def eosPrepare(directory=None, evname='EOS'):
if directory is None:
directory = os.getcwd()
currentdir = os.getcwd()
os.chdir(directory)
if not os.path.isfile('./1.0/POSCAR'):
return False
poscar = open('./1.0/POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
#Setup e-v.dat
eos = {}
with open(evname, 'w') as eosfile:
for i in sorted(os.listdir()):
if os.path.isdir(i) and i.replace('.', '', 1).isdigit():
E = execute(
'grep \'energy without entropy\' ' + i +
'/OUTCAR | tail -1 | awk \'{ print $7 }\'').strip()
V = execute(
'grep vol ' + i +
'/OUTCAR | tail -n 1 | awk \'{print $5}\'').strip()
eos[i] = (float(E) / numberofatoms, V)
eosfile.write(V + ' ' + str(E) + '\n')
os.chdir(currentdir)
return eos
def initialize(settings, hard=''):
#print 'write incar kpoints potcar, make directory?'
#inherit()
writeSettings(settings)
poscar = open('./POSCAR', 'r')
lines = poscar.readlines()
elements = lines[5][:-1].strip()
execute('POTgen' + str(hard) + ' ' + str(elements))
return 0
def decompress():
nodes = getNodeInfo()
ncore = min(nodes.values())
if os.path.isfile('CHGCAR.gz'):
print('Decompressing CHGCAR.gz in ' + os.getcwd() + '.')
execute('pigz -f -d -6 -p' + str(ncore) + ' CHGCAR.gz')
if os.path.isfile('WAVECAR.gz'):
print('Decompressing WAVECAR.gz in ' + os.getcwd() + '.')
execute('pigz -f -d -6 -p' + str(ncore) + ' WAVECAR.gz')
def readSettings(settings):
settings['INCAR'] = readINCAR()
settings['KPOINTS'] = readKPOINTS()
POTCAR_version = execute('grep -a \'TITEL\' POTCAR | awk \'{ print $4 }\'')
settings['POTCAR'] = POTCAR_version.strip().replace('\n', ', ')
#read/writePOTCAR would be useful
return settings
def eosPrepare(directory = None, evname = 'EOS'):
if directory == None:
directory = os.getcwd()
currentdir = os.getcwd()
os.chdir(directory)
os.chdir('../')
#Setup e-v.dat
eos = {}
with open(evname,'w') as eosfile:
for i in os.listdir():
if os.path.isdir(i) and i.replace('.','',1).isdigit():
E = execute('grep \'energy without entropy\' ' + i + '/OUTCAR | tail -1 | awk \'{ print $7 }\'').strip()
V = execute('grep vol ' + i + '/OUTCAR | tail -n 1 | awk \'{print $5}\'').strip()
eos[i] = (E,V)
eosfile.write(V + ' ' + E + '\n')
os.chdir(currentdir)
return eos
def run(ratio = 1,cwd = None):
global vasp
#could move hybrid to parallel setup
if cwd == None:
cwd = os.getcwd();
nodes = getNodeInfo()
#cores = mysql_query('SELECT `cores` FROM `clusters` WHERE `name` = ' + str(os.getenv('VSC_INSTITUTE_CLUSTER')))
hybrid = str(int(min(nodes.values())/int(ratio)))
return execute('mympirun -h ' + hybrid + ' --output ' + cwd + '/tempout ' + vasp)
def gather(results):
for key in results:
if key[0:2] == 'E0':
results[key] = float(execute('grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $7 }\''))
if 'atom' in key:
poscar = open('POSCAR','r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))/numberofatoms
results[key] /= numberofatoms
elif key == 'natoms':
poscar = open('POSCAR','r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))/numberofatoms
results[key] = numberofatoms
elif key == 'Ehull':
results[key] = float(execute('HTehull ./'))
elif key == 'Eatom':
#to be implemented
results[key] = float(execute('HTehull ./'))
elif key == 'Epure':
#to be implemented
results[key] = float(execute('HTehull ./'))
elif key == 'cellparams':
crystal = ase.io.read('CONTCAR')
results[key] = list(crystal.get_cell_lengths_and_angles())
elif key == 'volume':
results[key] = float(execute('grep vol OUTCAR | tail -n 1 | awk \'{print $5}\''))
elif key == 'eos':
eosPrepare()
v0, e0, B, BP, residuals = eosFit()
results[key] = {'V0' : v0, 'E0' : e0, 'B0' : B, 'BP' : BP, 'res' : residuals}
return results
print('Initializing job.')
inherit(cinfo,
cdir[inheritstep],
contcar=inheritcontcar,
chgcar=inheritchgcar,
wavecar=inheritwavecar,
grid=inheritgrid,
settingsmod=inheritmod,
rescale=rescale)
#Verify your potcardir, potgen should possibly just become a python function.
