def from_string(cls, string: str):
""" Reads an Incar object from a string.
This method is different from that of Incar superclass at it does not
support ";" semantic which split the incar flags.
Args:
string (str): Incar string
Returns:
ViseIncar object
"""
lines = list(clean_lines(string.splitlines()))
params = {}
for line in lines:
# YK: Support the split of ";" semantic in INCAR file
for sub_line in line.split(";"):
m = re.match(r'(\w+)\s*=\s*(.*)', sub_line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = ViseIncar.proc_val(key, val)
params[key] = val
return cls(params)
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Note: Checks to see if generated by pymatgen, if not it is impossible
to generate structure object so it is not possible to generate
header object and routine ends
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg == -1:
feffpmg = False
if feffpmg:
comment2 = " ".join(lines[1].split()[2:])
source = " ".join(lines[2].split()[2:])
basis_vec = lines[6].split(":")[-1].split()
# a, b, c
a = float(basis_vec[0])
b = float(basis_vec[1])
c = float(basis_vec[2])
lengths = [a, b, c]
# alpha, beta, gamma
basis_ang = lines[7].split(":")[-1].split()
alpha = float(basis_ang[0])
beta = float(basis_ang[1])
gamma = float(basis_ang[2])
angles = [alpha, beta, gamma]
lattice = Lattice.from_parameters(*lengths, *angles)
natoms = int(lines[8].split(":")[-1].split()[0])
atomic_symbols = []
for i in range(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in range(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
struct = Structure(lattice, atomic_symbols, coords, False, False,
False)
h = Header(struct, source, comment2)
return h
raise ValueError(
"Header not generated by pymatgen, cannot return header object")
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Note: Checks to see if generated by pymatgen, if not it is impossible
to generate structure object so it is not possible to generate
header object and routine ends
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg:
comment2 = ' '.join(lines[1].split()[2:])
source = ' '.join(lines[2].split()[2:])
basis_vec = lines[6].split(":")[-1].split()
# a, b, c
a = float(basis_vec[0])
b = float(basis_vec[1])
c = float(basis_vec[2])
lengths = [a, b, c]
# alpha, beta, gamma
basis_ang = lines[7].split(":")[-1].split()
alpha = float(basis_ang[0])
beta = float(basis_ang[1])
gamma = float(basis_ang[2])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
natoms = int(lines[8].split(":")[-1].split()[0])
atomic_symbols = []
for i in range(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in range(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
struct = Structure(lattice, atomic_symbols, coords, False,
False, False)
h = Header(struct, source, comment2)
return h
else:
return "Header not generated by pymatgen, cannot return header object"
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Args:
header_str:
pymatgen generated feff.inp header
Returns:
structure object.
"""
lines = tuple(clean_lines(header_str.split("\n"), False))
comment = lines[0]
feffpmg = comment.find("pymatgen")
if feffpmg > 0:
source = lines[1].split()[2]
natoms = int(lines[7].split()[2])
basis_vec = lines[5].split()
a = float(basis_vec[2])
b = float(basis_vec[3])
c = float(basis_vec[4])
lengths = [a, b, c]
basis_ang = lines[6].split()
alpha = float(basis_ang[2])
beta = float(basis_ang[3])
gamma = float(basis_ang[4])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
atomic_symbols = []
for i in xrange(8, 8 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in xrange(natoms):
toks = lines[i + 8].split()
coords.append([float(s) for s in toks[3:]])
struct_fromfile = Structure(lattice, atomic_symbols, coords, False,
False, False)
struct_fromfile.compound = lines[3].split()[2]
h = Header(struct_fromfile, comment)
h.set_source(source)
return h
else:
return "Header not generated by pymatgen, " \
"cannot return header object"
def from_file(filename="feff.inp"):
"""
Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.
Args:
filename: Filename for either PARAMETER or feff.inp file
Returns:
Feff_tag object
"""
with zopen(filename, "rt") as f:
lines = list(clean_lines(f.readlines()))
params = {}
eels_params = []
ieels = -1
ieels_max = -1
for i, line in enumerate(lines):
m = re.match(r"([A-Z]+\d*\d*)\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Tags.proc_val(key, val)
if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
if key in ["ELNES", "EXELFS"]:
ieels = i
ieels_max = ieels + 5
else:
params[key] = val
if ieels >= 0:
if ieels <= i <= ieels_max:
if i == ieels + 1:
if int(line.split()[1]) == 1:
ieels_max -= 1
eels_params.append(line)
if eels_params:
if len(eels_params) == 6:
eels_keys = [
"BEAM_ENERGY",
"BEAM_DIRECTION",
"ANGLES",
"MESH",
"POSITION",
]
else:
eels_keys = ["BEAM_ENERGY", "ANGLES", "MESH", "POSITION"]
eels_dict = {
"ENERGY": Tags._stringify_val(eels_params[0].split()[1:])
}
for k, v in zip(eels_keys, eels_params[1:]):
eels_dict[k] = str(v)
params[str(eels_params[0].split()[0])] = eels_dict
return Tags(params)
def from_file(filename="feff.inp"):
"""
Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.
Args:
filename: Filename for either PARAMETER or feff.inp file
Returns:
Feff_tag object
"""
with zopen(filename, "rt") as f:
lines = list(clean_lines(f.readlines()))
params = {}
eels_params = []
ieels = -1
ieels_max = -1
for i, line in enumerate(lines):
m = re.match(r"([A-Z]+\d*\d*)\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Tags.proc_val(key, val)
if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
if key in ["ELNES", "EXELFS"]:
ieels = i
ieels_max = ieels + 5
else:
params[key] = val
if ieels >= 0:
if i >= ieels and i <= ieels_max:
if i == ieels + 1:
if int(line.split()[1]) == 1:
ieels_max -= 1
eels_params.append(line)
if eels_params:
if len(eels_params) == 6:
eels_keys = ['BEAM_ENERGY', 'BEAM_DIRECTION', 'ANGLES', 'MESH', 'POSITION']
else:
eels_keys = ['BEAM_ENERGY', 'ANGLES', 'MESH', 'POSITION']
eels_dict = {"ENERGY": Tags._stringify_val(eels_params[0].split()[1:])}
for k, v in zip(eels_keys, eels_params[1:]):
eels_dict[k] = str(v)
params[str(eels_params[0].split()[0])] = eels_dict
return Tags(params)
def from_string(string):
"""
Reads an Incar object from a string.
