def __init__(self, sl_lrtddft, nrows, lr_comms):
self.mprocs, self.nprocs, self.block_size = tuple(sl_lrtddft)
self.lr_comms = lr_comms
# original grid, ie, how matrix is stored
self.matrix_grid = BlacsGrid(self.lr_comms.parent_comm,
self.lr_comms.dd_comm.size,
self.lr_comms.eh_comm.size)
# diagonalization grid
self.diag_grid = BlacsGrid(self.lr_comms.parent_comm, self.mprocs,
self.nprocs)
# -----------------------------------------------------------------
# for SCALAPACK we need TRANSPOSED MATRIX (and vector)
#
# M = rows, N = cols
M = nrows
N = nrows
mb = 1
nb = 1
self.matrix_descr = self.matrix_grid.new_descriptor(N, M, nb, mb)
bs = self.block_size
self.diag_descr = self.diag_grid.new_descriptor(N, M, bs, bs)
self.diag_in_redist = Redistributor(self.lr_comms.parent_comm,
self.matrix_descr, self.diag_descr)
self.diag_out_redist = Redistributor(self.lr_comms.parent_comm,
self.diag_descr,
self.matrix_descr)
def scalapack_diagonalize(self, H_sS):
mb = 32
N = self.nS
g1 = BlacsGrid(world, size, 1)
g2 = BlacsGrid(world, size // 2, 2)
nndesc1 = g1.new_descriptor(N, N, self.nS_local, N)
nndesc2 = g2.new_descriptor(N, N, mb, mb)
A_ss = nndesc2.empty(dtype=H_sS.dtype)
redistributor = Redistributor(world, nndesc1, nndesc2)
redistributor.redistribute(H_sS, A_ss)
# diagonalize
v_ss = nndesc2.zeros(dtype=A_ss.dtype)
w_S = np.zeros(N, dtype=float)
nndesc2.diagonalize_dc(A_ss, v_ss, w_S, 'L')
# distribute the eigenvectors to master
v_sS = np.zeros_like(H_sS)
redistributor = Redistributor(world, nndesc2, nndesc1)
redistributor.redistribute(v_ss, v_sS)
# v2_SS = np.zeros((self.nS, self.nS), dtype=complex)
# world.all_gather(v_sS, v2_SS)
return w_S, v_sS.conj()
def diagonalize(self):
print('Diagonalizing Hamiltonian', file=self.fd)
"""The t and T represent local and global
eigenstates indices respectively
"""
# Non-Hermitian matrix can only use linalg.eig
if not self.td:
print(' Using numpy.linalg.eig...', file=self.fd)
print(' Eliminated %s pair orbitals' % len(self.excludef_S),
file=self.fd)
self.H_SS = self.collect_A_SS(self.H_sS)
self.w_T = np.zeros(self.nS - len(self.excludef_S), complex)
if world.rank == 0:
self.H_SS = np.delete(self.H_SS, self.excludef_S, axis=0)
self.H_SS = np.delete(self.H_SS, self.excludef_S, axis=1)
self.w_T, self.v_ST = np.linalg.eig(self.H_SS)
world.broadcast(self.w_T, 0)
self.df_S = np.delete(self.df_S, self.excludef_S)
self.rhoG0_S = np.delete(self.rhoG0_S, self.excludef_S)
# Here the eigenvectors are returned as complex conjugated rows
else:
if world.size == 1:
print(' Using lapack...', file=self.fd)
from gpaw.utilities.lapack import diagonalize
self.w_T = np.zeros(self.nS)
diagonalize(self.H_sS, self.w_T)
self.v_St = self.H_sS.conj().T
else:
print(' Using scalapack...', file=self.fd)
nS = self.nS
ns = -(-self.kd.nbzkpts // world.size) * (self.nv * self.nc *
self.spins *
(self.spinors + 1)**2)
grid = BlacsGrid(world, world.size, 1)
desc = grid.new_descriptor(nS, nS, ns, nS)
