def setup(self, initdir, settings):
""" mv all files and directories (besides initdir) into initdir """
infilename = settings["infilename"]
print "Moving files into initial run directory:", initdir
initdir = os.path.abspath(initdir)
for p in os.listdir(self.relaxdir):
if (p in ([infilename] + self.settings["extra_input_files"])) and (
os.path.join(self.relaxdir, p) != initdir):
os.rename(os.path.join(self.relaxdir, p),
os.path.join(initdir, p))
print ""
sys.stdout.flush()
# Keep a backup copy of the base Infile
shutil.copyfile(os.path.join(initdir, infilename),
os.path.join(self.relaxdir, infilename + ".base"))
# If an initial infile is called for, copy it in and set the appropriate flag
if (self.settings["initial"] != None) and (os.path.isfile(
os.path.join(self.relaxdir, self.settings["initial"]))):
new_values = qeio.Infile(
os.path.join(self.relaxdir, self.settings["initial"])).tags
qeio.set_infile_tag(new_values, infilename, initdir)
print " Set Infile tags:", new_values, "\n"
sys.stdout.flush()
def run(self):
""" Perform a series of quantum espresso jobs to relax a structure. Performs a series of quantum espresso calculations until
convergence is reached according to the criteria in 'status()'. Then performs a final constant volume run
"""
print "Begin Quantum Espresso relaxation run"
sys.stdout.flush()
# get current status of the relaxation:
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
infilename = self.settings["infilename"]
outfilename = self.settings["outfilename"]
while status == "incomplete":
if task == "setup":
self.add_rundir()
self.setup(self.rundir[-1], self.settings)
elif task == "relax":
self.add_rundir()
quantumespresso.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
elif task == "constant":
self.add_rundir()
quantumespresso.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
# set Infile to calculation = relax
if (self.settings["final"] != None) and (os.path.isfile(
os.path.join(self.relaxdir, self.settings["final"]))):
new_values = qeio.Infile(
os.path.join(self.relaxdir,
self.settings["final"])).tags
else:
new_values = {"calculation": "'relax'"}
# set Infile title tag to denote 'final'
if qeio.get_infile_tag("title", infilename,
self.rundir[-1]) is None:
new_values["title"] = "'final'"
else:
new_values["title"] = "'{}'".format(
qeio.get_infile_tag("title", self.rundir[-1]) +
" final")
qeio.set_infile_tag(new_values, infilename, self.rundir[-1])
print " Set Infile tags:", new_values, "\n"
sys.stdout.flush()
else:
# probably hit walltime
self.add_rundir()
quantumespresso.continue_job(self.rundir[-2], self.rundir[-1],
self.settings)
while True:
# run quantum espresso
result = quantumespresso.run(
infilename,
outfilename,
self.rundir[-1],
command=self.settings["qe_cmd"],
ncpus=self.settings["ncpus"],
err_types=self.settings["err_types"])
# if no errors, continue
if result == None or self.not_converging():
break
# else, attempt to fix first error
self.add_errdir()
os.mkdir(self.rundir[-1])
# self.add_rundir()
err = result.itervalues().next()
print "\n++ status:", "error", " next task:", "fix_error"
sys.stdout.flush()
print "Attempting to fix error:", str(err)
err.fix(self.errdir[-1], self.rundir[-1], self.settings)
print ""
sys.stdout.flush()
if (self.settings["backup"] != None) and len(self.rundir) > 1:
print "Restoring from backups:"
for f in self.settings["backup"]:
if os.path.isfile(
os.path.join(self.rundir[-2],
f + "_BACKUP.gz")):
f_in = gzip.open(
os.path.join(self.rundir[-2], f + "_BACKUP.gz",
'rb'))
f_out = open(os.path.join(self.rundir[-1], f,
'wb'))
f_out.write(f_in.read())
f_in.close()
f_out.close()
print f, " restored!"
sys.stdout.flush()
(status, task) = self.status()
print "\n++ status:", status, " next task:", task
sys.stdout.flush()
if status == "complete":
if not os.path.isdir(self.finaldir):
# mv final results to relax.final
print "mv", os.path.basename(
self.rundir[-1]), os.path.basename(self.finaldir)
sys.stdout.flush()
os.rename(self.rundir[-1], self.finaldir)
self.rundir.pop()
quantumespresso.complete_job(self.finaldir, self.settings)
return (status, task)
def continue_job(jobdir, contdir, settings):
# def continue_job(jobdir,\
# contdir,\
# move = io.DEFAULT_VASP_MOVE_LIST,\
# copy = io.DEFAULT_VASP_COPY_LIST,\
# remove = io.DEFAULT_VASP_REMOVE_LIST,\
# compress = [], backup = []):
"""Use the files in vasp job directory 'jobdir', to setup a vasp job in directory 'contdir'.
Args:
jobdir: path to current job directory
contdir: path to new directory to continue the job
Settings:
copy: Files copied from 'jobdir' to 'contdir'
It also copies either CONTCAR, or if that does not exist POSCAR.
move: Files moved from 'jobdir' to 'contdir'
keep: Files (along with those in 'copy') to keep in 'jobdir'. The rest are removed.
Do not include "POSCAR" or "CONTCAR" in 'move' or 'copy'. jobdir/CONTCAR is copied
to contdir/POSCAR, unless it does not exist, in which case jobdir/POSCAR is copied
to contdir/POSCAR. jobdir/POSCAR and jobdir/CONTCAR are always kept.
