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[style] format and doc strings

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Alexander Hampel 2023-06-07 09:53:19 -04:00
parent 6df646ea0b
commit 5ae4949313
1 changed files with 155 additions and 147 deletions
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python/triqs_dft_tools/sumk_dft_tools.py
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@ -53,12 +53,11 @@ class SumkDFTTools(SumkDFT):
parproj_data=parproj_data, symmpar_data=symmpar_data, bands_data=bands_data, parproj_data=parproj_data, symmpar_data=symmpar_data, bands_data=bands_data,
transp_data=transp_data, misc_data=misc_data, cont_data=cont_data) transp_data=transp_data, misc_data=misc_data, cont_data=cont_data)
# Uses .data of only GfReFreq objects.
# Uses .data of only GfReFreq objects.
def density_of_states(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, proj_type=None, dosocc=False, save_to_file=True): def density_of_states(self, mu=None, broadening=None, mesh=None, with_Sigma=True, with_dc=True, proj_type=None, dosocc=False, save_to_file=True):
""" """
Calculates the density of states. The basis of the projected density of states is Calculates the density of states and the projected density of states.
specified by proj_type. The basis of the projected density of states is specified by proj_type.
Parameters Parameters
---------- ----------
mu : double, optional mu : double, optional
@ -96,51 +95,53 @@ class SumkDFTTools(SumkDFT):
DOS projected to atoms and resolved into orbital contributions. DOS projected to atoms and resolved into orbital contributions.
Empty if proj_type = None Empty if proj_type = None
""" """
if(proj_type!=None): if (proj_type != None):
#assert proj_type in ('wann', 'vasp','wien2k','elk'), "'proj_type' must be either 'wann', 'vasp', 'wien2k', or 'elk'" # assert proj_type in ('wann', 'vasp','wien2k','elk'), "'proj_type' must be either 'wann', 'vasp', 'wien2k', or 'elk'"
assert proj_type in ('wann', 'vasp','wien2k',), "'proj_type' must be either 'wann', 'vasp', 'wien2k'" assert proj_type in ('wann', 'vasp', 'wien2k',
if(proj_type!='wann'): ), "'proj_type' must be either 'wann', 'vasp', 'wien2k'"
assert proj_type==self.dft_code, "proj_type must be from the corresponding dft inputs." if (proj_type != 'wann'):
assert proj_type == self.dft_code, "proj_type must be from the corresponding dft inputs."
if (with_Sigma): if (with_Sigma):
assert isinstance(self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True" assert isinstance(
mesh=self.Sigma_imp[0].mesh self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True"
mesh = self.Sigma_imp[0].mesh
elif mesh is not None: elif mesh is not None:
assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq" assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq"
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
elif self.mesh is not None: elif self.mesh is not None:
assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq" assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq"
mesh=self.mesh mesh = self.mesh
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
else: else:
assert 0, "ReFreqMesh input required for calculations without real frequency self-energy" assert 0, "ReFreqMesh input required for calculations without real frequency self-energy"
mesh_val = numpy.linspace(mesh.w_min,mesh.w_max,len(mesh)) mesh_val = numpy.linspace(mesh.w_min, mesh.w_max, len(mesh))
n_om = len(mesh) n_om = len(mesh)
om_minplot = mesh_val[0] - 0.001 om_minplot = mesh_val[0] - 0.001
om_maxplot = mesh_val[-1] + 0.001 om_maxplot = mesh_val[-1] + 0.001
#Read in occupations from HDF5 file if required # Read in occupations from HDF5 file if required
if(dosocc): if (dosocc):
mpi.report('Reading occupations generated by self.occupations().') mpi.report('Reading occupations generated by self.occupations().')
