577, 0.63362427, 5.04668170],
[4.42895706, 3.29171414, 0.44623618]])
assert_allclose(np.asarray(atoms.cell),
cell1_ref,
atol=1e-4,
rtol=1e-4)
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
assert i < 80, 'Expected 59 iterations, got many more: {}'.format(i)
def test_Ar_minimize_multistep():
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
F1_numer = calc.calculate_numerical_forces(ar_nc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(), F1_numer, atol=1e-4, rtol=1e-4)
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.parameters = params
# set_atoms=True to read final coordinates after minimization
calc.run(set_atoms=True)
# get final coordinates after minimization
ar_nc.set_positions(calc.atoms.positions)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815887032201,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def relaxBend(bend, left_idxs, right_idxs, edge, bond, mdrelax):
constraints = []
constraints.append(FixAtoms(indices=left_idxs))
constraints.append(FixAtoms(indices=right_idxs))
#twist = twistConst_Rod(bend, 1, edge, bond ,F = 20)
#twist.set_angle(np.pi/3 + 2./180*np.pi)
#constraints.append(twist)
add_pot = LJ_potential_smooth(bend, bond)
constraints.append(add_pot)
calc = LAMMPS(parameters=get_lammps_params())
bend.set_calculator(calc)
# END CALCULATOR
# RELAX
bend.set_constraint(constraints)
dyn = BFGS(bend, trajectory=mdrelax)
dyn.run(fmax=0.05)
def all_lmp():
all_lmp_dict = {}
species = ["H", "He"]
specie_symbol_list = " ".join(species)
masses = [
f"{i} {_Z_to_mass[_element_to_Z[species[i]]]}"
for i in range(len(species))
]
parameters = {
"command": os.environ.get("lmp"), # set up executable for ASE
"newton": "off",
"pair_style": "mgp",
"mass": masses,
}
# set up input params
for bodies in body_list:
for multihyps in multi_list:
# create ASE calc
label = f"{bodies}{multihyps}"
files = [f"{label}.mgp"]
by = "yes" if bodies == "2" else "no"
ty = "yes" if bodies == "3" else "no"
parameters["pair_coeff"] = [
f"* * {label}.mgp {specie_symbol_list} {by} {ty}"
]
lmp_calc = LAMMPS(
label=label,
keep_tmp_files=True,
tmp_dir="./tmp/",
parameters=parameters,
files=files,
specorder=species,
)
all_lmp_dict[f"{bodies}{multihyps}"] = lmp_calc
yield all_lmp_dict
del all_lmp_dict
def test_Ar_minimize():
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
from ase.optimize import LBFGS
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.calc = calc
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
assert_allclose(ar_nc.get_potential_energy(),
-0.4791815886953914,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
def test_no_data_file_wrap():
"""
If 'create_atoms' hasn't been given the appropriate 'remap yes' option,
atoms falling outside of a periodic cell are not actually created. The
lammpsrun calculator will then look at the thermo output and determine a
discrepancy the number of atoms reported compared to the length of the
ASE Atoms object and raise a RuntimeError. This problem can only
possibly arise when the 'no_data_file' option for the calculator is set
to True. Furthermore, note that if atoms fall outside of the box along
non-periodic dimensions, create_atoms is going to refuse to create them
no matter what, so you simply can't use the 'no_data_file' option if you
want to allow for that scenario.
"""
from ase.atoms import Atoms
from ase.calculators.lammpsrun import LAMMPS
# Make a periodic box and put one atom outside of it
pos = [[0.0, 0.0, 0.0], [-2.0, 0.0, 0.0]]
atoms = Atoms(symbols=["Ar"] * 2,
positions=pos,
cell=[10.0, 10.0, 10.0],
pbc=True)
# Set parameters for calculator
params = {}
params["pair_style"] = "lj/cut 8.0"
params["pair_coeff"] = ["1 1 0.0108102 3.345"]
# Don't write a data file string. This will force
# ase.calculators.lammps.inputwriter.write_lammps_in to write a bunch of
# 'create_atoms' commands into the LAMMPS input file
params["no_data_file"] = True
with LAMMPS(specorder=["Ar"], **params) as calc:
atoms.calc = calc
atoms.get_potential_energy()
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)
# https://physics.stackexchange.com/questions/250018
pair_style = 'buck/coul/long 12.0'
pair_coeff = ['1 1 3796.9 0.2603 124.90']
pair_coeff += ['2 2 1227.2 0.3214 124.90']
pair_coeff += ['1 2 4117.9 0.3048 0.0']
masses = [
'1 {}'.format(atomic_masses[atomic_numbers['Na']]),
'2 {}'.format(atomic_masses[atomic_numbers['Cl']])
]
calc = LAMMPS(
specorder=['Na', 'Cl'],
pair_style=pair_style,
pair_coeff=pair_coeff,
masses=masses,
atom_style='charge',
kspace_style='pppm 1.0e-5',
keep_tmp_files=True,
)
for a in nacl:
if a.symbol == 'Na':
a.charge = +1.
