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#!/usr/bin/python
#=================================================================#
# Script to plot the bandstructure from an abinit bandstructure #
# _EIG.nc netcdf file or from a wannier bandstructure, or from #
# an _EIG.nc file+GW file+ bandstructure _EIG.nc file #
#=================================================================#
#########
#IMPORTS#
#########
import numpy as N
import matplotlib.pyplot as P
import matplotlib.ticker as mticker
import netCDF4 as nc
import sys
import os
import argparse
import time
#############
##VARIABLES##
#############
class VariableContainer:pass
#Constants
csts = VariableContainer()
csts.hartree2ev = N.float(27.211396132)
csts.ev2hartree = N.float(1/csts.hartree2ev)
csts.sqrtpi = N.float(N.sqrt(N.pi))
csts.invsqrtpi = N.float(1/csts.sqrtpi)
csts.TOLKPTS = N.float(0.00001)
###########
##CLASSES##
###########
class PolynomialFit(object):
def __init__(self):
self.degree = 2
class EigenvalueContainer(object):
nsppol = None
nkpt = None
mband = None
eigenvalues = None
units = None
wtk = None
filename = None
filefullpath = None
bd_indices = None
eigenvalue_type = None
kpoints = None
#kpoint_sampling_type: can be Monkhorst-Pack or Bandstructure
KPT_W90_TOL = N.float(1.0e-6)
KPT_DFT_TOL = N.float(1.0e-8)
kpoint_sampling_type = 'Monkhorst-Pack'
inputgvectors = None
gvectors = None
special_kpoints = None
special_kpoints_names = None
special_kpoints_indices = None
kpoint_path_values = None
kpoint_reduced_path_values = None
kpoint_path_length = None
#reduced_norm = None
norm_paths = None
norm_reduced_paths = None
def __init__(self,directory=None,filename=None):
if filename == None:return
if directory == None:directory='.'
self.filename = filename
self.filefullpath = '%s/%s' %(directory,filename)
self.file_open(self.filefullpath)
def set_kpoint_sampling_type(self,kpoint_sampling_type):
if kpoint_sampling_type != 'Monkhorst-Pack' and kpoint_sampling_type != 'Bandstructure':
print 'ERROR: kpoint_sampling_type "%s" does not exists' %kpoint_sampling_type
print ' it should be "Monkhorst-Pack" or "Bandstructure" ... exit'
sys.exit()
self.kpoint_sampling_type = kpoint_sampling_type
def correct_kpt(self,kpoint,tolerance=N.float(1.0e-6)):
kpt_correct = N.array(kpoint,N.float)
changed = False
for ii in range(3):
if N.allclose(kpoint[ii],N.float(1.0/3.0),atol=tolerance):
kpt_correct[ii] = N.float(1.0/3.0)
changed = True
elif N.allclose(kpoint[ii],N.float(1.0/6.0),atol=tolerance):
kpt_correct[ii] = N.float(1.0/6.0)
changed = True
elif N.allclose(kpoint[ii],N.float(-1.0/6.0),atol=tolerance):
kpt_correct[ii] = N.float(-1.0/6.0)
changed = True
elif N.allclose(kpoint[ii],N.float(-1.0/3.0),atol=tolerance):
kpt_correct[ii] = N.float(-1.0/3.0)
changed = True
if changed:
print 'COMMENT: kpoint %15.12f %15.12f %15.12f has been changed to %15.12f %15.12f %15.12f' %(kpoint[0],kpoint[1],kpoint[2],kpt_correct[0],kpt_correct[1],kpt_correct[2])
return kpt_correct
def find_special_kpoints(self,gvectors=None):
if self.kpoint_sampling_type != 'Bandstructure':
print 'ERROR: special kpoints are usefull only for bandstructures ... returning find_special_kpoints'
return
if self.eigenvalue_type == 'W90':
correct_kpt_tolerance = N.float(1.0e-4)
KPT_TOL = self.KPT_W90_TOL
elif self.eigenvalue_type == 'DFT':
correct_kpt_tolerance = N.float(1.0e-6)
KPT_TOL = self.KPT_DFT_TOL
else:
print 'ERROR: eigenvalue_type is "%s" while it should be "W90" or "DFT" ... returning find_special_kpoints' %self.eigenvalue_type
return
if gvectors == None:
self.inputgvectors = False
self.gvectors = N.identity(3,N.float)
else:
if N.shape(gvectors) != (3, 3):
print 'ERROR: wrong gvectors ... exiting now'
sys.exit()
self.inputgvectors = True
self.gvectors = gvectors
full_kpoints = N.zeros((self.nkpt,3),N.float)
for ikpt in range(self.nkpt):
full_kpoints[ikpt,:] = self.kpoints[ikpt,0]*self.gvectors[0,:]+self.kpoints[ikpt,1]*self.gvectors[1,:]+self.kpoints[ikpt,2]*self.gvectors[2,:]
delta_kpt = full_kpoints[1,:]-full_kpoints[0,:]
self.special_kpoints_indices = list()
self.special_kpoints = list()
self.special_kpoints_indices.append(0)
self.special_kpoints.append(self.correct_kpt(self.kpoints[0,:],tolerance=correct_kpt_tolerance))
for ikpt in range(1,self.nkpt-1):
thisdelta = full_kpoints[ikpt+1,:]-full_kpoints[ikpt,:]
if not N.allclose(thisdelta,delta_kpt,atol=KPT_TOL):
delta_kpt = thisdelta
self.special_kpoints_indices.append(ikpt)
self.special_kpoints.append(self.correct_kpt(self.kpoints[ikpt,:],tolerance=correct_kpt_tolerance))
self.special_kpoints_indices.append(N.shape(self.kpoints)[0]-1)
self.special_kpoints.append(self.correct_kpt(self.kpoints[-1,:],tolerance=correct_kpt_tolerance))
print 'Special Kpoints : '
print ' {0:d} : {1[0]: 8.8f} {1[1]: 8.8f} {1[2]: 8.8f}'.format(1,self.kpoints[0,:])
