def generateDOS(self, **kwargs):
""" Generate DOS input files for all the compounds created """
# Set default settings.
settings = {
'mode' : 'REL',
'nktab' : '250',
'NE' : '50',
'EMIN' : '-0.2',
'EMAX' : '1.0',
'ImE' : '0.01'
}
# Replace default settings with user defined settings.
for key, value in kwargs.iteritems():
settings[key] = value
print('Generating DOS input files.')
for dirname in os.listdir('.'):
if (os.path.exists(os.path.join(dirname, 'dos.inp'))
is True):
print(dirname + ' already contains dos.inp, '
+ 'it will not be overwritten.')
else:
reps = {
'tmpDATASET' : dirname,
'tmpMODE' : settings['mode'],
'tmpNKTAB' : settings['nktab'],
'tmpNE' : settings['NE'],
'tmpEMIN' : settings['EMIN'],
'tmpEMAX' : settings['EMAX'],
'tmpImE' : settings['ImE']
}
nmod.modFile(os.path.join(dirname, 'dos.inp'),
os.path.join(self.templatesDir, 'dos.inp'), reps)
print('Finish generating DOS input files.')
def create(self, fullConc, **kwargs):
""" Create the specified compound """
elementsFile = os.path.join(self.templatesDir, 'elements.txt')
# Set default settings.
settings = {
'mode' : 'REL',
'nktab' : '250',
'NE' : '30'
}
# Replace default settings with user defined settings.
for key, value in kwargs.iteritems():
settings[key] = value
# Set the different concentrations
concentrations = fullConc.split('_')
conc = [None]*5
for i in range(len(concentrations)):
conc[i] = concentrations[i]
# Set the different elements
IT = [None]*5
for i in range(len(self.elements)):
IT[i] = nmod.findLine(elementsFile, self.elements[i])
fullname = (
self.elements[0] + conc[0]
+ self.elements[1] + conc[1]
+ self.elements[2] + conc[2]
+ self.elements[3] + conc[3]
+ self.elements[4] + conc[4]
)
# Check if directory already exists, if not, carry on.
if os.path.isdir(fullConc):
print(fullConc + ' already exists, it will not be overwritten.')
else:
os.makedirs(fullConc)
# Start the creation process.
# Take all the template files, copy it to the new directory
# and replace the "tmp" strings with the settings.
# POT
reps = {
'tmpSYSTEM' : fullname,
'tmpALAT' : self.alat,
'tmpCONC1' : conc[0],
'tmpCONC2' : conc[1],
'tmpCONC3' : conc[2],
'tmpCONC4' : conc[3],
'tmpCONC5' : conc[4],
'tmpIT1' : IT[0],
'tmpIT2' : IT[1],
'tmpIT3' : IT[2],
'tmpIT4' : IT[3],
'tmpIT5' : IT[4]
}
nmod.modFile(os.path.join(fullConc, 'pot.pot'),
os.path.join(self.templatesDir, self.potFile + '.pot'), reps)
# SCF
reps = {
'tmpDATASET' : fullname,
'tmpMODE' : settings['mode'],
'tmpNKTAB' : settings['nktab'],
'tmpNE' : settings['NE']
}
nmod.modFile(os.path.join(fullConc, 'scf.inp'),
os.path.join(self.templatesDir, 'scf.inp'), reps)
print(fullname + " has been created.")
def generateBSF(self, **kwargs):
""" Generate BSF input files for all the compounds created """
settings = {
'nktab' : '250',
'NE' : '1',
'EMIN' : '1.0',
'EMAX' : '1.0',
'NK1' : '60',
'NK2' : '60',
'K1' : '{1.0, 0.0, 0.0}',
'K2' : '{0.0, 1.0, 0.0}',
'eRange': 0.01,
'iterations': 0
}
# Replace default settings with user defined settings.
for key, value in kwargs.iteritems():
settings[key] = value
print('Generating BSF input files.')
for dirname in os.listdir('.'):
if settings['iterations'] == 0:
if (os.path.exists(os.path.join(dirname, 'bsf.inp'))
is True):
print(dirname + ' already contains bsf.inp, '
+ 'it will not be overwritten.')