else:
a.charge = -1.
nacl.set_calculator(calc)
E = nacl.get_potential_energy()
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
from ase.optimize import LBFGS
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
calc = LAMMPS(specorder=['Ar'], **params)
ar_nc.set_calculator(calc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
dyn = LBFGS(ar_nc, force_consistent=False)
dyn.run(fmax=1E-6)
from ase.io import read, write
import numpy as np
from ase.calculators.lammpsrun import LAMMPS
from ase import units
from ase.stressbox import stressbox
import math
parameters = {
'units': 'metal',
'atom_style': 'atomic',
'boundary': 'p p p',
'pair_style': 'sw',
'pair_coeff': ['* * Si.sw Si']
}
lmp_calc = LAMMPS(parameters=parameters)
refatom = read('si_alpha_1000atoms_sw_relax.lmpdata',
format='lammps-data',
style="atomic")
patom = read('si_alpha_1000atoms_random.lmpdata',
format='lammps-data',
style="atomic")
patom.set_calculator(lmp_calc)
pstress = patom.get_cell() * 0.0
fixstrain = np.ones((3, 3))
def get_YoungAndTau3():
wis = range(
4, 120) #[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,25,28,30]
#wYt = np.zeros((len(wis), 4))
path_f = '/space/tohekorh/ShearSlide/pictures/Ytau3/%s/' % edge
wYt = np.zeros((len(wis) - len(bad_wis), 4))
j = 0
for wi in wis:
if wi not in bad_wis:
print 'width %i' % wi
atoms, fid = get_atoms(wi)
constraints = []
constraints.append(FixAtoms(indices=[0]))
for k in range(len(atoms)):
constraints.append(FixedPlane(k, [0, 0, 1]))
atoms.set_constraint(constraints)
# CALCULATOR
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
dyn = BFGS(
atoms,
logfile='/space/tohekorh/log_useless.log',
trajectory='/space/tohekorh/ShearSlide/opm_dx=%.3f_%s.traj' %
(dx, edge))
dyn.run(fmax=fmax, steps=maxSteps)
dedx = derivative(energy,
l0,
dx=dx,
n=1,
order=21,
args=(atoms, dyn))
tau = dedx / 2.
cparams.set_tau(tau)
print 'edge stress %s eV/Angst = %.3f' % (edge, tau)
qopm_l = (-2 * tau / (21 * cparams.get_w()) + 1) * l0
energy(qopm_l, atoms, dyn)
init_pos = atoms.positions.copy()
lxs_stre = np.linspace(1. * qopm_l, (1. + perVal) * qopm_l, N)
lxs_comp = np.linspace(1. * qopm_l, (1 - perVal) * qopm_l, N)
lxs = np.zeros(2 * N - 1)
energies = np.zeros(2 * N - 1)
cparams.set_w(wi)
n = 0
for lx in lxs_stre:
print lx / qopm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
atoms.positions = init_pos
for lx in lxs_comp[1:]:
print lx / qopm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
eps = (lxs - l0) / l0
atoms.positions = init_pos
e0 = energy(l0, atoms, dyn)
energies -= e0
Y_opm = curve_fit(energy_teor3, eps, energies, p0=[21])[0][:1]
l_opm = -2 * tau / (Y_opm * cparams.get_w()) * l0 + l0
eps0 = l_opm / l0 - 1
print 'Youngs mod eV/Angst2 = %.3f' % (Y_opm)
plt.scatter(eps, energies)
plt.plot(eps, 2 * tau * l0 * eps, label='tau = %.3f' % tau)
#plt.plot(eps, dedx*eps*l0, label = 'tau = %.3f' %tau)
plot_eps = np.linspace(np.min(eps), np.max(eps), 200)
plt.plot(plot_eps,
energy_teor3(plot_eps, Y_opm),
'-',
color='black',
label='fit, Y = %.3f eV/angst2' % (Y_opm))
# plt.plot([l_opm,l_opm], [-.1*np.max(energies), .1*np.max(energies)], '--',
# color = 'black', label = 'eps_opm = %.4f' %(l_opm/l0 - l0))
plt.plot([0, 0], [-.1 * np.max(energies), .1 * np.max(energies)],
'--',
color='black')
plt.plot([eps0, eps0],
[-.1 * np.max(energies), .1 * np.max(energies)],
'--',
color='black',
