def __init__(self, hud, urls, linkedin_user='******'):
self.bh = hud
self.urls = urls
self.current_url = self.urls[0]
from os import environ as os_environ
from os import path as os_path
from sys import path as py_path
py_path.append(os_path.join(os_environ['GIT_REPOS'], 'emt/src'))
from emt import EMT
self.x = EMT()
self.x.pg.check_db_config()
self.x.web.initiate_web_session(linkedin_user)
self.pg = self.x.pg
self.T = self.pg.T
def main():
asedb = connect('/scratch/users/ksb/db/ase.db')
initialQuestion = (
'\n%d relaxed bulk structure(s) passed filters+constraints.' %
(nBulk) + '\nDo you want to create %d slabs?\n(y/n)--> ' % (ncombo))
if raw_input(initialQuestion).lower() in ['y', 'yes']:
for combo in domainProduct:
print combo
ind, fac, xy, l, c, sym, vac, vacancy = combo
facList = [int(z) for z in str(fac)]
bare = makeSlab(ind, facList, l, sym, xy, vac)
img = plot(bare)
aseAtoms = AseAtomsAdaptor.get_atoms(bare)
taggedAtoms = tag_atoms(aseAtoms)
taggedAtoms.set_constraint(
FixAtoms(indices=constrainAtoms(taggedAtoms, c, sym)))
magmoms = [
magmomInit if (magmomInit and e in magElems) else 0
for e in taggedAtoms.get_chemical_symbols()
]
taggedAtoms.set_initial_magnetic_moments(magmoms)
taggedAtoms.set_calculator(EMT())
taggedAtoms.wrap()
for i in vacancy:
del taggedAtoms[i]
prettyfacet = '-'.join([x for x in str(fac)])
prettyxy = '%sx%s' % (str(xy)[0], str(xy)[1])
name = '%s_%s_%s' % (asedb.get(ind).get('name'), prettyfacet,
prettyxy)
info = {
'name': name,
'relaxed': False,
'emt': taggedAtoms.get_potential_energy() /
len(taggedAtoms) # normalize to per-atom basis
,
'comments': 'Autogenerated by initializeBareSurf',
'kind': 'surface' # vs bulk/molecule
,
'structure': asedb.get(ind).get('structure'),
'parent': ind #ase object surface was generated from
,
'sites': img,
'facet': fac,
'xy': xy,
'layers': l,
'constrained': c,
'symmetric': sym,
'vacuum': vac,
'vacancies': str(vacancy)
}
parentJob = db2object(query1('jobtableid', 'aseid', ind, 'result'))
if USER_APPROVAL: view(taggedAtoms)
question = (
'Does this structure look right?\nfacet= %s\nlayers = %d\nfixed = %d\n'
% (prettyfacet, l, c) +
'vacuum = %d\nxy = %s\n %s\n\n(y/n) --> ' %
(vac, prettyxy, parentJob.summary()))
if not USER_APPROVAL or raw_input(question).lower() in [
'y', 'yes'
]:
n = sum([
1 for x in asedb.select(parent=ind,
facet=fac,
xy=xy,
layers=l,
constrained=c,
symmetric=sym,
vacuum=vac,
vacancies=str(vacancy))
])
if n > 1:
raise ValueError, 'Two things already in database have same parameters???'
elif n == 1:
print "matching structure already in database!"
else:
asedb.write(taggedAtoms, key_value_pairs=info)
def main():
asedb = connect('/scratch/users/ksb/db/ase.db')
initialQuestion = ('\n%d relaxed surface structure(s) passed constraints.'%(len(surfaceDomain))
+'\nDo you want to create %d slabs?\n(y/n)--> '%(ncombo))
if raw_input(initialQuestion).lower() in ['y','yes']:
for combo in domainProduct:
ind,ads = combo
parent = asedb.get(ind).get('parent')
sites = asedb.get(ind).get('sites')
structure = asedb.get(ind).get('structure')
grandparent = asedb.get(ind).get('parent')
facet = asedb.get(ind).get('facet')
xy = asedb.get(ind).get('xy')
layers = asedb.get(ind).get('layers')
constrained = asedb.get(ind).get('constrained')
symmetric = asedb.get(ind).get('symmetric')
vacuum = asedb.get(ind).get('vacuum')
vacancies = literal_eval(asedb.get(ind).get('vacancies'))
facList = [int(z) for z in str(facet)]
bare = makeSlab(grandparent,facList,layers,symmetric,xy,vacuum)
adsSurf = adsorbedSurface(bare,ads)
aseAtoms = AseAtomsAdaptor.get_atoms(adsSurf)
taggedAtoms = tag_atoms(aseAtoms)
taggedAtoms.set_constraint(FixAtoms(indices=constrainAtoms(taggedAtoms,constrained,symmetric)))
magmoms = [magmomInit if (magmomInit and e in magElems) else 0 for e in taggedAtoms.get_chemical_symbols()]
taggedAtoms.set_initial_magnetic_moments(magmoms)
