def saveResults(jobID, cell, pos, magmom, e0, b, bFit, xc, t, nIter):
result = BulkResult(
jobID, cell, pos, magmom, e0, b, bFit, xc, t, nIter
) #lattice constants determined downstream, depending on structure'
if rank() == 0:
insertObject(result)
with open("result.json", "w") as f:
print >> f, result.toJSON()
updateStatus(jobID, 'running', 'completed')
def run_task(self,fw_spec):
jobID = fw_spec['jobID']
job = db2SurfaceJob(jobID)
resultNames = ['pos','magmom','e0','f0','xcContribs','avgtime','niter']
results = [fw_spec[x][0] for x in resultNames]
resultDict = {n:fw_spec[n] for n in resultNames}
result = SurfaceResult(*([jobID]+results))
result.addToASEdb(job)
insertObject(result) # add result to surface result table
updateDB('surfacejob','status','id',jobID,'complete')
return FWAction(stored_data= resultDict)
def increaseConvergence():
kohnsham = [x[0] for x in plotQuery(['jobid'], [KOHNSHAM])]
new = 0
for k in kohnsham:
jobj = db2object(k)
jobj.convid += 1
jobj.status = 'initialized'
jobj.error, jobj.comments = None, None
id, status = insertObject(jobj)
if status == 'inserted': new += 1
print 'added %d new jobs' % new
def main():
try:
deleteTable('tentative') #WHAT IS GOING ON HERE?
except:
pass
try:
createTentativeBulkTable()
except:
pass
domains = [
filteredTrajDomain, filteredXCDomain, filteredPSPDomain,
filteredPWDomain, filteredKPTDomain, filteredPreCalcXCDomain,
filteredDFTDomain
]
combos = product(*domains)
ncombo = reduce(mul, [len(x) for x in domains])
for i, c in enumerate(combos):
print '%f%' % (i / float(ncombo) * 100)
tentativeInput = c[:5] + tuple(defaults) + c[5:]
tentativeBulkjob = BulkJob(*tentativeInput)
if tentativeBulkjob.xc == 'mBEEF': #defaults slightly different for mBEEF
tentativeBulkjob.sigma += 0.1
tentativeBulkjob.sigma -= 0.05
ID, status = insertObject(tentativeBulkjob, tentative=True)
print "%d tentative jobs" % countDB('tentative')
valid = [
db2BulkJob(x[0], tentative=True)
for x in plotQuery('tentative', ['tentative.id'], constraints)
]
new = 0
for z in range(len(valid)):
ID, status = insertObject(valid[z])
if status == 'inserted': new += 1
print "%d valid jobs, %d are new" % (len(valid), new)
deleteTable('tentative')
def main():
dropTable('tentativejob')
dropTable('tentativedetails')
sqlexecute(jobTable('tentativejob'))
sqlexecute('INSERT INTO tentativejob SELECT * FROM job')
sqlexecute(tentativedetailstable)
for i,sID in enumerate(surfs):
p = asedb.get(sID).get('parent')
cols = ['xc','pw','kptden','psp','convid','precalc','dftcode']
allInfo = queryManyFromOne(cols,'aseid',p)
xc,pw,kptden,psp,convid,precalc,dftcode = allInfo
tentativeInput = [None,'surfrelax',sID,None,None,xc,pw,kptden,psp,None,None,convid,precalc,dftcode,None,None,'initialized']
tentativeSurfjob = Job(*tentativeInput)
insertObject(tentativeSurfjob,tentative=True)
applyDetails(tentative=True) #populate details table so that plotQuery works
valid = [db2object(x[0],'tentativejob','job') for x in plotQuery(['jobid'],constraints,tentativetable)]
new = 0
print "%d valid jobs, %d are new"%(len(valid),new)
question = "Do you want to insert %d new surface jobs?"%new
if raw_input(question) in ['y','yes']:
for z in range(len(valid)):
ID,status = insertObject(valid[z])
if status == 'inserted': new +=1
print "%d jobs are new"%new
applyDetails()
dropTable('tentativejob')
dropTable('tentativedetails')
def main():
try: dropTable('tentativejob') # uncomment if script fails in the middle
except: pass
sqlexecute(jobTable('tentativejob'))
copyTable('job','tentativejob')
