def output(self, extraConstraint='1'):
dom = db.queryCol('fwid',
pp.AND([extraConstraint, self.detail1constraint]))
pairs = db.query(['id0', 'id1'], self.detail2constraint, 'pairs')
if self.detail1constraint == '1' and extraConstraint == '1':
return pairs
return [(x, y) for (x, y) in pairs if (x in dom) and (y in dom)]
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 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 setWalltimeUnder40():
""" If too much time was requested accidentally (such that job is stuck in READY), use this to modify the job"""
details.load(['walltime'])
output = db.query(['fwid','queueadapter'],QOVER40)
print "Resetting walltime for %d jobs"%len(output)
for fw,fwpckl in output:
q=pickle.loads(fwpckl)['spec']['_queueadapter']
q['walltime'] = '39:59' + ':00' if q['walltime'].count(':')>1 else ''
lpad.update_spec([fw],{'_queueadapter':q})
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 makeTriples(self, idgroups, labelName):
args = [db.query(self.cols, FWIDS(x))
for x in idgroups] #[[(ARG1,ARG2,...)]]
labels = [db.queryCol(labelName, FWIDS(x))
for x in idgroups] #[[STRING]]
xy = [self.func(*zip(*arg)) for arg in args] #[[(FLOAT,FLOAT))
xy_l = [(zip(xy, l)) for xy, l in zip(xy, labels)]
filtered = [[(xyl[0][0], xyl[0][1], xyl[1]) for xyl in xyls
if not (xyl[0][0] is None or xyl[0][1] is None)]
for xyls in xy_l]
sortd = [sorted(x) for x in filtered if len(x) > 0]
return [zip(*x) for x in sortd]
def delete(constraint,check=True,comment=None):
output = db.query(['fwid','launchdir'],constraint)
question = 'Are you sure you want to delete %d jobs? (selected by constraint: %s)'%(len(output),constraint)
if (not check) or ask(question):
for fwid,launchdir in output:
db.updateDB('deleted','fwid',fwid,1,'job')
db.updateDB('status','fwid',fwid,'deleted','job')
if comment is not None: db.updateDB('comments','fwid',fwid,comment,'job')
if 'scratch' in launchdir:
with open(launchdir+'/deleted','w') as f: f.write('')
else:
subprocess.Popen(['ssh','*****@*****.**', 'touch %s/deleted'%launchdir], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
lpad.archive_wf(fwid)
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 duplicates(cnst='1',deleteFlag=False):
output = db.query(['fwid','strjob'],cnst)
rptDict={}
for fwid,strjob in output:
for f,s in output:
if strjob == s and f!=fwid:
if fwid not in list(itertools.chain.from_iterable(rptDict.values())):
if fwid in rptDict.keys(): rptDict[fwid].append(f)
else: rptDict[fwid] = [f]
print 'FWIDs with equal strjob entries: \n',abbreviateDict(rptDict)
if deleteFlag:
delfws = list(itertools.chain.from_iterable(rptDict.values()))
if ask('Are you sure you want to delete %d duplicates?'%len(delfws)):
for f in delfws: delete(FWID(f),False)
def barResults(ax, summaryFunc, labelFunc, eq, const='1'):
#Plots summaries of data as a bar graph
ids = [list(x) for x in eq.classes(extraConstraint=const)]
xs = [db.query1(labelFunc, 'fwid', i[0], 'job') for i in ids] # [String]
raw_ys = [db.query(summaryFunc.details, FWIDS(i))
for i in ids] # [[a,b,c,...]]
col_ys = zip(summaryFunc.details * len(raw_ys), raw_ys)
ys = [
summaryFunc.kind(summaryFunc.details, args) for cols, args in col_ys
] # [Float]
y_pos = np.arange(len(ids)) # bar locations
ax.bar(y_pos, ys, align='center', alpha=0.5)
ax.set_ylabel(summaryFunc.name)
ax.set_xticks(y_pos)
ax.set_xticklabels(xs)
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 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 fix():
output = db.query(['fwid','fwpckl'],AND([LATTICEOPT,GPAW]))
for fw,fwpckl in output:
q=pickle.loads(fwpckl)['spec']['_queueadapter']
q['pre_rocket'] = q['pre_rocket'].replace(';;',';')
lpad.update_spec([fw],{'_queueadapter':q})