taggedAtoms.set_calculator(EMT())
taggedAtoms.wrap()
for i in vacancies: del taggedAtoms[i] # hopefu
prettyfacet = '-'.join([x for x in str(facet)])
prettyxy = '%sx%s'%(str(xy)[0],str(xy)[1])
prettyAds = printAds(ads)
name = '%s_%s_%s'%(asedb.get(parent).get('name'),prettyfacet,prettyxy)
info = {'name': name
,'relaxed': False
,'emt': taggedAtoms.get_potential_energy()/len(taggedAtoms) # normalize to per-atom basis
,'comments': 'Autogenerated by initializeAdsSurf'
,'kind': 'surface' # vs bulk/molecule
,'structure': structure
,'parent': parent #ase object surface was generated from
,'sites': sites
,'facet': facet
,'xy': xy
,'layers': layers
,'constrained': constrained
,'symmetric': symmetric
,'vacuum': vacuum
,'vacancies': vacancies
,'adsorbates': prettyAds}
if USER_APPROVAL: view(taggedAtoms)
question = ('Does this structure look right?\nfacet= %s\nlayers = %d\nfixed = %d\n'%(prettyfacet,layers,constrained)
+'vacuum = %d\nxy = %s\nads = %s\n\n(y/n) --> '%(vacuum,prettyxy,prettyAds))
if not USER_APPROVAL or raw_input(question).lower() in ['y','yes']:
n = sum([1 for x in asedb.select(parent=ind,facet=fac,xy=xy,layers=l
,constrained=constrained,symmetric=symmetric,vacuum=vacuum,vacancies=str(vacancies),adsorbates= prettyAds)])
if n > 1: raise ValueError, 'Two things already in database have same parameters???'
elif n == 1: print "matching structure already in database!"
else:
asedb.write(taggedAtoms,key_value_pairs=info)
def main():
for x in fccs + bccs + hcps + diamonds + rocksalts + zincblendes + cscls:
f = x in fccs
b = x in bccs
h = x in hcps
d = x in diamonds
r = x in rocksalts
z = x in zincblendes
c = x in cscls
try:
if f: a = FaceCenteredCubic(x[0]).get_cell()[0][0] / 2
elif b: a = BodyCenteredCubic(x[0]).get_cell()[0][0] / 2
elif d: a = Diamond(x[0]).get_cell()[0][0] / 2
elif h:
cell = HexagonalClosedPacked(x[0]).get_cell()
a, c = cell[0][0], cell[2][2]
elif r | z | c:
a = dataLookup(x[0])
else:
raise NotImplementedError
except ValueError:
a = dataLookup(x[0]) / 2
#a = sum([radDict[e] for e in elems])/len(elems)
print "Had to guess lattice constant of " + x[0]
if f:
name, struc, pos, cell, n = '-fcc', 'fcc', [[0, 0, 0]], [[0, a, a],
[a, 0, a],
[a, a,
0]], 1
elif b:
name, struc, pos, cell, n = '-bcc', 'bcc', [[0, 0,
0]], [[a, a, -a],
[-a, a, a],
[a, -a, a]], 1
elif h:
name, struc, pos, cell, n = '-hcp', 'hexagonal', [[
0, 0, 0
], [2. / 3, 1. / 3, 1. / 2]], [a, a, c, 90, 90, 120], 2
elif d:
name, struc, pos, cell, n = '-diamond', 'diamond', [[
0, 0, 0
], [0.25, 0.25, 0.25]], [[0, a, a], [a, 0, a], [a, a, 0]], 2
elif z:
name, struc, pos, cell, n = '-zincblende', 'zincblende', [[
0, 0, 0
], [0.25, 0.25, 0.25]], [[0, a, a], [a, 0, a], [a, a, 0]], 1
elif r:
name, struc, pos, cell, n = '-rocksalt', 'rocksalt', [[
0, 0, 0
], [0.5, 0.5, 0.5]], [[0, a, a], [a, 0, a], [a, a, 0]], 1
elif c:
name, struc, pos, cell, n = '-cscl', 'cubic', [[0, 0, 0],
[0.5, 0.5, 0.5]], [
a, a, a, 90, 90,
90
], 1
mag = magLookup(x[0])
elems = parseChemicalFormula(x[0]).keys() * n
magmoms = [magmomInit if e in magElems else 0 for e in elems]
atoms = Atoms(elems,
scaled_positions=pos,
cell=cell,
pbc=[1, 1, 1],
magmoms=magmoms,
calculator=EMT())
info = {
'name': x[0] + name,
'relaxed': False,
'emt': atoms.get_potential_energy() /
len(elems) #normalized to per-atom basis
,
'comments': 'Autogenerated by createTrajs',
'kind': 'bulk' # vs surface/molecules
,
'structure': struc
}
db.write(atoms, key_value_pairs=info)
def __init__(self,
id,
pth,
name=None,
stoich=None,
bravais=None,
inita=None,
initb=None,
initc=None,
initalpha=None,
initbeta=None,
initgamma=None,
initpos=None,
mag=None,
emt=None,
comments=None):
if id is None:
# Creating object for first time
traj = io.read(pth)
traj.set_calculator(EMT())
cell = traj.get_cell()
atomList = traj.get_chemical_symbols()
self.atomList = atomList
self.initPos = traj.get_scaled_positions()