Args:
string (str): Incar string
Returns:
Incar object
"""
lines = list(clean_lines(string.splitlines()))
params = {}
for line in lines:
m = re.match(r'(\w+)\s*=\s*(.*)', line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Incar.proc_val(key, val)
params[key] = val
return Incar(params)
def from_file(filename):
"""
Reads an Incar object from a file.
Args:
filename - Filename for file
Returns:
Incar object
"""
with zopen(filename, "r") as f:
lines = list(clean_lines(f.readlines()))
params = {}
for line in lines:
m = re.match("(\w+)\s*=\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Incar.proc_val(key, val)
params[key] = val
return Incar(params)
def from_file(filename="feff.inp"):
"""
Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.
Args:
filename: Filename for either PARAMETER or feff.inp file
Returns:
Feff_tag object
"""
with zopen(filename, "r") as f:
lines = list(clean_lines(f.readlines()))
params = {}
for line in lines:
m = re.match("([A-Z]+\d*\d*)\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = FeffTags.proc_val(key, val)
if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
params[key] = val
return FeffTags(params)
def from_file(filename="feff.inp"):
"""
Creates a Feff_tag dictionary from a PARAMETER or feff.inp file.
Args:
filename: Filename for either PARAMETER or feff.inp file
Returns:
Feff_tag object
"""
with zopen(filename, "rt") as f:
lines = list(clean_lines(f.readlines()))
params = {}
for line in lines:
m = re.match("([A-Z]+\d*\d*)\s*(.*)", line)
if m:
key = m.group(1).strip()
val = m.group(2).strip()
val = Tags.proc_val(key, val)
if key not in ("ATOMS", "POTENTIALS", "END", "TITLE"):
params[key] = val
return Tags(params)
def from_string(string):
"""
Reads an PWInput object from a string.
Args:
string (str): PWInput string
Returns:
PWInput object
"""
lines = list(clean_lines(string.splitlines()))
def input_mode(line):
if line[0] == "&":
return ("sections", line[1:].lower())
elif "ATOMIC_SPECIES" in line:
return ("pseudo", )
elif "K_POINTS" in line:
return ("kpoints", line.split("{")[1][:-1])
elif "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
return ("structure", line.split("{")[1][:-1])
elif line == "/":
return None
else:
return mode
sections = {
"control": {},
"system": {},
"electrons": {},
"ions": {},
"cell": {}
}
pseudo = {}
pseudo_index = 0
lattice = []
species = []
coords = []
structure = None
site_properties = {"pseudo": []}
mode = None
for line in lines:
mode = input_mode(line)
if mode is None:
pass
elif mode[0] == "sections":
section = mode[1]
m = re.match(r'(\w+)\(?(\d*?)\)?\s*=\s*(.*)', line)
if m:
key = m.group(1).strip()
key_ = m.group(2).strip()
val = m.group(3).strip()
if key_ != "":
if sections[section].get(key, None) is None:
val_ = [0.0] * 20 # MAX NTYP DEFINITION
val_[int(key_) - 1] = PWInput.proc_val(key, val)
sections[section][key] = val_
site_properties[key] = []
else:
sections[section][key][int(key_) -
1] = PWInput.proc_val(
key, val)
else:
sections[section][key] = PWInput.proc_val(key, val)
elif mode[0] == "pseudo":
m = re.match(r'(\w+)\s+(\d*.\d*)\s+(.*)', line)
if m:
pseudo[m.group(1).strip()] = {}
pseudo[m.group(1).strip()]["index"] = pseudo_index
pseudo[m.group(1).strip()]["pseudopot"] = m.group(
3).strip()
pseudo_index += 1
elif mode[0] == "kpoints":
m = re.match(r'(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)',
line)
if m:
kpoints_grid = (int(m.group(1)), int(m.group(2)),
int(m.group(3)))
kpoints_shift = (int(m.group(4)), int(m.group(5)),
int(m.group(6)))
else:
kpoints_mode = mode[1]
elif mode[0] == "structure":
m_l = re.match(
r'(-?\d+\.?\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
m_p = re.match(
r'(\w+)\s+(-?\d+\.\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)',
line)
if m_l:
lattice += [
float(m_l.group(1)),
float(m_l.group(2)),
float(m_l.group(3))
]
elif m_p:
site_properties["pseudo"].append(
pseudo[m_p.group(1)]["pseudopot"])
species += [
pseudo[m_p.group(1)]["pseudopot"].split(".")[0]
]
coords += [[
float(m_p.group(2)),
float(m_p.group(3)),
float(m_p.group(4))
]]
for k, v in site_properties.items():
if k != "pseudo":
site_properties[k].append(sections['system'][k][
pseudo[m_p.group(1)]["index"]])
if mode[1] == "angstrom":
coords_are_cartesian = True
elif mode[1] == "crystal":
coords_are_cartesian = False
structure = Structure(Lattice(lattice),
species,
coords,
coords_are_cartesian=coords_are_cartesian,
site_properties=site_properties)
return PWInput(structure=structure,
control=sections["control"],
system=sections["system"],
electrons=sections["electrons"],
ions=sections["ions"],
cell=sections["cell"],
kpoints_mode=kpoints_mode,
kpoints_grid=kpoints_grid,
kpoints_shift=kpoints_shift)
def from_file(cls, filename, atom_style="full", sort_id=False):
"""
Constructor from parsing a file.
Args:
filename (str): Filename to read.
atom_style (str): Associated atom_style. Default to "full".
sort_id (bool): Whether sort each section by id. Default to
True.
