def _read_functions(fileobj, valence_orbitals):
"""
Read radial wave functions (R=u/r), self-consistent potentials,
confinements, etc. from given file.
"""
default = np.array([[0,0],[1,0],[2,0],[3,0]])
functions = {
'unl': {},
'Rnl': {}
}
for nl in valence_orbitals:
m = mix.find_value(fileobj, 'u_%s' % nl, fmt='matrix', default=default)
functions['unl'][nl]=Function('spline', m[:,0], m[:,1])
functions['Rnl'][nl]=Function('spline', m[:,0], m[:,1]/m[:,0])
m = mix.find_value(fileobj, 'effective_potential',
fmt='matrix', default=default)
functions['effective_potential'] = Function('spline', m[:,0], m[:,1])
m = mix.find_value(fileobj, 'confinement_potential',
fmt='matrix', default=default)
functions['confinement_potential'] = Function('spline', m[:,0], m[:,1])
return functions
def _read_functions(fileobj, valence_orbitals):
"""
Read radial wave functions (R=u/r), self-consistent potentials,
confinements, etc. from given file.
"""
default = np.array([[1, 0], [2, 0], [3, 0], [4, 0]])
functions = {'unl': {}, 'Rnl': {}}
for nl in valence_orbitals:
m = mix.find_value(fileobj, 'u_%s' % nl, fmt='matrix', default=default)
functions['unl'][nl] = Function('spline', m[:, 0], m[:, 1])
functions['Rnl'][nl] = Function('spline', m[:, 0], m[:, 1] / m[:, 0])
m = mix.find_value(fileobj,
'effective_potential',
fmt='matrix',
default=default)
functions['effective_potential'] = Function('spline', m[:, 0], m[:, 1])
m = mix.find_value(fileobj,
'confinement_potential',
fmt='matrix',
default=default)
functions['confinement_potential'] = Function('spline', m[:, 0], m[:, 1])
return functions
def read_table(parfile, s1, s2):
""" Read parameter table from file parfile for elements with symbols s1 and s2.
return list of tables [s1_s2_table,s2_s1_table] (or only other if s1==s2)
"""
if parfile.find('.skf') > 0:
if not parfile != '%s%s.skf':
raise NotImplementedError(
'Comparison assumes filename of type symbol1symbol2.skf.')
rgrid, table12 = read_skf_table('%s%s.skf' % (s1, s2), s1, s2)
rgrid, table21 = read_skf_table('%s%s.skf' % (s2, s1), s2, s1)
table = [table12]
if s1 != s2:
table.append(table21)
else:
f = open(parfile)
nel = [1, 2][s1 == s2]
tab = mix.find_value(parfile, '%s_%s_table' % (s1, s2), fmt='matrix')
rgrid = tab[:, 0]
table = [tab[:, 1:]]
if s1 != s2:
tab = mix.find_value(parfile,
'%s_%s_table' % (s2, s1),
fmt='matrix')
table.append(tab[:, 1:])
f.close()
return rgrid, table
def read_elm(filename, orbitals):
""" Read element data form .elm-file. """
f = open(filename, 'r')
data = {}
data['symbol'] = find_value(f, 'symbol')
data['energies'] = [
float(find_value(f, 'epsilon_%s' % orb)) for orb in orbitals
]
data['U'] = float(find_value(f, 'U'))
data['FWHM'] = float(find_value(f, 'FWHM'))
f.close()
return data
def read_par(el1, el2, filename):
""" Read parameter files. """
f = open(filename, 'r')
tables = {}
t12 = find_value(f, '%s_%s_table' % (el1, el2), fmt='matrix')
t21 = find_value(f, '%s_%s_table' % (el2, el1), fmt='matrix')
tables['N'] = len(t12[:, 0])
dr = t12[1, 0] - t12[0, 0]
dr2 = t21[1, 0] - t21[0, 0]
assert abs(dr - dr2) < 1E-13
tables['dr'] = dr
tables['grid'] = t12[:, 0]
tables['%s%s' % (el1, el2)] = t12[:, 1:]
tables['%s%s' % (el2, el1)] = t21[:, 1:]
rep = find_value(f, 'repulsion', fmt='matrix')
return tables, rep
def read_HS_from_par(fileobj, symboli, symbolj):
"""
Read Hamiltonian and overlap data from Hotbit-style .par file.