thingstoread = ['occik'] thingstoread = ['occik']
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.misc_data, things_to_read=thingstoread) subgrp=self.misc_data, things_to_read=thingstoread)
if len(values_not_read) > 0 and mpi.is_master_node: if len(values_not_read) > 0 and mpi.is_master_node:
raise ValueError( raise ValueError(
'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read) 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
#initialise projected DOS type if required # initialise projected DOS type if required
spn = self.spin_block_names[self.SO] spn = self.spin_block_names[self.SO]
n_shells=1 n_shells = 1
if (proj_type == 'wann'): if (proj_type == 'wann'):
n_shells = self.n_corr_shells n_shells = self.n_corr_shells
gf_struct = self.gf_struct_sumk.copy() gf_struct = self.gf_struct_sumk.copy()
dims = [self.corr_shells[ish]['dim'] for ish in range(n_shells)] dims = [self.corr_shells[ish]['dim'] for ish in range(n_shells)]
shells_type = 'corr' shells_type = 'corr'
elif (proj_type == 'vasp'): elif (proj_type == 'vasp'):
n_shells=1 n_shells = 1
gf_struct = [[(sp, list(range(self.proj_mat_csc.shape[2]))) for sp in spn]] gf_struct = [[(sp, list(range(self.proj_mat_csc.shape[2]))) for sp in spn]]
dims = [self.proj_mat_csc.shape[2]] dims = [self.proj_mat_csc.shape[2]]
shells_type = 'csc' shells_type = 'csc'
@ -148,10 +149,10 @@ class SumkDFTTools(SumkDFT):
self.load_parproj() self.load_parproj()
n_shells = self.n_shells n_shells = self.n_shells
gf_struct = [[(sp, self.shells[ish]['dim']) for sp in spn] gf_struct = [[(sp, self.shells[ish]['dim']) for sp in spn]
for ish in range(n_shells)] for ish in range(n_shells)]
dims = [self.shells[ish]['dim'] for ish in range(n_shells)] dims = [self.shells[ish]['dim'] for ish in range(n_shells)]
shells_type = 'all' shells_type = 'all'
# #commented out for now - unsure this produces DFT+DMFT PDOS # #commented out for now - unsure this produces DFT+DMFT PDOS
# elif (proj_type == 'elk'): # elif (proj_type == 'elk'):
# n_shells = self.n_shells # n_shells = self.n_shells
# dims = [self.shells[ish]['dim'] for ish in range(n_shells)] # dims = [self.shells[ish]['dim'] for ish in range(n_shells)]
@ -164,16 +165,16 @@ class SumkDFTTools(SumkDFT):
# raise ValueError( # raise ValueError(
# 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read) # 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
#set-up output arrays # set-up output arrays
DOS = {sp: numpy.zeros([n_om],float) for sp in spn} DOS = {sp: numpy.zeros([n_om], float) for sp in spn}
DOSproj = [{} for ish in range(n_shells)] DOSproj = [{} for ish in range(n_shells)]
DOSproj_orb = [{} for ish in range(n_shells)] DOSproj_orb = [{} for ish in range(n_shells)]
#set-up Green's function object # set-up Green's function object
if (proj_type != None): if (proj_type != None):
G_loc = [] G_loc = []
for ish in range(n_shells): for ish in range(n_shells):
glist = [GfReFreq(target_shape=(block_dim, block_dim), mesh=mesh) glist = [GfReFreq(target_shape=(block_dim, block_dim), mesh=mesh)
for block, block_dim in gf_struct[ish]] for block, block_dim in gf_struct[ish]]
G_loc.append( G_loc.append(
BlockGf(name_list=spn, block_list=glist, make_copies=False)) BlockGf(name_list=spn, block_list=glist, make_copies=False))
G_loc[ish].zero() G_loc[ish].zero()
@ -183,17 +184,17 @@ class SumkDFTTools(SumkDFT):
DOSproj_orb[ish][sp] = numpy.zeros( DOSproj_orb[ish][sp] = numpy.zeros(
[n_om, dim, dim], complex) [n_om, dim, dim], complex)
#calculate the DOS # calculate the DOS
ikarray = numpy.array(list(range(self.n_k))) ikarray = numpy.array(list(range(self.n_k)))
for ik in mpi.slice_array(ikarray): for ik in mpi.slice_array(ikarray):
G_latt_w = self.lattice_gf( G_latt_w = self.lattice_gf(
ik=ik, mu=mu, 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] G_latt_w *= self.bz_weights[ik]
#output occupied DOS if nk inputted # output occupied DOS if nk inputted
if(dosocc): if (dosocc):
for bname, gf in G_latt_w: for bname, gf in G_latt_w:
G_latt_w[bname].data[:,:,:] *= self.occik[bname][ik] G_latt_w[bname].data[:, :, :] *= self.occik[bname][ik]
# DOS # DOS
for bname, gf in G_latt_w: for bname, gf in G_latt_w:
DOS[bname] -= gf.data.imag.trace(axis1=1, axis2=2)/numpy.pi DOS[bname] -= gf.data.imag.trace(axis1=1, axis2=2)/numpy.pi
# Projected DOS: # Projected DOS:
@ -209,13 +210,13 @@ class SumkDFTTools(SumkDFT):
for bname in DOS: for bname in DOS:
DOS[bname] = mpi.all_reduce(DOS[bname]) DOS[bname] = mpi.all_reduce(DOS[bname])
# Collect data from mpi and put in projected arrays # Collect data from mpi and put in projected arrays
if(proj_type != None): if (proj_type != None):
for ish in range(n_shells): for ish in range(n_shells):
G_loc[ish] << mpi.all_reduce(G_loc[ish]) G_loc[ish] << mpi.all_reduce(G_loc[ish])
