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Merge pull request #177 from jkarp314/sumk_mesh

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have user specify frequency mesh when initializing SumKDFT object
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Alexander Hampel 2022-04-25 14:04:00 -04:00 committed by GitHub
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9 changed files with 254 additions and 271 deletions
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8
doc/tutorials/images_scripts/NiO_local_lattice_GF.py
View File

@ -12,9 +12,9 @@ import warnings
warnings.filterwarnings("ignore", category=FutureWarning)
filename = 'nio'
SK = SumkDFT(hdf_file = filename+'.h5', use_dft_blocks = False)
beta = 5.0
SK = SumkDFT(hdf_file = filename+'.h5', use_dft_blocks = False, beta=beta)
# We analyze the block structure of the Hamiltonian
Sigma = SK.block_structure.create_gf(beta=beta)
@ -79,12 +79,12 @@ for ik in mpi.slice_array(ikarray):
add_g_ik.zero()
add_g_ik << SK.downfold(ik, 0, bname, G_latt_KS[bname], gf, shells='csc', ir=None)
gf << gf + add_g_ik
G_latt_orb << mpi.all_reduce(
mpi.world, G_latt_orb, lambda x, y: x + y)
mpi.barrier()
if mpi.is_master_node():
if mpi.is_master_node():
ar['DMFT_results']['Iterations']['G_latt_orb_it'+str(iteration_offset-1)] = G_latt_orb
if mpi.is_master_node(): del ar

4
doc/tutorials/images_scripts/nio.py
View File

@ -17,9 +17,9 @@ warnings.filterwarnings("ignore", category=FutureWarning)
filename = 'nio'
SK = SumkDFT(hdf_file = filename+'.h5', use_dft_blocks = False)
beta = 5.0
SK = SumkDFT(hdf_file = filename+'.h5', use_dft_blocks = False, beta=beta)
Sigma = SK.block_structure.create_gf(beta=beta)
SK.put_Sigma([Sigma])

