def apply_constraints(mol_frm_tmp):
constraint_list = []
mol_indices = []
top_layer_indices = []
bottom_layer_indices = []
for atm in mol_frm_tmp:
if atm.symbol != 'Mo' and atm.symbol != 'S':
atm.position += frmwrk_com
mol_indices.append(atm.index)
else:
if atm.position[-1] > frmwrk_com[-1]:
top_layer_indices.append(atm.index)
else:
bottom_layer_indices.append(atm.index)
#Fix molecule to midpoint of bilayer
com_constraint = FixedPlane(mol_indices, [0, 0, 1])
top_layer = FixedPlane(top_layer_indices, [0, 0, 1])
bottom_layer = FixAtoms(bottom_layer_indices)
constraint_list.append(com_constraint)
constraint_list.append(top_layer)
constraint_list.append(bottom_layer)
#Set constraints
mol_frm_tmp.set_constraint(constraint_list)
return mol_frm_tmp
def get_atoms():
srf = Atoms('Cu64', [(1.2763, 1.2763, 4.0000), (3.8290, 1.2763, 4.0000),
(6.3816, 1.2763, 4.0000), (8.9343, 1.2763, 4.0000),
(1.2763, 3.8290, 4.0000), (3.8290, 3.8290, 4.0000),
(6.3816, 3.8290, 4.0000), (8.9343, 3.8290, 4.0000),
(1.2763, 6.3816, 4.0000), (3.8290, 6.3816, 4.0000),
(6.3816, 6.3816, 4.0000), (8.9343, 6.3816, 4.0000),
(1.2763, 8.9343, 4.0000), (3.8290, 8.9343, 4.0000),
(6.3816, 8.9343, 4.0000), (8.9343, 8.9343, 4.0000),
(0.0000, 0.0000, 5.8050), (2.5527, 0.0000, 5.8050),
(5.1053, 0.0000, 5.8050), (7.6580, 0.0000, 5.8050),
(0.0000, 2.5527, 5.8050), (2.5527, 2.5527, 5.8050),
(5.1053, 2.5527, 5.8050), (7.6580, 2.5527, 5.8050),
(0.0000, 5.1053, 5.8050), (2.5527, 5.1053, 5.8050),
(5.1053, 5.1053, 5.8050), (7.6580, 5.1053, 5.8050),
(0.0000, 7.6580, 5.8050), (2.5527, 7.6580, 5.8050),
(5.1053, 7.6580, 5.8050), (7.6580, 7.6580, 5.8050),
(1.2409, 1.2409, 7.6081), (3.7731, 1.2803, 7.6603),
(6.3219, 1.3241, 7.6442), (8.8935, 1.2669, 7.6189),
(1.2803, 3.7731, 7.6603), (3.8188, 3.8188, 7.5870),
(6.3457, 3.8718, 7.6649), (8.9174, 3.8340, 7.5976),
(1.3241, 6.3219, 7.6442), (3.8718, 6.3457, 7.6649),
(6.3945, 6.3945, 7.6495), (8.9576, 6.3976, 7.6213),
(1.2669, 8.8935, 7.6189), (3.8340, 8.9174, 7.5976),
(6.3976, 8.9576, 7.6213), (8.9367, 8.9367, 7.6539),
(0.0582, 0.0582, 9.4227), (2.5965, -0.2051, 9.4199),
(5.1282, 0.0663, 9.4037), (7.6808, -0.0157, 9.4235),
(-0.2051, 2.5965, 9.4199), (2.1913, 2.1913, 9.6123),
(5.0046, 2.5955, 9.4873), (7.5409, 2.5336, 9.4126),
(0.0663, 5.1282, 9.4037), (2.5955, 5.0046, 9.4873),
(5.3381, 5.3381, 9.6106), (7.8015, 5.0682, 9.4237),
(-0.0157, 7.6808, 9.4235), (2.5336, 7.5409, 9.4126),
(5.0682, 7.8015, 9.4237), (7.6155, 7.6155, 9.4317)])
c2 = Atoms('C2', [(3.2897, 3.2897, 10.6627), (4.2113, 4.2113, 10.6493)])
srf.extend(c2)
srf.pbc = (1, 1, 0)
srf.set_cell([10.2106, 10.2106, 20.6572], scale_atoms=False)
mask = [a.index < 32 for a in srf]
c1 = FixedPlane(-1, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
c2 = FixedPlane(-2, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
constraint = FixAtoms(mask=mask)
srf.set_constraint([constraint, c1, c2])
return srf
def test_siesta_zmat():
import os
from ase.calculators.siesta.siesta import Siesta
from ase.constraints import FixAtoms, FixedLine, FixedPlane
from ase import Atoms
pseudo_path = 'pseudos'
if not os.path.exists(pseudo_path): os.makedirs(pseudo_path)
