def __init__(self, configdir = None, convtype = None, auto = True, sort = True):
"""
Construct a VASP convergence job object.
Args:
configdir: path to configuration
convtype: type of convergence (e.g. 'kpoints' or 'encut')
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/project_settings.json' was not found.")
print "Constructing a CASM VASPWrapper Converge 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 converge.json settings file"
sys.stdout.flush()
setfile = casm.settings_path("converge.json",self.casm_settings["curr_calctype"],self.configdir)
if setfile == None:
raise vaspwrapper.VaspWrapperError("Could not find .../settings/" + self.casm_settings["curr_calctype"] + "/converge.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 "encut" in self.settings:
self.settings["encut"] = None
if not "kpoints" in self.settings:
self.settings["kpoints"] = None
if not "nrg_convergence" in self.settings:
self.settings["nrg_convergence"] = None
if not "run_limit" in self.settings:
self.settings["run_limit"] = None
self.auto = auto
self.sort = sort
print "VASP Converge object constructed\n"
sys.stdout.flush()
def __init__(self, configdir=None, auto=True, sort=True):
"""
Construct a VASP relaxation job object.
Arguments
----------
configdir: str, optional, default=None
Path to configuration directory. If None, uses the current working
directory
auto: boolean, optional, default=True,
Use True to use the pbs module's JobDB to manage pbs jobs
sort: boolean, optional, default=True,
Use True to sort atoms in POSCAR by type
"""
print "Construct a casm.vaspwrapper.Relax instance:"
if configdir is None:
configdir = os.getcwd()
print " Input directory:", configdir
# get the configname from the configdir path
_res = os.path.split(configdir)
self.configname = os.path.split(_res[0])[1] + "/" + _res[1]
print " Configuration:", self.configname
print " Reading CASM settings"
self.casm_directories = casm.project.DirectoryStructure(configdir)
self.casm_settings = casm.project.ProjectSettings(configdir)
if self.casm_settings is None:
raise vaspwrapper.VaspWrapperError(
"Not in a CASM project. The file '.casm' directory was not found."
)
if os.path.abspath(configdir) != self.configdir:
print ""
print "input configdir:", configdir
print "determined configname:", self.configname
print "expected configdir given configname:", self.configdir
raise vaspwrapper.VaspWrapperError(
"Mismatch between configname and configdir")
# fixed to default_clex for now
self.clex = self.casm_settings.default_clex
# store path to .../config/calctype.name, and create if not existing
self.calcdir = self.casm_directories.calctype_dir(
self.configname, self.clex)
try:
os.mkdir(self.calcdir)
except:
pass
print " Calculations directory:", self.calcdir
# read the settings json file
print " Reading relax.json settings file"
sys.stdout.flush()
setfile = self.casm_directories.settings_path_crawl(
"relax.json", self.configname, self.clex)
if setfile is None:
raise vaspwrapper.VaspWrapperError(
"Could not find \"relax.json\" in an appropriate \"settings\" directory"
)
sys.stdout.flush()
else:
print " Read settings from:", setfile
self.settings = vaspwrapper.read_settings(setfile)
# set default 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
if not "prerun" in self.settings:
self.settings["prerun"] = None
if not "postrun" in self.settings:
self.settings["postrun"] = None
self.auto = auto
self.sort = sort
print " DONE\n"
sys.stdout.flush()
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()
def __init__(self, configdir=None, auto=True, sort=True):
"""
Construct a VASP relaxation job object.
Arguments
----------
configdir: str, optional, default=None
Path to configuration directory. If None, uses the current working
directory
auto: boolean, optional, default=True,
Use True to use the pbs module's JobDB to manage pbs jobs
sort: boolean, optional, default=True,
Use True to sort atoms in POSCAR by type
"""
print "Construct a casm.vaspwrapper.Relax instance:"
if configdir is None:
configdir = os.getcwd()
print " Input directory:", configdir
# get the configname from the configdir path
_res = os.path.split(configdir)
self.configname = os.path.split(_res[0])[1] + "/" + _res[1]
print " Configuration:", self.configname
print " Reading CASM settings"
self.casm_directories=casm.project.DirectoryStructure(configdir)
self.casm_settings = casm.project.ProjectSettings(configdir)
if self.casm_settings is None:
raise vaspwrapper.VaspWrapperError("Not in a CASM project. The file '.casm' directory was not found.")
if os.path.abspath(configdir) != self.configdir:
print ""
print "input configdir:", configdir
print "determined configname:", self.configname
print "expected configdir given configname:", self.configdir
raise vaspwrapper.VaspWrapperError("Mismatch between configname and configdir")
# fixed to default_clex for now
self.clex = self.casm_settings.default_clex
# store path to .../config/calctype.name, and create if not existing
self.calcdir = self.casm_directories.calctype_dir(self.configname, self.clex)
try:
os.mkdir(self.calcdir)
except:
pass
print " Calculations directory:", self.calcdir
# read the settings json file
print " Reading relax.json settings file"
sys.stdout.flush()
setfile = self.casm_directories.settings_path_crawl("relax.json", self.configname, self.clex)
if setfile is None:
raise vaspwrapper.VaspWrapperError("Could not find \"relax.json\" in an appropriate \"settings\" directory")
sys.stdout.flush()
else:
print " Read settings from:", setfile
self.settings = vaspwrapper.read_settings(setfile)
# set default 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
if not "prerun" in self.settings:
self.settings["prerun"] = None
if not "postrun" in self.settings:
self.settings["postrun"] = None
self.auto = auto
self.sort = sort
print " DONE\n"
sys.stdout.flush()