def test_cpmd_parse_format():
name = 'cpmd_format'
head = ["&INFO\n",
"comment\n",
"&END\n",
"\n",
"!comment\n",
"&CPMD\n",
" MOLECULAR DYNAMICS CP\n",
" RESTART WAVEFUNCTION COORDINATES LATEST\n",
"&END",
"&SYSTEM\n",
"CUTOFF\n",
" 25.0\n",
"TESR\n",
" 2\n"]
tails = [["ANGSTROM\n",
"CELL VECTORS\n", "5.0000 0.0000 0.0000\n",
"0.0000 5.0000 0.0000\n", "0.0000 0.0000 5.0000\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 2.50000 2.50000 0.00000\n",
" 0.00000 2.50000 2.50000\n", " 2.50000 0.00000 2.50000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 2.50000 0.00000\n", " 2.50000 0.00000 0.00000\n",
" 0.00000 0.00000 2.50000\n", " 2.50000 2.50000 2.50000\n",
"&END\n"],
["CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 4.72432 4.72432 0.00000\n",
" 0.00000 4.72432 4.72432\n", " 4.72432 0.00000 4.72432\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 4.72432 0.00000\n", " 4.72432 0.00000 0.00000\n",
" 0.00000 0.00000 4.72432\n", " 4.72432 4.72432 4.72432\n",
"&END\n"],
["SCALE CARTESIAN\n",
"CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 0.50000 0.50000 0.00000\n",
" 0.00000 0.50000 0.50000\n", " 0.50000 0.00000 0.50000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.50000 0.00000\n", " 0.50000 0.00000 0.00000\n",
" 0.00000 0.00000 0.50000\n", " 0.50000 0.50000 0.50000\n",
"&END\n"],
["SCALE\n",
"CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 0.50000 0.50000 0.00000\n",
" 0.00000 0.50000 0.50000\n", " 0.50000 0.00000 0.50000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.50000 0.00000\n", " 0.50000 0.00000 0.00000\n",
" 0.00000 0.00000 0.50000\n", " 0.50000 0.50000 0.50000\n",
"&END\n"],
["SCALE S=0.5\n",
"CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 0.25000 0.25000 0.00000\n",
" 0.00000 0.25000 0.25000\n", " 0.25000 0.00000 0.25000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.25000 0.00000\n", " 0.25000 0.00000 0.00000\n",
" 0.00000 0.00000 0.25000\n", " 0.25000 0.25000 0.25000\n",
"&END\n"],
["SCALE SX=0.5\n",
"CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 0.25000 0.50000 0.00000\n",
" 0.00000 0.50000 0.50000\n", " 0.25000 0.00000 0.50000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.50000 0.00000\n", " 0.25000 0.00000 0.00000\n",
" 0.00000 0.00000 0.50000\n", " 0.25000 0.50000 0.50000\n",
"&END\n"],
["SCALE SX=0.5 SY=0.5 SZ=2\n",
"CELL VECTORS\n", "9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n", "0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.00000 0.00000\n", " 0.25000 0.25000 0.00000\n",
" 0.00000 0.25000 1.00000\n", " 0.25000 0.00000 1.00000\n",
"*Cl.uspp.pbe BINARY\n", " LMAX=F\n", " 4\n",
" 0.00000 0.25000 0.00000\n", " 0.25000 0.00000 0.00000\n",
" 0.00000 0.00000 1.00000\n", " 0.25000 0.25000 1.00000\n",
"&END\n"]]
formats = ['angstrom', 'bohr', 'alat', 'crystal',
'crystal', 'crystal', 'crystal']
targetp = newParam('cpmd')
targetp["name"] = name
targetp["&INFO"] = "comment\n"
targetp["&CPMD"] = " MOLECULAR DYNAMICS CP\n RESTART "\
"WAVEFUNCTION COORDINATES LATEST\n"
targetp["&SYSTEM"] = "CUTOFF\n 25.0\nTESR\n 2\n"
for f in range(len(formats)):
Mol, p = cpmd.parser(name, head + tails[f])
assert p == targetp
assert len(Mol) == 1
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ["Na", "Cl"]
assert Mol.getFmt() == formats[f]
assert Mol.getKpoints('active') == 'gamma'
assert vec_equal(Mol.getVec() * Mol.getCellDim(fmt='angstrom'),
((5, 0, 0), (0, 5, 0), (0, 0, 5)))
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)), ('Na', (2.5, 2.5, 0)), ('Na', (0, 2.5, 2.5)),