"""
with open(filename) as f:
lines = f.readlines()
clines = list(clean_lines(lines))
section_marks = [i for i, l in enumerate(clines) if l
in itertools.chain(*SECTION_KEYWORDS.values())]
parts = np.split(clines, section_marks)
# First, parse header
float_group = r'([0-9eE.+-]+)'
header_pattern = {}
header_pattern["counts"] = r'^\s*(\d+)\s+([a-zA-Z]+)$'
header_pattern["types"] = r'^\s*(\d+)\s+([a-zA-Z]+)\s+types$'
header_pattern["bounds"] = r'^\s*{}$'.format(r'\s+'.join(
[float_group] * 2 + [r"([xyz])lo \3hi"]))
header_pattern["tilt"] = r'^\s*{}$'.format(r'\s+'.join(
[float_group] * 3 + ["xy xz yz"]))
header = {"counts": {}, "types": {}}
bounds = {}
for l in parts[0]:
match = None
for k, v in header_pattern.items():
match = re.match(v, l)
if match:
break
else:
continue
if match and k in ["counts", "types"]:
header[k][match.group(2)] = int(match.group(1))
elif match and k == "bounds":
g = match.groups()
bounds[g[2]] = [float(i) for i in g[:2]]
elif match and k == "tilt":
header["tilt"] = [float(i) for i in match.groups()]
header["bounds"] = [bounds.get(i, [-0.5, 0.5]) for i in "xyz"]
# Then, parse each section
topo_sections = SECTION_KEYWORDS["molecule"]
def parse_section(single_section_lines):
kw = single_section_lines[0]
if kw in SECTION_KEYWORDS["ff"] and kw != "PairIJ Coeffs":
parse_line = lambda l: {"coeffs": [literal_eval(x)
for x in l[1:]]}
elif kw == "PairIJ Coeffs":
parse_line = lambda l: {"id1": int(l[0]), "id2": int(l[1]),
"coeffs": [literal_eval(x)
for x in l[2:]]}
elif kw in topo_sections:
n = {"Bonds": 2, "Angles": 3, "Dihedrals": 4, "Impropers": 4}
parse_line = lambda l: {"type": int(l[1]), kw[:-1].lower():
[int(x) for x in l[2:n[kw] + 2]]}
elif kw == "Atoms":
keys = ATOMS_LINE_FORMAT[atom_style][:]
sample_l = single_section_lines[1].split()
if len(sample_l) == len(keys) + 1:
pass
elif len(sample_l) == len(keys) + 4:
keys += ["nx", "ny", "nz"]
else:
warnings.warn("Atoms section format might be imcompatible"
" with atom_style %s." % atom_style)
float_keys = [k for k in keys if k in ATOMS_FLOATS]
parse_line = lambda l: {k: float(v) if k in float_keys
else int(v) for (k, v) in zip(keys, l[1:len(keys) + 1])}
elif kw == "Velocities":
parse_line = lambda l: {"velocity": [float(x)
for x in l[1:4]]}
elif kw == "Masses":
parse_line = lambda l: {"mass": float(l[1])}
else:
warnings.warn("%s section parser has not been implemented. "
"Skipping..." % kw)
return kw, []
section = []
splitted_lines = [l.split() for l in single_section_lines[1:]]
if sort_id and kw != "PairIJ Coeffs":
splitted_lines = sorted(splitted_lines,
key=lambda l: int(l[0]))
for l in splitted_lines:
line_data = parse_line(l)
if kw != "PairIJ Coeffs":
line_data["id"] = int(l[0])
section.append(line_data)
return kw, section
err_msg = "Bad LAMMPS data format where "
body = {}
seen_atoms = False
for part in parts[1:]:
name, section = parse_section(part)
if name == "Atoms":
seen_atoms = True
if name in ["Velocities"] + topo_sections and not seen_atoms:
raise RuntimeError(err_msg + "%s section appears before"
" Atoms section" % name)
body.update({name: section})
err_msg += "Nos. of {} do not match between header and {} section"
assert len(body["Masses"]) == header["types"]["atom"], \
err_msg.format("atom types", "Masses")
atom_sections = ["Atoms", "Velocities"] \
if body.get("Velocities") else ["Atoms"]
for s in atom_sections:
assert len(body[s]) == header["counts"]["atoms"], \
err_msg.format("atoms", s)
for s in topo_sections:
if header["counts"].get(s.lower(), 0) > 0:
assert len(body[s]) == header["counts"][s.lower()], \
err_msg.format(s.lower(), s)
items = {k.lower(): body[k] for k in ["Masses", "Atoms"]}
items["box_bounds"] = header["bounds"]
items["box_tilt"] = header.get("tilt")
items["velocities"] = body.get("Velocities")
ff_kws = [k for k in body.keys() if k in SECTION_KEYWORDS["ff"]]
items["force_field"] = {k: body[k] for k in ff_kws} if ff_kws \
else None
topo_kws = [k for k in body.keys()
if k in SECTION_KEYWORDS["molecule"]]
items["topology"] = {k: body[k] for k in topo_kws} \
if topo_kws else None
items["atom_style"] = atom_style
return cls(**items)
def from_string(data, default_names=None, read_velocities=True):
"""
Reads a Poscar from a string.
The code will try its best to determine the elements in the POSCAR in
the following order:
1. If default_names are supplied and valid, it will use those. Usually,
default names comes from an external source, such as a POTCAR in the
same directory.
2. If there are no valid default names but the input file is Vasp5-like
and contains element symbols in the 6th line, the code will use that.
3. Failing (2), the code will check if a symbol is provided at the end
of each coordinate.
If all else fails, the code will just assign the first n elements in
increasing atomic number, where n is the number of species, to the
Poscar. For example, H, He, Li, .... This will ensure at least a
unique element is assigned to each site and any analysis that does not
require specific elemental properties should work fine.
Args:
data (str): String containing Poscar data.
default_names ([str]): Default symbols for the POSCAR file,
usually coming from a POTCAR in the same directory.
read_velocities (bool): Whether to read or not velocities if they
are present in the POSCAR. Default is True.
Returns:
Poscar object.
"""
# "^\s*$" doesn't match lines with no whitespace
chunks = re.split(r"\n\s*\n", data.rstrip(), flags=re.MULTILINE)
try:
if chunks[0] == "":
chunks.pop(0)
chunks[0] = "\n" + chunks[0]
except IndexError:
raise ValueError("Empty POSCAR")
# Parse positions
lines = tuple(clean_lines(chunks[0].split("\n"), False))
comment = lines[0]
scale = float(lines[1])
lattice = np.array([[float(i) for i in line.split()]
for line in lines[2:5]])
if scale < 0:
# In vasp, a negative scale factor is treated as a volume. We need
# to translate this to a proper lattice vector scaling.
vol = abs(det(lattice))
lattice *= (-scale / vol)**(1 / 3)
else:
lattice *= scale
vasp5_symbols = False
try:
natoms = [int(i) for i in lines[5].split()]
ipos = 6
except ValueError:
vasp5_symbols = True
symbols = lines[5].split()
"""
Atoms and number of atoms in POSCAR written with vasp appear on
multiple lines when atoms of the same type are not grouped together
and more than 20 groups are then defined ...
Example :
Cr16 Fe35 Ni2
1.00000000000000
8.5415010000000002 -0.0077670000000000 -0.0007960000000000
-0.0077730000000000 8.5224019999999996 0.0105580000000000
-0.0007970000000000 0.0105720000000000 8.5356889999999996
Fe Cr Fe Cr Fe Cr Fe Cr Fe Cr Fe Cr Fe Cr Fe Ni Fe Cr Fe Cr
Fe Ni Fe Cr Fe
1 1 2 4 2 1 1 1 2 1 1 1 4 1 1 1 5 3 6 1
2 1 3 2 5
Direct
...
