def test_writestring(self):
# Test for the string export of s atructure into the exciting input xml schema
input_string = (
'<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'xsi:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput'
'.xsd">\n <title>Na4 Cl4</title>\n <structure speciespath="./">\n '
'<crystal scale="1.8897543768634038">\n <basevect> 5.62000000'
' 0.00000000 0.00000000</basevect>\n <basevect> '
'0.00000000 5.62000000 0.00000000</basevect>\n '
'<basevect> 0.00000000 0.00000000 5.62000000</basevect>'
'\n </crystal>\n <species speciesfile="Na.xml">\n <atom coord='
'" 0.00000000 0.00000000 0.00000000" />\n <atom coor'
'd=" 0.50000000 0.50000000 0.00000000" />\n <atom co'
'ord=" 0.50000000 0.00000000 0.50000000" />\n <atom '
'coord=" 0.00000000 0.50000000 0.50000000" />\n </spec'
'ies>\n <species speciesfile="Cl.xml">\n <atom coord=" 0.5000'
'0000 0.00000000 0.00000000" />\n <atom coord=" 0.00'
'000000 0.50000000 0.00000000" />\n <atom coord=" 0.'
'00000000 0.00000000 0.50000000" />\n <atom coord=" '
'0.50000000 0.50000000 0.50000000" />\n </species>\n </str'
'ucture>\n</input>\n')
lattice = Lattice.cubic('5.62')
structure = Structure(lattice, ['Na', 'Na', 'Na', 'Na',
'Cl', 'Cl', 'Cl', 'Cl'],
[[0, 0, 0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.0], [0.0, 0.5, 0.0],
[0.0, 0.0, 0.5], [0.5, 0.5, 0.5]])
excin = ExcitingInput(structure)
for l1, l2 in zip(input_string.split("\n"),
excin.write_string('unchanged').split("\n")):
if not l1.strip().startswith("<crystal scale"):
self.assertEqual(l1, l2)
def test_writebandstr(self):
filepath = os.path.join(test_dir, 'CsI3Pb.cif')
structure = Structure.from_file(filepath)
excin = ExcitingInput(structure)
string = excin.write_string('primitive', bandstr=True)
bandstr = string.split('<properties>')[1].split('</properties>')[0]
coord = []
label = []
coord_ref = [[0.0, 0.0, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.0], [0.0, 0.0, 0.5], [0.5, 0.0, 0.5],
[0.5, 0.5, 0.5],
[0.0, 0.5, 0.5], [0.0, 0.0, 0.5], [0.0, 0.5, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.5, 0.5, 0.5]]
label_ref = ['GAMMA', 'X', 'S', 'Y', 'GAMMA', 'Z', 'U', 'R', 'T', 'Z',
'Y', 'T',
'U', 'X', 'S', 'R']
root = ET.fromstring(bandstr)
for plot1d in root.iter('plot1d'):
for point in plot1d.iter('point'):
coord.append([float(i) for i in point.get('coord').split()])
label.append(point.get('label'))
self.assertEqual(label, label_ref)
self.assertEqual(coord, coord_ref)
def test_writebandstr(self):
filepath = os.path.join(test_dir, 'CsI3Pb.cif')
structure = Structure.from_file(filepath)
excin = ExcitingInput(structure)
string = excin.write_string('primitive', bandstr=True)
bandstr = string.split('<properties>')[1].split('</properties>')[0]
coord = []
label = []
coord_ref = [[0.0, 0.0, 0.0], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.0, 0.5, 0.0], [0.0, 0.0, 0.0], [0.0, 0.0, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.5], [0.0, 0.5, 0.5],
[0.0, 0.0, 0.5], [0.0, 0.5, 0.0], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.0, 0.0], [0.5, 0.5, 0.0],
[0.5, 0.5, 0.5]]
label_ref = [
'GAMMA', 'X', 'S', 'Y', 'GAMMA', 'Z', 'U', 'R', 'T', 'Z', 'Y', 'T',
'U', 'X', 'S', 'R'
]
root = ET.fromstring(bandstr)
for plot1d in root.iter('plot1d'):
for point in plot1d.iter('point'):
coord.append([float(i) for i in point.get('coord').split()])
label.append(point.get('label'))
self.assertEqual(label, label_ref)
self.assertEqual(coord, coord_ref)
def test_writestring(self):
# Test for the string export of s atructure into the exciting input xml schema
input_string = (
'<input xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" '
'xsi:noNamespaceSchemaLocation="http://xml.exciting-code.org/excitinginput'
'.xsd">\n <title>Na4 Cl4</title>\n <structure speciespath="./">\n '
'<crystal scale="1.8897543768634038">\n <basevect> 5.62000000'
' 0.00000000 0.00000000</basevect>\n <basevect> '
'0.00000000 5.62000000 0.00000000</basevect>\n '
'<basevect> 0.00000000 0.00000000 5.62000000</basevect>'
'\n </crystal>\n <species speciesfile="Na.xml">\n <atom coord='
'" 0.00000000 0.00000000 0.00000000" />\n <atom coor'
'd=" 0.50000000 0.50000000 0.00000000" />\n <atom co'
'ord=" 0.50000000 0.00000000 0.50000000" />\n <atom '
'coord=" 0.00000000 0.50000000 0.50000000" />\n </spec'
'ies>\n <species speciesfile="Cl.xml">\n <atom coord=" 0.5000'
'0000 0.00000000 0.00000000" />\n <atom coord=" 0.00'
'000000 0.50000000 0.00000000" />\n <atom coord=" 0.'
