def __init__(self, HDFfile, subgroup=None):
"""Initialises the class.
Reads the permutations and rotation matrizes from the file, and constructs the mapping for
the given orbitals. For each orbit a matrix is read!!!
SO: Flag for SO coupled calculations.
SP: Spin polarisation yes/no
"""
assert type(HDFfile) == StringType, "HDFfile must be a filename"
self.HDFfile = HDFfile
thingstoread = [
'Ns', 'Natoms', 'perm', 'orbits', 'SO', 'SP', 'timeinv', 'mat',
'mat_tinv'
]
for it in thingstoread:
exec "self.%s = 0" % it
if (MPI.IS_MASTER_NODE()):
#Read the stuff on master:
ar = HDF_Archive(HDFfile, 'a')
if (subgroup is None):
ar2 = ar
else:
ar2 = ar[subgroup]
for it in thingstoread:
exec "self.%s = ar2['%s']" % (it, it)
del ar2
del ar
#broadcasting
for it in thingstoread:
exec "self.%s = MPI.bcast(self.%s)" % (it, it)
# now define the mapping of orbitals:
# self.map[iorb]=jorb gives the permutation of the orbitals as given in the list, when the
# permutation of the atoms is done:
self.N_orbits = len(self.orbits)
self.map = [[0 for iorb in range(self.N_orbits)]
for iNs in range(self.Ns)]
for iNs in range(self.Ns):
for iorb in range(self.N_orbits):
srch = copy.deepcopy(self.orbits[iorb])
srch[0] = self.perm[iNs][self.orbits[iorb][0] - 1]
self.map[iNs][iorb] = self.orbits.index(srch)
# Define the Bravais Lattice : a square lattice in 2d
BL = bravais_lattice(Units=[(1, 0, 0), (0, 1, 0)],
Orbital_Positions={"": (0, 0, 0)})
# Prepare a nearest neighbour hopping on BL
t = -1.00 # First neighbour Hopping
tp = 0.0 * t # Second neighbour Hopping
# Hopping[ Displacement on the lattice] = [[t11,t12,t13....],[t21,t22,t23....],...,[....,tnn]]
# where n=Number_Orbitals
hop = {
(1, 0): [[t]],
(-1, 0): [[t]],
(0, 1): [[t]],
(0, -1): [[t]],
(1, 1): [[tp]],
(-1, -1): [[tp]],
(1, -1): [[tp]],
(-1, 1): [[tp]]
}
TB = tight_binding(BL, hop)
# Compute the density of states
d = dos(TB, nkpts=500, neps=101, Name='dos')[0]
from pytriqs.Base.Archive import HDF_Archive
R = HDF_Archive('dos1.output.h5', 'w')
R['SquareLatt'] = d
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see <http://www.gnu.org/licenses/>.
#
################################################################################
from pytriqs.Base.Archive import HDF_Archive
from pytriqs.Base.GF_Local import *
from pytriqs.Base.DMFT.Loop_Generic import *
from pytriqs.Base.GF_Local.Descriptors import iOmega_n, SemiCircular
#
# Example of DMFT single site solution with CTQMC
#
# Opens the results hdf5 file
Results = HDF_Archive("SingleSiteBethe.output.h5", 'w')
# set up a few parameters
Half_Bandwidth = 1.0
U = 2.5
Chemical_Potential = U / 2.0
Beta = 100
# Construct a CTQMC solver
from pytriqs.Solvers.Operators import * # imports the class manipulating C, C_dagger and N = C_dagger C
from pytriqs.Solvers.HybridizationExpansion import Solver # imports the solver class
S = Solver(
Beta=Beta, # inverse temperature
GFstruct=[('up', [1]), ('down', [1])], # Structure of the Green function
H_Local=U * N('up', 1) * N('down', 1), # Local Hamiltonian
from pytriqs.Base.GF_Local import GFBloc_ReFreq
from pytriqs.Base.Archive import HDF_Archive
from math import pi
R = HDF_Archive('myfile.h5', 'r')
from pytriqs.Base.Plot.MatplotlibPlotter import oplot, plt
plt.xrange(-1,1)
plt.yrange(0,7)
for name, g in R.items() : # iterate on the elements of R, like a dict ...
oplot( (- 1/pi * g).imag, "-o", Name = name)
p.savefig("./tut_ex3b.png")
def convert_DMFT_input(self):
"""
Reads the input files, and stores the data in the HDFfile
"""
if not (MPI.IS_MASTER_NODE()): return # do it only on master:
MPI.report("Reading input from %s..."%self.LDA_file)
# Read and write only on Master!!!
# R is a generator : each R.Next() will return the next number in the file
R = Read_Fortran_File(self.LDA_file)
try:
EnergyUnit = R.next() # read the energy convertion factor
Nk = int(R.next()) # read the number of k points
k_dep_projection = 1
SP = int(R.next()) # flag for spin-polarised calculation
SO = int(R.next()) # flag for spin-orbit calculation
charge_below = R.next() # total charge below energy window
Density_Required = R.next() # total density required, for setting the chemical potential
symm_op = 1 # Use symmetry groups for the k-sum
# the information on the non-correlated shells is not important here, maybe skip:
N_shells = int(R.next()) # number of shells (e.g. Fe d, As p, O p) in the unit cell,
# corresponds to index R in formulas
# now read the information about the shells:
shells = [ [ int(R.next()) for i in range(4) ] for icrsh in range(N_shells) ] # reads iatom, sort, l, dim
N_corr_shells = int(R.next()) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
# corresponds to index R in formulas
# now read the information about the shells:
corr_shells = [ [ int(R.next()) for i in range(6) ] for icrsh in range(N_corr_shells) ] # reads iatom, sort, l, dim, SO flag, irep
self.inequiv_shells(corr_shells) # determine the number of inequivalent correlated shells, has to be known for further reading...