"""
nlines_symbols = 1
for nlines_symbols in range(1, 11):
try:
int(lines[5 + nlines_symbols].split()[0])
break
except ValueError:
pass
for iline_symbols in range(6, 5 + nlines_symbols):
symbols.extend(lines[iline_symbols].split())
natoms = []
iline_natoms_start = 5 + nlines_symbols
for iline_natoms in range(iline_natoms_start,
iline_natoms_start + nlines_symbols):
natoms.extend([int(i) for i in lines[iline_natoms].split()])
atomic_symbols = list()
for i in range(len(natoms)):
atomic_symbols.extend([symbols[i]] * natoms[i])
ipos = 5 + 2 * nlines_symbols
postype = lines[ipos].split()[0]
sdynamics = False
# Selective dynamics
if postype[0] in "sS":
sdynamics = True
ipos += 1
postype = lines[ipos].split()[0]
cart = postype[0] in "cCkK"
nsites = sum(natoms)
# If default_names is specified (usually coming from a POTCAR), use
# them. This is in line with Vasp"s parsing order that the POTCAR
# specified is the default used.
if default_names:
try:
atomic_symbols = []
for i in range(len(natoms)):
atomic_symbols.extend([default_names[i]] * natoms[i])
vasp5_symbols = True
except IndexError:
pass
if not vasp5_symbols:
ind = 3 if not sdynamics else 6
try:
# Check if names are appended at the end of the coordinates.
atomic_symbols = [
l.split()[ind] for l in lines[ipos + 1:ipos + 1 + nsites]
]
# Ensure symbols are valid elements
if not all(
[Element.is_valid_symbol(sym) for sym in atomic_symbols]):
raise ValueError("Non-valid symbols detected.")
vasp5_symbols = True
except (ValueError, IndexError):
# Defaulting to false names.
atomic_symbols = []
for i in range(len(natoms)):
sym = Element.from_Z(i + 1).symbol
atomic_symbols.extend([sym] * natoms[i])
warnings.warn("Elements in POSCAR cannot be determined. "
"Defaulting to false names %s." %
" ".join(atomic_symbols))
# read the atomic coordinates
coords = []
selective_dynamics = list() if sdynamics else None
for i in range(nsites):
toks = lines[ipos + 1 + i].split()
crd_scale = scale if cart else 1
coords.append([float(j) * crd_scale for j in toks[:3]])
if sdynamics:
selective_dynamics.append(
[tok.upper()[0] == "T" for tok in toks[3:6]])
if read_velocities:
# Parse velocities if any
velocities = []
if len(chunks) > 1:
for line in chunks[1].strip().split("\n"):
velocities.append([float(tok) for tok in line.split()])
# Parse the predictor-corrector data
predictor_corrector = []
predictor_corrector_preamble = None
if len(chunks) > 2:
lines = chunks[2].strip().split("\n")
# There are 3 sets of 3xN Predictor corrector parameters
# So can't be stored as a single set of "site_property"
# First line in chunk is a key in CONTCAR
# Second line is POTIM
# Third line is the thermostat parameters
predictor_corrector_preamble = (lines[0] + "\n" + lines[1] +
"\n" + lines[2])
# Rest is three sets of parameters, each set contains
# x, y, z predictor-corrector parameters for every atom in orde
lines = lines[3:]
for st in range(nsites):
d1 = [float(tok) for tok in lines[st].split()]
d2 = [float(tok) for tok in lines[st + nsites].split()]
d3 = [float(tok) for tok in lines[st + 2 * nsites].split()]
predictor_corrector.append([d1, d2, d3])
else:
velocities = None
predictor_corrector = None
predictor_corrector_preamble = None
return Poscar_new(
atomic_symbols,
coords,
lattice,
comment,
selective_dynamics,
vasp5_symbols,
velocities=velocities,
predictor_corrector=predictor_corrector,
predictor_corrector_preamble=predictor_corrector_preamble)
def from_file(cls, filename, atom_style="full", sort_id=False):
"""
Constructor that parses a file.
Args:
filename (str): Filename to read.
atom_style (str): Associated atom_style. Default to "full".
sort_id (bool): Whether sort each section by id. Default to
True.
"""
with open(filename) as f:
lines = f.readlines()
kw_pattern = r"|".join(itertools.chain(*SECTION_KEYWORDS.values()))
section_marks = [i for i, l in enumerate(lines)
if re.search(kw_pattern, l)]
parts = np.split(lines, section_marks)
float_group = r"([0-9eE.+-]+)"
header_pattern = dict()
header_pattern["counts"] = r"^\s*(\d+)\s+([a-zA-Z]+)$"
header_pattern["types"] = r"^\s*(\d+)\s+([a-zA-Z]+)\s+types$"
header_pattern["bounds"] = r"^\s*{}$".format(r"\s+".join(
[float_group] * 2 + [r"([xyz])lo \3hi"]))
header_pattern["tilt"] = r"^\s*{}$".format(r"\s+".join(
[float_group] * 3 + ["xy xz yz"]))
header = {"counts": {}, "types": {}}
bounds = {}
for l in clean_lines(parts[0][1:]): # skip the 1st line
match = None
for k, v in header_pattern.items():
match = re.match(v, l)
if match:
break
else:
continue
if match and k in ["counts", "types"]:
header[k][match.group(2)] = int(match.group(1))
elif match and k == "bounds":
g = match.groups()
bounds[g[2]] = [float(i) for i in g[:2]]
elif match and k == "tilt":
header["tilt"] = [float(i) for i in match.groups()]
header["bounds"] = [bounds.get(i, [-0.5, 0.5]) for i in "xyz"]
def parse_section(sec_lines):
title_info = sec_lines[0].split("#", 1)
kw = title_info[0].strip()
sio = StringIO("".join(sec_lines[2:])) # skip the 2nd line
df = pd.read_csv(sio, header=None, comment="#",
delim_whitespace=True)
if kw.endswith("Coeffs") and not kw.startswith("PairIJ"):
names = ["id"] + ["coeff%d" % i
for i in range(1, df.shape[1])]
elif kw == "PairIJ Coeffs":
names = ["id1", "id2"] + ["coeff%d" % i
for i in range(1, df.shape[1] - 1)]
df.index.name = None
elif kw in SECTION_HEADERS:
names = ["id"] + SECTION_HEADERS[kw]
elif kw == "Atoms":
names = ["id"] + ATOMS_HEADERS[atom_style]
if df.shape[1] == len(names):
