def test_atoms_bohr():
Mol = Molecule()
Mol.setCellDim(2)
Mol.newAtom()
Mol.newAtom('H', (1, 1, 1), 1, [True, False], True)
assert Mol.nat == 2
assert Mol.ntyp == 2
assert Mol.getTypes() == ['H', 'C']
assert Mol.getCellDim() == 2
assert atom_equal(Mol.getAtom(0, charge=True, fix=True, hidden=True),
['C', (0, 0, 0), 0., [False, False, False], False])
assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True),
['H', (1, 1, 1), 1., [True, False, False], True])
assert list(map(len, Mol.getBonds(1.1))) == [1, 1, 1, 1, 1, 1, 1, 1]
Mol.delAtom(1)
assert Mol.nat == 1
assert Mol.getTypes() == ['C']
Mol.newAtoms(2)
assert Mol.getTypes() == ['X', 'C']
Mol.setAtom(1, 'O', (0.5, 0.5, 0.5), 2, [False, True], False)
Mol.setAtom(2, 'U', (1, 1, 1), 2, [True], False)
assert atom_equal(Mol.getAtom(1, charge=True, fix=True, hidden=True),
['O', (0.5, 0.5, 0.5), 2., [False, True, False], False])
assert atom_equal(Mol.getAtom(2, charge=True, fix=True, hidden=True),
['U', (1, 1, 1), 2., [True, False, False], False])
assert Mol.getTypes() == ['C', 'O', 'U']
target = (['C', (0, 0, 0), 0., [False, False, False], False],
['O', (0.5, 0.5, 0.5), 2., [False, True, False], False],
['U', (1, 1, 1), 2., [True, False, False], False])
for a, t in zip(Mol.getAtoms(True, True, True), target):
assert atom_equal(a, t)
def test_modify():
Mol = Molecule()
assert Mol.getUndo() == None
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('C', (0.5, 0.5, 0.5), fmt='crystal')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 1
Mol.mult(2, 1, 1)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 5, 0), (0, 0, 5)))
assert Mol.nat == 2
Mol.mult(1, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.crop()
assert Mol.nat == 1
Mol.mult(2, 2, 2)
assert vec_equal(Mol.getVec(), ((10, 0, 0), (0, 10, 0), (0, 0, 10)))
assert Mol.nat == 8
Mol.setVec(((7, 0, 0), (0, 7, 0), (0, 0, 7)))
Mol.wrap()
assert Mol.nat == 8
assert list(map(len, Mol.getBonds(1.1))) == [24, 0, 0, 0, 0, 0, 0, 0]
assert Mol.getUndo() == 'wrap atoms'
Mol.undo()
assert list(map(len, Mol.getBonds(1.1))) == [0, 4, 4, 4, 4, 4, 4, 0]
Mol.wrap()
Mol.reshape(((14, 7, 0), (0, 7, 0), (0, 0, 7)))
assert list(map(len, Mol.getBonds(1.1))) == [38, 0, 10, 0, 0, 0, 0, 0]
assert vec_equal(Mol.getVec(), ((14, 7, 0), (0, 7, 0), (0, 0, 7)))
Mol.undo()
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
assert atom_equal(Mol.getAtom(1, fmt="crystal"), ('C', (0.1, 0.5, 0.5)))
Mol.align(1, 'x')
assert vec_equal(Mol.getVec(), ((0, -5, 0), (5, 0, 0), (0, 0, 5)))
Mol.undo()
Mol.align(1, 'y')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.align(1, 'z')
assert vec_equal(Mol.getVec(), ((5, 0, 0), (0, 0, 5), (0, -5, 0)))
Mol.undo()
try:
Mol.align(0, 1)
except ValueError:
assert True
except:
assert False, "Wrong error"
else:
assert False, "Error missing"
def test_molecule():
Mol = Molecule(name="Test Mol", steps=0)
assert Mol.name == "Test Mol"
assert len(Mol) == 0
Mol.newStep()
assert len(Mol) == 1
Mol.newAtom('C', (1, 1, 1))
assert Mol.nat == 1