use_rotations = 1
rotmat = [numpy.identity(corr_shells[icrsh][3],numpy.complex_) for icrsh in xrange(N_corr_shells)]
# read the matrices
rotmat_timeinv = [0 for i in range(N_corr_shells)]
for icrsh in xrange(N_corr_shells):
for i in xrange(corr_shells[icrsh][3]): # read real part:
for j in xrange(corr_shells[icrsh][3]):
rotmat[icrsh][i,j] = R.next()
for i in xrange(corr_shells[icrsh][3]): # read imaginary part:
for j in xrange(corr_shells[icrsh][3]):
rotmat[icrsh][i,j] += 1j * R.next()
if (SP==1): # read time inversion flag:
rotmat_timeinv[icrsh] = int(R.next())
# Read here the infos for the transformation of the basis:
Nreps = [1 for i in range(self.N_inequiv_corr_shells)]
dim_reps = [0 for i in range(self.N_inequiv_corr_shells)]
T = []
for icrsh in range(self.N_inequiv_corr_shells):
Nreps[icrsh] = int(R.next()) # number of representatives ("subsets"), e.g. t2g and eg
dim_reps[icrsh] = [int(R.next()) for i in range(Nreps[icrsh])] # dimensions of the subsets
# The transformation matrix:
# it is of dimension 2l+1, if no SO, and 2*(2l+1) with SO!!
#T = []
#for ish in xrange(self.N_inequiv_corr_shells):
ll = 2*corr_shells[self.invshellmap[icrsh]][2]+1
lmax = ll * (corr_shells[self.invshellmap[icrsh]][4] + 1)
T.append(numpy.zeros([lmax,lmax],numpy.complex_))
# now read it from file:
for i in xrange(lmax):
for j in xrange(lmax):
T[icrsh][i,j] = R.next()
for i in xrange(lmax):
for j in xrange(lmax):
T[icrsh][i,j] += 1j * R.next()
# Spin blocks to be read:
Nspinblocs = SP + 1 - SO # number of spins to read for Norbs and Ham, NOT Projectors
# read the list of N_Orbitals for all k points
N_Orbitals = [ [0 for isp in range(Nspinblocs)] for ik in xrange(Nk)]
for isp in range(Nspinblocs):
for ik in xrange(Nk):
N_Orbitals[ik][isp] = int(R.next())
#print N_Orbitals
# Initialise the projectors:
Proj_Mat = [ [ [numpy.zeros([corr_shells[icrsh][3], N_Orbitals[ik][isp]], numpy.complex_)
for icrsh in range (N_corr_shells)]
for isp in range(Nspinblocs)]
for ik in range(Nk) ]
# Read the projectors from the file:
for ik in xrange(Nk):
for icrsh in range(N_corr_shells):
no = corr_shells[icrsh][3]
# first Real part for BOTH spins, due to conventions in dmftproj:
for isp in range(Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i,j] = R.next()
# now Imag part:
for isp in range(Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i,j] += 1j * R.next()
# now define the arrays for weights and hopping ...
BZ_weights = numpy.ones([Nk],numpy.float_)/ float(Nk) # w(k_index), default normalisation
Hopping = [ [numpy.zeros([N_Orbitals[ik][isp],N_Orbitals[ik][isp]],numpy.complex_)
for isp in range(Nspinblocs)] for ik in xrange(Nk) ]
# weights in the file
for ik in xrange(Nk) : BZ_weights[ik] = R.next()
# if the sum over spins is in the weights, take it out again!!
sm = sum(BZ_weights)
BZ_weights[:] /= sm
# Grab the H
# we use now the convention of a DIAGONAL Hamiltonian!!!!
for isp in range(Nspinblocs):
for ik in xrange(Nk) :
no = N_Orbitals[ik][isp]
for i in xrange(no):
Hopping[ik][isp][i,i] = R.next() * EnergyUnit
#keep some things that we need for reading parproj:
self.N_shells = N_shells
self.shells = shells
self.N_corr_shells = N_corr_shells
self.corr_shells = corr_shells
self.Nspinblocs = Nspinblocs
self.N_Orbitals = N_Orbitals
self.Nk = Nk
self.SO = SO
self.SP = SP
self.EnergyUnit = EnergyUnit
except StopIteration : # a more explicit error if the file is corrupted.
raise "SumK_LDA : reading file HMLT_file failed!"
