def trans_cal():
from mpi4py import MPI
from aces.App import App
m = App().m
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
print("my rank is: %d" % rank)
if rank == 0:
print("Reading force constants from cache")
d = np.load('fcbin.npz')
fccenter, fcleft, fcright = d['fccenter'], d['fcleft'], d['fcright']
#fccenter,fcleft,fcright = comm.bcast((fccenter,fcleft,fcright) if rank == 0 else None, root=0)
print rank, len(fccenter)
total = 400.0
fmax = m.fmax
dm = fmax / total
intval = dm * size
omega = np.arange(dm * rank, fmax, intval) # THz
factor = 1e12**2 * 1e-20 * 1e-3 / 1.6e-19 / 6.23e23
energies = (omega * 2.0 * np.pi)**2 * factor
mkdir('tmp')
from ase.transport.calculators import TransportCalculator
# important trick!
# if eta is too small , there would be infinite value in transmission
# while if eta is too large, the transmission will be curve.
#
if m.eta is None:
eta = np.abs(fccenter).max() * 1e-5
eta1 = np.abs(fcleft).max() * 1e-4
eta2 = np.abs(fcright).max() * 1e-4
else:
if hasattr(m.eta, 'extend'):
eta, eta1, eta2 = m.eta
else:
eta, eta1, eta2 = m.eta, m.eta, m.eta
tcalc = TransportCalculator(
h=fccenter,
h1=fcleft,
h2=fcright,
energies=energies,
dos=True,
logfile='tmp/negf.log' +
str(rank),
eta=eta,
eta1=eta1,
eta2=eta2)
if rank == 0:
print('Calculate Transmission')
trans = tcalc.get_transmission()
if rank == 0:
print('Calculate Dos')
dos = tcalc.get_dos() * omega
# np.savez('tmp/result%s.npz'%(rank),x=omega,trans=trans,dos=dos)
to_txt(['omega', 'trans', 'dos'], np.c_[
omega, trans, dos], 'tmp/result.txt' + str(rank))
def trans_cal():
from mpi4py import MPI
from aces.App import App
m = App().m
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
size = comm.Get_size()
print("my rank is: %d" % rank)
if rank == 0:
print("Reading force constants from cache")
d = np.load('fcbin.npz')
fccenter, fcleft, fcright = d['fccenter'], d['fcleft'], d['fcright']
#fccenter,fcleft,fcright = comm.bcast((fccenter,fcleft,fcright) if rank == 0 else None, root=0)
print rank, len(fccenter)
total = 400.0
fmax = m.fmax
dm = fmax / total
intval = dm * size
omega = np.arange(dm * rank, fmax, intval) # THz
factor = 1e12**2 * 1e-20 * 1e-3 / 1.6e-19 / 6.23e23
energies = (omega * 2.0 * np.pi)**2 * factor
mkdir('tmp')
from ase.transport.calculators import TransportCalculator
# important trick!
# if eta is too small , there would be infinite value in transmission
# while if eta is too large, the transmission will be curve.
#
if m.eta is None:
eta = np.abs(fccenter).max() * 1e-5
eta1 = np.abs(fcleft).max() * 1e-4
eta2 = np.abs(fcright).max() * 1e-4
else:
if hasattr(m.eta, 'extend'):
eta, eta1, eta2 = m.eta
else:
eta, eta1, eta2 = m.eta, m.eta, m.eta
tcalc = TransportCalculator(h=fccenter,
h1=fcleft,
h2=fcright,
energies=energies,
dos=True,
logfile='tmp/negf.log' + str(rank),
eta=eta,
eta1=eta1,
eta2=eta2)
if rank == 0:
print('Calculate Transmission')
trans = tcalc.get_transmission()
if rank == 0:
print('Calculate Dos')
dos = tcalc.get_dos() * omega
# np.savez('tmp/result%s.npz'%(rank),x=omega,trans=trans,dos=dos)
to_txt(['omega', 'trans', 'dos'], np.c_[omega, trans, dos],
'tmp/result.txt' + str(rank))
def test(self):
dm = .1
omega = np.arange(dm, 60, dm) #THz
factor = 1e12**2 * 1e-20 * 1e-3 / 1.6e-19 / 6.23e23
energies = (omega * 2.0 * np.pi)**2 * factor
#energies=np.arange(0,10,.01)
h = -np.array((-2, 1, 0, 1, -2, 1, 0, 1, -2)).reshape((3, 3))
h1 = -np.array((-2, 1, 1, -2)).reshape((2, 2))
#x=1.0/np.sqrt(2)
#h1=h=-np.array((-2,x,0,0,x,-1,x,0,0,x,-2,x,0,0,x,-1)).reshape((4,4))
#energies = np.arange(-3, 3, 0.1)
calc = TransportCalculator(h=h, h1=h1, energies=energies, dos=True)
T = calc.get_transmission()
#print T
dos = calc.get_dos() * omega
plot([omega, 'Frequency (THz)'], [T, 'Transmission'],
'test_green_transmission.png')
plot([omega, 'Frequency (THz)'], [dos, 'Phonon Density of State'],
'test_green_dos.png')
def generate(self):
self.m.xp = 1
leadm = self.preLead()