self.norm_paths = N.zeros((N.shape(self.special_kpoints_indices)[0]-1),N.float)
self.norm_reduced_paths = N.zeros((N.shape(self.special_kpoints_indices)[0]-1),N.float)
for ispkpt in range(1,N.shape(self.special_kpoints_indices)[0]):
self.norm_paths[ispkpt-1] = N.linalg.norm(full_kpoints[self.special_kpoints_indices[ispkpt]]-full_kpoints[self.special_kpoints_indices[ispkpt-1]])
self.norm_reduced_paths[ispkpt-1] = N.linalg.norm(self.special_kpoints[ispkpt]-self.special_kpoints[ispkpt-1])
print ' {2:d}-{3:d} path length : {0: 8.8f} | reduced path length : {1: 8.8f}'.\
format(self.norm_paths[ispkpt-1],self.norm_reduced_paths[ispkpt-1],ispkpt,ispkpt+1)
print ' {0:d} : {1[0]: 8.8f} {1[1]: 8.8f} {1[2]: 8.8f}'.format(ispkpt+1,self.kpoints[self.special_kpoints_indices[ispkpt],:])
self.kpoint_path_length = N.sum(self.norm_paths)
self.kpoint_reduced_path_length = N.sum(self.norm_reduced_paths)
self.normalized_kpoint_path_norm = self.norm_paths/self.kpoint_path_length
self.normalized_kpoint_reduced_path_norm = self.norm_reduced_paths/self.kpoint_reduced_path_length
kptredpathval = list()
kptpathval = list()
kptredpathval.append(N.float(0.0))
kptpathval.append(N.float(0.0))
curlen = N.float(0.0)
redcurlen = N.float(0.0)
for ispkpt in range(1,N.shape(self.special_kpoints_indices)[0]):
kptredpathval.extend(N.linspace(redcurlen,redcurlen+self.norm_reduced_paths[ispkpt-1],self.special_kpoints_indices[ispkpt]-self.special_kpoints_indices[ispkpt-1]+1)[1:])
kptpathval.extend(N.linspace(curlen,curlen+self.norm_paths[ispkpt-1],self.special_kpoints_indices[ispkpt]-self.special_kpoints_indices[ispkpt-1]+1)[1:])
redcurlen = redcurlen + self.norm_reduced_paths[ispkpt-1]
curlen = curlen + self.norm_paths[ispkpt-1]
self.kpoint_path_values = N.array(kptpathval,N.float)
self.kpoint_reduced_path_values = N.array(kptredpathval,N.float)
self.normalized_kpoint_path_values = self.kpoint_path_values/self.kpoint_path_length
self.normalized_kpoint_reduced_path_values = self.kpoint_reduced_path_values/self.kpoint_reduced_path_length
self.special_kpoints = N.array(self.special_kpoints,N.float)
def file_open(self,filefullpath):
if filefullpath[-3:] == '_GW':
self.gw_file_open(filefullpath)
elif filefullpath[-7:] == '_EIG.nc':
self.nc_eig_open(filefullpath)
elif filefullpath[-4:] == '.dat':
self.wannier_bs_file_open(filefullpath)
def has_eigenvalue(self,nsppol,isppol,kpoint,iband):
if self.nsppol != nsppol:
return False
for ikpt in range(self.nkpt):
if N.absolute(self.kpoints[ikpt,0]-kpoint[0]) < csts.TOLKPTS and \
N.absolute(self.kpoints[ikpt,1]-kpoint[1]) < csts.TOLKPTS and \
N.absolute(self.kpoints[ikpt,2]-kpoint[2]) < csts.TOLKPTS:
if iband >= self.bd_indices[isppol,ikpt,0]-1 and iband < self.bd_indices[isppol,ikpt,1]:
return True
return False
return False
def get_eigenvalue(self,nsppol,isppol,kpoint,iband):
for ikpt in range(self.nkpt):
if N.absolute(self.kpoints[ikpt,0]-kpoint[0]) < csts.TOLKPTS and \
N.absolute(self.kpoints[ikpt,1]-kpoint[1]) < csts.TOLKPTS and \
N.absolute(self.kpoints[ikpt,2]-kpoint[2]) < csts.TOLKPTS:
return self.eigenvalues[isppol,ikpt,iband]
def wannier_bs_file_open(self,filefullpath):
if not (os.path.isfile(filefullpath)):
print 'ERROR : file "%s" does not exists' %filefullpath
print '... exiting now ...'
sys.exit()
print 'WARNING: no spin polarization reading yet for Wannier90 bandstructure files!'
self.eigenvalue_type = 'W90'
self.nsppol = None
self.nkpt = None
self.mband = None
self.eigenvalues = None
self.units = None
self.filefullpath = filefullpath
reader = open(self.filefullpath,'r')
filedata = reader.readlines()
reader.close()
for iline in range(len(filedata)):
if filedata[iline].strip() == '':
self.nkpt = iline
break
self.mband = N.int(len(filedata)/self.nkpt)
self.nsppol = 1
self.eigenvalues = N.zeros([self.nsppol,self.nkpt,self.mband],N.float)
self.kpoints = N.zeros([self.nkpt,3],N.float)
iline = 0
kpt_file = '%s.kpt' %filefullpath[:-4]
if os.path.isfile(kpt_file):
reader = open(kpt_file,'r')
kptdata = reader.readlines()
reader.close()
if N.int(kptdata[0]) != self.nkpt:
print 'ERROR : the number of kpoints in file "%s" is not the same as in "%s" ... exit' %(self.filefullpath,kpt_file)
sys.exit()
for ikpt in range(self.nkpt):
linesplit = kptdata[ikpt+1].split()
self.kpoints[ikpt,0] = N.float(linesplit[0])
self.kpoints[ikpt,1] = N.float(linesplit[1])
self.kpoints[ikpt,2] = N.float(linesplit[2])
else:
for ikpt in range(self.nkpt):
self.kpoints[ikpt,0] = N.float(filedata[ikpt].split()[0])
for iband in range(self.mband):
for ikpt in range(self.nkpt):
self.eigenvalues[0,ikpt,iband] = N.float(filedata[iline].split()[1])
iline = iline+1
iline = iline+1
self.eigenvalues = self.eigenvalues*csts.ev2hartree
self.units = 'Hartree'
def gw_file_open(self,filefullpath):
if not (os.path.isfile(filefullpath)):
print 'ERROR : file "%s" does not exists' %filefullpath
print '... exiting now ...'
