def cont(calc):
import HighThroughput.manage.calculation as manage
baks = 0
bako = 0
bakx = 0
bakt = 0
for file in os.listdir(os.curdir):
if os.path.isfile(file) and file[0:10] == 'POSCAR.bak':
baks += 1
if os.path.isfile(file) and file[0:10] == 'OUTCAR.bak':
bako += 1
if os.path.isfile(file) and file[0:11] == 'XDATCAR.bak':
bakx += 1
if os.path.isfile(file) and file[0:11] == 'tempout.bak':
bakt += 1
if os.path.isfile('CONTCAR') and os.stat('CONTCAR').st_size > 0:
os.rename('POSCAR','POSCAR.bak' + str(baks))
os.rename('CONTCAR','POSCAR')
if os.path.isfile('OUTCAR') and os.stat('OUTCAR').st_size > 0:
os.rename('OUTCAR','OUTCAR.bak' + str(bako))
if os.path.isfile('XDATCAR') and os.stat('XDATCAR').st_size > 0:
os.rename('XDATCAR','XDATCAR.bak' + str(bakx))
if os.path.isfile('tempout') and os.stat('tempout').st_size > 0:
os.rename('tempout','tempout.bak' + str(bakt))
psettings = manage.getSettings(calc['parent'])
if 'continued' not in psettings.keys():
psettings['continued'] = 1
else:
psettings['continued'] += 1
manage.updateSettings(psettings, calc['parent'])
return calc
def cont(calc, settings):
import HighThroughput.manage.calculation as manage
bakc = 0
bakl = 0
for file in os.listdir(os.curdir):
if os.path.isfile(file) and file[6:10] == '.com':
baks += 1
if os.path.isfile(file) and file[6:10] == '.log':
bako += 1
if os.path.isfile(settings['name'] +
'.com') and os.stat(settings['name'] +
'.com').st_size > 0:
shutil.copy(COMname, COMname + '.bak' + str(baks))
# if 'SCF=Restart' not in settings['route']:
# settings['route'] += ' SCF=Restart'
if os.path.isfile(settings['name'] +
'.log') and os.stat(settings['name'] +
'.log').st_size > 0:
os.rename(settings['name'] + '.log',
settings['name'] + '.log' + '.bak' + str(bako))
psettings = manage.getSettings(calc['parent'])
if 'continued' not in psettings.keys():
psettings['continued'] = 1
else:
psettings['continued'] += 1
manage.updateSettings(psettings, calc['parent'])
return calc
def cont(calc):
import HighThroughput.manage.calculation as manage
baks = 0
bako = 0
bakx = 0
bakt = 0
for file in os.listdir(os.curdir):
if os.path.isfile(file) and file[0:10] == 'POSCAR.bak':
baks += 1
if os.path.isfile(file) and file[0:10] == 'OUTCAR.bak':
bako += 1
if os.path.isfile(file) and file[0:11] == 'XDATCAR.bak':
bakx += 1
if os.path.isfile(file) and file[0:11] == 'tempout.bak':
bakt += 1
if os.path.isfile('CONTCAR') and os.stat('CONTCAR').st_size > 0:
os.rename('POSCAR','POSCAR.bak' + str(baks))
os.rename('CONTCAR','POSCAR')
if os.path.isfile('OUTCAR') and os.stat('OUTCAR').st_size > 0:
os.rename('OUTCAR','OUTCAR.bak' + str(bako))
if os.path.isfile('XDATCAR') and os.stat('XDATCAR').st_size > 0:
os.rename('XDATCAR','XDATCAR.bak' + str(bakx))
if os.path.isfile('tempout') and os.stat('tempout').st_size > 0:
os.rename('tempout','tempout.bak' + str(bakt))
psettings = manage.getSettings(calc['parent'])
presults = manage.getResults(calc['parent'])
if 'continued' not in psettings.keys():
psettings['continued'] = 1
else:
psettings['continued'] += 1
if presults.get('settingsmod') != None:
if presults['settingsmod'].get('KPOINTS').get('K') != None and calc['settings']['KPOINTS'].get('K') != None:
curkp = [int(x) for x in calc['settings']['KPOINTS']['K'].split(' ')]
curmod = [int(x) for x in presults['settingsmod']['KPOINTS']['K'].split(' ')]
calc['settings']['KPOINTS']['K'] = ' '.join([str(curkp[x] + curmod[x]) for x in range(3)])