('Na', (2.5, 0, 2.5)), ('Cl', (0, 2.5, 0)), ('Cl', (2.5, 0, 0)),
('Cl', (0, 0, 2.5)), ('Cl', (2.5, 2.5, 2.5))))))
def test_cpmd_parse_symmetry():
name = 'cpmd_symmetry'
symm = ['0', '1', '2', '3', '4', '5', '6', '7', '8', '12', '14',
"ISOLATED", "CUBIC", "FACE CENTERED CUBIC", "FCC",
"BODY CENTERED CUBIC", "BCC", "HEXAGONAL", "TRIGONAL",
"RHOMBOHEDRAL", "TETRAGONAL", "BODY CENTERED TETRAGONAL",
"BCT", "ORTHORHOMBIC", "MONOCLINIC", "TRICLINIC", '14', '14', '14']
cell = [["CELL\n", "5 1 1 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 0 0 0.5 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 1.25 1.5 0 0 0\n"],
["CELL\n", "5 1.25 1.5 0.5 0 0\n"],
["CELL\n", "5 1.25 1.5 0.25 0.75 0.5\n"],
["CELL\n", "5 1 1 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 0 0 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 0 0 0.5 0 0\n"],
["CELL\n", "5 0 0 0.5 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 0 1.5 0 0 0\n"],
["CELL\n", "5 1.25 1.5 0 0 0\n"],
["CELL\n", "5 1.25 1.5 0.5 0 0\n"],
["CELL\n", "5 1.25 1.5 0.25 0.75 0.5\n"],
["CELL ABSOLUTE\n", "5 6.25 7.5 0.25 0.75 0.5\n"],
["CELL DEGREE\n", "5 1.25 1.5 75.5225 41.4096 60\n"],
["CELL ABSOLUTE DEGREE\n", "5 6.25 7.5 75.5225 41.4096 60\n"]]
head = ["&INFO\n",
"comment\n",
"&END\n",
"\n",
"!comment\n",
"&CPMD\n",
" MOLECULAR DYNAMICS CP\n",
" RESTART WAVEFUNCTION COORDINATES LATEST\n",
"&END",
"&SYSTEM\n",
"CUTOFF\n",
" 25.0\n",
"TESR\n",
" 2\n",
"ANGSTROM\n",
"SYMMETRY\n"]
tail = ["&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n",
" LMAX=F\n",
" 4\n",
" 0.00000 0.00000 0.00000\n",
" 0.50000 0.50000 0.00000\n",
" 0.00000 0.50000 0.50000\n",
" 0.50000 0.00000 0.50000\n",
"*Cl.uspp.pbe BINARY\n",
" LMAX=F\n",
" 4\n",
" 0.00000 0.50000 0.00000\n",
" 0.50000 0.00000 0.00000\n",
" 0.00000 0.00000 0.50000\n",
" 0.50000 0.50000 0.50000\n",
"&END\n"]
vectarget = [((1, 0, 0), (0, 1, 0), (0, 0, 1)),
((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)),
((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)),
((1, 0, 0), (0.625, 1.08253, 0), (0, 0, 1.5)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825)),
((1, 0, 0), (0, 1, 0), (0, 0, 1)),
((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, 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)),
((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)),
((0.5, -0.288675, 0.81650), (0, 0.57735, 0.81650),
(-0.5, -0.288675, 0.81650)),
((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)),
((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)),
((1, 0, 0), (0.625, 1.08253, 0), (0, 0, 1.5)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825)),
((1, 0, 0), (0.625, 1.082532, 0),
(1.125, -0.216506, 0.96825))]
for i in range(len(symm)):
Mol, _ = cpmd.parser(name, head + [symm[i]] + cell[i] + tail)
assert float_equal(Mol.getCellDim(fmt='angstrom'), 5)
assert vec_equal(Mol.getVec(), vectarget[i])
def test_cpmd_parse_constraints():
name = 'cpmd_constraints'
head = ["&INFO\n",
"comment\n",
"&END\n",
"\n",
"!comment\n",
"&CPMD\n",
" MOLECULAR DYNAMICS CP\n",
" RESTART WAVEFUNCTION COORDINATES LATEST\n",
"&END",
"&SYSTEM\n",
"CUTOFF\n",
" 25.0\n",
"TESR\n",
" 2\n",
"SCALE\n",
"CELL VECTORS\n",
"9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n",
"0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n",
" LMAX=F\n",
" 1\n",
" 0.00000 0.00000 0.00000\n",
"*Na_MT_PBE.psp KLEINMAN-BYLANDER\n",
" LMAX=P\n",
" 1\n",
" 0.50000 0.50000 0.00000\n",
"*Na.uspp.pbe BINARY\n",
" LMAX=F\n",
" 2\n",
" 0.00000 0.50000 0.00000\n",
" 0.50000 0.00000 0.00000\n",
"ISOTOPE\n",