sys.exit()
self.eigenvalue_type = 'GW'
self.nsppol = None
self.nkpt = None
self.mband = None
self.eigenvalues = None
self.units = None
self.filefullpath = filefullpath
reader = open(self.filefullpath,'r')
filedata = reader.readlines()
reader.close()
self.nkpt = N.int(filedata[0].split()[0])
self.kpoints = N.ones([self.nkpt,3],N.float)
self.nsppol = N.int(filedata[0].split()[1])
self.bd_indices = N.zeros((self.nsppol,self.nkpt,2),N.int)
icur = 1
nbd_kpt = N.zeros([self.nsppol,self.nkpt],N.int)
for isppol in range(self.nsppol):
for ikpt in range(self.nkpt):
self.kpoints[ikpt,:] = N.array(filedata[icur].split()[:],N.float)
icur = icur + 1
nbd_kpt[isppol,ikpt] = N.int(filedata[icur])
self.bd_indices[isppol,ikpt,0] = N.int(filedata[icur+1].split()[0])
self.bd_indices[isppol,ikpt,1] = N.int(filedata[icur+nbd_kpt[isppol,ikpt]].split()[0])
icur = icur + nbd_kpt[isppol,ikpt] + 1
self.mband = N.max(self.bd_indices[:,:,1])
self.eigenvalues = N.zeros([self.nsppol,self.nkpt,self.mband],N.float)
self.eigenvalues[:,:,:] = N.nan
ii = 3
for isppol in range(self.nsppol):
for ikpt in range(self.nkpt):
for iband in range(self.bd_indices[isppol,ikpt,0]-1,self.bd_indices[isppol,ikpt,1]):
self.eigenvalues[isppol,ikpt,iband] = N.float(filedata[ii].split()[1])
ii = ii + 1
ii = ii + 2
self.eigenvalues = csts.ev2hartree*self.eigenvalues
self.units = 'Hartree'
def pfit_gw_file_write(self,polyfitlist,directory=None,filename=None,bdgw=None,energy_pivots=None,gwec=None):
if filename == None:return
if directory == None:directory='.'
filefullpath = '%s/%s' %(directory,filename)
if (os.path.isfile(filefullpath)):
user_input = raw_input('WARNING : file "%s" exists, do you want to overwrite it ? (y/n)' %filefullpath)
if not (user_input == 'y' or user_input == 'Y'):
return
writer = open(filefullpath,'w')
writer.write('%12s%12s\n' %(self.nkpt,self.nsppol))
if gwec == None:
for ikpt in range(self.nkpt):
for isppol in range(self.nsppol):
writer.write('%10.6f%10.6f%10.6f\n' %(self.kpoints[ikpt,0],self.kpoints[ikpt,1],self.kpoints[ikpt,2]))
writer.write('%4i\n' %(bdgw[1]-bdgw[0]+1))
for iband in range(bdgw[0]-1,bdgw[1]):
delta = N.polyval(polyfitlist[-1],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
for ipivot in range(len(energy_pivots)):
if csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband] <= energy_pivots[ipivot]:
delta = N.polyval(polyfitlist[ipivot],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
break
writer.write('%6i%9.4f%9.4f%9.4f\n' %(iband+1,csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband]+delta,delta,0.0))
else:
for ikpt in range(self.nkpt):
for isppol in range(self.nsppol):
writer.write('%10.6f%10.6f%10.6f\n' %(self.kpoints[ikpt,0],self.kpoints[ikpt,1],self.kpoints[ikpt,2]))
writer.write('%4i\n' %(bdgw[1]-bdgw[0]+1))
for iband in range(bdgw[0]-1,bdgw[1]):
if gwec.has_eigenvalue(self.nsppol,isppol,self.kpoints[ikpt],iband):
gw_eig = gwec.get_eigenvalue(self.nsppol,isppol,self.kpoints[ikpt],iband)
writer.write('%6i%9.4f%9.4f%9.4f\n' %(iband+1,csts.hartree2ev*gw_eig,csts.hartree2ev*(gw_eig-self.eigenvalues[isppol,ikpt,iband]),0.0))
else:
delta = N.polyval(polyfitlist[-1],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
for ipivot in range(len(energy_pivots)):
if csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband] <= energy_pivots[ipivot]:
delta = N.polyval(polyfitlist[ipivot],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
break
writer.write('%6i%9.4f%9.4f%9.4f\n' %(iband+1,csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband]+delta,delta,0.0))
writer.close()
def pfit_dft_to_gw_bs_write(self,polyfitlist,directory=None,filename=None,bdgw=None,energy_pivots=None,gwec=None):
if filename == None:return
if directory == None:directory='.'
filefullpath = '%s/%s' %(directory,filename)
if (os.path.isfile(filefullpath)):
user_input = raw_input('WARNING : file "%s" exists, do you want to overwrite it ? (y/n)' %filefullpath)
if not (user_input == 'y' or user_input == 'Y'):
return
writer = open(filefullpath,'w')
if gwec == None:
for ikpt in range(self.nkpt):
writer.write('%s' %ikpt)
for isppol in range(self.nsppol):
for iband in range(bdgw[0]-1,bdgw[1]):
delta = N.polyval(polyfitlist[-1],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
for ipivot in range(len(energy_pivots)):
if csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband] <= energy_pivots[ipivot]:
delta = N.polyval(polyfitlist[ipivot],csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband])
break
writer.write(' %s' %(csts.hartree2ev*self.eigenvalues[isppol,ikpt,iband]+delta))
writer.write('\n')
else:
print 'NOT SUPPORTED YET'
sys.exit()
writer.close()
def nc_eig_open(self,filefullpath):
if not (os.path.isfile(filefullpath)):
print 'ERROR : file "%s" does not exists' %filefullpath
print '... exiting now ...'