combos = product(*domains)
nTot = reduce(mul,[len(x) for x in [trajDomain,xcDomain,pspDomain,pwDomain,kptDomain,preXcDomain,dftDomain]])
ncombo = reduce(mul,[len(x) for x in domains])
for i,c in enumerate(combos):
print '%f %%'%(i/float(ncombo)*100)
# jobid jobkind aseid vib neb xc pw kpt psp xtol strain convergence ID precalc dft comm err stat
tentativeInput = [None,'bulkrelax',c[0],None,None,c[1],c[2],c[3],c[4],0.005,0.03, 2 if c[1]=='mBEEF' else 1,c[5],c[6],None,None,'initialized']
tentativejob = Job(*tentativeInput)
insertObject(tentativejob,tentative=True)
nJobsInit,nJobsTent = countDB('job'),countDB('tentativejob')
print "%d tentative jobs after filtering %d jobs"%(ncombo,nTot)
applyDetails(tentative=True) #populate details table so that plotQuery works
valid = [db2object(x[0],'tentativejob') for x in plotQuery(['jobid'],CONSTRAINTS,tentativetable)]
new = 0
question = "Do you want to insert %d valid bulk jobs?\n(y/n)--> "%len(valid)
if raw_input(question) in ['y','yes']:
for z in range(len(valid)):
ID,status = insertObject(valid[z])
if status == 'inserted': new +=1
print "%d jobs are new"%new
applyDetails()
dropTable('tentativejob')
def main():
deleteTable('tentativesurf')
for i, sID in enumerate(surfs):
p = asedb.get(sID).get('parent')
table = ' bulkjob INNER JOIN bulkresult ON bulkresult.jobid=bulkjob.id '
cols = [
'xc', 'psp', 'pw', 'kptden', 'kpt', 'econv', 'mixing', 'nmix',
'maxstep', 'nbands', 'sigma', 'fmax', 'precalcxc', 'dftcode'
]
allInfo = queryManyFromOne(table, cols, 'aseid', p)
xc, psp, pw, kptden, kpt, econv, mixing, nmix, maxstep, nbands, sigma, fmax, precalcxc, dftcode = allInfo
tentativeInput = [
sID, xc, psp, pw, 10, kptden, None, econv, mixing, nmix, maxstep,
nbands, sigma, fmax, precalcxc, dftcode
]
tentativeSurfjob = SurfaceJob(*tentativeInput)
ID, status = insertObject(tentativeSurfjob, tentative=True)
valid = [
db2SurfaceJob(x[0], tentative=True)
for x in plotQuery('tentativesurf', ['tentativesurf.id'], constraints)
] # SurfaceJob objects that satisfy constraints
tot, new = len(valid), 0
question = '%d job(s) meet these criteria. Do you want to add them to surfacejobs in data.db?\n(y/n)--->' % tot
if raw_input(question).lower() in ['y', 'yes']:
for z in range(len(valid)):
ID, status = insertObject(valid[z])
if status == 'inserted': new += 1
deleteTable('tentativesurf')
print '%d jobs considered, %d are new' % (tot, new)
import os
import sqlite3 as sqlite
from db import insertObject
from itertools import product
commands = []
sherlockDB = '/scratch/users/ksb/db/data.db'
###########################
# Add PSP Paths to Database
###########################
# Define domain of psp's to consider
for p in pspDomain: insertObject(p)
################################
# Add XC Functionals to Database
################################
# Define domain of XC's to consider
PBE = XC('PBE', [[]])
BEEF = XC('BEEF', [[]])
mBEEF = XC('mBEEF',[[]])
xcDomain = [PBE,BEEF,mBEEF]
for x in xcDomain: insertObject(x)
################################
# Add Calculators to Database
def run_task(self,fw_spec):
jobID = fw_spec['jobID']
job = db2object(jobID)
if 'relax' in job.jobkind:
pos = fw_spec['pos'][0]
cell = fw_spec['cell'][0] if job.jobkind == 'bulkrelax' else job.cellinit()
magmom = fw_spec['magmom'][0]
db = connect('/scratch/users/ksb/db/ase.db')
info = {'name': job.name()
,'emt': 0 # EMT for relaxed structures useless, only relevant for deciding when to relax something
,'relaxed': True # Could always doing this be a problem?