" 21.994\n",
" 22.989\n",
" 23.990\n",
"CONSTRAINTS\n"]
cons = [[],
["FIX ALL\n"],
["FIX QM\n"],
["FIX MM\n"],
["FIX PPTY\n", "3\n"],
["FIX PPTY SEQUENCE\n", "3 1 3\n"],
["FIX ELEMENT\n", "11\n"],
["FIX ELEMENT SEQUENCE\n", "11 1 3\n"],
["FIX SEQUENCE\n", "1 3\n"],
["FIX ATOMS\n", "2\n", "1 3\n"],
["FIX COORDINATES\n", "3\n",
"1 0 1 1\n", "2 1 0 1\n", "3 1 1 0\n"],
["FIX COORDINATES\n", "4\n",
"1 0 0 1\n", "2 0 1 0\n", "3 1 0 0\n", "4 0 0 0\n"],
]
F = [False, False, False]
X = [True, False, False]
Y = [False, True, False]
Z = [False, False, True]
XY = [True, True, False]
XZ = [True, False, True]
YZ = [False, True, True]
A = [True, True, True]
fixtarget = [[F, F, F, F], [A, A, A, A], [A, A, A, A], [F, F, F, F],
[F, F, A, A], [F, F, A, F], [A, A, A, A], [A, A, A, F],
[A, A, A, F], [A, F, A, F], [X, Y, Z, F], [XY, XZ, YZ, A],
]
for i in range(len(cons)):
Mol, _ = cpmd.parser(name,
head + cons[i] + ["END CONSTRAINTS\n", "&END\n"])
assert Mol.nat == 4
assert Mol.ntyp == 3
assert Mol.getTypes() == ['Na', 'Na1', 'Na2']
assert Mol.pse['Na']['m'] == 21.994
assert Mol.pse['Na1']['m'] == 22.989
assert Mol.pse['Na2']['m'] == 23.990
assert list(map(lambda x: x[-1], Mol.getAtoms(fix=True))) ==\
fixtarget[i]
def test_cpmd_parse_kpoints():
name = 'cpmd_kpoints'
head = ["&INFO\n",
"comment\n",
"&END\n",
"\n",
"!comment\n",
"&CPMD\n",
" MOLECULAR DYNAMICS CP\n",
" RESTART WAVEFUNCTION COORDINATES LATEST\n",
"&END",
"&SYSTEM\n"]
tail = ["CUTOFF\n",
" 25.0\n",
"TESR\n",
" 2\n",
"SCALE\n",
"CELL VECTORS\n",
"9.4486 0.0000 0.0000\n",
"0.0000 9.4486 0.0000\n",
"0.0000 0.0000 9.4486\n",
"&END\n",
"&ATOMS\n",
"*Na.uspp.pbe BINARY\n",
" LMAX=F\n",
" 4\n",
" 0.00000 0.00000 0.00000\n",
" 0.50000 0.50000 0.00000\n",
" 0.00000 0.50000 0.50000\n",
" 0.50000 0.00000 0.50000\n",
"*Cl.uspp.pbe BINARY\n",
" LMAX=F\n",
" 4\n",
" 0.00000 0.50000 0.00000\n",
" 0.50000 0.00000 0.00000\n",
" 0.00000 0.00000 0.50000\n",
" 0.50000 0.50000 0.50000\n",
"&END\n"]
ksys = [[],
["KPOINTS MONKHORST-PACK\n", "2 0 0\n"],
["KPOINTS MONKHORST-PACK SHIFT=0 0 0\n", "2 0 0\n"],
["KPOINTS\n", "2\n", "0.0 0.0 0.0 2\n", "0.5 0.5 0.5 0\n"],
["KPOINTS SCALED\n", "2\n", "0.0 0.0 0.0 2\n", "0.5 0.5 0.5 0\n"],
["KPOINTS BANDS\n", "2 0.0 0.0 0.0 0.5 0.5 0.5\n",
"0 0 0 0 0 0 0\n"],
["KPOINTS SCALED BANDS\n", "2 0.0 0.0 0.0 0.5 0.5 0.5\n",
"0 0 0 0 0 0 0\n"]]
kfmt = ['gamma', 'mpg', 'mpg', 'discrete',
'discrete', 'discrete', 'discrete']
opttarget = [{'crystal': False, 'bands': False},
{'crystal': True, 'bands': False},
{'crystal': False, 'bands': True},
{'crystal': True, 'bands': True}]
targetp = newParam('cpmd')
targetp["name"] = name
targetp["&INFO"] = "comment\n"
targetp["&CPMD"] = " MOLECULAR DYNAMICS CP\n RESTART "\
"WAVEFUNCTION COORDINATES LATEST\n"
targetp["&SYSTEM"] = "CUTOFF\n 25.0\nTESR\n 2\n"
for k in range(len(kfmt)):
Mol, p = cpmd.parser(name, head + ksys[k] + tail)
assert p == targetp
assert len(Mol) == 1
assert Mol.name == name
assert Mol.nat == 8
assert Mol.ntyp == 2
assert Mol.getTypes() == ["Na", "Cl"]
assert Mol.getFmt() == 'crystal'
assert vec_equal(Mol.getVec() * Mol.getCellDim(fmt='angstrom'),
((5, 0, 0), (0, 5, 0), (0, 0, 5)))
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)), ('Na', (2.5, 2.5, 0)), ('Na', (0, 2.5, 2.5)),
('Na', (2.5, 0, 2.5)), ('Cl', (0, 2.5, 0)), ('Cl', (2.5, 0, 0)),
('Cl', (0, 0, 2.5)), ('Cl', (2.5, 2.5, 2.5))))))
assert Mol.getKpoints('active') == kfmt[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', '2'],
['0.5', '0.5', '0.5', '0']]
assert Mol.getKpoints('options') == opttarget[k - 3]
