def get_structures(mydir, namelist):
"""Get structures from list
Args:
mydir <str>: Ingredient directory
namelist <list: List of file names of structures
Returns:
return_structures <list of Structure objects>
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
return_structures = list()
for strline in namelist:
tryline = strline.strip()
if os.path.isfile(tryline):
str_path = tryline
else:
trypath = os.path.join(mydir, tryline)
if os.path.isfile(trypath):
str_path = trypath
else:
logger.error("No file found at %s" % tryline)
continue
one_structure = pymatgen.io.smartio.read_structure(str_path)
return_structures.append(one_structure)
return return_structures
def get_structures(mydir, namelist):
"""Get structures from list
Args:
mydir <str>: Ingredient directory
namelist <list: List of file names of structures
Returns:
return_structures <list of Structure objects>
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
return_structures = list()
for strline in namelist:
tryline = strline.strip()
if os.path.isfile(tryline):
str_path = tryline
else:
trypath = os.path.join(mydir, tryline)
if os.path.isfile(trypath):
str_path = trypath
else:
logger.error("No file found at %s" % tryline)
continue
one_structure = pymatgen.io.smartio.read_structure(str_path)
return_structures.append(one_structure)
return return_structures
def main(mydir="", fname="", startat=0, childdir=""):
"""This method makes POSCAR-containing subfolders from a
list of structures,
in childdir if a child directory is given, or in
mydir otherwise.
File fname must reside in directory mydir.
Args:
mydir <str>: Ingredient directory
fname <str>: File containing list of structures
startat <str, will be converted to int>:
0 (default) - start subfolders at 00
1 - start subfolders at 01
childdir <str>: Child directory (optional)
If xyz files, fname is required to be of the form:
"xyz"
<float a> <float b> <float c for box size>
fileone.xyz
filetwo.xyz
...
If POSCAR or other structure files, fname may simply
start with file names:
POSCAR_01
POSCAR_02
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
if childdir == "":
childdir = mydir
fpath = os.path.join(mydir, fname)
if not os.path.isfile(fpath):
logger.error("No file found at %s" % fpath)
return "File not found. No effect."
str_list_file = MASTFile(fpath)
if str_list_file.data[0].strip().lower() == "xyz":
namelist = list(str_list_file.data[2:])
structure_list = get_xyz_structures(mydir, str_list_file.data[1],
namelist)
else:
namelist = list(str_list_file.data)
structure_list = get_structures(mydir, namelist)
if not (len(structure_list) == len(namelist)):
logger.error("Not all structures in file %s found." % fname)
return "Not all structures found. No effect."
strct = int(startat)
for one_structure in structure_list:
subname = str(strct).zfill(2)
subpath = os.path.join(childdir, subname)
if not os.path.isdir(subpath):
os.mkdir(subpath)
one_poscar = pymatgen.io.vaspio.Poscar(one_structure)
pospath = os.path.join(subpath, "POSCAR")
if os.path.isfile(pospath):
logger.error("POSCAR file already exists at %s" % subpath)
else:
one_poscar.write_file(os.path.join(subpath, "POSCAR"))
strct = strct + 1
return "Wrote all POSCAR files to subdirectories in %s" % childdir
def main(mydir="", fname="", startat=0, childdir=""):
"""This method makes POSCAR-containing subfolders from a
list of structures,
in childdir if a child directory is given, or in
mydir otherwise.
File fname must reside in directory mydir.
Args:
mydir <str>: Ingredient directory
fname <str>: File containing list of structures
startat <str, will be converted to int>:
0 (default) - start subfolders at 00
1 - start subfolders at 01
childdir <str>: Child directory (optional)
If xyz files, fname is required to be of the form:
"xyz"
<float a> <float b> <float c for box size>
fileone.xyz
filetwo.xyz
...
If POSCAR or other structure files, fname may simply
start with file names:
POSCAR_01
POSCAR_02
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
if childdir == "":
childdir = mydir
fpath = os.path.join(mydir, fname)
if not os.path.isfile(fpath):
logger.error("No file found at %s" % fpath)
return "File not found. No effect."
str_list_file = MASTFile(fpath)
if str_list_file.data[0].strip().lower() == "xyz":
namelist = list(str_list_file.data[2:])
structure_list = get_xyz_structures(mydir, str_list_file.data[1], namelist)
else:
namelist = list(str_list_file.data)
structure_list = get_structures(mydir, namelist)
if not (len(structure_list) == len(namelist)):
logger.error("Not all structures in file %s found." % fname)
return "Not all structures found. No effect."
strct = int(startat)
for one_structure in structure_list:
subname = str(strct).zfill(2)
subpath = os.path.join(childdir, subname)
if not os.path.isdir(subpath):
os.mkdir(subpath)
one_poscar = pymatgen.io.vaspio.Poscar(one_structure)
pospath = os.path.join(subpath, "POSCAR")
if os.path.isfile(pospath):
logger.error("POSCAR file already exists at %s" % subpath)
else:
one_poscar.write_file(os.path.join(subpath, "POSCAR"))
strct = strct + 1
return "Wrote all POSCAR files to subdirectories in %s" % childdir
def get_xyz_structures(mydir, boxline, namelist):
"""Get xyz structures from list
Args:
mydir <str>: Ingredient directory
boxline <str>: Box size line, example:
2.0 3.0 4.0
for an orthorhombic box with lattice vector
a = 2.0, b = 3.0, and c = 4.0
namelist <list: List of file names of structures
Returns:
return_structures <list of Structure objects>
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
return_structures = list()
boxline = boxline.strip()
boxsplit = boxline.split()
boxa = float(boxsplit[0])
boxb = float(boxsplit[1])
boxc = float(boxsplit[2])
for strline in namelist:
tryline = strline.strip()
if os.path.isfile(tryline):
str_path = tryline
else:
trypath = os.path.join(mydir, tryline)
if os.path.isfile(trypath):
str_path = trypath
else:
logger.error("No file found at %s" % tryline)
continue
one_mol = pymatgen.io.smartio.read_mol(str_path)
one_structure = one_mol.get_boxed_structure(boxa, boxb, boxc)
return_structures.append(one_structure)
return return_structures
def get_xyz_structures(mydir, boxline, namelist):
"""Get xyz structures from list
Args:
mydir <str>: Ingredient directory
boxline <str>: Box size line, example:
2.0 3.0 4.0
for an orthorhombic box with lattice vector
a = 2.0, b = 3.0, and c = 4.0
namelist <list: List of file names of structures
Returns:
return_structures <list of Structure objects>
"""
logger = logging.getLogger(mydir)
logger = loggerutils.add_handler_for_recipe(mydir, logger)
return_structures = list()
boxline = boxline.strip()
boxsplit = boxline.split()
boxa = float(boxsplit[0])
boxb = float(boxsplit[1])
boxc = float(boxsplit[2])
for strline in namelist:
tryline = strline.strip()
if os.path.isfile(tryline):
str_path = tryline
else:
trypath = os.path.join(mydir, tryline)
if os.path.isfile(trypath):
str_path = trypath
else:
logger.error("No file found at %s" % tryline)
continue
one_mol = pymatgen.io.smartio.read_mol(str_path)
one_structure = one_mol.get_boxed_structure(boxa, boxb, boxc)
return_structures.append(one_structure)
return return_structures