def converge(calc):
presults = getResults(calc['parent'])
if 'settingsmod' not in presults.keys():
presults['settingsmod'] = {}
for propset in presults['convergence']:
total = len(propset)
prop = propset[0]
for i in range(1,total):
(crit,cond,current,converged) = propset[i]
if converged == 1:
continue;
elif crit == 'K':
if 'KPOINTS' not in presults['settingsmod'].keys():
presults['settingsmod']['KPOINTS'] = {}
if 'K' not in presults['settingsmod']['KPOINTS'].keys():
presults['settingsmod']['KPOINTS']['K'] = '2 2 2'
else:
presults['settingsmod']['KPOINTS']['K'] = ' '.join([str(int(x) + 2) for x in presults['settingsmod']['KPOINTS']['K'].split(' ')])
#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)])
break;
elif crit == 'ENCUT':
if 'INCAR' not in presults['settingsmod'].keys():
presults['settingsmod']['INCAR'] = {}
if 'ENCUT' not in presults['settingsmod']['INCAR']:
presults['settingsmod']['INCAR']['ENCUT'] = 100
else:
presults['settingsmod']['INCAR']['ENCUT'] += 100
# calc['settings']['INCAR']['ENCUT'] = int(calc['settings']['INCAR']['ENCUT']) + presults['settingsmod']['INCAR']['ENCUT']
break;
updateResults(presults,calc['parent'])
return True
def toggleISYM(calc):
presults = getResults(calc['parent'])
if 'ISYM' not in calc['settings']['INCAR'].keys():
calc['settings']['INCAR']['ISYM'] = 1
calc['settings']['INCAR']['ISYM'] = (
int(calc['settings']['INCAR']['ISYM']) + 1) % 2
return True
def halveSigmaInherit(calc):
presults = getResults(calc['parent'])
if 'settingsmod' not in presults.keys():
presults['settingsmod'] = {"INCAR": {}}
if 'INCAR' not in presults['settingsmod'].keys():
presults['settingsmod']['INCAR'] = {}
elif presults['settingsmod'].get('INCAR').get('SIGMA') != None:
presults['settingsmod']['INCAR']['SIGMA'] = float(
presults['settingsmod']['INCAR']['SIGMA']) / 2
else:
presults['settingsmod']['INCAR']['SIGMA'] = float(
calc['settings']['INCAR']['SIGMA']) / 2
updateResults(presults, calc['parent'])
return True
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 changeSpinInherit(calc):
presults = getResults(calc['parent'])
if 'settingsmod' not in presults.keys():
presults['settingsmod'] = {"INCAR": {}}
if 'INCAR' not in presults['settingsmod'].keys():
presults['settingsmod']['INCAR'] = {}
if presults['settingsmod'].get('INCAR').get('ISPIN') != None:
presults['settingsmod']['INCAR']['ISPIN'] = (
int(presults['settingsmod']['INCAR']['ISPIN']) - 2) % 2 + 1
else:
presults['settingsmod']['INCAR']['ISPIN'] = (
int(calc['settings']['INCAR']['ISPIN']) - 2) % 2 + 1
print('Setting spin to ' + str(presults['settingsmod']['INCAR']['ISPIN']))
updateResults(presults, calc['parent'])
return True
def raiseSYMPREC(calc):
presults = getResults(calc['parent'])
if 'settingsmod' not in presults.keys():
presults['settingsmod'] = {}
if 'SYMPREC' not in calc['settings']['INCAR'].keys():
calc['settings']['INCAR']['SYMPREC'] = 1e-5
if 'INCAR' not in presults['settingsmod'].keys():
presults['settingsmod']['INCAR'] = {}
if 'ENCUT' not in presults['settingsmod']['INCAR']:
presults['settingsmod']['INCAR']['SYMPREC'] = np.float32(
calc['settings']['INCAR']['SYMPREC']) * 10.
else:
presults['settingsmod']['INCAR']['SYMPREC'] = np.float32(
calc['settings']['INCAR']['SYMPREC']) * 10.
return True
def notConverged(calc):
presults = getResults(calc['parent'])
error = False
if 'convergence' not in presults.keys():
return False
else:
#"convergence": [["Ehull", ["K", 0.01, [], 0]]] format, could add more than two els to each tuple to determine how to increase the settings and so on
new = []
for propset in presults['convergence']:
total = len(propset)
prop = propset[0]
pnew = (prop,)
for i in range(1,total):
(crit,cond,current,converged) = propset[i]
if converged == 1:
propset[i][-1] = 1
pnew += (tuple(propset[i]),)
continue;
print('Checking ' + prop + ' convergence ' + ' with respect to ' + crit + '.')
newval = gather({ prop : ''})[prop]
current.append(newval)
if len(current) == 1:
error = True
else:
delta = np.abs(current[-1] - current[-2])
if delta > cond:
print('Not converged. Remaining error of ' + str(delta) + ' on ' + prop + '.')