Parameters:
-----------
fileobj: filename of file-object to read from
symboli: chemical symbol of the first element
symbolj: chemical symbol of the second element
"""
if mix.find_value(fileobj, 'X_X_table', fmt='test'):
table = mix.find_value(fileobj,
'X_X_table' % ( symboli, symbolj ),
fmt='matrix')
else:
table = mix.find_value(fileobj,
'%s_%s_table' % ( symboli, symbolj ),
fmt='matrix')
return table[:, 0], table[:, 1:]
def read_HS_from_par(fileobj, symboli, symbolj):
"""
Read Hamiltonian and overlap data from Hotbit-style .par file.
Parameters:
-----------
fileobj: filename of file-object to read from
symboli: chemical symbol of the first element
symbolj: chemical symbol of the second element
"""
if mix.find_value(fileobj, 'X_X_table', fmt='test'):
table = mix.find_value(fileobj,
'X_X_table' % (symboli, symbolj),
fmt='matrix')
else:
table = mix.find_value(fileobj,
'%s_%s_table' % (symboli, symbolj),
fmt='matrix')
return table[:, 0], table[:, 1:]
def read_element_from_elm(fileobj, symbol):
"""
Read element data from Hotbit-style .elm file.
Parameters:
-----------
fileobj: filename of file-object to read from
symbol: chemical symbol of the element
"""
if isinstance(fileobj, str):
fileobj = open(fileobj)
symb = mix.find_value(fileobj, 'symbol').strip()
assert symb == symbol
data = copy(box_data[symbol])
data['U'] = float(mix.find_value(fileobj, 'U'))
data['FWHM'] = float(mix.find_value(fileobj, 'FWHM'))
data['epsilon'] = { }
for orbital in data['valence_orbitals']:
data['epsilon'][orbital] = float(
mix.find_value(fileobj, 'epsilon_%s' % orbital)
)
data['comment'] = mix.find_value(fileobj, 'comment',
fmt='strings',
default=['no comment'])
functions = _read_functions(fileobj, data['valence_orbitals'])
energies=[]
for orbital in data['valence_orbitals']:
eps = data['epsilon'][orbital]
if 's' in orbital: n=1
elif 'p' in orbital: n=3
elif 'd' in orbital: n=5
energies.extend( [eps]*n )
data['onsite_energies'] = energies
data['nr_basis_orbitals'] = len(energies)
data['valence_energies'] = np.array(energies, dtype=float)
# vdW correction
data['C6'] = mix.find_value(fileobj, 'C6', default=-1.0)
data['p'] = mix.find_value(fileobj, 'p', default=-1.0)
data['R0'] = mix.find_value(fileobj, 'R0', default=-1.0)
return data, functions
def read_element_from_elm(fileobj, symbol):
"""
Read element data from Hotbit-style .elm file.