R.close()
#print Proj_Mat[0]
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile,'a')
if not (self.LDASubGrp in ar): ar.create_group(self.LDASubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
ar[self.LDASubGrp]['EnergyUnit'] = EnergyUnit
ar[self.LDASubGrp]['Nk'] = Nk
ar[self.LDASubGrp]['k_dep_projection'] = k_dep_projection
ar[self.LDASubGrp]['SP'] = SP
ar[self.LDASubGrp]['SO'] = SO
ar[self.LDASubGrp]['charge_below'] = charge_below
ar[self.LDASubGrp]['Density_Required'] = Density_Required
ar[self.LDASubGrp]['symm_op'] = symm_op
ar[self.LDASubGrp]['N_shells'] = N_shells
ar[self.LDASubGrp]['shells'] = shells
ar[self.LDASubGrp]['N_corr_shells'] = N_corr_shells
ar[self.LDASubGrp]['corr_shells'] = corr_shells
ar[self.LDASubGrp]['use_rotations'] = use_rotations
ar[self.LDASubGrp]['rotmat'] = rotmat
ar[self.LDASubGrp]['rotmat_timeinv'] = rotmat_timeinv
ar[self.LDASubGrp]['Nreps'] = Nreps
ar[self.LDASubGrp]['dim_reps'] = dim_reps
ar[self.LDASubGrp]['T'] = T
ar[self.LDASubGrp]['N_Orbitals'] = N_Orbitals
ar[self.LDASubGrp]['Proj_Mat'] = Proj_Mat
ar[self.LDASubGrp]['BZ_weights'] = BZ_weights
ar[self.LDASubGrp]['Hopping'] = Hopping
del ar
# Symmetries are used,
# Now do the symmetries for correlated orbitals:
self.read_Symmetry_input(orbits=corr_shells,symmfile=self.Symm_file,SymmSubGrp=self.SymmSubGrp,SO=SO,SP=SP)
def read_Symmetry_input(self,orbits,symmfile,SymmSubGrp,SO,SP):
"""
Reads input for the symmetrisations from symmfile, which is case.sympar or case.symqmc.
"""
if not (MPI.IS_MASTER_NODE()): return
MPI.report("Reading symmetry input from %s..."%symmfile)
N_orbits = len(orbits)
R=Read_Fortran_File(symmfile)
try:
Ns = int(R.next()) # Number of symmetry operations
Natoms = int(R.next()) # number of atoms involved
perm = [ [int(R.next()) for i in xrange(Natoms)] for j in xrange(Ns) ] # list of permutations of the atoms
if SP:
timeinv = [ int(R.next()) for j in xrange(Ns) ] # timeinversion for SO xoupling
else:
timeinv = [ 0 for j in xrange(Ns) ]
# Now read matrices:
mat = []
for iNs in xrange(Ns):
mat.append( [ numpy.zeros([orbits[orb][3], orbits[orb][3]],numpy.complex_) for orb in xrange(N_orbits) ] )
for orb in range(N_orbits):
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[iNs][orb][i,j] = R.next() # real part
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[iNs][orb][i,j] += 1j * R.next() # imaginary part
# determine the inequivalent shells:
#SHOULD BE FINALLY REMOVED, PUT IT FOR ALL ORBITALS!!!!!
#self.inequiv_shells(orbits)
mat_tinv = [numpy.identity(orbits[orb][3],numpy.complex_)
for orb in range(N_orbits)]
if ((SO==0) and (SP==0)):
# here we need an additional time inversion operation, so read it:
for orb in range(N_orbits):
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat_tinv[orb][i,j] = R.next() # real part
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat_tinv[orb][i,j] += 1j * R.next() # imaginary part
except StopIteration : # a more explicit error if the file is corrupted.
raise "Symmetry : reading file failed!"
R.close()
# Save it to the HDF:
ar=HDF_Archive(self.HDFfile,'a')
if not (SymmSubGrp in ar): ar.create_group(SymmSubGrp)
thingstowrite = ['Ns','Natoms','perm','orbits','SO','SP','timeinv','mat','mat_tinv']
for it in thingstowrite: exec "ar['%s']['%s'] = %s"%(SymmSubGrp,it,it)
del ar
def convert_bands_input(self,BandsSubGrp = 'SumK_LDA_Bands'):
"""
Converts the input for momentum resolved spectral functions, and stores it in BandsSubGrp in the
HDF5.
"""
if not (MPI.IS_MASTER_NODE()): return
self.BandsSubGrp = BandsSubGrp
MPI.report("Reading bands input from %s..."%self.Band_file)
R = Read_Fortran_File(self.Band_file)
try:
Nk = int(R.next())
# read the list of N_Orbitals for all k points
N_Orbitals = [ [0 for isp in range(self.Nspinblocs)] for ik in xrange(Nk)]
for isp in range(self.Nspinblocs):
for ik in xrange(Nk):
N_Orbitals[ik][isp] = int(R.next())
# Initialise the projectors:
Proj_Mat = [ [ [numpy.zeros([self.corr_shells[icrsh][3], N_Orbitals[ik][isp]], numpy.complex_)
for icrsh in range (self.N_corr_shells)]
for isp in range(self.Nspinblocs)]
for ik in range(Nk) ]
# Read the projectors from the file:
for ik in xrange(Nk):
for icrsh in range(self.N_corr_shells):
no = self.corr_shells[icrsh][3]
# first Real part for BOTH spins, due to conventions in dmftproj:
for isp in range(self.Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i,j] = R.next()
# now Imag part:
for isp in range(self.Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i,j] += 1j * R.next()
Hopping = [ [numpy.zeros([N_Orbitals[ik][isp],N_Orbitals[ik][isp]],numpy.complex_)
for isp in range(self.Nspinblocs)] for ik in xrange(Nk) ]
# Grab the H
# we use now the convention of a DIAGONAL Hamiltonian!!!!
for isp in range(self.Nspinblocs):
for ik in xrange(Nk) :
no = N_Orbitals[ik][isp]
for i in xrange(no):
Hopping[ik][isp][i,i] = R.next() * self.EnergyUnit
# now read the partial projectors:
N_parproj = [int(R.next()) for i in range(self.N_shells)]
# Initialise P, here a double list of matrices:
Proj_Mat_pc = [ [ [ [numpy.zeros([self.shells[ish][3], N_Orbitals[ik][isp]], numpy.complex_)
for ir in range(N_parproj[ish])]
for ish in range (self.N_shells) ]
for isp in range(self.Nspinblocs) ]
for ik in range(Nk) ]
for ish in range(self.N_shells):
for ik in xrange(Nk):
for ir in range(N_parproj[ish]):
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][i,j] = R.next()
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][i,j] += 1j * R.next()
except StopIteration : # a more explicit error if the file is corrupted.
raise "SumK_LDA : reading file HMLT_file failed!"
