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():
from numpy import all, abs, dot, identity
from pylada.dftcrystal import Crystal, External
from pylada.crystal import which_site
orig = Crystal(227, 5.43).add_atom(0.125, 0.125, 0.125, 'Si')
b = External(copy=orig.eval())
assert all(abs(orig.eval().cell - b.initial.cell) < 1e-8)
assert len(b.initial) == 2
assert repr(b) == repr( eval(repr(b), {'External': External}) )
assert len(b.print_input().splitlines()) == 2
assert b.print_input().splitlines()[0] == 'EXTERNAL'
assert b.print_input().splitlines()[1] == 'END EXTERNAL'
# check that symmetries as extracted are ok.
for atom in b.initial:
for op in orig.symmetry_operators:
assert all(abs(identity(3, dtype='float64') - dot(op[:3].T, op[:3])) < 1e-8)
assert which_site(dot(op[:3], atom.pos) + op[3], b.initial) != -1
# Check that running structure through crystal works
c = b.eval()
assert all(abs(c.cell - b.cell) < 1e-8)
assert len(c) == 2
assert all(abs(abs(c[0].pos) - [0.67875]*3) < 1e-8)
assert all(abs(abs(c[1].pos) - [0.67875]*3) < 1e-8)
assert all(abs(c[0].pos + c[1].pos) < 1e-8)
def test(): """ Tests functional prints and reads itself """ from pylada.dftcrystal.functional import Functional from pylada.dftcrystal import Crystal from pylada.dftcrystal.parse import parse parsed = parse(string) structure = Crystal() structure.read_input(parsed['rutile']['CRYSTAL']) a = Functional() a.read_input(parsed) assert a.scfdir assert a.maxcycle == 300 assert a.exchsize == 6937578 # need structure otherwise parse can't find beginning of input. otherstring = a.print_input(structure=structure) otherparsed = parse(otherstring) b = Functional() b.read_input(otherparsed) assert otherstring == b.print_input(structure=structure)
def test_output_map():
from pylada.dftcrystal import Functional, Crystal
from pylada.dftcrystal.parse import parse
a = Functional()
parsed = parse(input)['']
a.basis.read_input(parsed['BASISSET'])
structure = Crystal()
structure.read_input(parsed['CRYSTAL'])
o = a.basis.output_map(structure=structure)
assert len(o) == 1
assert o[0] == ('ghosts', '2\n1 2')
a.basis.ghosts.breaksym = False
o = a.basis.output_map(structure=structure)
assert len(o) == 2
assert o[0] == ('keepsymm', True)
assert o[1] == ('ghosts', '2\n1 2')
b = Functional()
b.basis.raw = o.prefix
assert set(b.basis) == set(['O', 'Ti'])
assert repr(b.basis['O']) == repr(a.basis['O'])
assert repr(b.basis['Ti']) == repr(a.basis['Ti'])
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