pass
elif df.shape[1] == len(names) + 3:
names += ["nx", "ny", "nz"]
else:
raise ValueError("Format in Atoms section inconsistent"
" with atom_style %s" % atom_style)
else:
raise NotImplementedError("Parser for %s section"
" not implemented" % kw)
df.columns = names
if sort_id:
sort_by = "id" if kw != "PairIJ Coeffs" else ["id1", "id2"]
df.sort_values(sort_by, inplace=True)
if "id" in df.columns:
df.set_index("id", drop=True, inplace=True)
df.index.name = None
return kw, df
err_msg = "Bad LAMMPS data format where "
body = {}
seen_atoms = False
for part in parts[1:]:
name, section = parse_section(part)
if name == "Atoms":
seen_atoms = True
if name in ["Velocities"] + SECTION_KEYWORDS["topology"] and \
not seen_atoms: # Atoms must appear earlier than these
raise RuntimeError(err_msg + "%s section appears before"
" Atoms section" % name)
body.update({name: section})
err_msg += "Nos. of {} do not match between header and {} section"
assert len(body["Masses"]) == header["types"]["atom"], \
err_msg.format("atom types", "Masses")
atom_sections = ["Atoms", "Velocities"] \
if "Velocities" in body else ["Atoms"]
for s in atom_sections:
assert len(body[s]) == header["counts"]["atoms"], \
err_msg.format("atoms", s)
for s in SECTION_KEYWORDS["topology"]:
if header["counts"].get(s.lower(), 0) > 0:
assert len(body[s]) == header["counts"][s.lower()], \
err_msg.format(s.lower(), s)
items = {k.lower(): body[k] for k in ["Masses", "Atoms"]}
items["box_bounds"] = header["bounds"]
items["box_tilt"] = header.get("tilt")
items["velocities"] = body.get("Velocities")
ff_kws = [k for k in body if k
in SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]]
items["force_field"] = {k: body[k] for k in ff_kws} if ff_kws \
else None
topo_kws = [k for k in body if k in SECTION_KEYWORDS["topology"]]
items["topology"] = {k: body[k] for k in topo_kws} \
if topo_kws else None
items["atom_style"] = atom_style
return cls(**items)
def struct_import_pymatgen(filename,ubin=""):
""" import structure from QE input/output into Pymatgen structure
adapted from pymatgen native PWio method
pymatgen.io.pwscf from_file and from_string methods
DOES NOT WORK ATM
filname: (string) input/output QE file containing structure
ubin: (string) dummy variable; for consistency with remaining scripts
"""
import re
from monty.io import zopen
from monty.re import regrep
from pymatgen.util.io_utils import clean_lines
from pymatgen.io.pwscf import PWInput
print("# Reading atomic coordinates from: ", filename)
with zopen(filename, "rt") as f:
string = f.read()
lines = list(clean_lines(string.splitlines()))
print(lines)
def input_mode(line):
if line[0] == "&":
return ("sections", line[1:].lower())
elif "ATOMIC_SPECIES" in line:
return ("pseudo", )
elif "K_POINTS" in line:
return ("kpoints", line.split("{")[1][:-1])
elif "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
return ("structure", line.split("{")[1][:-1])
elif line == "/":
return None
else:
return mode
sections = {"control": {}, "system": {}, "electrons": {},
"ions": {}, "cell":{}}
pseudo = {}
pseudo_index = 0
lattice = []
species = []
coords = []
structure = None
site_properties = {"pseudo":[]}
mode = None
for line in lines:
mode = input_mode(line)
if mode == None:
pass
elif mode[0] == "sections":
section = mode[1]
m = re.match(r'(\w+)\(?(\d*?)\)?\s*=\s*(.*)', line)
if m:
key = m.group(1).strip()
key_ = m.group(2).strip()
val = m.group(3).strip()
if key_ != "":
if sections[section].get(key, None) == None:
val_ = [0.0]*20 # MAX NTYP DEFINITION
val_[int(key_)-1] = PWInput.proc_val(key, val)
sections[section][key] = val_
site_properties[key] = []
else:
sections[section][key][int(key_)-1] = PWInput.proc_val(key, val)
else:
sections[section][key] = PWInput.proc_val(key, val)
# elif mode[0] == "pseudo":
# m = re.match(r'(\w+)\s+(\d*.\d*)\s+(.*)', line)
# if m:
# pseudo[m.group(1).strip()] = {}
# pseudo[m.group(1).strip()]["index"] = pseudo_index
# pseudo[m.group(1).strip()]["pseudopot"] = m.group(3).strip()
# pseudo_index += 1
# elif mode[0] == "kpoints":
# m = re.match(r'(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)', line)
# if m:
# kpoints_grid = (int(m.group(1)), int(m.group(2)), int(m.group(3)))
# kpoints_shift = (int(m.group(4)), int(m.group(5)), int(m.group(6)))
# else:
# kpoints_mode = mode[1]
elif mode[0] == "structure":
m_l = re.match(r'(-?\d+\.?\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
m_p = re.match(r'(\w+)\s+(-?\d+\.\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
if m_l:
lattice += [ float(m_l.group(1)), float(m_l.group(2)), float(m_l.group(3)) ]
elif m_p:
site_properties["pseudo"].append(pseudo[m_p.group(1)]["pseudopot"])
species += [pseudo[m_p.group(1)]["pseudopot"].split(".")[0]]
coords += [[float(m_p.group(2)), float(m_p.group(3)), float(m_p.group(4))]]
for k, v in site_properties.items():
if k != "pseudo":
site_properties[k].append(sections['system'][k][pseudo[m_p.group(1)]["index"]])
if mode[1] == "angstrom":
coords_are_cartesian = True
elif mode[1] == "crystal":
coords_are_cartesian = False
structure = Structure(Lattice(lattice), species, coords,
coords_are_cartesian=coords_are_cartesian,
site_properties=site_properties)
return structure
def from_file(cls, filename, atom_style="full", sort_id=False):
"""
Constructor that parses a file.
Args:
filename (str): Filename to read.
atom_style (str): Associated atom_style. Default to "full".
sort_id (bool): Whether sort each section by id. Default to
True.
