################################################################################
#
# TRIQS: a Toolbox for Research in Interacting Quantum Systems
#
# Copyright (C) 2011 by M. Aichhorn, L. Pourovskii, V. Vildosola
#
# TRIQS is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# TRIQS is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details.
#
# You should have received a copy of the GNU General Public License along with
# TRIQS. If not, see .
#
################################################################################
#=======================================================================================================================
# #################################################################
# Code for Transport/Optic calculations based on SumK_LDA... class
# by Xiaoyu Deng
# The code read in files needed for transport/Optic calculations from Wien outputs.
# including: symmetry, velocity, lattice constants.
# The HDF convention is not adopted here since momentum file from Wien output is usually quite large
# and it is not necessary to keep in in the HDF file.
# #################################################################
#=======================================================================================================================
import numpy, sys, os.path
def Read_Fortran_File (filename):
""" Returns a generator that yields all numbers in the Fortran file as float, one by one"""
import os.path
if not(os.path.exists(filename)) : raise IOError, "File %s does not exists" % filename
for line in open(filename, 'r') :
for x in line.replace('D', 'E').split() :
yield string.atof(x)
class Velocity_k:
"""momentum matrix for a single k points.
"""
def __init__(self):
self.kp = [0.0, 0.0, 0.0]
self.bandwin = [999, 0]
# here a matrix for 3 vels. use list since the size of vel is to be determined.
self.vel = []
class Velocities:
"""Class containig the velocities.
Provides container for velocities
as a function of k and method to read them from case.pmat Wien2k file
use as ClassInstance.vks[ik].vel[iband][jband][ix]
"""
def __init__(self, wiencase, spinbl=""):
if not(os.path.exists(wiencase + ".pmat" + spinbl)) : raise IOError, "File %s does not exists" % wiencase + ".pmat"
# expected format:
# k nu nu2 (k denotes k-point, nu1 starting band index, nu2 ending band index
# kpos ( read in if needed.
# (real, im) (of velocity for all nu <=nu_prime within nu1 and nu2)
# ... ...
# k nu nu2
# ...
f = open(wiencase + ".pmat" + spinbl)
self.vks = []
while 1:
try:
s = f.readline()
if (s == ""):
break
except:
break
try:
vec = Velocity_k()
[k, nu1, nu2] = [int (x) for x in s.strip().split()]
vec.bandwin[0] = nu1
vec.bandwin[1] = nu2
vec.kp = f.readline().strip().split()
dim = vec.bandwin[1] - vec.bandwin[0] + 1
shape = (dim, dim, 3)
vxyz = numpy.zeros(shape, dtype=complex)
for nu in xrange(dim):
for nu_prime in xrange(nu, dim):
for i in xrange(3):
s = f.readline().strip("\n ()").split(',')
vxyz[nu][nu_prime][i] = float(s[0]) + float(s[1]) * 1j
if(nu_prime != nu):
vxyz[nu_prime][nu][i] = vxyz[nu][nu_prime][i].conjugate()
vec.vel = vxyz
self.vks.append(vec)
except IOError:
print("Reading case.pmat error. Wrong format?\n ")
raise
f.close()
def getvel(self, k):
# should return array at a given k. use as [iband][jband][i]
return self.vks[k].vel
def plot(self):
f = open("velband.dat", "w")
bandid = numpy.array([vk.bandwin for vk in self.vks]).flatten()
minb = bandid.min()
maxb = bandid.max()
for ib in range(minb, maxb + 1):
ik = 0
for vk in self.vks:
if(vk.bandwin[0] <= ib and vk.bandwin[1] >= ib):
f.write(str(ik) + " ")
for i in range(3):
f.write(str(vk.vel[ib - vk.bandwin[0]][ib - vk.bandwin[0]][i].real) + " ")
f.write("\n")
ik = ik + 1
f.write("&\n")
f.close()
class SGsymmetry():
""" read in symmetry of space group from wiencase.outputs other than wiencase.struct since
in this file there are also symmetry operations in xyz coordinates..
