def initialize(self):
self.ini = True
BASECHI.initialize(self)
self.txtname = self.gwtxtname
self.output_init()
self.printtxt('GPAW version %s' % (version))
self.printtxt('-----------------------------------------------')
self.printtxt('GW calculation started at:')
self.printtxt(ctime())
self.printtxt('-----------------------------------------------')
self.starttime = time()
calc = self.calc
kd = self.kd
# band init
if self.gwnbands is None:
if self.npw > calc.wfs.bd.nbands:
self.nbands = calc.wfs.bd.nbands
else:
self.nbands = self.npw
# eigenvalue init
if self.user_skn is not None:
self.printtxt('Use eigenvalues from user.')
assert np.shape(
self.user_skn
)[0] == self.nspins, 'Eigenvalues not compatible with .gpw file!'
assert np.shape(
self.user_skn
)[1] == self.kd.nibzkpts, 'Eigenvalues not compatible with .gpw file!'
assert np.shape(
self.user_skn)[2] >= self.nbands, 'Too few eigenvalues!'
self.e_skn = self.user_skn
else:
self.printtxt('Use eigenvalues from the calculator.')
# q point init
self.bzq_kc = kd.get_bz_q_points()
self.ibzq_qc = self.bzq_kc # q point symmetry is not used at the moment.
self.nqpt = np.shape(self.bzq_kc)[0]
# frequency points init
self.static = False
if self.ppa: # Plasmon Pole Approximation
if self.E0 is None:
self.E0 = Hartree
self.E0 /= Hartree
self.w_w = np.array([0., 1j * self.E0])
self.hilbert_trans = False
self.wpar = 1
elif self.w_w is None: # static COHSEX
self.w_w = np.array([0.])
self.static = True
self.hilbert_trans = False
self.wpar = 1
self.eta = 0.0001 / Hartree
else:
# create nonlinear frequency grid
# grid is linear from 0 to wcut with spacing dw
# spacing is linearily increasing between wcut and wmax
# Hilbert transforms are still carried out on linear grid
wcut = self.w_w[0]
wmax = self.w_w[1]
dw = self.w_w[2]
w_w = np.linspace(0., wcut, wcut / dw + 1)
i = 1
wi = wcut
while wi < wmax:
wi += i * dw
w_w = np.append(w_w, wi)
i += 1
while len(w_w) % self.wpar != 0:
wi += i * dw
w_w = np.append(w_w, wi)
i += 1
dw_w = np.zeros(len(w_w))
dw_w[0] = dw
dw_w[1:] = w_w[1:] - w_w[:-1]
self.w_w = w_w / Hartree
self.dw_w = dw_w / Hartree
self.eta_w = dw_w * 4 / Hartree
self.wcut = wcut
self.wmax = self.w_w[-1]
self.wmin = self.w_w[0]
self.dw = self.w_w[1] - self.w_w[0]
self.Nw = len(self.w_w)
# self.wpar = int(self.Nw * self.npw**2 * 16. / 1024**2) // 1500 + 1 # estimate memory and parallelize over frequencies
for s in range(self.nspins):
emaxdiff = self.e_skn[s][:, self.nbands -
1].max() - self.e_skn[s][:, 0].min()
assert (self.wmax > emaxdiff
), 'Maximum frequency must be larger than %f' % (
emaxdiff * Hartree)
# GW kpoints init
if self.kpoints is None:
self.gwnkpt = self.kd.nibzkpts
self.gwkpt_k = kd.ibz2bz_k
else:
self.gwnkpt = np.shape(self.kpoints)[0]
self.gwkpt_k = self.kpoints
# GW bands init
if self.bands is None:
self.gwnband = self.nbands
self.bands = self.gwbands_n = np.arange(self.nbands)
else:
self.gwnband = np.shape(self.bands)[0]
self.gwbands_n = self.bands
self.alpha = 1j / (2 * pi * self.vol * self.kd.nbzkpts)
# parallel init
assert len(self.w_w) % self.wpar == 0
self.wcommsize = self.wpar
self.qcommsize = size // self.wpar
assert self.qcommsize * self.wcommsize == size, 'wpar must be integer divisor of number of requested cores'
if self.nqpt != 1: # parallelize over q-points
self.wcomm, self.qcomm, self.worldcomm = set_communicator(
world, rank, size, self.wpar)
self.ncomm = serial_comm
self.dfcomm = self.wcomm
self.kcommsize = 1
else: # parallelize over bands
self.wcomm, self.ncomm, self.worldcomm = set_communicator(