"""
with open(filename) as f:
lines = f.readlines()
kw_pattern = r"|".join(itertools.chain(*SECTION_KEYWORDS.values()))
section_marks = [i for i, l in enumerate(lines)
if re.search(kw_pattern, l)]
parts = np.split(lines, section_marks)
float_group = r"([0-9eE.+-]+)"
header_pattern = dict()
header_pattern["counts"] = r"^\s*(\d+)\s+([a-zA-Z]+)$"
header_pattern["types"] = r"^\s*(\d+)\s+([a-zA-Z]+)\s+types$"
header_pattern["bounds"] = r"^\s*{}$".format(r"\s+".join(
[float_group] * 2 + [r"([xyz])lo \3hi"]))
header_pattern["tilt"] = r"^\s*{}$".format(r"\s+".join(
[float_group] * 3 + ["xy xz yz"]))
header = {"counts": {}, "types": {}}
bounds = {}
for l in clean_lines(parts[0][1:]): # skip the 1st line
match = None
for k, v in header_pattern.items():
match = re.match(v, l)
if match:
break
else:
continue
if match and k in ["counts", "types"]:
header[k][match.group(2)] = int(match.group(1))
elif match and k == "bounds":
g = match.groups()
bounds[g[2]] = [float(i) for i in g[:2]]
elif match and k == "tilt":
header["tilt"] = [float(i) for i in match.groups()]
header["bounds"] = [bounds.get(i, [-0.5, 0.5]) for i in "xyz"]
box = LammpsBox(header["bounds"], header.get("tilt"))
def parse_section(sec_lines):
title_info = sec_lines[0].split("#", 1)
kw = title_info[0].strip()
sio = StringIO("".join(sec_lines[2:])) # skip the 2nd line
df = pd.read_csv(sio, header=None, comment="#",
delim_whitespace=True)
if kw.endswith("Coeffs") and not kw.startswith("PairIJ"):
names = ["id"] + ["coeff%d" % i
for i in range(1, df.shape[1])]
elif kw == "PairIJ Coeffs":
names = ["id1", "id2"] + ["coeff%d" % i
for i in range(1, df.shape[1] - 1)]
df.index.name = None
elif kw in SECTION_HEADERS:
names = ["id"] + SECTION_HEADERS[kw]
elif kw == "Atoms":
names = ["id"] + ATOMS_HEADERS[atom_style]
if df.shape[1] == len(names):
pass
elif df.shape[1] == len(names) + 3:
names += ["nx", "ny", "nz"]
else:
raise ValueError("Format in Atoms section inconsistent"
" with atom_style %s" % atom_style)
else:
raise NotImplementedError("Parser for %s section"
" not implemented" % kw)
df.columns = names
if sort_id:
sort_by = "id" if kw != "PairIJ Coeffs" else ["id1", "id2"]
df.sort_values(sort_by, inplace=True)
if "id" in df.columns:
df.set_index("id", drop=True, inplace=True)
df.index.name = None
return kw, df
err_msg = "Bad LAMMPS data format where "
body = {}
seen_atoms = False
for part in parts[1:]:
name, section = parse_section(part)
if name == "Atoms":
seen_atoms = True
if name in ["Velocities"] + SECTION_KEYWORDS["topology"] and \
not seen_atoms: # Atoms must appear earlier than these
raise RuntimeError(err_msg + "%s section appears before"
" Atoms section" % name)
body.update({name: section})
err_msg += "Nos. of {} do not match between header and {} section"
assert len(body["Masses"]) == header["types"]["atom"], \
err_msg.format("atom types", "Masses")
atom_sections = ["Atoms", "Velocities"] \
if "Velocities" in body else ["Atoms"]
for s in atom_sections:
assert len(body[s]) == header["counts"]["atoms"], \
err_msg.format("atoms", s)
for s in SECTION_KEYWORDS["topology"]:
if header["counts"].get(s.lower(), 0) > 0:
assert len(body[s]) == header["counts"][s.lower()], \
err_msg.format(s.lower(), s)
items = {k.lower(): body[k] for k in ["Masses", "Atoms"]}
items["velocities"] = body.get("Velocities")
ff_kws = [k for k in body if k
in SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]]
items["force_field"] = {k: body[k] for k in ff_kws} if ff_kws \
else None
topo_kws = [k for k in body if k in SECTION_KEYWORDS["topology"]]
items["topology"] = {k: body[k] for k in topo_kws} \
if topo_kws else None
items["atom_style"] = atom_style
items["box"] = box
return cls(**items)
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
# Checks to see if generated by pymatgen, if not it is impossible to
# generate structure object so it is not possible to generate header
# object and routine ends
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg > 0:
comment2 = ' '.join(lines[1].split()[2:])
#This sec section gets information to create structure object
source = ' '.join(lines[2].split()[2:])
natoms = int(lines[8].split()[2])
basis_vec = lines[6].split()
a = float(basis_vec[2])
b = float(basis_vec[3])
c = float(basis_vec[4])
lengths = [a, b, c]
basis_ang = lines[7].split()
alpha = float(basis_ang[2])
beta = float(basis_ang[3])
gamma = float(basis_ang[4])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
atomic_symbols = []
for i in range(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in range(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
#Structure object is now generated and Header object returned
struct_fromfile = Structure(lattice, atomic_symbols, coords, False,
False, False)
h = Header(struct_fromfile, source, comment2)
return h
else:
return "Header not generated by pymatgen, " \
"cannot return header object"
def from_file(cls, filename, atom_style="full", sort_id=False):
"""
Constructor from parsing a file.
Args:
filename (str): Filename to read.
atom_style (str): Associated atom_style. Default to "full".
sort_id (bool): Whether sort each section by id. Default to
True.