R.close()
# reading done!
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile,'a')
if not (self.BandsSubGrp in ar): ar.create_group(self.BandsSubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
thingstowrite = ['Nk','N_Orbitals','Proj_Mat','Hopping','N_parproj','Proj_Mat_pc']
for it in thingstowrite: exec "ar['%s']['%s'] = %s"%(self.BandsSubGrp,it,it)
#ar[self.BandsSubGrp]['Nk'] = Nk
#ar[self.BandsSubGrp]['N_Orbitals'] = N_Orbitals
#ar[self.BandsSubGrp]['Proj_Mat'] = Proj_Mat
#self.Proj_Mat = Proj_Mat
#self.N_Orbitals = N_Orbitals
#self.Nk = Nk
#self.Hopping = Hopping
del ar
def convert_DMFT_input(self):
"""
Reads the input files, and stores the data in the HDFfile
"""
if not (MPI.IS_MASTER_NODE()): return # do it only on master:
MPI.report("Reading input from %s..." % self.LDA_file)
# Read and write only on Master!!!
# R is a generator : each R.Next() will return the next number in the file
R = Read_Fortran_File(self.LDA_file)
try:
EnergyUnit = R.next() # read the energy convertion factor
Nk = int(R.next()) # read the number of k points
k_dep_projection = 1
SP = int(R.next()) # flag for spin-polarised calculation
SO = int(R.next()) # flag for spin-orbit calculation
charge_below = R.next() # total charge below energy window
Density_Required = R.next(
) # total density required, for setting the chemical potential
symm_op = 1 # Use symmetry groups for the k-sum
# the information on the non-correlated shells is not important here, maybe skip:
N_shells = int(R.next(
)) # number of shells (e.g. Fe d, As p, O p) in the unit cell,
# corresponds to index R in formulas
# now read the information about the shells:
shells = [[int(R.next()) for i in range(4)]
for icrsh in range(N_shells)
] # reads iatom, sort, l, dim
N_corr_shells = int(R.next(
)) # number of corr. shells (e.g. Fe d, Ce f) in the unit cell,
# corresponds to index R in formulas
# now read the information about the shells:
corr_shells = [[int(R.next()) for i in range(6)]
for icrsh in range(N_corr_shells)
] # reads iatom, sort, l, dim, SO flag, irep
self.inequiv_shells(
corr_shells
) # determine the number of inequivalent correlated shells, has to be known for further reading...
use_rotations = 1
rotmat = [
numpy.identity(corr_shells[icrsh][3], numpy.complex_)
for icrsh in xrange(N_corr_shells)
]
# read the matrices
rotmat_timeinv = [0 for i in range(N_corr_shells)]
for icrsh in xrange(N_corr_shells):
for i in xrange(corr_shells[icrsh][3]): # read real part:
for j in xrange(corr_shells[icrsh][3]):
rotmat[icrsh][i, j] = R.next()
for i in xrange(corr_shells[icrsh][3]): # read imaginary part:
for j in xrange(corr_shells[icrsh][3]):
rotmat[icrsh][i, j] += 1j * R.next()
if (SP == 1): # read time inversion flag:
rotmat_timeinv[icrsh] = int(R.next())
# Read here the infos for the transformation of the basis:
Nreps = [1 for i in range(self.N_inequiv_corr_shells)]
dim_reps = [0 for i in range(self.N_inequiv_corr_shells)]
T = []
for icrsh in range(self.N_inequiv_corr_shells):
Nreps[icrsh] = int(R.next(
)) # number of representatives ("subsets"), e.g. t2g and eg
dim_reps[icrsh] = [int(R.next()) for i in range(Nreps[icrsh])
] # dimensions of the subsets
# The transformation matrix:
# it is of dimension 2l+1, if no SO, and 2*(2l+1) with SO!!
#T = []
#for ish in xrange(self.N_inequiv_corr_shells):
ll = 2 * corr_shells[self.invshellmap[icrsh]][2] + 1
lmax = ll * (corr_shells[self.invshellmap[icrsh]][4] + 1)
T.append(numpy.zeros([lmax, lmax], numpy.complex_))
# now read it from file:
for i in xrange(lmax):
for j in xrange(lmax):
T[icrsh][i, j] = R.next()
for i in xrange(lmax):
for j in xrange(lmax):
T[icrsh][i, j] += 1j * R.next()
# Spin blocks to be read:
Nspinblocs = SP + 1 - SO # number of spins to read for Norbs and Ham, NOT Projectors
# read the list of N_Orbitals for all k points
N_Orbitals = [[0 for isp in range(Nspinblocs)]
for ik in xrange(Nk)]
for isp in range(Nspinblocs):
for ik in xrange(Nk):
N_Orbitals[ik][isp] = int(R.next())
#print N_Orbitals
# Initialise the projectors:
Proj_Mat = [[[
numpy.zeros([corr_shells[icrsh][3], N_Orbitals[ik][isp]],
numpy.complex_) for icrsh in range(N_corr_shells)
] for isp in range(Nspinblocs)] for ik in range(Nk)]
# Read the projectors from the file:
for ik in xrange(Nk):
for icrsh in range(N_corr_shells):
no = corr_shells[icrsh][3]
# first Real part for BOTH spins, due to conventions in dmftproj:
for isp in range(Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i, j] = R.next()
# now Imag part:
for isp in range(Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i, j] += 1j * R.next()