world, rank, size, self.wpar)
self.qcomm = serial_comm
if self.wpar > 1:
self.dfcomm = self.wcomm
self.kcommsize = 1
else:
self.dfcomm = self.ncomm
self.kcommsize = self.ncomm.size
nq, self.nq_local, self.q_start, self.q_end = parallel_partition(
self.nqpt, self.qcomm.rank, self.qcomm.size, reshape=False)
nb, self.nbands_local, self.m_start, self.m_end = parallel_partition(
self.nbands, self.ncomm.rank, self.ncomm.size, reshape=False)
def parallel_init(self):
"""Parallel initialization. By default, only use kcomm and wcomm.
Parameters:
kcomm:
kpoint communicator
wScomm:
spectral function communicator
wcomm:
frequency communicator
"""
if extra_parameters.get("df_dry_run"):
from gpaw.mpi import DryRunCommunicator
size = extra_parameters["df_dry_run"]
world = DryRunCommunicator(size)
rank = world.rank
self.comm = world
else:
world = self.comm
rank = self.comm.rank
size = self.comm.size
wcommsize = int(self.NwS * self.npw ** 2 * 16.0 / 1024 ** 2) // 1500 # megabyte
wcommsize += 1
if size < wcommsize:
raise ValueError("Number of cpus are not enough ! ")
if self.kcommsize is None:
self.kcommsize = world.size
if wcommsize > size // self.kcommsize: # if matrix too large, overwrite kcommsize and distribute matrix
self.printtxt("kcommsize is over written ! ")
while size % wcommsize != 0:
wcommsize += 1
self.kcommsize = size // wcommsize
assert self.kcommsize * wcommsize == size
if self.kcommsize < 1:
raise ValueError("Number of cpus are not enough ! ")
self.kcomm, self.wScomm, self.wcomm = set_communicator(world, rank, size, self.kcommsize)
if self.kd.nbzkpts >= world.size:
self.nkpt_reshape = self.kd.nbzkpts
self.nkpt_reshape, self.nkpt_local, self.kstart, self.kend = parallel_partition(
self.nkpt_reshape, self.kcomm.rank, self.kcomm.size, reshape=True, positive=True
)
self.mband_local = self.nvalbands
self.mlist = np.arange(self.nbands)
else:
# if number of kpoints == 1, use band parallelization
self.nkpt_local = self.kd.nbzkpts
self.kstart = 0
self.kend = self.kd.nbzkpts
self.nkpt_reshape = self.kd.nbzkpts
self.nbands, self.mband_local, self.mlist = parallel_partition_list(
self.nbands, self.kcomm.rank, self.kcomm.size
)
if self.NwS % size != 0:
self.NwS -= self.NwS % size
self.NwS, self.NwS_local, self.wS1, self.wS2 = parallel_partition(
self.NwS, self.wScomm.rank, self.wScomm.size, reshape=False
)
if self.hilbert_trans:
self.Nw, self.Nw_local, self.wstart, self.wend = parallel_partition(
self.Nw, self.wcomm.rank, self.wcomm.size, reshape=True
)
else:
if self.Nw > 1:
# assert self.Nw % (self.comm.size / self.kcomm.size) == 0
self.wcomm = self.wScomm
self.Nw, self.Nw_local, self.wstart, self.wend = parallel_partition(
self.Nw, self.wcomm.rank, self.wcomm.size, reshape=False
)
else:
# if frequency point is too few, then dont parallelize
self.wcomm = serial_comm
self.wstart = 0
self.wend = self.Nw
self.Nw_local = self.Nw
return
def initialize(self):
self.ini = True
BASECHI.initialize(self)
self.txtname = self.gwtxtname
self.output_init()
self.printtxt('GPAW version %s' %(version))
self.printtxt('-----------------------------------------------')
self.printtxt('GW calculation started at:')
self.printtxt(ctime())
self.printtxt('-----------------------------------------------')
self.starttime = time()
calc = self.calc
kd = self.kd
# band init
if self.gwnbands is None:
if self.npw > calc.wfs.bd.nbands:
self.nbands = calc.wfs.bd.nbands
else:
self.nbands = self.npw
# eigenvalue init
if self.user_skn is not None:
self.printtxt('Use eigenvalues from user.')