# Symmetrize and rotate to local coord. system if needed: # Symmetrize and rotate to local coord. system if needed:
if((proj_type!='vasp') and (proj_type!='elk')): if ((proj_type != 'vasp') and (proj_type != 'elk')):
if self.symm_op != 0: if self.symm_op != 0:
if proj_type=='wann': if proj_type == 'wann':
G_loc = self.symmcorr.symmetrize(G_loc) G_loc = self.symmcorr.symmetrize(G_loc)
else: else:
G_loc = self.symmpar.symmetrize(G_loc) G_loc = self.symmpar.symmetrize(G_loc)
@ -223,13 +224,13 @@ class SumkDFTTools(SumkDFT):
for ish in range(n_shells): for ish in range(n_shells):
for bname, gf in G_loc[ish]: for bname, gf in G_loc[ish]:
G_loc[ish][bname] << self.rotloc( G_loc[ish][bname] << self.rotloc(
ish, gf, direction='toLocal',shells=shells_type) ish, gf, direction='toLocal', shells=shells_type)
# G_loc can now also be used to look at orbitally-resolved quantities # G_loc can now also be used to look at orbitally-resolved quantities
for ish in range(n_shells): for ish in range(n_shells):
for bname, gf in G_loc[ish]: # loop over spins for bname, gf in G_loc[ish]: # loop over spins
DOSproj[ish][bname] = -gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi DOSproj[ish][bname] = -gf.data.imag.trace(axis1=1, axis2=2) / numpy.pi
DOSproj_orb[ish][bname][ DOSproj_orb[ish][bname][
:, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:,:,:] :, :, :] += (1.0j*(gf-gf.conjugate().transpose())/2.0/numpy.pi).data[:, :, :]
# Write to files # Write to files
if save_to_file and mpi.is_master_node(): if save_to_file and mpi.is_master_node():
@ -239,9 +240,9 @@ class SumkDFTTools(SumkDFT):
f.write("%s %s\n" % (mesh_val[iom], DOS[sp][iom])) f.write("%s %s\n" % (mesh_val[iom], DOS[sp][iom]))
f.close() f.close()
# Partial # Partial
if(proj_type!=None): if (proj_type != None):
for ish in range(n_shells): for ish in range(n_shells):
f = open('DOS_' + proj_type + '_%s_proj%s.dat' % (sp, ish), 'w') f = open('DOS_' + proj_type + '_%s_proj%s.dat' % (sp, ish), 'w')
for iom in range(n_om): for iom in range(n_om):
f.write("%s %s\n" % f.write("%s %s\n" %
(mesh_val[iom], DOSproj[ish][sp][iom])) (mesh_val[iom], DOSproj[ish][sp][iom]))
@ -249,18 +250,17 @@ class SumkDFTTools(SumkDFT):
# Orbitally-resolved # Orbitally-resolved
for i in range(dims[ish]): for i in range(dims[ish]):
for j in range(dims[ish]): for j in range(dims[ish]):
#For Elk with parproj - skip off-diagonal elements # For Elk with parproj - skip off-diagonal elements
#if(proj_type=='elk') and (i!=j): continue # if(proj_type=='elk') and (i!=j): continue
f = open('DOS_' + proj_type + '_' + sp + '_proj' + str(ish) + f = open('DOS_' + proj_type + '_' + sp + '_proj' + str(ish) +
'_' + str(i) + '_' + str(j) + '.dat', 'w') '_' + str(i) + '_' + str(j) + '.dat', 'w')
for iom in range(n_om): for iom in range(n_om):
f.write("%s %s %s\n" % ( f.write("%s %s %s\n" % (
mesh_val[iom], DOSproj_orb[ish][sp][iom, i, j].real,DOSproj_orb[ish][sp][iom, i, j].imag)) mesh_val[iom], DOSproj_orb[ish][sp][iom, i, j].real, DOSproj_orb[ish][sp][iom, i, j].imag))
f.close() f.close()
return DOS, DOSproj, DOSproj_orb return DOS, DOSproj, DOSproj_orb
def proj_type_G_loc(self, G_latt, G_inp, ik, ish, proj_type=None): def proj_type_G_loc(self, G_latt, G_inp, ik, ish, proj_type=None):
""" """
Internal routine which calculates the project Green's function subject to the Internal routine which calculates the project Green's function subject to the
@ -292,7 +292,7 @@ class SumkDFTTools(SumkDFT):
if (proj_type == 'wann'): if (proj_type == 'wann'):
for bname, gf in G_proj: for bname, gf in G_proj:
G_proj[bname] << self.downfold(ik, ish, bname, G_proj[bname] << self.downfold(ik, ish, bname,
G_latt[bname], gf) # downfolding G G_latt[bname], gf) # downfolding G
elif (proj_type == 'vasp'): elif (proj_type == 'vasp'):
for bname, gf in G_latt: for bname, gf in G_latt:
G_proj[bname] << self.downfold(ik, ish, bname, gf, G_proj[bname], shells='csc') G_proj[bname] << self.downfold(ik, ish, bname, gf, G_proj[bname], shells='csc')
@ -302,7 +302,7 @@ class SumkDFTTools(SumkDFT):
tmp.zero() tmp.zero()
for bname, gf in tmp: for bname, gf in tmp:
tmp[bname] << self.downfold(ik, ish, bname, tmp[bname] << self.downfold(ik, ish, bname,
G_latt[bname], gf, shells='all', ir=ir) G_latt[bname], gf, shells='all', ir=ir)
G_proj += tmp G_proj += tmp
# elif (proj_type == 'elk'): # elif (proj_type == 'elk'):
# dim = self.shells[ish]['dim'] # dim = self.shells[ish]['dim']
@ -328,7 +328,7 @@ class SumkDFTTools(SumkDFT):
return G_proj return G_proj
def load_parproj(self,data_type=None): def load_parproj(self, data_type=None):
""" """
Internal routine which loads the n_parproj, proj_mat_all, rot_mat_all and Internal routine which loads the n_parproj, proj_mat_all, rot_mat_all and
rot_mat_all_time_inv from parproj data from .h5 file. rot_mat_all_time_inv from parproj data from .h5 file.