364
python/triqs_dft_tools/sumk_dft.py
View File

@ -25,7 +25,7 @@ General SumK class and helper functions for combining ab-initio code and triqs
"""
from types import *
import numpy
import numpy as np
import triqs.utility.dichotomy as dichotomy
from triqs.gf import *
import triqs.utility.mpi as mpi
@ -42,7 +42,7 @@ from scipy.optimize import minimize
class SumkDFT(object):
"""This class provides a general SumK method for combining ab-initio code and triqs."""
def __init__(self, hdf_file, h_field=0.0, use_dft_blocks=False,
def __init__(self, hdf_file, h_field=0.0, mesh=None, beta=40, n_iw=1025, use_dft_blocks=False,
dft_data='dft_input', symmcorr_data='dft_symmcorr_input', parproj_data='dft_parproj_input',
symmpar_data='dft_symmpar_input', bands_data='dft_bands_input', transp_data='dft_transp_input',
misc_data='dft_misc_input',bc_data='dft_bandchar_input',fs_data='dft_fs_input'):
@ -57,6 +57,11 @@ class SumkDFT(object):
The value of magnetic field to add to the DFT Hamiltonian.
The contribution -h_field*sigma is added to diagonal elements of the Hamiltonian.
It cannot be used with the spin-orbit coupling on; namely h_field is set to 0 if self.SO=True.
mesh: MeshImFreq or MeshReFreq, optional. Frequency mesh of Sigma.
beta : real, optional
Inverse temperature. Used to construct imaginary frequency if mesh is not given.
n_iw : integer, optional
Number of Matsubara frequencies. Used to construct imaginary frequency if mesh is not given.
use_dft_blocks : boolean, optional
If True, the local Green's function matrix for each spin is divided into smaller blocks
with the block structure determined from the DFT density matrix of the corresponding correlated shell.
@ -99,6 +104,22 @@ class SumkDFT(object):
self.fs_data = fs_data
self.h_field = h_field
if mesh is None:
self.mesh = MeshImFreq(beta=beta, S='Fermion', n_max=n_iw)
self.mesh_values = np.linspace(self.mesh(self.mesh.first_index()),
self.mesh(self.mesh.last_index()),
len(self.mesh))
elif isinstance(mesh, MeshImFreq):
self.mesh = mesh
self.mesh_values = np.linspace(self.mesh(self.mesh.first_index()),
self.mesh(self.mesh.last_index()),
len(self.mesh))
elif isinstance(mesh, MeshReFreq):
self.mesh = mesh
self.mesh_values = np.linspace(self.mesh.omega_min, self.mesh.omega_max, len(self.mesh))
else:
raise ValueError('mesh must be a triqs mesh of type MeshImFreq or MeshReFreq')
self.block_structure = BlockStructure()
# Read input from HDF:
@ -467,7 +488,7 @@ class SumkDFT(object):
return gf_rotated
def lattice_gf(self, ik, mu=None, iw_or_w="iw", beta=40, broadening=None, mesh=None, with_Sigma=True, with_dc=True):
def lattice_gf(self, ik, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True):
r"""
Calculates the lattice Green function for a given k-point from the DFT Hamiltonian and the self energy.
@ -478,19 +499,11 @@ class SumkDFT(object):
mu : real, optional
Chemical potential for which the Green's function is to be calculated.
If not provided, self.chemical_potential is used for mu.
iw_or_w : string, optional
- `iw_or_w` = 'iw' for a imaginary-frequency self-energy
- `iw_or_w` = 'w' for a real-frequency self-energy
beta : real, optional
Inverse temperature.
broadening : real, optional
Imaginary shift for the axis along which the real-axis GF is calculated.
If not provided, broadening will be set to double of the distance between mesh points in 'mesh'.
mesh : list, optional
Data defining mesh on which the real-axis GF will be calculated, given in the form
(om_min,om_max,n_points), where om_min is the minimum omega, om_max is the maximum omega and n_points is the number of points.
mesh : MeshReFreq or MeshImFreq, optional
Mesh to be used if with_Sigma=False. If with Sigma=False and mesh is none then self.mesh is used.
with_Sigma : boolean, optional
If True the GF will be calculated with the self-energy stored in self.Sigmaimp_(w/iw), for real/Matsubara GF, respectively.
In this case the mesh is taken from the self.Sigma_imp object.
@ -508,9 +521,7 @@ class SumkDFT(object):
mu = self.chemical_potential
ntoi = self.spin_names_to_ind[self.SO]
spn = self.spin_block_names[self.SO]
if (iw_or_w != "iw") and (iw_or_w != "w"):
raise ValueError("lattice_gf: Implemented only for Re/Im frequency functions.")
if not hasattr(self, "Sigma_imp_" + iw_or_w):
if not hasattr(self, "Sigma_imp"):
with_Sigma = False
if broadening is None:
if mesh is None:
@ -518,45 +529,48 @@ class SumkDFT(object):
else: # broadening = 2 * \Delta omega, where \Delta omega is the spacing of omega points
broadening = 2.0 * ((mesh[1] - mesh[0]) / (mesh[2] - 1))
# Are we including Sigma?
if with_Sigma:
Sigma_imp = getattr(self, "Sigma_imp_" + iw_or_w)
sigma_minus_dc = [s.copy() for s in Sigma_imp]
if with_dc:
sigma_minus_dc = self.add_dc(iw_or_w)
if iw_or_w == "iw":
# override beta if Sigma_iw is present
beta = Sigma_imp[0].mesh.beta
mesh = Sigma_imp[0].mesh
elif iw_or_w == "w":
mesh = Sigma_imp[0].mesh
if broadening>0 and mpi.is_master_node():
warn('lattice_gf called with Sigma and broadening > 0 (broadening = {}). You might want to explicitly set the broadening to 0.'.format(broadening))
else:
if iw_or_w == "iw":
if beta is None:
raise ValueError("lattice_gf: Give the beta for the lattice GfReFreq.")
# Default number of Matsubara frequencies
mesh = MeshImFreq(beta=beta, S='Fermion', n_max=1025)
elif iw_or_w == "w":
if mesh is None:
raise ValueError("lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq.")
mesh = MeshReFreq(mesh[0], mesh[1], mesh[2])
# Check if G_latt is present
set_up_G_latt = False # Assume not
if not hasattr(self, "G_latt_" + iw_or_w):
if not hasattr(self, "G_latt" ):
# Need to create G_latt_(i)w
set_up_G_latt = True
else: # Check that existing GF is consistent
G_latt = getattr(self, "G_latt_" + iw_or_w)
G_latt = self.G_latt
GFsize = [gf.target_shape[0] for bname, gf in G_latt]
unchangedsize = all([self.n_orbitals[ik, ntoi[spn[isp]]] == GFsize[
isp] for isp in range(self.n_spin_blocks[self.SO])])
if not unchangedsize:
if (not mesh is None) or (not unchangedsize):
set_up_G_latt = True
if (iw_or_w == "iw") and (self.G_latt_iw.mesh.beta != beta):
set_up_G_latt = True # additional check for ImFreq
# Are we including Sigma?
if with_Sigma:
Sigma_imp = self.Sigma_imp
if with_dc:
sigma_minus_dc = self.add_dc()
else:
sigma_minus_dc = [s for s in Sigma_imp]
if not mesh is None:
warn('lattice_gf called with Sigma and given mesh. Mesh will be taken from Sigma.')
if self.mesh != Sigma_imp[0].mesh:
mesh = Sigma_imp[0].mesh
if isinstance(mesh, MeshImFreq):
mesh_values = np.linspace(mesh(mesh.first_index()), mesh(mesh.last_index()), len(mesh))
else:
mesh_values = np.linspace(mesh.omega_min, mesh.omega_max, len(mesh))
else:
mesh = self.mesh
mesh_values = self.mesh_values
elif not mesh is None:
assert isinstance(mesh, MeshReFreq) or isinstance(mesh, MeshImFreq), "mesh must be a triqs MeshReFreq or MeshImFreq"
if isinstance(mesh, MeshImFreq):
mesh_values = np.linspace(mesh(mesh.first_index()), mesh(mesh.last_index()), len(mesh))
else:
mesh_values = np.linspace(mesh.omega_min, mesh.omega_max, len(mesh))
else:
mesh = self.mesh