assert atom_equal(Mol.getAtom(0, fmt='crystal'), ['C', (1, 1, 1)])
Mol.copyStep()
assert len(Mol) == 2
for s in Mol.steps:
assert s.nat == 1
assert s.getCellDim() == 1
assert Mol.curStep == 1
Mol.changeStep(0)
assert Mol.curStep == 0
Mol.setCellDimAll(1, fmt='angstrom', scale=True)
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
assert atom_equal(s.getAtom(0, fmt='angstrom'), ['C', (1, 1, 1)])
Mol.setVecAll(((2, 0, 0), (0, 2, 0), (0, 0, 2)), scale=True)
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((2, 0, 0), (0, 2, 0), (0, 0, 2)))
assert atom_equal(s.getAtom(0, fmt='angstrom'), ['C', (2, 2, 2)])
Mol.setVecAll(((1, 0, 0), (0, 1, 0), (0, 0, 1)))
for s in Mol.steps:
assert float_equal(s.getCellDim(fmt='angstrom'), 1)
assert vec_equal(s.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
assert atom_equal(s.getAtom(0, fmt='crystal'), ['C', (2, 2, 2)])
assert Mol.getKpoints('active') == 'gamma'
assert Mol.getKpoints('mpg') == ['1', '1', '1', '0', '0', '0']
assert Mol.getKpoints('discrete') == []
assert Mol.getKpoints('options') == {'crystal': False, 'bands': False}
Mol.setKpoints('active', 'mpg')
assert Mol.getKpoints('active') == 'mpg'
Mol1 = Mol.copy()
assert len(Mol1) == 1
assert Mol1.name == "Copy of Test Mol"
Mol2 = Mol.copyAll()
assert len(Mol2) == 2
assert Mol2.name == "Copy of Test Mol"
def test_atoms_fmt():
Mol = Molecule()
# standard: bohr:
assert Mol.getFmt() == 'bohr'
assert float_equal(Mol.getCellDim(), 1)
assert vec_equal(Mol.getVec(), ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
Mol.newAtom('C', (1, 1, 1))
assert atom_equal(Mol.getAtom(0), ('C', (1, 1, 1)))
# transition to angstrom:
Mol.setFmt("angstrom", scale=True)
assert Mol.getFmt() == 'angstrom'
Mol.setCellDim(1)
assert float_equal(Mol.getCellDim(), 1)
assert atom_equal(Mol.getAtom(0, fmt="angstrom"), ('C', (1, 1, 1)))
Mol.setCellDim(2.5, scale=True, fmt='angstrom')
Mol.newAtom('C', (2.5, 2.5, 2.5), fmt='angstrom')
for at in Mol.getAtoms():
assert atom_equal(at, ('C', (2.5, 2.5, 2.5)))
Mol.setVec(((2, 0, 0), (0, 2, 0), (0, 0, 2)), scale=True)
assert vec_equal(Mol.getVec(), ((2, 0, 0), (0, 2, 0), (0, 0, 2)))
Mol.newAtom('C', (5, 5, 5), fmt='angstrom')
Mol.newAtom('C', (2, 2, 2), fmt='alat')
Mol.newAtom('C', (1, 1, 1), fmt='crystal')
for at in Mol.getAtoms():
assert atom_equal(at, ('C', (5, 5, 5)))
for at in Mol.getAtoms(fmt='alat'):
assert atom_equal(at, ('C', (2, 2, 2)))
for at in Mol.getAtoms(fmt='crystal'):
assert atom_equal(at, ('C', (1, 1, 1)))
# scale back down to bohr
Mol.setCellDim(2.5, scale=True, fmt='bohr')
for at in Mol.getAtoms(fmt='bohr'):
assert atom_equal(at, ('C', (5, 5, 5)))
Mol.setFmt('alat', scale=True)
for at in Mol.getAtoms(fmt='bohr'):
assert atom_equal(at, ('C', (12.5, 12.5, 12.5)))
Mol.setFmt('crystal', scale=True)
for at in Mol.getAtoms(fmt='bohr'):
assert atom_equal(at, ('C', (62.5, 62.5, 62.5)))
assert vec_equal(Mol.getCenter(), (2.5, 2.5, 2.5))
assert vec_equal(Mol.getCenter(com=True), (62.5, 62.5, 62.5))
def test_selection():
