def failPwi(f):
try:
MolFail, _ = pwInput.parser(name, header + f + tail)
except ValueError:
return True
else:
return False
def test_pwi_parse_formats():
name = "pwi_parse_formats"
header = ["&control\n",
" calculation='scf'\n",
"/\n",
"&system\n",
" nat=8\n",
" ntyp=2\n",
" ibrav=0\n",
" celldm(1)=9.448631\n",
" ecutwfc=30.0\n",
"/\n",
"&electrons\n",
" diagonalization='david'\n",
" conv_thr=1.0e-8\n",
"/\n",
"\n",
"ATOMIC_SPECIES\n",
"Na 22.99 Na.uspp736.pbe.UPF\n",
"Cl 35.45 Cl.uspp736.pbe.UPF\n",
"\n"]
formats = {"bohr": ["ATOMIC_POSITIONS bohr\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 4.7243 0.0000 0.0000\n",
"Na 4.7243 4.7243 0.0000\n",
"\n",
"Cl 0.0000 4.7243 0.0000\n",
"Cl 0.0000 0.0000 4.7243\n",
"Na 4.7243 0.0000 4.7243\n",
"Cl 4.7243 4.7243 4.7243\n",
"Na 0.0000 4.7243 4.7243\n",
"\n"],
"alat": ["ATOMIC_POSITIONS alat\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 0.5000 0.0000 0.0000\n",
"Na 0.5000 0.5000 0.0000\n",
"Cl 0.0000 0.5000 0.0000\n",
"Cl 0.0000 0.0000 0.5000\n",
"Na 0.5000 0.0000 0.5000\n",
"Cl 0.5000 0.5000 0.5000\n",
"Na 0.0000 0.5000 0.5000\n",
"\n"],
"angstrom": ["ATOMIC_POSITIONS angstrom\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 2.5000 0.0000 0.0000\n",
"Na 2.5000 2.5000 0.0000\n",
"Cl 0.0000 2.5000 0.0000\n",
"Cl 0.0000 0.0000 2.5000\n",
"Na 2.5000 0.0000 2.5000\n",
"Cl 2.5000 2.5000 2.5000\n",
"Na 0.0000 2.5000 2.5000\n",
"\n"],
"crystal": ["ATOMIC_POSITIONS crystal\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 0.5000 0.0000 0.0000\n",
"Na 0.5000 0.5000 0.0000\n",
"Cl 0.0000 0.5000 0.0000\n",
"Cl 0.0000 0.0000 0.5000\n",
"Na 0.5000 0.0000 0.5000\n",
"Cl 0.5000 0.5000 0.5000\n",
"Na 0.0000 0.5000 0.5000\n",
"\n"]}
tail = ["K_POINTS gamma\n",
"\n",
"CELL_PARAMETERS\n",
"1.00000 0.00000 0.00000\n",
"0.00000 1.00000 0.00000\n",
"0.00000 0.00000 1.00000\n"]
tparam = {"type": "pwi", "name": name,
"&control": {"calculation": "'scf'"},
"&system": {"ibrav": "0", "ecutwfc": "30.0"},
"&electrons": {"diagonalization": "'david'",
"conv_thr": "1.0e-8"}}
for f in formats:
target = header + formats[f] + tail
Mol, p = pwInput.parser(name, target)
assert p == tparam
assert len(Mol) == 1
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ['Na', 'Cl']
assert Mol.getFmt() == f
assert Mol.getKpoints('active') == 'gamma'
assert float_equal(Mol.getCellDim(fmt='angstrom'), 5)
assert vec_equal(Mol.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
assert list(map(len, Mol.getBonds(1.1))) == [12, 4, 4, 0, 4, 0, 0, 0]
assert all(map(lambda x: atom_equal(*x), zip(
Mol.getAtoms(fmt='angstrom'),
(('Na', (0, 0, 0)), ('Cl', (2.5, 0, 0)), ('Na', (2.5, 2.5, 0)),
('Cl', (0, 2.5, 0)), ('Cl', (0, 0, 2.5)), ('Na', (2.5, 0, 2.5)),
('Cl', (2.5, 2.5, 2.5)), ('Na', (0, 2.5, 2.5))))))
def test_pwi_parse_ibrav():
name = "pwi_parse_ibrav"
