from ase.dft.bee import BEEF_Ensemble
import numpy as np
ens = BEEF_Ensemble()
def read_beef(filename):
energy, ensemble = ens.read(filename)
return energy, ensemble
# read out the energy and the ensemble of energies for each calculation
E_N2, E_ens_N2 = read_beef('folder_name/N2.bee')
E_cluster, E_ens_cluster = read_beef('folder_name/cluster.bee')
E_2N_cluster, E_ens_2N_cluster = read_beef('folder_name/2N_cluster.bee')
# compute the energy
E_2N = E_2N_cluster - E_cluster - E_N2
# computer the standard deviation (the error) from the ensembles
dE_2N = np.std(E_ens_2N_cluster - E_ens_cluster - E_ens_N2)
print "Reaction energy:", E_2N
print "Error:", dE_2N
'removewf': True,
'wf_collect': False
},
outdir='calcdir',
dipole={'status': True})
#if qn.traj exists, restart from the last steps
if os.path.exists('qn.traj') and os.path.getsize('qn.traj') != 0:
Slab = read('qn.traj', index=-1)
from math import sqrt
Slab.set_calculator(calc)
write('Initial_Slab_with_constraint.traj', Slab)
dyn = QuasiNewton(Slab, logfile='out_scf.log', trajectory='qn.traj')
dyn.run(fmax=fmaxout)
energy = Slab.get_potential_energy()
ens = BEEF_Ensemble(calc)
d_energy = ens.get_ensemble_energies()
calc.stop()
print 'Final SCF energy: %18f [eV]' % (energy)
print 'Deviation in energy: %18f [eV]' % (d_energy.std())
print '\n'
Slab.write('final_' + Slab.get_chemical_formula() + '.traj')
relaxed_atoms = calc.get_final_structure()
psppath = '/home/users/vossj/suncat/psp/gbrv1.5pbe'
pseudos = psppath.split('/')[-1]
print 'Potential Energy:', energy, 'eV'
print 'Maximum force:', fmaxout, 'eV/A'
print 'Final Structure:', relaxed_atoms
def run_geo_opt(bulk_name, final_traj_name, site_coord):
'''
This function runs the DFT calculations for the given trajectory name. It puts the adsorbate on the
passed site coordinate.
'''
time2= time.time()
f.write('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
f.write('Starting calculations: %30s\n'
%(final_traj_name.split('.')[0]))
f.write('+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
db=connect('/home/mamunm/DATABASE/adsorbate-slab.db')
######Calculations parameters#######
pw=500.
dw=5000.
xc='BEEF-vdW'
kpts=(6,6,1)
code='Qunatum-Espresso'
facet=(1,1,1)
layer=3
vacuum=10
a = final_traj_name.split('_')
adsorbate = a[1]
site = a[2] + '_' + a[3] + '_' + a[4]
slab_name = a[5].split('.')[0]
height = get_height(adsorbate, a[4])
f.write('\nComputed initial adsorption height: %4.2f Angstrom\n' %(height))
if '6' in slab_name:
SBS_symbol = 'L10' #Strukterbericht symbol
PS_symbol = 'tP2' #Pearson symbol
else:
SBS_symbol = 'L12' #Strukterbericht symbol
PS_symbol = 'cP4' #Pearson symbol
supercell='2x2'
fmaxout=0.05
crystal='fcc'
pol_metal = ['Fe', 'Ni', 'Co', 'Mn']
spinpol = False
DB_dir = '/scratch/users/mamunm/DATABASE/Binary_Alloy_Project/Surface/'
if '6' in slab_name:
metal1 = slab_name.split('6')[0]
metal2 = slab_name.split('6')[1]
path_to_slab = DB_dir + '/AB/'
if os.path.exists(path_to_slab + bulk_name):
slab = read(path_to_slab + bulk_name +
'/Initial_Slab_with_constraint.traj')
if metal1 in pol_metal or metal2 in pol_metal:
spinpol = True
slab.set_initial_magnetic_moments([2.0 if atom.symbol in pol_metal else 0 for atom in slab])
else:
metal1 = slab_name.split('9')[0]
metal2 = slab_name.split('9')[1].split('3')[0]
path_to_slab = DB_dir + '/A3B/'
if os.path.exists(path_to_slab + bulk_name):
slab = read(path_to_slab + bulk_name +
'/Initial_Slab_with_constraint.traj')
if metal1 in pol_metal or metal2 in pol_metal:
spinpol = True
slab.set_initial_magnetic_moments([2.0 if atom.symbol in pol_metal else 0 for atom in slab])
calc = espresso(pw = pw,
dw = dw,
xc = xc,
kpts = kpts,
spinpol = spinpol,
nbands = -10,
occupations = 'smearing', #'smeraing', 'fixed', 'tetrahedra'
smearing = 'fd', #Fermi-Dirac
sigma = 0.15,
calcstress = True,
mode = 'relax',
nosym = True,
beefensemble = True,
convergence= {'energy' : 1e-5*13.6,
'mixing' : 0.3,
'nmix' : 10,
'mix' : 4,
'maxsteps' : 2000,
'diag' : 'david'
},
psppath='/home/vossj/suncat/psp/gbrv1.5pbe',
output = {'avoidio':False,'removewf':True,'wf_collect':False},
outdir='Calculations/'+ adsorbate + '_' + site + '/calcdir',
dipole={'status':True})
#Add adsorbate on the surface
add_adsorbate(slab, adsorbate, height, site_coord)
slab.write('Initial_slab_with_adsorbate.traj')
#if qn.traj exists, restart from the last steps
if os.path.exists('qn.traj') and os.path.getsize('qn.traj') != 0:
slab=read('qn.traj',index=-1)
slab.set_calculator(calc)
dyn = QuasiNewton(slab,logfile='out_scf.log',trajectory='qn.traj')
dyn.run(fmax=fmaxout)
energy = slab.get_potential_energy()
ens=BEEF_Ensemble(calc)
d_energy=ens.get_ensemble_energies()
calc.stop()
f.write('Final SCF energy: %18f [eV]\n'%(energy))
f.write('Deviation in energy: %18f [eV]\n'%(d_energy.std()))
slab.write(final_traj_name)
relaxed_atoms = calc.get_final_structure()
psppath='/home/vossj/suncat/psp/gbrv1.5pbe'
pseudos = psppath.split('/')[-1]
f.write('Potential Energy: %2.10E eV\n' %(energy))
f.write('Maximum force: %2.6f eV/A\n' %(fmaxout))
f.write('Final Structure: %-300s\n' %(str(relaxed_atoms)))
db.write(relaxed_atoms,
crystal = crystal,
epot = energy,
supercell = supercell,
layer = layer,
SBS_symbol = SBS_symbol,
vacuum = vacuum,
facet = str(facet),
PS_symbol = PS_symbol,
slab_name = slab_name,
adsorbate = adsorbate,
site = site,
name=str(slab.get_chemical_formula()),
fmaxout = fmaxout,
xc = xc,
pw = pw,
dw = dw,
Ensemble_energy = d_energy.std(),
code = code,
psp = pseudos)
f.write('+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
f.write("Elapsed time for %20s :: %s seconds\n"
%(final_traj_name.split('.')[0], time.time()-time2))
f.write('+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