Mol = Molecule()
Mol.newAtom('C', (0, 0, 0))
Mol.addSelection([1, (0, 0, 0)])
Mol.addSelection([1, (1, 0, 0)])
assert Mol.getSelection() == [[1, (0, 0, 0)], [1, (1, 0, 0)]]
Mol.addSelection([1, (1, 0, 0)])
assert Mol.getSelection() == [[1, (0, 0, 0)]]
Mol.delSelection()
assert Mol.getSelection() == []
def test_scripting():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.newAtom('C', (0, 0, 0))
Mol.newAtom('O', (1, 1, 0))
Mol.newAtom('B', (2, 2, 0))
Mol.newAtom('U', (0, 2, 0))
Mol.evalScript("def g all tU\n"
"shi g 1-3 2")
assert atom_equal(Mol.getAtom(3), ('U', (2, 0, 0)))
Mol.undo()
Mol.evalScript("rot 3 90 2-0 1")
assert atom_equal(Mol.getAtom(3), ('U', (1, 1, np.sqrt(2))))
Mol.undo()
Mol.evalScript("rot 3 90 2-0\n"
"mir 3 (1,0,0) (0,0,1,'angstrom') (1,0,0)")
assert atom_equal(Mol.getAtom(3), ('U', (1, -1, np.sqrt(2))))
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(15)
Mol.newAtom('C1', (0, 0, 0))
Mol.newAtom('C1', (1, 0, 0))
Mol.newAtom('C1', (1, 0, 0))
Mol.newAtom('C2', (0, 0, 3))
Mol.newAtom('C2', (1, 0, 3))
Mol.newAtom('C2', (1, 0, 3))
Mol.evalScript("rot [2, 5] 60 (0, 0, 1)")
Mol.evalScript("rot 3-5 90 (1, 0, 0) 3")
assert len(Mol.getBonds(1.1)[0]) == 6
Mol.evalScript("sel all tC2\npar sel sel 0-2")
atoms = Mol.getAtoms()
assert vec_equal(atoms[0][1], atoms[3][1]-(0,0,3))
assert vec_equal(atoms[1][1], atoms[4][1]-(0,0,3))
assert vec_equal(atoms[2][1], atoms[5][1]-(0,0,3))
Mol.evalScript("rot sel 45 (1, 0, 0) 3")
Mol.evalScript("pshift 0-2 (0,0,1) sel")
assert atom_equal(Mol.getAtom(0), ['C1', (0, np.sqrt(2)/2, -np.sqrt(2)/2)])
assert atom_equal(Mol.getAtom(1), ['C1', (1, np.sqrt(2)/2, -np.sqrt(2)/2)])
assert atom_equal(Mol.getAtom(2), ['C1', (0.5, (np.sqrt(3)+np.sqrt(2))/2, -np.sqrt(2)/2)])
def test_cpmd_write_kpoints_constraints():
Mol = Molecule()
Mol.newAtom('Na', (0, 0, 0), fix=[True])
Mol.newAtom('Na', (1, 1, 1), fix=[True, True, True])
p = newParam('cpmd')
p["&ATOMS"] = "CONSTRAINTS\n"\
"FIX COM\n"\
"END CONSTRAINTS\n"
head = "&CPMD\n"\
"&END\n"\
"&SYSTEM\n"\
" CELL VECTORS\n"\
" 1.0000 0.0000 0.0000\n"\
" 0.0000 1.0000 0.0000\n"\
" 0.0000 0.0000 1.0000\n"
tail = "&END\n"\
"&ATOMS\n"\
"*Na.uspp736.pbe BINARY\n"\
" LMAX=F\n"\
" 2\n"\
" 0.0000 0.0000 0.0000\n"\
" 1.0000 1.0000 1.0000\n"\
"CONSTRAINTS\n"\
"FIX ATOMS\n"\
"1\n"\
" 2\n"\
"FIX COORDINATES\n"\
"1\n"\
"1 0 1 1\n"\
"\n"\
"FIX COM\n"\
"END CONSTRAINTS\n"\
"ISOTOPE\n"\
"22.99\n"\
"&END\n"
def assertKpoint():
f = StringIO()
cpmd.writer(Mol, f, p)
f = f.getvalue()
assert f == target
Mol.setKpoints('active', 'gamma')
target = head + tail
assertKpoint()
Mol.setKpoints('active', 'mpg')
Mol.setKpoints('mpg', ('2', '0', '0', '0', '0', '0'))
target = head +\
" KPOINTS MONKHORST-PACK\n 2 0 0 \n" +\
tail
assertKpoint()
Mol.setKpoints('mpg', ('2', '0', '0', '0', '0', '0.5'))
target = head +\
" KPOINTS MONKHORST-PACK SHIFT=0 0 0.5 \n" +\
" 2 0 0 \n" +\
tail
assertKpoint()
Mol.setKpoints('active', 'discrete')
Mol.setKpoints('discrete',
[['0.0', '0.0', '0.0', '0.75'],
