def vary(constraint, param, rang, check=True):
# verify that constraint uniquely picks out a job
readJobs.readJobs()
defaults = RELAXORLAT
output = dbase.queryCol('params_json', AND([defaults, constraint]))
assert len(
output
) == 1, 'Constraint %s is not specific enough, the following sets of params are returned: %s' % (
constraint, '\n\n'.join([abbreviateDict(z) for z in output]))
params = json.loads(output[0])
assert param in params.keys(), 'param %s not in keys: %s' % (
abbreviateDict(param), params.keys())
print 'Param dict with %s being varied over the range %s: %s' % (
param, str(rang), abbreviateDict(params))
jbs = []
for v in rang:
ps = copy.deepcopy(params)
assert not (jobs.assignJob(ps).new()
), 'varying a job that isn\'t complete or doesn\'t exist'
ps[param] = v
job = jobs.assignJob(ps)
if job.new(): jbs.append(job)
if not check or ask('Do you want to launch %d new jobs?' % len(jbs)):
for j in jbs:
j.check()
j.submit()
if check: misc.launch()
def addAdsorbate(constraint="1"):
constrnts = AND([COMPLETED, RELAX, SURFACE, SYMMETRIC(False), constraint])
ads = {'H': ['O1']}
details.load('finaltraj_pckl', constrnts)
output = dbase.query(['fwid', 'params_json', 'finaltraj_pckl'], constrnts)
question = 'Are you sure you want to add adsorbates to %d slabs?' % len(
output)
if ask(question):
for fw, paramStr, ftraj in output:
params = json.loads(paramStr)
newsurf = surfFuncs.adsorbedSurface(
ftraj, json.loads(params['facet_json']), ads)
if jobs.assignJob(params).spinpol():
newsurf.set_initial_magnetic_moments([
3 if e in misc.magElems else 0
for e in newsurf.get_chemical_symbols()
])
ase.visualize.view(newsurf)
params['name'] += '_' + printAds(ads)
params['surfparent'] = fw
params['inittraj_pckl'] = pickle.dumps(newsurf)
params['adsorbates_json'] = json.dumps(ads)
job = jobs.assignJob(params)
if job.new():
viz.view(newsurf)
question = 'Does this structure look right?\n' + abbreviateDict(
params)
if ask(question):
job.check()
job.submit()
misc.launch()
def initialize(fwspec):
clearOldFiles()
prms = fwspec['params']
jb = jobs.assignJob(prms)
atms = jb.atoms().copy()
ase.io.write('init.traj',atms)
return jb,prms,atms
def getVibs(constraint="1"):
cons = AND([QE, COMPLETED, RELAXORLAT, NONMETAL, constraint])
details.load('finaltraj_pckl', cons)
output = dbase.query(
['fwid', 'params_json', 'finaltraj_pckl', 'natoms', 'numbers_pckl'],
cons)
question = 'Are you sure you want to calculate vibrations for %d structures?' % len(
output)
if ask(question):
newjbs = []
for fwid, paramStr, ftraj, n, ns in output:
param = json.loads(paramStr)
nums = zip(range(n), pickle.loads(ns))
nonmetal = [x for x, y in nums if y in misc.nonmetals
] #default do vibrations only on nonmetal atoms
if len(nonmetal) > 0:
param['jobkind'] = 'vib'
param['relax'] = fwid
param['inittraj_pckl'] = misc.restoreMagmom(ftraj)
param['vibids_json'] = json.dumps(nonmetal)
param['delta'] = 0.04
job = jobs.assignJob(param)
print abbreviateDict(param)
if job.new(): newjbs.append(job)
if ask("launch %d new jobs?" % len(newjbs)):
for j in newjbs:
j.check()
j.submit()
misc.launch()
def calculateBulkModulus(constraint="1"):
details.load(['finaltraj_pckl'], incomplete=False)
cons = AND([COMPLETED, LATTICEOPT,
constraint]) # necessary for bulkmodulus calc to be valid
output = dbase.query(['fwid', 'params_json', 'finaltraj_pckl'], cons)
question = 'Are you sure you want to calculate bulk modulus for %d structures?' % len(
output)
if ask(question):
newjbs = []
for fwid, paramStr, ftraj in output:
param = json.loads(paramStr)
del param['xtol']
param['jobkind'] = 'bulkmod'
param['strain'] = 0.03
param['relax'] = fwid
param['inittraj_pckl'] = misc.restoreMagmom(ftraj)
