Python Phonopy.set_force_constants方法代碼示例

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_force_constants [as 別名]
def get_phonopy_qha(energies, volumes, force_constants, structure, t_min, t_step, t_max, mesh, eos,
                      pressure=0):
    """
    Return phonopy QHA interface.

    Args:
        energies (list):
        volumes (list):
        force_constants (list):
        structure (Structure):
        t_min (float): min temperature
        t_step (float): temperature step
        t_max (float): max temperature
        mesh (list/tuple): reciprocal space density
        eos (str): equation of state used for fitting the energies and the volumes.
            options supported by phonopy: vinet, murnaghan, birch_murnaghan
        pressure (float): in GPa, optional.

    Returns:
        PhonopyQHA
    """
    from phonopy import Phonopy
    from phonopy.structure.atoms import Atoms as PhonopyAtoms
    from phonopy import PhonopyQHA
    from phonopy.units import EVAngstromToGPa

    phon_atoms = PhonopyAtoms(symbols=[str(s.specie) for s in structure],
                              scaled_positions=structure.frac_coords,
                              cell=structure.lattice.matrix)
    scell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
    phonon = Phonopy(phon_atoms, scell)
    # compute the required phonon thermal properties
    temperatures = []
    free_energy = []
    entropy = []
    cv = []
    for f in force_constants:
        phonon.set_force_constants(-np.array(f))
        phonon.set_mesh(list(mesh))
        phonon.set_thermal_properties(t_step=t_step, t_min=t_min, t_max=t_max)
        t, g, e, c = phonon.get_thermal_properties()
        temperatures.append(t)
        free_energy.append(g)
        entropy.append(e)
        cv.append(c)

    # add pressure contribution
    energies = np.array(energies) + np.array(volumes) * pressure / EVAngstromToGPa
    # quasi-harmonic approx
    return PhonopyQHA(volumes, energies, eos=eos, temperatures=temperatures[0],
                      free_energy=np.array(free_energy).T, cv=np.array(cv).T,
                      entropy=np.array(entropy).T, t_max=np.max(temperatures[0]))

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_force_constants [as 別名]
from phonopy import Phonopy
from phonopy.interface.vasp import read_vasp
from phonopy.file_IO import parse_FORCE_SETS
from phonopy.file_IO import parse_FORCE_CONSTANTS, write_FORCE_CONSTANTS

cell = read_vasp("POSCAR")
phonon = Phonopy(cell, [[2, 0, 0], [0, 2, 0], [0, 0, 2]])
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS")

force_constants = parse_FORCE_CONSTANTS()
phonon.set_force_constants(force_constants)
phonon.symmetrize_force_constants(iteration=1)
write_FORCE_CONSTANTS(phonon.get_force_constants(), filename="FORCE_CONSTANTS_NEW")

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_force_constants [as 別名]
 def __init__(self, numbatom=125, supercell=5):
     
     #species = 'WRe_0.25_conv'
     species = 'WRe_0.00'
     #species = 'Re'
     ###read force constants from vasprun.xml###
     vasprun = etree.iterparse('vasprun.xml', tag='varray')
     #fc = vasp.get_force_constants_vasprun_xml(vasprun,1) #pass xml input and species atomic weight.
     ###########################################
     
     ########### read positionsl ###############
     primitive = vasp.get_atoms_from_poscar(open('POSCAR-p'),'W')
     superc =  vasp.get_atoms_from_poscar(open('POSCAR'),'W')
     ###########################################
     numbatom =  superc.get_number_of_atoms()
     #print primitive.get_cell()
     #print primitive.get_scaled_positions()
     #print superc.get_scaled_positions()
     
     print numbatom, species, os.getcwd()
     if species=='W':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,0,64)
         s = 4.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
         
     elif species=='W_conv_2x2x2':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
         s = 2.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W','W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
     