"""
def __init__(self, wiencase):
structfile = wiencase + ".outputs"
self.nsymm = 1
self.symm = []
self.tau = []
self.bravaismatrix = numpy.zeros((3, 3), dtype=numpy.float_)
self.symmcartesian = []
self.taucartesian = []
with open(structfile, "r") as f:
f.readline()
f.readline()# bravais matrix
for i in range(3):
line = f.readline().strip().split()
self.bravaismatrix[i, :] = numpy.array([numpy.float(item) for item in line])[:]
print "bravais matrix", self.bravaismatrix
while 1:
s = f.readline().strip(" ").split()
try:
if(s[0] == "PGBSYM:"):
self.nsymm = int(s[-1])
break
except:
continue
f.readline()
f.readline()
for i in range(self.nsymm):
f.readline()
## read symmcartesian
symmt = numpy.zeros((3, 3), dtype=float)
taut = numpy.zeros((3), dtype=float)
for ir in range(3):
s = f.readline().strip().split()
for ic in range(3):
symmt[ir, ic] = float(s[ic])
s = f.readline().strip().split()
for ir in range(3):
taut[ir] = float(s[ir])
self.symmcartesian.append(symmt)
self.taucartesian.append(taut)
##read symm
symmt = numpy.zeros((3, 3), dtype=float)
taut = numpy.zeros((3), dtype=float)
for ir in range(3):
s = f.readline().strip().split()
for ic in range(3):
symmt[ir, ic] = float(s[ic])
taut[ir] = float(s[3])
self.symm.append(symmt)
self.tau.append(taut)
f.readline()
# end
f.close()
print "Read wiencase.outputs done!"
def checksymmxyz(self):
''' This is to check symm in cartesian coordinates and in primitive cell lattice
For details of symm, one should check wien/SRC_symmetry/, latsym.f, pglsym.f,pgbsym.f
In general, if a lattice is orthorhombic, then symmcartesian is the same as symmprimitive
(at most different by a transpose (or inversion)). If a lattice is not orthorhombic, these two symms could
be related by bravais matrix.
One special case is CXZ lattice. In Wien CXZ lattice contains two cases: orthorhombic, and
monoclinic (with only gamma not equal to 90). For CXZ lattice monoclinic, symmcartesian is also the same as
symmprimitive (or with transpose (or inversion)).
'''
for i in range(self.nsymm):
mat = self.symmcartesian[i].transpose() # according to wien2k, why?
bm = self.bravaismatrix
bminv = numpy.linalg.inv(bm)#.transpose()
res = numpy.dot(bminv, numpy.dot(mat, bm)) - self.symm[i]
print i, res
def size(self):
return self.nsymm
def cellvolume(latticetype, latticeconstants, latticeangle):
""" calculate cell volume: volumecc conventional cell, volumepc, primitive cell.
"""
for i in range(3):
latticeangle[i] *= 1.0 / 180 * numpy.pi
a = latticeconstants[0]
b = latticeconstants[1]
c = latticeconstants[2]
c_al = numpy.cos(latticeangle[0])
c_be = numpy.cos(latticeangle[1])
c_ga = numpy.cos(latticeangle[2])
volumecc = a * b * c * numpy.sqrt(1 + 2 * c_al * c_be * c_ga - c_al ** 2 - c_be * 82 - c_ga ** 2)
det = {"P":1,
"F":4,
"B":2,
"R":3,
"H":1,
"CXY":2,
"CYZ":2,
"CXZ":2
}
volumepc = volumecc / det[latticetype]
return volumecc, volumepc
class WienStruct():
""" parsing Wien Struct file
"""
def __init__(self, wiencase):
structfile = wiencase + ".struct"
with open(structfile, "r") as infile:
print "read in Wien case file %s" % structfile
infile.readline()#title
tem = infile.readline() #lattice
self.latticetype = tem[0:10].split()[0]
self.ineqvsite = int(tem[27:30])
try:
self.sgrnumber = int(tem[30:33])
except:
self.sgrnumber = None
try:
self.sgrlabel = tem[34:38]
except:
self.sgrlabel = None
print self.latticetype, self.ineqvsite, self.sgrnumber, self.sgrlabel
infile.readline()
tem = infile.readline() # lattice constants
self.latticeconstants = [float(tem[0:10]), float(tem[10:20]), float(tem[20:30])]
self.latticeangle = [float(tem[30:40]), float(tem[40:50]), float(tem[50:60])]
print "Cell"
print self.latticeconstants[:]
print self.latticeangle[:]
self.positions = []
self.atomsymbols = []
self.multi = []
self.atomnumbers = []
self.locrotmatrix = []
for isite in range(self.ineqvsite):
tem = infile.readline()
positions = []
positions.append([float(tem[12:22]), float(tem[25:35]), float(tem[38:48])])
tem = infile.readline()
multi = int(tem[15:17])
self.multi.append(multi)
for im in range(multi - 1):
tem = infile.readline()