label='eps0 = %.5f' % (eps0))
plt.legend(frameon=False)
#plt.show()
plt.savefig(path_f + 'w=%i_dx=%.3f.png' % (wi, dx))
plt.clf()
wYt[j] = [cparams.get_w(), Y_opm, tau, eps0]
plt.scatter(wYt[:j + 1, 0],
wYt[:j + 1, 1],
label='Y',
color='black')
plt.legend(loc=2, frameon=False)
plt.twinx()
plt.plot(wYt[:j + 1, 0], wYt[:j + 1, 2], '-o', label='tau')
plt.xlabel('width')
plt.title('Young s modulus and edge stress')
plt.legend(frameon=False)
plt.savefig(path_f + 'Ytau.png')
plt.clf()
np.savetxt(path_f + 'Ytau.txt',
wYt,
header='width, Y, tau, eps_opm')
#plt.show()
j += 1
import os
from ase.calculators.lammpsrun import LAMMPS
os.environ[
"ASE_LAMMPSRUN_COMMAND"] = "/Users/Cas/gits/lammps-ace/src/lmp_serial"
model_dir = os.path.dirname(os.path.realpath(__file__))
parameters = {
'pair_style': 'pace',
'pair_coeff': ['* * Si_B8_N4_18_07_lap_dia_1.1_rep_2B+ACE.ace Si']
}
files = [os.path.join(model_dir, "Si_B8_N4_18_07_lap_dia_1.1_rep_2B+ACE.ace")]
calculator = LAMMPS(parameters=parameters, files=files)
name = "ACE"
no_checkpoint = 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)
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)
lammpsrun calculator will then look at the thermo output and determine a
discrepancy the number of atoms reported compared to the length of the
ASE Atoms object and raise a RuntimeError. This problem can only
possibly arise when the 'no_data_file' option for the calculator is set
to True. Furthermore, note that if atoms fall outside of the box along
non-periodic dimensions, create_atoms is going to refuse to create them
no matter what, so you simply can't use the 'no_data_file' option if you
want to allow for that scenario.
"""
from ase.atoms import Atoms
from ase.calculators.lammpsrun import LAMMPS
# Make a periodic box and put one atom outside of it
pos = [[0.0, 0.0, 0.0], [-2.0, 0.0, 0.0]]
atoms = Atoms(symbols=["Ar"] * 2, positions=pos, cell=[10.0, 10.0, 10.0],
pbc=True)
# Set parameters for calculator
params = {}
params["pair_style"] = "lj/cut 8.0"
params["pair_coeff"] = ["1 1 0.0108102 3.345"]
# Don't write a data file string. This will force
# ase.calculators.lammps.inputwriter.write_lammps_in to write a bunch of
# 'create_atoms' commands into the LAMMPS input file
params["no_data_file"] = True
with LAMMPS(specorder=["Ar"], **params) as calc:
atoms.calc = calc
energy = atoms.get_potential_energy()
def corr_KC(width, edge):
params0 = get_simulParams(edge)[-1]
bond = params0['bond']
'''
atoms = graphene_nanoribbon(1, 1, type= 'armchair', C_C=bond, saturated = False)
atoms.rotate([1,0,0], np.pi/2, rotate_cell = True)
atoms.rotate([0,0,1], -np.pi/2, rotate_cell = True)
atoms.set_cell([20, 20, 10])
atoms.center()
del atoms[[2,3]]
'''
atoms = create_stucture(2, width, edge, key='top', a=bond)[0]
atoms.set_cell([70, 70, 20])
atoms.center()
atoms.positions[:, 2] = 3.4
h_t = []
for i in range(len(atoms)):
if atoms[i].number == 1:
h_t.append(i)
del atoms[h_t]
#view(atoms)
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
params['no_edge_neigh'] = True
add_KC = KC_potential_p(params)
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[0], edge, bond)
atoms.translate(trans_vec)
#plot_posits(atoms, edge, bond)
#exit()
init_pos = atoms.positions.copy()
r_around = init_pos[1]
thetas = np.linspace(0, np.pi / 3, 61)
n = 15
lat_vec1 = np.array([3. / 2 * bond, np.sqrt(3) / 2 * bond, 0.])
