def test_doubleatomsymm():
""" Bugs when calling atomsymm twice. """
from tempfile import mkdtemp
from shutil import rmtree
from os.path import exists
from pylada.dftcrystal import Crystal
from pylada.misc import Changedir
c = Crystal(136, 4.63909875, 2.97938395,
ifhr=0,
shift=0) \
.add_atom(0, 0, 0, 'Ti') \
.add_atom(0.306153, 0.306153, 0, 'O') \
.append('ATOMSYMM')
directory = '/tmp/test' #mkdtemp()
if directory == '/tmp/test':
if exists(directory): rmtree(directory)
with Changedir(directory) as cwd: pass
try:
c.append('ATOMSYMM')
c.eval()
finally:
if directory != '/tmp/test': rmtree(directory)
def test_breaksym():
from pylada.dftcrystal import Crystal, Functional, Shell, DisplaceAtoms, read
functional = Functional()
functional.basis['Si'] = [
Shell('s', a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325]),
Shell('sp', a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496]),
Shell('sp', 4.0, a0=[1.22, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.55, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.27, 1.0, 1.0]) ]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.optgeom.keepsymm = True
functional.optgeom.enabled = True
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
crystal.append('breaksym')
crystal.append(DisplaceAtoms().add_atom(0.01, 0, 0, 1))
string = functional.print_input(structure=crystal)
assert string.splitlines()[10] == 'KEEPSYMM'
cry, func = read(string)
assert cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.keepsymm
functional.optgeom.keepsymm = False
string = functional.print_input(structure=crystal)
assert string.splitlines()[10] == 'OPTGEOM'
cry, func = read(string)
assert cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.breaksym
crystal[0] = 'keepsymm'
string = functional.print_input(structure=crystal)
assert string.splitlines()[11] == 'BREAKSYM'
cry, func = read(string)
assert not cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.breaksym
functional.optgeom.keepsymm = True
string = functional.print_input(structure=crystal)
assert string.splitlines()[11] == 'OPTGEOM'
cry, func = read(string)
assert not cry.is_breaksym
assert func.optgeom.enabled
assert func.optgeom.keepsymm
string = crystal.print_input()
crystal.append('keepsymm')
crystal.append('keepsymm')
assert crystal.print_input() == string
crystal.append('breaksym')
assert crystal.print_input() != string
assert len(crystal.print_input().splitlines()) == len(string.splitlines()) + 1
def test():
from tempfile import mkdtemp
from numpy import array, all, abs
from shutil import rmtree
from os.path import exists
from os import mkdir
from pylada.dftcrystal import Crystal, relax, Shell, DisplaceAtoms
from pylada import default_comm
functional = relax.Relax()
functional.basis['Si'] = [
Shell('s', a0=[16120.0, 0.001959],
a1=[2426.0, 0.01493],
a2=[553.9, 0.07285],
a3=[156.3, 0.2461],
a4=[50.07, 0.4859],
a5=[17.02, 0.325]),
Shell('sp', a0=[292.7, -0.002781, 0.004438],
a1=[69.87, -0.03571, 0.03267],
a2=[22.34, -0.115, 0.1347],
a3=[8.15, 0.09356, 0.3287],
a4=[3.135, 0.603, 0.4496]),
Shell('sp', 4.0, a0=[1.22, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.55, 1.0, 1.0]),
Shell('sp', 0.0, a0=[0.27, 1.0, 1.0]) ]
functional.dft.pbe0 = True
functional.fmixing = 30
functional.optgeom.fulloptg = True
functional.shrink = 8, 16
functional.levshift = 5, True
functional.maxcycle = 600
functional.guessp = True
functional.optgeom.keepsymm = True
crystal = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
crystal.append('fraction')
crystal.append('keepsymm')
crystal.append(DisplaceAtoms().add_atom(0.01, 0, 0, 1))
directory = mkdtemp()
if directory == '/tmp/test/' and exists(directory):
rmtree(directory)
mkdir(directory)
try:
results = functional(crystal, outdir=directory, comm=default_comm)
assert results.success
# check that final crystals are same as final structures.
for crystal, structure in zip(results.details.crystal.itervalues(),
results.details.structure.itervalues()):
estruc = crystal.eval()
assert all(abs(estruc.cell - structure.cell) < 1e-8)
assert all(abs( array([a.pos for a in estruc])
- array([a.pos for a in structure]) ) < 1e-8)
assert all( array([a.type for a in estruc])
== array([a.type for a in structure]) )
instruc = results.details.input_crystal.values()[1:] + [results.crystal]
outstruc = results.details.structure.values()
for a, b in zip(instruc, outstruc):
a = a.eval()
assert all(abs(a.cell - b.cell) < 1e-8)
assert all(abs( array([v.pos for v in a])
- array([v.pos for v in b]) ) < 1e-8)
assert all( array([v.type for v in a])
== array([v.type for v in b]) )
finally:
if directory != '/tmp/test/': rmtree(directory)
pass