positions.append([float(tem[12:22]), float(tem[25:35]), float(tem[38:48])])
#print positions
self.positions.append(positions)
#print self.positions
tem = infile.readline().strip(" ").split()
self.atomsymbols.append(tem[0])
self.atomnumbers.append(float(tem[-1]))
mat = numpy.zeros((3, 3), dtype=numpy.float_)
tem = infile.readline().strip(" ").split()
#print tem[-3:],mat[0,:]
mat[0, :] = tem[-3:]
tem = infile.readline().strip(" ").split()
mat[1, :] = tem[-3:]
tem = infile.readline().strip(" ").split()
mat[2, :] = tem[-3:]
self.locrotmatrix.append(mat)
for ia in range(len(self.atomsymbols)):
print "atom symbol : %s atom number: %d atom multi: %d" % (self.atomsymbols[ia], self.atomnumbers[ia], self.multi[ia])
print "positions:"
for im in self.positions[ia]:
print im[:]
# symmetry with lattice vector
tem = infile.readline().strip(" ").split()
self.symm = []
self.tau = []
self.Nsymm = int(tem[0])
for isymm in range(self.Nsymm):
symmt = numpy.zeros((3, 3), dtype=float)
taut = numpy.zeros((3), dtype=float)
for ir in range(3):
s = infile.readline()
for ic in range(3):
symmt[ir][ic] = float(s[ic * 2:ic * 2 + 2])
taut[ir] = float(s[7:17])
self.symm.append(symmt)
self.tau.append(taut)
infile.readline()
#############
print "Read in %s.struct done!" % wiencase
## convential Cell Volume and primitive Cell. In bohr^3 unit
self.VolumeCC, self.VolumePC = cellvolume(self.latticetype, self.latticeconstants, self.latticeangle)
def readSGsymm(self, wiencase):
""" read in symmetry of space group from wiencase.outputs other than wiencase.struct since
in this file there are also symmetry operations in xyz coordinates..
"""
structfile = wiencase + ".outputs"
self.nsymm = 1
self.symm = []
self.tau = []
# note bravaismatrix is not accurate enough in wiencase.outputs file. Just use it for test.
self.bravaismatrix = numpy.zeros((3, 3), dtype=numpy.float_)
self.symmcartesian = []
self.taucartesian = []
with open(structfile, "r") as f:
f.readline()
f.readline()# bravais matrix
for i in range(3):
line = f.readline().strip().split()
self.bravaismatrix[i, :] = numpy.array([numpy.float(item) for item in line])[:]
print "bravais matrix", self.bravaismatrix
while 1:
try:
s = f.readline().strip(" ").split()
if(s[0] == "PGBSYM:"):
self.nsymm = int(s[-1])
break
except:
assert "Error in read case.outputs"
#f.readline()
#f.readline()
for i in range(self.nsymm):
while 1:
s = f.readline().strip().split()
if s[0] == "Symmetry":
break
## read symmcartesian
symmt = numpy.zeros((3, 3), dtype=float)
taut = numpy.zeros((3), dtype=float)
for ir in range(3):
s = f.readline().strip().split()
for ic in range(3):
symmt[ir, ic] = float(s[ic])
s = f.readline().strip().split()
for ir in range(3):
taut[ir] = float(s[ir])
self.symmcartesian.append(symmt)
self.taucartesian.append(taut)
##read symm
symmt = numpy.zeros((3, 3), dtype=float)
taut = numpy.zeros((3), dtype=float)
for ir in range(3):
s = f.readline().strip().split()
for ic in range(3):
symmt[ir, ic] = numpy.float(s[ic])
taut[ir] = numpy.float(s[3])
self.symm.append(symmt)
self.tau.append(taut)
# end
f.close()
def checksymmxyz(self):
''' This is to check symm in cartesian coordinates and in primitive cell lattice
For details of symm, should check wien/SRC_symmetry/, latsym.f, pglsym.f,pgbsym.f
In general, if a lattice is orthorhombic, then symmcartesian is the same as symmprimitive
(at most different by a transpose (or inversion)). If a lattice is not orthorhombic, these two symms could
be related by bravais matrix.
One special case is CXZ lattice. In Wien CXZ lattice contains two cases: orthorhombic, and
monoclinic (with only gamma not equal to 90). For CXZ lattice monoclinic, symmcartesian is also the same as
symmprimitive (or with transpose (or inversion)).
'''
ortho = numpy.abs(numpy.array(self.latticeangle) - 90.0).sum() <= 1e-6
for i in range(self.nsymm):
mat = self.symmcartesian[i].transpose() # according to wien2k, why?
res = mat
if (not ortho) and (self.latticetype != "CXZ") :
bm = self.bravaismatrix
bminv = numpy.linalg.inv(bm)#.transpose()
res = numpy.dot(bminv, numpy.dot(mat, bm))
res -= self.symm[i]
print i, numpy.abs(res).sum()
## primitive cell vectors.+