def apply_l0(self, sab, comega=1j * 0.0):
""" This applies the non-interacting four point Green's function to a suitable vector (e.g. dipole matrix elements)"""
assert sab.size == (self.norbs2), "%r,%r" % (sab.size, self.norbs2)
sab = sab.reshape([self.norbs, self.norbs])
self.l0_ncalls += 1
nb2v = np.dot(self.xocc, sab)
nm2v = blas.cgemm(1.0, nb2v, np.transpose(self.xvrt))
if use_numba:
div_eigenenergy_numba(self.ksn2e, self.ksn2f, self.nfermi,
self.vstart, comega, nm2v.real, nm2v.imag,
self.ksn2e.shape[2])
else:
for n, [en, fn] in enumerate(
zip(self.ksn2e[0, 0, :self.nfermi],
self.ksn2f[0, 0, :self.nfermi])):
for j, [em, fm] in enumerate(
zip(self.ksn2e[0, 0, n + 1:], self.ksn2f[0, 0,
n + 1:])):
m = j + n + 1 - self.vstart
nm2v[n,m] = nm2v[n,m] * (fn-fm) *\
( 1.0 / (comega - (em - en)) - 1.0 / (comega + (em - en)) )
nb2v = blas.cgemm(1.0, nm2v, self.xvrt)
ab2v = blas.cgemm(1.0, np.transpose(self.xocc), nb2v)
return ab2v
def computeQ(kij, vels, om, idsl, idsr, nl, nr, tn, dt, s):
"""
Compute the spectral heat current across the interface
"""
vfft = np.fft.fft(vels, axis=0) * dt
qom = np.zeros(tn).astype(complex)
vl = np.zeros((tn, nl * 3)).astype(complex)
vr = np.zeros((tn, nr * 3)).astype(complex)
vl[:, 0::3] = vfft[:, idsl * 3]
vl[:, 1::3] = vfft[:, idsl * 3 + 1]
vl[:, 2::3] = vfft[:, idsl * 3 + 2]
vr[:, 0::3] = vfft[:, idsr * 3]
vr[:, 1::3] = vfft[:, idsr * 3 + 1]
vr[:, 2::3] = vfft[:, idsr * 3 + 2]
vl = np.asfortranarray(vl)
vr = np.asfortranarray(vr)
kij = np.asfortranarray(kij)
print('\n\tNow computing heat current for block ' + str(s + 1) + '\n')
num = tn / 10
for j in range(tn):
if j != 0 and j % (num) == 0: #print progress updates
print('\t\tNow ' + str(10 * np.round(j / num, decimals=1)) +
'% done computing heat current for block ' + str(s + 1))
if j == 0:
qom[j] = 0 + 0j
else:
qom[j] = -(blas.cgemm((1 + 0j), vr[j, None].conj(),
blas.cgemm(
(1 + 0j), kij, vl[j, None].T))) / om[j]
return qom
def apply_l0(self, sab, comega=1j * 0.0):
""" This applies the non-interacting four point Green's function to a suitable vector (e.g. dipole matrix elements)"""
assert sab.size == (self.nspin * self.norbs2)
self.l0_ncalls += 1
sab = sab.reshape((self.nspin, self.norbs, self.norbs))
ab2v = np.zeros_like(sab, dtype=self.dtypeComplex)
for s, (ab, xv, xo, x, n2e, n2f) in enumerate(
zip(sab, self.xvrt_l0, self.xocc_l0, self.x_l0, self.ksn2e_l0,
self.ksn2f_l0)):
nm2v = zeros((self.norbs, self.norbs), self.dtypeComplex)
nm2v[self.vstart_l0[s]:, :self.nfermi_l0[s]] = blas.cgemm(
1.0, dot(xv, ab), xo.T)
nm2v[:self.nfermi_l0[s],
self.vstart_l0[s]:] = blas.cgemm(1.0, dot(xo, ab), xv.T)
for n, (en, fn) in enumerate(zip(n2e, n2f)):
for m, (em, fm) in enumerate(zip(n2e, n2f)):
nm2v[n, m] = nm2v[n, m] * (fn - fm) / (comega - (em - en))
