Python Vasp.clone方法代码示例

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
for U in [2.0, 4.0, 6.0]:
    ## Cu2O ########################################
    calc = Vasp('bulk/Cu2O')
    calc.clone('bulk/Cu2O-U={0}'.format(U))
    calc.set(ldau=True,   # turn DFT+U on
             ldautype=2,  # select simplified rotationally invariant option
             ldau_luj={'Cu':{'L':2,  'U':U, 'J':0.0},
                       'O':{'L':-1, 'U':0.0, 'J':0.0}},
             ldauprint=1,
             ibrion=-1,  # do not rerelax
             nsw=0)
    atoms1 = calc.get_atoms()
    cu2o_energy = atoms1.get_potential_energy() / (len(atoms1) / 3)
    ## CuO ########################################
    calc = Vasp('bulk/CuO')
    calc.clone('bulk/CuO-U={0}'.format(U))
    calc.set(ldau=True,   # turn DFT+U on
             ldautype=2,  # select simplified rotationally invariant option
             ldau_luj={'Cu':{'L':2,  'U':U, 'J':0.0},
                       'O':{'L':-1, 'U':0.0, 'J':0.0}},
             ldauprint=1,
             ibrion=-1,  # do not rerelax
             nsw=0)
    atoms2 = calc.get_atoms()
    cuo_energy = atoms2.get_potential_energy() / (len(atoms2) / 2)
    ## O2 ########################################
    # make sure to use the same cutoff energy for the O2 molecule!
    calc = Vasp('molecules/O2-sp-triplet-400')
    atoms = calc.get_atoms()
    o2_energy = atoms.get_potential_energy()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('bulk/tio2/step1-0.90')
calc.clone('bulk/tio2/step2-0.90')
#calc.set(isif=4)
print calc.set(isif=4)
print calc.calculation_required()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('bulk/CuPd-cls-0')
calc.clone('bulk/CuPd-cls-1')
calc.set(ibrion=None,
         isif=None,
         nsw=None,
         setups=[[0, 'Cu']],  # Create separate entry in POTCAR for atom index 0
         icorelevel=2,        # Perform core level shift calculation
         clnt=0,              # Excite atom index 0
         cln=2,               # 2p3/2 electron for Cu core level shift
         cll=1,
         clz=1)
calc.update()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('bulk/tio2/step3')
atoms = calc.get_atoms()
print 'default ismear: ', atoms.get_potential_energy()
calc.clone('bulk/tio2/step4')
calc.set(ismear=-5,
         nsw=0)
atoms = calc.get_atoms()
print 'ismear=-5:      ', atoms.get_potential_energy()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
wd = 'bulk/Si-bandstructure'
calc = Vasp('bulk/Si-selfconsistent')
calc.clone(wd)
kpts = [[0.5, 0.5, 0.0],   # L
        [0, 0, 0],         # Gamma
        [0, 0, 0],
        [0.5, 0.5, 0.5]]  # X
calc.set(kpts=kpts,
         reciprocal=True,
         kpts_nintersections=10,
         icharg=11)
print calc.run()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
from enthought.mayavi import mlab
from ase.data import vdw_radii
from ase.data.colors import cpk_colors
calc = Vasp('molecules/simple-co')
calc.clone('molecules/co-chg')
calc.set(lcharg=True)
calc.stop_if(calc.potential_energy is None)
atoms = calc.get_atoms()
x, y, z, cd = calc.get_charge_density()
# make a white figure
mlab.figure(1, bgcolor=(1, 1, 1))
# plot the atoms as spheres
for atom in atoms:
    mlab.points3d(atom.x,
                  atom.y,
                  atom.z,
                  #this determines the size of the atom
                  scale_factor=vdw_radii[atom.number] / 5.,
                  resolution=20,
                  # a tuple is required for the color
                  color=tuple(cpk_colors[atom.number]),
                  scale_mode='none')
# draw the unit cell - there are 8 corners, and 12 connections
a1, a2, a3 = atoms.get_cell()
origin = [0, 0, 0]
cell_matrix = [[origin,  a1],
               [origin,  a2],
               [origin,  a3],
               [a1,      a1 + a2],
               [a1,      a1 + a3],

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
# perform a climbing image NEB calculation
from vasp import Vasp
calc = Vasp('surfaces/Pt-O-fcc-hcp-neb')
calc.clone('surfaces/Pt-O-fcc-hcp-cineb')
calc.set(ichain=0, lclimb=True)
images, energies = calc.get_neb()
calc.plot_neb(show=False)
import matplotlib.pyplot as plt
plt.savefig('images/pt-o-cineb.svg')
plt.show()

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
factors = [0.9, 0.95, 1.0, 1.05, 1.1]  # to change volume by
energies1, volumes1 = [], []  # from step 1
energies, volumes = [], []  # for step 2
ready = True
for f in factors:
    calc = Vasp('bulk/tio2/step1-{0:1.2f}'.format(f))
    atoms = calc.get_atoms()
    energies1.append(atoms.get_potential_energy())
    volumes1.append(atoms.get_volume())
    calc.clone('bulk/tio2/step2-{0:1.2f}'.format(f))
    calc.set(isif=4)
    # You have to get the atoms again.
    atoms = calc.get_atoms()
    energies.append(atoms.get_potential_energy())
    volumes.append(atoms.get_volume())
print(energies, volumes)
calc.stop_if(None in energies)
import matplotlib.pyplot as plt
plt.plot(volumes1, energies1, volumes, energies)
plt.xlabel('Vol. ($\AA^3)$')
plt.ylabel('Total energy (eV)')
plt.legend(['step 1', 'step 2'], loc='best')
plt.savefig('images/tio2-step2.png')