# now define the arrays for weights and hopping ...
BZ_weights = numpy.ones([Nk], numpy.float_) / float(
Nk) # w(k_index), default normalisation
Hopping = [[
numpy.zeros([N_Orbitals[ik][isp], N_Orbitals[ik][isp]],
numpy.complex_) for isp in range(Nspinblocs)
] for ik in xrange(Nk)]
# weights in the file
for ik in xrange(Nk):
BZ_weights[ik] = R.next()
# if the sum over spins is in the weights, take it out again!!
sm = sum(BZ_weights)
BZ_weights[:] /= sm
# Grab the H
# we use now the convention of a DIAGONAL Hamiltonian!!!!
for isp in range(Nspinblocs):
for ik in xrange(Nk):
no = N_Orbitals[ik][isp]
for i in xrange(no):
Hopping[ik][isp][i, i] = R.next() * EnergyUnit
#keep some things that we need for reading parproj:
self.N_shells = N_shells
self.shells = shells
self.N_corr_shells = N_corr_shells
self.corr_shells = corr_shells
self.Nspinblocs = Nspinblocs
self.N_Orbitals = N_Orbitals
self.Nk = Nk
self.SO = SO
self.SP = SP
self.EnergyUnit = EnergyUnit
except StopIteration: # a more explicit error if the file is corrupted.
raise "SumK_LDA : reading file HMLT_file failed!"
R.close()
#print Proj_Mat[0]
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile, 'a')
if not (self.LDASubGrp in ar): ar.create_group(self.LDASubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
ar[self.LDASubGrp]['EnergyUnit'] = EnergyUnit
ar[self.LDASubGrp]['Nk'] = Nk
ar[self.LDASubGrp]['k_dep_projection'] = k_dep_projection
ar[self.LDASubGrp]['SP'] = SP
ar[self.LDASubGrp]['SO'] = SO
ar[self.LDASubGrp]['charge_below'] = charge_below
ar[self.LDASubGrp]['Density_Required'] = Density_Required
ar[self.LDASubGrp]['symm_op'] = symm_op
ar[self.LDASubGrp]['N_shells'] = N_shells
ar[self.LDASubGrp]['shells'] = shells
ar[self.LDASubGrp]['N_corr_shells'] = N_corr_shells
ar[self.LDASubGrp]['corr_shells'] = corr_shells
ar[self.LDASubGrp]['use_rotations'] = use_rotations
ar[self.LDASubGrp]['rotmat'] = rotmat
ar[self.LDASubGrp]['rotmat_timeinv'] = rotmat_timeinv
ar[self.LDASubGrp]['Nreps'] = Nreps
ar[self.LDASubGrp]['dim_reps'] = dim_reps
ar[self.LDASubGrp]['T'] = T
ar[self.LDASubGrp]['N_Orbitals'] = N_Orbitals
ar[self.LDASubGrp]['Proj_Mat'] = Proj_Mat
ar[self.LDASubGrp]['BZ_weights'] = BZ_weights
ar[self.LDASubGrp]['Hopping'] = Hopping
del ar
# Symmetries are used,
# Now do the symmetries for correlated orbitals:
self.read_Symmetry_input(orbits=corr_shells,
symmfile=self.Symm_file,
SymmSubGrp=self.SymmSubGrp,
SO=SO,
SP=SP)
def convert_bands_input(self, BandsSubGrp='SumK_LDA_Bands'):
"""
Converts the input for momentum resolved spectral functions, and stores it in BandsSubGrp in the
HDF5.
"""
if not (MPI.IS_MASTER_NODE()): return
self.BandsSubGrp = BandsSubGrp
MPI.report("Reading bands input from %s..." % self.Band_file)
R = Read_Fortran_File(self.Band_file)
try:
Nk = int(R.next())
# read the list of N_Orbitals for all k points
N_Orbitals = [[0 for isp in range(self.Nspinblocs)]
for ik in xrange(Nk)]
for isp in range(self.Nspinblocs):
for ik in xrange(Nk):
N_Orbitals[ik][isp] = int(R.next())
# Initialise the projectors:
Proj_Mat = [[[
numpy.zeros([self.corr_shells[icrsh][3], N_Orbitals[ik][isp]],
numpy.complex_)
for icrsh in range(self.N_corr_shells)
] for isp in range(self.Nspinblocs)] for ik in range(Nk)]
# Read the projectors from the file:
for ik in xrange(Nk):
for icrsh in range(self.N_corr_shells):
no = self.corr_shells[icrsh][3]
# first Real part for BOTH spins, due to conventions in dmftproj:
for isp in range(self.Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i, j] = R.next()
# now Imag part:
for isp in range(self.Nspinblocs):
for i in xrange(no):
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat[ik][isp][icrsh][i, j] += 1j * R.next()
Hopping = [[
numpy.zeros([N_Orbitals[ik][isp], N_Orbitals[ik][isp]],
numpy.complex_) for isp in range(self.Nspinblocs)
] for ik in xrange(Nk)]