     elif species=='W_conv':
     #Tungsten
         fc = vasp.get_force_constants_vasprun_xml(vasprun,1,2)
         s = 4.
         a = superc.get_cell()[0][0]*2.
         print a
         bulk = PhonopyAtoms(symbols=['W','W'] * 1,
                             scaled_positions= primitive.get_scaled_positions())
         bulk.set_cell(np.diag((a, a, a)))
         phonon = Phonopy(bulk,
                          [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                          primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                          distance=0.01, factor=15.633302)
         print fc
         phonon.set_force_constants(fc[0])
         phonon.set_dynamical_matrix()
         #print phonon.get_dynamical_matrix_at_q([0,0,0])
         mesh = [100, 100, 100]
         phonon.set_mesh(mesh)
         qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
         print frequencies
         phonon.set_total_DOS()
         
         phonon.set_thermal_properties(t_step=10,
                                       t_max=3700,
                                       t_min=0)
#.........這裏部分代碼省略.........

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_force_constants [as 別名]
phonon.set_qpoints_phonon(com_points,
                          is_eigenvectors=True)
frequencies, eigenvectors = phonon.get_qpoints_phonon()
dynmat2fc.set_dynamical_matrices(frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
fc = dynmat2fc.get_force_constants()

phonon2 = Phonopy(bulk,
                  [[2, 0, 0],
                   [0, 2, 0],
                   [0, 0, 2]],
                  primitive_matrix=[[0, 0.5, 0.5],
                                    [0.5, 0, 0.5],
                                    [0.5, 0.5, 0]],
                  is_auto_displacements=False)
phonon2.set_force_constants(fc)
bands = []
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.0, 0.0])
append_band(bands, [0.5, 0.0, 0.0], [0.5, 0.5, 0.0])
append_band(bands, [0.5, 0.5, 0.0], [0.0, 0.0, 0.0])
append_band(bands, [0.0, 0.0, 0.0], [0.5, 0.5, 0.5])
phonon2.set_band_structure(bands)
phonon2.plot_band_structure().show()

 # Artificially increase phonon frequency of the highest band(s) at Gamma
frequencies[0, 3:] = 7.5
dynmat2fc.set_dynamical_matrices(frequencies / VaspToTHz, eigenvectors)
dynmat2fc.run()
fc = dynmat2fc.get_force_constants()
phonon3 = Phonopy(bulk,
                  [[2, 0, 0],

# 需要導入模塊: from phonopy import Phonopy [as 別名]
# 或者: from phonopy.Phonopy import set_force_constants [as 別名]
###########################################
numbatom =  superc.get_number_of_atoms()
#print primitive.get_cell()
#print primitive.get_scaled_positions()
#print superc.get_scaled_positions()
s = 5.
a = superc.get_cell()[0][0]*2.
bulk = PhonopyAtoms(symbols=['W'] * 1,
                    scaled_positions= primitive.get_scaled_positions())
bulk.set_cell(np.diag((a, a, a)))
phonon = Phonopy(bulk,
                 [[s,0.,0.],[0.,s,0.],[0.,0.,s]],
                 primitive_matrix=[[-0.5, 0.5, 0.5],[0.5, -0.5, 0.5],[0.5, 0.5, -0.5]],
                 distance=0.01, factor=15.633302)

phonon.set_force_constants(fc[0])
phonon.set_dynamical_matrix()
#print phonon.get_dynamical_matrix_at_q([0,0,0])
mesh = [100, 100, 100]
phonon.set_mesh(mesh)
qpoints, weights, frequencies, eigvecs = phonon.get_mesh()
print frequencies
phonon.set_total_DOS()

phonon.set_thermal_properties(t_step=10,
                              t_max=1000,
                              t_min=0)
f = open('F_TV','w')
for t, free_energy, entropy, cv in np.array(phonon.get_thermal_properties()).T:
    print ("%12.3f " + "%15.7f" * 3) % ( t, free_energy, entropy, cv )
    f.write(("%12.3f " + "%15.7f" + "\n") % ( t, free_energy))