def get_gauges(self, bands, verbose=True):
wfn = self.wfn
nbands = len(bands)
ng_max = np.amax(wfn.ngk)
gvec = np.empty((3, ng_max), dtype=int, order='F')
data = np.empty((ng_max, wfn.ns),
dtype=get_numpy_flavor(wfn.flavor),
order='F')
gauges = np.empty((nbands, wfn.nk), dtype=get_numpy_flavor(wfn.flavor))
k_done = 0
for ik in range(wfn.nk):
k_done += 1
if verbose:
print k_done, '/', wfn.nk
#wfn.read_gvectors(gvec)
#Assume G-vectors are order by kinetic energy
wfn.read_gvectors()
ib_ = 0
for ib in range(wfn.nbands):
if ib in bands:
wfn.read_data(data)
gauges[ib_, ik] = data[0]
ib_ += 1
else:
wfn.read_data()
return gauges
def get_data_buffer(self):
'''Results an ndarray that serves as buffer for calls to read_data'''
if self.flavor == common.flavor.NONE:
raise Exception('Flavor is unknown.')
dtype = common.get_numpy_flavor(self.flavor)
return empty((self.ngkmax, self.ns), dtype=dtype, order='F')
def truncate(wfn_in, fname_out, ik_keep):
print
print 'Truncating', wfn_in.fname, '->', fname_out
wfn_out = wfnIO()
wfn_out.__dict__ = wfn_in.__dict__.copy()
wfn_out.nk = len(ik_keep)
wfn_out.ngk = wfn_out.ngk[ik_keep]
wfn_out.ngkmax = amax(wfn_out.ngk)
wfn_out.kw = wfn_out.kw[ik_keep]
wfn_out.kw[:] = 1.0 / wfn_out.nk
wfn_out.kpt = wfn_out.kpt[:, ik_keep]
#HACK!
#wfn_out.ifmin[:] = 1
#wfn_out.ifmax[:] = 4
wfn_out.ifmin = wfn_out.ifmin[ik_keep, :]
wfn_out.ifmax = wfn_out.ifmax[ik_keep, :]
wfn_out.energies = wfn_out.energies[:, ik_keep, :]
wfn_out.occupations = wfn_out.occupations[:, ik_keep, :]
wfn_out.f = None
wfn_out.fname = fname_out
wfn_out.write_header(full=True)
ng_max = amax(wfn_in.ngk)
gvec = empty((3, ng_max), dtype=int, order='F')
data = empty((ng_max, wfn_in.ns),
dtype=get_numpy_flavor(wfn_in.flavor),
order='F')
k_done = 0
for ik in range(wfn_in.nk):
if ik in ik_keep:
k_done += 1
print k_done, '/', wfn_out.nk
wfn_in.read_gvectors(gvec)
wfn_out.write_gvectors(gvec[:, :wfn_in.ngk[ik]])
for ib in range(wfn_in.nbands):
wfn_in.read_data(data)
wfn_out.write_data(data[:wfn_in.ngk[ik], :])
if k_done == wfn_out.nk:
break
else:
wfn_in.read_gvectors()
for ib in range(wfn_in.nbands):
wfn_in.read_data()
print wfn_out
def decimate_to(self, fname_out, verbose=True):
wfn_in = self.wfn_in
keep_k = self.keep_k
nk_out = np.sum(keep_k)
wfn_out = wfnIO()
wfn_out.__dict__ = wfn_in.__dict__.copy()
wfn_out.nk = nk_out
wfn_out.ngk = wfn_out.ngk[keep_k]
wfn_out.ngkmax = np.amax(wfn_out.ngk)
wfn_out.kw = wfn_out.kw[keep_k]
wfn_out.kw[:] = 1.0 / wfn_out.nk
wfn_out.kpt = wfn_out.kpt[:, keep_k]
wfn_out.ifmin = wfn_out.ifmin[keep_k, :]
wfn_out.ifmax = wfn_out.ifmax[keep_k, :]
wfn_out.energies = wfn_out.energies[:, keep_k, :]
wfn_out.occupations = wfn_out.occupations[:, keep_k, :]
