Source code for dpdata.formats.xyz.quip_gap_xyz
#!/usr/bin/env python3
# %%
from __future__ import annotations
import re
from collections import OrderedDict
import numpy as np
from dpdata.periodic_table import Element
[docs]
class QuipGapxyzSystems:
"""deal with QuipGapxyzFile."""
def __init__(self, file_name):
self.file_object = open(file_name)
self.block_generator = self.get_block_generator()
def __iter__(self):
return self
def __next__(self):
return self.handle_single_xyz_frame(next(self.block_generator))
def __del__(self):
self.file_object.close()
[docs]
def get_block_generator(self):
p3 = re.compile(r"^\s*(\d+)\s*")
while True:
line = self.file_object.readline()
if not line:
break
if p3.match(line):
atom_num = int(p3.match(line).group(1))
lines = []
lines.append(line)
for ii in range(atom_num + 1):
lines.append(self.file_object.readline())
if not lines[-1]:
raise RuntimeError(
f"this xyz file may lack of lines, should be {atom_num + 2};lines:{lines}"
)
yield lines
[docs]
@staticmethod
def handle_single_xyz_frame(lines):
atom_num = int(lines[0].strip("\n").strip())
if len(lines) != atom_num + 2:
raise RuntimeError(
f"format error, atom_num=={atom_num}, {len(lines)}!=atom_num+2"
)
data_format_line = lines[1].strip("\n").strip() + " "
field_value_pattern = re.compile(
r"(?P<key>\S+)=(?P<quote>[\'\"]?)(?P<value>.*?)(?P=quote)\s+"
)
prop_pattern = re.compile(
r"(?P<key>\w+?):(?P<datatype>[a-zA-Z]):(?P<value>\d+)"
)
data_format_list = [
kv_dict.groupdict()
for kv_dict in field_value_pattern.finditer(data_format_line)
]
field_dict = {}
for item in data_format_list:
field_dict[item["key"]] = item["value"]
Properties = field_dict["Properties"]
prop_list = [
kv_dict.groupdict() for kv_dict in prop_pattern.finditer(Properties)
]
data_lines = []
for line in lines[2:]:
data_lines.append(list(filter(bool, line.strip().split())))
data_array = np.array(data_lines)
used_colomn = 0
type_array = None
coords_array = None
Z_array = None
force_array = None
virials = None
for kv_dict in prop_list:
if kv_dict["key"] == "species":
if kv_dict["datatype"] != "S":
raise RuntimeError(
"datatype for species must be 'S' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
type_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "pos":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
coords_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
continue
elif kv_dict["key"] == "Z":
if kv_dict["datatype"] != "I":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
Z_array = data_array[
:, used_colomn : used_colomn + field_length
].flatten()
used_colomn += field_length
continue
elif kv_dict["key"] == "force":
if kv_dict["datatype"] != "R":
raise RuntimeError(
"datatype for pos must be 'R' instead of {}".format(
kv_dict["datatype"]
)
)
field_length = int(kv_dict["value"])
force_array = data_array[:, used_colomn : used_colomn + field_length]
used_colomn += field_length
continue
else:
raise RuntimeError("unknown field {}".format(kv_dict["key"]))
type_num_dict = OrderedDict()
atom_type_list = []
type_map = {}
temp_atom_max_index = 0
if type_array is None:
raise RuntimeError("type_array can't be None type, check .xyz file")
for ii in type_array:
if ii not in type_map:
type_map[ii] = temp_atom_max_index
temp_atom_max_index += 1
temp_atom_index = type_map[ii]
atom_type_list.append(temp_atom_index)
type_num_dict[ii] = 1
else:
temp_atom_index = type_map[ii]
atom_type_list.append(temp_atom_index)
type_num_dict[ii] += 1
type_num_list = []
for atom_type, atom_num in type_num_dict.items():
type_num_list.append((atom_type, atom_num))
type_num_array = np.array(type_num_list)
if field_dict.get("virial", None):
virials = np.array(
[
np.array(
list(filter(bool, field_dict["virial"].split(" ")))
).reshape(3, 3)
]
).astype(np.float64)
else:
virials = None
info_dict = {}
info_dict["atom_names"] = list(type_num_array[:, 0])
info_dict["atom_numbs"] = list(type_num_array[:, 1].astype(int))
info_dict["atom_types"] = np.array(atom_type_list).astype(int)
info_dict["cells"] = np.array(
[
np.array(list(filter(bool, field_dict["Lattice"].split(" ")))).reshape(
3, 3
)
]
).astype(np.float64)
info_dict["coords"] = np.array([coords_array]).astype(np.float64)
info_dict["energies"] = np.array([field_dict["energy"]]).astype(np.float64)
info_dict["forces"] = np.array([force_array]).astype(np.float64)
if virials is not None:
info_dict["virials"] = virials
info_dict["orig"] = np.zeros(3)
return info_dict