sys.exit()
ncdata = nc.Dataset(filefullpath)
self.eigenvalue_type = 'DFT'
self.nsppol = None
self.nkpt = None
self.mband = None
self.eigenvalues = None
self.units = None
self.filefullpath = filefullpath
for dimname,dimobj in ncdata.dimensions.iteritems():
if dimname == 'nsppol':self.nsppol = N.int(len(dimobj))
if dimname == 'nkpt':self.nkpt = N.int(len(dimobj))
if dimname == 'mband':self.mband = N.int(len(dimobj))
for varname in ncdata.variables:
if varname == 'Eigenvalues':
varobj = ncdata.variables[varname]
varshape = N.shape(varobj[:])
self.units = None
for attrname in varobj.ncattrs():
if attrname == 'units':
self.units = varobj.getncattr(attrname)
if self.units == None:
print 'WARNING : units are not specified'
print '... assuming "Hartree" units ...'
self.units = 'Hartree'
elif self.units != 'Hartree':
print 'ERROR : units are unknown : "%s"' %self.units
print '... exiting now ...'
sys.exit()
self.eigenvalues = N.reshape(N.array(varobj,N.float),varshape)
self.nsppol = varshape[0]
self.nkpt = varshape[1]
self.kpoints = -1*N.ones((self.nkpt,3),N.float)
self.mband = varshape[2]
self.bd_indices = N.zeros((self.nsppol,self.nkpt,2),N.int)
self.bd_indices[:,:,0] = 1
self.bd_indices[:,:,1] = self.mband
break
for varname in ncdata.variables:
if varname == 'Kptns':
varobj = ncdata.variables[varname]
varshape = N.shape(varobj[:])
self.kpoints = N.reshape(N.array(varobj,N.float),varshape)
def write_bandstructure_to_file(self,filename,option_kpts='bohrm1_units'):
#if option_kpts is set to 'normalized', the path of the bandstructure will be normalized to 1 (and special k-points correctly chosen)
if self.kpoint_sampling_type != 'Bandstructure':
print 'ERROR: kpoint_sampling_type is not "Bandstructure" ... returning from write_bandstructure_to_file'
return
if self.nsppol > 1:
print 'ERROR: number of spins is more than 1, this is not yet coded ... returning from write_bandstructure_to_file'
return
writer = open(filename,'w')
writer.write('# BANDSTRUCTURE FILE FROM DAVID\'S SCRIPT\n')
writer.write('# nsppol = %s\n' %self.nsppol)
writer.write('# nband = %s\n' %self.mband)
writer.write('# eigenvalue_type = %s\n' %self.eigenvalue_type)
if self.inputgvectors:
writer.write('# inputgvectors = 1 (%s)\n' %self.inputgvectors)
else:
writer.write('# inputgvectors = 0 (%s)\n' %self.inputgvectors)
writer.write('# gvectors(1) = %20.17f %20.17f %20.17f \n' %(self.gvectors[0,0],self.gvectors[0,1],self.gvectors[0,2]))
writer.write('# gvectors(2) = %20.17f %20.17f %20.17f \n' %(self.gvectors[1,0],self.gvectors[1,1],self.gvectors[1,2]))
writer.write('# gvectors(3) = %20.17f %20.17f %20.17f \n' %(self.gvectors[2,0],self.gvectors[2,1],self.gvectors[2,2]))
writer.write('# special_kpoints_number = %s\n' %(len(self.special_kpoints_indices)))
writer.write('# list of special kpoints : (given in reduced coordinates, value_path is in Bohr^-1, value_red_path has its total path normalized to 1)\n')
for ii in range(len(self.special_kpoints_indices)):
ispkpt = self.special_kpoints_indices[ii]
spkpt = self.special_kpoints[ii]
writer.write('# special_kpt_index %5s : %20.17f %20.17f %20.17f (value_path = %20.17f | value_red_path = %20.17f)\n' %(ispkpt,spkpt[0],spkpt[1],spkpt[2],self.kpoint_path_values[ispkpt],self.kpoint_reduced_path_values[ispkpt]))
writer.write('# special_kpoints_names :\n')
for ii in range(len(self.special_kpoints_indices)):
ispkpt = self.special_kpoints_indices[ii]
spkpt = self.special_kpoints[ii]
writer.write('# special_kpt_name %3s : "%s" : %20.17f %20.17f %20.17f\n' %(ii+1,self.special_kpoints_names[ii],spkpt[0],spkpt[1],spkpt[2]))
writer.write('# kpoint_path_length = %20.17f \n' %(self.kpoint_path_length))
writer.write('# kpoint_path_number = %s \n' %(self.nkpt))
if self.inputgvectors:
writer.write('# kpoint_path_units = %s\n' %(option_kpts))
else:
writer.write('# kpoint_path_units = %s (!!! CONSIDERING UNITARY GVECTORS MATRIX !!!)\n' %(option_kpts))
writer.write('#BEGIN\n')
if option_kpts == 'bohrm1_units':
values_path = self.kpoint_path_values
elif option_kpts == 'reduced':
values_path = self.kpoint_reduced_path_values
elif option_kpts == 'bohrm1_units_normalized':
values_path = self.normalized_kpoint_path_values
elif option_kpts == 'reduced_normalized':
values_path = self.normalized_kpoint_reduced_path_values
else:
print 'ERROR: wrong option_kpts ... exit'
writer.write('... CANCELLED (wrong option_kpts)')
writer.close()
sys.exit()
for isppol in range(self.nsppol):
writer.write('#isppol %s\n' %isppol)
for iband in range(self.mband):
writer.write('#iband %5s (band number %s)\n' %(iband,iband+1))
for ikpt in range(self.nkpt):
writer.write('%20.17f %20.17f\n' %(values_path[ikpt],self.eigenvalues[isppol,ikpt,iband]))
writer.write('\n')
writer.write('#END\n')
writer.close()
def print_bandstructure_info(self):
print 'Bandstructure file'
print 'nsppol : %s' %self.nsppol
print 'nband : %s' %self.mband
print 'eigenvalue type : %s' %self.eigenvalue_type
print 'special kpoints :'
for ispkpt in range(len(self.special_kpoints)):
print ' %2d : %15.12f %15.12f %15.12f' %(ispkpt+1,self.special_kpoints[ispkpt,0],self.special_kpoints[ispkpt,1],self.special_kpoints[ispkpt,2])
print 'kpoint path length : %s' %self.kpoint_path_length
print 'kpoint path units : %s' %self.kpoint_path_units
if self.inputgvectors == 1:
print 'kpoint path made with these gvectors :'
print ' gvectors(1) : %15.12f %15.12f %15.12f' %(self.gvectors[0,0],self.gvectors[0,1],self.gvectors[0,2])
print ' gvectors(2) : %15.12f %15.12f %15.12f' %(self.gvectors[1,0],self.gvectors[1,1],self.gvectors[1,2])
print ' gvectors(3) : %15.12f %15.12f %15.12f' %(self.gvectors[2,0],self.gvectors[2,1],self.gvectors[2,2])
else:
print ' !!! gvectors are unitary !!!'
