Beispiel #1
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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
Beispiel #2
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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
Beispiel #3
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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
Beispiel #4
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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
Beispiel #5
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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
Beispiel #6
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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:]
Beispiel #7
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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:]
Beispiel #8
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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
Beispiel #9
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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
Beispiel #10
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 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
Beispiel #11
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 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
Beispiel #12
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 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
Beispiel #13
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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]
Beispiel #14
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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]
Beispiel #15
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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