@ -339,20 +339,20 @@ class SumkDFTTools(SumkDFT):
'band' - reads data converted by bands_convert() 'band' - reads data converted by bands_convert()
None - reads data converted by parproj_convert() None - reads data converted by parproj_convert()
""" """
#read in the projectors # read in the projectors
things_to_read = ['n_parproj', 'proj_mat_all'] things_to_read = ['n_parproj', 'proj_mat_all']
if data_type == 'band': if data_type == 'band':
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.bands_data, things_to_read=things_to_read) subgrp=self.bands_data, things_to_read=things_to_read)
else: else:
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.parproj_data, things_to_read=things_to_read) subgrp=self.parproj_data, things_to_read=things_to_read)
if self.symm_op: if self.symm_op:
self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data) self.symmpar = Symmetry(self.hdf_file, subgroup=self.symmpar_data)
if len(values_not_read) > 0 and mpi.is_master_node: if len(values_not_read) > 0 and mpi.is_master_node:
raise ValueError( raise ValueError(
'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read) 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
#read general data # read general data
things_to_read = ['rot_mat_all', 'rot_mat_all_time_inv'] things_to_read = ['rot_mat_all', 'rot_mat_all_time_inv']
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.parproj_data, things_to_read=things_to_read) subgrp=self.parproj_data, things_to_read=things_to_read)
@ -364,6 +364,7 @@ class SumkDFTTools(SumkDFT):
""" """
Calculates the band resolved density matrices (occupations) from the Matsubara Calculates the band resolved density matrices (occupations) from the Matsubara
frequency self-energy. frequency self-energy.
Parameters Parameters
---------- ----------
mu : double, optional mu : double, optional
@ -376,7 +377,8 @@ class SumkDFTTools(SumkDFT):
save_occ : boolean, optional save_occ : boolean, optional
If True, saves the band resolved density matrix in misc_data. If True, saves the band resolved density matrix in misc_data.
save_to_file : boolean, optional save_to_file : boolean, optional
If True, text files with the calculated data will be created. If True, text files with the calculated data will be created.\
Returns Returns
------- -------
occik : Dict of numpy arrays occik : Dict of numpy arrays
@ -387,7 +389,8 @@ class SumkDFTTools(SumkDFT):
mesh = self.Sigma_imp[0].mesh mesh = self.Sigma_imp[0].mesh
else: else:
mesh = self.mesh mesh = self.mesh
assert isinstance(mesh, MeshImFreq), "SumkDFT.mesh must be real if with_Sigma is True or mesh is not given" assert isinstance(
mesh, MeshImFreq), "SumkDFT.mesh must be real if with_Sigma is True or mesh is not given"
if mu is None: if mu is None:
mu = self.chemical_potential mu = self.chemical_potential
@ -395,20 +398,21 @@ class SumkDFTTools(SumkDFT):
spn = self.spin_block_names[self.SO] spn = self.spin_block_names[self.SO]
occik = {} occik = {}
for sp in spn: for sp in spn:
#same format as gf.data ndarray # same format as gf.data ndarray
occik[sp] = [numpy.zeros([1, self.n_orbitals[ik, ntoi[sp]], self.n_orbitals[ik, ntoi[sp]]], numpy.double) for ik in range(self.n_k)] occik[sp] = [numpy.zeros([1, self.n_orbitals[ik, ntoi[sp]],
#calculate the occupations self.n_orbitals[ik, ntoi[sp]]], numpy.double) for ik in range(self.n_k)]
# calculate the occupations
ikarray = numpy.array(range(self.n_k)) ikarray = numpy.array(range(self.n_k))
for ik in range(self.n_k): for ik in range(self.n_k):
G_latt = self.lattice_gf( G_latt = self.lattice_gf(
ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc) ik=ik, mu=mu, with_Sigma=with_Sigma, with_dc=with_dc)
for bname, gf in G_latt: for bname, gf in G_latt:
occik[bname][ik][0,:,:] = gf.density().real occik[bname][ik][0, :, :] = gf.density().real
# Collect data from mpi: # Collect data from mpi:
for sp in spn: for sp in spn:
occik[sp] = mpi.all_reduce(occik[sp]) occik[sp] = mpi.all_reduce(occik[sp])
mpi.barrier() mpi.barrier()
#save to HDF5 file (if specified) # save to HDF5 file (if specified)
if save_occ and mpi.is_master_node(): if save_occ and mpi.is_master_node():
things_to_save_misc = ['occik'] things_to_save_misc = ['occik']
# Save it to the HDF: # Save it to the HDF:
@ -420,7 +424,6 @@ class SumkDFTTools(SumkDFT):
