def toString(self, string=None):
if string != None:
qeConf = QEInput(config=string)
qeConf.parse()
else:
if self.qeConf != None:
qeConf = self.qeConf
else:
qeConf = QEInput(config='')
self.updatePWInput(qeConf)
return qeConf.toString()
def test_filter_apply(self):
input = QEInput(config=fixtures.textMain)
# Filter that adds parameters to input
fp = Filter("fPlus")
fp.setParam("control", "prefix", "'ni'")
fp.setParam("control", "pseudo_dir", "''")
fp.setParam("control", "outdir", "''")
fp.setCard({
"name": "occupations",
"lines": ("New line", )
}) # Add new card
fp.setNamelist({
"name": "cell",
"params": {
"hello": "world"
}
}) # Add new namelist
fp.setNamelist({"name": "phonon"})
fp.apply(input, "plus")
self.assertEqual(input.toString(), fixtures.assertPlus)
# Filter that removes parameters from input
fm = Filter("fMinus")
fm.setCard({"name": "atomic_species"})
fm.setNamelist({"name": "phonon"}) # Remove namelist
fm.setParam("cell",
"hello") # Remove parameter that makes namelist empty
fm.setParam("control", "prefix") # Remove parameter
fm.apply(input, "minus")
self.assertEqual(input.toString(), fixtures.assertMinus)
def test_qeinput_card_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
card = input.card("SOME_CARD")
self.assertFalse(input.cardExists("some_card"))
card = input.card("occupations")
self.assertTrue(input.cardExists("occupations"))
def test_qeinput_namelist_exists(self):
input = QEInput(config=fixtures.textMain)
# If non-standard card is requested, it will not add it!
nl = input.namelist("SOME_NAMELIST")
self.assertFalse(input.namelistExists("some_namelist"))
nl = input.namelist("cell")
self.assertTrue(input.namelistExists("cell"))
def test_qeinput_namelist(self):
input = QEInput()
nl = Namelist("control")
nl.set("title", "'Ni'")
input.addNamelist(nl)
nl2 = input.namelist("phonon")
self.assertEqual(input.toString(), fixtures.assertNewNamelist)
input.removeNamelist("control")
self.assertEqual(input.toString(), fixtures.assertNewNamelist2)
def test_qeinput_save(self):
fname = "temp.in"
input = QEInput(config=fixtures.textMain)
input.save(fname)
self.assertTrue(filecmp.cmp(fname, "ref.in"))
try:
os.remove(fname)
except OSError:
pass # Doesn't exist
def test_qeinput_card(self):
input = QEInput()
c = Card("atomic_species")
c.setArg("temp")
c.addLine("Ni 26.98 Ni.pbe-nd-rrkjus.UPF")
input.addCard(c)
c2 = input.card("atomic_positions")
self.assertEqual(input.toString(), fixtures.assertNewCard)
input.removeCard("atomic_species")
self.assertEqual(input.toString(), fixtures.assertNewCard2)
def save(self, fname=None):
"""Writes/updates structure into PW config file,
if the file does not exist, new one will be created"""
if fname != None:
filename = fname
self.lattice.save(filename)
qeConf = QEInput(fname)
qeConf.parse()
else:
filename = self.filename
self.lattice.save(filename)
qeConf = self.qeConf
self.updatePWInput(qeConf)
qeConf.save(filename)
def save(self, fname=None):
"""Will save the lattice either into its own file or into supplied with fname.