lat_vec2 = np.array([3. / 2 * bond, -np.sqrt(3) / 2 * bond, 0.])
for i, theta in enumerate(thetas):
fname = path + 'corr_%s_theta=%.2f.data' % (edge, theta /
(2 * np.pi) * 360)
#if not os.path.isfile(fname):
print 'Calculating theta = %.2f' % (theta / (2 * np.pi) * 360)
atoms.positions = init_pos
atoms.rotate([0, 0, 1], theta, center=r_around)
R = np.array([[np.cos(theta), -np.sin(theta), 0.],
[np.sin(theta), np.cos(theta), 0.], [0., 0., 1.]])
lat_vec_theta1 = np.dot(R, lat_vec1.copy())
lat_vec_theta2 = np.dot(R, lat_vec2.copy())
#trans_vec1 = lat_vec_theta1.copy()/n
trans_vec2 = lat_vec_theta2.copy() / n
data = np.zeros((n, n))
#plot_posits(atoms, edge, bond, vecs = [lat_vec_theta1, lat_vec_theta2])
for k in range(n):
atoms.positions = init_pos
atoms.translate(lat_vec_theta1 * float(k) / n)
#plot_posits(atoms, edge, bond, vecs = [lat_vec_theta1, lat_vec_theta2])
#print trans_vec1*float(k)/n, k, n, float(k)/n
for l in range(n):
atoms.translate(trans_vec2)
emin, hmin = get_optimal_h(atoms, len(atoms), dyn=False)
#data[k,l,:] = [emin, hmin]
data[k, l] = emin #atoms.get_potential_energy()/len(atoms)
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 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))) + '%'
from ase.test.eam_pot import Pt_u3
from ase.build import fcc111
import os
pot_fn = 'Pt_u3.eam'
f = open(pot_fn, 'w')
f.write(Pt_u3)
f.close()
slab = fcc111('Pt', size=(10, 10, 5), vacuum=30.0)
params = {}
params['pair_style'] = 'eam'
params['pair_coeff'] = ['1 1 {}'.format(pot_fn)]
calc = LAMMPS(specorder=['Pt'], parameters=params, files=[pot_fn])
slab.set_calculator(calc)
E = slab.get_potential_energy()
F = slab.get_forces()
assert abs(E - -2758.63) < 1E-2
assert abs(norm(F) - 11.3167) < 1E-4
assert abs(norm(slab.positions) - 955.259) < 1E-3
params['group'] = [
'lower_atoms id ' +
' '.join([str(i + 1) for i, tag in enumerate(slab.get_tags()) if tag >= 4])
]
params['fix'] = ['freeze_lower_atoms lower_atoms setforce 0.0 0.0 0.0']
params['run'] = 100
params['timestep'] = 0.0005
def get_YoungAndTau2():
wis = range(5, 120)
path_f = '/space/tohekorh/ShearSlide/pictures/Ytau2/%s/' % edge
wYt = np.zeros((len(wis) - len(bad_wis), 5))
j = 0
fa, fb = 0.09, 0
for wi in wis:
if wi not in bad_wis:
print wi, edge
atoms, fid = get_atoms(wi)
constraints = []
constraints.append(FixAtoms(indices=[0]))
for k in range(len(atoms)):
constraints.append(FixedPlane(k, [0, 0, 1]))
#constraints.append(FixedPlane(fid[0], [0,0,1]))
#constraints.append(FixedPlane(fid[1], [0,0,1]))
atoms.set_constraint(constraints)
# CALCULATOR
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
dyn = BFGS(
atoms,
trajectory='/space/tohekorh/ShearSlide/opm_dx=%.3f_%s.traj' %
(dx, edge),
maxstep=.01,
logfile='/space/tohekorh/log_useless.log')
dyn.run(fmax=fmax, steps=10 * maxSteps)
cparams.set_w(wi)
#derivative(energy, l0, dx=dx, n=1, order=5)
#opm_l = fmin(energy, l0, xtol = 1e-6, ftol = 1e-6, args = (atoms, dyn))[0]
cont = True
cont = False
try:
#opm_l = fmin_cg(energy, l0, args=(atoms, dyn), gtol=1e-03,
# epsilon=1.4901161193847656e-03,
# full_output=0, disp=1)
#qopm_l = (-2*(-.2)/(21*cparams.get_w()) + 1)*l0
qopm_l = oneOverR(cparams.get_w(), fa, fb) * l0 + l0
#qopm_l = l0