print 'kpoint path number : %s' %self.nkpt
def read_bandstructure_from_file(self,filename):
reader = open(filename,'r')
bs_data = reader.readlines()
reader.close()
self.gvectors = N.identity(3,N.float)
self.kpoint_sampling_type = 'Bandstructure'
self.special_kpoints_indices = list()
self.special_kpoints = list()
for ii in range(len(bs_data)):
if bs_data[ii] == '#BEGIN\n':
ibegin = ii
break
elif bs_data[ii][:10] == '# nsppol =':
self.nsppol = N.int(bs_data[ii][10:])
elif bs_data[ii][:9] == '# nband =':
self.mband = N.int(bs_data[ii][9:])
elif bs_data[ii][:19] == '# eigenvalue_type =':
self.eigenvalue_type = bs_data[ii][19:].strip()
elif bs_data[ii][:17] == '# inputgvectors =':
tt = N.int(bs_data[ii][18])
if tt == 1:
self.inputgvectors = True
elif tt == 0:
self.inputgvectors = False
else:
print 'ERROR: reading inputgvectors ... exit'
sys.exit()
elif bs_data[ii][:15] == '# gvectors(1) =':
sp = bs_data[ii][15:].split()
self.gvectors[0,0] = N.float(sp[0])
self.gvectors[0,1] = N.float(sp[1])
self.gvectors[0,2] = N.float(sp[2])
elif bs_data[ii][:15] == '# gvectors(2) =':
sp = bs_data[ii][15:].split()
self.gvectors[1,0] = N.float(sp[0])
self.gvectors[1,1] = N.float(sp[1])
self.gvectors[1,2] = N.float(sp[2])
elif bs_data[ii][:15] == '# gvectors(3) =':
sp = bs_data[ii][15:].split()
self.gvectors[2,0] = N.float(sp[0])
self.gvectors[2,1] = N.float(sp[1])
self.gvectors[2,2] = N.float(sp[2])
elif bs_data[ii][:26] == '# special_kpoints_number =':
special_kpoints_number = N.int(bs_data[ii][26:])
self.special_kpoints_names = ['']*special_kpoints_number
elif bs_data[ii][:22] == '# special_kpt_index':
sp = bs_data[ii][22:].split()
self.special_kpoints_indices.append(N.int(sp[0]))
self.special_kpoints.append(N.array([sp[2],sp[3],sp[4]]))
elif bs_data[ii][:21] == '# special_kpt_name':
sp = bs_data[ii][21:].split()
ispkpt = N.int(sp[0])-1
self.special_kpoints_names[ispkpt] = sp[2][1:-1]
elif bs_data[ii][:22] == '# kpoint_path_length =':
self.kpoint_path_length = N.float(bs_data[ii][22:])
elif bs_data[ii][:22] == '# kpoint_path_number =':
self.nkpt = N.int(bs_data[ii][22:])
elif bs_data[ii][:21] == '# kpoint_path_units =':
self.kpoint_path_units = bs_data[ii][21:].split()[0]
self.special_kpoints_indices = N.array(self.special_kpoints_indices,N.int)
self.special_kpoints = N.array(self.special_kpoints,N.float)
if len(self.special_kpoints_indices) != special_kpoints_number or len(self.special_kpoints) != special_kpoints_number:
print 'ERROR: reading the special kpoints ... exit'
sys.exit()
self.kpoint_path_values = N.zeros([self.nkpt],N.float)
self.kpoint_reduced_path_values = N.zeros([self.nkpt],N.float)
if self.kpoint_path_units == 'bohrm1_units':
jj = 0
for ii in range(ibegin+1,len(bs_data)):
if bs_data[ii][:7] == '#isppol' or bs_data[ii][:6] == '#iband':continue
if bs_data[ii] == '\n':
break
self.kpoint_path_values[jj] = N.float(bs_data[ii].split()[0])
jj = jj + 1
if jj != self.nkpt:
print 'ERROR: reading bandstructure file ... exit'
sys.exit()
self.normalized_kpoint_path_values = self.kpoint_path_values/self.kpoint_path_length
if self.kpoint_path_units == 'bohrm1_units_normalized':
jj = 0
for ii in range(ibegin+1,len(bs_data)):
if bs_data[ii][:7] == '#isppol' or bs_data[ii][:6] == '#iband':continue
if bs_data[ii] == '\n':
break
self.normalized_kpoint_path_values[jj] = N.float(bs_data[ii].split()[0])
jj = jj + 1
if jj != self.nkpt:
print 'ERROR: reading bandstructure file ... exit'
sys.exit()
self.kpoint_path_values = self.normalized_kpoint_path_values*self.kpoint_path_length
elif self.kpoint_path_units == 'reduced_normalized':
jj = 0
for ii in range(ibegin+1,len(bs_data)):
if bs_data[ii][:7] == '#isppol' or bs_data[ii][:6] == '#iband':continue
if bs_data[ii] == '\n':
break
self.normalized_kpoint_reduced_path_values[jj] = N.float(bs_data[ii].split()[0])
jj = jj + 1
if jj != self.nkpt:
print 'ERROR: reading bandstructure file ... exit'
sys.exit()
self.kpoint_reduced_path_values = self.normalized_kpoint_reduced_path_values/self.kpoint_reduced_path_length
elif self.kpoint_path_units == 'reduced':
jj = 0
for ii in range(ibegin+1,len(bs_data)):
if bs_data[ii][:7] == '#isppol' or bs_data[ii][:6] == '#iband':continue
if bs_data[ii] == '\n':
break
self.kpoint_reduced_path_values[jj] = N.float(bs_data[ii].split()[0])
jj = jj + 1
if jj != self.nkpt:
print 'ERROR: reading bandstructure file ... exit'
sys.exit()
self.normalized_kpoint_reduced_path_values = self.kpoint_reduced_path_values/self.kpoint_reduced_path_length
self.eigenvalues = N.zeros([self.nsppol,self.nkpt,self.mband],N.float)
check_nband = 0
for ii in range(ibegin+1,len(bs_data)):
if bs_data[ii][:7] == '#isppol':
isppol = N.int(bs_data[ii][7:])
elif bs_data[ii][:6] == '#iband':
iband = N.int(bs_data[ii][6:].split()[0])
ikpt = 0
elif bs_data[ii][:4] == '#END':
break
elif bs_data[ii] == '\n':