It will also create all relevant sections/cards"""
from os.path import exists
if fname != None:
filename = fname
if not exists(filename):
f = open(filename, 'w')
qeConf = QEInput(fname)
qeConf.parse()
else:
qeConf = self.qeConf
filename = qeConf.filename
self.updatePWInput(qeConf)
qeConf.save(filename)
def test_qeinput_filter(self):
input = QEInput(config=fixtures.textMain)
f = Filter("fPlus")
f.setParam("control", "calculation", "'md'")
f.setCard({"name": "occupations", "lines": ("New line", )})
input.applyFilter(f, "plus")
self.assertEqual(input.toString(), fixtures.assertInputFilterPlus)
f = Filter("fMinus")
f.setNamelist({"name": "control"})
f.setCard({"name": "k_points"})
input.applyFilter(f, "minus")
self.assertEqual(input.toString(), fixtures.assertInputFilterMinus)
def write(self, filename=None, format="pwinput"):
"""Save structure to file in the specified format
format -- structure formats
'pwinput' ( pw.x input, default), 'pwoutput' (pw.x output),
'bratoms', 'cif', 'discus', 'pdb', 'pdffit', 'rawxyz',
'xcfg', 'xyz'
No return value.
"""
if format == "pwinput":
self._qeInput.update(forceUpdate=True)
if filename == None:
filename = self._qeInput.filename
input = QEInput(config=self._qeInput.toString(), type='pw')
input.save(filename=filename)
else:
self.matter().write(filename=filename, format=format)
return
def test_qeinput_read(self):
input = QEInput()
input.readString(fixtures.textMain) # Load input from string
self.assertEqual(input.config, fixtures.textMain) # config is set
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
input.readFile("matdyn.in")
self.assertEqual(input.filename, "matdyn.in") # filename is set
input.readFile("ni.scf.in") # Load input from file
nl = input.namelist("control")
c = input.card("atomic_positions")
self.assertEqual(nl.get("calculation"), "'scf'")
self.assertEqual(c.line(0), "Ni 0.00 0.00 0.00")
def getLatticeParamsFromPWSCF(self, ibrav, fname):
qeConf = QEInput(fname)
qeConf.parse()
return self.parsePWInput(ibrav, qeConf)
def test_qeinput_remove(self):
input = QEInput(config=fixtures.textMain)
input.removeCard("atomic_species") # Remove non-existing card
input.removeNamelist("control") # Remove non-existing namelist
def setLatticeFromPWSCF(self, fname):
self.qeConf = QEInput(fname)
self.qeConf.parse()
setLatticeFromPWInput(self, qeConf)
base = self._base / self._a
self.setLattice(ibrav=self._ibrav, a=self._a, base=base)
else:
if self._ibrav == 0:
pass
else:
self._type = value
type = property(_get_type,
_set_type,
doc="""QE lattice type: 'celldm',
'traditional' or 'generic cubic', 'generic hexagonal'(implies ibrav = 0""")
if __name__ == '__main__':
pwInput = QEInput('scf.in', type='pw')
pwInput.parse()
qeLattice = QELattice(qeConf=pwInput)
print qeLattice.latticeParams()
# qeLattice = QELattice(fname = 'qwe.in')
# qeLattice.setLatticeFromPrimitiveVectors(12,qeLattice.lattice().base)
# print qeLattice.latticeParams()
# qeLattice.latticeType = 'generic hexagonal'
# qeLattice.bb = 12
qeLattice.a = 13.0
qeLattice.b = 24.0
qeLattice.c = 3.
qeLattice.ibrav = 4
print qeLattice.b, qeLattice.c,
print qeLattice.latticeParams()
qeLattice.saveLatticeToPWSCF('./scf_2.in')
def test_qeinput_attach(self):
"This unit test is useful for matdyn simulation type"
input = QEInput()
input.addAttach("176\n\
0.000000 0.000000 0.456392 0.000000")
self.assertEqual(input.toString(), fixtures.assertAttach)
def test_qeinput_parse(self):
input = QEInput(config=fixtures.textMain, parse=False)
self.assertEqual(input.toString(), "")
input = QEInput(config=fixtures.textMain, parse=True)
self.assertEqual(input.namelistExists("control"), True)
def test_qeinput_type(self):
input = QEInput(type="ph")
self.assertEqual(input.type(), "ph")