res = minimize(energy, [qopm_l],
args=(atoms, dyn),
method='L-BFGS-B',
jac=None,
bounds=[(l0 * .995, l0 * 1.005)],
tol=None,
callback=None,
options={
'disp': None,
'iprint': -1,
'gtol': 1e-012 * wi,
'eps': 1e-04,
'maxiter': 15,
'ftol': 2.220446049250313e-09,
'maxcor': 10,
'maxfun': 100
}) #['x'][0] 'factr': 10000
'''
options={'disp': None, 'iprint': -1,
'gtol': 1e-03*wi, 'eps': 1e-04,
'maxiter': 15,
'ftol': 2.220446049250313e-09,
'maxcor': 10,
'maxfun': 100})
'''
opm_l = res['x'][0]
eopm = res['fun']
print 'number of iterations = %i' % res['nit']
init_pos = atoms.positions.copy()
cont = True
except Exception as e:
print e
if cont:
eps0 = (opm_l - l0) / l0
print wi, opm_l, l0, opm_l - l0, eps0
#qopm_l = (-2*(-.2)/(21*cparams.get_w()) + 1)*l0
lxs_stre = np.linspace(1. * opm_l, (1. + perVal) * opm_l, N)
lxs_comp = np.linspace(1. * opm_l, (1 - perVal) * opm_l, N)
lxs = np.zeros(2 * N - 1)
energies = np.zeros(2 * N - 1)
cparams.set_eps0(eps0)
n = 0
for lx in lxs_stre:
print lx / opm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
atoms.positions = init_pos
for lx in lxs_comp[1:]:
print lx / opm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
#min_e = energy(opm_l, atoms, dyn)
energies = energies - np.min(energies) #- min_e
eps = (lxs - l0) / l0
Y_opm = curve_fit(energy_teor2, eps, energies, p0=[21])[0][:1]
tau = -Y_opm * cparams.get_w() * eps0 / 2
tau2 = (eopm - energy(l0, atoms, dyn)) / (eps0 * l0)
plt.scatter(eps, energies)
plt.plot([eps0, eps0],
[-.1 * np.max(energies), .1 * np.max(energies)],
'--',
color='black',
label='eps_opm = %.4f' % eps0)
plot_eps = np.linspace(np.min(eps), np.max(eps), 200)
plt.plot(
plot_eps,
energy_teor(plot_eps, Y_opm, eps0),
'-',
color='black',
label='fit, Y = %.3f eV/angst2, \n tau = %.3f eV/Angst' %
(Y_opm, tau))
plt.legend(frameon=False)
plt.xlabel('eps')
plt.ylabel('energy eV')
plt.title('Energy and sheet elasticity fit to it')
wYt[j] = [cparams.get_w(), Y_opm, tau, eps0, tau2]
plt.savefig(path_f + 'w=%i.png' % wi)
plt.clf()
#plt.show()
if j > 2:
fa, fb = curve_fit(oneOverR,
wYt[:j, 0],
wYt[:j, 3],
p0=[1, 0])[0][:2]
#if j%5 == 0:
# plt.scatter(wYt[:j,0], wYt[:j,3])
# plt.plot(wYt[:j,0], oneOverR(wYt[:j,0], fa, fb))
# plt.show()
#print fa, fb
plt.scatter(wYt[:j + 1, 0],
wYt[:j + 1, 1],
label='Y',
color='black')
plt.legend(loc=2, frameon=False)
plt.twinx()
plt.plot(wYt[:j + 1, 0], wYt[:j + 1, 2], '-o', label='tau')
plt.plot(wYt[:j + 1, 0], wYt[:j + 1, 4], '-o', label='tau2')
plt.xlabel('width')
plt.title('Young s modulus and edge stress')
plt.legend(frameon=False)
plt.savefig(path_f + 'Ytau.png')
plt.clf()
#np.savetxt(path_f + 'Ytau.txt', wYt,
# header = 'width, Y, tau, eps_opm')
j += 1
def get_YoungAndTau():
wis = range(5, 120)
wYt = np.zeros((len(wis) - len(bad_wis), 4))
j = 0
for wi in wis:
if wi not in bad_wis:
print wi, edge
atoms, fid = get_atoms(wi)
constraints = []
constraints.append(FixAtoms(indices=[0]))
for k in range(len(atoms)):
constraints.append(FixedPlane(k, [0, 0, 1]))
#constraints.append(FixedPlane(fid[0], [0,0,1]))
#constraints.append(FixedPlane(fid[1], [0,0,1]))
atoms.set_constraint(constraints)
# CALCULATOR
calc = LAMMPS(parameters=parameters)
atoms.set_calculator(calc)
dyn = BFGS(
atoms,
