Exemplos de Atoms.extended_copy em Python

Exemplo n.º 1

Arquivo: C6H6_wedge.py Projeto: molguin-qc/hotbit

from box.md import check_energy_conservation
from hotbit.test.misc import default_param


# check that C1H1-presentation of C6H6 goes right
SCC=True
cut=3.0
atoms = Atoms('CH',[(1.42,0,0),(2.0,1.0,0.2)],container='Wedge')
atoms.set_container(M=6,height=10)

calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()

atoms6 = ase_Atoms(pbc=False)
atoms6 += atoms.extended_copy([(i-2,0,0) for i in range(6)])
#view(atoms)
calc = Hotbit(SCC=SCC,txt='tmp.cal',gamma_cut=cut,**default_param)
atoms6.set_calculator(calc)
e6 = atoms6.get_potential_energy()

assert abs(6*e1-e6)<1E-5


#
# energy conservation
#
atoms = Atoms('CH',[(1.42,0,0),(2.0,0.5,0.3)],container='Wedge')
atoms.set_container(M=6,height=10)
calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
atoms.set_calculator(calc)

Exemplo n.º 2

Arquivo: C6H6_cell_game.py Projeto: molguin-qc/hotbit

from ase import *
from ase import Atoms as ase_Atoms
from hotbit import *
from hotbit.atoms import Atoms
from box.md import check_energy_conservation
from hotbit.test.misc import default_param

SCC=True
cut=3.0
atoms = Atoms('CH',[(1.42,0,0),(2.42,0,0)],container='Wedge')
atoms.set_container(M=6,height=10)

calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()

 
aux = atoms.extended_copy((3,1,1))
atoms2 = Atoms(container='Wedge')
atoms2 += aux[0]
atoms2 += aux[-1]
atoms2.set_container(M=6,height=10)

#view(atoms2)
calc = Hotbit(SCC=SCC,txt='tmp.cal',kpts=(6,1,1),gamma_cut=cut,**default_param)
atoms2.set_calculator(calc)
e2 = atoms.get_potential_energy()

assert abs(e1-e2)<1E-5

Exemplo n.º 3

Arquivo: mulliken.py Projeto: pastewka/hotbit

    sm = 0.0
    for i in range(calc.st.norb):
        for j in range(i, calc.st.norb):
            x1, y1 = calc.get_covalent_energy('orbitals', i=i, j=j)
            sm += y1.sum()
    assert abs(y.sum() - sm) < eps

if True:
    # check that C1H1-presentation of C6H6 goes right
    n1 = 4
    SCC = True
    cut = 1E10
    a1 = Atoms('CH', [(1.42, 0, 0), (2.42, 0.1, 0.1)], container='Wedge')
    a1.set_container(M=6, height=10)
    aux = a1.extended_copy([(1, 0, 0)])
    a1 += aux
    a1.set_container(M=3, height=10)

    n2 = 12
    c1 = Hotbit(SCC=SCC,
                txt='-',
                kpts=(3, 1, 1),
                gamma_cut=cut,
                **default_param)
    a1.set_calculator(c1)
    a1.get_potential_energy()

    a2 = a1.extended_copy((3, 1, 1))
    c2 = Hotbit(SCC=SCC,
                txt='-',

Exemplo n.º 4

Arquivo: C6H6_wedge.py Projeto: nateharms/hotbit

# check that C1H1-presentation of C6H6 goes right
SCC = True
cut = 3.0
atoms = Atoms('CH', [(1.42, 0, 0), (2.0, 1.0, 0.2)], container='Wedge')
atoms.set_container(M=6, height=10)

calc = Hotbit(SCC=SCC,
              txt='tmp.cal',
              kpts=(6, 1, 1),
              gamma_cut=cut,
              **default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()

atoms6 = ase_Atoms(pbc=False)
atoms6 += atoms.extended_copy([(i - 2, 0, 0) for i in range(6)])
#view(atoms)
calc = Hotbit(SCC=SCC, txt='tmp.cal', gamma_cut=cut, **default_param)
atoms6.set_calculator(calc)
e6 = atoms6.get_potential_energy()

assert abs(6 * e1 - e6) < 1E-5

#
# energy conservation
#
atoms = Atoms('CH', [(1.42, 0, 0), (2.0, 0.5, 0.3)], container='Wedge')
atoms.set_container(M=6, height=10)
calc = Hotbit(SCC=SCC,
              txt='tmp.cal',
              kpts=(6, 1, 1),

Exemplo n.º 5

from hotbit.test.misc import default_param

SCC = True
cut = 3.0
atoms = Atoms('CH', [(1.42, 0, 0), (2.42, 0, 0)], container='Wedge')
atoms.set_container(M=6, height=10)

calc = Hotbit(SCC=SCC,
              txt='tmp.cal',
              kpts=(6, 1, 1),
              gamma_cut=cut,
              **default_param)
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()

aux = atoms.extended_copy((3, 1, 1))
atoms2 = Atoms(container='Wedge')
atoms2 += aux[0]
atoms2 += aux[-1]
atoms2.set_container(M=6, height=10)

#view(atoms2)
calc = Hotbit(SCC=SCC,
              txt='tmp.cal',
              kpts=(6, 1, 1),
              gamma_cut=cut,
              **default_param)
atoms2.set_calculator(calc)
e2 = atoms.get_potential_energy()

assert abs(e1 - e2) < 1E-5

Exemplo n.º 6

Arquivo: mulliken.py Projeto: molguin-qc/hotbit

    sm = 0.0
    for i in range(calc.st.norb):
        for j in range(i,calc.st.norb):
            x1,y1 = calc.get_covalent_energy('orbitals',i=i,j=j) 
            sm += y1.sum()
    assert abs(y.sum()-sm)<eps


if True:
    # check that C1H1-presentation of C6H6 goes right
    n1 = 4
    SCC=True
    cut=1E10
    a1 = Atoms('CH',[(1.42,0,0),(2.42,0.1,0.1)],container='Wedge')
    a1.set_container(M=6,height=10)
    aux = a1.extended_copy([(1,0,0)])
    a1 += aux
    a1.set_container(M=3,height=10)
    
    
    n2 = 12
    c1 = Hotbit(SCC=SCC,txt='-',kpts=(3,1,1),gamma_cut=cut,**default_param)
    a1.set_calculator(c1)
    a1.get_potential_energy()
    
    
    a2 = a1.extended_copy((3,1,1))
    c2 = Hotbit(SCC=SCC,txt='-',kpts=(1,1,1),gamma_cut=cut,**default_param)
    a2.set_calculator(c2)
    a2.get_potential_energy()