# Grab the H
# we use now the convention of a DIAGONAL Hamiltonian!!!!
for isp in range(self.Nspinblocs):
for ik in xrange(Nk):
no = N_Orbitals[ik][isp]
for i in xrange(no):
Hopping[ik][isp][i, i] = R.next() * self.EnergyUnit
# now read the partial projectors:
N_parproj = [int(R.next()) for i in range(self.N_shells)]
# Initialise P, here a double list of matrices:
Proj_Mat_pc = [[[[
numpy.zeros([self.shells[ish][3], N_Orbitals[ik][isp]],
numpy.complex_) for ir in range(N_parproj[ish])
] for ish in range(self.N_shells)]
for isp in range(self.Nspinblocs)]
for ik in range(Nk)]
for ish in range(self.N_shells):
for ik in xrange(Nk):
for ir in range(N_parproj[ish]):
for isp in range(self.Nspinblocs):
for i in xrange(
self.shells[ish][3]): # read real part:
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][
i, j] = R.next()
for i in xrange(self.shells[ish]
[3]): # read imaginary part:
for j in xrange(N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][
i, j] += 1j * R.next()
except StopIteration: # a more explicit error if the file is corrupted.
raise "SumK_LDA : reading file HMLT_file failed!"
R.close()
# reading done!
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile, 'a')
if not (self.BandsSubGrp in ar): ar.create_group(self.BandsSubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
thingstowrite = [
'Nk', 'N_Orbitals', 'Proj_Mat', 'Hopping', 'N_parproj',
'Proj_Mat_pc'
]
for it in thingstowrite:
exec "ar['%s']['%s'] = %s" % (self.BandsSubGrp, it, it)
#ar[self.BandsSubGrp]['Nk'] = Nk
#ar[self.BandsSubGrp]['N_Orbitals'] = N_Orbitals
#ar[self.BandsSubGrp]['Proj_Mat'] = Proj_Mat
#self.Proj_Mat = Proj_Mat
#self.N_Orbitals = N_Orbitals
#self.Nk = Nk
#self.Hopping = Hopping
del ar
def read_Symmetry_input(self, orbits, symmfile, SymmSubGrp, SO, SP):
"""
Reads input for the symmetrisations from symmfile, which is case.sympar or case.symqmc.
"""
if not (MPI.IS_MASTER_NODE()): return
MPI.report("Reading symmetry input from %s..." % symmfile)
N_orbits = len(orbits)
R = Read_Fortran_File(symmfile)
try:
Ns = int(R.next()) # Number of symmetry operations
Natoms = int(R.next()) # number of atoms involved
perm = [[int(R.next()) for i in xrange(Natoms)]
for j in xrange(Ns)] # list of permutations of the atoms
if SP:
timeinv = [int(R.next()) for j in xrange(Ns)
] # timeinversion for SO xoupling
else:
timeinv = [0 for j in xrange(Ns)]
# Now read matrices:
mat = []
for iNs in xrange(Ns):
mat.append([
numpy.zeros([orbits[orb][3], orbits[orb][3]],
numpy.complex_) for orb in xrange(N_orbits)
])
for orb in range(N_orbits):
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[iNs][orb][i, j] = R.next() # real part
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat[iNs][orb][i,
j] += 1j * R.next() # imaginary part
# determine the inequivalent shells:
#SHOULD BE FINALLY REMOVED, PUT IT FOR ALL ORBITALS!!!!!
#self.inequiv_shells(orbits)
mat_tinv = [
numpy.identity(orbits[orb][3], numpy.complex_)
for orb in range(N_orbits)
]
if ((SO == 0) and (SP == 0)):
# here we need an additional time inversion operation, so read it:
for orb in range(N_orbits):
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat_tinv[orb][i, j] = R.next() # real part
for i in xrange(orbits[orb][3]):
for j in xrange(orbits[orb][3]):
mat_tinv[orb][i,
j] += 1j * R.next() # imaginary part
except StopIteration: # a more explicit error if the file is corrupted.
raise "Symmetry : reading file failed!"
R.close()
# Save it to the HDF:
ar = HDF_Archive(self.HDFfile, 'a')
if not (SymmSubGrp in ar): ar.create_group(SymmSubGrp)
thingstowrite = [
'Ns', 'Natoms', 'perm', 'orbits', 'SO', 'SP', 'timeinv', 'mat',
'mat_tinv'
]
for it in thingstowrite:
exec "ar['%s']['%s'] = %s" % (SymmSubGrp, it, it)
del ar
def convert_Parproj_input(self,
ParProjSubGrp='SumK_LDA_ParProj',
SymmParSubGrp='SymmPar'):
"""
Reads the input for the partial charges projectors from case.parproj, and stores it in the SymmParSubGrp
group in the HDF5.