trajectory='/space/tohekorh/ShearSlide/opm_dx=%.3f_%s.traj' %
(dx, edge),
maxstep=.01,
logfile='/space/tohekorh/log_useless.log')
dyn.run(fmax=fmax, steps=10 * maxSteps)
qopm_l = (-2 * (-.2) / (21 * cparams.get_w()) + 1) * l0
energy(qopm_l, atoms, dyn)
init_pos = atoms.positions.copy()
lxs_stre = np.linspace(1. * qopm_l, (1. + perVal) * qopm_l, N)
lxs_comp = np.linspace(1. * qopm_l, (1 - perVal) * qopm_l, N)
lxs = np.zeros(2 * N - 1)
energies = np.zeros(2 * N - 1)
cparams.set_w(wi)
n = 0
for lx in lxs_stre:
print lx / qopm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
atoms.positions = init_pos
for lx in lxs_comp[1:]:
print lx / qopm_l
energies[n] = energy(lx, atoms, dyn)
lxs[n] = lx
n += 1
energies = energies - np.min(energies)
eps = (lxs - l0) / l0
Y_opm, eps0 = curve_fit(energy_teor,
eps,
energies,
p0=[21, qopm_l / l0 - 1])[0][:2]
tau = -Y_opm * cparams.get_w() * eps0 / 2.
plt.scatter(eps, energies)
plt.plot([eps0, eps0],
[-.1 * np.max(energies), .1 * np.max(energies)],
'--',
color='black',
label='eps_opm = %.4f' % eps0)
plot_eps = np.linspace(np.min(eps), np.max(eps), 200)
plt.plot(plot_eps,
energy_teor(plot_eps, Y_opm, eps0),
'-',
color='black',
label='fit, Y = %.3f eV/angst2, \n tau = %.3f eV/Angst' %
(Y_opm, tau))
plt.legend(frameon=False)
plt.xlabel('eps')
plt.ylabel('energy eV')
plt.title('Energy and sheet elasticity fit to it')
wYt[j] = [cparams.get_w(), Y_opm, tau, eps0]
plt.savefig(
'/space/tohekorh/ShearSlide/pictures/Ytau/%s/w=%i.png' %
(edge, wi))
plt.clf()
#plt.show()
plt.scatter(wYt[:j + 1, 0],
wYt[:j + 1, 1],
label='Y',
color='black')
plt.legend(loc=2, frameon=False)
plt.twinx()
plt.plot(wYt[:j + 1, 0], wYt[:j + 1, 2], '-o', label='tau')
plt.xlabel('width')
plt.title('Young s modulus and edge stress')
plt.legend(frameon=False)
plt.savefig(
'/space/tohekorh/ShearSlide/pictures/Ytau/%s/Ytau.png' % edge)
plt.clf()
np.savetxt('/space/tohekorh/ShearSlide/pictures/Ytau/%s/Ytau.txt' %
edge,
wYt,
header='width, Y, tau, eps_opm')
j += 1
def calc(self, **kwargs):
from ase.calculators.lammpsrun import LAMMPS
return LAMMPS(command=self.executable, **kwargs)
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(width, edge):
#width = 5
#edge = 'ac'
params0 = get_simulParams(edge)[-1]
bond = params0['bond']
atoms = create_stucture(1, width, edge, key='top', a=bond)[0]
atoms.set_cell([40, 40, 20])
atoms.center()
atoms.positions[:, 2] = 3.4
h_t = []
for i in range(len(atoms)):
if atoms[i].number == 1:
h_t.append(i)
del atoms[h_t]
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)
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)
trans_vec = trans_atomsKC(atoms.positions[0], edge, bond)
atoms.translate(trans_vec)
init_pos = atoms.positions.copy()
middle = [
np.average(init_pos[:, 0]),
np.average(init_pos[:, 1]),
np.average(init_pos[:, 2])
]
thetas = np.linspace(np.pi / 2, np.pi, 91)
L = 4 * bond
ds = .05
n = int(L / ds)
for i, theta in enumerate(thetas):
fname = path + 'corr_w=%02d_%s_theta=%.2f.data' % (width, edge, theta /
(2 * np.pi) * 360)
if not os.path.isfile(fname):
print 'Calculating w=%i, theta = %.2f' % (width, theta /
(2 * np.pi) * 360)
atoms.positions = init_pos
atoms.rotate([0, 0, 1], theta, center=middle)
trans_vec = np.array([-np.sin(theta), np.cos(theta), 0])