# Make dummy pseudopotentials.
for symbol in 'HCO':
with open('{0}/{1}.lda.psf'.format(pseudo_path, symbol), 'w') as fd:
fd.close()
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0),
(1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = Siesta(label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.set_calculator(siesta)
siesta.write_input(atoms, properties=['energy'])
assert os.path.isfile(os.path.join(custom_dir, 'C.lda.1.psf'))
assert os.path.isfile(os.path.join(custom_dir, 'O.lda.2.psf'))
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
assert ['cartesian'] in lsl
assert ['%block', 'Zmatrix'] in lsl
assert ['%endblock', 'Zmatrix'] in lsl
assert ['MD.TypeOfRun', 'CG'] in lsl
assert any(
[line.split()[4:9] == ['0', '0', '0', '1', 'C'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '0', '2', 'O'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '1', '3', 'O'] for line in lines])
def traj(tmpdir_factory):
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
mask = [atom.tag > 1 for atom in slab]
fixlayers = FixAtoms(mask=mask)
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
slab.set_calculator(EMT())
fn = tmpdir_factory.mktemp("data").join("AlAu.traj") # see /tmp/pytest-xx
qn = QuasiNewton(slab, trajectory=str(fn))
qn.run(fmax=0.02)
return fn
def traj(tmp_path_factory):
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
mask = [atom.tag > 1 for atom in slab]
fixlayers = FixAtoms(mask=mask)
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
slab.calc = EMT()
temp_path = tmp_path_factory.mktemp("data")
trajectory = temp_path / 'AlAu.traj'
qn = QuasiNewton(slab, trajectory=str(trajectory))
qn.run(fmax=0.02)
return str(trajectory)
def slabCalculation():
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
# Make sure the structure is correct:
#from ase.visualize import view
#view(slab)
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
#print mask
fixlayers = FixAtoms(mask=mask)
# Constrain the last atom (Au atom) to move only in the yz-plane:
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
print(slab.cell / Bohr)
def test_siesta_zmat(siesta_factory):
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0),
(1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = siesta_factory.calc(label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.calc = siesta
siesta.write_input(atoms, properties=['energy'])
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
assert ['cartesian'] in lsl
assert ['%block', 'Zmatrix'] in lsl
assert ['%endblock', 'Zmatrix'] in lsl
assert ['MD.TypeOfRun', 'CG'] in lsl
assert any(
[line.split()[4:9] == ['0', '0', '0', '1', 'C'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '0', '2', 'O'] for line in lines])
assert any(
[line.split()[4:9] == ['0', '1', '1', '3', 'O'] for line in lines])
from ase.optimize import QuasiNewton
# 2x2-Al(001) surface with 3 layers and an
# Au atom adsorbed in a hollow site:
slab = fcc100('Al', size=(2, 2, 3))
add_adsorbate(slab, 'Au', 1.7, 'hollow')
slab.center(axis=2, vacuum=4.0)
# Make sure the structure is correct:
#from ase.visualize import view
#view(slab)
# Fix second and third layers:
mask = [atom.tag > 1 for atom in slab]
#print mask
fixlayers = FixAtoms(mask=mask)
# Constrain the last atom (Au atom) to move only in the yz-plane:
plane = FixedPlane(-1, (1, 0, 0))
slab.set_constraint([fixlayers, plane])
# Use EMT potential:
slab.set_calculator(EMT())
for i in range(5):
qn = QuasiNewton(slab, trajectory='mep%d.traj' % i)
qn.run(fmax=0.05)
# Move gold atom along x-axis:
slab[-1].x += slab.get_cell()[0, 0] / 8
return x_grid,y_grid,z_grid
c = []
# Read initial and final states:
initial = read_vasp('POSCAR')
pos = initial.get_positions()
ucell = initial.get_cell()
type = initial.get_chemical_symbols()
atoms = Atoms(positions=pos, symbols=type, cell=ucell, pbc=[True,True,True])
#c = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == 'Hf'])
