def export_qwalk(self):
''' Export QWalk input files into current directory.
Returns:
bool: whether it was successful.'''
self.recover(pkl.load(open(self.path + self.pickle, 'rb')))
ready = False
if len(self.qwfiles['slater']) == 0:
self.nextstep()
if not self.completed:
return False
cwd = os.getcwd()
os.chdir(self.path)
print(self.logname,
": %s attempting to generate QWalk files." % self.name)
# Check on the properties run
status = resolve_status(self.prunner, self.preader, self.propoutfn)
print(self.logname, ": properties status= %s" % (status))
if status == 'not_started':
ready = False
self.prunner.add_command("cp %s INPUT" % self.propinpfn)
self.prunner.add_task("%s &> %s" %
(paths['Pproperties'], self.propoutfn))
if self.bundle:
self.scriptfile = "%s.run" % self.name
self.bundle_ready = self.prunner.script(
self.scriptfile, self.driverfn)
else:
qsubfile = self.runner.submit(
self.path.replace('/', '-') + self.name)
elif status == 'ready_for_analysis':
self.preader.collect(self.propoutfn)
if self.preader.completed:
ready = True
print(self.logname, ": converting crystal to QWalk input now.")
self.qwfiles = crystal2qmc.convert_crystal(
base=self.name, propoutfn=self.propoutfn)
else:
ready = False
print(
self.logname,
": conversion postponed because properties is not finished."
)
os.chdir(cwd)
else:
ready = True
with open(self.path + self.pickle, 'wb') as outf:
pkl.dump(self, outf)
return ready
def status(self):
''' Determine the course of action based on info from reader and runner.'''
current_status = resolve_status(self.runner, self.reader, self.outfile)
if current_status == 'done':
return 'ok'
elif current_status == 'retry':
return 'retry'
else:
return 'not_finished'
def nextstep(self):
''' Perform next step in calculation. trialfunc managers are updated if they aren't completed yet.'''
# Recover old data.
self.recover(pkl.load(open(self.path + self.pickle, 'rb')))
print(self.logname, ": next step.")
# Check dependency is completed first.
if self.writer.trialfunc == '':
print(self.logname, ": checking trial function.")
self.writer.trialfunc = self.trialfunc.export(self.path)
# Work on this job.
cwd = os.getcwd()
os.chdir(self.path)
# Write the input file.
if not self.writer.completed:
self.writer.qwalk_input(self.infile)
status = resolve_status(self.runner, self.reader, self.outfile)
print(self.logname, ": %s status= %s" % (self.name, status))
if status == "not_started" and self.writer.completed:
exestr = "%s %s &> %s" % (paths['qwalk'], self.infile, self.stdout)
self.runner.add_task(exestr)
print(self.logname, ": %s status= submitted" % (self.name))
elif status == "ready_for_analysis":
#This is where we (eventually) do error correction and resubmits
status = self.reader.collect(self.outfile)
if status == 'ok':
print(self.logname,
": %s status= %s, task complete." % (self.name, status))
self.completed = True
else:
print(
self.logname,
": %s status= %s, attempting rerun." % (self.name, status))
exestr = "%s %s &> %s" % (paths['qwalk'], self.infile,
self.stdout)
self.runner.add_task(exestr)
elif status == 'done':
self.completed = True
# Ready for bundler or else just submit the jobs as needed.
if self.bundle:
self.scriptfile = "%s.run" % self.name
self.bundle_ready = self.runner.script(self.scriptfile)
else:
qsubfile = self.runner.submit(
self.path.replace('/', '-') + self.name)
# Update the file.
with open(self.pickle, 'wb') as outf:
pkl.dump(self, outf)
os.chdir(cwd)
def nextstep(self):
''' Determine and perform the next step in the calculation.'''
# Recover old data.
self.recover(pkl.load(open(self.path + self.pickle, 'rb')))
print(self.logname, ": next step.")
cwd = os.getcwd()
os.chdir(self.path)
if not self.writer.completed:
self.writer.pyscf_input(self.driverfn, self.chkfile)
status = resolve_status(self.runner, self.reader, self.outfile)
print(self.logname, ": %s status= %s" % (self.name, status))
if status == "not_started":
self.runner.add_task("python3 %s > %s" %
(self.driverfn, self.outfile))
elif status == "ready_for_analysis":
status = self.reader.collect(self.outfile, self.chkfile)
if status == 'killed':
print(
self.logname,
": attempting restart (%d previous restarts)." %
self.restarts)
sh.copy(self.driverfn,
"%d.%s" % (self.restarts, self.driverfn))
sh.copy(self.outfile, "%d.%s" % (self.restarts, self.outfile))
sh.copy(self.chkfile, "%d.%s" % (self.restarts, self.chkfile))
if os.path.exists(self.chkfile):
self.writer.dm_generator = dm_from_chkfile(
"%d.%s" % (self.restarts, self.chkfile))
self.writer.pyscf_input(self.driverfn, self.chkfile)
self.runner.add_task("/usr/bin/python3 %s > %s" %
(self.driverfn, self.outfile))
self.restarts += 1
elif status == 'done':
print(self.logname,
": %s status= %s, task complete." % (self.name, status))