data = np.zeros((n, 3))
for j in range(n):
atoms.translate(ds * trans_vec)
emin, hmin = get_optimal_h(atoms, len(atoms), dyn=False)
data[j, :] = [j * ds, emin, hmin]
#plot_posits(atoms, edge, bond)
header = '%s runs along x-dir, angle measured from x-axis, natoms = %i. x (Angs), e (eV/atom), hmin' % (
edge, len(atoms))
np.savetxt(fname, data, header=header)
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
from numpy.testing import assert_allclose
from ase.calculators.lammpsrun import LAMMPS
from ase.build import bulk
from ase.test.eam_pot import Pt_u3
from ase.constraints import ExpCellFilter
from ase.optimize import BFGS
# (For now) reuse eam file stuff from other lammps test:
pot_fn = 'Pt_u3.eam'
f = open(pot_fn, 'w')
f.write(Pt_u3)
f.close()
params = {}
params['pair_style'] = 'eam'
params['pair_coeff'] = ['1 1 {}'.format(pot_fn)]
calc = LAMMPS(specorder=['Pt'], files=[pot_fn], **params)
rng = np.random.RandomState(17)
atoms = bulk('Pt') * (2, 2, 2)
atoms.rattle(stdev=0.1)
atoms.cell += 2 * rng.rand(3, 3)
atoms.calc = calc
assert_allclose(atoms.get_stress(),
calc.calculate_numerical_stress(atoms),
atol=1e-4,
rtol=1e-4)
opt = BFGS(ExpCellFilter(atoms), trajectory='opt.traj')
for i, _ in enumerate(opt.irun(fmax=0.05)):
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.linalg import norm
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['mass'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
calc = LAMMPS(specorder=['Ar'], parameters=params)
ar_nc.set_calculator(calc)
E = ar_nc.get_potential_energy()
F = ar_nc.get_forces()
assert abs(E - -0.47) < 1E-2
assert abs(norm(F) - 0.0574) < 1E-4
assert abs(norm(ar_nc.positions) - 23.588) < 1E-3
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.params = params
# set_atoms=True to read final coordinates after minimization
calc.run(set_atoms=True)
#!/usr/bin/env python3
import os, wget
from ase import Atom, Atoms
from ase.build import bulk
from ase.calculators.lammpsrun import LAMMPS #基于文件的ASE计算器
from ase.calculators.lammpslib import LAMMPSlib #基于LAMMPS原生的Python接口
# 势函数下载
url = "https://openkim.org/files/MO_418978237058_005/NiAlH_jea.eam.alloy"
pot_fname = wget.filename_from_url(url)
if not os.path.exists(pot_fname):
pot_fname = wget.download(url)
# 模型构建
Ni = bulk('Ni', cubic=True)
H = Atom('H', position=Ni.cell.diagonal() / 2)
NiH = Ni + H
NiH.pbc = True
# 开始计算
lammps = LAMMPS(files=[pot_fname],
parameters={
'pair_style': 'eam/alloy',
'pair_coeff': ['* * {} H Ni'.format(pot_fname)]
})
lammps.set(command="/usr/bin/lmp")
NiH.calc = lammps
print("Energy ", NiH.get_potential_energy())
from ase import Atoms, Atom
from ase.calculators.lammpsrun import LAMMPS
a = [6.5, 6.5, 7.7]
d = 2.3608
NaCl = Atoms([Atom('Na', [0, 0, 0]), Atom('Cl', [0, 0, d])], cell=a, pbc=True)
calc = LAMMPS(tmp_dir='./', keep_tmp_files=True)
NaCl.set_calculator(calc)
print NaCl.get_stress()
def LAMMPSRunCalculator(model_name, model_type, supported_species, options,
debug, **kwargs):
"""
Used for Portable Models or LAMMPS Simulator Models if specifically requested
"""
def get_params(model_name, supported_units, supported_species, atom_style):
"""
Extract parameters for LAMMPS calculator from model definition lines.
