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 submit(self):
"""Submit a PBS job for this VASP relaxation"""
# first, check if the job has already been submitted and is not completed
db = pbs.JobDB()
print "rundir", self.calcdir
id = db.select_regex_id("rundir", self.calcdir)
print "id:", id
sys.stdout.flush()
if id != []:
for j in id:
job = db.select_job(j)
# taskstatus = ["Incomplete","Complete","Continued","Check","Error:.*","Aborted"]
# jobstatus = ["C","Q","R","E","W","H","M"]
if job["jobstatus"] != "C":
print "JobID:", job["jobid"], " Jobstatus:", job["jobstatus"], " Not submitting."
sys.stdout.flush()
return
#elif job["taskstatus"] in ["Complete", "Check"] or re.match( "Error:.*", job["taskstatus"]):
# print "JobID:", job["jobid"], " Taskstatus:", job["taskstatus"], " Not submitting."
# sys.stdout.flush()
# return
# second, only submit a job if relaxation status is "incomplete"
# construct the Relax object
relaxation = vasp.Relax(self.calcdir, self.run_settings())
# check the current status
(status, task) = relaxation.status()
if status == "complete":
print "Status:", status, " Not submitting."
sys.stdout.flush()
# ensure job marked as complete in db
if self.auto:
for j in id:
job = db.select_job(j)
if job["taskstatus"] == "Incomplete":
try:
pbs.complete_job(jobid=j)
except (pbs.PBSError, pbs.JobDBError, pbs.EligibilityError) as e:
print str(e)
sys.stdout.flush()
# ensure results report written
if not os.path.isfile(os.path.join(self.calcdir, "properties.calc.json")):
self.report()
return
elif status == "not_converging":
print "Status:", status, " Not submitting."
sys.stdout.flush()
return
elif status != "incomplete":
raise vaspwrapper.VaspWrapperError("unexpected relaxation status: '" + status + "' and task: '" + task + "'")
sys.stdout.flush()
return
print "Preparing to submit a VASP relaxation PBS job"
sys.stdout.flush()
# cd to configdir, submit jobs from configdir, then cd back to currdir
currdir = os.getcwd()
os.chdir(self.calcdir)
# determine the number of atoms in the configuration
print " Counting atoms in the POSCAR"
sys.stdout.flush()
pos = vasp.io.Poscar(os.path.join(self.configdir,"POS"))
N = len(pos.basis)
print " Constructing a PBS job"
sys.stdout.flush()
# construct a pbs.Job
job = pbs.Job(name=casm.jobname(self.configdir),\
account=self.settings["account"],\
nodes=int(math.ceil(float(N)/float(self.settings["atom_per_proc"])/float(self.settings["ppn"]))),\
ppn=int(self.settings["ppn"]),\
walltime=self.settings["walltime"],\
pmem=self.settings["pmem"],\
qos=self.settings["qos"],\
queue=self.settings["queue"],\
message=self.settings["message"],\
email=self.settings["email"],\
priority=self.settings["priority"],\
command="python -c \"import casm.vaspwrapper; casm.vaspwrapper.Relax('" + self.configdir + "').run()\"",\
auto=self.auto)
print " Submitting"
sys.stdout.flush()
# submit the job
job.submit()
# return to current directory
os.chdir(currdir)
print "CASM VASPWrapper relaxation PBS job submission complete\n"
sys.stdout.flush()
def run(self):
""" Setup input files, run a vasp relaxation, and report results """
# construct the Relax object
relaxation = vasp.Relax(self.calcdir, self.run_settings())
# check the current status
(status, task) = relaxation.status()
if status == "complete":
print "Status:", status
sys.stdout.flush()
# mark job as complete in db
if self.auto:
try:
pbs.complete_job()
except (pbs.PBSError, pbs.JobDBError, pbs.EligibilityError) as e:
print str(e)
sys.stdout.flush()
# write results to output.VASP
self.report()
return
elif status == "not_converging":
print "Status:", status
print "Returning"
sys.stdout.flush()
return
elif status == "incomplete":
if task == "setup":
self.setup()
(status, task) = relaxation.run()
else:
raise vaspwrapper.VaspWrapperError("unexpected relaxation status: '" + status + "' and task: '" + task + "'")
sys.stdout.flush()
# once the run is done, update database records accordingly
if status == "not_converging":
# mark error
if self.auto:
try:
pbs.error_job("Not converging")
except (pbs.PBSError, pbs.JobDBError) as e:
print str(e)
sys.stdout.flush()
print "Not Converging!"
sys.stdout.flush()
# print a local settings file, so that the run_limit can be extended if the
# convergence problems are fixed
try:
os.makedirs(os.path.join(self.configdir, "settings", self.casm_settings["curr_calctype"]))
except:
pass
settingsfile = os.path.join(self.configdir, "settings", self.casm_settings["curr_calctype"], "relax.json")
vaspwrapper.write_settings(self.settings, settingsfile)
print "Writing:", settingsfile
print "Edit the 'run_limit' property if you wish to continue."
sys.stdout.flush()
return
elif status == "complete":
# mark job as complete in db
if self.auto:
try:
pbs.complete_job()
except (pbs.PBSError, pbs.JobDBError, pbs.EligibilityError) as e:
print str(e)
sys.stdout.flush()
# write results to output.VASP
self.report()
else:
raise vaspwrapper.VaspWrapperError("vasp relaxation complete with unexpected status: '" + status + "' and task: '" + task + "'")
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()