,'comments': 'Generated from #%d'%(job.aseidinitial)
,'parent': job.aseidinitial
,'jobid': job.jobid # Int
###Unchanged Things###
,'kind': job.kind()} # String
if job.structure() is not None: info['structure'] = job.structure()
if job.vacancies() is not None: info['vacancies'] = job.vacancies()
if job.sites() is not None: info['sites'] = job.sites()
if job.facet() is not None: info['facet'] = job.facet()
if job.xy() is not None: info['xy'] = job.xy()
if job.layers() is not None: info['layers'] = job.layers()
if job.constrained() is not None: info['constrained'] = job.constrained()
if job.symmetric() is not None: info['symmetric'] = job.symmetric()
if job.vacuum() is not None: info['vacuum'] = job.vacuum()
if job.adsorbates() is not None: info['adsorbates'] = job.adsorbates()
optAtoms = Atoms(symbols = job.symbols()
,scaled_positions = pos
,cell = cell
,magmoms = magmom
,constraint = job.constraints()
,tags = job.tags())
aseid = db.write(optAtoms,key_value_pairs=info)
else:
aseid = None
launchdir = fw_spec['_launch_dir']
energy = fw_spec['e0'][0] if 'relax' in job.jobkind else None
forces = fw_spec['f0'][0] if 'relax' in job.jobkind else None
bulkmodulus = fw_spec['b0'][0] if job.jobkind == 'bulkrelax' else None
bfit = fw_spec['quadR2'][0] if job.jobkind == 'bulkrelax' else None
xccoeffs = fw_spec['xcContribs'][0] if 'relax' in job.jobkind else None
viblist = fw_spec['vibs'][0] if job.jobkind == 'vib' else None
dos = fw_spec['dos'][0] if job.jobkind == 'dos' else None
barrier = fw_spec['barrier'][0] if job.jobkind == 'neb' else None
time = fw_spec['avgtime'][0]
niter = fw_spec['niter'][0] if 'relax' in job.jobkind else None
result = Result(jobID,launchdir,aseid=aseid,energy=energy,forces=forces
,bulkmodulus=bulkmodulus,bfit=bfit,xccoeffs=xccoeffs,viblist=viblist
,dos=dos,barrier=barrier,time=time,niter=niter)
resultDict = {'_launch_dir':launchdir,'aseid':aseid,'energy':energy
,'forces':str(forces),'bulkmodulus':bulkmodulus
,'bfit':bfit,'xccoeffs':xccoeffs,'time':time
,'niter':niter,'viblist':viblist,'barrier':barrier}
insertObject(result) # add result to bulkresult table
updateDB('status','jobid',jobID,'complete')
return FWAction(stored_data= resultDict)
def main():
for conv in convs:
insertObject(conv)
def main():
jIDs = [x[0] for x in plotQuery(['jobid'], CONSTRAINTS)]
question = "Going to add an %s interstitial to %d bulk objects.\n(y/n)--> " % (
inter, len(jIDs))
if raw_input(question).lower() in ['y', 'yes']:
for j in jIDs:
aseinitID = query1('aseid', 'jobid', j)
aseinit = asedb.get_atoms(id=aseinitID)
# Access information about previous Job / Atoms object
jobinit = db2object(j)
xc, pw, kptden = jobinit.xc, jobinit.pw, jobinit.kptden
psp, xtol, strain = jobinit.psp, jobinit.xtol, jobinit.strain
precalc, dftcode = jobinit.precalc, jobinit.dftcode
nameinit = jobinit.name()
structure = jobinit.structure()
vacancies = jobinit.vacancies()
# Create conventional PyMatGen Object
pmg_init = AseAtomsAdaptor.get_structure(aseinit)
pmg_init2 = SpacegroupAnalyzer(
pmg_init).get_conventional_standard_structure()
interstitial = Interstitial(
pmg_init2, None, covalent_radii) #accuracy=high breaks...