Returns a dictionary with entries for "pair_style" and "pair_coeff".
Expects there to be only one "pair_style" line. There can be multiple
"pair_coeff" lines (result is returned as a list).
"""
parameters = {}
# In case the SM supplied its own atom_style in its model-init -- only needed
# because lammpsrun writes data files and needs to know the proper format
if atom_style:
parameters["atom_style"] = atom_style
# Set units to prevent them from defaulting to metal
parameters["units"] = supported_units
parameters["model_init"] = [
"kim_init {} {}{}".format(model_name, supported_units, os.linesep)
]
parameters["kim_interactions"] = "kim_interactions {}{}".format(
(" ").join(supported_species), os.linesep)
# For every species in "supported_species", add an entry to the
# "masses" key in dictionary "parameters".
parameters["masses"] = []
for i, species in enumerate(supported_species):
if species not in atomic_numbers:
raise KIMCalculatorError(
"Could not determine mass of unknown species "
"{} listed as supported by model".format(species))
massstr = str(
convert(
atomic_masses[atomic_numbers[species]],
"mass",
"ASE",
supported_units,
))
parameters["masses"].append(str(i + 1) + " " + massstr)
return parameters
options_not_allowed = [
"parameters", "files", "specorder", "keep_tmp_files"
]
_check_conflict_options(options,
options_not_allowed,
simulator="lammpsrun")
# If no atom_style kwarg is passed, lammpsrun will default to atom_style atomic,
# which is what we want for KIM Portable Models
atom_style = kwargs.get("atom_style", None)
# Simulator Models will supply their own units from their metadata. For Portable
# Models, we use "metal" units.
supported_units = kwargs.get("supported_units", "metal")
# Set up kim_init and kim_interactions lines
parameters = get_params(model_name, supported_units, supported_species,
atom_style)
return LAMMPS(**parameters,
specorder=supported_species,
keep_tmp_files=debug,
**options)
from ase.calculators.lammpsrun import LAMMPS
from ase.cluster.icosahedron import Icosahedron
from ase.data import atomic_numbers, atomic_masses
from numpy.testing import assert_allclose
ar_nc = Icosahedron('Ar', noshells=2)
ar_nc.cell = [[300, 0, 0], [0, 300, 0], [0, 0, 300]]
ar_nc.pbc = True
params = {}
params['pair_style'] = 'lj/cut 8.0'
params['pair_coeff'] = ['1 1 0.0108102 3.345']
params['masses'] = ['1 {}'.format(atomic_masses[atomic_numbers['Ar']])]
with LAMMPS(specorder=['Ar'], **params) as calc:
ar_nc.set_calculator(calc)
F1_numer = calc.calculate_numerical_forces(ar_nc)
assert_allclose(ar_nc.get_potential_energy(),
-0.468147667942117,
atol=1e-4,
rtol=1e-4)
assert_allclose(ar_nc.get_forces(),
calc.calculate_numerical_forces(ar_nc),
atol=1e-4,
rtol=1e-4)
params['minimize'] = '1.0e-15 1.0e-6 2000 4000' # add minimize
calc.parameters = params
# set_atoms=True to read final coordinates after minimization