def __init__(self, directory):
super(PwscfParser, self).__init__(directory)
self.settings = {}
parser = PwscfStdOutputParser()
with open(os.path.join(directory, self.outputf), "r") as f:
for line in parser.parse(f.readlines()):
self.settings.update(line)
def test_energy_contributions():
"""Test that rules which are generated by a function work"""
lines = """
! total energy = -439.62704582 Ry
Harris-Foulkes estimate = -439.62704606 Ry
estimated scf accuracy < 0.00000033 Ry
The total energy is the sum of the following terms:
one-electron contribution = -13.58082604 Ry
hartree contribution = 68.24717960 Ry
xc contribution = -123.45729278 Ry
ewald contribution = -370.83610660 Ry
smearing contrib. (-TS) = 0.00000000 Ry
convergence has been achieved in 8 iterations
""".split("\n")
parser = PwscfStdOutputParser()
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["total energy"] == -439.62704582
assert flattened["total energy units"] == "Ry"
assert flattened["one-electron energy contribution"] == -13.58082604
assert flattened["one-electron energy contribution units"] == "Ry"
def __init__(self, files):
super(PwscfParser, self).__init__(files)
self.settings = {}
self.all_parsed_data = {}
parser = PwscfStdOutputParser()
# Look for appropriate files
self.inputf = self.outputf = None
for f in self._files:
try:
if self._get_line('Program PWSCF', f, return_string=False):
if self.outputf is not None:
raise InvalidIngesterException('More than one output file!')
self.outputf = f
elif self._get_line('&control', f, return_string=False, case_sens=False):
if self.inputf is not None:
raise InvalidIngesterException('More than one input file')
self.inputf = f
except UnicodeDecodeError as e:
pass
if self.inputf is None:
raise InvalidIngesterException('Failed to find input file')
if self.outputf is None:
raise InvalidIngesterException('Failed to find output file')
# Read in the settings
with open(self.outputf, "r") as f:
for line in parser.parse(f.readlines()):
self.settings.update(line)
for k, v in line.items():
if k in self.all_parsed_data:
self.all_parsed_data[k].append(v)
else:
self.all_parsed_data[k] = [v]
def test_simple():
"""Test that parsing simple one-line rules works"""
parser = PwscfStdOutputParser()
lines = """
bravais-lattice index = 0
lattice parameter (alat) = 7.1517 a.u.
unit-cell volume = 919.5821 (a.u.)^3
""".split("\n")
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["lattice parameter"] == 7.1517
assert flattened["bravais-lattice index"] == 0
assert flattened["unit-cell volume"] == 919.5821
assert flattened["unit-cell volume units"] == "(a.u.)^3"
def test_parse_stress():
"""Test that parses multiple lines into a list output"""
lines = """
total stress (Ry/bohr**3) (kbar) P= -77.72
-0.00055293 0.00000000 0.00000000 -81.34 0.00 0.00
0.00000000 -0.00055293 0.00000000 0.00 -81.34 0.00
0.00000000 0.00000000 -0.00047917 0.00 0.00 -70.49
""".split("\n")
parser = PwscfStdOutputParser()
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["pressure"] == -77.72
assert flattened["pressure units"] == "kbar"
assert len(flattened["stress"]) == 3
assert flattened["stress"][1][1] == -81.34
assert flattened["stress units"] == "kbar"
def test_ldaU():
"""Test parsing simplified LDA+U calculations"""
lines = """
Simplified LDA+U calculation (l_max = 2) with parameters (eV):
atomic species L U alpha J0 beta
Fe1 2 4.3000 0.0000 0.0000 0.0000
Fe2 2 4.3000 0.0000 0.0000 0.0000
""".split("\n")
parser = PwscfStdOutputParser()
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["LDA+U l_max"] == 2
assert flattened["LDA+U parameters"]["Fe1"]["L"] == 2
assert flattened["LDA+U parameters"]["Fe1"]["U"] == 4.3
assert flattened["LDA+U parameters"]["Fe2"]["L"] == 2
assert flattened["LDA+U parameters"]["Fe2"]["U"] == 4.3
def test_parse_force():
"""Test that force parsing works"""
lines = """
Forces acting on atoms (Ry/au):
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000054
The non-local contrib. to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 -0.00000016
The ionic contribution to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000000
The local contribution to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000187
The core correction contribution to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000000
The Hubbard contrib. to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 0.00000000
The SCF correction term to forces
atom 1 type 1 force = 0.00000000 0.00000000 0.00000000
atom 2 type 2 force = 0.00000000 0.00000000 -0.00000117
Total force = 0.011752 Total SCF correction = 0.000072
""".split("\n")
parser = PwscfStdOutputParser()
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["force units"] == "(Ry/au)"
assert flattened["total force"] == 0.011752
assert flattened["total SCF correction"] == 0.000072
assert flattened["forces"][1][2] == 0.00000054
assert flattened["non-local contribution to forces"][1][2] == -0.00000016
assert flattened["Atomic species index for forces"][1] == 2
def test_parse_force_short():
"""Test that force parsing without the contributions works"""
lines = """
Forces acting on atoms (Ry/au):
atom 1 type 1 force = -0.00147138 0.00084950 0.00000000
atom 2 type 1 force = 0.00137999 -0.00079673 0.00000000
atom 3 type 1 force = 0.00147138 -0.00084950 0.00000000
atom 4 type 1 force = -0.00137999 0.00079673 0.00000000
Total force = 0.003294 Total SCF correction = 0.000014
""".split("\n")
parser = PwscfStdOutputParser()
results = list(parser.parse(lines))
flattened = {}
for r in results:
flattened.update(r)
assert flattened["force units"] == "(Ry/au)"
assert flattened["total force"] == 0.003294
assert flattened["total SCF correction"] == 0.000014
assert flattened["forces"][3][0] == -0.00137999
assert flattened["Atomic species index for forces"][3] == 1