os.system('cls' if os.name == 'nt' else 'clear')
for i, site in enumerate(interstitial.enumerate_defectsites()):
coordination = int(
round(interstitial.get_defectsite_coordination_number(i)))
mult = 0 # interstitial.get_defectsite_multiplicity(i) -- broken ???
insert = InsertSitesTransformation([inter], [site.coords],
coords_are_cartesian=True)
pmg_new = insert.apply_transformation(pmg_init2.copy())
ase_new = AseAtomsAdaptor.get_atoms(pmg_new)
ase_new.set_calculator(EMT())
emt = ase_new.get_potential_energy()
if coordination == 4: siteName = 'T'
elif coordination == 6: siteName = 'O'
else: siteName = '%d-fold' % coordination
question = ('site: %s\ncoordination: %s\nmultiplicity: %s' %
(site.coords, coordination, mult) +
'\ninitial ase id: %d \nxc: %s \npw: %d ' %
(aseinitID, xc, pw) +
'\nkptden: %f \npsp: %s\nxtol: %f\nstrain: %f' %
(kptden, psp, xtol, strain) +
'\nprecalc: %s \ndftcode: %s' %
(precalc, dftcode) +
'\n\nDoes this structure look good?\n(y/n)--> ')
view(ase_new)
if raw_input(question).lower() in ['y', 'yes']:
if checkForDuplicates(ase_new, structure, emt):
newquestion = 'What structure does this have?\n(leave blank for general triclinic case)\n--> '
structure = raw_input(newquestion)
if structure is '': structure = 'triclinic'
info = {
'name': nameinit + '_%s-%s' % (inter, siteName),
'emt':
emt # EMT for relaxed structures useless, only relevant for deciding when to relax something
,
'relaxed':
False # Could always doing this be a problem?
,
'comments': 'Generated from initializeHydride.py',
'parent': aseinitID,
'kind': 'bulk',
'structure': structure,
'interstitial': siteName
}
if vacancies is not None: info['vacancies'] = vacancies
newaseid = asedb.write(ase_new, key_value_pairs=info)
newjob = Job(None, 'bulkrelax', newaseid, None, None,
xc, pw, kptden, psp, xtol, strain,
2 if xc == 'mBEEF' else 1, precalc,
dftcode, None, None, 'initialized')
insertObject(newjob)
0, 0, 0, 0, 0, 0, 12, 13, 11, 15, 16, 15, 16, 11, 12, 13, 14, 8, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 8, 8
])
sgs15 = PSP(
'sgs_15', '/scratch/users/ksb/gpaw/gpaw_sg15/norm_conserving_setups', [
1, 0, 3, 4, 3, 4, 5, 6, 7, 0, 9, 10, 3, 4, 5, 6, 7, 0, 9, 10, 11, 12,
13, 14, 15, 16, 17, 18, 19, 20, 19, 12, 5, 6, 7, 0, 9, 10, 11, 12, 13,
14, 15, 16, 15, 16, 19, 12, 13, 14, 15, 6, 7, 0, 9, 10, 11, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 12, 13, 11, 15, 16, 15, 16, 11, 12, 13,
14, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 8
])
pspDomain = [gbrv15pbe, sgs15]
for p in pspDomain:
insertObject(p)
################################
# Add XC Functionals to Database
################################
# Define domain of XC's to consider
PBE = XC('PBE', [[]])
BEEF = XC('BEEF', [[]])
mBEEF = XC('mBEEF', [[]])
xcDomain = [PBE, BEEF, mBEEF]
for x in xcDomain:
insertObject(x)
################################