Exemplo n.º 1
0
def check_db(db, params):
    if debug:
        print "%10s %10s %10s ( %10s )" \
            % ( "bond", "value", "reference", "error" )
    for mol, values in db.iteritems():
        #if mol == 'H2O':
        if 1:
            if debug:
                print mol

            a = molecule(mol)
            a.center(vacuum=10.0)
            a.set_pbc(False)

            #print a.get_chemical_symbols()

            calc = Hotbit(
                charge_density = 'Slater',
                SCC = True,
                width = 1e-6,
                txt = 'mio.out',
                **params)
            a.set_calculator(calc)

            #calc.ia.plot_table('H', 'H')
            #calc.rep.get_repulsion('H', 'H').plot()

            OPT(a, logfile='opt.log').run(fmax=FMAX)

            #print a.get_charges()
            
            for name, ( ( i1, i2 ), refvalue ) in values.iteritems():
                value = a.get_distance(i1, i2)
                if debug:
                    print '%10s %10.3f %10.3f ( %10.3f )' % \
                        ( name, value, refvalue, abs(value-refvalue) )
                assert abs(value-refvalue) < 0.01
Exemplo n.º 2
0
import numpy as np

import ase
from ase.units import Hartree
from hotbit import Hotbit

###

dir1 = '/Users/pas/Sourcen/hotbit/param/'
#dir2 = '/Users/pas/Sourcen/hotbit/param/'
dir2 = '/Users/pas/Sourcen/mdcore/data/slater_koster_tables/Frauenheim/download-2009-10-23/mio-0-1/'

###

a = ase.molecule('C6H6')
a.center(vacuum=6.0)

c = Hotbit(elements={
    'H': dir2 + 'H-H.skf',
    'C': dir2 + 'C-C.skf'
},
           tables={
               'HH': dir2 + 'H-H.skf',
               'CH': dir2 + 'C-H.skf',
               'CC': dir2 + 'C-C.skf'
           },
           SCC=False)
a.set_calculator(c)

ase.FIRE(a).run(fmax=0.01)
Exemplo n.º 3
0
import numpy as np

import ase
from ase.units import Hartree
from hotbit import Hotbit

###


dir1 = '/Users/pas/Sourcen/hotbit/param/'
#dir2 = '/Users/pas/Sourcen/hotbit/param/'
dir2 = '/Users/pas/Sourcen/mdcore/data/slater_koster_tables/Frauenheim/download-2009-10-23/mio-0-1/'

###

a = ase.molecule('C6H6')
a.center(vacuum=6.0)

c = Hotbit(
    elements = {
        'H': dir2 + 'H-H.skf',
        'C': dir2 + 'C-C.skf'
        },
    tables   = {
        'HH': dir2 + 'H-H.skf',
        'CH': dir2 + 'C-H.skf',
        'CC': dir2 + 'C-C.skf'
        },
    SCC      = False
    )
a.set_calculator(c)
Exemplo n.º 4
0
import os

import numpy as np

from time import time
from ase import molecule
from gpaw import GPAW
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs

if not os.path.isfile('C6H6.gpw'):
    atoms = molecule('C6H6')
    atoms.center(vacuum=2.5)
    calc = GPAW(h=0.2, basis='szp', width=0.05, convergence={'bands': 17})
    atoms.set_calculator(calc)
    atoms.get_potential_energy()
    calc.write('C6H6.gpw', 'all')
calc = GPAW('C6H6.gpw', txt=None, basis='sz')

ibzk_kc = calc.wfs.ibzk_kc
nk = len(ibzk_kc)
Ef = calc.get_fermi_level()
eps_kn = np.asarray([calc.get_eigenvalues(k) for k in range(nk)])
eps_kn -= Ef

V_knM, H_kMM, S_kMM, P_aqMi = get_phs(calc, s=0)
H_kMM -= Ef * S_kMM

pwf = ProjectedWannierFunctions(V_knM,
                                h_lcao=H_kMM,
                                s_lcao=S_kMM,
                                eigenvalues=eps_kn,
Exemplo n.º 5
0
import os

import numpy as np

from time import time
from ase import molecule
from gpaw import GPAW
from gpaw.lcao.projected_wannier import ProjectedWannierFunctions, get_phs

if not os.path.isfile('C6H6.gpw'):
    atoms = molecule('C6H6')
    atoms.center(vacuum=2.5)
    calc = GPAW(h=0.2, basis='szp', width=0.05, convergence={'bands':17})
    atoms.set_calculator(calc)
    atoms.get_potential_energy()
    calc.write('C6H6.gpw', 'all')
calc = GPAW('C6H6.gpw', txt=None, basis='sz')

ibzk_kc = calc.wfs.ibzk_kc
nk = len(ibzk_kc)
Ef = calc.get_fermi_level()
eps_kn = np.asarray([calc.get_eigenvalues(k) for k in range(nk)])
eps_kn -= Ef

V_knM, H_kMM, S_kMM, P_aqMi = get_phs(calc, s=0)
H_kMM -= Ef * S_kMM 

pwf = ProjectedWannierFunctions(V_knM, 
                                h_lcao=H_kMM, 
                                s_lcao=S_kMM, 
                                eigenvalues=eps_kn,
Exemplo n.º 6
0
def run_molecule(adsorbate, geometry, xc, code):

    parameters = initialize_parameters(code, 0.01, h)
    parameters['xc'] = xc

    molecules = {
        'None': ('NO', 8),
        'N': ('N2', 8),
        'O': ('O2', 8),
    }

    for name, nbands in [molecules[adsorbate]]:
        if code != 'elk':
            parameters['nbands'] = nbands
        if geometry == 'fix':
            mol = read_trajectory(code + '_' + name + '.traj')
        else:
            mol = molecule(name)
        mol.center(vacuum=3.0 + add_vacuum)
        if name == 'NO':
            mol.translate((0, 0.1, 0))
        #
        if code == 'gpaw':
            from gpaw import GPAW as Calculator
            from gpaw.mpi import rank
            parameters['txt'] = code + '_' + name + '.txt'
            from gpaw.mixer import Mixer, MixerSum
            #if name == 'N2':
            #    parameters['mixer'] = Mixer(beta=0.1, nmaxold=5, metric='new', weight=100.0)
            #else:
            #    #parameters['eigensolver'] = 'cg'
            #    parameters['mixer'] = MixerSum(beta=0.2, nmaxold=5, metric='new', weight=100.0)
        if code == 'dacapo':
            from ase.calculators.dacapo import Dacapo as Calculator
            rank = 0
            parameters['txtout'] = code + '_' + name + '.txt'
        if code == 'abinit':
            from ase.calculators.abinit import Abinit as Calculator
            rank = 0
            parameters['label'] = code + '_' + name
        if code == 'elk':
            from ase.calculators.elk import ELK as Calculator
            rank = 0
            elk_dir = 'elk_' + str(parameters['rgkmax'])
            conv_param = 1.0
            parameters['dir'] = elk_dir + '_' + name
        #
        calc = Calculator(**parameters)
        #
        mol.set_calculator(calc)
        try:
            if geometry == 'fix':
                mol.get_potential_energy()
                traj = PickleTrajectory(code + '_' + name + '.traj', mode='w')
                traj.write(mol)
            else:
                opt = QuasiNewton(mol,
                                  logfile=code + '_' + name + '.qn',
                                  trajectory=code + '_' + name + '.traj')
                opt.run(fmax=fmax)
        except:
            raise