nb2v = blas.cgemm(1.0, nm2v, x)
ab2v[s] += blas.cgemm(1.0, x.T, nb2v)
return ab2v.reshape(-1)
def apply_l0_ref(self, sab, comega=1j*0.0):
""" This applies the non-interacting four point Green's function to a suitable vector (e.g. dipole matrix elements)"""
assert sab.size==(self.norbs2), "%r,%r"%(sab.size,self.norbs2)
sab = sab.reshape([self.norbs,self.norbs])
self.l0_ncalls+=1
nb2v = dot(self.x[0], sab)
nm2v = blas.cgemm(1.0, nb2v, self.x[0].T)
for n,[en,fn] in enumerate(zip(self.ksn2e[0,0,:],self.ksn2f[0,0,:])):
for m,[em,fm] in enumerate(zip(self.ksn2e[0,0,:],self.ksn2f[0,0,:])):
nm2v[n,m] = nm2v[n,m] * (fn-fm) * ( 1.0 / (comega - (em - en)))
nb2v = blas.cgemm(1.0, nm2v, self.x[0])
ab2v = blas.cgemm(1.0, self.x[0].T, nb2v)
return ab2v
def apply_l0_exp(self, sab, comega=1j*0.0):
""" This applies the non-interacting four point Green's function to a suitable vector (e.g. dipole matrix elements)"""
assert sab.size==(self.norbs2), "%r,%r"%(sab.size,self.norbs2)
sab = sab.reshape([self.norbs,self.norbs])
self.l0_ncalls+=1
nb2v = dot(self.x[0], sab)
nm2v = blas.cgemm(1.0, nb2v, self.x[0].T)
print(nm2v.dtype)
print(nm2v[self.vstart[0]:, :self.nfermi[0]])
print(nm2v[:self.nfermi[0], self.vstart[0]:])
nm2v = zeros((self.norbs,self.norbs), self.dtypeComplex)
nb2v1 = dot(self.xocc[0], sab)
nm2v1 = blas.cgemm(1.0, nb2v1, self.xvrt[0].T)
nb2v2 = dot(self.xvrt[0], sab)
nm2v2 = blas.cgemm(1.0, nb2v2, self.xocc[0].T)
nm2v[self.vstart[0]:, :self.nfermi[0]] = nm2v2
nm2v[:self.nfermi[0], self.vstart[0]:] = nm2v1
print(nm2v.dtype, nm2v1.shape, nm2v1.dtype)
print(nm2v[self.vstart[0]:, :self.nfermi[0]])
print(nm2v[:self.nfermi[0], self.vstart[0]:])
#raise RuntimeError('11')
#nm2v2 = np.copy(nm2v1)
#for n,[en,fn] in enumerate(zip(self.ksn2e[0,0,:self.nfermi],self.ksn2f[0,0,:self.nfermi])):
#for m,[em,fm] in enumerate(zip(self.ksn2e[0,0,self.vstart:],self.ksn2f[0,0,self.vstart:])):
#nm2v1[n,m] = nm2v1[n,m] * (fn-fm) * ( 1.0 / (comega - (em - en)))
#for n,[en,fn] in enumerate(zip(self.ksn2e[0,0,:self.nfermi],self.ksn2f[0,0,:self.nfermi])):
#for m,[em,fm] in enumerate(zip(self.ksn2e[0,0,self.vstart:],self.ksn2f[0,0,self.vstart:])):
#nm2v2[n,m] = nm2v2[n,m] * (fm-fn) * ( 1.0 / (comega - (en - em)))
for n,[en,fn] in enumerate(zip(self.ksn2e[0,0,:],self.ksn2f[0,0,:])):
for m,[em,fm] in enumerate(zip(self.ksn2e[0,0,:],self.ksn2f[0,0,:])):
nm2v[n,m] = nm2v[n,m] * (fn-fm) * ( 1.0 / (comega - (em - en)))
nb2v = blas.cgemm(1.0, nm2v, self.x[0])
ab2v = blas.cgemm(1.0, self.x[0].T, nb2v)
return ab2v
def apply_rf0(self, v, comega=1j * 0.0):
""" This applies the non-interacting response function to a vector (a set of vectors?) """
assert len(v) == len(self.moms0), "%r, %r " % (len(v), len(self.moms0))