# """Constrain an atom index *a* to move in a given plane only.
#for atom in atoms:
# c.append( FixedPlane(atom.index, ( 0, 0, 1)) )
c = [ FixedPlane( atom.index, ( 0, 0, 1) ) for atom in atoms ]
atoms.set_constraint(c)
write_vasp("OUT.vasp", atoms=atoms, vasp5=True, ignore_constraints=False)
#print (c)
fig = plt.figure()
ax = fig.add_subplot(111)
#ax.set_aspect("auto")
ax.set(xlim=(-1, 1), ylim = (-1, 1) )
a_circle = plt.Circle((23, 11.7), 2.7, alpha = 0.5,fill=False, ec='red')
a1_circle = plt.Circle((23, 11.7), 0.2,fill=False, ec='red')
ax.add_artist(a_circle)
ax.add_artist(a1_circle)
plot_atoms(atoms, ax, radii=0.5, rotation=('0x,0y,00z'))
plt.savefig("test.eps", format="eps", dpi=600)
plt.show()
benz.set_pbc(False)
tags = np.zeros_like(benz)
benz.set_tags(tags)
benz.center(vacuum=4.0)
cell = benz.get_cell()
calc = GPAW(nbands=-1,
h=h,
xc=xc,
occupations=FermiDirac(0.0),
txt=molname + '_relax.txt')
benz.set_calculator(calc)
# qn constraint
for i in range(len(benz)):
plane = FixedPlane(i, (0, 0, 1))
benz.set_constraint(plane)
qn = QuasiNewton(benz,
logfile=molname + '_relax.log',
trajectory=molname + '_relax.traj')
qn.run(fmax=0.01)
e_mol = benz.get_potential_energy()
del calc
#-------------------------------------
# mapping out the benzene dimer (T-shaped) intermolecular distance
e_array = np.zeros(20)
d_array = np.zeros(20)
(6.3976, 8.9576, 7.6213), (8.9367, 8.9367, 7.6539),
(0.0582, 0.0582, 9.4227), (2.5965, -0.2051, 9.4199),
(5.1282, 0.0663, 9.4037), (7.6808, -0.0157, 9.4235),
(-0.2051, 2.5965, 9.4199), (2.1913, 2.1913, 9.6123),
(5.0046, 2.5955, 9.4873), (7.5409, 2.5336, 9.4126),
(0.0663, 5.1282, 9.4037), (2.5955, 5.0046, 9.4873),
(5.3381, 5.3381, 9.6106), (7.8015, 5.0682, 9.4237),
(-0.0157, 7.6808, 9.4235), (2.5336, 7.5409, 9.4126),
(5.0682, 7.8015, 9.4237), (7.6155, 7.6155, 9.4317)])
c2 = Atoms('C2', [(3.2897, 3.2897, 10.6627), (4.2113, 4.2113, 10.6493)])
srf.extend(c2)
srf.pbc = (1, 1, 0)
srf.set_cell([10.2106, 10.2106, 20.6572], scale_atoms=False)
mask = [a.index < 32 for a in srf]
c1 = FixedPlane(-1, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
c2 = FixedPlane(-2, (1 / np.sqrt(2), 1 / np.sqrt(2), 1))
constraint = FixAtoms(mask=mask)
srf.set_constraint([constraint, c1, c2])
systems.append((srf, 'C2/Cu(100)'))
def create_database():
db = connect('systems.db', append=False)
for atoms, description in systems:
db.write(atoms, description=description)
if __name__ == '__main__':
create_database()
def do_one_interstitial(bulk_supercell,
bulk_supercell_pe,
interstitial_Z,
interstitial_pos,
label,
relax_radial=0.0,
relax_symm_break=0.0,
nn_cutoff=0.0,
tol=1.0e-2):
interst = bulk_supercell.copy()
interst += Atoms(numbers=[interstitial_Z], positions=[interstitial_pos])
interstitial_i = len(interst) - 1
if relax_radial != 0.0 or relax_symm_break != 0.0:
nl = NeighborList([nn_cutoff / 2.0] * len(bulk_supercell),
self_interaction=False,
bothways=True)
nl.update(bulk_supercell)
indices, offsets = nl.get_neighbors(interstitial_i)
offset_factor = relax_radial
for i, offset in zip(indices, offsets):
ri = interst.positions[interstitial_i] - (
interst.positions[i] + np.dot(offset, interst.get_cell()))
interst.positions[i] += offset_factor * ri
offset_factor += relax_symm_break
if "interstitial_constraint" in bulk_supercell.info:
(constr_type, constr_subtype
) = bulk_supercell.info["interstitial_constraint"].split()[0:2]
if constr_type == "plane":
if constr_subtype == "atoms":
indices = [
int(i) for i in
bulk_supercell.info["interstitial_constraint"].split()[2:]
]
if len(indices) != 3:
raise ValueError(
"number of indices not 3 for plane atoms '{}'".format(
bulk_supercell.info["interstitial_constraint"]))
p = interst.get_positions()
constr_normal = np.cross(p[indices[0]] - p[indices[1]],
p[indices[0]] - p[indices[2]])
elif constr_subtype == "vector":
constr_normal = np.array(
bulk_supercell.info["interstitial_constraint"].split()[2:])
else:
raise ValueError(
"unknown interstitial constraint subtype for plane '{}'".