assert np.shape(self.user_skn)[0] == self.nspins, 'Eigenvalues not compatible with .gpw file!'
assert np.shape(self.user_skn)[1] == self.kd.nibzkpts, 'Eigenvalues not compatible with .gpw file!'
assert np.shape(self.user_skn)[2] >= self.nbands, 'Too few eigenvalues!'
self.e_skn = self.user_skn
else:
self.printtxt('Use eigenvalues from the calculator.')
# q point init
self.bzq_kc = kd.get_bz_q_points()
self.ibzq_qc = self.bzq_kc # q point symmetry is not used at the moment.
self.nqpt = np.shape(self.bzq_kc)[0]
# frequency points init
self.static=False
if self.ppa: # Plasmon Pole Approximation
if self.E0 is None:
self.E0 = Hartree
self.E0 /= Hartree
self.w_w = np.array([0., 1j*self.E0])
self.hilbert_trans=False
self.wpar=1
elif self.w_w is None: # static COHSEX
self.w_w = np.array([0.])
self.static=True
self.hilbert_trans=False
self.wpar=1
self.eta = 0.0001 / Hartree
else:
# create nonlinear frequency grid
# grid is linear from 0 to wcut with spacing dw
# spacing is linearily increasing between wcut and wmax
# Hilbert transforms are still carried out on linear grid
wcut = self.w_w[0]
wmax = self.w_w[1]
dw = self.w_w[2]
w_w = np.linspace(0., wcut, wcut/dw+1)
i=1
wi=wcut
while wi < wmax:
wi += i*dw
w_w = np.append(w_w, wi)
i+=1
while len(w_w) % self.wpar != 0:
wi += i*dw
w_w = np.append(w_w, wi)
i+=1
dw_w = np.zeros(len(w_w))
dw_w[0] = dw
dw_w[1:] = w_w[1:] - w_w[:-1]
self.w_w = w_w / Hartree
self.dw_w = dw_w / Hartree
self.eta_w = dw_w * 4 / Hartree
self.wcut = wcut
self.wmax = self.w_w[-1]
self.wmin = self.w_w[0]
self.dw = self.w_w[1] - self.w_w[0]
self.Nw = len(self.w_w)
# self.wpar = int(self.Nw * self.npw**2 * 16. / 1024**2) // 1500 + 1 # estimate memory and parallelize over frequencies
for s in range(self.nspins):
emaxdiff = self.e_skn[s][:,self.nbands-1].max() - self.e_skn[s][:,0].min()
assert (self.wmax > emaxdiff), 'Maximum frequency must be larger than %f' %(emaxdiff*Hartree)
# GW kpoints init
if self.kpoints is None:
self.gwnkpt = self.kd.nibzkpts
self.gwkpt_k = kd.ibz2bz_k
else:
self.gwnkpt = np.shape(self.kpoints)[0]
self.gwkpt_k = self.kpoints
# GW bands init
if self.bands is None:
self.gwnband = self.nbands
self.bands = self.gwbands_n = np.arange(self.nbands)
else:
self.gwnband = np.shape(self.bands)[0]
self.gwbands_n = self.bands
self.alpha = 1j/(2*pi * self.vol * self.kd.nbzkpts)
# parallel init
assert len(self.w_w) % self.wpar == 0
self.wcommsize = self.wpar
self.qcommsize = size // self.wpar
assert self.qcommsize * self.wcommsize == size, 'wpar must be integer divisor of number of requested cores'
if self.nqpt != 1: # parallelize over q-points
self.wcomm, self.qcomm, self.worldcomm = set_communicator(world, rank, size, self.wpar)
self.ncomm = serial_comm
self.dfcomm = self.wcomm
self.kcommsize = 1
else: # parallelize over bands
self.wcomm, self.ncomm, self.worldcomm = set_communicator(world, rank, size, self.wpar)
self.qcomm = serial_comm
if self.wpar > 1:
self.dfcomm = self.wcomm
self.kcommsize = 1
else:
self.dfcomm = self.ncomm
self.kcommsize = self.ncomm.size
nq, self.nq_local, self.q_start, self.q_end = parallel_partition(
self.nqpt, self.qcomm.rank, self.qcomm.size, reshape=False)