# Ready for bundler or else just submit the jobs as needed.
if self.bundle:
self.scriptfile = "%s.run" % self.name
self.bundle_ready = self.runner.script(self.scriptfile,
self.driverfn)
else:
qsubfile = self.runner.submit(jobname=self.path.replace('/', '-') +
self.name,
ppath=[paths['pyscf']])
self.completed = self.reader.completed
# Update the file.
with open(self.pickle, 'wb') as outf:
pkl.dump(self, outf)
os.chdir(cwd)
def nextstep(self):
''' Determine and perform the next step in the calculation.'''
self.recover(pkl.load(open(self.path + self.pickle, 'rb')))
print(self.logname, ": next step.")
cwd = os.getcwd()
os.chdir(self.path)
# Generate input files.
if not self.writer.completed:
if self.writer.guess_fort is not None:
sh.copy(self.writer.guess_fort, 'fort.20')
with open(self.crysinpfn, 'w') as f:
self.writer.write_crys_input(self.crysinpfn)
with open(self.propinpfn, 'w') as f:
self.writer.write_prop_input(self.propinpfn)
# Check on the CRYSTAL run
status = resolve_status(self.runner, self.creader, self.crysoutfn)
print(self.logname, ": status= %s" % (status))
if status == "not_started":
self.runner.add_command("cp %s INPUT" % self.crysinpfn)
self.runner.add_task("%s &> %s" %
(paths['Pcrystal'], self.crysoutfn))
elif status == "ready_for_analysis":
#This is where we (eventually) do error correction and resubmits
status = self.creader.collect(self.crysoutfn)
print(self.logname, ": status %s" % status)
if status == 'killed':
if self.restarts >= self.max_restarts:
print(
self.logname,
": restarts exhausted (%d previous restarts). Human intervention required."
% self.restarts)
else:
print(
self.logname,
": attempting restart (%d previous restarts)." %
self.restarts)
self.writer.restart = True
if self.trylev:
print(self.logname, ": trying LEVSHIFT.")
self.writer.levshift = [10, 1] # No mercy.
self.savebroy = deepcopy(self.writer.broyden)
self.writer.broyden = []
self.lev = True
sh.copy(self.crysinpfn,
"%d.%s" % (self.restarts, self.crysinpfn))
sh.copy(self.crysoutfn,
"%d.%s" % (self.restarts, self.crysoutfn))
sh.copy('fort.79', "%d.fort.79" % (self.restarts))
self.writer.guess_fort = './fort.79'
sh.copy(self.writer.guess_fort, 'fort.20')
self.writer.write_crys_input(self.crysinpfn)
sh.copy(self.crysinpfn, 'INPUT')
self.runner.add_task("%s &> %s" %
(paths['Pcrystal'], self.crysoutfn))
self.restarts += 1
elif status == 'done' and self.lev:
# We used levshift to converge. Now let's restart to be sure.
print("Recovering from LEVSHIFTer.")
self.writer.restart = True
self.writer.levshift = []
self.creader.completed = False
self.lev = False
sh.copy(self.crysinpfn, "%d.%s" % (self.restarts, self.crysinpfn))
sh.copy(self.crysoutfn, "%d.%s" % (self.restarts, self.crysoutfn))
sh.copy('fort.79', "%d.fort.79" % (self.restarts))
self.writer.guess_fort = './fort.79'
sh.copy(self.writer.guess_fort, 'fort.20')
self.writer.write_crys_input(self.crysinpfn)
sh.copy(self.crysinpfn, 'INPUT')
self.runner.add_task("%s &> %s" %
(paths['Pcrystal'], self.crysoutfn))
self.restarts += 1
# Ready for bundler or else just submit the jobs as needed.
if self.bundle:
self.scriptfile = "%s.run" % self.name
self.bundle_ready = self.runner.script(self.scriptfile)
else:
qsubfile = self.runner.submit(
self.path.replace('/', '-') + self.name)
self.completed = self.creader.completed
# Update the file.
with open(self.pickle, 'wb') as outf:
pkl.dump(self, outf)
os.chdir(cwd)