format(bulk_supercell.info["interstitial_constraint"]))
print("setting constraint FixedPlane with normal", constr_normal)
interst.set_constraint(FixedPlane(interstitial_i, constr_normal))
else:
raise ValueError(
"unknown interstitial constraint type '{}'".format(
bulk_supercell.info["interstitial_constraint"]))
evaluate(interst)
unrelaxed_interstitial_pe = interst.get_potential_energy()
if len(set(bulk_supercell.get_atomic_numbers())) == 1:
Ebulk = float(len(interst)) / float(
len(bulk_supercell)) * bulk_supercell_pe
else:
Ebulk = bulk_supercell_pe
Ef0 = unrelaxed_interstitial_pe - Ebulk
unrelaxed_filename = run_root + "-%s-unrelaxed.xyz" % label
ase.io.write(os.path.join("..", unrelaxed_filename),
interst,
format='extxyz')
print("got unrelaxed interstitial {} cell energy".format(label),
unrelaxed_interstitial_pe)
try:
interst = relax_config(interst,
relax_pos=True,
relax_cell=False,
tol=tol,
save_traj=True,
config_label=label,
from_base_model=True,
save_config=True,
try_restart=True)
relaxed_filename = run_root + "-%s-relaxed.xyz" % label
ase.io.write(os.path.join("..", relaxed_filename),
interst,
format='extxyz')
interstitial_pe = interst.get_potential_energy()
Ef = interstitial_pe - Ebulk
print("got relaxed interstitial {} cell energy".format(label),
interstitial_pe)
except:
relaxed_filename = None
Ef = None
print("got bulk energy", Ebulk)
return (unrelaxed_filename, Ef0, relaxed_filename, Ef, interstitial_i)
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
# User inputs
input_structure = "str.cif"
atoms = read(input_structure)
maxstep = 0.1
fmaxx = 0.01
kpoints = [6, 12, 3]
gpoints = [32, 16, 72]
index = [1,1,0]
calc = GPAW(xc='BEEF-vdW', gpts=gpoints, kpts=kpoints) #symmetry={'point_group': False})
atoms.set_calculator(calc)
# Set constraints- Fix carbon atoms, move Li,F atoms only in plane normal to displacement direction given by index
constraints = []
constraints.append(FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == 'C']))
sym = atoms.get_chemical_symbols()
for i in range(len(sym)):
if sym[i] != 'C':
constraints.append(FixedPlane(i,index))
atoms.set_constraint(constraints)
atoms.calc.set(txt='bfgs.txt')
dyn=BFGS(atoms=atoms, trajectory='traj.traj', logfile = 'qn.log', maxstep=maxstep)
dyn.run(fmax=fmaxx)
atoms = bulk('NaCl', crystalstructure='rocksalt', a=5) * (2, 1, 1)
atoms.set_initial_magnetic_moments([1.1] * len(atoms))
l = SPARC(atoms=atoms,
h=0.1,
label='in1',
xc='GGA',
spin_typ=1,
pseudo_dir='.')
l.write_input(atoms=atoms, h=0.1, spin_typ=1, pseudo_dir='.', SPIN_TYP=1)
print('input writing functional')
# check reading and writing .ion files
atoms.set_constraint(
[FixAtoms([0]),
FixedLine(1, [0, 1, 0]),
FixedPlane(2, [1, 0, 0])])
write_ion(open('in1.ion', 'w'), atoms, pseudo_dir='.')