mesh_values = self.mesh_values
# Set up G_latt
if set_up_G_latt:
@ -565,41 +579,38 @@ class SumkDFT(object):
gf_struct = [(spn[isp], block_structure[isp])
for isp in range(self.n_spin_blocks[self.SO])]
block_ind_list = [block for block, inner in gf_struct]
if iw_or_w == "iw":
if isinstance(mesh, MeshImFreq):
glist = lambda: [GfImFreq(indices=inner, mesh=mesh)
for block, inner in gf_struct]
elif iw_or_w == "w":
else:
glist = lambda: [GfReFreq(indices=inner, mesh=mesh)
for block, inner in gf_struct]
G_latt = BlockGf(name_list=block_ind_list,
block_list=glist(), make_copies=False)
G_latt.zero()
if iw_or_w == "iw":
G_latt << iOmega_n
elif iw_or_w == "w":
G_latt << Omega + 1j * broadening
idmat = [numpy.identity(
self.n_orbitals[ik, ntoi[sp]], numpy.complex_) for sp in spn]
M = copy.deepcopy(idmat)
for ibl in range(self.n_spin_blocks[self.SO]):
idmat = [np.identity(
self.n_orbitals[ik, ntoi[sp]], np.complex_) for sp in spn]
# fill Glatt
for ibl, (block, gf) in enumerate(G_latt):
ind = ntoi[spn[ibl]]
n_orb = self.n_orbitals[ik, ind]
M[ibl] = self.hopping[ik, ind, 0:n_orb, 0:n_orb] - \
(idmat[ibl] * mu) - (idmat[ibl] * self.h_field * (1 - 2 * ibl))
G_latt -= M
if isinstance(mesh, MeshImFreq):
gf.data[:, :, :] = (idmat[ibl] * (mesh_values[:, None, None] + mu + self.h_field*(1-2*ibl))
- self.hopping[ik, ind, 0:n_orb, 0:n_orb])
else:
gf.data[:, :, :] = (idmat[ibl] *
(mesh_values[:, None, None] + mu + self.h_field*(1-2*ibl) + 1j*broadening)
- self.hopping[ik, ind, 0:n_orb, 0:n_orb])
if with_Sigma:
for icrsh in range(self.n_corr_shells):
for bname, gf in G_latt:
gf -= self.upfold(ik, icrsh, bname,
sigma_minus_dc[icrsh][bname], gf)
if with_Sigma:
for icrsh in range(self.n_corr_shells):
gf -= self.upfold(ik, icrsh, block,
sigma_minus_dc[icrsh][block], gf)
G_latt.invert()
setattr(self, "G_latt_" + iw_or_w, G_latt)
self.G_latt = G_latt
return G_latt
@ -629,19 +640,19 @@ class SumkDFT(object):
assert len(Sigma_imp) == self.n_corr_shells,\
"put_Sigma: give exactly one Sigma for each corr. shell!"
if all((isinstance(gf, Gf) and isinstance(gf.mesh, MeshImFreq)) for bname, gf in Sigma_imp[0]):
if isinstance(self.mesh, MeshImFreq) and all(isinstance(gf.mesh, MeshImFreq) and isinstance(gf, Gf) and gf.mesh == self.mesh for bname, gf in Sigma_imp[0]):
# Imaginary frequency Sigma:
self.Sigma_imp_iw = [self.block_structure.create_gf(ish=icrsh, mesh=Sigma_imp[icrsh].mesh, space='sumk')
self.Sigma_imp = [self.block_structure.create_gf(ish=icrsh, mesh=Sigma_imp[icrsh].mesh, space='sumk')
for icrsh in range(self.n_corr_shells)]
SK_Sigma_imp = self.Sigma_imp_iw
elif all(isinstance(gf, Gf) and isinstance(gf.mesh, MeshReFreq) for bname, gf in Sigma_imp[0]):
SK_Sigma_imp = self.Sigma_imp
elif isinstance(self.mesh, MeshReFreq) and all(isinstance(gf, Gf) and isinstance(gf.mesh, MeshReFreq) and gf.mesh == self.mesh for bname, gf in Sigma_imp[0]):
# Real frequency Sigma:
self.Sigma_imp_w = [self.block_structure.create_gf(ish=icrsh, mesh=Sigma_imp[icrsh].mesh, gf_function=GfReFreq, space='sumk')
self.Sigma_imp = [self.block_structure.create_gf(ish=icrsh, mesh=Sigma_imp[icrsh].mesh, gf_function=GfReFreq, space='sumk')
for icrsh in range(self.n_corr_shells)]
SK_Sigma_imp = self.Sigma_imp_w
SK_Sigma_imp = self.Sigma_imp
else:
raise ValueError("put_Sigma: This type of Sigma is not handled, give either BlockGf of GfReFreq or GfImFreq.")
raise ValueError("put_Sigma: Sigma_imp must have the same mesh as SumKDFT.mesh.")
# rotation from local to global coordinate system:
for icrsh in range(self.n_corr_shells):
@ -654,13 +665,12 @@ class SumkDFT(object):
gf << Sigma_imp[icrsh][bname]
#warning if real frequency self energy is within the bounds of the band energies
if isinstance(Sigma_imp[0].mesh, MeshReFreq):
if isinstance(self.mesh, MeshReFreq):
if self.min_band_energy is None or self.max_band_energy is None:
self.calculate_min_max_band_energies()
for gf in Sigma_imp:
Sigma_mesh = numpy.array([i for i in gf.mesh.values()])
if Sigma_mesh[0] > (self.min_band_energy - self.chemical_potential) or Sigma_mesh[-1] < (self.max_band_energy - self.chemical_potential):
warn('The given Sigma is on a mesh which does not cover the band energy range. The Sigma MeshReFreq runs from %f to %f, while the band energy (minus the chemical potential) runs from %f to %f'%(Sigma_mesh[0], Sigma_mesh[-1], self.min_band_energy, self.max_band_energy))
mesh = np.array([i for i in self.mesh.values()])
if mesh[0] > (self.min_band_energy - self.chemical_potential) or mesh[-1] < (self.max_band_energy - self.chemical_potential):
warn('The given Sigma is on a mesh which does not cover the band energy range. The Sigma MeshReFreq runs from %f to %f, while the band energy (minus the chemical potential) runs from %f to %f'%(mesh[0], mesh[-1], self.min_band_energy, self.max_band_energy))
def transform_to_sumk_blocks(self, Sigma_imp, Sigma_out=None):
r""" transform Sigma from solver to sumk space
@ -703,7 +713,7 @@ class SumkDFT(object):
G_out=Sigma_out[icrsh])
return Sigma_out
def extract_G_loc(self, mu=None, iw_or_w='iw', with_Sigma=True, with_dc=True, broadening=None,
def extract_G_loc(self, mu=None, with_Sigma=True, with_dc=True, broadening=None,
transform_to_solver_blocks=True, show_warnings=True):
r"""
Extracts the local downfolded Green function by the Brillouin-zone integration of the lattice Green's function.
@ -739,14 +749,22 @@ class SumkDFT(object):
if mu is None:
mu = self.chemical_potential
if iw_or_w == "iw":
G_loc = [self.Sigma_imp_iw[icrsh].copy() for icrsh in range(
if with_Sigma:
mesh = self.Sigma_imp[0].mesh
if mesh != self.mesh:
warn('self.mesh and self.Sigma_imp[0].mesh are differen! Using mesh from Sigma')
else:
mesh = self.mesh
if isinstance(mesh, MeshImFreq):
G_loc = [self.Sigma_imp[icrsh].copy() for icrsh in range(
self.n_corr_shells)] # this list will be returned
beta = G_loc[0].mesh.beta
G_loc_inequiv = [BlockGf(name_block_generator=[(block, GfImFreq(target_shape=(block_dim, block_dim), mesh=G_loc[0].mesh)) for block, block_dim in self.gf_struct_solver[ish].items()],
make_copies=False) for ish in range(self.n_inequiv_shells)]
elif iw_or_w == "w":
G_loc = [self.Sigma_imp_w[icrsh].copy() for icrsh in range(
else:
G_loc = [self.Sigma_imp[icrsh].copy() for icrsh in range(
self.n_corr_shells)] # this list will be returned
mesh = G_loc[0].mesh
G_loc_inequiv = [BlockGf(name_block_generator=[(block, GfReFreq(target_shape=(block_dim, block_dim), mesh=mesh)) for block, block_dim in self.gf_struct_solver[ish].items()],
@ -755,24 +773,20 @@ class SumkDFT(object):
for icrsh in range(self.n_corr_shells):
G_loc[icrsh].zero() # initialize to zero
ikarray = numpy.array(list(range(self.n_k)))
ikarray = np.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
if iw_or_w == 'iw':
if isinstance(self.mesh, MeshImFreq):
G_latt = self.lattice_gf(
ik=ik, mu=mu, iw_or_w=iw_or_w, with_Sigma=with_Sigma, with_dc=with_dc, beta=beta)
elif iw_or_w == 'w':
mesh_parameters = (G_loc[0].mesh.omega_min,G_loc[0].mesh.omega_max,len(G_loc[0].mesh))
ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc)
else:
G_latt = self.lattice_gf(
ik=ik, mu=mu, iw_or_w=iw_or_w, with_Sigma=with_Sigma, with_dc=with_dc, broadening=broadening, mesh=mesh_parameters)
ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc, broadening=broadening)
G_latt *= self.bz_weights[ik]
for icrsh in range(self.n_corr_shells):
# init temporary storage
tmp = G_loc[icrsh].copy()
for bname, gf in tmp:
tmp[bname] << self.downfold(
ik, icrsh, bname, G_latt[bname], gf)
G_loc[icrsh] += tmp
for bname, gf in G_loc[icrsh]:
gf += self.downfold(ik, icrsh, bname, G_latt[bname], gf)
# Collect data from mpi
for icrsh in range(self.n_corr_shells):
@ -932,8 +946,8 @@ class SumkDFT(object):
dm = {}
for block, block_dim in self.gf_struct_solver[ish].items():
# get dm for the blocks:
dm[block] = numpy.zeros(
[block_dim, block_dim], numpy.complex_)
dm[block] = np.zeros(
[block_dim, block_dim], complex)
for ind1 in range(block_dim):
for ind2 in range(block_dim):
block_sumk, ind1_sumk = self.solver_to_sumk[
@ -994,7 +1008,7 @@ class SumkDFT(object):
gf = [g_sh.copy() for g_sh in G]
for ish in range(len(gf)):
for name, g in gf[ish]:
g << 1.0j*(g-g.conjugate().transpose())/2.0/numpy.pi
g << 1.0j*(g-g.conjugate().transpose())/2.0/np.pi
elif all(isinstance(g_sh.mesh, MeshReTime) for g_sh in G):
def get_delta_from_mesh(mesh):
w0 = None
@ -1004,15 +1018,15 @@ class SumkDFT(object):
else:
return w-w0
gf = [BlockGf(name_block_generator = [(name, GfReFreq(
window=(-numpy.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh)),
numpy.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh))),
window=(-np.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh)),
np.pi*(len(block.mesh)-1) / (len(block.mesh)*get_delta_from_mesh(block.mesh))),
n_points=len(block.mesh), indices=block.indices)) for name, block in g_sh], make_copies=False)
for g_sh in G]
for ish in range(len(gf)):
for name, g in gf[ish]:
g.set_from_fourier(G[ish][name])
g << 1.0j*(g-g.conjugate().transpose())/2.0/numpy.pi
g << 1.0j*(g-g.conjugate().transpose())/2.0/np.pi
else:
raise Exception("G must be a list of BlockGf of either GfImFreq, GfImTime, GfReFreq or GfReTime")
return gf
@ -1063,7 +1077,7 @@ class SumkDFT(object):
for ish in range(self.n_inequiv_shells)]
# the maximum value of each matrix element of each block and shell
max_gf = [{name:numpy.max(numpy.abs(g.data),0) for name, g in gf[ish]} for ish in range(self.n_inequiv_shells)]
max_gf = [{name:np.max(np.abs(g.data),0) for name, g in gf[ish]} for ish in range(self.n_inequiv_shells)]
if include_shells is None:
# include all shells
@ -1162,7 +1176,7 @@ class SumkDFT(object):
# helper function
def null(A, eps=1e-15):
""" Calculate the null-space of matrix A """
u, s, vh = numpy.linalg.svd(A)
u, s, vh = np.linalg.svd(A)
null_mask = (s <= eps)
null_space = compress(null_mask, vh, axis=0)
return null_space.conjugate().transpose()
@ -1217,9 +1231,9 @@ class SumkDFT(object):
# one block to make it equal to the other (at least
# for tau=0).
e1 = numpy.linalg.eigvalsh(gf1.data[0])
e2 = numpy.linalg.eigvalsh(gf2.data[0])
if numpy.any(abs(e1-e2) > threshold): continue
e1 = np.linalg.eigvalsh(gf1.data[0])
e2 = np.linalg.eigvalsh(gf2.data[0])
if np.any(abs(e1-e2) > threshold): continue
for conjugate in [False,True]:
if conjugate:
@ -1238,21 +1252,21 @@ class SumkDFT(object):
# product to get a linear problem, which consists
# of finding the null space of M vec T = 0.
M = numpy.kron(numpy.eye(*gf1.target_shape),gf2.data[0])-numpy.kron(gf1.data[0].transpose(),numpy.eye(*gf1.target_shape))
M = np.kron(np.eye(*gf1.target_shape),gf2.data[0])-np.kron(gf1.data[0].transpose(),np.eye(*gf1.target_shape))
N = null(M, threshold)
# now we get the intersection of the null spaces
# of all values of tau
for i in range(1,len(gf1.data)):
M = numpy.kron(numpy.eye(*gf1.target_shape),gf2.data[i])-numpy.kron(gf1.data[i].transpose(),numpy.eye(*gf1.target_shape))
M = np.kron(np.eye(*gf1.target_shape),gf2.data[i])-np.kron(gf1.data[i].transpose(),np.eye(*gf1.target_shape))
# transform M into current null space
M = numpy.dot(M, N)
N = numpy.dot(N, null(M, threshold))
if numpy.size(N) == 0:
M = np.dot(M, N)
N = np.dot(N, null(M, threshold))
if np.size(N) == 0:
break
# no intersection of the null spaces -> no symmetry
if numpy.size(N) == 0: continue
if np.size(N) == 0: continue
# reshape N: it then has the indices matrix, matrix, number of basis vectors of the null space
N = N.reshape(gf1.target_shape[0], gf1.target_shape[1], -1).transpose([1, 0, 2])
@ -1270,7 +1284,7 @@ class SumkDFT(object):
sum y[i] N[:,:,i] y[j].conjugate() N[:,:,j].conjugate().transpose() = eye.
The object N[:,:,i] N[:,:,j] is a four-index object which we call Z.
"""
Z = numpy.einsum('aci,bcj->abij', N, N.conjugate())
Z = np.einsum('aci,bcj->abij', N, N.conjugate())
"""
function chi2
@ -1280,16 +1294,16 @@ class SumkDFT(object):
"""
def chi2(y):
# reinterpret y as complex number
y = y.view(numpy.complex_)
y = y.view(np.complex_)
ret = 0.0
for a in range(Z.shape[0]):
for b in range(Z.shape[1]):
ret += numpy.abs(numpy.dot(y, numpy.dot(Z[a, b], y.conjugate()))
ret += np.abs(np.dot(y, np.dot(Z[a, b], y.conjugate()))
- (1.0 if a == b else 0.0))**2
return ret
# use the minimization routine from scipy
res = minimize(chi2, numpy.ones(2 * N.shape[-1]))
res = minimize(chi2, np.ones(2 * N.shape[-1]))
# if the minimization fails, there is probably no symmetry
if not res.success: continue
@ -1297,10 +1311,10 @@ class SumkDFT(object):
if res.fun > threshold: continue
# reinterpret the solution as a complex number
y = res.x.view(numpy.complex_)
y = res.x.view(np.complex_)
# reconstruct the T matrix
T = numpy.zeros(N.shape[:-1], dtype=numpy.complex_)
T = np.zeros(N.shape[:-1], dtype=np.complex_)
for i in range(len(y)):
T += N[:, :, i] * y[i]
@ -1338,9 +1352,9 @@ class SumkDFT(object):
# C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
if (ind1 < 0) and (ind2 >= 0):
if conjugate:
self.deg_shells[ish][ind2][block1] = numpy.dot(T.conjugate().transpose(), v2[0].conjugate()), not v2[1]
self.deg_shells[ish][ind2][block1] = np.dot(T.conjugate().transpose(), v2[0].conjugate()), not v2[1]
else:
self.deg_shells[ish][ind2][block1] = numpy.dot(T.conjugate().transpose(), v2[0]), v2[1]
self.deg_shells[ish][ind2][block1] = np.dot(T.conjugate().transpose(), v2[0]), v2[1]
# the first block is already present
# set v2 and C2 so that they are compatible with
# C(T gf1 T^dagger) = gf2
@ -1348,9 +1362,9 @@ class SumkDFT(object):
# C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
elif (ind1 >= 0) and (ind2 < 0):
if conjugate:
self.deg_shells[ish][ind1][block2] = numpy.dot(T.conjugate(), v1[0].conjugate()), not v1[1]
self.deg_shells[ish][ind1][block2] = np.dot(T.conjugate(), v1[0].conjugate()), not v1[1]
else:
self.deg_shells[ish][ind1][block2] = numpy.dot(T, v1[0]), v1[1]
self.deg_shells[ish][ind1][block2] = np.dot(T, v1[0]), v1[1]
# the blocks are not already present
# we arbitrarily choose v1=eye and C1=False and
# set v2 and C2 so that they are compatible with
@ -1359,7 +1373,7 @@ class SumkDFT(object):
# C1(v1^dagger G1 v1) = C2(v2^dagger G2 v2)
elif (ind1 < 0) and (ind2 < 0):