del ar del ar
return occik return occik
# Uses .data of only GfReFreq objects.
def spectral_contours(self, mu=None, broadening=None, mesh=None, plot_range=None, FS=True, with_Sigma=True, with_dc=True, proj_type=None, save_to_file=True): def spectral_contours(self, mu=None, broadening=None, mesh=None, plot_range=None, FS=True, with_Sigma=True, with_dc=True, proj_type=None, save_to_file=True):
""" """
Calculates the correlated spectral function at the Fermi level (relating to the Fermi Calculates the correlated spectral function at the Fermi level (relating to the Fermi
@ -465,13 +468,13 @@ class SumkDFTTools(SumkDFT):
(Correlated) k-resolved spectral function projected to atoms and (Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions. Empty if proj_type = None resolved into orbital contributions. Empty if proj_type = None
""" """
if(proj_type!=None): if (proj_type != None):
assert proj_type in ('wann'), "'proj_type' must be 'wann' if not None" assert proj_type in ('wann'), "'proj_type' must be 'wann' if not None"
#read in the energy contour energies and projectors # read in the energy contour energies and projectors
things_to_read = ['n_k','bmat','BZ_n_k','BZ_iknr','BZ_vkl', things_to_read = ['n_k', 'bmat', 'BZ_n_k', 'BZ_iknr', 'BZ_vkl',
'n_orbitals', 'proj_mat', 'hopping'] 'n_orbitals', 'proj_mat', 'hopping']
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.cont_data, things_to_read=things_to_read) subgrp=self.cont_data, things_to_read=things_to_read)
if len(values_not_read) > 0 and mpi.is_master_node: if len(values_not_read) > 0 and mpi.is_master_node:
raise ValueError( raise ValueError(
'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read) 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
@ -479,107 +482,110 @@ class SumkDFTTools(SumkDFT):
if mu is None: if mu is None:
mu = self.chemical_potential mu = self.chemical_potential
if (with_Sigma): if (with_Sigma):
assert isinstance(self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True" assert isinstance(
mesh=self.Sigma_imp[0].mesh self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True"
mesh = self.Sigma_imp[0].mesh
elif mesh is not None: elif mesh is not None:
assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq" assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq"
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
elif self.mesh is not None: elif self.mesh is not None:
assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq" assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq"
mesh=self.mesh mesh = self.mesh
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
else: else:
assert 0, "ReFreqMesh input required for calculations without real frequency self-energy" assert 0, "ReFreqMesh input required for calculations without real frequency self-energy"
mesh_val = numpy.linspace(mesh.w_min,mesh.w_max,len(mesh)) mesh_val = numpy.linspace(mesh.w_min, mesh.w_max, len(mesh))
n_om = len(mesh) n_om = len(mesh)
om_minplot = mesh_val[0] - 0.001 om_minplot = mesh_val[0] - 0.001
om_maxplot = mesh_val[-1] + 0.001 om_maxplot = mesh_val[-1] + 0.001
#for Fermi Surface calculations # for Fermi Surface calculations
if FS: if FS:
dw = abs(mesh_val[1]-mesh_val[0]) dw = abs(mesh_val[1]-mesh_val[0])
#ensure that a few frequencies around the Fermi level are included # ensure that a few frequencies around the Fermi level are included
plot_range = [-2*dw, 2*dw] plot_range = [-2*dw, 2*dw]
mpi.report('Generated A(k,w) will be evaluted at closest frequency to 0.0 in given mesh ') mpi.report('Generated A(k,w) will be evaluted at closest frequency to 0.0 in given mesh ')
if plot_range is None: if plot_range is None:
n_om = len(mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)]) n_om = len(mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)])
mesh_val2 = mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)] mesh_val2 = mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)]
else: else:
om_minplot = plot_range[0] om_minplot = plot_range[0]
om_maxplot = plot_range[1] om_maxplot = plot_range[1]
n_om = len(mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)]) n_om = len(mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)])
mesh_val2 = mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)] mesh_val2 = mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)]