self.phonopy('lead', leadm)
centerm = self.preCenter()
self.phonopy('center', centerm)
fccenter, fclead = self.collect()
dm = .5
omega = np.arange(dm, 60, dm) #THz
factor = 1e12**2 * 1e-20 * 1e-3 / 1.6e-19 / 6.23e23
energies = (omega * 2.0 * np.pi)**2 * factor
tcalc = TransportCalculator(h=fccenter,
h1=fclead,
h2=fclead,
energies=energies,
logfile='negf.log',
dos=True)
print 'Calculate Transmission'
trans = tcalc.get_transmission()
print 'Calculate Dos'
dos = tcalc.get_dos() * omega
print 'Calculate Thermal Conductance'
self.post()
def test_transport_calculator():
H_lead = np.zeros([4, 4])
# On-site energies are zero
for i in range(4):
H_lead[i, i] = 0.0
# Nearest neighbor hopping is -1.0
for i in range(3):
H_lead[i, i + 1] = -1.0
H_lead[i + 1, i] = -1.0
# Next-nearest neighbor hopping is 0.2
for i in range(2):
H_lead[i, i + 2] = 0.2
H_lead[i + 2, i] = 0.2
H_scat = np.zeros([6, 6])
# Principal layers on either side of S
H_scat[:2, :2] = H_lead[:2, :2]
H_scat[-2:, -2:] = H_lead[:2, :2]
# Scattering region
H_scat[2, 2] = 0.0
H_scat[3, 3] = 0.0
H_scat[2, 3] = -0.8
H_scat[3, 2] = -0.8
# External coupling
H_scat[1, 2] = 0.2
H_scat[2, 1] = 0.2
H_scat[3, 4] = 0.2
H_scat[4, 3] = 0.2
energies = np.arange(-3, 3, 0.02)
tcalc = TransportCalculator(h=H_scat,
h1=H_lead,
eta=0.02,
energies=energies)
T = tcalc.get_transmission()
tcalc.set(pdos=[2, 3])
pdos = tcalc.get_pdos()
tcalc.set(dos=True)
dos = tcalc.get_dos()
write('T.dat', tcalc.energies, T)
write('pdos0.dat', tcalc.energies, pdos[0])
write('pdos1.dat', tcalc.energies, pdos[1])
#subdiagonalize
h_rot, s_rot, eps, u = tcalc.subdiagonalize_bfs([2, 3], apply=True)
T_rot = tcalc.get_transmission()
dos_rot = tcalc.get_dos()
pdos_rot = tcalc.get_pdos()
write('T_rot.dat', tcalc.energies, T_rot)
write('pdos0_rot.dat', tcalc.energies, pdos_rot[0])
write('pdos1_rot.dat', tcalc.energies, pdos_rot[1])
print('Subspace eigenvalues:', eps)
assert sum(abs(eps - (-0.8, 0.8))) < 2.0e-15, 'Subdiagonalization. error'
print('Max deviation of T after the rotation:', np.abs(T - T_rot).max())
assert max(abs(T - T_rot)) < 2.0e-15, 'Subdiagonalization. error'
#remove coupling
h_cut, s_cut = tcalc.cutcoupling_bfs([2], apply=True)
T_cut = tcalc.get_transmission()
dos_cut = tcalc.get_dos()
pdos_cut = tcalc.get_pdos()
write('T_cut.dat', tcalc.energies, T_cut)
write('pdos0_cut.dat', tcalc.energies, pdos_cut[0])
write('pdos1_cut.dat', tcalc.energies, pdos_cut[1])
# External coupling
H_scat[1, 2] = 0.2
H_scat[2, 1] = 0.2
H_scat[3, 4] = 0.2
H_scat[4, 3] = 0.2
energies = np.arange(-3, 3, 0.02)
tcalc = TransportCalculator(h=H_scat, h1=H_lead, eta=0.02, energies=energies)
T = tcalc.get_transmission()
tcalc.set(pdos=[2, 3])
pdos = tcalc.get_pdos()
tcalc.set(dos=True)
dos = tcalc.get_dos()
write('T.dat', tcalc.energies, T)
write('pdos0.dat', tcalc.energies, pdos[0])
write('pdos1.dat', tcalc.energies, pdos[1])
#subdiagonalize
h_rot, s_rot, eps, u = tcalc.subdiagonalize_bfs([2, 3], apply=True)
T_rot = tcalc.get_transmission()
dos_rot = tcalc.get_dos()
pdos_rot = tcalc.get_pdos()
write('T_rot.dat', tcalc.energies, T_rot)
write('pdos0_rot.dat', tcalc.energies, pdos_rot[0])
write('pdos1_rot.dat', tcalc.energies, pdos_rot[1])
H_scat[2,1] = 0.2
H_scat[3,4] = 0.2
H_scat[4,3] = 0.2
energies = np.arange(-3,3,0.02)
tcalc = TransportCalculator(h=H_scat,
h1=H_lead,
h2=H_lead,
energies=energies)
T = tcalc.get_transmission()
tcalc.set(pdos=[2, 3])
pdos = tcalc.get_pdos()
tcalc.set(dos=True)
dos = tcalc.get_dos()
write('T.dat',tcalc.energies,T)
write('pdos0.dat', tcalc.energies,pdos[0])
write('pdos1.dat', tcalc.energies,pdos[1])
#subdiagonalize
h_rot, s_rot, eps, u = tcalc.subdiagonalize_bfs([2, 3])
tcalc.set(h=h_rot,s=s_rot)
T_rot = tcalc.get_transmission()
dos_rot = tcalc.get_dos()
pdos_rot = tcalc.get_pdos()
write('T_rot.dat', tcalc.energies,T_rot)
write('pdos0_rot.dat', tcalc.energies, pdos_rot[0])
write('pdos1_rot.dat', tcalc.energies, pdos_rot[1])
