def setup(self):
""" Setup initial relaxation run
Uses the following files from the most local .../settings/calctype.name directory:
INCAR: VASP input settings
KPOINTS: VASP kpoints settings
POSCAR: reference for KPOINTS if KPOINTS mode is not A/AUTO/Automatic
SPECIES: info for each species such as which POTCAR files to use, MAGMOM, GGA+U, etc.
Uses the following files from the .../config directory:
POS: structure of the configuration to be relaxed
"""
# Find required input files in CASM project directory tree
vaspfiles=casm.vaspwrapper.vasp_input_file_names(self.casm_directories, self.configname, self.clex)
incarfile,prim_kpointsfile,prim_poscarfile,super_poscarfile,speciesfile=vaspfiles
# Find optional input files
extra_input_files = []
for s in self.settings["extra_input_files"]:
extra_input_files.append(self.casm_directories.settings_path_crawl(s, self.configname, self.clex))
if extra_input_files[-1] is None:
raise vasp.VaspError("Relax.setup failed. Extra input file " + s + " not found in CASM project.")
if self.settings["initial"]:
extra_input_files += [ self.casm_directories.settings_path_crawl(self.settings["initial"], self.configname, self.clex) ]
if extra_input_files[-1] is None:
raise vasp.VaspError("Relax.setup failed. No initial INCAR file " + self.settings["initial"] + " found in CASM project.")
if self.settings["final"]:
extra_input_files += [ self.casm_directories.settings_path_crawl(self.settings["final"], self.configname, self.clex) ]
if extra_input_files[-1] is None:
raise vasp.VaspError("Relax.setup failed. No final INCAR file " + self.settings["final"] + " found in CASM project.")
sys.stdout.flush()
vasp.io.write_vasp_input(self.calcdir, incarfile, prim_kpointsfile, prim_poscarfile, super_poscarfile, speciesfile, self.sort, extra_input_files,self.settings["strict_kpoints"])
def setup(self):
""" Setup initial relaxation run
Uses the following files from the most local .../settings/calctype.name directory:
INCAR: VASP input settings
KPOINTS: VASP kpoints settings
POSCAR: reference for KPOINTS if KPOINTS mode is not A/AUTO/Automatic
SPECIES: info for each species such as which POTCAR files to use, MAGMOM, GGA+U, etc.
Uses the following files from the .../config directory:
POS: structure of the configuration to be relaxed
"""
incarfile = casm.settings_path("INCAR",
self.casm_settings["curr_calctype"],
self.configdir)
prim_kpointsfile = casm.settings_path(
"KPOINTS", self.casm_settings["curr_calctype"], self.configdir)
prim_poscarfile = casm.settings_path(
"POSCAR", self.casm_settings["curr_calctype"], self.configdir)
super_poscarfile = os.path.join(self.configdir, "POS")
speciesfile = casm.settings_path("SPECIES",
self.casm_settings["curr_calctype"],
self.configdir)
if incarfile == None or not os.path.isfile(incarfile):
raise vasp.VaspError("Relax.setup failed. No incar file: '" +
incarfile + "'")
if prim_kpointsfile == None or not os.path.isfile(prim_kpointsfile):
raise vasp.VaspError("Relax.setup failed. No kpoints file: '" +
prim_kpointsfile + "'")
if prim_poscarfile == None or not os.path.isfile(prim_poscarfile):
# raise vasp.VaspError("Relax.setup failed. No prim poscar file: '" + prim_poscarfile + "'")
warnings.warn(
"No prim poscar file: '" + prim_poscarfile +
"', I hope your KPOINTS mode is A/AUTO/Automatic \
or this will fail!!!", vasp.VaspWarning)
prim_poscarfile = None
if super_poscarfile == None or not os.path.isfile(super_poscarfile):
raise vasp.VaspError("Relax.setup failed. No pos file: '" +
super_poscarfile + "'")
if speciesfile == None or not os.path.isfile(speciesfile):
raise vasp.VaspError("Relax.setup failed. No species file: '" +
speciesfile + "'")
sys.stdout.flush()
vasp.io.write_vasp_input(self.calcdir, incarfile, prim_kpointsfile,
prim_poscarfile, super_poscarfile,
speciesfile, self.sort)
def __init__(self, configdir=None, auto = True, sort = True):
"""
Construct a VASP relaxation job object.
Args:
configdir: path to configuration
auto: True if using pbs module's JobDB to manage pbs jobs
"""
if configdir == None:
configdir = os.getcwd()
print "Reading CASM settings"
self.casm_settings = casm.casm_settings(configdir)
if self.casm_settings == None:
raise vaspwrapper.VaspWrapperError("Not in a CASM project. The file '.casm' directory was not found.")
print "Constructing a CASM VASPWrapper Relax object"
sys.stdout.flush()
print " Setting up directories"
sys.stdout.flush()
# store path to .../config, if not existing raise
self.configdir = os.path.abspath(configdir)
if not os.path.isdir(self.configdir):
raise vasp.VaspError("Error in casm.vasp.relax: Did not find directory: " + self.configdir)
sys.stdout.flush()
# store path to .../config/calctype.name, and create if not existing
self.calcdir = os.path.join(self.configdir, self.casm_settings["curr_calctype"])
try:
os.mkdir(self.calcdir)
except:
pass
# read the settings json file
print " Reading relax.json settings file"
sys.stdout.flush()
setfile = casm.settings_path("relax.json",self.casm_settings["curr_calctype"],self.configdir)
if setfile == None:
raise vaspwrapper.VaspWrapperError("Could not find .../settings/" + self.casm_settings["curr_calctype"] + "/relax.json file.")
sys.stdout.flush()
self.settings = vaspwrapper.read_settings(setfile)
# add required keys to settings if not present
if not "ncore" in self.settings:
self.settings["ncore"] = None
if not "npar" in self.settings:
self.settings["npar"] = None
if not "kpar" in self.settings:
self.settings["kpar"] = None
if not "vasp_cmd" in self.settings:
self.settings["vasp_cmd"] = None
if not "ncpus" in self.settings:
self.settings["ncpus"] = None
if not "run_limit" in self.settings:
self.settings["run_limit"] = None
self.auto = auto
self.sort = sort
print "VASP Relax object constructed\n"
sys.stdout.flush()