def __init__(self,
incarfile,
ref_kpointsfile,
ref_structurefile,
structurefile,
speciesfile,
sort=False):
""" Construct a VaspIO object
Args:
incarfile: path to INCAR file
ref_kpointsfile: path to a reference KPOINTS file
ref_structurefile: path to a reference CASM structure.json or VASP POSCAR file, used for scaling k-points
structurefile: path to CASM structure.json or VASP POSCAR file
for the configuration
speciesfile: path to SPECIES file
This functions reads the input files and generates self.kpoints appropriate for self.poscar given that 'ref_kpointsfile' is for 'ref_structurefile'.
"""
ref_structure = poscar.Poscar(ref_structurefile)
ref_kpoints = kpoints.Kpoints(ref_kpointsfile)
self.species = species.species_settings(speciesfile)
self.poscar = poscar.Poscar(structurefile, self.species)
self.incar = incar.Incar(incarfile, self.species, self.poscar, sort)
self.kpoints = ref_kpoints.super_kpoints(ref_structure, self.poscar)
def __init__(self,
incarfile,
prim_kpointsfile,
prim_poscarfile,
super_poscarfile,
speciesfile,
sort=False):
""" Construct a VaspIO object
Args:
incarfile: path to INCAR file
prim_kpointsfile: path to primitive KPOINTS file
prim_poscarfile: path to primitive POSCAR file
super_poscarfile: path to POSCAR file for this configuration
speciesfile: path to SPECIES file
This functions reads the input files and generates self.kpoints appropriate for self.poscar
given that 'prim_kpointsfile' is for 'prim_poscarfile'.
"""
prim = poscar.Poscar(prim_poscarfile)
prim_kpoints = kpoints.Kpoints(prim_kpointsfile)
self.species = species.species_settings(speciesfile)
self.poscar = poscar.Poscar(super_poscarfile, self.species)
self.incar = incar.Incar(incarfile, self.species, self.poscar, sort)
self.kpoints = prim_kpoints.super_kpoints(prim, self.poscar)
def get_incar_tag(key, jobdir=None):
"""Opens INCAR in 'jobdir' and returns 'key' value."""
if jobdir is None:
jobdir = os.getcwd()
tincar = incar.Incar(os.path.join(jobdir,"INCAR"))
for k in tincar.tags:
if key.lower() == k.lower():
return tincar.tags[k]
return None
def write_vasp_input(dirpath,
incarfile,
prim_kpointsfile,
prim_poscarfile,
super_poscarfile,
speciesfile,
sort=True,
extra_input_files=[],
strict_kpoints=False):
""" Write VASP input files in directory 'dirpath' """
print("Setting up VASP input files:", dirpath)
# read prim and prim kpoints
print(" Reading KPOINTS:", prim_kpointsfile)
prim_kpoints = kpoints.Kpoints(prim_kpointsfile)
if prim_poscarfile != None:
print(" Reading KPOINTS reference POSCAR:", prim_poscarfile)
prim = poscar.Poscar(prim_poscarfile)
else:
prim = None
# read species, super poscar, incar, and generate super kpoints
print(" Reading SPECIES:", speciesfile)
species_settings = species.species_settings(speciesfile)
print(" Reading supercell POS:", super_poscarfile)
super = poscar.Poscar(super_poscarfile, species_settings)
print(" Reading INCAR:", incarfile)
super_incar = incar.Incar(incarfile, species_settings, super, sort)
print(" Generating supercell KPOINTS")
if strict_kpoints:
super_kpoints = prim_kpoints
else:
super_kpoints = prim_kpoints.super_kpoints(prim, super)
# write main input files
print(" Writing supercell POSCAR:", os.path.join(dirpath, 'POSCAR'))
super.write(os.path.join(dirpath, 'POSCAR'), sort)
print(" Writing INCAR:", os.path.join(dirpath, 'INCAR'))
super_incar.write(os.path.join(dirpath, 'INCAR'))
print(" Writing supercell KPOINTS:", os.path.join(dirpath, 'KPOINTS'))
super_kpoints.write(os.path.join(dirpath, 'KPOINTS'))
print(" Writing POTCAR:", os.path.join(dirpath, 'POTCAR'))
write_potcar(os.path.join(dirpath, 'POTCAR'), super, species_settings,
sort)
# copy extra input files
if len(extra_input_files):
print(" Copying extra input files", end=' ')
for s in extra_input_files:
print(" ", s)
shutil.copy(s, dirpath)
print(" DONE\n")
sys.stdout.flush()
def set_incar_tag(tag_dict,jobdir=None, name=None):
"""Opens INCAR in 'jobdir', sets 'key' value, and writes INCAR
If 'val' is None, the tag is removed from the INCAR.