['0.5', '0.5', '0.5', '0.25']])
Mol.setKpoints('options', {'crystal': False, 'bands': False})
target = head +\
" KPOINTS\n 2\n 0.0 0.0 0.0 0.75\n 0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
Mol.setKpoints('options', {'crystal': True, 'bands': False})
target = head +\
" KPOINTS SCALED\n 2\n 0.0 0.0 0.0 0.75\n"\
" 0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
Mol.setKpoints('discrete',
[['0.0', '0.0', '0.0', '2'],
['0.5', '0.5', '0.5', '0']])
Mol.setKpoints('options', {'crystal': False, 'bands': True})
target = head +\
" 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" +\
tail
assertKpoint()
Mol.setKpoints('options', {'crystal': True, 'bands': True})
target = head +\
" 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" +\
tail
assertKpoint()
Mol.newAtom('Na', (2, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (3, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (4, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (5, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (6, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (7, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (8, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (9, 1, 1), fix=[True, True, True])
Mol.newAtom('Na', (1, 2, 1), fix=[True, True, True])
Mol.newAtom('Na', (1, 3, 1), fix=[True, True, True])
Mol.setKpoints('active', 'gamma')
tail2 = "&END\n"\
"&ATOMS\n"\
"*Na.uspp736.pbe BINARY\n"\
" LMAX=F\n"\
" 12\n"\
" 0.0000 0.0000 0.0000\n"\
" 1.0000 1.0000 1.0000\n"\
" 2.0000 1.0000 1.0000\n"\
" 3.0000 1.0000 1.0000\n"\
" 4.0000 1.0000 1.0000\n"\
" 5.0000 1.0000 1.0000\n"\
" 6.0000 1.0000 1.0000\n"\
" 7.0000 1.0000 1.0000\n"\
" 8.0000 1.0000 1.0000\n"\
" 9.0000 1.0000 1.0000\n"\
" 1.0000 2.0000 1.0000\n"\
" 1.0000 3.0000 1.0000\n"\
"CONSTRAINTS\n"\
"FIX ATOMS\n"\
"11\n"\
" 2 3 4 5 6 7 8 9 10 11\n"\
" 12\n"\
"FIX COORDINATES\n"\
"1\n"\
"1 0 1 1\n"\
"END CONSTRAINTS\n"\
"ISOTOPE\n"\
"22.99\n"\
"&END\n"
target = head + tail2
f = StringIO()
cpmd.writer(Mol, f, newParam('cpmd'))
for i in range(len(target.split('\n'))):
print(f.getvalue().split('\n')[i], target.split('\n')[i])
assert f.getvalue().split('\n')[i] == target.split('\n')[i]
assert f.getvalue() == target
def test_empire_write():
target = "3\n"\
"Hamil=PM3 calc=spt Periodic\n"\
"O 0.0000 0.0000 0.0000\n"\
"H 0.9572 0.0000 0.0000\n"\
"H -0.2400 0.9266 0.0000\n"\
"\n"\
"1.0000 0.0000 0.0000\n"\
"0.0000 2.0000 0.0000\n"\
"0.0000 0.0000 3.0000\n"
f = StringIO()
Mol = Molecule()
Mol.newAtom('O', (0, 0, 0), fmt='angstrom')
Mol.newAtom('H', (0.9572, 0, 0), fmt='angstrom')
Mol.newAtom('H', (-0.23999, 0.926627, 0), fmt='angstrom')
Mol.setCellDim(1, fmt='angstrom')
Mol.setVec(((1, 0, 0), (0, 2, 0), (0, 0, 3)))
empire.writer(Mol, f, None)
assert f.getvalue() == target
def test_pwi_write_kpoints():
body = "&control\n"\
"/\n"\
"\n"\
"&system\n"\
" nat=2\n"\
" ntyp=1\n"\
" celldm(1)=2.0\n"\
" ibrav=0\n"\
" ecutwfc=30.0\n"\
"/\n"\
"\n"\
"&electrons\n"\
"/\n"\
"\n"\
"ATOMIC_SPECIES\n"\