'00000000 0.00000000 0.50000000" />\n <atom coord=" '
'0.50000000 0.50000000 0.50000000" />\n </species>\n </str'
'ucture>\n</input>\n')
lattice = Lattice.cubic('5.62')
structure = Structure(
lattice, ['Na', 'Na', 'Na', 'Na', 'Cl', 'Cl', 'Cl', 'Cl'],
[[0, 0, 0], [0.5, 0.5, 0.0], [0.5, 0.0, 0.5], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.0], [0.0, 0.5, 0.0], [0.0, 0.0, 0.5],
[0.5, 0.5, 0.5]])
excin = ExcitingInput(structure)
for l1, l2 in zip(input_string.split("\n"),
excin.write_string('unchanged').split("\n")):
if not l1.strip().startswith("<crystal scale"):
self.assertEqual(l1.strip(), l2.strip())
def test_writebandstr(self):
filepath = os.path.join(test_dir, "CsI3Pb.cif")
structure = Structure.from_file(filepath)
excin = ExcitingInput(structure)
string = excin.write_string("primitive", bandstr=True)
bandstr = string.split("<properties>")[1].split("</properties>")[0]
coord = []
label = []
coord_ref = [
[0.0, 0.0, 0.0],
[0.5, 0.0, 0.0],
[0.5, 0.5, 0.0],
[0.0, 0.5, 0.0],
[0.0, 0.0, 0.0],
[0.0, 0.0, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.5, 0.5],
[0.0, 0.5, 0.5],
[0.0, 0.0, 0.5],
[0.0, 0.5, 0.0],
[0.0, 0.5, 0.5],
[0.5, 0.0, 0.5],
[0.5, 0.0, 0.0],
[0.5, 0.5, 0.0],
[0.5, 0.5, 0.5],
]
label_ref = [
"GAMMA",
"X",
"S",
"Y",
"GAMMA",
"Z",
"U",
"R",
"T",
"Z",
"Y",
"T",
"U",
"X",
"S",
"R",
]
root = ET.fromstring(bandstr)
for plot1d in root.iter("plot1d"):
for point in plot1d.iter("point"):
coord.append([float(i) for i in point.get("coord").split()])
label.append(point.get("label"))
self.assertEqual(label, label_ref)
self.assertEqual(coord, coord_ref)
def test_paramdict(self):
coords = [[0.0, 0.0, 0.0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84,
b=3.84,
c=3.84,
alpha=120,
beta=90,
gamma=60)
struct = Structure(lattice, ["Si", "Si"], coords)
paradir = {
"grst": {
"do": "fromscratch",
"ngridk": "8 8 8",
"xctype": "GGA_PBE_SOL",
"gmaxvr": "14.0",
},
"xs": {
"xstype": "BSE",
"ngridk": "4 4 4",
"ngridq": "4 4 4",
"nempty": "30",
"gqmax": "3.0",
"broad": "0.07",
"tevout": "true",
"energywindow": {
"intv": "0.0 1.0",
"points": "1200"
},
"screening": {
"screentype": "full",
"nempty": "100"
},
"BSE": {
"bsetype": "singlet",
"nstlbse": "1 5 1 4"
},
},
}
test_input = ExcitingInput(struct)
test_string = test_input.write_string("unchanged", **paradir)
# read reference file
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR,
"input_exciting2.xml")
tree = ET.parse(filepath)
root = tree.getroot()
ref_string = ET.tostring(root, encoding="unicode")
self.assertEqual(ref_string.strip(), test_string.strip())
def test_fromfile(self):
# Test for the import of a structure directly from an exciting
# input file
filepath = os.path.join(test_dir, 'input1.xml')
excin = ExcitingInput.from_file(filepath)
lattice = [[0.0, 2.81, 2.81], [2.81, 0.0, 2.81], [2.81, 2.81, 0.0]]
atoms = ['Na', 'Cl']
fraccoords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
self.assertEqual(lattice, excin.structure.lattice.matrix.tolist())
self.assertEqual(atoms,
[site.specie.symbol for site in excin.structure])
self.assertEqual(fraccoords, [site.frac_coords.tolist() for site in
excin.structure])
def test_fromfile(self):
# Test for the import of a structure directly from an exciting
# input file
filepath = os.path.join(test_dir, 'input1.xml')
excin = ExcitingInput.from_file(filepath)
lattice = [[0.0, 2.81, 2.81], [2.81, 0.0, 2.81], [2.81, 2.81, 0.0]]
atoms = ['Na', 'Cl']
fraccoords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
self.assertEqual(lattice, excin.structure.lattice.matrix.tolist())
self.assertEqual(atoms,
[site.specie.symbol for site in excin.structure])
self.assertEqual(
fraccoords,
[site.frac_coords.tolist() for site in excin.structure])
def parse(self, options, *args, **kwargs):
path = self.raw_value
if exists(path):
if isfile(path):
filename = basename(path)
if filename.lower().endswith('.cif'):
from pymatgen.io.cif import CifParser
try:
result = CifParser(path).get_structures()[0]
except:
self.write_message(
'Could not parse CIF file: "{0}"'.format(path))
raise InvalidOption
elif filename.lower().endswith('.cssr'):
from pymatgen.io.cssr import Cssr
try:
result = Cssr.from_file(path).structure
except:
self.write_message(
'Could not parse CSSR file: "{0}"'.format(path))
raise InvalidOption
elif filename.lower().endswith('.xml'):
from pymatgen.io.exciting import ExcitingInput
try:
result = ExcitingInput.from_file(path).structure
except:
self.write_message(
'Could not parse Exciting input file: "{0}"'.