desc2 = grid.new_descriptor(nS, nS, 2, 2)
H_tmp = desc2.zeros(dtype=complex)
r = Redistributor(world, desc, desc2)
r.redistribute(self.H_sS, H_tmp)
self.w_T = np.empty(nS)
v_tmp = desc2.empty(dtype=complex)
desc2.diagonalize_dc(H_tmp, v_tmp, self.w_T)
r = Redistributor(grid.comm, desc2, desc)
self.v_St = desc.zeros(dtype=complex)
r.redistribute(v_tmp, self.v_St)
self.v_St = self.v_St.conj().T
if self.write_v and self.td:
# Cannot use par_save without td
self.par_save('v_TS.ulm', 'v_TS', self.v_St.T)
return
def __init__(self,
gd,
bd,
block_comm,
dtype,
mcpus,
ncpus,
blocksize,
nao,
timer=nulltimer):
BlacsLayouts.__init__(self, gd, bd, block_comm, dtype, mcpus, ncpus,
blocksize, timer)
nbands = bd.nbands
self.blocksize = blocksize
self.mynbands = mynbands = bd.mynbands
self.orbital_comm = self.bd.comm
self.naoblocksize = naoblocksize = -((-nao) // self.orbital_comm.size)
self.nao = nao
# Range of basis functions for BLACS distribution of matrices:
self.Mmax = nao
self.Mstart = bd.comm.rank * naoblocksize
self.Mstop = min(self.Mstart + naoblocksize, self.Mmax)
self.mynao = self.Mstop - self.Mstart
# Column layout for one matrix per band rank:
self.columngrid = BlacsGrid(bd.comm, bd.comm.size, 1)
self.mMdescriptor = self.columngrid.new_descriptor(
nao, nao, naoblocksize, nao)
self.nMdescriptor = self.columngrid.new_descriptor(
nbands, nao, mynbands, nao)
#parallelprint(world, (mynao, self.mMdescriptor.shape))
# Column layout for one matrix in total (only on grid masters):
self.single_column_grid = BlacsGrid(self.column_comm, bd.comm.size, 1)
self.mM_unique_descriptor = self.single_column_grid.new_descriptor( \
nao, nao, naoblocksize, nao)
# nM_unique_descriptor is meant to hold the coefficients after
# diagonalization. BLACS requires it to be nao-by-nao, but
# we only fill meaningful data into the first nbands columns.
#
# The array will then be trimmed and broadcast across
# the grid descriptor's communicator.
self.nM_unique_descriptor = self.single_column_grid.new_descriptor( \
nbands, nao, mynbands, nao)
# Fully blocked grid for diagonalization with many CPUs:
self.mmdescriptor = self.blockgrid.new_descriptor(
nao, nao, blocksize, blocksize)
#self.nMdescriptor = nMdescriptor
self.mM2mm = Redistributor(self.block_comm, self.mM_unique_descriptor,
self.mmdescriptor)
self.mm2nM = Redistributor(self.block_comm, self.mmdescriptor,
self.nM_unique_descriptor)
def test_overlaps_nonhermitian(self):
alpha = np.random.normal(size=1).astype(self.dtype)
if self.dtype == complex:
alpha += 1j * np.random.normal(size=1)
world.broadcast(alpha, 0)
# Set up non-Hermitian overlap operator:
S = lambda x: alpha * x
dS = lambda a, P_ni: np.dot(alpha * P_ni, self.setups[a].dO_ii)
nblocks = self.get_optimal_number_of_blocks(self.blocking)
overlap = MatrixOperator(self.ksl, nblocks, self. async, False)
if 0: #XXX non-hermitian case so Nn2nn not just uplo='L' but rather 'G'
blockcomm = self.ksl.nndescriptor.blacsgrid.comm
