def read(self,filepath):
print 'reading Procar',
lines = nstrip(readfile(filepath))
self.nk = int(lines[1].split(':')[1].split()[0])
self.nbands = int(lines[1].split(':')[2].split()[0])
self.nions = int(lines[1].split(':')[3])
#initialize
self.kvecs = zeros((3,self.nk),dtype = float)
self.kweights = zeros((self.nk),dtype = float)
self.ener = zeros((self.nk, self.nbands, self.nspin),dtype = float)
self.occ = zeros((self.nk, self.nbands,self.nspin),dtype = float)
self.weights = zeros((self.nk,self.nbands,self.nions,len(self.orbs),self.nspin),dtype = float)
#read weights
ipos = 2
for ispin in range(self.nspin):
ipos += 1; # print 'ipos for spin %i: %i' % (ispin,ipos)
for ik in range(self.nk):
self.kvecs[:,ik] = lines[ipos].split()[3:6]
self.kweights[ik] = float(lines[ipos].split()[8])
ipos += 2
for ib in range(self.nbands):
self.ener[ik,ib,ispin] = float(lines[ipos].split()[4])
self.occ[ik,ib,ispin] = float(lines[ipos].split()[7])
ipos += 3
for i in range(self.nions):
if mod(ipos,1e4)==0: print '-', #progress bar
tempw = lines[ipos].split()[1:self.norbs+1]
self.weights[ik,ib,i,:,ispin] = tempw
ipos += 1
ipos += 2
ipos += 1
print
def rd_ibzkpt(self,dir): #only extracts the kpoint vectors
self.vecs = zeros((3,self.nk),dtype = float64)
lines = nstrip(readfile(dir+'IBZKPT'))
nk2 = int(lines[1].split()[0])
if nk2 != self.nk: print nk2,self.nk, 'Warning! Nkpts in IBZKPTS differs from this program''s'
for ik in range(self.nk):
self.vecs[:,ik] = lines[ik+3].split()[:3] #don't read weights'
def get_eigen(self,dir):
lines = nstrip(readfile(dir+'eigenv'))
self.nk = int(lines[0].split()[0])
self.nbands = int(lines[0].split()[1])
self.ener = zeros((self.nk,self.nbands),dtype = float64)
for ik in range(self.nk):
for ib in range(self.nbands):
self.ener[ik,ib] = lines[ik+1].split()[ib+1]
def get_tetweights(self,dir):
lines = nstrip(readfile(dir+'tetwgt'))
self.ntet = int(lines[0].split()[0])
self.nbands = int(lines[0].split()[1])
# nspin = int(lines[0][2]) #haven't added spin yet
self.fwgt = zeros((self.ntet,self.nbands),dtype = float64)
for it in range(self.ntet):
for ib in range(self.nbands):
self.fwgt[it,ib] = lines[it+1].split()[ib+1] #First line and first column are not weights
def rd_ibzkpt(self,dir): #only extracts the tets ids
self.idk = zeros((4,self.ntet),dtype = int)
self.vwgt = zeros(self.ntet,dtype = float64)
lines = nstrip(readfile(dir+'IBZKPT'))
nk = int(lines[1].split()[0])
ntet2 = int(lines[4+nk].split()[0])
self.volscale = float(lines[4+nk].split()[1])
print 'VASP volume scale', self.volscale
if ntet2 != self.ntet: print 'Warning! NTET in IBZKPTS differs from this program''s'
for it in range(self.ntet):
self.vwgt[it] = lines[5+nk+it].split()[0]
self.idk[:,it] = lines[5+nk+it].split()[1:]
self.idk = self.idk -1 #(converting from Fortran counting to python)
def get_tetvecs(self,dir):
lines = nstrip(readfile(dir+'tetvecs'))
self.vecs = zeros((3,4,self.ntet),dtype = float64)
self.vol = zeros(self.ntet,dtype = float64)
print shape(self.vecs)
for it in range(self.ntet):
for ic in range(4):
print it, ic,lines[5*it+ic+1]
self.vecs[:,ic,it] = lines[5*it+ic+1].split()
va = self.vecs[:,1,it]-self.vecs[:,0,it]
vb = self.vecs[:,2,it]-self.vecs[:,0,it]
vc = self.vecs[:,3,it]-self.vecs[:,0,it]
self.vol[it] = abs(dot(va,cross(vb,vc))/2.0)
def incar(self,dir):
print 'reading ISPIN and LORBIT from INCAR'
lines = nstrip(readfile(dir+'INCAR'))
for line in lines:
if ('ISPIN' in line) or ('ispin' in line): self.nspin = int(line.split('=')[1])
if ('LORBIT' in line) or ('lorbit' in line):
lorbit = int(line.split('=')[1])
if lorbit in [0,10]: #no lm decomposition
self.orbs = ['s','p','d']
elif lorbit in [1,2,11,12]:
self.orbs = ['s','py','pz','px','dxy','dyz','dz2','dxz','dx2']
else:
sys.exit('Unrecognized LORBIT in INCAR')
self.norbs = len(self.orbs)
def incar(self, dir):
print 'reading ISPIN and LORBIT from INCAR'
lines = nstrip(readfile(dir + 'INCAR'))
for line in lines:
if ('ISPIN' in line) or ('ispin' in line):