format(path))
raise InvalidOption
else:
from pymatgen.io.vasp import Poscar
try:
result = Poscar.from_file(path).structure
except:
self.write_message(
'Could not parse POSCAR file "{0}"'.format(path))
raise InvalidOption
if not 'result' in locals():
write_message('File format not supported')
raise InvalidOption
else:
return result
else:
self.write_message('"{0}" is a directory!'.format(path))
raise InvalidOption
else:
self.write_message('Cannot locate file "{0}"'.format(path))
raise InvalidOption
def test_fromfile(self):
# Test for the import of a structure directly from an exciting
# input file
filepath = os.path.join(PymatgenTest.TEST_FILES_DIR,
"input_exciting1.xml")
excin = ExcitingInput.from_file(filepath)
lattice = [[0.0, 2.81, 2.81], [2.81, 0.0, 2.81], [2.81, 2.81, 0.0]]
atoms = ["Na", "Cl"]
fraccoords = [[0.0, 0.0, 0.0], [0.5, 0.5, 0.5]]
self.assertArrayAlmostEqual(lattice,
excin.structure.lattice.matrix.tolist())
self.assertEqual(atoms,
[site.specie.symbol for site in excin.structure])
self.assertEqual(
fraccoords,
[site.frac_coords.tolist() for site in excin.structure])
def from_file(cls, filename, primitive=False, sort=False, merge_tol=0.0):
"""
Reads a structure from a file. For example, anything ending in
a "cif" is assumed to be a Crystallographic Information Format file.
Supported formats include CIF, POSCAR/CONTCAR, CHGCAR, LOCPOT,
vasprun.xml, CSSR, Netcdf and pymatgen's JSON serialized structures.
Args:
filename (str): The filename to read from.
primitive (bool): Whether to convert to a primitive cell
Only available for cifs. Defaults to False.
sort (bool): Whether to sort sites. Default to False.
merge_tol (float): If this is some positive number, sites that
are within merge_tol from each other will be merged. Usually
0.01 should be enough to deal with common numerical issues.
Returns:
Structure.
"""
filename = str(filename)
if filename.endswith(".nc"):
# Read Structure from a netcdf file.
from pymatgen.io.abinit.netcdf import structure_from_ncdata
s = structure_from_ncdata(filename, cls=cls)
if sort:
s = s.get_sorted_structure()
return s
from pymatgen.io.lmto import LMTOCtrl
from pymatgen.io.vasp import Vasprun, Chgcar
from pymatgen.io.exciting import ExcitingInput
from monty.io import zopen
fname = os.path.basename(filename)
with zopen(filename, "rt") as f:
contents = f.read()
if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
return cls.from_str(contents, fmt="cif",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*POSCAR*") or fnmatch(fname, "*CONTCAR*") or fnmatch(fname, "*.vasp"):
s = cls.from_str(contents, fmt="poscar",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "CHGCAR*") or fnmatch(fname, "LOCPOT*"):
s = Chgcar.from_file(filename).structure
elif fnmatch(fname, "vasprun*.xml*"):
s = Vasprun(filename).final_structure
elif fnmatch(fname.lower(), "*.cssr*"):
return cls.from_str(contents, fmt="cssr",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
return cls.from_str(contents, fmt="json",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.yaml*"):
return cls.from_str(contents, fmt="yaml",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "*.xsf"):
return cls.from_str(contents, fmt="xsf",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "input*.xml"):
return ExcitingInput.from_file(fname).structure
elif fnmatch(fname, "*rndstr.in*") \
or fnmatch(fname, "*lat.in*") \
or fnmatch(fname, "*bestsqs*"):
return cls.from_str(contents, fmt="mcsqs",
primitive=primitive, sort=sort,
merge_tol=merge_tol)
elif fnmatch(fname, "CTRL*"):
return LMTOCtrl.from_file(filename=filename).structure
else:
raise ValueError("Unrecognized file extension!")
if sort:
s = s.get_sorted_structure()
if merge_tol:
s.merge_sites(merge_tol)
s.__class__ = cls
return s