check_nband = check_nband + 1
else:
self.eigenvalues[isppol,ikpt,iband] = N.float(bs_data[ii].split()[1])
ikpt = ikpt + 1
def check_gw_vs_dft_parameters(dftec,gwec):
if gwec.eigenvalue_type != 'GW' or dftec.eigenvalue_type != 'DFT':
print 'ERROR: eigenvalue files do not contain GW and DFT eigenvalues ... exiting now'
sys.exit()
if dftec.nsppol != gwec.nsppol or dftec.nkpt != gwec.nkpt:
print 'ERROR: the number of spins/kpoints is not the same in the GW and DFT files used to make the interpolation ... exiting now'
sys.exit()
for ikpt in range(dftec.nkpt):
if N.absolute(dftec.kpoints[ikpt,0]-gwec.kpoints[ikpt,0]) > csts.TOLKPTS or \
N.absolute(dftec.kpoints[ikpt,1]-gwec.kpoints[ikpt,1]) > csts.TOLKPTS or \
N.absolute(dftec.kpoints[ikpt,2]-gwec.kpoints[ikpt,2]) > csts.TOLKPTS:
print 'ERROR: the kpoints are not the same in the GW and DFT files used to make the interpolation ... exiting now'
sys.exit()
def plot_gw_vs_dft_eig(dftec,gwec,vbm_index,energy_pivots=None,polyfit_degrees=None):
if gwec.eigenvalue_type != 'GW' or dftec.eigenvalue_type != 'DFT':
print 'ERROR: eigenvalue containers do not contain GW and DFT eigenvalues ... exiting now'
sys.exit()
if dftec.nsppol != gwec.nsppol or dftec.nkpt != gwec.nkpt:
print 'ERROR: the number of spins/kpoints is not the same in the GW and DFT containers ... exiting now'
sys.exit()
valdftarray = N.array([],N.float)
conddftarray = N.array([],N.float)
valgwarray = N.array([],N.float)
condgwarray = N.array([],N.float)
for isppol in range(dftec.nsppol):
for ikpt in range(dftec.nkpt):
ibdmin = N.max([dftec.bd_indices[isppol,ikpt,0],gwec.bd_indices[isppol,ikpt,0]])-1
ibdmax = N.min([dftec.bd_indices[isppol,ikpt,1],gwec.bd_indices[isppol,ikpt,1]])-1
valdftarray = N.append(valdftarray,csts.hartree2ev*dftec.eigenvalues[isppol,ikpt,ibdmin:vbm_index])
valgwarray = N.append(valgwarray,csts.hartree2ev*gwec.eigenvalues[isppol,ikpt,ibdmin:vbm_index])
conddftarray = N.append(conddftarray,csts.hartree2ev*dftec.eigenvalues[isppol,ikpt,vbm_index:ibdmax+1])
condgwarray = N.append(condgwarray,csts.hartree2ev*gwec.eigenvalues[isppol,ikpt,vbm_index:ibdmax+1])
if energy_pivots == None:
if plot_figures == 1:
P.figure(1)
P.hold(True)
P.grid(True)
P.plot(valdftarray,valgwarray,'bx')
P.plot(conddftarray,condgwarray,'rx')
P.xlabel('DFT eigenvalues (in eV)')
P.ylabel('GW eigenvalues (in eV)')
P.figure(2)
P.hold(True)
P.grid(True)
P.plot(valdftarray,valgwarray-valdftarray,'bx')
P.plot(conddftarray,condgwarray-conddftarray,'rx')
P.xlabel('DFT eigenvalues (in eV)')
P.ylabel('GW correction to the DFT eigenvalues (in eV)')
P.show()
return
polyfitlist = list()
if len(polyfit_degrees) == 1:
print 'ERROR: making a fit with only one interval is not allowed ... exiting now'
sys.exit()
dftarray = N.append(valdftarray,conddftarray)
gwarray = N.append(valgwarray,condgwarray)
dftarray_list = list()
gwarray_list = list()
for iinterval in range(len(polyfit_degrees)):
tmpdftarray = N.array([],N.float)
tmpgwarray = N.array([],N.float)
if iinterval == 0:
emin = None
emax = energy_pivots[0]
for ii in range(len(dftarray)):
if dftarray[ii] <= emax:
tmpdftarray = N.append(tmpdftarray,[dftarray[ii]])
tmpgwarray = N.append(tmpgwarray,[gwarray[ii]])
elif iinterval == len(polyfit_degrees)-1:
emin = energy_pivots[-1]
emax = None
for ii in range(len(dftarray)):
if dftarray[ii] >= emin:
tmpdftarray = N.append(tmpdftarray,[dftarray[ii]])
tmpgwarray = N.append(tmpgwarray,[gwarray[ii]])
else:
emin = energy_pivots[iinterval-1]
emax = energy_pivots[iinterval]
for ii in range(len(dftarray)):
if dftarray[ii] >= emin and dftarray[ii] <= emax:
tmpdftarray = N.append(tmpdftarray,[dftarray[ii]])
tmpgwarray = N.append(tmpgwarray,[gwarray[ii]])
dftarray_list.append(tmpdftarray)
gwarray_list.append(tmpgwarray)
pfit = N.polyfit(tmpdftarray,tmpgwarray-tmpdftarray,polyfit_degrees[iinterval])
polyfitlist.append(pfit)
if plot_figures == 1:
linspace_npoints = 200
valpoly_x = N.linspace(N.min(valdftarray),N.max(valdftarray),linspace_npoints)
condpoly_x = N.linspace(N.min(conddftarray),N.max(conddftarray),linspace_npoints)
P.figure(3)
P.hold(True)
P.grid(True)
P.plot(valdftarray,valgwarray-valdftarray,'bx')
P.plot(conddftarray,condgwarray-conddftarray,'rx')
[x_min,x_max] = P.xlim()
for iinterval in range(len(polyfit_degrees)):
if iinterval == 0:
tmppoly_x = N.linspace(x_min,energy_pivots[iinterval],linspace_npoints)
elif iinterval == len(polyfit_degrees)-1:
tmppoly_x = N.linspace(energy_pivots[iinterval-1],x_max,linspace_npoints)
else:
tmppoly_x = N.linspace(energy_pivots[iinterval-1],energy_pivots[iinterval],linspace_npoints)
P.plot(tmppoly_x,N.polyval(polyfitlist[iinterval],tmppoly_x),'k')
for ipivot in range(len(energy_pivots)):
en = energy_pivots[ipivot]
P.plot([en,en],[N.polyval(polyfitlist[ipivot],en),N.polyval(polyfitlist[ipivot+1],en)],'k-.')