header = ["&control\n",
" calculation='scf'\n",
"/\n",
"&system\n",
" nat=4\n",
" ntyp=1\n",
" ecutwfc=30.0\n"]
tail = ["/\n",
"&electrons\n",
" diagonalization='david'\n",
" conv_thr=1.0e-8\n",
"/\n",
"\n",
"ATOMIC_SPECIES\n",
"C 12.0107 C.uspp736.pbe.UPF\n",
"/\n",
"\n",
"ATOMIC_POSITIONS crystal\n",
"C 0.0 0.0 0.0 0 1 0\n",
"C 0.25 0.75 0.5 1 0\n",
"C 0.5 0.25 0.75\n",
"C 0.75 0.5 0.25\n",
"/\n",
"\n",
"K_POINTS gamma\n"]
fails = [["ibrav=1\n"],
["ibrav=4\n", "celldm(1)=9.448631\n"],
["ibrav=0\n"]]
celld = [["ibrav=1\n", "celldm(1)=9.448631\n"],
["ibrav=2\n", "celldm(1)=9.448631\n"],
["ibrav=3\n", "celldm(1)=9.448631\n"],
["ibrav=4\n", "celldm(1)=9.448631\n", "celldm(3)=1.5\n"],
["ibrav=5\n", "celldm(1)=9.448631\n", "celldm(4)=0.5\n"],
["ibrav=-5\n", "celldm(1)=9.448631\n", "celldm(4)=0.5\n"],
["ibrav=6\n", "celldm(1)=9.448631\n", "celldm(3)=1.5\n"],
["ibrav=7\n", "celldm(1)=9.448631\n", "celldm(3)=1.5\n"],
["ibrav=8\n", "celldm(1)=9.448631\n",
"celldm(2)=1.25\n", "celldm(3)=1.5\n"],
["ibrav=9\n", "celldm(1)=9.448631\n",
"celldm(2)=1.25\n", "celldm(3)=1.5\n"],
["ibrav=10\n", "celldm(1)=9.448631\n",
"celldm(2)=1.25\n", "celldm(3)=1.5\n"],
["ibrav=11\n", "celldm(1)=9.448631\n",
"celldm(2)=1.25\n", "celldm(3)=1.5\n"],
["ibrav=12\n", "celldm(1)=9.448631\n", "celldm(2)=1.25\n",
"celldm(3)=1.5\n", "celldm(4)=0.5\n"],
["ibrav=-12\n", "celldm(1)=9.448631\n", "celldm(2)=1.25\n",
"celldm(3)=1.5\n", "celldm(5)=0.75\n"],
["ibrav=13\n", "celldm(1)=9.448631\n", "celldm(2)=1.25\n",
"celldm(3)=1.5\n", "celldm(4)=0.5\n"],
["ibrav=14\n", "celldm(1)=9.448631\n", "celldm(2)=1.25\n",
"celldm(3)=1.5\n", "celldm(4)=0.25\n",
"celldm(5)=0.75\n", "celldm(6)=0.5\n"]]
cryst = [["ibrav=1\n", "A=5\n"],
["ibrav=2\n", "A=5\n"],
["ibrav=3\n", "A=5\n"],
["ibrav=4\n", "A=5\n", "C=7.5\n"],
["ibrav=5\n", "A=5\n", "cosAB=0.5\n"],
["ibrav=-5\n", "A=5\n", "cosAB=0.5\n"],
["ibrav=6\n", "A=5\n", "C=7.5\n"],
["ibrav=7\n", "A=5\n", "C=7.5\n"],
["ibrav=8\n", "A=5\n", "B=6.25\n", "C=7.5\n"],
["ibrav=9\n", "A=5\n", "B=6.25\n", "C=7.5\n"],
["ibrav=10\n", "A=5\n", "B=6.25\n", "C=7.5\n"],
["ibrav=11\n", "A=5\n", "B=6.25\n", "C=7.5\n"],
["ibrav=12\n", "A=5\n", "B=6.25\n", "C=7.5\n", "cosAB=0.5\n"],
["ibrav=-12\n", "A=5\n", "B=6.25\n", "C=7.5\n", "cosAC=0.75\n"],
["ibrav=13\n", "A=5\n", "B=6.25\n", "C=7.5\n", "cosAB=0.5\n"],
["ibrav=14\n", "A=5\n", "B=6.25\n", "C=7.5\n",
"cosAB=0.5\n", "cosAC=0.75\n", "cosBC=0.25\n"]]
vectarget = [((1, 0, 0), (0, 1, 0), (0, 0, 1)),
((-0.5, 0, 0.5), (0, 0.5, 0.5), (-0.5, 0.5, 0)),
((0.5, 0.5, 0.5), (-0.5, 0.5, 0.5), (-0.5, -0.5, 0.5)),
((1, 0, 0), (-0.5, np.sqrt(3) * 0.5, 0), (0, 0, 1.5)),
((0.5, -0.288675, 0.81650), (0, 0.57735, 0.81650),
(-0.5, -0.288675, 0.81650)),
((0, 0.70711, 0.70711), (0.70711, 0, 0.70711),
(0.70711, 0.70711, 0)),
((1, 0, 0), (0, 1, 0), (0, 0, 1.5)),