initialize(cinfo['settings'])
#Post setup modifications.
encutlow = 1.25 * float(
execute(
'grep ENMAX POTCAR | awk \'{print $3}\' | cut -d\; -f1 | sort -n | tail -n1'
))
if step < 12:
cinfo['settings']['INCAR']['ENCUT'] = encutlow
else:
cinfo['settings']['INCAR']['ENCUT'] = 520
if detectSP('POSCAR'):
# This could be abstracted further, though the magnetic elements chosen in
# detectSP are not uniquely chosen either.
cinfo['settings']['INCAR']['ISPIN'] = 2
#Redivide KP AFTER initializing for settingsmod
setupKP(cinfo['settings'], minkp)
#Setup parallellization settings
def gather(results):
if 'Ehull' in results.keys():
results['Ehullold'] = 0
results['potcorr'] = 0
results['path'] = ''
resultkeys = list(results.keys()).copy()
results['Edisp'] = 0
for key in resultkeys:
print(key)
if key[0:2] == 'E0' and 'disp' not in key:
try:
vdw = float(
execute('grep \'Edisp\' OUTCAR | awk \'{print $3}\''))
except ValueError:
vdw = 0
results['Edisp'] = vdw
results[key + 'disp'] = float(
execute(
'grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $7 }\''
))
results[key] = results[key + 'disp'] - vdw
if 'atom' in key:
poscar = open('POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
results[key] /= numberofatoms
results[key + 'disp'] /= numberofatoms
elif key == 'natoms':
poscar = open('POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
results[key] = numberofatoms
elif key == 'Ehull':
results[key + 'old'] = float(getEhull().split(' ')[0])
ehull, path = tuple(
[x.strip() for x in getEhull(new='1').split(' ', maxsplit=1)])
potcorr = getPotCorr(
) #float(execute('HTpotcorr ./ 1 | tail -n 1'))
results[key] = float(ehull) + potcorr
results['path'] = path
results['potcorr'] = potcorr
elif key == 'Eatom':
#to be implemented
results[key] = float(
execute(
'grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $7 }\''
))
poscar = open('POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
results[key] /= numberofatoms
results[key] -= float(execute('HTeatom ./ | tail -n 1'))
elif key == 'Epure':
#to be implemented
results[key] = float(
execute(
'grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $7 }\''
))
poscar = open('POSCAR', 'r')
lines = poscar.readlines()
numberofatoms = lines[6][:-1].lstrip()
numberofatoms = " ".join(numberofatoms.split())
numberofatoms = sum(map(int, numberofatoms.split(' ')))
results[key] /= numberofatoms
results[key] -= float(execute('HTepure ./ | tail -n 1'))
elif key == 'Eelectro':
results[key] = execute('HTelectro ./')
elif key == 'cellparams':
crystal = ase.io.read('CONTCAR')
results[key] = list(crystal.get_cell_lengths_and_angles())
elif key == 'volume':
results[key] = float(
execute('grep vol OUTCAR | tail -n 1 | awk \'{print $5}\''))
elif key == 'eos':
test = eosPrepare(directory='../')
if not test:
continue
v0, e0, B, BP, residuals = eosFit()
results[key] = {
'V0': v0,
'E0': e0,
'B0': B,
'BP': BP,
'res': residuals
}
elif key == 'BG':
vr = Vasprun('vasprun.xml', occu_tol=0.1)
results[key] = vr.eigenvalue_band_properties[0]
elif key == 'smearerr':
s0 = float(
execute(
'grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $7 }\''
))
s = float(
execute(
'grep \'energy without entropy\' OUTCAR | tail -1 | awk \'{ print $4 }\''
))
results[key] = s0 - s
elif key == 'magmom':
magmom = execute(
'grep number.*magnetization OUTCAR | tail -n 1 | awk \'{print $6}\''
).isdigit()
if isfloat(magmom):
results[key] = np.abs(float(magmom))
else:
results[key] = 0
return results
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
# Error catching
finderrors(cinfo)
# Checkpoint cleanup
if os.path.isfile('STOPCAR'):
os.remove('STOPCAR')
print('Ending Calculation')
# Checkpoint abortion
if os.path.isfile('aborted'):
print('Calculation aborted')
if cinfo['server'] != 'breniac':
execute(submitscript + ' ' + str(qid) + ' ' + str(submit_arg))
else:
execute('ssh login1 "' + submitscript + ' ' + str(qid) + ' ' + str(submit_arg) + '"')
sys.exit()
# Post-processing (run hooks? or extra functions in VASP module)
# Gather results and settings and end calculation
# Nowadays I take the energy with sigma -> 0, while in theory without entropy should be nearly the same,
# this seems more robust and is also used by the VASP group
# Store detected errors
if 'error' in locals():
HT.updateResults({'error':error}, cinfo['id'])
else:
