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 assertKpoint():
f = StringIO()
cpmd.writer(Mol, f, p)
f = f.getvalue()
assert f == target
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