error = True
else:
print('Property ' + prop + ' is converged up to ' + str(delta) + '.')
if crit == 'K':
presults['settingsmod']['KPOINTS']['K'] = ' '.join([str(int(x) - 2) for x in presults['settingsmod']['KPOINTS']['K'].split(' ')])
elif crit == 'ENCUT':
presults['settingsmod']['INCAR']['ENCUT'] -= 100
converged = 1
pnew += ((crit,cond,current,converged),)
new.append(pnew)
# presults['convergence'] = json.dumps(new).translate(str.maketrans({"'": r"\'"}))
updateResults(presults,calc['parent'])
return error
def changeSmearInherit(calc):
presults = getResults(calc['parent'])
if 'settingsmod' not in presults.keys():
presults['settingsmod'] = {"INCAR": {}}
if 'INCAR' not in presults['settingsmod'].keys():
presults['settingsmod']['INCAR'] = {}
if presults['settingsmod'].get('INCAR').get('ISMEAR') != None:
if presults['settingsmod'].get('INCAR').get('ISMEAR') == 0:
presults['settingsmod']['INCAR']['ISMEAR'] = 1
presults['settingsmod']['INCAR']['SIGMA'] = 0.2
elif presults['settingsmod'].get('INCAR').get('ISMEAR') == 1:
presults['settingsmod']['INCAR']['ISMEAR'] = 0
presults['settingsmod']['INCAR']['SIGMA'] = 0.05
else:
if calc['settings']['INCAR']['ISMEAR'] == 0:
presults['settingsmod']['INCAR']['ISMEAR'] = 1
presults['settingsmod']['INCAR']['SIGMA'] = 0.2
elif calc['settings']['INCAR']['ISMEAR'] == 1:
presults['settingsmod']['INCAR']['ISMEAR'] = 0
presults['settingsmod']['INCAR']['SIGMA'] = 0.05
updateResults(presults, calc['parent'])
return True
step = int(np.ceil(float(cinfo['stat']) / 2))
# Configure settings per step
# By default always inherit
inheritcontcar = True
inheritchgcar = True
inheritwavecar = True
# Can define this by default, though I've added an if statement for each step anyways
inheritstep = step - 1
parent = HT.get(cinfo['parent'])
inheritmod = None
inheritgrid = False
rescale = 1.0
if parent['parent'] != '0':
pparent = HT.getResults(parent['parent'])
inheritmod = pparent.get('settingsmod')
print('The following settingsmod will be inherited: ')
print(inheritmod)
#==============================================================================
# In this section you can also make manual changes to the settings, for example:
# if int(qid) == 167 or int(qid) == 171:
# cinfo['settings']['KPOINTS']['K'] = '12 12 12'
# cinfo['settings']['INCAR']['NKRED'] = '2'
# cinfo['settings']['INCAR']['LSUBROT'] = '.TRUE.'
# if int(cfile) == 10025486:
# cinfo['settings']['INCAR']['ALGO'] = 'A'
# cinfo['settings']['INCAR']['NELM'] = 30
# cinfo['settings']['INCAR']['TIME'] = 1.95
# if int(cfile) == 10031153:
def inherit(calc,
path,
contcar=True,
chgcar=True,
wavecar=True,
settingsmod=None,
grid=False,
rescale=1.0):
#pstep = int(math.ceil(float(stat)/2.)) -1
if path is None:
return True
#inputfile = os.path.join(qdir, 'import', str(cfile) + '.vasp')
#qdir, 'CALCULATIONS/' + cfile + '/STEP' + str(pstep)
if contcar:
contcarnames = [
'CONTCAR', 'POSCAR' + calc['file'] + '.vasp',
'POSCAR' + calc['file'], calc['file'], calc['file'] + '.vasp'
]
for name in contcarnames:
temp = os.path.join(path, name)
if os.path.isfile(temp):
inputfile = temp
print('Inheriting geometry from ' + inputfile + '.')
shutil.copy(inputfile, './POSCAR')
rescalePOSCAR('POSCAR', rescale)
break
if chgcar:
chgcarnames = [
'CHGCAR.gz', 'CHGCAR', 'CHGCAR' + calc['file'] + '.gz',
'CHGCAR' + calc['file']
]
for name in chgcarnames:
temp = os.path.join(path, name)
if os.path.isfile(temp):
density = temp
out = 'CHGCAR'
if density[-3:] == '.gz':
out += '.gz'
print('Inheriting charge density from ' + density + '.')
shutil.copy(density, out)
if calc['settings']['INCAR'].get('ICHARG') is None:
calc['settings']['INCAR']['ICHARG'] = 1
break
if wavecar:
wavecarnames = [
'WAVECAR.gz', 'WAVECAR', 'WAVECAR' + calc['file'] + '.gz',
'WAVECAR' + calc['file']
]
for name in wavecarnames:
temp = os.path.join(path, name)
if os.path.isfile(temp):
wavecar = temp
out = 'WAVECAR'
if wavecar[-3:] == '.gz':
out += '.gz'
print('Inheriting wave functions from ' + wavecar + '.')