nb, self.nbands_local, self.m_start, self.m_end = parallel_partition(
self.nbands, self.ncomm.rank, self.ncomm.size, reshape=False)
def parallel_init(self):
"""Parallel initialization. By default, only use kcomm and wcomm.
Parameters:
kcomm:
kpoint communicator
wScomm:
spectral function communicator
wcomm:
frequency communicator
"""
if extra_parameters.get('df_dry_run'):
from gpaw.mpi import DryRunCommunicator
size = extra_parameters['df_dry_run']
world = DryRunCommunicator(size)
rank = world.rank
self.comm = world
else:
world = self.comm
rank = self.comm.rank
size = self.comm.size
wcommsize = int(self.NwS * self.npw**2 * 16. / 1024**2) // 1500 # megabyte
wcommsize += 1
if size < wcommsize:
raise ValueError('Number of cpus are not enough ! ')
if self.kcommsize is None:
self.kcommsize = world.size
if wcommsize > size // self.kcommsize: # if matrix too large, overwrite kcommsize and distribute matrix
self.printtxt('kcommsize is over written ! ')
while size % wcommsize != 0:
wcommsize += 1
self.kcommsize = size // wcommsize
assert self.kcommsize * wcommsize == size
if self.kcommsize < 1:
raise ValueError('Number of cpus are not enough ! ')
self.kcomm, self.wScomm, self.wcomm = set_communicator(world, rank, size, self.kcommsize)
if self.kd.nbzkpts >= world.size:
self.nkpt_reshape = self.kd.nbzkpts
self.nkpt_reshape, self.nkpt_local, self.kstart, self.kend = parallel_partition(
self.nkpt_reshape, self.kcomm.rank, self.kcomm.size, reshape=True, positive=True)
self.mband_local = self.nvalbands
self.mlist = np.arange(self.nbands)
else:
# if number of kpoints == 1, use band parallelization
self.nkpt_local = self.kd.nbzkpts
self.kstart = 0
self.kend = self.kd.nbzkpts
self.nkpt_reshape = self.kd.nbzkpts
self.nbands, self.mband_local, self.mlist = parallel_partition_list(
self.nbands, self.kcomm.rank, self.kcomm.size)
if self.NwS % size != 0:
self.NwS -= self.NwS % size
self.NwS, self.NwS_local, self.wS1, self.wS2 = parallel_partition(
self.NwS, self.wScomm.rank, self.wScomm.size, reshape=False)
if self.hilbert_trans:
self.Nw, self.Nw_local, self.wstart, self.wend = parallel_partition(
self.Nw, self.wcomm.rank, self.wcomm.size, reshape=True)
else:
if self.Nw > 1:
# assert self.Nw % (self.comm.size / self.kcomm.size) == 0
self.wcomm = self.wScomm
self.Nw, self.Nw_local, self.wstart, self.wend = parallel_partition(
self.Nw, self.wcomm.rank, self.wcomm.size, reshape=False)
else:
# if frequency point is too few, then dont parallelize
self.wcomm = serial_comm
self.wstart = 0
self.wend = self.Nw
self.Nw_local = self.Nw
return
def get_rpa_correlation_energy(self,
kcommsize=None,
dfcommsize=world.size,
directions=None,
skip_gamma=False,
ecut=10,
nbands=None,
gauss_legendre=None,
frequency_cut=None,
frequency_scale=None,
w=None,
restart=None):
self.initialize_calculation(w,
ecut,
nbands,
kcommsize,
gauss_legendre,
frequency_cut,
frequency_scale)
if dfcommsize == world.size:
self.dfcomm = world
E_q = []
if restart is not None:
assert type(restart) is str
try:
f = paropen(restart, 'r')
lines = f.readlines()
for line in lines:
E_q.append(eval(line))
f.close()
print >> self.txt, 'Correlation energy obtained ' \