self.rf0_ncalls += 1
# np.require may perform a copy of v, is it really necessary??
vdp = self.cc_da * np.require(v, dtype=np.complex64)
no = self.norbs
sab = csr_matrix((np.transpose(vdp) * self.v_dab).reshape([no, no]))
if self.tddft_iter_gpu.GPU:
vdp = self.tddft_iter_gpu.apply_rf0_gpu(self.xocc, sab, comega)
else:
#
# WARNING!!!!
# nb2v is column major, while self.xvrt is row major
# What a mess!!
nb2v = self.xocc * sab
nm2v = blas.cgemm(1.0, nb2v, np.transpose(self.xvrt))
if use_numba:
div_eigenenergy_numba(self.ksn2e, self.ksn2f, self.nfermi,
self.vstart, comega, nm2v,
self.ksn2e.shape[2])
else:
for n, [en, fn] in enumerate(
zip(self.ksn2e[0, 0, :self.nfermi],
self.ksn2f[0, 0, :self.nfermi])):
for j, [em, fm] in enumerate(
zip(self.ksn2e[0, 0, n + 1:], self.ksn2f[0, 0,
n + 1:])):
m = j + n + 1 - self.vstart
nm2v[n,m] = nm2v[n,m] * (fn-fm) *\
( 1.0 / (comega - (em - en)) - 1.0 / (comega + (em - en)) )
nb2v = blas.cgemm(1.0, nm2v, self.xvrt)
ab2v = blas.cgemm(1.0, np.transpose(self.xocc),
nb2v).reshape(no * no)
vdp = self.v_dab * ab2v
return vdp * self.cc_da
def apply_l0_ref(self, sab, comega=1j * 0.0):
""" This applies the non-interacting four point Green's function to a suitable vector (e.g. dipole matrix elements)"""
assert sab.size == (self.nspin * self.norbs2)
self.l0_ncalls += 1
sab = sab.reshape((self.nspin, self.norbs, self.norbs))
ab2v = np.zeros_like(sab, dtype=self.dtypeComplex)
for s in range(self.nspin):
nb2v = dot(self.x_l0[s], sab[s])
nm2v = blas.cgemm(1.0, nb2v, self.x_l0[s].T)
for n, [en, fn] in enumerate(
zip(self.ksn2e_l0[s, :], self.ksn2f_l0[s, :])):
for m, [em, fm] in enumerate(
zip(self.ksn2e_l0[s, :], self.ksn2f_l0[s, :])):
nm2v[n, m] = nm2v[n, m] * (fn - fm) * (1.0 / (comega -
(em - en)))
nb2v = blas.cgemm(1.0, nm2v, self.x_l0[s])
ab2v[s] += blas.cgemm(1.0, self.x_l0[s].T, nb2v)
return ab2v.reshape(-1)
def apply_l0_spin_non_diag(self, sab, comega=1j * 0.0):
""" The definition of L0 which is not spin-diagonal even for parallel-spin references"""
assert sab.size == (self.nspin * self.norbs2)
self.l0_ncalls += 1
sab = sab.reshape((self.nspin, self.norbs, self.norbs))
ab2v = np.zeros_like(sab, dtype=self.dtypeComplex)
for ns in range(self.nspin):
for ms in range(self.nspin):
nb2v = dot(self.x_l0[ns], sab[ns])
nm2v = blas.cgemm(1.0, nb2v, self.x_l0[ms].T)
for n, [en, fn] in enumerate(
zip(self.ksn2e_l0[ns, :], self.ksn2f_l0[ns, :])):