#\omega ~= 0.0 index for FS file # \omega ~= 0.0 index for FS file
abs_mesh_val = [abs(i) for i in mesh_val2] abs_mesh_val = [abs(i) for i in mesh_val2]
jw=[i for i in range(len(abs_mesh_val)) if abs_mesh_val[i] == numpy.min(abs_mesh_val[:])] jw = [i for i in range(len(abs_mesh_val)) if abs_mesh_val[i]
== numpy.min(abs_mesh_val[:])]
# calculate the spectral functions for the irreducible set of k-points
[Akw, pAkw, pAkw_orb] = self.gen_Akw(mu=mu, broadening=broadening, mesh=mesh,
plot_shift=0.0, plot_range=plot_range,
shell_list=None, with_Sigma=with_Sigma, with_dc=with_dc,
proj_type=proj_type)
#calculate the spectral functions for the irreducible set of k-points
[Akw, pAkw, pAkw_orb] = self.gen_Akw(mu=mu, broadening=broadening, mesh=mesh, \
plot_shift=0.0, plot_range=plot_range, \
shell_list=None, with_Sigma=with_Sigma, with_dc=with_dc, \
proj_type=proj_type)
if save_to_file and mpi.is_master_node(): if save_to_file and mpi.is_master_node():
spn = self.spin_block_names[self.SO] spn = self.spin_block_names[self.SO]
vkc = numpy.zeros(3, float) vkc = numpy.zeros(3, float)
mesh_val2 = mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)] mesh_val2 = mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)]
if FS: if FS:
n_om = 1 n_om = 1
else: else:
n_om = len(mesh_val2) n_om = len(mesh_val2)
for sp in spn: for sp in spn:
# Open file for storage: # Open file for storage:
for iom in range(n_om): for iom in range(n_om):
if FS: if FS:
f = open('Akw_FS_' + sp + '.dat', 'w') f = open('Akw_FS_' + sp + '.dat', 'w')
jom=jw[0] jom = jw[0]
else: else:
f = open('Akw_omega_%s_%s.dat' % (iom, sp), 'w') f = open('Akw_omega_%s_%s.dat' % (iom, sp), 'w')
jom=iom jom = iom
f.write("#Spectral function evaluated at frequency = %s\n" %mesh_val2[jom]) f.write("#Spectral function evaluated at frequency = %s\n" % mesh_val2[jom])
for ik in range(self.BZ_n_k): for ik in range(self.BZ_n_k):
jk=self.BZ_iknr[ik] jk = self.BZ_iknr[ik]
vkc[:] = numpy.matmul(self.bmat,self.BZ_vkl[ik,:]) vkc[:] = numpy.matmul(self.bmat, self.BZ_vkl[ik, :])
f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2], Akw[sp][jk, jom])) f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2], Akw[sp][jk, jom]))
f.close() f.close()
if (proj_type!=None): if (proj_type != None):
n_shells = len(pAkw[:]) n_shells = len(pAkw[:])
for iom in range(n_om): for iom in range(n_om):
for sp in spn: for sp in spn:
for ish in range(n_shells): for ish in range(n_shells):
if FS: if FS:
strng = 'Akw_FS' + '_' + proj_type + '_' + sp + '_proj' + str(ish) strng = 'Akw_FS' + '_' + proj_type + '_' + sp + '_proj' + str(ish)
jom=jw[0] jom = jw[0]
else: else:
strng = 'Akw_omega_' + str(iom) + '_' + proj_type + '_' + sp + '_proj' + str(ish) strng = 'Akw_omega_' + str(iom) + '_' + proj_type + \
jom=iom '_' + sp + '_proj' + str(ish)
jom = iom
f = open(strng + '.dat', 'w') f = open(strng + '.dat', 'w')
f.write("#Spectral function evaluated at frequency = %s\n" %mesh_val2[jom]) f.write("#Spectral function evaluated at frequency = %s\n" % mesh_val2[jom])
for ik in range(self.BZ_n_k): for ik in range(self.BZ_n_k):
jk=self.BZ_iknr[ik] jk = self.BZ_iknr[ik]
vkc[:] = numpy.matmul(self.bmat,self.BZ_vkl[ik,:]) vkc[:] = numpy.matmul(self.bmat, self.BZ_vkl[ik, :])
f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2], f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2],
pAkw[ish][sp][jk, jom])) pAkw[ish][sp][jk, jom]))
f.close() f.close()
dim=len(pAkw_orb[ish][sp][0, 0, 0, :]) dim = len(pAkw_orb[ish][sp][0, 0, 0, :])
for i in range(dim): for i in range(dim):
for j in range(dim): for j in range(dim):
#For Elk with parproj - skip off-diagonal elements # For Elk with parproj - skip off-diagonal elements
if(proj_type=='elk') and (i!=j): continue if (proj_type == 'elk') and (i != j):
continue
strng2 = strng + '_' + str(i) + '_' + str(j) strng2 = strng + '_' + str(i) + '_' + str(j)
# Open file for storage: # Open file for storage:
f = open(strng2 + '.dat', 'w') f = open(strng2 + '.dat', 'w')
for ik in range(self.BZ_n_k): for ik in range(self.BZ_n_k):
jk=self.BZ_iknr[ik] jk = self.BZ_iknr[ik]
vkc[:] = numpy.matmul(self.bmat,self.BZ_vkl[ik,:]) vkc[:] = numpy.matmul(self.bmat, self.BZ_vkl[ik, :])
f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2], f.write("%s %s %s %s\n" % (vkc[0], vkc[1], vkc[2],
pAkw_orb[ish][sp][jk, jom, i, j])) pAkw_orb[ish][sp][jk, jom, i, j]))
f.close() f.close()