+'from %s q-points obtained from restart file: ' \
% len(E_q), restart
print >> self.txt
except:
IOError
for index, q in zip(range(len(E_q), len(self.ibz_q_points)),
self.ibz_q_points[len(E_q):]):
if abs(np.dot(q, q))**0.5 < 1.e-5:
E_q0 = 0.
if skip_gamma:
print >> self.txt, \
'Not calculating q at the Gamma point'
print >> self.txt
else:
if directions is None:
directions = [[0, 1/3.], [1, 1/3.], [2, 1/3.]]
for d in directions:
E_q0 += self.E_q(q,
index=index,
direction=d[0]) * d[1]
E_q.append(E_q0)
else:
E_q.append(self.E_q(q, index=index))
if restart is not None:
f = paropen(restart, 'a')
print >> f, E_q[-1]
f.close()
E = np.dot(np.array(self.q_weights), np.array(E_q).real)
else: # parallelzation over q points
print >> self.txt, 'parallelization over q point ! '
# creates q list
qlist = []
qweight = []
id = 0
for iq, q in enumerate(self.ibz_q_points):
if abs(np.dot(q, q))**0.5 < 1.e-5:
if skip_gamma:
continue
else:
if directions is None:
directions = [[0, 1/3.], [1, 1/3.], [2, 1/3.]]
for d in directions:
qlist.append((id, q, d[0], d[1]))
qweight.append(self.q_weights[iq])
id += 1
continue
qlist.append((id, q, 0, 1))
qweight.append(self.q_weights[iq])
id += 1
nq = len(qlist)
# distribute q list
self.dfcomm, qcomm = set_communicator(world,
world.rank,
world.size,
kcommsize=dfcommsize)[:2]
nq, nq_local, qlist_local = parallel_partition_list(nq,
qcomm.rank,
qcomm.size)
E_q = np.zeros(nq)
for iq in qlist_local:
try:
ff = open('E_q_%s_%s.dat' %(self.tag,iq), 'r')
E_q[iq] = ff.readline().split()[-2]
print >> self.txt, 'Reading E_q[%s] '%(iq), E_q[iq]
except:
E_q[iq] = self.E_q(qlist[iq][1],
index=iq,
direction=qlist[iq][2]) * qlist[iq][3]
if self.tag is not None and self.dfcomm.rank == 0:
ff = open('E_q_%s_%s.dat' %(self.tag,iq), 'a')
print >> ff, qlist[iq][1:4], E_q[iq], qweight[iq]
ff.close()
qcomm.sum(E_q)
print >> self.txt, '(q, direction, weight), E_q, qweight'
for iq in range(nq):
print >> self.txt, qlist[iq][1:4], E_q[iq], qweight[iq]
E = np.dot(np.array(qweight), np.array(E_q))
print >> self.txt, 'RPA correlation energy:'
print >> self.txt, 'E_c = %s eV' % E
print >> self.txt
print >> self.txt, 'Calculation completed at: ', ctime()
print >> self.txt
print >> self.txt, \
'------------------------------------------------------'
print >> self.txt
return E
def get_rpa_correlation_energy(self,
kcommsize=None,
dfcommsize=world.size,
directions=None,
skip_gamma=False,
ecut=10,
nbands=None,
gauss_legendre=None,
frequency_cut=None,
frequency_scale=None,
w=None,
restart=None):
self.initialize_calculation(w, ecut, nbands, kcommsize, gauss_legendre,
frequency_cut, frequency_scale)
if dfcommsize == world.size:
self.dfcomm = world
E_q = []
if restart is not None:
assert type(restart) is str
try:
f = paropen(restart, 'r')
lines = f.readlines()
for line in lines:
E_q.append(eval(line))
f.close()
print('Correlation energy obtained ' \
+'from %s q-points obtained from restart file: ' \
% len(E_q), restart, file=self.txt)
print(file=self.txt)
except:
IOError
for index, q in zip(range(len(E_q), len(self.ibz_q_points)),
self.ibz_q_points[len(E_q):]):
if abs(np.dot(q, q))**0.5 < 1.e-5:
E_q0 = 0.