"C 12.0107 C.uspp736.pbe.UPF\n"\
"\n"\
"ATOMIC_POSITIONS alat\n"\
"C 0.00000 0.00000 0.00000 1 0 1\n"\
"C 0.50000 7.50000 7.50000\n"\
"\n"
tail = "\n"\
"CELL_PARAMETERS\n"\
" 1.00000 2.00000 0.00000\n"\
" 0.00000 5.00000 6.00000\n"\
" 0.00000 8.00000 9.00000\n"
Param = pwInput.param['default'].copy()
Mol = Molecule()
Mol.setFmt('alat')
Mol.setCellDim(2)
Mol.setVec(((1, 2, 0), (0, 5, 6), (0, 8, 9)))
Mol.newAtom('C', (0, 0, 0), fix=[False, True])
Mol.newAtom('C', [0.5, 0.5, 0.5], fmt='crystal')
def assertKpoint():
f = StringIO()
pwInput.writer(Mol, f, Param)
assert f.getvalue() == target
Mol.setKpoints('active', 'gamma')
target = body + "K_POINTS gamma\n" + tail
assertKpoint()
Mol.setKpoints('active', 'mpg')
Mol.setKpoints('mpg', ('2', '0', '0', '0', '0', '0'))
target = body +\
"K_POINTS automatic\n2 0 0 0 0 0 \n" +\
tail
assertKpoint()
Mol.setKpoints('active', 'discrete')
Mol.setKpoints('discrete',
[['0.0', '0.0', '0.0', '0.75'],
['0.5', '0.5', '0.5', '0.25']])
Mol.setKpoints('options', {'crystal': False, 'bands': False})
target = body +\
"K_POINTS tpiba\n2\n0.0 0.0 0.0 0.75\n0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
Mol.setKpoints('options', {'crystal': False, 'bands': True})
target = body +\
"K_POINTS tpiba_b\n2\n0.0 0.0 0.0 0.75\n0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
Mol.setKpoints('options', {'crystal': True, 'bands': False})
target = body +\
"K_POINTS crystal\n2\n0.0 0.0 0.0 0.75\n0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
Mol.setKpoints('options', {'crystal': True, 'bands': True})
target = body +\
"K_POINTS crystal_b\n2\n0.0 0.0 0.0 0.75\n0.5 0.5 0.5 0.25\n" +\
tail
assertKpoint()
def test_cpmd_write_format():
Mol = Molecule()
Mol.setCellDim(1, fmt='angstrom')
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('Na', (0, 0, 0), fmt='crystal')
Mol.newAtom('Cl', (0.5, 0.5, 0.5), fmt='crystal')
p = newParam('cpmd')
p["&INFO"] = "comment\n"
p["&CPMD"] = " MOLECULAR DYNAMICS CP\n RESTART "\
"WAVEFUNCTION COORDINATES LATEST\n"
fmts = ['bohr', 'angstrom', 'crystal', 'alat']
head = "&INFO\n"\
"comment\n"\
"&END\n"\
"&CPMD\n"\
" MOLECULAR DYNAMICS CP\n RESTART "\
"WAVEFUNCTION COORDINATES LATEST\n"\
"&END\n"\
"&SYSTEM\n"
body = [" 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.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.0000 0.0000 0.0000\n"
"*Cl.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 4.7243 4.7243 4.7243\n",
" 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.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.0000 0.0000 0.0000\n"
"*Cl.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 2.5000 2.5000 2.5000\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.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.0000 0.0000 0.0000\n"
"*Cl.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.5000 0.5000 0.5000\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.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.0000 0.0000 0.0000\n"
"*Cl.uspp736.pbe BINARY\n" " LMAX=F\n" " 1\n"