else:
reps = {
'tmpDATASET' : dirname,
'tmpNKTAB' : settings['nktab'],
'tmpNE' : settings['NE'],
'tmpEMIN' : settings['EMIN'],
'tmpEMAX' : settings['EMAX'],
'tmpNK1' : settings['NK1'],
'tmpNK2' : settings['NK1'],
'tmpK1' : settings['K1'],
'tmpK2' : settings['K2']
}
nmod.modFile(os.path.join(dirname, 'bsf.inp'),
os.path.join(self.templatesDir, 'bsf.inp'), reps)
else:
energy = (settings['EMIN'] - 0.5*float(settings['eRange']))
for i in range(settings['iterations']):
tmpnum = str(i + 1)
bsfFile = 'bsf_' + tmpnum + '.inp'
if (os.path.exists(os.path.join(dirname, bsfFile))
is True):
print(dirname + ' already contains ' + bsfFile + ', '
+ 'it will not be overwritten.')
else:
energy += settings['eRange'] / settings['iterations']
reps = {
'tmpDATASET' : dirname + '_' + tmpnum,
'tmpNKTAB' : settings['nktab'],
'tmpNE' : 1,
'tmpEMIN' : energy,
'tmpEMAX' : energy,
'tmpNK1' : settings['NK1'],
'tmpNK2' : settings['NK1'],
'tmpK1' : settings['K1'],
'tmpK2' : settings['K2']
}
nmod.modFile(os.path.join(dirname, bsfFile),
os.path.join(self.templatesDir, 'bsf.inp'), reps)
print('Finish generating BSF input files.')
def submitArray(mainDir, pbsFile, start, end, **kwargs):
""" Submit many array jobs without overloading the task farm """
# Define all the required directories.
baseDir = os.path.join(os.path.dirname(os.path.realpath(
inspect.getfile(inspect.currentframe()))), '..')
templatesDir = os.path.join(baseDir, 'templates')
jobsDir = os.path.join(baseDir, mainDir, 'jobs')
# Set default settings.
settings = {
'step': 10,
'interval': 300
}
# Replace default settings with user defined settings.
for key, value in kwargs.iteritems():
settings[key] = value
if checkRequired(mainDir, templatesDir, jobsDir):
nmod.nexit()
else:
os.chdir(jobsDir)
iterations = int(math.ceil((end - start) / settings['step']))
last = iterations - 1 # Last iteration point for checks later.
subCmd = ['qsub', pbsFile]
checkInterval = settings['interval']
timeStart = int(time.time())
timePrev = timeStart
# Submit the first batch of jobs.
reps = {
'tmpTSTART' : start,
'tmpTEND' : settings['step'] + start - 1
}
nmod.modFile(pbsFile,
os.path.join(templatesDir, pbsFile), reps)
subprocess.Popen(subCmd)
for i in range(1, iterations):
# Check if any jobs are still idle or blocked.
# If there are, check again after an interval.
# Only submit the next batch of jobs when there are no queued jobs.
time.sleep(3) # Sleep to make sure the jobs are submitted.
while True:
# Read in the showq command as an array separated by newline.
p = subprocess.Popen(['showq', '-u', 'phukgm'],
stdout = subprocess.PIPE,
stderr = subprocess.PIPE)
stdout, _ = p.communicate()
stdout = stdout.decode()
stdout = stdout.split('\n')
# Check if queued jobs are non-zero.
if ('Idle Jobs: 0' in stdout[-2]
and 'Blocked Jobs: 0' in stdout[-2]):
timePrev = time.time()
break
else:
print('There are still idle and blocked jobs after '
+ nmod.seconds2str(time.time() - timePrev) + '.')
timePrev = time.time()
time.sleep(checkInterval) # Check jobs interval.
# Submit the next batch of jobs.
# Make sure the last iteration has the correct
# ending point of -t (tempTEND).
if i == last:
print('Submitting -t ' + str(i * settings['step'] + start)
+ '-' + str(end) + '...')
reps = {
'tmpTSTART' : i * settings['step'] + start,
'tmpTEND' : end
}
else:
print('Submitting -t ' + str(i * settings['step'] + start)
+ '-' + str((i+1) * settings['step'] + start - 1) + '...')
reps = {
'tmpTSTART' : i * settings['step'] + start,
'tmpTEND' : (i+1) * settings['step'] + start - 1
}
nmod.modFile(pbsFile,
os.path.join(templatesDir, pbsFile), reps)
subprocess.Popen(subCmd)
timeTaken = nmod.seconds2str(time.time() - timeStart)
print('All jobs submitted. Time taken: ' + timeTaken + '.')