wfn_out.f = None
wfn_out.fname = fname_out
wfn_out.write_header(full=True)
ng_max = np.amax(wfn_in.ngk)
gvec = np.empty((3, ng_max), dtype=int, order='F')
data = np.empty((ng_max, wfn_in.ns),
dtype=get_numpy_flavor(wfn_in.flavor),
order='F')
k_done = 0
for ik in range(wfn_in.nk):
if keep_k[ik]:
k_done += 1
if verbose:
print k_done, '/', wfn_out.nk
wfn_in.read_gvectors(gvec)
wfn_out.write_gvectors(gvec[:, :wfn_in.ngk[ik]])
for ib in range(wfn_in.nbands):
wfn_in.read_data(data)
wfn_out.write_data(data[:wfn_in.ngk[ik], :])
if k_done == wfn_out.nk:
break
else:
wfn_in.read_gvectors()
for ib in range(wfn_in.nbands):
wfn_in.read_data()
def write_decimated(wfn,keep,bz,use_symmetries):
if use_symmetries:
keep_reduced = keep
else:
keep_reduced = bz.indr[keep]-1
keep = keep[argsort(keep_reduced)] # sort k's by reduced index
wfn_out = wfnIO()
wfn_out.__dict__ = wfn.__dict__.copy()
wfn_out.nk = len(keep)
if use_symmetries:
wfn_out.ngk = wfn_out.ngk[keep]
wfn_out.kw = wfn_out.kw[keep]
else:
wfn_out.ngk = wfn_out.ngk[bz.indr[keep]-1]
wfn_out.kw = wfn_out.kw[bz.indr[keep]-1]
wfn_out.ngkmax = amax(wfn_out.ngk)
wfn_out.kw[:] = 1.0/wfn_out.nk
if use_symmetries:
wfn_out.kpt = wfn_out.kpt[:, keep]
wfn_out.ifmin = wfn_out.ifmin[keep, :]
wfn_out.ifmax = wfn_out.ifmax[keep, :]
wfn_out.energies = wfn_out.energies[:, keep, :]
wfn_out.occupations = wfn_out.occupations[:, keep, :]
else:
wfn_out.kpt = bz.fk[:, keep]
wfn_out.ifmin = wfn_out.ifmin[bz.indr[keep]-1, :]
wfn_out.ifmax = wfn_out.ifmax[bz.indr[keep]-1, :]
wfn_out.energies = wfn_out.energies[:, bz.indr[keep]-1, :]
wfn_out.occupations = wfn_out.occupations[:, bz.indr[keep]-1, :]
wfn_out.f = None
wfn_out.fname = fname_out
wfn_out.write_header(full=True)
ng_max = amax(wfn_in.ngk)
gvec = empty((3, ng_max), dtype=int, order='F')
if use_symmetries:
data = empty((ng_max, wfn_in.ns), dtype=get_numpy_flavor(wfn_in.flavor), order='F')
else:
data = empty((wfn_in.nbands,ng_max, wfn_in.ns), dtype=get_numpy_flavor(wfn_in.flavor), order='F')
k_done = 0
for ik in range(wfn_in.nk):
if ik in keep_reduced:
k_done += 1
print k_done,'/',wfn_out.nk
wfn_in.read_gvectors(gvec)
if use_symmetries:
wfn_out.write_gvectors(gvec[:,:wfn_in.ngk[ik]])
for ib in range(wfn_in.nbands):
wfn_in.read_data(data)
wfn_out.write_data(data[:wfn_in.ngk[ik],:])
if k_done==wfn_out.nk:
break
else:
# ik is the reduced index
# find places where ik occurs in indr
idx_k = where(keep_reduced==ik)[0]
for kk in range(len(idx_k)):
wfn_out.write_gvectors(gvec[:,:wfn_in.ngk[ik]])
for ib in range(wfn_in.nbands):
if kk==0:
wfn_in.read_data(data[ib,:,:])
wfn_out.write_data(data[ib,:wfn_in.ngk[ik],:])
if k_done==wfn_out.nk:
break
else:
wfn_in.read_gvectors()