" 0.5000 0.5000 0.5000\n"]
tail = "ISOTOPE\n"\
"22.99\n"\
"35.453\n"\
"&END\n"
for i in range(len(body)):
target = head + body[i] + tail
Mol.setFmt(fmts[i])
f = StringIO()
cpmd.writer(Mol, f, p)
assert f.getvalue() == target
def test_pwi_write_calc():
calcs = ["'scf'",
"'relax'",
"'vc-relax'"]
adnl = ["",
"&ions\n ion_dynamics='bfgs'\n/\n\n",
"&ions\n ion_dynamics='bfgs'\n/\n\n"
"&cell\n cell_dynamics='bfgs'\n/\n\n"]
head = "&control\n calculation="
body = "\n/\n\n"\
"&system\n"\
" nat=2\n"\
" ntyp=1\n"\
" celldm(1)=2.0\n"\
" ibrav=0\n"\
" ecutwfc=30.0\n"\
"/\n"\
"\n"\
"&electrons\n"\
" diagonalization='david'\n"\
" conv_thr=1.0e-8\n"\
"/\n"\
"\n"
tail = "ATOMIC_SPECIES\n"\
"C 12.0107 C.uspp736.pbe.UPF\n"\
"\n"\
"ATOMIC_POSITIONS crystal\n"\
"C 0.00000 0.00000 0.00000 1 0 1\n"\
"C 0.50000 0.50000 0.50000\n"\
"\n"\
"K_POINTS automatic\n"\
"2 0 0 0 0 0 \n"\
"\n"\
"CELL_PARAMETERS\n"\
" 1.00000 2.00000 0.00000\n"\
" 0.00000 5.00000 6.00000\n"\
" 0.00000 8.00000 9.00000\n"
Mol = Molecule()
Mol.setFmt('crystal')
Mol.setCellDim(2)
Mol.setVec(((1, 2, 0), (0, 5, 6), (0, 8, 9)))
Mol.newAtom('C', (0, 0, 0), fix=[False, True])
Mol.newAtom('C', [0.5, 0.5, 0.5], fmt='crystal')
Mol.setKpoints('active', 'mpg')
Mol.setKpoints('mpg', ('2', '0', '0', '0', '0', '0'))
def failWrite(p):
try:
pwInput.writer(Mol, f, p)
except KeyError:
return True
else:
return False
for c in range(3):
for a in range(3):
Param = newParam('pwi')
Param['&control']['calculation'] = calcs[c]
Param['&electrons']['diagonalization'] = "'david'"
Param['&electrons']['conv_thr'] = "1.0e-8"
if a > 0:
Param['&ions'] = {'ion_dynamics': "'bfgs'"}
if a > 1:
Param['&cell'] = {'cell_dynamics': "'bfgs'"}
f = StringIO()
if a < c:
failWrite(Param)
else:
pwInput.writer(Mol, f, Param)
target = head + calcs[c] + body + adnl[a] + tail
assert f.getvalue() == target
# default to scf when nothing present:
Param = newParam('pwi')
Param['&electrons']['diagonalization'] = "'david'"
Param['&electrons']['conv_thr'] = "1.0e-8"
f = StringIO()
pwInput.writer(Mol, f, Param)
target = "&control" + body + tail
assert f.getvalue() == target
def test_lmp_write_skew():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(1)
Mol.setVec(((5, 0, 0), (1, 5, 0), (2, 3, 5)))
Mol.newAtom('Na', (0, 0, 0))
p = newParam('lmp')
f = StringIO()
lammpsData.writer(Mol, f, p)
print(f.getvalue())
target = "\n"\
"1 atoms\n"\
"1 atom types\n"\
"\n"\
" 0.0000 5.0000 xlo xhi\n"\
" 0.0000 5.0000 ylo yhi\n"\
" 0.0000 5.0000 zlo zhi\n"\
" 1.0000 2.0000 3.0000 xy xz yz\n"\
"\n"\
"Masses\n"\
"\n"\
"1 22.9900 #Na\n"\
"\n"\
"Atoms # atomic\n"\
"\n"\
"1 1 0.0000 0.0000 0.0000\n"\
"\n"
assert f.getvalue() == target
Mol.setVec(((5, 3, 2), (0, 5, 1), (0, 0, 5)))
try:
lammpsData.writer(Mol, f, p)
except ValueError:
assert True
except:
assert False
else:
assert False
def test_lmp_write_proper():
Mol = Molecule()
Mol.setFmt('angstrom')
Mol.setCellDim(1)
Mol.setVec(((5, 0, 0), (0, 5, 0), (0, 0, 5)))
Mol.newAtom('Na', (0.0, 0.0, 0.0), charge=1.)