"""
if not (MPI.IS_MASTER_NODE()): return
self.ParProjSubGrp = ParProjSubGrp
self.SymmParSubGrp = SymmParSubGrp
MPI.report("Reading parproj input from %s..." % self.Parproj_file)
Dens_Mat_below = [[
numpy.zeros([self.shells[ish][3], self.shells[ish][3]],
numpy.complex_) for ish in range(self.N_shells)
] for isp in range(self.Nspinblocs)]
R = Read_Fortran_File(self.Parproj_file)
#try:
N_parproj = [int(R.next()) for i in range(self.N_shells)]
# Initialise P, here a double list of matrices:
Proj_Mat_pc = [[[[
numpy.zeros([self.shells[ish][3], self.N_Orbitals[ik][isp]],
numpy.complex_) for ir in range(N_parproj[ish])
] for ish in range(self.N_shells)] for isp in range(self.Nspinblocs)]
for ik in range(self.Nk)]
rotmat_all = [
numpy.identity(self.shells[ish][3], numpy.complex_)
for ish in xrange(self.N_shells)
]
rotmat_all_timeinv = [0 for i in range(self.N_shells)]
for ish in range(self.N_shells):
#print ish
# read first the projectors for this orbital:
for ik in xrange(self.Nk):
for ir in range(N_parproj[ish]):
for isp in range(self.Nspinblocs):
for i in xrange(
self.shells[ish][3]): # read real part:
for j in xrange(self.N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][i, j] = R.next()
for isp in range(self.Nspinblocs):
for i in xrange(
self.shells[ish][3]): # read imaginary part:
for j in xrange(self.N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][
i, j] += 1j * R.next()
# now read the Density Matrix for this orbital below the energy window:
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(self.shells[ish][3]):
Dens_Mat_below[isp][ish][i, j] = R.next()
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(self.shells[ish][3]):
Dens_Mat_below[isp][ish][i, j] += 1j * R.next()
if (self.SP == 0): Dens_Mat_below[isp][ish] /= 2.0
# Global -> local rotation matrix for this shell:
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(self.shells[ish][3]):
rotmat_all[ish][i, j] = R.next()
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(self.shells[ish][3]):
rotmat_all[ish][i, j] += 1j * R.next()
#print Dens_Mat_below[0][ish],Dens_Mat_below[1][ish]
if (self.SP):
rotmat_all_timeinv[ish] = int(R.next())
#except StopIteration : # a more explicit error if the file is corrupted.
# raise "SumK_LDA_Wien2k_input: reading file for Projectors failed!"
R.close()
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile, 'a')
if not (self.ParProjSubGrp in ar): ar.create_group(self.ParProjSubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
thingstowrite = [
'Dens_Mat_below', 'N_parproj', 'Proj_Mat_pc', 'rotmat_all',
'rotmat_all_timeinv'
]
for it in thingstowrite:
exec "ar['%s']['%s'] = %s" % (self.ParProjSubGrp, it, it)
del ar
# Symmetries are used,
# Now do the symmetries for all orbitals:
self.read_Symmetry_input(orbits=self.shells,
symmfile=self.Symmpar_file,
SymmSubGrp=self.SymmParSubGrp,
SO=self.SO,
SP=self.SP)
from pytriqs.Base.Archive import HDF_Archive
from pytriqs.Base.GF_Local import GFBloc_ImFreq
# Define a Green function
G = GFBloc_ImFreq ( Indices = [1], Beta = 10, NFreqMatsubara = 1000)
# Opens the file myfile.h5, in read/write mode
R = HDF_Archive('myfile.h5', 'w')
# Store the object G under the name 'g1' and mu
R['g1'] = G
R['mu'] = 1.29
del R # closing the files (optional : file is closed when the R reference is deleted)
from pytriqs.Base.GF_Local import *
from pytriqs.Base.GF_Local.Descriptors import iOmega_n
g = GFBloc_ImFreq(Indices = [1], Beta = 300, NFreqMatsubara = 1000, Name = "g")
g <<= inverse( iOmega_n + 0.5 )
print " van plot"
oplot (g, '-o', x_window = (0,3) )
print "plot done"
g<<= inverse( iOmega_n + 0.5 )
print "ok ----------------------"
from pytriqs.Base.Archive import HDF_Archive
R = HDF_Archive('myfile.h5', 'r')
for n, calculation in R.items() :
#g = calculation['g']
g <<= inverse( iOmega_n + 0.5 )
print "pokokook"
X,Y = g.x_data_view (x_window = (0,0.2), flatten_y = True )
#fitl = Fit ( X,Y.imag, linear )
g <<= inverse( iOmega_n + 0.5 )
print " van plot"
oplot (g, '-o', x_window = (0,3) )
g <<= inverse( iOmega_n + 0.5 )
from pytriqs.Base.Archive import HDF_Archive
from pytriqs.Base.GF_Local import GFBloc_ImFreq
R = HDF_Archive('myfile.h5', 'r') # Opens the file myfile.h5 in readonly mode
G = R['g1'] # Retrieve the object named g1 in the file as G
# ... ok now I can work with G
def convert_Parproj_input(self,ParProjSubGrp='SumK_LDA_ParProj',SymmParSubGrp='SymmPar'):
"""
Reads the input for the partial charges projectors from case.parproj, and stores it in the SymmParSubGrp
group in the HDF5.
