def getEng(strpth):
def getENG_GPAW(log):
return float(parseLine(log, 'Extrapolated:', -1).split()[-1])
def getENG_QE(log):
return float(parseLine(log, 'total energy', -2).split()[-2])
dftcode = getDFTcode(strpth)
if dftcode == 'gpaw': return getENG_GPAW(readOnSherOrSlac(strpth + 'log'))
elif dftcode == 'quantumespresso':
return getENG_QE(readOnSherOrSlac(strpth + 'log'))
else:
return None
def getPSPpath(storagepath, dftcode):
def getPSPpath_QE(log):
return parseLine(log, 'pseudo_dir').split("='")[1][:-2]
def getPSPpath_GPAW(log):
return parseLine(log, 'setups').split(': ')[-1].strip()
if dftcode == 'gpaw':
return getPSPpath_GPAW(readOnSherOrSlac(storagepath + 'log'))
elif dftcode == 'quantumespresso':
return getPSPpath_QE(readOnSherOrSlac(storagepath + 'pw.inp'))
else:
raise NotImplementedError, 'unknown dftcode?'
def varies(constraint, param, rang):
"""
varies("xc='BEEF' and name like '%Pd%'",'pw',range(500,1000,100))
--> create jobs varying planewave_cutoff (500,600,...,1000) for all BEEF jobs with Pd
"""
jbs = []
defaults = RELAXORLAT
cnst = AND(defaults, constraint)
output = db.queryCol('storage_directory', cnst)
existing = manage.listOfIncompleteJobStrs()
if ask('Do you want to vary %s over range %s for %d jobs?' %
(param, str(rang), len(output))):
for stordir in output:
params = json.loads(misc.readOnSherOrSlac(stordir + 'params.json'))
for v in rang:
ps = copy.deepcopy(params)
assert not (jobs.Job(ps).new(
)), 'varying a job that isn\'t complete or doesn\'t exist'
ps[param] = v
job = jobs.Job(ps)
if job.new(existing): jbs.append(job)
if ask('Do you want to launch %d new jobs?' % len(jbs)):
for j in jbs:
j.submit()
misc.launch()
def getAtoms(storedpath):
import pickle
return pickle.loads(readOnSherOrSlac(storedpath + 'raw.pckl'))
def getDFTcode(strpth):
if 'espresso' in readOnSherOrSlac(strpth + 'log'): return 'quantumespresso'
elif 'gpaw' in readOnSherOrSlac(strpth + 'log'): return 'gpaw'
else: raise NotImplementedError, 'Vasp?'
def getTPS(user, jobkind, storedpath, fwid):
if user != 'ksb' or jobkind not in ['latticeopt', 'relax']: return None
n = readOnSherOrSlac(storedpath + 'qn.log').count('BFGS')
return lastLaunch(fwid)['runtime_secs'] / float(n)
def getFWID(user, storedpath):
if user != 'ksb': return None
out = readOnSherOrSlac(storedpath + 'FW_submit.script')
return int(parseLine(out, '--fw_id').split()[-1])
raise ValueError, 'No fw_id found in FW_submit.script: \n\n%s' % out
def makeStrJob(user, storedpath):
if user != 'ksb': return None
import jobs, json
params = json.loads(readOnSherOrSlac(storedpath + 'params.json'))
return str(jobs.Job(params))
def result(storagepath, key):
import json
return json.loads(readOnSherOrSlac(storagepath + 'result.json'))[key]
def getBareSlab(constraint="1", check=True):
"""Create a bare slab for some set of relaxed bulk structures. Alter parameters below as necessary"""
cons = AND(RELAXORLAT, BULK, MBEEF, PAWPSP, BCC, PW(1500), KPTDEN(2),
constraint)
facet = [1, 0, 0]
xy = [1, 1]
layers = 6
constrained = 2
symmetric = 1
vacuum = 10
vacancies = []
output = db.query([
'fwid', 'storage_directory', 'job_name', 'structure_ksb',
'planewave_cutoff', 'xc', 'kptden_ksb', 'psp_ksb', 'dwrat_ksb',
'econv_ksb', 'mixing_ksb', 'nmix_ksb', 'maxstep_ksb', 'nbands_ksb',
'sigma_ksb', 'fmax_ksb', 'dftcode'
], cons)
question = 'Are you sure you want to create bare slabs for %d structures?' % len(
output)
if ask(question):
existing = manage.listOfIncompleteJobStrs()
newjbs = []
for fwid, stor_dir, name, structure, pw, xc, kptden, psp, dwrat, econv, mixing, nmix, maxstep, nbands, sigma, fmax, dftcode in output:
ftraj = misc.readOnSherOrSlac(stor_dir + 'raw.pckl')
surf, img = surfFuncs.bulk2surf(ftraj, facet, xy, layers,
constrained, symmetric, vacuum,
vacancies)
name += '_' + ','.join(map(str, facet)) + '_' + 'x'.join(
map(str, (xy + [layers])))
params = {
'jobkind': 'relax',
'inittraj_pckl': pickle.dumps(surf),
'name': name,
'kind': 'surface',
'dftcode': dftcode,
'structure': structure # don't need bulk vacancies/scale?
,
'pw': pw,
'xc': xc,
'kptden': kptden,
'psp': psp,
'bulkparent': fwid,
'dwrat': dwrat,
'econv': econv,
'mixing': mixing,
'nmix': nmix,
'maxstep': maxstep,
'nbands': nbands,
'sigma': sigma,
'fmax': fmax,
'sites_base64': img,
'facet_json': json.dumps(facet),
'xy_json': json.dumps(xy),
'layers': layers,
'constrained': constrained,
'symmetric': symmetric,
'vacuum': vacuum,
'vacancies_json': json.dumps(vacancies),
'adsorbates_json': json.dumps({})
}
job = jobs.Job(params)
if job.new(existing):
if check: viz.view(surf)
question = 'Does this structure look right?\n' + misc.abbreviateDict(
params)
if not check or ask(question): job.submit()
misc.launch()