"""
with open(filename) as f:
lines = f.readlines()
clines = list(clean_lines(lines))
section_marks = [
i for i, l in enumerate(clines)
if l in itertools.chain(*SECTION_KEYWORDS.values())
]
parts = np.split(clines, section_marks)
# First, parse header
float_group = r'([0-9eE.+-]+)'
header_pattern = {}
header_pattern["counts"] = r'^\s*(\d+)\s+([a-zA-Z]+)$'
header_pattern["types"] = r'^\s*(\d+)\s+([a-zA-Z]+)\s+types$'
header_pattern["bounds"] = r'^\s*{}$'.format(
r'\s+'.join([float_group] * 2 + [r"([xyz])lo \3hi"]))
header_pattern["tilt"] = r'^\s*{}$'.format(
r'\s+'.join([float_group] * 3 + ["xy xz yz"]))
header = {"counts": {}, "types": {}}
bounds = {}
for l in parts[0]:
match = None
for k, v in header_pattern.items():
match = re.match(v, l)
if match:
break
else:
continue
if match and k in ["counts", "types"]:
header[k][match.group(2)] = int(match.group(1))
elif match and k == "bounds":
g = match.groups()
bounds[g[2]] = [float(i) for i in g[:2]]
elif match and k == "tilt":
header["tilt"] = [float(i) for i in match.groups()]
header["bounds"] = [bounds.get(i, [-0.5, 0.5]) for i in "xyz"]
# Then, parse each section
topo_sections = SECTION_KEYWORDS["molecule"]
def parse_section(single_section_lines):
kw = single_section_lines[0]
if kw in SECTION_KEYWORDS["ff"] and kw != "PairIJ Coeffs":
parse_line = lambda l: {
"coeffs": [literal_eval(x) for x in l[1:]]
}
elif kw == "PairIJ Coeffs":
parse_line = lambda l: {
"id1": int(l[0]),
"id2": int(l[1]),
"coeffs": [literal_eval(x) for x in l[2:]]
}
elif kw in topo_sections:
n = {"Bonds": 2, "Angles": 3, "Dihedrals": 4, "Impropers": 4}
parse_line = lambda l: {
"type": int(l[1]),
kw[:-1].lower(): [int(x) for x in l[2:n[kw] + 2]]
}
elif kw == "Atoms":
keys = ATOMS_LINE_FORMAT[atom_style][:]
sample_l = single_section_lines[1].split()
if len(sample_l) == len(keys) + 1:
pass
elif len(sample_l) == len(keys) + 4:
keys += ["nx", "ny", "nz"]
else:
warnings.warn("Atoms section format might be imcompatible"
" with atom_style %s." % atom_style)
float_keys = [k for k in keys if k in ATOMS_FLOATS]
parse_line = lambda l: {
k: float(v) if k in float_keys else int(v)
for (k, v) in zip(keys, l[1:len(keys) + 1])
}
elif kw == "Velocities":
parse_line = lambda l: {"velocity": [float(x) for x in l[1:4]]}
elif kw == "Masses":
parse_line = lambda l: {"mass": float(l[1])}
else:
warnings.warn("%s section parser has not been implemented. "
"Skipping..." % kw)
return kw, []
section = []
splitted_lines = [l.split() for l in single_section_lines[1:]]
if sort_id and kw != "PairIJ Coeffs":
splitted_lines = sorted(splitted_lines,
key=lambda l: int(l[0]))
for l in splitted_lines:
line_data = parse_line(l)
if kw != "PairIJ Coeffs":
line_data["id"] = int(l[0])
section.append(line_data)
return kw, section
err_msg = "Bad LAMMPS data format where "
body = {}
seen_atoms = False
for part in parts[1:]:
name, section = parse_section(part)
if name == "Atoms":
seen_atoms = True
if name in ["Velocities"] + topo_sections and not seen_atoms:
raise RuntimeError(err_msg + "%s section appears before"
" Atoms section" % name)
body.update({name: section})
err_msg += "Nos. of {} do not match between header and {} section"
assert len(body["Masses"]) == header["types"]["atom"], \
err_msg.format("atom types", "Masses")
atom_sections = ["Atoms", "Velocities"] \
if body.get("Velocities") else ["Atoms"]
for s in atom_sections:
assert len(body[s]) == header["counts"]["atoms"], \
err_msg.format("atoms", s)
for s in topo_sections:
if header["counts"].get(s.lower(), 0) > 0:
assert len(body[s]) == header["counts"][s.lower()], \
err_msg.format(s.lower(), s)
items = {k.lower(): body[k] for k in ["Masses", "Atoms"]}
items["box_bounds"] = header["bounds"]
items["box_tilt"] = header.get("tilt")
items["velocities"] = body.get("Velocities")
ff_kws = [k for k in body.keys() if k in SECTION_KEYWORDS["ff"]]
items["force_field"] = {k: body[k] for k in ff_kws} if ff_kws \
else None
topo_kws = [
k for k in body.keys() if k in SECTION_KEYWORDS["molecule"]
]
items["topology"] = {k: body[k] for k in topo_kws} \
if topo_kws else None
items["atom_style"] = atom_style
return cls(**items)
def from_string(header_str):
"""
Reads Header string and returns Header object if header was
generated by pymatgen.
Args:
header_str: pymatgen generated feff.inp header
Returns:
Structure object.
"""
# Checks to see if generated by pymatgen, if not it is impossible to
# generate structure object so it is not possible to generate header
# object and routine ends
lines = tuple(clean_lines(header_str.split("\n"), False))
comment1 = lines[0]
feffpmg = comment1.find("pymatgen")
if feffpmg > 0:
comment2 = ' '.join(lines[1].split()[2:])
#This sec section gets information to create structure object
source = ' '.join(lines[2].split()[2:])
natoms = int(lines[8].split()[2])
basis_vec = lines[6].split()
a = float(basis_vec[2])
b = float(basis_vec[3])
c = float(basis_vec[4])
lengths = [a, b, c]
basis_ang = lines[7].split()
alpha = float(basis_ang[2])
beta = float(basis_ang[3])
gamma = float(basis_ang[4])
angles = [alpha, beta, gamma]
lattice = Lattice.from_lengths_and_angles(lengths, angles)
atomic_symbols = []
for i in xrange(9, 9 + natoms):
atomic_symbols.append(lines[i].split()[2])
# read the atomic coordinates
coords = []
for i in xrange(natoms):
toks = lines[i + 9].split()
coords.append([float(s) for s in toks[3:]])
#Structure object is now generated and Header object returned
struct_fromfile = Structure(lattice, atomic_symbols, coords, False,
False, False)
h = Header(struct_fromfile, source, comment2)
return h
else:
return "Header not generated by pymatgen, " \
"cannot return header object"
def from_string(string):
"""
Reads an PWInput object from a string.
Args:
string (str): PWInput string
Returns:
PWInput object
"""
lines = list(clean_lines(string.splitlines()))
def input_mode(line):
if line[0] == "&":
return ("sections", line[1:].lower())
elif "ATOMIC_SPECIES" in line:
return ("pseudo", )
elif "K_POINTS" in line:
return ("kpoints", line.split("{")[1][:-1])
elif "CELL_PARAMETERS" in line or "ATOMIC_POSITIONS" in line:
return ("structure", line.split("{")[1][:-1])
elif line == "/":
return None
else:
return mode
sections = {"control": {}, "system": {}, "electrons": {},
"ions": {}, "cell":{}}
pseudo = {}
pseudo_index = 0
lattice = []
species = []
coords = []
structure = None
site_properties = {"pseudo":[]}
mode = None
for line in lines:
mode = input_mode(line)
if mode == None:
pass
elif mode[0] == "sections":
section = mode[1]
m = re.match(r'(\w+)\(?(\d*?)\)?\s*=\s*(.*)', line)
if m:
key = m.group(1).strip()
key_ = m.group(2).strip()
val = m.group(3).strip()
if key_ != "":
if sections[section].get(key, None) == None:
val_ = [0.0]*20 # MAX NTYP DEFINITION
val_[int(key_)-1] = PWInput.proc_val(key, val)
sections[section][key] = val_
site_properties[key] = []
else:
sections[section][key][int(key_)-1] = PWInput.proc_val(key, val)
else:
sections[section][key] = PWInput.proc_val(key, val)
elif mode[0] == "pseudo":
m = re.match(r'(\w+)\s+(\d*.\d*)\s+(.*)', line)
if m:
pseudo[m.group(1).strip()] = {}
pseudo[m.group(1).strip()]["index"] = pseudo_index
pseudo[m.group(1).strip()]["pseudopot"] = m.group(3).strip()
pseudo_index += 1
elif mode[0] == "kpoints":
m = re.match(r'(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)', line)
if m:
kpoints_grid = (int(m.group(1)), int(m.group(2)), int(m.group(3)))
kpoints_shift = (int(m.group(4)), int(m.group(5)), int(m.group(6)))
else:
kpoints_mode = mode[1]
elif mode[0] == "structure":
m_l = re.match(r'(-?\d+\.?\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
m_p = re.match(r'(\w+)\s+(-?\d+\.\d*)\s+(-?\d+\.?\d*)\s+(-?\d+\.?\d*)', line)
if m_l:
lattice += [ float(m_l.group(1)), float(m_l.group(2)), float(m_l.group(3)) ]
elif m_p:
site_properties["pseudo"].append(pseudo[m_p.group(1)]["pseudopot"])
species += [pseudo[m_p.group(1)]["pseudopot"].split(".")[0]]
coords += [[float(m_p.group(2)), float(m_p.group(3)), float(m_p.group(4))]]
for k, v in site_properties.items():
if k != "pseudo":
site_properties[k].append(sections['system'][k][pseudo[m_p.group(1)]["index"]])
if mode[1] == "angstrom":
coords_are_cartesian = True
elif mode[1] == "crystal":
coords_are_cartesian = False
structure = Structure(Lattice(lattice), species, coords,
coords_are_cartesian=coords_are_cartesian,
site_properties=site_properties)
return PWInput(structure=structure, control=sections["control"],
system=sections["system"], electrons=sections["electrons"],
ions=sections["ions"], cell=sections["cell"], kpoints_mode=kpoints_mode,
kpoints_grid=kpoints_grid, kpoints_shift=kpoints_shift)
def from_string(data, default_names=None):
"""
Reads a Poscar from a string.
The code will try its best to determine the elements in the POSCAR in
the following order:
1. If default_names are supplied and valid, it will use those. Usually,
default names comes from an external source, such as a POTCAR in the
same directory.
2. If there are no valid default names but the input file is Vasp5-like
and contains element symbols in the 6th line, the code will use that.
3. Failing (2), the code will check if a symbol is provided at the end
of each coordinate.
If all else fails, the code will just assign the first n elements in
increasing atomic number, where n is the number of species, to the
Poscar. For example, H, He, Li, .... This will ensure at least a
unique element is assigned to each site and any analysis that does not
require specific elemental properties should work fine.
Args:
data:
string containing Poscar data.
default_names:
default symbols for the POSCAR file, usually coming from a
POTCAR in the same directory.
Returns:
Poscar object.
"""
chunks = re.split("^\s*$", data.strip(), flags=re.MULTILINE)
#Parse positions
lines = tuple(clean_lines(chunks[0].split("\n"), False))
comment = lines[0]
scale = float(lines[1])
lattice = np.array([map(float, line.split())
for line in lines[2:5]])
if scale < 0:
# In vasp, a negative scale factor is treated as a volume. We need
# to translate this to a proper lattice vector scaling.
vol = abs(det(lattice))
lattice *= (-scale / vol) ** (1 / 3)
else:
lattice *= scale
vasp5_symbols = False
try:
natoms = map(int, lines[5].split())
ipos = 6
except ValueError:
vasp5_symbols = True
symbols = lines[5].split()
natoms = map(int, lines[6].split())
atomic_symbols = list()
for i in xrange(len(natoms)):
atomic_symbols.extend([symbols[i]] * natoms[i])
ipos = 7
postype = lines[ipos].split()[0]
sdynamics = False
# Selective dynamics
if postype[0] in "sS":
sdynamics = True
ipos += 1
postype = lines[ipos].split()[0]
cart = postype[0] in "cCkK"
nsites = sum(natoms)
# If default_names is specified (usually coming from a POTCAR), use
# them. This is in line with Vasp"s parsing order that the POTCAR
# specified is the default used.
if default_names:
try:
atomic_symbols = []
for i in xrange(len(natoms)):
atomic_symbols.extend([default_names[i]] * natoms[i])
vasp5_symbols = True
except IndexError:
pass
if not vasp5_symbols:
ind = 3 if not sdynamics else 6
try:
#check if names are appended at the end of the coordinates.
atomic_symbols = [l.split()[ind]
for l in lines[ipos + 1:ipos + 1 + nsites]]
#Ensure symbols are valid elements
if not all([Element.is_valid_symbol(sym)
for sym in atomic_symbols]):
raise ValueError("Non-valid symbols detected.")
vasp5_symbols = True
except (ValueError, IndexError):
#Defaulting to false names.
atomic_symbols = []
for i in xrange(len(natoms)):
sym = Element.from_Z(i + 1).symbol
atomic_symbols.extend([sym] * natoms[i])
warnings.warn("Elements in POSCAR cannot be determined. "
"Defaulting to false names {}."
.format(" ".join(atomic_symbols)))
# read the atomic coordinates
coords = []
selective_dynamics = list() if sdynamics else None
for i in xrange(nsites):
toks = lines[ipos + 1 + i].split()
coords.append(map(float, toks[:3]))
if sdynamics:
selective_dynamics.append([tok.upper()[0] == "T"
for tok in toks[3:6]])
struct = Structure(lattice, atomic_symbols, coords, False, False, cart)
#parse velocities if any
velocities = []
if len(chunks) > 1:
for line in chunks[1].strip().split("\n"):
velocities.append([float(tok) for tok in line.split()])
predictor_corrector = []
if len(chunks) > 2:
lines = chunks[2].strip().split("\n")
predictor_corrector.append([int(lines[0])])
for line in lines[1:]:
predictor_corrector.append([float(tok)
for tok in line.split()])
return Poscar(struct, comment, selective_dynamics, vasp5_symbols,
velocities=velocities,
predictor_corrector=predictor_corrector)