"""
print "Continue Quantum Espresso job:\n Original: " + jobdir + "\n Continuation: " + contdir
sys.stdout.flush()
infilename = settings["infilename"]
outfilename = settings["outfilename"]
# remove duplicates
move = list(set(settings['move'] + settings['extra_input_files']))
copy = list(set(settings['copy'] + [infilename]))
remove = list(set(settings['remove']))
compress = list(set(settings['compress']))
backup = list(set(settings['backup']))
# Check that necessary files are being moved/copied
if not infilename in (move + copy):
warnings.warn(
"Warning: Infile not found in either 'move' or 'copy'. Copying " +
infilename + " by default", QuantumEspressoWarning)
copy += [infilename]
# Check that the user isn't being contradictory or silly
for f in move:
if f in remove:
warnings.warn(
"Warning: %s found in both 'move' and 'remove'. The file will not be removed."
% f, QuantumEspressoWarning)
remove = list(set(remove) - set([f]))
if f in copy:
warnings.warn(
"Warning: %s found in both 'move' and 'copy'. The file will be copied only."
% f, QuantumEspressoWarning)
move = list(set(move) - set([f]))
if f in compress:
raise QuantumEspressoError(
"Error in casm.quantumespresso.continue_job(). %s found in both 'move' and 'compress', but these options contradict. Did you mean 'backup'?"
% f)
for f in copy:
if re.match(".*.wfc.*", f) or re.match(".*.igk.*", f):
warnings.warn(
"Warning: %s can be rather huge. It is suggested to include %s in 'move', rather than 'copy'. If you're worried about corruption due to interrupted runs, add %s to 'backup' as well."
% (f, f, f), QuantumEspressoWarning)
if f in remove:
warnings.warn(
"Warning: %sfound in 'copy' and 'remove', which is the same as 'move'."
% f, QuantumEspressoWarning)
move += f
copy = list(set(copy) - set([f]))
remove = list(set(copy) - set([f]))
if f in compress:
warnings.warn(
"Warning: %s found in 'copy' and 'compress'. It is suggested to include %s in 'move' and 'backup' instead."
% (f, f), QuantumEspressoWarning)
if f in backup:
warnings.warn(
"Warning: %s found in 'copy' and 'backup'. This will result in three copies of your file being made (old, old_BACKUP.gz, and copy)!"
% f, QuantumEspressoWarning)
for f in remove:
if f in compress:
warnings.warn(
"Warning: %s found in both 'compress' and 'remove'. Defaulting to 'compress' only!"
% f, QuantumEspressoWarning)
remove = list(set(remove) - set([f]))
for f in compress:
if f in backup:
warnings.warn(
"Warning: %s found in 'compress' and 'backup'. Defaulting to ompressing only!"
% f, QuantumEspressoWarning)
backup = list(set(backup) - set([f]))
for f in backup:
if (f not in move) and (f in remove):
warnings.warn(
"Warning: 'backup' is meant for files being moved, but %s is found under 'remove' only. Did you maybe mean 'compress'?",
QuantumEspressoWarning)
elif (f not in move):
warnings.warn(
"Warning: %s not found in 'move', so you'll just end up with 2 copies of the file..."
% f, QuantumEspressoWarning)
# make the new contdir
try:
os.mkdir(contdir)
except:
pass
# make compressed backups of files sensitive to corruption
print " backup:"
for file in backup:
if os.path.isfile(os.path.join(jobdir, file)):
print file,
# Open target file, target file.gz
f_in = open(os.path.join(jobdir, file), 'rb')
f_out = gzip.open(os.path.join(jobdir, file) + '_BACKUP.gz', 'wb')
# Compress, close files
f_out.writelines(f_in)
f_out.close()
f_in.close()
print ""
# move files
print " mv:",
for file in move:
print file,
os.rename(os.path.join(jobdir, file), os.path.join(contdir, file))
print ""
# copy files
print " cp:",
for file in copy:
print file,
shutil.copyfile(os.path.join(jobdir, file),
os.path.join(contdir, file))
print ""
# Rewrite new positions into infile if necessary
if os.path.isfile(os.path.join(jobdir, outfilename)) and os.path.isfile(
os.path.join(contdir, infilename)):
postpos = qeio.Poscar(os.path.join(jobdir, outfilename))
newinfile = qeio.Infile(os.path.join(contdir, infilename))
newinfile.rewrite_poscar_info(postpos)
newinfile.write(os.path.join(contdir, infilename))
print "Overwrote " + infilename + " positions and lattice with positions and lattice from " + outfilename
else:
print " no calculated positions to overwrite"
# remove files
print " rm:",
for file in remove:
if os.path.isfile(os.path.join(jobdir, file)):
print file,
os.remove(os.path.join(jobdir, file))
print ""
# compress files
print " gzip:",
for file in compress:
if os.path.isfile(os.path.join(jobdir, file)):
print file,
# Open target file, target file.gz
f_in = open(os.path.join(jobdir, file), 'rb')
f_out = gzip.open(os.path.join(jobdir, file) + '.gz', 'wb')
# Compress, close files
f_out.writelines(f_in)
f_out.close()
f_in.close()
# Remove original target file
os.remove(os.path.join(jobdir, file))
print ""
print ""
sys.stdout.flush()