for ib in range(wfn_in.nbands):
wfn_in.read_data()
print wfn_out
from bgwtools.IO.wfn import wfnIO
from bgwtools.common.common import get_numpy_flavor
import sys
from numpy import amax, empty, empty_like
fname1 = sys.argv[1]
print('File #1: %s'%(fname1))
fname2 = sys.argv[2]
print('File #2: %s'%(fname2))
wfn1 = wfnIO(fname1)
wfn2 = wfnIO(fname2)
ng_max = amax(wfn1.ngk) * wfn1.nspinor
gvec = empty((3, ng_max), dtype=int, order='F')
data1 = empty((ng_max, wfn1.ns), dtype=get_numpy_flavor(wfn1.flavor), order='F')
data2 = empty_like(data1)
for ik in range(wfn1.nk):
print('ik = %d'%ik)
wfn1.read_gvectors(gvec)
wfn2.read_gvectors(gvec)
ngk = wfn1.ngk[ik] * wfn1.nspinor
for ib in range(wfn1.nbands):
wfn1.read_data(data1)
wfn2.read_data(data2)
diff = (data2 - data1)[:ngk]
max_diff = amax(abs(diff))
print(' band %d:'%(ib))
print(' ||cg2 - cg1||_inf = %e'%max_diff)
wfn_in = wfnIO(fname_in, full=True)
nb_out = np.amax(wfn_in.ifmax) + 1
wfn_out = wfnIO()
wfn_out.__dict__ = wfn_in.__dict__.copy()
wfn_out.energies = wfn_out.energies[:nb_out, :, :]
wfn_out.occupations = wfn_out.occupations[:nb_out, :, :]
wfn_out.f = None
wfn_out.fname = fname_out
wfn_out.nbands = nb_out
wfn_out.write_header(full=True)
ng_max = np.amax(wfn_in.ngk)
gvec = np.empty((3, ng_max), dtype=int, order='F')
data = np.empty((ng_max, wfn_in.ns),
dtype=get_numpy_flavor(wfn_in.flavor),
order='F')
k_done = 0
for ik in range(wfn_in.nk):
k_done += 1
print k_done, '/', wfn_out.nk
wfn_in.read_gvectors(gvec)
wfn_out.write_gvectors(gvec[:, :wfn_in.ngk[ik]])
for ib in range(nb_out):
wfn_in.read_data(data)
wfn_out.write_data(data[:wfn_in.ngk[ik], :])
for ib in range(nb_out, wfn_in.nbands):
wfn_in.read_data()
print wfn_out
wfn_out.ngk = wfn_out.ngk[should_keep]
wfn_out.ngkmax = amax(wfn_out.ngk)
wfn_out.kw = wfn_out.kw[should_keep]
wfn_out.kw[:] = 1.0/wfn_out.nk
wfn_out.kpt = wfn_out.kpt[:, should_keep]
wfn_out.ifmin = wfn_out.ifmin[should_keep, :]
wfn_out.ifmax = wfn_out.ifmax[should_keep, :]
wfn_out.energies = wfn_out.energies[:, should_keep, :]
wfn_out.occupations = wfn_out.occupations[:, should_keep, :]
wfn_out.f = None
wfn_out.fname = fname_out
wfn_out.write_header(full=True)
ng_max = amax(wfn_in.ngk)
gvec = empty((3, ng_max), dtype=int, order='F')
data = empty((ng_max, wfn_in.ns), dtype=get_numpy_flavor(wfn_in.flavor), order='F')
k_done = 0
for ik in range(wfn_in.nk):
if ik in should_keep:
k_done += 1
print k_done,'/',wfn_out.nk
wfn_in.read_gvectors(gvec)
wfn_out.write_gvectors(gvec[:,:wfn_in.ngk[ik]])
for ib in range(wfn_in.nbands):
wfn_in.read_data(data)
wfn_out.write_data(data[:wfn_in.ngk[ik],:])
if k_done==wfn_out.nk:
break
else:
wfn_in.read_gvectors()
for ib in range(wfn_in.nbands):