P.xlabel('DFT eigenvalues (in eV)')
P.ylabel('GW correction to the DFT eigenvalues (in eV)')
P.figure(4)
P.hold(True)
P.grid(True)
for iinterval in range(len(polyfit_degrees)):
P.plot(dftarray_list[iinterval],gwarray_list[iinterval]-dftarray_list[iinterval]-N.polyval(polyfitlist[iinterval],dftarray_list[iinterval]),'bx')
[x_min,x_max] = P.xlim()
P.plot([x_min,x_max],[0,0],'k-')
P.xlabel('DFT eigenvalues (in eV)')
P.ylabel('Error in the fit (in eV)')
P.show()
return polyfitlist
def compare_bandstructures(ec_ref,ec_test,label_ref=None,label_test=None):
if label_ref == None:
labref = 'Reference'
else:
labref = label_ref
if label_test == None:
labtest = 'Test'
else:
labtest = label_test
nspkpt_ref = len(ec_ref.special_kpoints)
nspkpt_test = len(ec_test.special_kpoints)
if nspkpt_ref != nspkpt_test:
print 'ERROR: The number of special kpoints is different in the two files ... exit'
sys.exit()
eig_type_ref = ec_ref.eigenvalue_type
eig_type_test = ec_test.eigenvalue_type
if eig_type_ref == 'DFT' and eig_type_test == 'W90':
TOL_KPTS = N.float(1.0e-4)
else:
TOL_KPTS = N.float(1.0e-6)
for ispkpt in range(nspkpt_ref):
if not N.allclose(ec_ref.special_kpoints[ispkpt,:],ec_test.special_kpoints[ispkpt,:],atol=TOL_KPTS):
print 'ERROR: The kpoints are not the same :'
print ' Kpt #%s ' %ispkpt
print ' Reference => %20.17f %20.17f %20.17f' %(ec_ref.special_kpoints[ispkpt,0],ec_ref.special_kpoints[ispkpt,1],ec_ref.special_kpoints[ispkpt,2])
print ' Compared => %20.17f %20.17f %20.17f' %(ec_test.special_kpoints[ispkpt,0],ec_test.special_kpoints[ispkpt,1],ec_test.special_kpoints[ispkpt,2])
print ' ... exit'
sys.exit()
mband_comparison = N.min([ec_ref.mband,ec_test.mband])
if mband_comparison < ec_ref.mband:
print 'Number of bands in the test bandstructure is lower than the number of bands in the reference (%s)' %ec_ref.mband
print ' => Comparison will proceed with %s bands' %ec_test.mband
elif mband_comparison < ec_test.mband:
print 'Number of bands in the reference bandstructure is lower than the number of bands in the test bandstructure (%s)' %ec_test.mband
print ' => Comparison will only proceed with %s bands of the test bandstructure' %ec_ref.mband
else:
print 'Number of bands in the reference and test bandstructure is the same'
print ' => Comparison will proceed with %s bands' %mband_comparison
# eig_test_ref_path = ec_ref.eigenvalues[:,:,:mband_comparison]
rmsd_per_band = N.zeros([ec_ref.nsppol,mband_comparison],N.float)
nrmsd_per_band = N.zeros([ec_ref.nsppol,mband_comparison],N.float)
mae_per_band = N.zeros([ec_ref.nsppol,mband_comparison],N.float)
maxabserror_per_band = N.zeros([ec_ref.nsppol,mband_comparison],N.float)
for isppol in range(ec_ref.nsppol):
for iband in range(mband_comparison):
interp = N.interp(ec_ref.normalized_kpoint_path_values,ec_test.normalized_kpoint_path_values,ec_test.eigenvalues[isppol,:,iband])
rmsd_per_band[isppol,iband] = N.sqrt(N.sum((csts.hartree2ev*interp-csts.hartree2ev*ec_ref.eigenvalues[isppol,:,iband])**2)/ec_ref.nkpt)
mae_per_band[isppol,iband] = N.sum(N.abs(csts.hartree2ev*interp-csts.hartree2ev*ec_ref.eigenvalues[isppol,:,iband]))/ec_ref.nkpt
maxabserror_per_band[isppol,iband] = N.max(N.abs(csts.hartree2ev*interp-csts.hartree2ev*ec_ref.eigenvalues[isppol,:,iband]))
minorxticks = mticker.FixedLocator(N.arange(1,mband_comparison+1))
mae_figure=P.figure(1)
mae_ax=mae_figure.add_subplot(111)
mae_ax.set_title('Errors made "%s" vs "%s"' %(labref,labtest))
mae_plot=mae_ax.plot(N.arange(1,len(mae_per_band[0,:])+1),mae_per_band[0,:],'bx-',linewidth=2,markersize=10,markeredgewidth=2)
mae_ax.xaxis.set_minor_locator(minorxticks)
mae_ax.set_xlabel('Band index')
mae_ax.set_ylabel('Error (in eV)')
mae_ax.grid(True)
rmsd_plot=mae_ax.plot(N.arange(1,len(rmsd_per_band[0,:])+1),rmsd_per_band[0,:],'go-',linewidth=2,markersize=10)
maxabserror_plot=mae_ax.plot(N.arange(1,len(rmsd_per_band[0,:])+1),maxabserror_per_band[0,:],'r+-',linewidth=2,markersize=10,markeredgewidth=2)
mae_ax.legend([mae_plot,rmsd_plot,maxabserror_plot],['Mean absolute error','Root mean square deviation','Maximum absolute error'],loc='upper left')
P.show()
# Parse the command line options
parser = argparse.ArgumentParser(description='Tool for plotting dft bandstructures')
parser.add_argument('files',help='files to be opened',nargs='*')
parser.add_argument('--align_vbm_index',help='script will align the bandstructures with respect to the given vbm index',nargs=1)
args = parser.parse_args()
args_dict = vars(args)
if args_dict['files']:
print 'will open the file'
else:
print 'ERROR: you should provide some bandstructure file ! exiting now ...'