recovered_atoms = read_ion(open('in1.ion', 'r'))
assert compare_atoms(atoms, recovered_atoms) == []
calc = SPARC(atoms=atoms, pseudo_dir='.', SPIN_TYP=1)
try: # check that `h` is required
calc.write_input()
raise Exception('test failed')
except CalculatorSetupError:
pass
print('.ion reading test passed')
calc = SPARC.read('read_input')
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 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
from ase.constraints import FixAtoms, FixedLine, FixedPlane
from ase import Atoms
pseudo_path = 'pseudos'
if not os.path.exists(pseudo_path): os.makedirs(pseudo_path)
# Make dummy pseudopotentials.
for symbol in 'HCO':
with open('{0}/{1}.lda.psf'.format(pseudo_path, symbol), 'w') as fd:
fd.close()
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0), (1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = Siesta(label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.set_calculator(siesta)
def get_constraints(atoms, edge, bond, idxs, key='shear_p', pot='LJ'):
if key == 'shear':
# FIXES
constraints = []
if edge == 'zz': fixL = np.sqrt(3) * bond * .51 #1.05
if edge == 'ac': fixL = 1.01 * bond
rend_b, rend_t = get_posInds(atoms, 'redge')[1:]
lend_s, lend_h = get_posInds(atoms, 'ledge', fixL)
#view(atoms)
if idxs == None:
for i in lend_s:
constraints.append(FixedLine(i, (0, 0, 1)))
constraints.append(FixAtoms(indices=lend_h))
else:
for i in idxs:
constraints.append(FixedLine(i, (0, 0, 1)))
for i in rend_b:
constraints.append(FixedPlane(i, (0, 1, 0)))
# KC
add_LJ = LJ_potential_smooth(bond)
constraints.append(add_LJ)
# END FIXES
return constraints, add_LJ, rend_b, rend_t
elif key == 'twist_F':
# FIXES
constraints = []
if edge == 'zz': fixL = np.sqrt(3) * bond * 2.05
if edge == 'ac': fixL = 5 * bond
rend_b, rend_t = get_posInds(atoms, 'redge')[1:]
lend_s, lend_h = get_posInds(atoms, 'ledge', fixL)
#view(atoms)
if idxs == None:
for i in lend_s:
constraints.append(FixedLine(i, (0, 0, 1)))
constraints.append(FixAtoms(indices=lend_h))
else:
for i in idxs:
constraints.append(FixedLine(i, (0, 0, 1)))
# KC
add_LJ = LJ_potential_smooth(bond)
if len(rend_b) != len(rend_t) != 1: raise
twist = twist_const_F(rend_b[0], rend_t[0], np.zeros(3))
constraints.append(FixedPlane(rend_b[0], (0, 0, 1)))
constraints.append(FixedPlane(rend_t[0], (0, 0, 1)))
constraints.append(add_LJ)
constraints.append(twist)
# END FIXES
return constraints, add_LJ, twist, rend_b, rend_t
elif key == 'twist_p':
# FIXES
constraints = []
if edge == 'zz': fixL = np.sqrt(3) * bond * .51
if edge == 'ac': fixL = 1.1 * bond
rend_b, rend_t = get_posInds(atoms, 'redge')[1:]
lend_s, lend_h = get_posInds(atoms, 'ledge', fixL)
#view(atoms)
if idxs == None:
for i in lend_s:
constraints.append(FixedLine(i, (0, 0, 1)))
constraints.append(FixAtoms(indices=lend_h))
else:
for i in idxs:
constraints.append(FixedLine(i, (0, 0, 1)))
# KC
if pot == 'KC':
params = {}
params['positions'] = atoms.positions
params['chemical_symbols'] = atoms.get_chemical_symbols()
params['ia_dist'] = 10
params['edge'] = edge
params['bond'] = bond
params['ncores'] = 1
add_pot = KC_potential_p(params)
elif pot == 'LJ':
add_pot = LJ_potential_smooth(atoms, bond)
if len(rend_b) != len(rend_t) != 1: raise
#dist = np.linalg.norm(atoms.positions[rend_b[0]] - atoms.positions[rend_t[0]])
#twist = twistConst_Rod(rend_b[0], rend_t[0], dist)
twist = twistConst_Rod(atoms, 4, edge, bond)
constraints.append(FixedPlane(rend_b[0], (0, 0, 1)))
constraints.append(add_pot)
constraints.append(twist)
# END FIXES
return constraints, add_pot, twist, rend_b[0], rend_t[0]