job = jobs.assignJob(param)
if job.new(): newjbs.append(job)
if ask("launch %d new jobs?" % len(newjbs)):
for j in newjbs:
j.check()
j.submit()
misc.launch()
def varies(constraint, param, rang):
readJobs.readJobs()
jbs = []
defaults = RELAXORLAT
cnst = AND([defaults, constraint])
output = dbase.queryCol('params_json', cnst)
if ask('Do you want to vary %s over range %s for %d jobs?' %
(param, str(rang), len(output))):
for params in map(json.loads, output):
for v in rang:
ps = copy.deepcopy(params)
assert not (jobs.assignJob(ps).new(
)), 'varying a job that isn\'t complete or doesn\'t exist'
ps[param] = v
job = jobs.assignJob(ps)
if job.new(): jbs.append(job)
if ask('Do you want to launch %d new jobs?' % len(jbs)):
for j in jbs:
j.check()
j.submit()
misc.launch()
def getBareSlab(constraint="1",
facet=[1, 1, 1],
xy=[1, 1],
layers=4,
constrained=2,
symmetric=0,
vacuum=10,
vacancies=[]):
cons = AND([COMPLETED, LATTICEOPT, constraint])
details.load('finaltraj_pckl', cons)
output = dbase.query(['fwid', 'params_json', 'finaltraj_pckl'], cons)
question = 'Are you sure you want to create bare slabs for %d structures?' % len(
output)
if ask(question):
newjbs = []
for fwid, paramStr, ftraj in output:
param = json.loads(paramStr)
surf, img = surfFuncs.bulk2surf(ftraj, facet, xy, layers,
constrained, symmetric, vacuum,
vacancies)
param['jobkind'] = 'relax'
param['kind'] = 'surface'
param['name'] += '_' + ','.join(map(str, facet)) + '_' + 'x'.join(
map(str, (xy + [layers])))
param['relax'] = 0
param['bulkparent'] = fwid
param['inittraj_pckl'] = pickle.dumps(surf)
param['sites_base64'] = img
param['facet_json'] = json.dumps(facet)
param['xy_json'] = json.dumps(xy)
param['layers'] = layers
param['constrained'] = constrained
param['symmetric'] = symmetric
param['vacuum'] = vacuum
param['vacancies_json'] = json.dumps(vacancies)
param['adsorbates_json'] = json.dumps({})
job = jobs.assignJob(param)
if job.new():
viz.view(surf)
question = 'Does this structure look right?\n' + abbreviateDict(
param)
if ask(question):
job.check()
job.submit()
misc.launch()
def molecule(molname=None):
readJobs.readJobs()
for name, m in gas.aseMolDict.items():
if molname is None or name == molname:
mol = pickle.dumps(m)
variableParams = {
'pw': 500,
'xc': 'RPBE',
'psp': 'gbrv15pbe',
'fmax': 0.05,
'dftcode': 'quantumespresso'
}
defaultParams = {
'jobkind': 'relax',
'inittraj_pckl': mol,
'comments': 'created by gendata.molecule()',
'trajcomments': '',
'name': name,
'relaxed': 0,
'kind': 'molecule',
'kptden':
1 #doesn't matter, will be ignored. Use 1 to be safe.
,
'dwrat': 10,
'econv': 5e-4,
'mixing': 0.1,
'nmix': 10,
'maxstep': 500,
'nbands': -12,
'sigma': 0.1
}
p = misc.mergeDicts([variableParams, defaultParams])
if molname is None or ask(
'Do you want to run a gas phase calculation with these params?\n%s'
% (abbreviateDict(p))):
j = jobs.assignJob(p)
if j.new():
j.check()
j.submit()
misc.launch()
def relaunch(cnst = '1',expiration_secs=80000,skip_load=False):
"""Relaunch timed out jobs and unconverged GPAW jobs"""
lpad.detect_lostruns(expiration_secs=expiration_secs, fizzle=True)
lpad.detect_unreserved(expiration_secs=3600*24*7, rerun=True)
if not skip_load: details.load('status fwpckl status trace',NOTCOMPLETED)
unconverged = AND([NOTCOMPLETED,KOHNSHAM,cnst])
timedout = AND([TIMEOUT,NOTKOHN,cnst])
launchflag = False
tOutput = db.query(['fwid','fwpckl'],timedout)
uOutput = db.query(['fwid','params_json'],unconverged)
tQuestion = "Do you want to relaunch %d timed out runs?"%len(tOutput)
uQuestion = "Do you want to relaunch %d unconverged jobs?"%len(uOutput)
if ask(tQuestion):
launchflag = True
for fid,fwpckl in tOutput:
if lpad.get_fw_dict_by_id(fid)['state']=='FIZZLED':
q = pickle.loads(fwpckl)['spec']['_queueadapter']
wallT = q['walltime']
q['walltime'] = doubleTime(wallT)
lpad.update_spec([fid],{'_queueadapter':q})
lpad.rerun_fw(fid)
else: print ("Wait up to 24 hours to relaunch fwid %d, or change default expiration time for detect_lostruns"%(fid))
if ask(uQuestion):
launchflag = True
for fw,paramstr in uOutput:
p = json.loads(paramstr)
p['sigma'] += 0.1
p['mixing'] = p['mixing']*0.5
job= jobs.assignJob(p)
if job.new():
job.check();job.submit()
delete(FWID(fw),check=False)
readJobs.readJobs()
if launchflag:
misc.launch()
duplicates()
def getXCcontribs(constraint="1"):
details.load(['finaltraj_pckl'], incomplete=False)
cons = AND([COMPLETED, GPAW, RELAXORLAT, constraint])
output = dbase.query(['fwid', 'params_json', 'finaltraj_pckl'], cons)
question = 'Are you sure you want to calculate XC contributions for %d structures?' % len(
output)
if ask(question):
newjbs = []
for fwid, paramStr, ftraj in output:
param = json.loads(paramStr)
param['jobkind'] = 'xc'
param['inittraj_pckl'] = misc.restoreMagmom(ftraj)
param['relax'] = fwid
job = jobs.assignJob(param)
if job.new(): newjbs.append(job)
if ask("launch %d new jobs?" % len(newjbs)):
for j in newjbs:
j.check()
j.submit()
misc.launch()
def fromJob(params): try: return f((jobs.assignJob(json.loads(params)))) except AttributeError: return None
def getStoichDirectly(launchdir,deleteFlag): fwid = getFWID(launchdir,deleteFlag) fwpckl = getFWpckl(fwid) params = json.loads(pickle.loads(fwpckl)['spec']['params_json']) job = jobs.assignJob(params) return job.numbers()
def getInitData(fid): params = lpad.get_fw_dict_by_id(fid)['spec']['params'] return jobs.assignJob(params).generalSummary()
def addInterstitial(constraint="1", load=True, emttol=0.2):
inter, num = 'H', 2
cons = AND([COMPLETED, LATTICEOPT, QE, constraint])
if load: details.load(['finaltraj_pckl'], cons)
else: readJobs.readJobs()
output = dbase.query(['fwid', 'params_json', 'finaltraj_pckl'], cons)
question = 'Are you sure you want to add interstitials to %d structures?' % len(
output)
if ask(question):
jbs = []
for fwid, paramStr, ftraj in output:
param = json.loads(paramStr)
spnpl = jobs.assignJob(param).spinpol()
param['structure'] = 'triclinic'
param['jobkind'] = 'vcrelax'
param['relaxed'] = fwid
if 'xtol' in param.keys(): del param['xtol']
trajs = [[(pickle.loads(ftraj), '')]]
for i in range(num):
lastround = trajs[-1]
trajs.append([])
for inputtraj, strname in lastround:
for newtraj, newname in interstitialFuncs.getInterstitials(
inputtraj, inter, spnpl):
trajs[-1].append((newtraj, strname + newname))
def modParams(par, trj, nam):
p = copy.deepcopy(par)
p['name'] += nam
p['inittraj_pckl'] = pickle.dumps(trj)
return p
onelevel = [item for sublist in trajs[1:] for item in sublist]
tentativejoblist = [
jobs.assignJob(modParams(param, t, n)) for t, n in onelevel
]
addJobs, efilt = [], 0
for j in tentativejoblist:
if any([abs(j.emt() - x.emt()) < emttol for x in addJobs]):
efilt += 1
else:
addJobs.append(j)
jbs.extend(addJobs)
newjbs = [j for j in jbs if j.new()]
for j in newjbs:
print j.symbols(), j.emt()
check = ask(
'Do you want to check %d/%d new jobs? (%d filtered by emt)' %
(len(newjbs), len(jbs) + efilt, efilt))
if not check and ask('Do you want to exit?'): return 0
for jb in newjbs:
question = 'Does this structure look right?\n' + abbreviateDict(
j.params)
if check: viz.view(newtraj)
if not check or ask(question):
jb.check()
jb.submit()
misc.launch()
def toDo():
params = db.queryCol('params_json',VIB,deleted=True)
for p in params:
j = jobs.assignJob(json.loads(p))
if j.new(): j.check();j.submit()
misc.launch()