sys.exit()
file_list = args_dict['files']
ec_list = list()
input_labels = False
if len(file_list) > 1:
test = raw_input('Do you want to enter labels for the bandstructures ? (y/n)\n')
if test == 'y':
input_labels = True
labels = list()
else:
input_labels = False
for ifile in range(len(file_list)):
ec_dft = EigenvalueContainer()
ec_dft.read_bandstructure_from_file(file_list[ifile])
if args_dict['align_vbm_index']:
ec_dft.eigenvalues = ec_dft.eigenvalues-N.max(ec_dft.eigenvalues[:,:,args_dict['align_vbm_index'][0]])
ec_dft.print_bandstructure_info()
if input_labels:
test = raw_input('Label for bandstructure file "%s" : \n' %file_list[ifile])
labels.append(test)
ec_list.append(ec_dft)
print 'Minimum and maximum energies of the bandstructures :'
for ifile in range(len(file_list)):
if input_labels:
print ' => %18s : minenergy = %8.5f maxenergy = %8.5f (file "%s")' %(labels[ifile],N.min(ec_list[ifile].eigenvalues)*csts.hartree2ev,N.max(ec_list[ifile].eigenvalues)*csts.hartree2ev,file_list[ifile])
else:
print ' => minenergy = %8.5f maxenergy = %8.5f for file "%s"' %(N.min(ec_list[ifile].eigenvalues)*csts.hartree2ev,N.max(ec_list[ifile].eigenvalues)*csts.hartree2ev,file_list[ifile])
test = raw_input('Enter the minimum and maximum energy for the bandstructure plot (<ENTER> : default) :\n')
if test == '':
energy_default = True
else:
energy_default = False
energy_limits = N.array([N.float(test.split()[0]),N.float(test.split()[1])],N.float)
style = ['k-','r--','b-.','g:']
onebsstyle = ['k-','r-']
P.figure(1,figsize=(3.464,5))
P.hold('on')
P.grid('on')
P.xticks(N.take(ec_list[0].kpoint_path_values,N.array(ec_list[0].special_kpoints_indices,N.int))/ec_list[0].kpoint_path_length,ec_list[0].special_kpoints_names)
ax_list = list()
if len(ec_list) == 1:
ibs = 0
if ec_list[ibs].nsppol == 1:
updown = False
for iband in range(ec_list[ibs].mband):
if iband == 0:
ax = P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,onebsstyle[0],linewidth=2)
ax_list.append(ax)
else:
P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,onebsstyle[0],linewidth=2)
elif ec_list[ibs].nsppol == 2:
test = raw_input('Put "Up/Down" legend for this spin polarized system ?\n')
if test == 'y':
updown = True
else:
updown = False
for iband in range(ec_list[ibs].mband):
if iband == 0:
axup = P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,onebsstyle[0],linewidth=2)
axdown = P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[1,:,iband]*csts.hartree2ev,onebsstyle[1],linewidth=2)
ax_list.append(axup)
ax_list.append(axdown)
else:
P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,onebsstyle[0],linewidth=2)
P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[1,:,iband]*csts.hartree2ev,onebsstyle[1],linewidth=2)
else:
print 'WARNING: when several bandstructures are to be plotted, care must be taken with spins ... not yet fully tested ... !'
updown = False
for ibs in range(len(ec_list)):
for iband in range(ec_list[ibs].mband):
if iband == 0:
ax = P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,style[ibs],linewidth=2)
ax_list.append(ax)
else:
P.plot(ec_list[ibs].kpoint_path_values/ec_list[ibs].kpoint_path_length,ec_list[ibs].eigenvalues[0,:,iband]*csts.hartree2ev,style[ibs],linewidth=2)
P.xlim([0,1])
if not energy_default:
P.ylim(energy_limits)
if input_labels:
P.legend(ax_list,labels)
if updown:
P.legend(ax_list,['Up','Down'])
P.xlim([0,1])
P.show()
if len(ec_list) > 1:
test = raw_input('Do you want to compare the bandstructures ? (y/n)')
if test == 'y':
print 'Bandstructure list :'
if input_labels:
for iec in range(len(ec_list)):
print ' %3d => %20s (file "%s")' %(iec,labels[iec],file_list[iec])
else:
for iec in range(len(ec_list)):
print ' %3d => bandstructure from file "%s"' %(iec,file_list[iec])
test = raw_input('Enter the index of the "reference" band structure (<ENTER> : default = 0)\n')
if test == '':
ref_index = 0
else:
ref_index = N.int(test)
for iec in range(len(ec_list)):
if iec != ref_index:
if input_labels:
compare_bandstructures(ec_list[ref_index],ec_list[iec],label_ref=labels[ref_index],label_test=labels[iec])
else:
compare_bandstructures(ec_list[ref_index],ec_list[iec],label_ref=file_list[ref_index],label_test=file_list[iec])
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