shutil.copy(wavecar, out)
break
if grid:
outcar = os.path.join(path, 'OUTCAR')
ng = execute('grep "dimension x,y,z NGX" ' + outcar +
' | head -n 1').strip().split()
calc['settings']['INCAR']['NGX'] = int(ng[4])
calc['settings']['INCAR']['NGY'] = int(ng[7])
calc['settings']['INCAR']['NGZ'] = int(ng[10])
if settingsmod:
presults = manage.getResults(calc['parent'])
presults['settingsmod'] = settingsmod
manage.updateResults(presults, calc['parent'])
print('These setting mods are inherited:')
print(presults['settingsmod'])
if settingsmod.get('KPOINTS') is not None and calc['settings'].get(
'KPOINTS').get('K') is not None:
curkp = [
int(x) for x in calc['settings']['KPOINTS']['K'].split(' ')
]
curmod = [int(x) for x in settingsmod['KPOINTS']['K'].split(' ')]
calc['settings']['KPOINTS']['K'] = ' '.join(
[str(curkp[x] + curmod[x]) for x in range(3)])
print(curkp, curmod)
print('Calibration update to kpoints executed.')
if settingsmod.get('INCAR') is not None:
if settingsmod.get('INCAR').get('ENCUT') is not None:
calc['settings']['INCAR']['ENCUT'] = int(
calc['settings']['INCAR']
['ENCUT']) + settingsmod['INCAR']['ENCUT']
if settingsmod.get('INCAR').get('SIGMA') is not None:
calc['settings']['INCAR']['SIGMA'] = settingsmod['INCAR'][
'SIGMA']
if settingsmod.get('INCAR').get('ISMEAR') is not None:
if int(calc['settings']['INCAR']['ISMEAR']) != -5:
calc['settings']['INCAR']['ISMEAR'] = settingsmod['INCAR'][
'ISMEAR']
if settingsmod.get('INCAR').get('ISPIN') is not None:
calc['settings']['INCAR']['ISPIN'] = settingsmod['INCAR'][
'ISPIN']
#if os.path.isfile('CHGCAR'):
# os.rename('CHGCAR','CHGCAR.prec')
return calc
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
while (ended == 0 and tries < 10):
ended = HT.end(cid)
tries = tries + 1
print tries
time.sleep(random.randint(10, 100))
if (ended == 0):
print('ERROR: I tried to end calculation ' + str(cid) + str(tries) +
' times, but no succes.') #tries should always be 10
HT.updateResults({'error': 'Ending calculation failed'}, cid)
else:
if status < 15:
#os.remove('CHGCAR')
os.remove('CHG')
results = HT.getResults(cid)
#could leave this out when working with QZP's
poscar = open('POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
energy = float(energy)
Eatom = energy / numberofatoms
results['Eatom'] = Eatom
if 'error' in locals():
HT.updateResults({'error':error}, cid)
elif energy=='' or not 'energy' in locals():
HT.updateResults({'error':'Energy missing'}, cid)
print('Energy missing! Error...')
elif not os.path.isfile('CHGCAR') and not os.path.isfile('CHG'):
HT.updateResults({'error':'CHGCAR and CHG missing. VASP Error?'}, cid)
print('CHGCAR/CHG missing. VASP Error?')
else:
print('Energy OK. Ending calculation, deleting junk files and fetching results.')
HT.end(cid)
if status<19:
os.remove('CHG')
results = HT.getResults(cid)
#could leave this out when working with QZP's
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
energy = float(energy)
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 }\''))
cinfo['settings']['INCAR']['NKRED'] = '2'
cinfo['settings']['INCAR']['LSUBROT'] = '.TRUE.'
if int(cfile) == 10025486:
cinfo['settings']['INCAR']['ALGO'] = 'A'
cinfo['settings']['INCAR']['NELM'] = 30
cinfo['settings']['INCAR']['TIME'] = 1.95
if int(cfile) == 10031153:
cinfo['settings']['INCAR']['MAGMOM'] = '2*1.0000 2*-1.0000'
if int(cfile) == 10031210:
cinfo['settings']['INCAR']['MAGMOM'] = '1. 1. -1. -1.'
parallelSetup(cinfo['settings'])
if os.getenv('VSC_INSTITUTE_CLUSTER') == 'muk':
cinfo['settings']['INCAR']['NCORE'] = '16'
perror = HT.getResults(cinfo['parent'])
if perror.get('errors') != None:
fixerrors(cinfo)
writeSettings(cinfo['settings'])
run()
finderrors(cinfo)
if os.path.isfile('STOPCAR'):
os.remove('STOPCAR')
print('END STATUS ' + cinfo['stat'])
#UPDATE POTCAR INFO
POTCAR_version = execute('grep -a \'TITEL\' POTCAR | awk \'{ print $4 }\'')
cinfo['settings']['POTCAR'] = POTCAR_version.strip().replace('\n', ', ')