d = dict()
d[block1] = numpy.eye(*gf1.target_shape), False
d[block1] = np.eye(*gf1.target_shape), False
if conjugate:
d[block2] = T.conjugate(), True
else:
@ -1420,7 +1434,7 @@ class SumkDFT(object):
"calculate_diagonalization_matrix: Choices for prop_to_be_diagonal are 'eal' or 'dm'.")
return 0
trans = [{block: numpy.eye(block_dim) for block, block_dim in gfs} for gfs in self.gf_struct_sumk]
trans = [{block: np.eye(block_dim) for block, block_dim in gfs} for gfs in self.gf_struct_sumk]
for ish in shells:
trafo = {}
@ -1429,10 +1443,10 @@ class SumkDFT(object):
prop[ish] = self.block_structure.convert_matrix(prop[ish], space_from='sumk', space_to='solver')
# Get diagonalisation matrix, if not already diagonal
for name in prop[ish]:
if numpy.sum(abs(prop[ish][name]-numpy.diag(numpy.diagonal(prop[ish][name])))) > 1e-13:
trafo[name] = numpy.linalg.eigh(prop[ish][name])[1].conj().T
if np.sum(abs(prop[ish][name]-np.diag(np.diagonal(prop[ish][name])))) > 1e-13:
trafo[name] = np.linalg.eigh(prop[ish][name])[1].conj().T
else:
trafo[name] = numpy.identity(numpy.shape(prop[ish][name])[0])
trafo[name] = np.identity(np.shape(prop[ish][name])[0])
# Transform back to sumk if necessay, blocks change in this step!
if calc_in_solver_blocks:
trafo = self.block_structure.convert_matrix(trafo, space_from='solver', space_to='sumk')
@ -1446,7 +1460,7 @@ class SumkDFT(object):
return trans
def density_matrix(self, method='using_gf', beta=40.0):
def density_matrix(self, method='using_gf'):
"""Calculate density matrices in one of two ways.
Parameters
@ -1469,16 +1483,15 @@ class SumkDFT(object):
dens_mat = [{} for icrsh in range(self.n_corr_shells)]
for icrsh in range(self.n_corr_shells):
for sp in self.spin_block_names[self.corr_shells[icrsh]['SO']]:
dens_mat[icrsh][sp] = numpy.zeros(
[self.corr_shells[icrsh]['dim'], self.corr_shells[icrsh]['dim']], numpy.complex_)
dens_mat[icrsh][sp] = np.zeros(
[self.corr_shells[icrsh]['dim'], self.corr_shells[icrsh]['dim']], np.complex_)
ikarray = numpy.array(list(range(self.n_k)))
ikarray = np.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
if method == "using_gf":
G_latt_iw = self.lattice_gf(
ik=ik, mu=self.chemical_potential, iw_or_w="iw", beta=beta)
G_latt_iw = self.lattice_gf(ik=ik, mu=self.chemical_potential)
G_latt_iw *= self.bz_weights[ik]
dm = G_latt_iw.density()
MMat = [dm[sp] for sp in self.spin_block_names[self.SO]]
@ -1488,7 +1501,7 @@ class SumkDFT(object):
ntoi = self.spin_names_to_ind[self.SO]
spn = self.spin_block_names[self.SO]
dims = {sp:self.n_orbitals[ik, ntoi[sp]] for sp in spn}
MMat = [numpy.zeros([dims[sp], dims[sp]], numpy.complex_) for sp in spn]
MMat = [np.zeros([dims[sp], dims[sp]], np.complex_) for sp in spn]
for isp, sp in enumerate(spn):
ind = ntoi[sp]
@ -1511,10 +1524,10 @@ class SumkDFT(object):
n_orb = self.n_orbitals[ik, ind]
projmat = self.proj_mat[ik, ind, icrsh, 0:dim, 0:n_orb]
if method == "using_gf":
dens_mat[icrsh][sp] += numpy.dot(numpy.dot(projmat, MMat[isp]),
dens_mat[icrsh][sp] += np.dot(np.dot(projmat, MMat[isp]),
projmat.transpose().conjugate())
elif method == "using_point_integration":
dens_mat[icrsh][sp] += self.bz_weights[ik] * numpy.dot(numpy.dot(projmat, MMat[isp]),
dens_mat[icrsh][sp] += self.bz_weights[ik] * np.dot(np.dot(projmat, MMat[isp]),
projmat.transpose().conjugate())
# get data from nodes:
@ -1533,7 +1546,7 @@ class SumkDFT(object):
for sp in dens_mat[icrsh]:
if self.rot_mat_time_inv[icrsh] == 1:
dens_mat[icrsh][sp] = dens_mat[icrsh][sp].conjugate()
dens_mat[icrsh][sp] = numpy.dot(numpy.dot(self.rot_mat[icrsh].conjugate().transpose(), dens_mat[icrsh][sp]),
dens_mat[icrsh][sp] = np.dot(np.dot(self.rot_mat[icrsh].conjugate().transpose(), dens_mat[icrsh][sp]),
self.rot_mat[icrsh])
return dens_mat
@ -1568,8 +1581,8 @@ class SumkDFT(object):
eff_atlevels = [{} for ish in range(self.n_inequiv_shells)]
for ish in range(self.n_inequiv_shells):
for sp in self.spin_block_names[self.corr_shells[self.inequiv_to_corr[ish]]['SO']]:
eff_atlevels[ish][sp] = numpy.identity(
self.corr_shells[self.inequiv_to_corr[ish]]['dim'], numpy.complex_)
eff_atlevels[ish][sp] = np.identity(
self.corr_shells[self.inequiv_to_corr[ish]]['dim'], np.complex_)
eff_atlevels[ish][sp] *= -self.chemical_potential
eff_atlevels[ish][
sp] -= self.dc_imp[self.inequiv_to_corr[ish]][sp]
@ -1582,18 +1595,18 @@ class SumkDFT(object):
for icrsh in range(self.n_corr_shells):
dim = self.corr_shells[icrsh]['dim']
for sp in self.spin_block_names[self.corr_shells[icrsh]['SO']]:
self.Hsumk[icrsh][sp] = numpy.zeros(
[dim, dim], numpy.complex_)
self.Hsumk[icrsh][sp] = np.zeros(
[dim, dim], np.complex_)
for isp, sp in enumerate(self.spin_block_names[self.corr_shells[icrsh]['SO']]):
ind = self.spin_names_to_ind[
self.corr_shells[icrsh]['SO']][sp]
for ik in range(self.n_k):
n_orb = self.n_orbitals[ik, ind]
MMat = numpy.identity(n_orb, numpy.complex_)
MMat = np.identity(n_orb, np.complex_)
MMat = self.hopping[
ik, ind, 0:n_orb, 0:n_orb] - (1 - 2 * isp) * self.h_field * MMat
projmat = self.proj_mat[ik, ind, icrsh, 0:dim, 0:n_orb]
self.Hsumk[icrsh][sp] += self.bz_weights[ik] * numpy.dot(numpy.dot(projmat, MMat),
self.Hsumk[icrsh][sp] += self.bz_weights[ik] * np.dot(np.dot(projmat, MMat),
projmat.conjugate().transpose())
# symmetrisation:
if self.symm_op != 0:
@ -1606,7 +1619,7 @@ class SumkDFT(object):
if self.rot_mat_time_inv[icrsh] == 1:
self.Hsumk[icrsh][sp] = self.Hsumk[
icrsh][sp].conjugate()
self.Hsumk[icrsh][sp] = numpy.dot(numpy.dot(self.rot_mat[icrsh].conjugate().transpose(), self.Hsumk[icrsh][sp]),
self.Hsumk[icrsh][sp] = np.dot(np.dot(self.rot_mat[icrsh].conjugate().transpose(), self.Hsumk[icrsh][sp]),
self.rot_mat[icrsh])
# add to matrix:
@ -1631,7 +1644,7 @@ class SumkDFT(object):
dim = self.corr_shells[icrsh]['dim']
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
for sp in spn:
self.dc_imp[icrsh][sp] = numpy.zeros([dim, dim], numpy.float_)
self.dc_imp[icrsh][sp] = np.zeros([dim, dim], np.float_)
self.dc_energ = [0.0 for icrsh in range(self.n_corr_shells)]
def set_dc(self, dc_imp, dc_energ):
@ -1709,7 +1722,7 @@ class SumkDFT(object):
Ncr[bl] += dens_mat[block].real.trace()
Ncrtot = sum(Ncr.values())
for sp in spn:
self.dc_imp[icrsh][sp] = numpy.identity(dim, numpy.float_)
self.dc_imp[icrsh][sp] = np.identity(dim, np.float_)
if self.SP == 0: # average the densities if there is no SP:
Ncr[sp] = Ncrtot / len(spn)
# correction for SO: we have only one block in this case, but
@ -1774,10 +1787,10 @@ class SumkDFT(object):
if transform:
for sp in spn:
T = self.block_structure.effective_transformation_sumk[icrsh][sp]
self.dc_imp[icrsh][sp] = numpy.dot(T.conjugate().transpose(),
numpy.dot(self.dc_imp[icrsh][sp], T))
self.dc_imp[icrsh][sp] = np.dot(T.conjugate().transpose(),
np.dot(self.dc_imp[icrsh][sp], T))
def add_dc(self, iw_or_w="iw"):
def add_dc(self):
r"""
Subtracts the double counting term from the impurity self energy.
@ -1796,18 +1809,15 @@ class SumkDFT(object):
"""
# Be careful: Sigma_imp is already in the global coordinate system!!
sigma_minus_dc = [s.copy()
for s in getattr(self, "Sigma_imp_" + iw_or_w)]