Mol.newAtom('Na', (2.5, 2.5, 0.0), charge=1.)
Mol.newAtom('Na', (0.0, 2.5, 2.5), charge=1.)
Mol.newAtom('Na', (2.5, 0.0, 2.5), charge=1.)
Mol.newAtom('Cl', (0.0, 2.5, 0.0), charge=-1.)
Mol.newAtom('Cl', (2.5, 0.0, 0.0), charge=-1.)
Mol.newAtom('Cl', (0.0, 0.0, 2.5), charge=-1.)
Mol.newAtom('Cl', (2.5, 2.5, 2.5), charge=-1.)
p = newParam('lmp')
p['atom_style'] = 'full'
p['bonds'] = True
p['angles'] = True
p['dihedrals'] = True
p['impropers'] = True
head = "\n"\
"8 atoms\n"\
"2 atom types\n"\
"12 bonds\n"\
"1 bond types\n"\
"#1 Cl Na\n"\
"24 angles\n"\
"2 angle types\n"\
"#1 Cl Na Cl\n"\
"#2 Na Cl Na\n"\
"48 dihedrals\n"\
"1 dihedral types\n"\
"#1 Cl Na Cl Na\n"\
"8 impropers\n"\
"2 improper types\n"\
"#1 Cl Na Na Na\n"\
"#2 Na Cl Cl Cl\n"\
"\n"\
" 0.0000 5.0000 xlo xhi\n"\
" 0.0000 5.0000 ylo yhi\n"\
" 0.0000 5.0000 zlo zhi\n"\
"\n"\
"Masses\n"\
"\n"\
"1 22.9900 #Na\n"\
"2 35.4530 #Cl\n"\
"\n"
tail = "\nBonds\n\n"\
"1 1 1 5\n2 1 1 6\n3 1 1 7\n4 1 2 5\n5 1 2 6\n"\
"6 1 2 8\n7 1 3 5\n8 1 3 7\n9 1 3 8\n10 1 4 6\n"\
"11 1 4 7\n12 1 4 8\n"\
"\nAngles\n\n"\
"1 1 5 1 6\n2 1 5 1 7\n3 2 1 5 2\n4 2 1 5 3\n"\
"5 1 6 1 7\n6 2 1 6 2\n7 2 1 6 4\n8 2 1 7 3\n"\
"9 2 1 7 4\n10 1 5 2 6\n11 1 5 2 8\n12 2 2 5 3\n"\
"13 1 6 2 8\n14 2 2 6 4\n15 2 2 8 3\n16 2 2 8 4\n"\
"17 1 5 3 7\n18 1 5 3 8\n19 1 7 3 8\n20 2 3 7 4\n"\
"21 2 3 8 4\n22 1 6 4 7\n23 1 6 4 8\n24 1 7 4 8\n"\
"\nDihedrals\n\n"\
"1 1 6 1 5 2\n2 1 6 1 5 3\n3 1 5 1 6 2\n4 1 5 1 6 4\n"\
"5 1 7 1 5 2\n6 1 7 1 5 3\n7 1 5 1 7 3\n8 1 5 1 7 4\n"\
"9 1 1 5 2 6\n10 1 1 5 2 8\n11 1 1 5 3 7\n12 1 1 5 3 8\n"\
"13 1 7 1 6 2\n14 1 7 1 6 4\n15 1 6 1 7 3\n16 1 6 1 7 4\n"\
"17 1 1 6 2 5\n18 1 1 6 2 8\n19 1 1 6 4 7\n20 1 1 6 4 8\n"\
"21 1 1 7 3 5\n22 1 1 7 3 8\n23 1 1 7 4 6\n24 1 1 7 4 8\n"\
"25 1 6 2 5 3\n26 1 5 2 6 4\n27 1 8 2 5 3\n28 1 5 2 8 3\n"\