self.nspin = int(line.split('=')[1])
if ('LORBIT' in line) or ('lorbit' in line):
lorbit = int(line.split('=')[1])
if lorbit in [0, 10]: #no lm decomposition
self.orbs = ['s', 'p', 'd']
elif lorbit in [1, 2, 11, 12]:
self.orbs = [
's', 'py', 'pz', 'px', 'dxy', 'dyz', 'dz2', 'dxz',
'dx2'
]
else:
sys.exit('Unrecognized LORBIT in INCAR')
self.norbs = len(self.orbs)
def read(self, filepath):
print 'reading Procar',
lines = nstrip(readfile(filepath))
self.nk = int(lines[1].split(':')[1].split()[0])
self.nbands = int(lines[1].split(':')[2].split()[0])
self.nions = int(lines[1].split(':')[3])
#initialize
self.kvecs = zeros((3, self.nk), dtype=float)
self.kweights = zeros((self.nk), dtype=float)
self.ener = zeros((self.nk, self.nbands, self.nspin), dtype=float)
self.occ = zeros((self.nk, self.nbands, self.nspin), dtype=float)
self.weights = zeros(
(self.nk, self.nbands, self.nions, len(self.orbs), self.nspin),
dtype=float)
#read weights
ipos = 2
for ispin in range(self.nspin):
ipos += 1
# print 'ipos for spin %i: %i' % (ispin,ipos)
for ik in range(self.nk):
self.kvecs[:, ik] = lines[ipos].split()[3:6]
self.kweights[ik] = float(lines[ipos].split()[8])
ipos += 2
for ib in range(self.nbands):
self.ener[ik, ib, ispin] = float(lines[ipos].split()[4])
self.occ[ik, ib, ispin] = float(lines[ipos].split()[7])
ipos += 3
for i in range(self.nions):
if mod(ipos, 1e4) == 0: print '-', #progress bar
tempw = lines[ipos].split()[1:self.norbs + 1]
self.weights[ik, ib, i, :, ispin] = tempw
ipos += 1
ipos += 2
ipos += 1
print
deviations = abs(parts - means) + 1e-16 #last term to handle zero entries
#print'deviations';print deviations
try:
file2 = open('lattype', 'r')
lattype = file2.read()
file2.close()
except:
lattype = ''
################# summary #################
outfile = open('vary_N.csv', 'w')
outfile.write('pf,energy,el converged, el steps, Nkpoints, NIBZ,cputime(min\n')
#os.chdir(mainDir)
file = open(maindir + 'names', 'r')
names = nstrip(file.readlines())
file.close()
file = open(maindir + 'energies', 'r')
energies = nstrip(file.readlines())
file.close()
file = open(maindir + 'Nk', 'r')
Nk = nstrip(file.readlines())
file.close()
file = open(maindir + 'NkIBZ', 'r')
NkIBZ = nstrip(file.readlines())
file.close()
file = open(maindir + 'elsteps', 'r')
writeElConverge(dirsfull)
writeElSteps(dirsfull)
writeCPUtime(dirsfull)
parts = enerparts(dirsfull)
dets = getdata(dirsfull,'detL') #supercell volume in terms of unit cell volume
dets = [float(dets[i]) for i in range(len(dets))]
NkfullBZ = getdata(dirsfull,'detM') #Nk without symmetry reduction
lattypes = getdata(dirsfull,'lattype')
ms = array(getms(dirsfull),dtype = int)
filesstructselect = sorted([f for f in os.listdir(os.getcwd())])
#os.chdir(mainDir)
file = open(tempdir+'energies','r')
energies = nstrip(file.readlines())
file.close()
os.system('mv %s %s' % ('energies', 'energies'+structi))
file = open(tempdir+'efermi','r')
efermis = nstrip(file.readlines())
file.close()
os.system('mv %s %s' % ('efermi', 'efermi'+structi))
file = open(tempdir+'NkIBZ','r')
NkIBZ = nstrip(file.readlines())
file.close()
os.system('mv %s %s' % ('NkIBZ', 'NkIBZ'+structi))
file = open(tempdir+'elsteps','r')
elsteps = nstrip(file.readlines())
#print'means';print means
deviations = abs(parts - means) + 1e-16 #last term to handle zero entries
#print'deviations';print deviations
try:
file2 = open('lattype','r'); lattype = file2.read(); file2.close()
except:
lattype = ''
################# summary #################
outfile = open('vary_pf.csv','w')
outfile.write('pf,energy,el converged, el steps, Nkpoints, NIBZ,cputime(min\n')
#os.chdir(mainDir)
file = open(maindir+'names','r')
names = nstrip(file.readlines())
file.close()
file = open(maindir+'energies','r')
energies = nstrip(file.readlines())
file.close()
file = open(maindir+'Nk','r')
Nk = nstrip(file.readlines())
file.close()
file = open(maindir+'NkIBZ','r')
NkIBZ = nstrip(file.readlines())
file.close()
file = open(maindir+'elsteps','r')