sigma_minus_dc = [s.copy() for s in self.Sigma_imp]
for icrsh in range(self.n_corr_shells):
for bname, gf in sigma_minus_dc[icrsh]:
# Transform dc_imp to global coordinate system
if self.use_rotations:
dccont = numpy.dot(self.rot_mat[icrsh], numpy.dot(self.dc_imp[icrsh][
bname], self.rot_mat[icrsh].conjugate().transpose()))
gf -= np.dot(self.rot_mat[icrsh], np.dot(self.dc_imp[icrsh][
bname], self.rot_mat[icrsh].conjugate().transpose()))
else:
dccont = self.dc_imp[icrsh][bname]
sigma_minus_dc[icrsh][bname] -= dccont
gf -= self.dc_imp[icrsh][bname]
return sigma_minus_dc
@ -1848,7 +1858,7 @@ class SumkDFT(object):
v, C = degsh[key]
else:
# for backward compatibility, allow degsh to be a list
v = numpy.eye(*ss.target_shape)
v = np.eye(*ss.target_shape)
C = False
# the helper is in the basis where the blocks are all equal
helper.from_L_G_R(v.conjugate().transpose(), gf_to_symm[key], v)
@ -1862,14 +1872,14 @@ class SumkDFT(object):
v, C = degsh[key]
else:
# for backward compatibility, allow degsh to be a list
v = numpy.eye(*ss.target_shape)
v = np.eye(*ss.target_shape)
C = False
if C:
gf_to_symm[key].from_L_G_R(v, ss.transpose().copy(), v.conjugate().transpose())
else:
gf_to_symm[key].from_L_G_R(v, ss, v.conjugate().transpose())
def total_density(self, mu=None, iw_or_w="iw", with_Sigma=True, with_dc=True, broadening=None):
def total_density(self, mu=None, with_Sigma=True, with_dc=True, broadening=None):
r"""
Calculates the total charge within the energy window for a given chemical potential.
The chemical potential is either given by parameter `mu` or, if it is not specified,
@ -1919,10 +1929,10 @@ class SumkDFT(object):
if mu is None:
mu = self.chemical_potential
dens = 0.0
ikarray = numpy.array(list(range(self.n_k)))
ikarray = np.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
G_latt = self.lattice_gf(
ik=ik, mu=mu, iw_or_w=iw_or_w, with_Sigma=with_Sigma, with_dc=with_dc, broadening=broadening)
ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc, broadening=broadening)
dens += self.bz_weights[ik] * G_latt.total_density()
# collect data from mpi:
dens = mpi.all_reduce(mpi.world, dens, lambda x, y: x + y)
@ -2050,16 +2060,16 @@ class SumkDFT(object):
# Convert Fermi weights to a density matrix
dens_mat_dft = {}
for sp in spn:
dens_mat_dft[sp] = [fermi_weights[ik, ntoi[sp], :].astype(numpy.complex_) for ik in range(self.n_k)]
dens_mat_dft[sp] = [fermi_weights[ik, ntoi[sp], :].astype(np.complex_) for ik in range(self.n_k)]
# Set up deltaN:
deltaN = {}
for sp in spn:
deltaN[sp] = [numpy.zeros([self.n_orbitals[ik, ntoi[sp]], self.n_orbitals[
ik, ntoi[sp]]], numpy.complex_) for ik in range(self.n_k)]
deltaN[sp] = [np.zeros([self.n_orbitals[ik, ntoi[sp]], self.n_orbitals[
ik, ntoi[sp]]], np.complex_) for ik in range(self.n_k)]
ikarray = numpy.arange(self.n_k)
ikarray = np.arange(self.n_k)
for ik in mpi.slice_array(ikarray):
G_latt_iw = self.lattice_gf(
ik=ik, mu=self.chemical_potential, iw_or_w="iw")
@ -2079,11 +2089,11 @@ class SumkDFT(object):
if dm_type in ['vasp','qe']:
# In 'vasp'-mode subtract the DFT density matrix
nb = self.n_orbitals[ik, ntoi[bname]]
diag_inds = numpy.diag_indices(nb)
diag_inds = np.diag_indices(nb)
deltaN[bname][ik][diag_inds] -= dens_mat_dft[bname][ik][:nb]
if self.charge_mixing and self.deltaNOld is not None:
G2 = numpy.sum(self.kpts_cart[ik,:]**2)
G2 = np.sum(self.kpts_cart[ik,:]**2)
# Kerker mixing
mix_fac = self.charge_mixing_alpha * G2 / (G2 + self.charge_mixing_gamma**2)
deltaN[bname][ik][diag_inds] = (1.0 - mix_fac) * self.deltaNOld[bname][ik][diag_inds] + mix_fac * deltaN[bname][ik][diag_inds]
@ -2092,7 +2102,7 @@ class SumkDFT(object):
b1, b2 = band_window[isp][ik, :2]
nb = b2 - b1 + 1
assert nb == self.n_orbitals[ik, ntoi[bname]], "Number of bands is inconsistent at ik = %s"%(ik)
band_en_correction += numpy.dot(deltaN[bname][ik], self.hopping[ik, isp, :nb, :nb]).trace().real * self.bz_weights[ik]
band_en_correction += np.dot(deltaN[bname][ik], self.hopping[ik, isp, :nb, :nb]).trace().real * self.bz_weights[ik]
# mpi reduce:
for bname in deltaN:
@ -2161,9 +2171,9 @@ class SumkDFT(object):
fout.close()
elif dm_type == 'vasp':
if kpts_to_write is None:
kpts_to_write = numpy.arange(self.n_k)
kpts_to_write = np.arange(self.n_k)
else:
assert numpy.min(kpts_to_write) >= 0 and numpy.max(kpts_to_write) < self.n_k
assert np.min(kpts_to_write) >= 0 and np.max(kpts_to_write) < self.n_k
assert self.SP == 0, "Spin-polarized density matrix is not implemented"
@ -2192,7 +2202,7 @@ class SumkDFT(object):
with open(filename, 'w') as f:
# determine the number of spin blocks
n_spin_blocks = self.SP + 1 - self.SO
nbmax = numpy.max(self.n_orbitals)
nbmax = np.max(self.n_orbitals)
# output beta and mu in Hartrees
beta = G_latt_iw.mesh.beta * self.energy_unit
mu = self.chemical_potential/self.energy_unit
@ -2227,7 +2237,7 @@ class SumkDFT(object):
assert self.SP == 0, "Spin-polarized density matrix is not implemented"
subgrp = 'dft_update'
delta_N = numpy.zeros([self.n_k, max(self.n_orbitals[:,0]), max(self.n_orbitals[:,0])], dtype=complex)
delta_N = np.zeros([self.n_k, max(self.n_orbitals[:,0]), max(self.n_orbitals[:,0])], dtype=complex)
mpi.report(" %i -1 ! Number of k-points, default number of bands\n"%(self.n_k))
for ik in range(self.n_k):
ib1 = band_window[0][ik, 0]
@ -2259,10 +2269,10 @@ class SumkDFT(object):
def calculate_min_max_band_energies(self):
hop = self.hopping
diag_hop = numpy.zeros(hop.shape[:-1])
diag_hop = np.zeros(hop.shape[:-1])
hop_slice = mpi.slice_array(hop)
diag_hop_slice = mpi.slice_array(diag_hop)
diag_hop_slice[:] = numpy.linalg.eigvalsh(hop_slice)
diag_hop_slice[:] = np.linalg.eigvalsh(hop_slice)
diag_hop = mpi.all_reduce(mpi.world, diag_hop, lambda x, y: x + y)
min_band_energy = diag_hop.min().real
max_band_energy = diag_hop.max().real
@ -2301,7 +2311,7 @@ class SumkDFT(object):
def check_projectors(self):
"""Calculated the density matrix from projectors (DM = P Pdagger) to check that it is correct and
specifically that it matches DFT."""
dens_mat = [numpy.zeros([self.corr_shells[icrsh]['dim'], self.corr_shells[icrsh]['dim']], numpy.complex_)
dens_mat = [np.zeros([self.corr_shells[icrsh]['dim'], self.corr_shells[icrsh]['dim']], np.complex_)
for icrsh in range(self.n_corr_shells)]
for ik in range(self.n_k):
@ -2310,7 +2320,7 @@ class SumkDFT(object):
n_orb = self.n_orbitals[ik, 0]
projmat = self.proj_mat[ik, 0, icrsh, 0:dim, 0:n_orb]
dens_mat[icrsh][
:, :] += numpy.dot(projmat, projmat.transpose().conjugate()) * self.bz_weights[ik]
:, :] += np.dot(projmat, projmat.transpose().conjugate()) * self.bz_weights[ik]
if self.symm_op != 0:
dens_mat = self.symmcorr.symmetrize(dens_mat)
@ -2320,7 +2330,7 @@ class SumkDFT(object):
for icrsh in range(self.n_corr_shells):
if self.rot_mat_time_inv[icrsh] == 1:
dens_mat[icrsh] = dens_mat[icrsh].conjugate()
dens_mat[icrsh] = numpy.dot(numpy.dot(self.rot_mat[icrsh].conjugate().transpose(), dens_mat[icrsh]),
dens_mat[icrsh] = np.dot(np.dot(self.rot_mat[icrsh].conjugate().transpose(), dens_mat[icrsh]),
self.rot_mat[icrsh])
return dens_mat