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('surfaces/Pt-slab-O-fcc')
calc.clone('surfaces/Pt-slab-O-fcc-vib')
calc.set(ibrion=5,     # finite differences with selective dynamics
         nfree=2,      # central differences (default)
         potim=0.015,  # default as well
         ediff=1e-8,
         nsw=1)
atoms = calc.get_atoms()
f, v = calc.get_vibrational_modes(0)
print 'Elapsed time = {0} seconds'.format(calc.get_elapsed_time())
allfreq = calc.get_vibrational_modes()[0]
from ase.units import meV
c = 3e10  # cm/s
h = 4.135667516e-15  # eV*s
print 'vibrational energy = {0} eV'.format(f)
print 'vibrational energy = {0} meV'.format(f/meV)
print 'vibrational freq   = {0} 1/s'.format(f/h)
print 'vibrational freq   = {0} cm^{{-1}}'.format(f/(h*c))
print
print 'All energies = ', allfreq

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
from ase.dft import DOS
calc = Vasp('bulk/pd-dos')
calc.clone('bulk/pd-dos-ismear-5')
bulk = calc.get_atoms()
calc.set(ismear=-5)
bulk.get_potential_energy()
dos = DOS(calc, width=0.2)
d = dos.get_dos()
e = dos.get_energies()
import pylab as plt
plt.plot(e, d)
plt.xlabel('energy [eV]')
plt.ylabel('DOS')
plt.savefig('images/pd-dos-ismear-5.png')

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
slab.center()
calc = Vasp('surfaces/Al-Na-dip',
            xc='PBE',
            encut=340,
            kpts=[2, 2, 1],
            lcharg=True,
            idipol=3,   # only along z-axis
            lvtot=True,  # write out local potential
            lvhar=True,  # write out only electrostatic potential, not xc pot
            atoms=slab)
calc.stop_if(calc.potential_energy is None)
x, y, z, cd = calc.get_charge_density()
n0, n1, n2 = cd.shape
nelements = n0 * n1 * n2
voxel_volume = slab.get_volume() / nelements
total_electron_charge = cd.sum() * voxel_volume
electron_density_center = np.array([(cd * x).sum(),
                                    (cd * y).sum(),
                                    (cd * z).sum()])
electron_density_center *= voxel_volume
electron_density_center /= total_electron_charge
print 'electron-density center = {0}'.format(electron_density_center)
uc = slab.get_cell()
# get scaled electron charge density center
sedc = np.dot(np.linalg.inv(uc.T), electron_density_center.T).T
# we only write 4 decimal places out to the INCAR file, so we round here.
sedc = np.round(sedc, 4)
calc.clone('surfaces/Al-Na-dip-step2')
# now run step 2 with dipole set at scaled electron charge density center
calc.set(ldipol=True, dipol=sedc)
print(calc.potential_energy)

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('bulk/Fe-bulk')
calc.clone('bulk/Fe-elastic')
calc.set(ibrion=6,    #
         isif=3,      # gets elastic constants
         potim=0.05,  # displacements
         nsw=1,
         nfree=2)
print(calc.potential_energy)

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
calc = Vasp('bulk/Al-bulk')
calc.clone('bulk/Al-elastic')
calc.set(ibrion=6,    #
         isif=3,      # gets elastic constants
         potim=0.015,  # displacements
         nsw=1,
         nfree=2)
calc.wait(abort=True)
EM = calc.get_elastic_moduli()
print(EM)
c11 = EM[0, 0]
c12 = EM[0, 1]
B = (c11 + 2 * c12) / 3.0
print(B)

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
atoms[0].magmom = 1
calc = Vasp('bulk/Ni-PBE',
            ismear=-5,
            kpts=[5, 5, 5],
            xc='PBE',
            ispin=2,
            lorbit=11,
            lwave=True, lcharg=True,  # store for reuse
            atoms=atoms)
e = atoms.get_potential_energy()
print('PBE energy:   ',e)
calc.stop_if(e is None)
dos = DOS(calc, width=0.2)
e_pbe = dos.get_energies()
d_pbe = dos.get_dos()
calc.clone('bulk/Ni-PBE0')
calc.set(xc='pbe0')
atoms = calc.get_atoms()
pbe0_e = atoms.get_potential_energy()
if atoms.get_potential_energy() is not None:
    dos = DOS(calc, width=0.2)
    e_pbe0 = dos.get_energies()
    d_pbe0 = dos.get_dos()
## HSE06
calc = Vasp('bulk/Ni-PBE')
calc.clone('bulk/Ni-HSE06')
calc.set(xc='hse06')
atoms = calc.get_atoms()
hse06_e = atoms.get_potential_energy()
if hse06_e is not None:
    dos = DOS(calc, width=0.2)

# 需要导入模块: from vasp import Vasp [as 别名]
# 或者: from vasp.Vasp import clone [as 别名]
from vasp import Vasp
from ase import Atom, Atoms
import logging
calc = Vasp('bulk/Cu2O')
calc.clone('bulk/Cu2O-U=4.0')
calc.set(ldau=True,   # turn DFT+U on
         ldautype=2,  # select simplified rotationally invariant option
         ldau_luj={'Cu':{'L':2,  'U':4.0, 'J':0.0},
                   'O':{'L':-1, 'U':0.0, 'J':0.0}},
         ldauprint=1,
         ibrion=-1,  #do not rerelax
         nsw=0)
atoms = calc.get_atoms()
print(atoms.get_potential_energy())
#print calc