for m, [em, fm] in enumerate(
zip(self.ksn2e_l0[ms, :], self.ksn2f_l0[ms, :])):
nm2v[n,
m] = nm2v[n, m] * (fn - fm) * (1.0 / (comega -
(em - en)))
nb2v = blas.cgemm(1.0, nm2v, self.x_l0[ms])
ab2v[ns] += blas.cgemm(0.5, self.x_l0[ns].T, nb2v)
return ab2v.reshape(-1)
vk = np.asfortranarray(vk[freq, :].T)
for i in range(1): #nl) #loop over left atoms
if i != 0 and i % (nl / 10) == 0: #print progress updates
print('\t\tNow ' + str(10 * np.round(i /
(nl / 10), 1)) + '% done '
'comptuting spectral conductance for block ' +
str(s + 1))
phix = np.asfortranarray(fijk[i * 3, ...]) #phi on i in x
phiy = np.asfortranarray(fijk[i * 3 + 1, ...]) #phi on i in y
phiz = np.asfortranarray(fijk[i * 3 + 2, ...]) #phi on i in z
#faster to compute this dot product only once per atom
for w in range(nfreq): #loop over omega prime
pxdotvk[:, w] = blas.cgemm((1 + 0j), phix,
vk[:, w]).reshape(nr * 3)
pydotvk[:, w] = blas.cgemm((1 + 0j), phiy,
vk[:, w]).reshape(nr * 3)
pzdotvk[:, w] = blas.cgemm((1 + 0j), phiz,
vk[:, w]).reshape(nr * 3)
# vj = np.flipud(vj[freq,:]).conj() #(freqmax,-freqmax)
# vj = np.roll(vj,1,axis=0) #roll once to start at 0 in the loop
# om = om[freq]
# omp = np.roll(np.flipud(om),1,axis=0)
# for w in range(nfreq):
# if w != 0 and w%(nfreq/100) == 0: #print progress updates
# print('\t\tNow '+str(np.round(w/(nfreq/100),1))+'% done '
# 'comptuting the etc term for block '+str(s+1))
# fx.toc()
#
rvelsfft[:,1::3] = velsfft[:,idsR*3+1] #vy
rvelsfft[:,2::3] = velsfft[:,idsR*3+2] #vz
########################################
lvelsfft = np.asfortranarray(lvelsfft) #faster blas dot product
rvelsfft = np.asfortranarray(rvelsfft) #faster blas dot product
kij = np.asfortranarray(kij) #faster blas dot product
for j in range(tn):
if j%(tn/10) == 0:
print('\t\t'+str(((j/(tn/10))+1)*10)+'% done with chunk '+
str(i+1))
if j == 0: #avoid divide by zero
qom[j,0] = 0+0j
else:
qom[j,0] = -(blas.cgemm((1+0j),lvelsfft[j,np.newaxis],
blas.cgemm((1+0j),kij,rvelsfft[j,np.newaxis].conj().T))
/om[j])
#######################################
# for j in range(tn):
# if j%(tn/10) == 0:
# print('\t\t'+str(((j/(tn/10))+1)*10)+'% done with chunk '+
# str(i+1))
# if j == 0: #avoid divide by zero
# qom[j,0] = 0+0j
# else:
# qom[j,0] = -(np.dot(lvelsfft[j,:],
# np.dot(kij,rvelsfft[j,:].transpose().conj()))/om[j])
qom = -2*1j*qom/(tn*dt*dn)
qom = qom*1.602e-19/1e-24 #convert to J/s. Units are F*v^2 =