def calc_BEalloy(natoms, layer, **args):
'''
Return BE of alloy slab and ads
'''
filename = './data/{}-{}-{}-{}-{}.csv'.format(args['fac'], args['host'],
args['cov'], args['ads'],
args['site'])
nf = open(filename, 'w')
nf.write('molid,deltaz,inert,active,delBE_dft,delBE_alc\n')
refBE = calc_BEref(**args)
geom = dft.ref()
slabdir = 'slab/{1}/{0}-slab-{1}'.format(args['host'], args['cov'])
adsdir = '{0}_BE/{1}/{2}/{3}-slab-{2}-{0}-{1}'.format(
args['ads'], args['site'], args['cov'], args['host'])
slab_esp = geom.ret_esp(slabdir, cov=int(args['cov'][-1]))
ads_esp = geom.ret_esp(adsdir, ads=args['ads'], cov=int(args['cov'][-1]))
delta_esp = []
for i in range(len(ads_esp)):
delta_esp.append(float(ads_esp[i]) - float(slab_esp[i]))
mol_energy = e_mol_dict[args['ads']]
if args['root'] == None:
nullstr = 'is null'
queryargs = [
args['host'], args['fac'], args['cov'], args['alloytype'],
args['ads'], args['site']
]
else:
nullstr = '= ?'
queryargs = [
args['host'], args['fac'], args['cov'], args['root'],
args['alloytype'], args['ads'], args['site']
]
ads_data = fetchDB(queryargs, nullstr, jobtype='alloy', calctype='ads')
for alloyentry in ads_data:
alloyid = alloyentry[5]
ads_energy = alloyentry[-3]
con = lite.connect(sql_file)
cur = con.cursor()
query = [alloyid, args['cov'], args['fac']]
try:
cur.execute(
'SELECT * from alloydata WHERE '
'alloy = ? and ads is NULL and cov=? and '
'facet = ? ', (query))
rows = cur.fetchall()
except lite.Error, e:
print "Error %s:" % e.args[0]
sys.exit(1)
print alloyid #, len(rows), rows
if len(rows) == 1:
slab_energy = rows[0][-3]
spBE = slab_energy + mol_energy - ads_energy
inert_sol = alloyid.split('-')[0].split('_')[-1]
deltaz = ele_dict[inert_sol] - ele_dict[args['host']]
isite = [int(i) for i in alloyentry[7].split('.')]
asite = [int(i) for i in alloyentry[8].split('.')]
aesp = util.esp_layer(delta_esp, natoms, layer)
iesp = util.esp_layer(delta_esp, natoms, 1)
#print alloyid, asite, isite, delta_esp, aesp, iesp
alcder = calc_alcder(isite, asite, iesp, aesp, deltaz)
istr = ':'.join([str(s) for s in isite])
astr = ':'.join([str(s) for s in asite])
nf.write('{},{},{},{},{},{}\n'.format(alloyid, abs(deltaz), istr,
astr, spBE - refBE, alcder))
else:
print 'Non unique alloy found'
host = 'Pt'
cov = [2, 2]
lat_const = lat_dict[host]
facet = 111
root = None
ads_dict = {'CH3': 'ontop'}
# Slab setup
slab_args = {
'host': host,
'cov': cov,
'lat': lat_const,
'fac': facet,
'ads': None,
'site': None,
'root': root
}
slabdir = 'slab/{1}x{2}/{0}-slab-{1}x{2}'.format(host, cov[0], cov[1])
geom = dft.ref()
en = geom.read_energy(slabdir)
archiver.add_refdata(energy=en, **slab_args)
# Ads setup
for ads, site in ads_dict.iteritems():
adsdir = '{2}_BE/{3}/{0}x{1}/{4}-slab-{0}x{0}-{2}-{3}'.format(
cov[0], cov[1], ads, site, host)
ads_args = dict(slab_args)
ads_args.update({'ads': ads, 'site': site})
en = geom.read_energy(adsdir)
archiver.add_refdata(energy=en, **ads_args)
def calc_Eballoy(natoms, layer, **args):
'''
Return Eb (activation energy) of alloy
'''
filename = './data/CH4_CH3_ts.csv'
nf = open(filename, 'w')
nf.write('molid,deltaz,inert,active,delEb_dft,delEb_alc\n')
rctdir = '00/'
tsdir = '05/'
# Calculating ref Eb
s = Popen("grep 'F=' {0}/OSZICAR | tail -n 1".format(rctdir),
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=STDOUT,
close_fds=True)
rctenergy = float(s.communicate()[0].split()[4])
s = Popen("grep 'F=' {0}/OSZICAR | tail -n 1".format(tsdir),
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=STDOUT,
close_fds=True)
tsenergy = float(s.communicate()[0].split()[4])
ref_Eb = tsenergy - rctenergy
geom = dft.ref()
rct_esp = geom.ret_esp(rctdir, ads=args['ads'], cov=int(args['cov'][-1]))
ts_esp = geom.ret_esp(tsdir, ads=args['ads'], cov=int(args['cov'][-1]))
delta_esp = []
for i in range(len(ts_esp)):
delta_esp.append(float(rct_esp[i]) - float(ts_esp[i]))
alloys = [s for s in os.listdir(rctdir) if 'Au' in s]
for alloyid in alloys:
with jasp(rctdir + '/' + alloyid) as calc:
try:
atoms = calc.get_atoms()
rct_sp_energy = atoms.get_potential_energy()
except:
print alloyid, 'Something went wrong: RCT'
with jasp(tsdir + '/' + alloyid) as calc:
try:
atoms = calc.get_atoms()
ts_sp_energy = atoms.get_potential_energy()
except:
print alloyid, 'Something went wrong: TS'
sp_Eb = ts_sp_energy - rct_sp_energy
inert_sol = alloyid.split('-')[0].split('_')[-1]
deltaz = ele_dict[inert_sol] - ele_dict[args['host']]
allsites = [string.split('_') for string in alloyid.split('-')]
isite = allsites[0][0]
asite = allsites[1][0]
isite = [int(i) for i in allsites[0][0].split('.')]
asite = [int(i) for i in allsites[1][0].split('.')]
aesp = util.esp_layer(delta_esp, natoms, layer)
iesp = util.esp_layer(delta_esp, natoms, 1)
istr = ':'.join([str(s) for s in isite])
astr = ':'.join([str(s) for s in asite])
alcder = calc_alcder(isite, asite, iesp, aesp, deltaz)
print alloyid, sp_Eb - ref_Eb, alcder
nf.write('{},{},{},{},{},{}\n'.format(alloyid, abs(deltaz), istr, astr,
sp_Eb - ref_Eb, alcder))