"29 1 5 2 8 4\n30 1 2 5 3 7\n31 1 2 5 3 8\n32 1 8 2 6 4\n"\
"33 1 6 2 8 3\n34 1 6 2 8 4\n35 1 2 6 4 7\n36 1 2 6 4 8\n"\
"37 1 2 8 3 5\n38 1 2 8 3 7\n39 1 2 8 4 6\n40 1 2 8 4 7\n"\
"41 1 5 3 7 4\n42 1 5 3 8 4\n43 1 8 3 7 4\n44 1 7 3 8 4\n"\
"45 1 3 7 4 6\n46 1 3 7 4 8\n47 1 3 8 4 6\n48 1 3 8 4 7\n"\
"\nImpropers\n\n"\
"1 2 1 5 6 7\n2 2 2 5 6 8\n3 2 3 5 7 8\n4 2 4 6 7 8\n"\
"5 1 5 1 2 3\n6 1 6 1 2 4\n7 1 7 1 3 4\n8 1 8 2 3 4\n"\
"\n"
atoms = "Atoms # full\n"\
"\n"\
"1 1 1 1.0000 0.0000 0.0000 0.0000\n"\
"2 1 1 1.0000 2.5000 2.5000 0.0000\n"\
"3 1 1 1.0000 0.0000 2.5000 2.5000\n"\
"4 1 1 1.0000 2.5000 0.0000 2.5000\n"\
"5 1 2 -1.0000 0.0000 2.5000 0.0000\n"\
"6 1 2 -1.0000 2.5000 0.0000 0.0000\n"\
"7 1 2 -1.0000 0.0000 0.0000 2.5000\n"\
"8 1 2 -1.0000 2.5000 2.5000 2.5000\n"
f = StringIO()
lammpsData.writer(Mol, f, p)
target = head + atoms + tail
assert f.getvalue() == target
def grapheneOrtho(x, y, z):
"""
Create an orthogonal cell of graphene
x -> x-dimension
y -> sqrt(3)*y-dimension
z -> interlayer distance
"""
mol = Molecule(name="({:},{:})-ortho graphene".format(x, y))
mol.setCellDim(Agraph)
mol.setVec([vecX, sq3 * vecY, z * vecZ])
mol.newAtom('C', [0, 0, 0])
mol.newAtom('C', [0, 1. / 3., 0])
mol.newAtom('C', [0.5, 0.5, 0])
mol.newAtom('C', [0.5, 5. / 6., 0])
# mol.scaleAtoms("crystal")
# mol.setFmt("crystal")
mol.setFmt("crystal", scale=True)
mol.mult(x, y, 1)
return mol
def grapheneHex(x, y, z):
"""
Create a hexagonal cell of graphene
x -> x-dimension
y -> 0.5*x+0.5*sqrt(3)*y-dimension
z -> interlayer distance
"""
mol = Molecule(name="({:},{:})-hex graphene".format(x, y))
mol.setCellDim(Agraph)
mol.setVec([vecX, vecYh, z * vecZ])
mol.newAtom('C', [1. / 3., 2. / 3., 0])
mol.newAtom('C', [2. / 3., 1. / 3., 0])
# mol.scaleAtoms("crystal")
# mol.setFmt("crystal")
mol.setFmt("crystal", scale=True)
mol.mult(x, y, 1)
return mol