if skip_gamma:
print('Not calculating q at the Gamma point',
file=self.txt)
print(file=self.txt)
else:
if directions is None:
directions = [[0, 1 / 3.], [1, 1 / 3.],
[2, 1 / 3.]]
for d in directions:
E_q0 += self.E_q(q, index=index,
direction=d[0]) * d[1]
E_q.append(E_q0)
else:
E_q.append(self.E_q(q, index=index))
if restart is not None:
f = paropen(restart, 'a')
print(E_q[-1], file=f)
f.close()
E = np.dot(np.array(self.q_weights), np.array(E_q).real)
else: # parallelzation over q points
print('parallelization over q point ! ', file=self.txt)
# creates q list
qlist = []
qweight = []
id = 0
for iq, q in enumerate(self.ibz_q_points):
if abs(np.dot(q, q))**0.5 < 1.e-5:
if skip_gamma:
continue
else:
if directions is None:
directions = [[0, 1 / 3.], [1, 1 / 3.],
[2, 1 / 3.]]
for d in directions:
qlist.append((id, q, d[0], d[1]))
qweight.append(self.q_weights[iq])
id += 1
continue
qlist.append((id, q, 0, 1))
qweight.append(self.q_weights[iq])
id += 1
nq = len(qlist)
# distribute q list
self.dfcomm, qcomm = set_communicator(world,
world.rank,
world.size,
kcommsize=dfcommsize)[:2]
nq, nq_local, qlist_local = parallel_partition_list(
nq, qcomm.rank, qcomm.size)
E_q = np.zeros(nq)
for iq in qlist_local:
try:
ff = open('E_q_%s_%s.dat' % (self.tag, iq), 'r')
E_q[iq] = ff.readline().split()[-2]
print('Reading E_q[%s] ' % (iq), E_q[iq], file=self.txt)
except:
E_q[iq] = self.E_q(qlist[iq][1],
index=iq,
direction=qlist[iq][2]) * qlist[iq][3]
if self.tag is not None and self.dfcomm.rank == 0:
ff = open('E_q_%s_%s.dat' % (self.tag, iq), 'a')
print(qlist[iq][1:4], E_q[iq], qweight[iq], file=ff)
ff.close()
qcomm.sum(E_q)
print('(q, direction, weight), E_q, qweight', file=self.txt)
for iq in range(nq):
print(qlist[iq][1:4], E_q[iq], qweight[iq], file=self.txt)
E = np.dot(np.array(qweight), np.array(E_q))
print('RPA correlation energy:', file=self.txt)
print('E_c = %s eV' % E, file=self.txt)
print(file=self.txt)
print('Calculation completed at: ', ctime(), file=self.txt)
print(file=self.txt)
print('------------------------------------------------------',
file=self.txt)
print(file=self.txt)
return E