109
python/triqs_dft_tools/sumk_dft_tools.py
View File

@ -41,17 +41,17 @@ class SumkDFTTools(SumkDFT):
Extends the SumkDFT class with some tools for analysing the data.
"""
def __init__(self, hdf_file, h_field=0.0, use_dft_blocks=False, dft_data='dft_input', symmcorr_data='dft_symmcorr_input',
def __init__(self, hdf_file, h_field=0.0, mesh=None, beta=40, n_iw=1025, use_dft_blocks=False, dft_data='dft_input', symmcorr_data='dft_symmcorr_input',
parproj_data='dft_parproj_input', symmpar_data='dft_symmpar_input', bands_data='dft_bands_input',
transp_data='dft_transp_input', misc_data='dft_misc_input'):
"""
Initialisation of the class. Parameters are exactly as for SumKDFT.
"""
SumkDFT.__init__(self, hdf_file=hdf_file, h_field=h_field, use_dft_blocks=use_dft_blocks,
dft_data=dft_data, symmcorr_data=symmcorr_data, parproj_data=parproj_data,
symmpar_data=symmpar_data, bands_data=bands_data, transp_data=transp_data,
misc_data=misc_data)
SumkDFT.__init__(self, hdf_file=hdf_file, h_field=h_field, mesh=mesh, beta=beta, n_iw=n_iw,
use_dft_blocks=use_dft_blocks, dft_data=dft_data, symmcorr_data=symmcorr_data,
parproj_data=parproj_data, symmpar_data=symmpar_data, bands_data=bands_data,
transp_data=transp_data, misc_data=misc_data)
# Uses .data of only GfReFreq objects.
def dos_wannier_basis(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, save_to_file=True):
@ -82,10 +82,9 @@ class SumkDFTTools(SumkDFT):
DOSproj_orb : Dict of numpy arrays
DOS projected to atoms and resolved into orbital contributions.
"""
if (mesh is None) and (not with_Sigma):
raise ValueError("lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq.")
if mesh is None:
om_mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
if mesh is None or with_Sigma:
assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
om_mesh = [x.real for x in self.mesh]
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
@ -119,7 +118,7 @@ class SumkDFTTools(SumkDFT):
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
# Non-projected DOS
@ -218,10 +217,9 @@ class SumkDFTTools(SumkDFT):
DOSproj_orb : Dict of numpy arrays
DOS projected to atoms and resolved into orbital contributions.
"""
if (mesh is None) and (not with_Sigma):
raise ValueError("lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq.")
if mesh is None:
om_mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
if mesh is None or with_Sigma:
assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
om_mesh = [x.real for x in self.mesh]
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
@ -255,7 +253,7 @@ class SumkDFTTools(SumkDFT):
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
# Non-projected DOS
@ -350,10 +348,9 @@ class SumkDFTTools(SumkDFT):
if self.symm_op:
self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
if (mesh is None) and (not with_Sigma):
raise ValueError("lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq.")
if mesh is None:
om_mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
if mesh is None or with_Sigma:
assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
om_mesh = [x.real for x in self.mesh]
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
@ -389,7 +386,7 @@ class SumkDFTTools(SumkDFT):
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
# Non-projected DOS
@ -502,10 +499,9 @@ class SumkDFTTools(SumkDFT):
if not value_read:
return value_read
if (mesh is None) and (not with_Sigma):
raise ValueError("lattice_gf: Give the mesh=(om_min,om_max,n_points) for the lattice GfReFreq.")
if mesh is None:
om_mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
if mesh is None or with_Sigma:
assert isinstance(self.mesh, MeshReFreq), "mesh must be given if self.mesh is a MeshImFreq"
om_mesh = [x.real for x in self.mesh]
om_min = om_mesh[0]
om_max = om_mesh[-1]
n_om = len(om_mesh)
@ -532,7 +528,7 @@ class SumkDFTTools(SumkDFT):
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_w *= self.bz_weights[ik]
if(nk!=None):
for iom in range(n_om):
@ -667,8 +663,9 @@ class SumkDFTTools(SumkDFT):
if not value_read:
return value_read
if with_Sigma is True:
om_mesh = [x.real for x in self.Sigma_imp_w[0].mesh]
if with_Sigma is True or mesh is None:
assert isinstance(self.mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True or mesh is not given"
om_mesh = [x.real for x in self.mesh]
#for Fermi Surface calculations
if FS:
jw=[i for i in range(len(om_mesh)) if om_mesh[i] == 0.0]
@ -690,17 +687,6 @@ class SumkDFTTools(SumkDFT):
mesh = (om_min, om_max, n_om)
if broadening is None:
broadening=0.0
elif mesh is None:
#default is to set "mesh" to be just for the Fermi surface - omega=0.0
om_min = 0.000
om_max = 0.001
n_om = 3
mesh = (om_min, om_max, n_om)
om_mesh = numpy.linspace(om_min, om_max, n_om)
if broadening is None:
broadening=0.01
FS=True
jw=[i for i in range(len(om_mesh)) if((om_mesh[i]<=om_max)and(om_mesh[i]>=om_min))]
else:
#a range of frequencies can be used if desired
om_min, om_max, n_om = mesh
@ -732,7 +718,7 @@ class SumkDFTTools(SumkDFT):
vkc[ik,:] = numpy.matmul(self.bmat,self.vkl[ik,:])
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
ik=ik, mu=mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma, with_dc=with_dc)
for iom in range(n_om):
for bname, gf in G_latt_w:
@ -836,8 +822,9 @@ class SumkDFTTools(SumkDFT):
Data as it is also written to the files.
"""
assert hasattr(
self, "Sigma_imp_w"), "spaghettis: Set Sigma_imp_w first."
# check if ReFreqMesh is given
assert isinstance(self.mesh, MeshReFreq)
things_to_read = ['n_k', 'n_orbitals', 'proj_mat',
'hopping', 'n_parproj', 'proj_mat_all']
value_read = self.read_input_from_hdf(
@ -854,7 +841,8 @@ class SumkDFTTools(SumkDFT):
if mu is None:
mu = self.chemical_potential
spn = self.spin_block_names[self.SO]
mesh = numpy.array([x.real for x in self.Sigma_imp_w[0].mesh])
mesh = numpy.array([x.value for x in self.mesh])
n_om = len(mesh)
if plot_range is None:
om_minplot = mesh[0] - 0.001
@ -871,18 +859,17 @@ class SumkDFTTools(SumkDFT):
Akw = {sp: numpy.zeros(
[self.shells[ishell]['dim'], self.n_k, n_om], numpy.float_) for sp in spn}
if not ishell is None:
if ishell is not None:
gf_struct_parproj = [
(sp, self.shells[ishell]['dim']) for sp in spn]
G_loc = BlockGf(name_block_generator=[(block, GfReFreq(target_shape=(block_dim, block_dim), mesh=self.Sigma_imp_w[0].mesh))
G_loc = BlockGf(name_block_generator=[(block, GfReFreq(target_shape=(block_dim, block_dim), mesh=self.Sigma_imp[0].mesh))
for block, block_dim in gf_struct_parproj], make_copies=False)
G_loc.zero()
ikarray = numpy.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="w", broadening=broadening)
G_latt_w = self.lattice_gf(ik=ik, mu=mu, broadening=broadening)
if ishell is None:
# Non-projected A(k,w)
@ -953,7 +940,7 @@ class SumkDFTTools(SumkDFT):
return Akw
def partial_charges(self, beta=40, mu=None, with_Sigma=True, with_dc=True):
def partial_charges(self, mu=None, with_Sigma=True, with_dc=True):
"""
Calculates the orbitally-resolved density matrix for all the orbitals considered in the input, consistent with
the definition of Wien2k. Hence, (possibly non-orthonormal) projectors have to be provided in the partial projectors subgroup of
@ -964,8 +951,6 @@ class SumkDFTTools(SumkDFT):
with_Sigma : boolean, optional
If True, the self energy is used for the calculation. If false, partial charges are calculated without self-energy correction.
beta : double, optional
In case the self-energy correction is not used, the inverse temperature where the calculation should be done has to be given here.
mu : double, optional
Chemical potential, overrides the one stored in the hdf5 archive.
with_dc : boolean, optional
@ -995,23 +980,16 @@ class SumkDFTTools(SumkDFT):
# Set up G_loc
gf_struct_parproj = [[(sp, self.shells[ish]['dim']) for sp in spn]
for ish in range(self.n_shells)]
if with_Sigma:
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(target_shape=(block_dim, block_dim), mesh=self.Sigma_imp_iw[0].mesh))
for block, block_dim in gf_struct_parproj[ish]], make_copies=False)
for ish in range(self.n_shells)]
beta = self.Sigma_imp_iw[0].mesh.beta
else:
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(target_shape=(block_dim, block_dim), beta=beta))
for block, block_dim in gf_struct_parproj[ish]], make_copies=False)
for ish in range(self.n_shells)]
G_loc = [BlockGf(name_block_generator=[(block, GfImFreq(target_shape=(block_dim, block_dim), mesh=self.mesh))
for block, block_dim in gf_struct_parproj[ish]], make_copies=False)
for ish in range(self.n_shells)]
for ish in range(self.n_shells):
G_loc[ish].zero()
ikarray = numpy.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
G_latt_iw = self.lattice_gf(
ik=ik, mu=mu, iw_or_w="iw", beta=beta, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_iw = self.lattice_gf(ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc)
G_latt_iw *= self.bz_weights[ik]
for ish in range(self.n_shells):
tmp = G_loc[ish].copy()
@ -1207,7 +1185,7 @@ class SumkDFTTools(SumkDFT):
# Define mesh for Green's function and in the specified energy window
if (with_Sigma == True):
self.omega = numpy.array([round(x.real, 12)
for x in self.Sigma_imp_w[0].mesh])
for x in self.mesh])
mesh = None
mu = self.chemical_potential
n_om = len(self.omega)
@ -1225,13 +1203,13 @@ class SumkDFTTools(SumkDFT):
# In the future there should be an option in gf to manipulate the mesh (e.g. truncate) directly.
# For now we stick with this:
for icrsh in range(self.n_corr_shells):
Sigma_save = self.Sigma_imp_w[icrsh].copy()
Sigma_save = self.Sigma_imp[icrsh].copy()
spn = self.spin_block_names[self.corr_shells[icrsh]['SO']]
glist = lambda: [GfReFreq(target_shape=(block_dim, block_dim), window=(self.omega[
0], self.omega[-1]), n_points=n_om) for block, block_dim in self.gf_struct_sumk[icrsh]]
self.Sigma_imp_w[icrsh] = BlockGf(
self.Sigma_imp[icrsh] = BlockGf(
name_list=spn, block_list=glist(), make_copies=False)
for i, g in self.Sigma_imp_w[icrsh]:
for i, g in self.Sigma_imp[icrsh]:
for iL in g.indices[0]:
for iR in g.indices[0]:
for iom in range(n_om):
@ -1267,8 +1245,7 @@ class SumkDFTTools(SumkDFT):
ikarray = numpy.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray):
# Calculate G_w for ik and initialize A_kw
G_w = self.lattice_gf(ik, mu, iw_or_w="w", beta=beta,
broadening=broadening, mesh=mesh, with_Sigma=with_Sigma)
G_w = self.lattice_gf(ik, mu, broadening=broadening, mesh=mesh, with_Sigma=with_Sigma)
A_kw = [numpy.zeros((self.n_orbitals[ik][isp], self.n_orbitals[ik][isp], n_om), dtype=numpy.complex_)
for isp in range(n_inequiv_spin_blocks)]