if 'ENCUT' in presults['settingsmod'].keys():
calc['settings']['INCAR']['ENCUT'] = int(calc['settings']['INCAR']['ENCUT']) + presults['settingsmod']['INCAR']['ENCUT']
manage.updateSettings(psettings, calc['parent'])
manage.updateResults(presults, calc['parent'])
return calc
def cont(calc,settings):
import HighThroughput.manage.calculation as manage
bakc = 0
bakl = 0
for file in os.listdir(os.curdir):
if os.path.isfile(file) and file[6:10] == '.com':
baks += 1
if os.path.isfile(file) and file[6:10] == '.log':
bako += 1
if os.path.isfile(settings['name'] + '.com') and os.stat(settings['name'] + '.com').st_size > 0:
shutil.copy(COMname,COMname + '.bak' + str(baks))
# if 'SCF=Restart' not in settings['route']:
# settings['route'] += ' SCF=Restart'
if os.path.isfile(settings['name'] + '.log') and os.stat(settings['name'] + '.log').st_size > 0:
os.rename(settings['name'] + '.log',settings['name'] + '.log' + '.bak' + str(bako))
psettings = manage.getSettings(calc['parent'])
if 'continued' not in psettings.keys():
psettings['continued'] = 1
else:
psettings['continued'] += 1
manage.updateSettings(psettings, calc['parent'])
return calc
print(
'Energy OK. Ending calculation, deleting junk files and fetching results.'
)
HT.end(cinfo['id'])
#cleanup function
# Can change this to a step dictionary
os.remove('CHG')
print('Updating settings.')
# Update POTCAR INFO
POTCAR_version = execute('grep -a \'TITEL\' POTCAR | awk \'{ print $4 }\'')
cinfo['settings']['POTCAR'] = POTCAR_version.strip().replace('\n', ', ')
HT.updateSettings(cinfo['settings'], cinfo['id'])
# Update priority with Machine Learning model
#if step == 21:
# updateMLPriority(cinfo['queue'], 42)
stat_info = os.stat(qdir)
uid = stat_info.st_uid
gid = stat_info.st_gid
for root, dirs, files in os.walk(
os.path.join(qdir, 'CALCULATIONS', cinfo['file'])):
for momo in dirs:
try:
os.chown(os.path.join(root, momo), -1, gid)
os.chmod(os.path.join(root, momo), 0o774)
def cont(calc):
print('DEBUG: continue')
baks = 0
bako = 0
bakx = 0
bakt = 0
bakv = 0
for file in os.listdir(os.curdir):
if os.path.isfile(file) and file[0:10] == 'POSCAR.bak':
baks += 1
if os.path.isfile(file) and file[0:10] == 'OUTCAR.bak':
bako += 1
if os.path.isfile(file) and file[0:11] == 'XDATCAR.bak':
bakx += 1
if os.path.isfile(file) and file[0:11] == 'tempout.bak':
bakt += 1
if os.path.isfile(file) and file[0:11] == 'vasprun.bak':
bakv += 1
if os.path.isfile('CONTCAR') and os.stat('CONTCAR').st_size > 0:
os.rename('POSCAR', 'POSCAR.bak' + str(baks))
os.rename('CONTCAR', 'POSCAR')
if os.path.isfile('OUTCAR') and os.stat('OUTCAR').st_size > 0:
os.rename('OUTCAR', 'OUTCAR.bak' + str(bako))
if os.path.isfile('XDATCAR') and os.stat('XDATCAR').st_size > 0:
os.rename('XDATCAR', 'XDATCAR.bak' + str(bakx))
if os.path.isfile('tempout') and os.stat('tempout').st_size > 0:
os.rename('tempout', 'tempout.bak' + str(bakt))
if os.path.isfile('vasprun.xml') and os.stat('vasprun.xml').st_size > 0:
os.rename('vasprun.xml', 'vasprun.bak' + str(bakv))
psettings = manage.getSettings(calc['parent'])
presults = manage.getResults(calc['parent'])
if 'continued' not in psettings.keys():
psettings['continued'] = 1
else:
psettings['continued'] += 1
if presults.get('settingsmod') is not None:
if presults['settingsmod'].get('KPOINTS') is not None and calc[
'settings'].get('KPOINTS') is not None:
if presults['settingsmod'].get('KPOINTS').get(
'K') is not None and calc['settings']['KPOINTS'].get(
'K') is not None:
curkp = [
int(x) for x in calc['settings']['KPOINTS']['K'].split(' ')
]
curmod = [
int(x)
for x in presults['settingsmod']['KPOINTS']['K'].split(' ')
]
calc['settings']['KPOINTS']['K'] = ' '.join(
[str(curkp[x] + curmod[x]) for x in range(3)])
if presults.get('settingsmod').get('INCAR') is not None:
if presults.get('settingsmod').get('INCAR').get(
'ENCUT') is not None:
calc['settings']['INCAR']['ENCUT'] = int(calc['settings']['INCAR']['ENCUT']) + \
presults['settingsmod']['INCAR']['ENCUT']
if presults.get('settingsmod').get('INCAR').get(
'SIGMA') is not None:
calc['settings']['INCAR']['SIGMA'] = presults['settingsmod'][
'INCAR']['SIGMA']
if presults.get('settingsmod').get('INCAR').get(
'ISMEAR') is not None:
if int(calc['settings']['INCAR']['ISMEAR']) != -5:
calc['settings']['INCAR']['ISMEAR'] = presults[
'settingsmod']['INCAR']['ISMEAR']
if presults.get('settingsmod').get('INCAR').get(
'ISPIN') is not None:
calc['settings']['INCAR']['ISPIN'] = presults['settingsmod'][
'INCAR']['ISPIN']
manage.updateSettings(psettings, calc['parent'])
manage.updateResults(presults, calc['parent'])
return calc
nc = round(norm(c), 3)
results['a'] = na
results['b'] = nb
results['c'] = nc
results['alpha'] = round(degrees(arccos(dot(b, c) / nb / nc)), 1)
results['beta'] = round(degrees(arccos(dot(c, a) / nc / na)), 1)
results['gamma'] = round(degrees(arccos(dot(a, b) / na / nb)), 1)
print('Updating results')
print results
HT.updateResults(results, cid)
print('Updating settings')
print settings
HT.updateSettings(settings, cid)
#RELOOP to the script
#exit() #No new calculations allowed.
cid_new = HT.fetch(qid)
print('Fetched calculation ' + str(cid_new) + ' from queue ' + str(qid) + '.')
os.chdir(qdir + '/LOGFILES')
if int(cid_new) > 0:
print('Queue not empty: submit new job.')
execute(' ssh login1 "~/bin/HTtools/QZPsubmit_reeosleuven ' + str(qid) +
' ' + str(argv[2]) + ' ' + str(argv[3]) + ' ' + str(argv[4]) + '"')
if step == 1:
results['E0PBE'] = energy
else:
results['E0HSE06'] = energy
results['E0PBE'] = float(execute('grep \'energy without entropy\' ../STEP1/OUTCAR | tail -1 | awk \'{ print $4 }\''))
print('Updating results')
print results
# updateresults could be assumed from dictionary keys and automated.
HT.updateResults(results, cid)
print('Updating settings')
print settings
HT.updateSettings(settings, cid)
#RELOOP to the script
cid_new = HT.fetch(qid)
print('Fetched calculation '+str(cid_new)+' from queue '+str(qid)+'.')
os.chdir(qdir+'/LOGFILES')
if int(cid_new) > 0:
# print('Script ONCE: do not submit new job')
#execute('vaspsubmit ' + str(qid) + ' ' + str(submit_arg))
else:
print('No calculations left; end script without submitting new job.')
)
HT.end(cid)
#cleanup function
os.remove('CHG')
results = json.loads(cinfo['results'])
#could leave this out when working with QZP's
energy = float(energy)
if status == 1:
results['E0PBE'] = energy
else:
results['E0HSE06'] = energy
results['E0PBE'] = float(
execute(
'grep \'energy without entropy\' ../STEP1/OUTCAR | tail -1 | awk \'{ print $4 }\''
))
print('Updating results')
# updateresults could be assumed from dictionary keys and automated.
HT.updateResults(results, cid)
print('Updating settings')
HT.updateSettings(cinfo['settings'], cid)
newcalc = int(HT.fetch(str(qid)))
print(str(newcalc))
if int(HT.fetch(str(qid))) > 0 and int(qid) != 167 and int(qid) != 171:
execute('betaHSE ' + str(qid) + ' ' + str(submit_arg))
# -*- coding: utf-8 -*-