def __call__(self, *args):
if os.path.exists(self.fn):
print 'Reading configuration from checkpoint file %s...' % self.fn
a = io.read(self.fn)
else:
a = self.func(*args)
io.write(self.fn, a)
return a
def __call__(self, *args):
if os.path.exists(self.fn):
print 'Reading configuration from checkpoint file %s...' % self.fn
a = io.read(self.fn)
else:
a = self.func(*args)
io.write(self.fn, a)
return a
def test_no_pbc_small_cell(self):
a = io.read('aC.cfg')
a.set_calculator(Tersoff())
a.set_pbc(False)
e1 = a.get_potential_energy()
i1, j1, r1 = a.calc.nl.get_neighbors(a.calc.particles)
a.set_cell(a.cell*0.9, scale_atoms=False)
e2 = a.get_potential_energy()
self.assertAlmostEqual(e1, e2)
i2, j2, r2 = a.calc.nl.get_neighbors(a.calc.particles)
for k in range(len(a)):
neigh1 = np.array(sorted(j1[i1==k]))
neigh2 = np.array(sorted(j2[i2==k]))
self.assertTrue(np.all(neigh1 == neigh2))
def test_pbc_shift_by_multiple_cells(self):
a = io.read('aC.cfg')
a.set_calculator(Tersoff())
e1 = a.get_potential_energy()
i1, j1, r1 = a.calc.nl.get_neighbors(a.calc.particles)
a[100].position += 3*a.cell[0]
e2 = a.get_potential_energy()
i2, j2, r2 = a.calc.nl.get_neighbors(a.calc.particles)
for i in range(len(a)):
n1 = np.array(sorted(j1[i1==i]))
n2 = np.array(sorted(j2[i2==i]))
if np.any(n1 != n2):
print(i, n1, n2)
a[100].position += a.cell.T.dot([1,3,-4])
e3 = a.get_potential_energy()
self.assertAlmostEqual(e1, e2)
self.assertAlmostEqual(e1, e3)
def test_neighbor_list(self):
a = io.read('aC.cfg')
an = native.from_atoms(a)
nl = native.Neighbors(100)
nl.request_interaction_range(5.0)
i, j, abs_dr_no_vec = nl.get_neighbors(an)
i, j, dr, abs_dr = nl.get_neighbors(an, vec=True)
self.assertTrue(np.all(np.abs(abs_dr_no_vec-abs_dr) < 1e-12))
r = a.get_positions()
dr_direct = mic(r[i]-r[j], a.cell)
abs_dr_from_dr = np.sqrt(np.sum(dr*dr, axis=1))
abs_dr_direct = np.sqrt(np.sum(dr_direct*dr_direct, axis=1))
self.assertTrue(np.all(np.abs(abs_dr-abs_dr_from_dr) < 1e-12))
self.assertTrue(np.all(np.abs(abs_dr-abs_dr_direct) < 1e-12))
self.assertTrue(np.all(np.abs(dr-dr_direct) < 1e-12))
nbins = int(value)
elif key == '--cutoff':
cutoff = float(value)
elif key == '--avgn':
avgn = int(value)
###
print '# fn = ', fn
print '# nbins = ', nbins
print '# cutoff = ', cutoff
print '# avgn = ', avgn
###
a = read(fn)
print '{0} atoms.'.format(len(a))
p = native.from_atoms(a)
nl = native.neighbor_list(p, cutoff, avgn=avgn)
i, j, dr, abs_dr = nl.get_neighbors(p, vec=True)
pavg, pvar = native.pair_distribution(i, abs_dr, nbins, cutoff)
r = np.linspace(0.0, cutoff, nbins + 1)
r = (r[1:] + r[:-1]) / 2
rho = len(a) / a.get_volume()
np.savetxt('g2.out', np.transpose([r, pavg, pvar, pavg / rho]))
rho = np.sum(a.get_masses()) / a.get_volume()
(opt, args) = parser.parse_args()
###
convlen = None
if opt.toA:
convlen = ase.units.Bohr
elif opt.toBohr:
convlen = 1.0 / ase.units.Bohr
infn = args[0]
outfn = args[1]
a = io.read(infn)
if 'shear_dx' in a.info:
cx, cy, cz = a.cell
assert abs(cx[1]) < 1e-12
assert abs(cx[2]) < 1e-12
assert abs(cy[0]) < 1e-12
assert abs(cy[2]) < 1e-12
assert abs(cz[0]) < 1e-12
assert abs(cz[1]) < 1e-12
dx, dy, dz = a.info['shear_dx']
sx, sy, sz = a.cell.diagonal()
a.set_cell([[sx, 0, 0], [0, sy, 0], [dx, dy, sz]], scale_atoms=False)
if opt.cell is not None:
cell = map(float, opt.cell.split(','))
nbins = int(value)
elif key == '--cutoff':
cutoff = float(value)
elif key == '--avgn':
avgn = int(value)
###
print '# fn = ', fn
print '# nbins = ', nbins
print '# cutoff = ', cutoff
print '# avgn = ', avgn
###
a = read(fn)
print '{0} atoms.'.format(len(a))
p = native.from_atoms(a)
nl = native.neighbor_list(p, cutoff, avgn=avgn)
i, j, dr, abs_dr = nl.get_neighbors(p, vec=True)
pavg, pvar = native.pair_distribution(i, abs_dr, nbins, cutoff)
r = np.linspace(0.0, cutoff, nbins+1)
r = (r[1:]+r[:-1])/2
rho = len(a)/a.get_volume()
np.savetxt('g2.out', np.transpose([r, pavg, pvar, pavg/rho]))
rho = np.sum(a.get_masses())/a.get_volume()
assert len(args) == 1
infn = args[0]
for key, value in optlist:
if key == '--pot':
potstr = value
elif key == '--fmax':
fmax = float(value)
elif key == '--outfn':
outfn = value
###
print '# infn = ', infn
print '# outfn = ', outfn
print '# pot = ', potstr
print '# fmax = ', fmax
###
a = read(infn)
print '{0} atoms.'.format(len(a))
potclass = getattr(atomistica, potstr)
a.set_calculator(potclass())
FIRE(a).run(fmax=fmax)
write(outfn, a)
assert len(args) == 1
infn = args[0]
for key, value in optlist:
if key == '--pot':
potstr = value
elif key == '--fmax':
fmax = float(value)
elif key == '--outfn':
outfn = value
###
print '# infn = ', infn
print '# outfn = ', outfn
print '# pot = ', potstr
print '# fmax = ', fmax
###
a = read(infn)
print '{0} atoms.'.format(len(a))
potclass = getattr(atomistica, potstr)
a.set_calculator(potclass())
FIRE(a).run(fmax=fmax)
write(outfn, a)
(opt, args) = parser.parse_args()
###
convlen = None
if opt.toA:
convlen = ase.units.Bohr
elif opt.toBohr:
convlen = 1.0/ase.units.Bohr
infn = args[0]
outfn = args[1]
a = io.read(infn)
if 'shear_dx' in a.info:
cx, cy, cz = a.cell
assert abs(cx[1]) < 1e-12
assert abs(cx[2]) < 1e-12
assert abs(cy[0]) < 1e-12
assert abs(cy[2]) < 1e-12
assert abs(cz[0]) < 1e-12
assert abs(cz[1]) < 1e-12
dx, dy, dz = a.info['shear_dx']
sx, sy, sz = a.cell.diagonal()
a.set_cell([[sx,0,0],[0,sy,0],[dx,dy,sz]], scale_atoms=False)
if opt.cell is not None:
cell = map(float, opt.cell.split(','))