"""
if not (MPI.IS_MASTER_NODE()): return
self.ParProjSubGrp = ParProjSubGrp
self.SymmParSubGrp = SymmParSubGrp
MPI.report("Reading parproj input from %s..."%self.Parproj_file)
Dens_Mat_below = [ [numpy.zeros([self.shells[ish][3],self.shells[ish][3]],numpy.complex_) for ish in range(self.N_shells)]
for isp in range(self.Nspinblocs) ]
R = Read_Fortran_File(self.Parproj_file)
#try:
N_parproj = [int(R.next()) for i in range(self.N_shells)]
# Initialise P, here a double list of matrices:
Proj_Mat_pc = [ [ [ [numpy.zeros([self.shells[ish][3], self.N_Orbitals[ik][isp]], numpy.complex_)
for ir in range(N_parproj[ish])]
for ish in range (self.N_shells) ]
for isp in range(self.Nspinblocs) ]
for ik in range(self.Nk) ]
rotmat_all = [numpy.identity(self.shells[ish][3],numpy.complex_) for ish in xrange(self.N_shells)]
rotmat_all_timeinv = [0 for i in range(self.N_shells)]
for ish in range(self.N_shells):
#print ish
# read first the projectors for this orbital:
for ik in xrange(self.Nk):
for ir in range(N_parproj[ish]):
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(self.N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][i,j] = R.next()
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(self.N_Orbitals[ik][isp]):
Proj_Mat_pc[ik][isp][ish][ir][i,j] += 1j * R.next()
# now read the Density Matrix for this orbital below the energy window:
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(self.shells[ish][3]):
Dens_Mat_below[isp][ish][i,j] = R.next()
for isp in range(self.Nspinblocs):
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(self.shells[ish][3]):
Dens_Mat_below[isp][ish][i,j] += 1j * R.next()
if (self.SP==0): Dens_Mat_below[isp][ish] /= 2.0
# Global -> local rotation matrix for this shell:
for i in xrange(self.shells[ish][3]): # read real part:
for j in xrange(self.shells[ish][3]):
rotmat_all[ish][i,j] = R.next()
for i in xrange(self.shells[ish][3]): # read imaginary part:
for j in xrange(self.shells[ish][3]):
rotmat_all[ish][i,j] += 1j * R.next()
#print Dens_Mat_below[0][ish],Dens_Mat_below[1][ish]
if (self.SP):
rotmat_all_timeinv[ish] = int(R.next())
#except StopIteration : # a more explicit error if the file is corrupted.
# raise "SumK_LDA_Wien2k_input: reading file for Projectors failed!"
R.close()
#-----------------------------------------
# Store the input into HDF5:
ar = HDF_Archive(self.HDFfile,'a')
if not (self.ParProjSubGrp in ar): ar.create_group(self.ParProjSubGrp)
# The subgroup containing the data. If it does not exist, it is created.
# If it exists, the data is overwritten!!!
thingstowrite = ['Dens_Mat_below','N_parproj','Proj_Mat_pc','rotmat_all','rotmat_all_timeinv']
for it in thingstowrite: exec "ar['%s']['%s'] = %s"%(self.ParProjSubGrp,it,it)
del ar
# Symmetries are used,
# Now do the symmetries for all orbitals:
self.read_Symmetry_input(orbits=self.shells,symmfile=self.Symmpar_file,SymmSubGrp=self.SymmParSubGrp,SO=self.SO,SP=self.SP)
N_Legendre_Coeffs=50, # Number of Legendre coefficients
Random_Generator_Name='mt19937', # Name of the random number generator
Use_Segment_Picture=True, # Use the segment picture
Measured_Operators={ # Operators to be averaged
'Nimp': N('up', 1) + N('down', 1)
},
Global_Moves=[ # Global move in the QMC
(0.05, lambda (a, alpha, dag): ({
'up': 'down',
'down': 'up'
}[a], alpha, dag))
],
)
# Initialize the non-interacting Green's function S.G0
for spin, g0 in S.G0:
g0 <<= inverse(iOmega_n - e_f - V**2 * Wilson(D))
# Run the solver. The result will be in S.G
S.Solve()
# Save the results in an hdf5 file (only on the master node)
from pytriqs.Base.Archive import HDF_Archive
import pytriqs.Base.Utility.MPI as MPI
if MPI.IS_MASTER_NODE():
Results = HDF_Archive("solution.h5", 'w')
Results["G"] = S.G
Results["Gl"] = S.G_Legendre
Results["Nimp"] = S.Measured_Operators_Results['Nimp']
GFstruct = [ ('up',[1]), ('down',[1]) ], # Structure of the Green's function
H_Local = U * N('up',1) * N('down',1), # Local Hamiltonian
Quantum_Numbers = { # Quantum Numbers
'Nup' : N('up',1), # (operators commuting with H_Local)
'Ndown' : N('down',1) },
N_Cycles = 100000, # Number of QMC cycles
Length_Cycle = 200, # Length of one cycle
N_Warmup_Iteration = 10000, # Warmup cycles
Use_Segment_Picture = True, # Use the segment picture
Global_Moves = [ # Global move in the QMC
(0.05, lambda (a,alpha,dag) : ( {'up':'down','down':'up'}[a],alpha,dag ) ) ],
)
from pytriqs.Base.Archive import HDF_Archive
import pytriqs.Base.Utility.MPI as MPI
for random_name in ['mt11213b','lagged_fibonacci607']:
# Solve using random_name as a generator
S.Random_Generator_Name = random_name
for spin, g0 in S.G0 :
g0 <<= inverse( iOmega_n - e_f - V**2 * Wilson(D) )
S.Solve()
# Save the results in an hdf5 file (only on the master node)
if MPI.IS_MASTER_NODE():
Results = HDF_Archive("random.h5")
Results["G_%s"%(random_name)] = S.G
del Results