"""
if name is None:
name = "INCAR"
if jobdir is None:
jobdir = os.getcwd()
incarfile = os.path.join(jobdir,name)
tincar = incar.Incar(incarfile)
for key, val in six.iteritems(tag_dict):
for k in tincar.tags:
if key.lower() == k.lower():
if (val is None) or (str(val).strip() == ""):
del tincar.tags[k]
else:
tincar.tags[k] = val
break
if val != None and str(val).strip() != "":
tincar.tags[key] = val
tincar.write(incarfile)
def write_vasp_input(dirpath,
incarfile,
ref_kpointsfile,
ref_structurefile,
structurefile,
speciesfile,
sort=True,
extra_input_files=[],
strict_kpoints=False):
""" Write VASP input files in directory 'dirpath'
Parameters
----------
ref_structurefile: str
Path to a CASM structure.json file or VASP POS/POSCAR file representing a reference structure used for scaling incar and k-point parameters.
structurefile: str
Path to a CASM structure.json file or VASP POS/POSCAR file representing the structure to be calculated.
"""
print("Setting up VASP input files:", dirpath)
# read reference structure and kpoints
print(" Reading reference KPOINTS:", ref_kpointsfile)
ref_kpoints = kp.Kpoints(ref_kpointsfile)
if ref_structurefile != None:
print(" Reading reference POSCAR:", ref_structurefile)
ref_structure = poscar.Poscar(ref_structurefile)
else:
ref_structure = None
# read species, prim structure.json/POS, and to-be-calculated
# structure.json/POS, and use to construct incar and kpoints for
# the to-be-calculated structure
print(" Reading SPECIES:", speciesfile)
species_settings = species.species_settings(speciesfile)
if structurefile != None:
print(" Reading structure:", structurefile)
structure = poscar.Poscar(structurefile, species_settings)
else:
structure = None
## Reading DOF information present in the structure.json file
## Examples include: Cmagspin, NCmagspin, SOmagspin, etc
## Also contains information about atom types, and mol types
print(" Reading DOF information from structure: ", structurefile)
dof_info = attribute_info.AttributeInfo(structurefile)
print(" Reading INCAR:", incarfile)
incar = inc.Incar(incarfile, species_settings, structure, sort, dof_info)
print(" Generating KPOINTS")
if strict_kpoints:
kpoints = ref_kpoints
else:
kpoints = ref_kpoints.super_kpoints(ref_structure, structure)
# write main input files
if structurefile != None:
print(" Writing POSCAR:", os.path.join(dirpath, 'POSCAR'))
structure.write(os.path.join(dirpath, 'POSCAR'), sort)
print(" Writing INCAR:", os.path.join(dirpath, 'INCAR'))
incar.write(os.path.join(dirpath, 'INCAR'))
print(" Writing KPOINTS:", os.path.join(dirpath, 'KPOINTS'))
kpoints.write(os.path.join(dirpath, 'KPOINTS'))
if structurefile != None:
print(" Writing POTCAR:", os.path.join(dirpath, 'POTCAR'))
write_potcar(os.path.join(dirpath, 'POTCAR'), structure,
species_settings, sort)
# copy extra input files
if len(extra_input_files):
print(" Copying extra input files", end=' ')
for s in extra_input_files:
print(" ", s)
shutil.copy(s, dirpath)
print(" DONE\n")
sys.stdout.flush()