self.ksl.Nn2nn = Redistributor(blockcomm, self.ksl.Nndescriptor,
self.ksl.nndescriptor)
S_nn = overlap.calculate_matrix_elements(self.psit_nG, self.P_ani, S,
dS)
if memstats:
self.mem_test = record_memory()
S_NN = self.ksl.nndescriptor.collect_on_master(S_nn)
if self.bd.comm.rank == 0 and self.gd.comm.rank == 0:
assert S_NN.shape == (self.bd.nbands, ) * 2
S_NN = S_NN.T.copy() # Fortran -> C indexing
else:
assert S_NN.nbytes == 0
S_NN = np.empty((self.bd.nbands, ) * 2, dtype=S_NN.dtype)
if self.bd.comm.rank == 0:
self.gd.comm.broadcast(S_NN, 0)
self.bd.comm.broadcast(S_NN, 0)
self.check_and_plot(S_NN, alpha * self.S0_nn, 9,
'overlaps,nonhermitian')
def calculate_blocked_density_matrix(self, f_n, C_nM):
nbands = self.bd.nbands
nao = self.nao
dtype = C_nM.dtype
self.nMdescriptor.checkassert(C_nM)
if self.gd.rank == 0:
Cf_nM = (C_nM * f_n[:, None]).conj()
else:
C_nM = self.nM_unique_descriptor.zeros(dtype=dtype)
Cf_nM = self.nM_unique_descriptor.zeros(dtype=dtype)
r = Redistributor(self.block_comm, self.nM_unique_descriptor,
self.mmdescriptor)
Cf_mm = self.mmdescriptor.zeros(dtype=dtype)
r.redistribute(Cf_nM, Cf_mm, nbands, nao)
del Cf_nM
C_mm = self.mmdescriptor.zeros(dtype=dtype)
r.redistribute(C_nM, C_mm, nbands, nao)
# no use to delete C_nM as it's in the input...
rho_mm = self.mmdescriptor.zeros(dtype=dtype)
pblas_simple_gemm(self.mmdescriptor,
self.mmdescriptor,
self.mmdescriptor,
Cf_mm,
C_mm,
rho_mm,
transa='T')
return rho_mm
def parallel_eigh(matrixfile, blacsgrid=(4, 2), blocksize=64):
"""Diagonalize matrix in parallel"""
assert np.prod(blacsgrid) == world.size
grid = BlacsGrid(world, *blacsgrid)
if world.rank == MASTER:
H_MM = np.load(matrixfile)
assert H_MM.ndim == 2
assert H_MM.shape[0] == H_MM.shape[1]
NM = len(H_MM)
else:
NM = 0
NM = world.sum(NM) # Distribute matrix shape to all nodes
# descriptor for the individual blocks
block_desc = grid.new_descriptor(NM, NM, blocksize, blocksize)
# descriptor for global array on MASTER
local_desc = grid.new_descriptor(NM, NM, NM, NM)
# Make some dummy array on all the slaves
if world.rank != MASTER:
H_MM = local_desc.zeros()
assert local_desc.check(H_MM)
# The local version of the matrix
H_mm = block_desc.empty()
# Distribute global array to smaller blocks
redistributor = Redistributor(world, local_desc, block_desc)
redistributor.redistribute(H_MM, H_mm)
# Allocate arrays for eigenvalues and -vectors
eps_M = np.empty(NM)
C_mm = block_desc.empty()
block_desc.diagonalize_ex(H_mm, C_mm, eps_M)
# Collect eigenvectors on MASTER
C_MM = local_desc.empty()
redistributor2 = Redistributor(world, block_desc, local_desc)
redistributor2.redistribute(C_mm, C_MM)
# Return eigenvalues and -vectors on Master
if world.rank == MASTER:
return eps_M, C_MM
else:
return None, None
def test_multiply_nonhermitian(self):
alpha = np.random.normal(size=1).astype(self.dtype)
if self.dtype == complex:
alpha += 1j * np.random.normal(size=1)
world.broadcast(alpha, 0)