self.pth = pth
self.name = (pth.split('.traj')[0]).split('traj/')[1]
self.traj = traj
try:
self.bravais = traj.info['bravais']
except KeyError:
self.bravais = 'triclinic' # default is most general (and expensive) case
try:
self.mag = traj.info['mag']
except KeyError:
self.mag = False # Default nonmag
try:
self.comments = traj.info['comments']
except KeyError:
self.comments = None
self.initEMT = traj.get_potential_energy()
a, b, c, alpha, beta, gamma = cell2param(cell)
self.inita = a
self.initb = b
self.initc = c
self.initalpha = alpha
self.initbeta = beta
self.initgamma = gamma
else:
self.id = id
self.pth = pth
self.name = name
self.stoich = stoich
self.bravais = bravais
self.inita = inita
self.initb = initb
self.initc = initc
self.initalpha = initalpha
self.initbeta = initbeta
self.initgamma = initgamma
self.initpos = initpos
self.mag = mag
self.emt = emt
self.comments = comments
traj = io.read(pth)
atomList = traj.get_chemical_symbols()
self.atomList = atomList
def main():
asedb = connect('/scratch/users/ksb/db/ase.db')
initialQuestion = (
'\n%d relaxed bulk structure(s) passed filters+constraints.' %
(nBulk) + '\nDo you want to create %d slabs?\n(y/n)--> ' % (ncombo))
if raw_input(initialQuestion).lower() in ['y', 'yes']:
for combo in domainProduct:
ind, fac, xy, l, c, sym, vac, vacancy = combo
a = asedb.get_atoms(id=ind)
pmg_a = AseAtomsAdaptor.get_structure(a)
unit = SpacegroupAnalyzer(
pmg_a, symprec=0.1,
angle_tolerance=5).get_conventional_standard_structure()
gen = SlabGenerator(unit,
fac,
findHeight(unit, fac, l, sym),
vac,
center_slab=sym,
primitive=True,
lll_reduce=True)
slabs = gen.get_slabs()
if len(slabs) > 1: print "Warning, multiple slabs generated..."
slab = slabs[0]
slab.make_supercell(list(xy) + [1])
bare = reorient_z(slab)
img = plot(bare)
aseAtoms = AseAtomsAdaptor.get_atoms(bare)
taggedAtoms = tag_atoms(aseAtoms)
taggedAtoms.set_constraint(
FixAtoms(indices=constrainAtoms(taggedAtoms, c, sym)))
magmoms = [
magmomInit if (magmomInit and e in magElems) else 0
for e in taggedAtoms.get_chemical_symbols()
]
taggedAtoms.set_initial_magnetic_moments(magmoms)
taggedAtoms.set_calculator(EMT())
taggedAtoms.wrap()
for i in vacancy:
del taggedAtoms[i]
info = {
'name':
'%s_%s_%s' % (asedb.get(ind).get('name'), '-'.join(
[str(x) for x in fac]), 'x'.join([str(x) for x in xy])),
'kind':
'surface',
'structure':
asedb.get(ind).get('structure'),
'sites':
img,
'bare':
True,
'parent':
ind #ase object surface was generated from
,
'facet':
str(fac),
'xy':
str(xy),
'layers':
l,
'constrained':
c,
'symmetric':
sym,
'vacuum':
vac,
'vacancies':
str(vacancy),
'surfcomments':
'Autogenerated by initializeBareSurf',
'emt':
taggedAtoms.get_potential_energy(),
'relaxed':
False
}
if USER_APPROVAL:
view(taggedAtoms)
question = (
'Does this structure look right?\nfacet= %s\nlayers = %d\nfixed = %d\n'
% ('-'.join([str(x) for x in fac]), l, c) +
'vacuum = %d\nxy = %s\n(y/n) --> ' %
(vac, 'x'.join([str(x) for x in xy])))
if raw_input(question).lower() in ['y', 'yes']:
asedb.write(taggedAtoms, key_value_pairs=info)
else:
asedb.write(taggedAtoms, key_value_pairs=info)
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)
eDict={}
for i in range(9): eDict[i]=[]
for i,c in enumerate(list(configs)):
print i
a = Atoms(c,positions=positions,cell=cell,pbc=1,calculator=EMT())
e = a.get_potential_energy()
nPd = c.count('Pd')
eDict[nPd].append(e)
"""
positions = np.array([[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
cell = np.array([[0, 2, 2], [2, 0, 2], [2, 2, 0]])
elements = ['Pd', 'Au']
configs = itertools.product(elements, repeat=4)
eDict = {}
for i in range(5):
eDict[i] = []
for i, c in enumerate(list(configs)):
print i
a = Atoms(c, positions=positions, cell=cell, pbc=1, calculator=EMT())
e = a.get_potential_energy()
nPd = c.count('Pd')
eDict[nPd].append(e)
print eDict
# plt.hist(eDict[3],nbins=256)