BIN
test/python/SrVO3_Sigma_transport.h5 Normal file
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Binary file not shown.

2
test/python/sigma_from_file.py
View File

@ -40,7 +40,7 @@ for name, s in Sigma_hdf:
np.savetxt('Sigma_' + name + '.dat', mesh_a_data)
# Read self energy from txt files
SK = SumkDFTTools(hdf_file = 'SrVO3.ref.h5', use_dft_blocks = True)
SK = SumkDFTTools(hdf_file='SrVO3.ref.h5', mesh=Sigma_hdf.mesh, use_dft_blocks=True)
# the order in the orig SrVO3 file is not assured, hence order it here
a_list = sorted([a for a,al in SK.gf_struct_solver[0].items()])

24
test/python/srvo3_spectral.py
View File

@ -1,20 +1,16 @@
from triqs_dft_tools.sumk_dft_tools import *
from triqs.utility.h5diff import h5diff
from triqs.utility.h5diff import h5diff
from h5 import HDFArchive
beta = 40
SK = SumkDFTTools(hdf_file='SrVO3_spectral.h5', use_dft_blocks=True)
if mpi.is_master_node():
with HDFArchive('SrVO3_Sigma.h5', 'a') as ar:
with HDFArchive('SrVO3_Sigma.h5', 'r') as ar:
Sigma = ar['dmft_transp_input']['Sigma_w']
SK.chemical_potential = ar['dmft_transp_input']['chemical_potential']
SK.dc_imp = ar['dmft_transp_input']['dc_imp']
chemical_potential = ar['dmft_transp_input']['chemical_potential']
dc_imp = ar['dmft_transp_input']['dc_imp']
Sigma = mpi.bcast(Sigma)
SK.chemical_potential = mpi.bcast(SK.chemical_potential)
SK.dc_imp = mpi.bcast(SK.dc_imp)
SK = SumkDFTTools(hdf_file='SrVO3_spectral.h5', use_dft_blocks=True, mesh = Sigma.mesh)
SK.chemical_potential = chemical_potential
SK.dc_imp = dc_imp
SK.set_Sigma([Sigma])
dos_wannier = SK.dos_wannier_basis(broadening=0.01, with_Sigma=True, with_dc=True, save_to_file=False)
@ -24,12 +20,12 @@ spaghetti = SK.spaghettis(broadening=0.01, plot_shift=0.0, plot_range=(-1,1), is
if mpi.is_master_node():
# with HDFArchive('srvo3_spectral.ref.h5', 'a') as ar:
# ar['dos_wannier'] = dos_wannier
# ar['dos_wannier'] = dos_wannier
# ar['dos_parproj'] = dos_parproj
# ar['spaghetti'] = spaghetti
with HDFArchive('srvo3_spectral.out.h5', 'a') as ar:
ar['dos_wannier'] = dos_wannier
ar['dos_wannier'] = dos_wannier
ar['dos_parproj'] = dos_parproj
ar['spaghetti'] = spaghetti

10
test/python/srvo3_transp.py
View File

@ -20,11 +20,12 @@
################################################################################
from numpy import *
from h5 import HDFArchive
from triqs_dft_tools.converters.wien2k import *
from triqs_dft_tools.sumk_dft import *
from triqs_dft_tools.sumk_dft_tools import *
from triqs.utility.comparison_tests import *
from triqs.utility.h5diff import h5diff
from triqs.utility.h5diff import h5diff
beta = 40
@ -32,10 +33,9 @@ Converter = Wien2kConverter(filename='SrVO3', repacking=True)
Converter.convert_dft_input()
Converter.convert_transport_input()
SK = SumkDFTTools(hdf_file='SrVO3.ref.h5', use_dft_blocks=True)
with HDFArchive('SrVO3_Sigma.h5', 'a') as ar:
with HDFArchive('SrVO3_Sigma_transport.h5', 'a') as ar:
Sigma = ar['dmft_transp_input']['Sigma_w']
SK = SumkDFTTools(hdf_file='SrVO3.ref.h5', mesh=Sigma.mesh, use_dft_blocks=True)
SK.set_Sigma([Sigma])
SK.chemical_potential = ar['dmft_transp_input']['chemical_potential']
SK.dc_imp = ar['dmft_transp_input']['dc_imp']
@ -48,4 +48,4 @@ SK.hdf_file = 'srvo3_transp.out.h5'
SK.save(['seebeck','optic_cond','kappa'])
if mpi.is_master_node():
h5diff("srvo3_transp.out.h5","srvo3_transp.ref.h5")
h5diff("srvo3_transp.out.h5","srvo3_transp.ref.h5")

4
test/python/sumkdft_basic.py
View File

@ -28,8 +28,8 @@ from triqs.utility.h5diff import h5diff
SK = SumkDFTTools(hdf_file = 'SrVO3.ref.h5')
dm = SK.density_matrix(method = 'using_gf', beta = 40)
dm_pc = SK.partial_charges(beta=40,with_Sigma=False,with_dc=False)
dm = SK.density_matrix(method = 'using_gf')
dm_pc = SK.partial_charges(with_Sigma=False, with_dc=False)
with HDFArchive('sumkdft_basic.out.h5','w') as ar:
ar['dm'] = dm