Parameters:
-----------
fileobj: filename of file-object to read from
symbol: chemical symbol of the element
"""
if isinstance(fileobj, str):
fileobj = open(fileobj)
symb = mix.find_value(fileobj, 'symbol').strip()
assert symb == symbol
data = copy(box_data[symbol])
data['U'] = float(mix.find_value(fileobj, 'U'))
data['FWHM'] = float(mix.find_value(fileobj, 'FWHM'))
data['epsilon'] = {}
for orbital in data['valence_orbitals']:
data['epsilon'][orbital] = float(
mix.find_value(fileobj, 'epsilon_%s' % orbital))
data['comment'] = mix.find_value(fileobj,
'comment',
fmt='strings',
default=['no comment'])
functions = _read_functions(fileobj, data['valence_orbitals'])
energies = []
for orbital in data['valence_orbitals']:
eps = data['epsilon'][orbital]
if 's' in orbital: n = 1
elif 'p' in orbital: n = 3
elif 'd' in orbital: n = 5
energies.extend([eps] * n)
data['onsite_energies'] = energies
data['nr_basis_orbitals'] = len(energies)
data['valence_energies'] = np.array(energies, dtype=float)
# vdW correction
data['C6'] = mix.find_value(fileobj, 'C6', default=-1.0)
data['p'] = mix.find_value(fileobj, 'p', default=-1.0)
data['R0'] = mix.find_value(fileobj, 'R0', default=-1.0)
return data, functions
def greetings(self):
""" Return the repulsion documentations. """
txt='Repulsions:\n'
for i,s1 in enumerate(self.calc.el.present):
for s2 in self.calc.el.present[i:]:
file = self.files[s1+s2]
if file==None:
txt+=' %s%s: None\n' %(s1,s2)
else:
txt+=' %s%s in %s\n' %(s1,s2,file)
doc=mix.find_value(file,'repulsion_comment',fmt='strings',default=['no repulsion doc'])
for line in doc:
txt+=' *'+line.lstrip()+'\n'
return txt
def greetings(self):
""" Return the interaction specifications """
txt='Interactions:\n'
for i,s1 in enumerate(self.present):
for s2 in self.present:
file = self.files[s1+s2]
if file==None:
txt+=' %s%s: None\n' %(s1,s2)
else:
txt+=' %s%s in %s\n' %(s1,s2,file)
doc=mix.find_value(file,'slako_comment',fmt='strings',default=['no slako doc'])
for line in doc:
txt+=' *'+line.lstrip()+'\n'
return txt
def greetings(self):
""" Return the repulsion documentations. """
txt='Repulsions:\n'
for i,s1 in enumerate(self.calc.el.present):
for s2 in self.calc.el.present[i:]:
file = self.files[s1+s2]
if file==None:
txt+=' %s%s: None\n' %(s1,s2)
else:
txt+=' %s%s in %s\n' %(s1,s2,file)
doc=mix.find_value(file,'repulsion_comment',fmt='strings',default=['no repulsion doc'])
for line in doc:
txt+=' *'+line.lstrip()+'\n'
return txt
def read_repulsion_from_par(fileobj):
"""
Read repulsion data from Hotbit-style .par file.
Parameters:
-----------
fileobj: filename of file-object to read from
"""
try:
v = mix.find_value(fileobj, 'repulsion', fmt='matrix')
except:
v = np.array([[0,0],[1,0],[2,0],[3,0]])
return v[:, 0], v[:, 1]
def read_repulsion_from_par(fileobj):
"""
Read repulsion data from Hotbit-style .par file.
Parameters:
-----------
fileobj: filename of file-object to read from
"""
try:
v = mix.find_value(fileobj, 'repulsion', fmt='matrix')
except:
v = np.array([[0, 0], [1, 0], [2, 0], [3, 0]])
return v[:, 0], v[:, 1]
def read_table(parfile,s1,s2):
""" Read parameter table from file parfile for elements with symbols s1 and s2.
return list of tables [s1_s2_table,s2_s1_table] (or only other if s1==s2)
"""
if parfile.find('.skf')>0:
if not parfile!='%s%s.skf':
raise NotImplementedError('Comparison assumes filename of type symbol1symbol2.skf.')
rgrid, table12 = read_skf_table('%s%s.skf' %(s1,s2),s1,s2)
rgrid, table21 = read_skf_table('%s%s.skf' %(s2,s1),s2,s1)
table = [table12]
if s1!=s2:
table.append(table21)
else:
f=open(parfile)
nel=[1,2][s1==s2]
tab=mix.find_value(parfile,'%s_%s_table' %(s1,s2),fmt='matrix')
rgrid=tab[:,0]
table=[tab[:,1:]]
if s1!=s2:
tab=mix.find_value(parfile,'%s_%s_table' %(s2,s1),fmt='matrix')
table.append(tab[:,1:])
f.close()
return rgrid, table