((0.5, -0.5, 0.75), (0.5, 0.5, 0.75), (-0.5, -0.5, 0.75)),
((1, 0, 0), (0, 1.25, 0), (0, 0, 1.5)),
((0.5, 0.625, 0), (-0.5, 0.625, 0), (0, 0, 1.5)),
((0.5, 0, 0.75), (0.5, 0.625, 0), (0, 0.625, 0.75)),
((0.5, 0.625, 0.75), (-0.5, 0.625, 0.75),
(-0.5, -0.625, 0.75)),
((1, 0, 0), (0.625, 1.08253, 0), (0, 0, 1.5)),
((1, 0, 0), (0, 1.25, 0), (1.125, 0, 0.992157)),
((0.5, 0, -0.75), (0.625, 1.08253, 0), (0.5, 0, 0.75)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825))]
for i in range(len(cryst)):
MolCell, _ = pwInput.parser(name, header + celld[i] + tail)
MolCrys, _ = pwInput.parser(name, header + cryst[i] + tail)
assert float_equal(MolCell.getCellDim(fmt='angstrom'), 5)
assert vec_equal(MolCell.getVec(), vectarget[i])
assert float_equal(MolCell.getCellDim(), MolCrys.getCellDim())
assert vec_equal(MolCell.getVec(), MolCrys.getVec())
def failPwi(f):
try:
MolFail, _ = pwInput.parser(name, header + f + tail)
except ValueError:
return True
else:
return False
for f in fails:
assert failPwi(f)
def test_pwi_parse_kpoints():
name = 'pwi_parse_kpoints'
body = ["&control\n",
" calculation='scf'\n",
"/\n",
"&system\n",
" nat=8\n",
" ntyp=2\n",
" ibrav=0\n",
" celldm(1)=9.448631\n",
" ecutwfc=30.0\n",
"/\n",
"&electrons\n",
" diagonalization='david'\n",
" conv_thr=1.0e-8\n",
"/\n",
"\n",
"ATOMIC_SPECIES\n",
"Na 22.99 Na.uspp736.pbe.UPF\n",
"Cl 35.45 Cl.uspp736.pbe.UPF\n",
"\n",
"ATOMIC_POSITIONS alat\n",
"Na 0.0000 0.0000 0.0000\n",
"Cl 0.5000 0.0000 0.0000\n",
"Na 0.5000 0.5000 0.0000\n",
"Cl 0.0000 0.5000 0.0000\n",
"Cl 0.0000 0.0000 0.5000\n",
"Na 0.5000 0.0000 0.5000\n",
"Cl 0.5000 0.5000 0.5000\n",
"Na 0.0000 0.5000 0.5000\n",
"\n",
"CELL_PARAMETERS\n",
"1.00000 0.00000 0.00000\n",
"0.00000 1.00000 0.00000\n",
"0.00000 0.00000 1.00000\n",
"\n"]
kpoints = [["K_POINTS gamma\n"],
["K_POINTS automatic\n",
"2 0 0 0 0 0 \n"],
["K_POINTS tpiba\n",
"2\n",
"0.0 0.0 0.0 0.75\n",
"0.5 0.5 0.5 0.25\n"],
["K_POINTS tpiba_b\n",
"2\n",
"0.0 0.0 0.0 0.75\n",
"0.5 0.5 0.5 0.25\n"],
["K_POINTS crystal\n",
"2\n",
"0.0 0.0 0.0 0.75\n",
"0.5 0.5 0.5 0.25\n"],
["K_POINTS crystal_b\n",
"2\n",
"0.0 0.0 0.0 0.75\n",
"0.5 0.5 0.5 0.25\n"]]
activetarget = ['gamma', 'mpg', 'discrete',
'discrete', 'discrete', 'discrete']
opttarget = [{'crystal': False, 'bands': False},
{'crystal': False, 'bands': True},
{'crystal': True, 'bands': False},
{'crystal': True, 'bands': True}]
for k in range(6):
Mol, p = pwInput.parser(name, body + kpoints[k])
assert Mol.getKpoints('active') == activetarget[k]
if Mol.getKpoints('active') == 'mpg':
assert Mol.getKpoints('mpg') == ['2', '0', '0', '0', '0', '0']
elif Mol.getKpoints('active') == 'discrete':
assert Mol.getKpoints('discrete') ==\
[['0.0', '0.0', '0.0', '0.75'],
['0.5', '0.5', '0.5', '0.25']]
assert Mol.getKpoints('options') == opttarget[k - 2]