return Akw, pAkw, pAkw_orb return Akw, pAkw, pAkw_orb
# Uses .data of only GfReFreq objects.
def spaghettis(self, mu=None, broadening=None, mesh=None, plot_shift=0.0, plot_range=None, shell_list=None, with_Sigma=True, with_dc=True, proj_type=None, save_to_file=True): def spaghettis(self, mu=None, broadening=None, mesh=None, plot_shift=0.0, plot_range=None, shell_list=None, with_Sigma=True, with_dc=True, proj_type=None, save_to_file=True):
""" """
Calculates the k-resolved spectral function A(k,w) (band structure) Calculates the k-resolved spectral function A(k,w) (band structure)
@ -597,12 +603,12 @@ class SumkDFTTools(SumkDFT):
plot_shift : double, optional plot_shift : double, optional
Offset for each A(k,w) for stacked plotting of spectra. Offset for each A(k,w) for stacked plotting of spectra.
plot_range : list of double, optional plot_range : list of double, optional
Sets the energy window for plotting to (plot_range[0],plot_range[1]). Sets the energy window for plotting to (plot_range[0],plot_range[1]).
If not provided, the min and max values of the energy mesh is used. If not provided, the min and max values of the energy mesh is used.
shell_list : list of integers, optional shell_list : list of integers, optional
Contains the indices of the shells of which the projected spectral function Contains the indices of the shells of which the projected spectral function
is calculated for. is calculated for.
If shell_list = None and proj_type is not None, then the projected spectral If shell_list = None and proj_type is not None, then the projected spectral
function is calculated for all shells. function is calculated for all shells.
with_Sigma : boolean, optional with_Sigma : boolean, optional
If True, the self energy is used for the calculation. If True, the self energy is used for the calculation.
@ -620,44 +626,45 @@ class SumkDFTTools(SumkDFT):
Akw : Dict of numpy arrays Akw : Dict of numpy arrays
(Correlated) k-resolved spectral function (Correlated) k-resolved spectral function
pAkw : Dict of numpy arrays pAkw : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms. (Correlated) k-resolved spectral function projected to atoms.
Empty if proj_type = None Empty if proj_type = None
pAkw_orb : Dict of numpy arrays pAkw_orb : Dict of numpy arrays
(Correlated) k-resolved spectral function projected to atoms and (Correlated) k-resolved spectral function projected to atoms and
resolved into orbital contributions. Empty if proj_type = None resolved into orbital contributions. Empty if proj_type = None
""" """
#initialisation # initialisation
if(proj_type!=None): if (proj_type != None):
assert proj_type in ('wann', 'wien2k'), "'proj_type' must be either 'wann', 'wien2k'" assert proj_type in ('wann', 'wien2k'), "'proj_type' must be either 'wann', 'wien2k'"
if(proj_type!='wann'): if (proj_type != 'wann'):
assert proj_type==self.dft_code, "proj_type must be from the corresponding dft inputs." assert proj_type == self.dft_code, "proj_type must be from the corresponding dft inputs."
things_to_read = ['n_k', 'n_orbitals', 'proj_mat', 'hopping'] things_to_read = ['n_k', 'n_orbitals', 'proj_mat', 'hopping']
subgroup_present, values_not_read = self.read_input_from_hdf( subgroup_present, values_not_read = self.read_input_from_hdf(
subgrp=self.bands_data, things_to_read=things_to_read) subgrp=self.bands_data, things_to_read=things_to_read)
if len(values_not_read) > 0 and mpi.is_master_node: if len(values_not_read) > 0 and mpi.is_master_node:
raise ValueError( raise ValueError(
'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read) 'ERROR: One or more necessary SumK input properties have not been found in the given h5 archive:', self.values_not_read)
if(proj_type=='wien2k'): if (proj_type == 'wien2k'):
self.load_parproj(data_type='band') self.load_parproj(data_type='band')
if mu is None: if mu is None:
mu = self.chemical_potential mu = self.chemical_potential
if (with_Sigma): if (with_Sigma):
assert isinstance(self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True" assert isinstance(
mesh=self.Sigma_imp[0].mesh self.Sigma_imp[0].mesh, MeshReFreq), "SumkDFT.mesh must be real if with_Sigma is True"
mesh = self.Sigma_imp[0].mesh
elif mesh is not None: elif mesh is not None:
assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq" assert isinstance(mesh, MeshReFreq), "mesh must be of form MeshReFreq"
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
elif self.mesh is not None: elif self.mesh is not None:
assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq" assert isinstance(self.mesh, MeshReFreq), "self.mesh must be of form MeshReFreq"
mesh=self.mesh mesh = self.mesh
if broadening is None: if broadening is None:
broadening=0.001 broadening = 0.001
else: else:
assert 0, "ReFreqMesh input required for calculations without real frequency self-energy" assert 0, "ReFreqMesh input required for calculations without real frequency self-energy"
mesh_val = numpy.linspace(mesh.w_min,mesh.w_max,len(mesh)) mesh_val = numpy.linspace(mesh.w_min, mesh.w_max, len(mesh))
n_om = len(mesh) n_om = len(mesh)
om_minplot = mesh_val[0] - 0.001 om_minplot = mesh_val[0] - 0.001
om_maxplot = mesh_val[-1] + 0.001 om_maxplot = mesh_val[-1] + 0.001
@ -667,52 +674,53 @@ class SumkDFTTools(SumkDFT):
else: else:
om_minplot = plot_range[0] om_minplot = plot_range[0]
om_maxplot = plot_range[1] om_maxplot = plot_range[1]
n_om = len(mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)]) n_om = len(mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)])
[Akw, pAkw, pAkw_orb] = self.gen_Akw(mu=mu, broadening=broadening, mesh=mesh, \ [Akw, pAkw, pAkw_orb] = self.gen_Akw(mu=mu, broadening=broadening, mesh=mesh,
plot_shift=plot_shift, plot_range=plot_range, \ plot_shift=plot_shift, plot_range=plot_range,
shell_list=shell_list, with_Sigma=with_Sigma, with_dc=with_dc, \ shell_list=shell_list, with_Sigma=with_Sigma, with_dc=with_dc,
proj_type=proj_type) proj_type=proj_type)
if save_to_file and mpi.is_master_node(): if save_to_file and mpi.is_master_node():
mesh_val2 = mesh_val[(mesh_val > om_minplot)&(mesh_val < om_maxplot)] mesh_val2 = mesh_val[(mesh_val > om_minplot) & (mesh_val < om_maxplot)]
spn = self.spin_block_names[self.SO] spn = self.spin_block_names[self.SO]
for sp in spn: for sp in spn:
# Open file for storage: # Open file for storage:
f = open('Akw_' + sp + '.dat', 'w') f = open('Akw_' + sp + '.dat', 'w')
for ik in range(self.n_k): for ik in range(self.n_k):
for iom in range(n_om): for iom in range(n_om):
f.write('%s %s %s\n' %(ik, mesh_val2[iom], Akw[sp][ik, iom])) f.write('%s %s %s\n' % (ik, mesh_val2[iom], Akw[sp][ik, iom]))
f.write('\n') f.write('\n')
f.close() f.close()
if (proj_type!=None): if (proj_type != None):
n_shells = len(pAkw[:]) n_shells = len(pAkw[:])
if shell_list==None: if shell_list == None:
shell_list=[ish for ish in range(n_shells)] shell_list = [ish for ish in range(n_shells)]
for sp in spn: for sp in spn:
for ish in range(n_shells): for ish in range(n_shells):
jsh=shell_list[ish] jsh = shell_list[ish]
f = open('Akw_' + proj_type + '_' + f = open('Akw_' + proj_type + '_' +
sp + '_proj' + str(jsh) + '.dat', 'w') sp + '_proj' + str(jsh) + '.dat', 'w')
for ik in range(self.n_k): for ik in range(self.n_k):
for iom in range(n_om): for iom in range(n_om):
f.write('%s %s %s\n' % ( f.write('%s %s %s\n' % (
ik, mesh_val2[iom], pAkw[ish][sp][ik, iom])) ik, mesh_val2[iom], pAkw[ish][sp][ik, iom]))
f.write('\n') f.write('\n')
f.close() f.close()
#get orbital dimension from the length of dimension of the array # get orbital dimension from the length of dimension of the array
dim=len(pAkw_orb[ish][sp][0, 0, 0, :]) dim = len(pAkw_orb[ish][sp][0, 0, 0, :])
for i in range(dim): for i in range(dim):
for j in range(dim): for j in range(dim):
#For Elk with parproj - skip off-diagonal elements # For Elk with parproj - skip off-diagonal elements
if(proj_type=='elk') and (i!=j): continue if(proj_type =='elk') and (i!=j):
continue
# Open file for storage: # Open file for storage:
f = open('Akw_' + proj_type + '_' + sp + '_proj' + str(jsh) f = open('Akw_' + proj_type + '_' + sp + '_proj' + str(jsh)
+ '_' + str(i) + '_' + str(j) + '.dat', 'w') + '_' + str(i) + '_' + str(j) + '.dat', 'w')
for ik in range(self.n_k): for ik in range(self.n_k):
for iom in range(n_om): for iom in range(n_om):
f.write('%s %s %s\n' % ( f.write('%s %s %s\n' % (
ik, mesh_val2[iom], pAkw_orb[ish][sp][ik, iom, i, j])) ik, mesh_val2[iom], pAkw_orb[ish][sp][ik, iom, i, j]))
f.write('\n') f.write('\n')
f.close() f.close()