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_supercell(path):
from os.path import join
from numpy import all, abs, array, set_printoptions
from pylada.dftcrystal import read, Supercell, Crystal, Slabcut, BreakSym, \
KeepSymm, DisplaceAtoms, InsertAtoms
set_printoptions(precision=12)
crystal, functional = read(join(path, 'supercell.d12'))
assert isinstance(crystal, Crystal)
assert all(abs(array(crystal.params) - [4.63909875, 2.97938395]) < 1e-6)
assert crystal.symmgroup == 136
assert len(crystal) == 8
assert isinstance(crystal[0], Slabcut)
assert crystal[0].isup == 2
assert crystal[0].nl == 15
assert all(crystal[0].hkl == [1, 1, 0])
assert isinstance(crystal[1], BreakSym)
assert isinstance(crystal[2], DisplaceAtoms)
assert all(array([u.type for u in crystal[2].atoms]) == range(1, 31))
disp = array([[ 0. , 0. , 0.00496008 ],
[ 0. , 0. , -0.152840221],
[ 0. , 0. , 0.216529621],
[ 0. , -0.052728927, 0.185587552],
[ 0. , 0.052728927, 0.185587552],
[ 0. , 0. , -0.004768893],
[ 0. , 0. , 0.034440171],
[ 0. , 0. , 0.136085018],
[ 0. , 0. , -0.069420272],
[ 0. , 0.035782986, 0.022806847],
[ 0. , -0.035782986, 0.022806847],
[ 0. , 0. , 0.018900892],
[ 0. , 0. , 0.002450591],
[ 0. , 0. , 0. ],
[ 0. , 0. , 0. ],
[ 0. , -0.027503191, 0. ],
[ 0. , 0.027503191, 0. ],
[ 0. , 0. , -0.002450591],
[ 0. , 0. , -0.018900892],
[ 0. , 0. , -0.136085018],
[ 0. , 0. , 0.069420272],
[ 0. , 0.035782986, -0.022806847],
[ 0. , -0.035782986, -0.022806847],
[ 0. , 0. , -0.034440171],
[ 0. , 0. , 0.004768893],
[ 0. , 0. , 0.152840221],
[ 0. , 0. , -0.216529621],
[ 0. , -0.052728927, -0.185587552],
[ 0. , 0.052728927, -0.185587552],
[ 0. , 0. , -0.00496008 ]])
assert all(abs( array([u.pos for u in crystal[2].atoms]) - disp) < 1e-8)
assert isinstance(crystal[3], BreakSym)
assert isinstance(crystal[4], DisplaceAtoms)
assert all(array([u.type for u in crystal[4].atoms]) == range(1, 31))
disp = array([[ 0. , 0. , -0.005827511],
[ 0. , 0. , -0.00382378 ],
[ 0. , 0. , -0.000865488],
[ 0. , 0.001041455, -0.002644481],
[ 0. , -0.001041455, -0.002644481],
[ 0. , 0. , -0.004243966],
[ 0. , 0. , 0.001098565],
[ 0. , 0. , 0.00118787 ],
[ 0. , 0. , -0.002160436],
[ 0. , 0.000613051, -0.000776595],
[ 0. , -0.000613051, -0.000776595],
[ 0. , 0. , 0.00162428 ],
[ 0. , 0. , -0.000458678],
[ 0. , 0. , 0. ],
[ 0. , 0. , 0. ],
[ 0. , -0.000733281, 0. ],
[ 0. , 0.000733281, 0. ],
[ 0. , 0. , 0.000458678],
[ 0. , 0. , -0.00162428 ],
[ 0. , 0. , -0.00118787 ],
[ 0. , 0. , 0.002160436],
[ 0. , 0.000613051, 0.000776595],
[ 0. , -0.000613051, 0.000776595],
[ 0. , 0. , -0.001098565],
[ 0. , 0. , 0.004243966],
[ 0. , 0. , 0.00382378 ],
[ 0. , 0. , 0.000865488],
[ 0. , 0.001041455, 0.002644481],
[ 0. , -0.001041455, 0.002644481],
[ 0. , 0. , 0.005827511]])
assert all(abs( array([u.pos for u in crystal[4].atoms]) - disp) < 1e-8)
assert crystal[5].keyword.lower() == 'supercel'
assert isinstance(crystal[5], Supercell)
assert all(abs(crystal[5].matrix - [[2, 0], [0, 1]]) < 1e-8)
assert isinstance(crystal[6], KeepSymm)
assert isinstance(crystal[7], InsertAtoms)
assert len(crystal[7].atoms) == 2
assert crystal[7].atoms[0].type == 'H'
assert crystal[7].atoms[1].type == 'H'
assert all(abs(crystal[7].atoms[0].pos - [0.0, 3.28033818472, 8.731578688]) < 1e-8)
assert all(abs(crystal[7].atoms[1].pos - [2.97938395, 3.28033818472, 8.731578688]) < 1e-8)
assert all(functional.atomspin.up == [3, 4, 15, 16, 39, 40, 51, 52])
assert functional.biposize == 9701800
assert functional.dft.b3lyp == True
assert functional.dft.spin == True
assert functional.dft.xxlgrid == True
assert functional.exchsize == 6937578
assert functional.fmixing == 60
assert functional.levshift.lock == True
assert functional.levshift.shift == 5.0
assert functional.maxcycle == 300
assert functional.mpp == True
assert functional.nobipola == True
assert functional.nofmwf == True
assert functional.optgeom.breaksym == False
assert functional.optgeom.enabled == True
assert functional.optgeom.maxcycle == 10
assert functional.ppan == True
assert functional.scfdir == True
assert all(functional.shrink.mp == [4, 8])
assert functional.shrink.gallat == 8
assert functional.spinlock.ncycles == 30
assert functional.spinlock.nspin == 4
assert functional.title == 'rutile'
assert functional.toldee == 7
assert all(functional.tolinteg == [7, 7, 7, 7, 14])