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_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_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_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