# Known starting point of S_nn = <psit_m|S|psit_n>
S_NN = alpha * self.S0_nn
if self.dtype == complex:
C_NN = np.random.uniform(size=self.nbands**2) * \
np.exp(1j*np.random.uniform(0,2*np.pi,size=self.nbands**2))
else:
C_NN = np.random.normal(size=self.nbands**2)
C_NN = C_NN.reshape(
(self.nbands, self.nbands)) / np.linalg.norm(C_NN, 2)
world.broadcast(C_NN, 0)
# Set up Hermitian overlap operator:
S = lambda x: alpha * x
dS = lambda a, P_ni: np.dot(alpha * P_ni, self.setups[a].dO_ii)
nblocks = self.get_optimal_number_of_blocks(self.blocking)
overlap = MatrixOperator(self.ksl, nblocks, self. async, False)
if 0: #XXX non-hermitian case so Nn2nn not just uplo='L' but rather 'G'
blockcomm = self.ksl.nndescriptor.blacsgrid.comm
self.ksl.Nn2nn = Redistributor(blockcomm, self.ksl.Nndescriptor,
self.ksl.nndescriptor)
if self.bd.comm.rank == 0 and self.gd.comm.rank == 0:
assert C_NN.shape == (self.bd.nbands, ) * 2
tmp_NN = C_NN.T.copy() # C -> Fortran indexing
else:
tmp_NN = self.ksl.nndescriptor.as_serial().empty(dtype=C_NN.dtype)
C_nn = self.ksl.nndescriptor.distribute_from_master(tmp_NN)
self.psit_nG = overlap.matrix_multiply(C_nn, self.psit_nG, self.P_ani)
D_nn = overlap.calculate_matrix_elements(self.psit_nG, self.P_ani, S,
dS)
if memstats:
self.mem_test = record_memory()
D_NN = self.ksl.nndescriptor.collect_on_master(D_nn)
if self.bd.comm.rank == 0 and self.gd.comm.rank == 0:
assert D_NN.shape == (self.bd.nbands, ) * 2
D_NN = D_NN.T.copy() # Fortran -> C indexing
else:
assert D_NN.nbytes == 0
D_NN = np.empty((self.bd.nbands, ) * 2, dtype=D_NN.dtype)
if self.bd.comm.rank == 0:
self.gd.comm.broadcast(D_NN, 0)
self.bd.comm.broadcast(D_NN, 0)
# D_nn = C_nn^dag * S_nn * C_nn
D0_NN = np.dot(C_NN.T.conj(), np.dot(S_NN, C_NN))
self.check_and_plot(D_NN, D0_NN, 9, 'multiply,nonhermitian')
def scal_diagonalize(A, nodes='master'):
# Diagonalize matrix A (size N*N) with scalapack
# Usage: eps, B = scal_diagonalize(A)
# eps and B and the eigenvalues and eigenvectors
# nodes = 'master': eigenvectors only available on master node
# nodes = 'all': eigenvectors broadcast to all nodes
# make sure A is N*N, and hermitian
N = A.shape[0]
assert A.shape[0] == A.shape[1]
for i in range(N):
for j in range(i, N):
assert A[i, j] == A[j, i].conj()
# create blacs descriptor
mb = 64
g = BlacsGrid(world, 2, size // 2)
nndesc1 = g.new_descriptor(N, N, N, N)
nndesc2 = g.new_descriptor(N, N, mb, mb)
# distribute A to blacs grid A_
if rank != 0:
A = nndesc1.zeros(dtype=A.dtype)
A_ = nndesc2.empty(dtype=A.dtype)
redistributor = Redistributor(world, nndesc1, nndesc2)
redistributor.redistribute(A, A_)
# diagonalize
B_ = nndesc2.zeros(dtype=A.dtype)
eps = np.zeros(N, dtype=A.dtype)
nndesc2.diagonalize_dc(A_, B_, eps, 'L')
# distribute the eigenvectors to master
B = np.zeros_like(A)
redistributor = Redistributor(world, nndesc2, nndesc1)
redistributor.redistribute(B_, B)
if nodes == 'master':
return eps, B
elif nodes == 'all':
if rank != 0:
B = np.zeros((N, N))
world.broadcast(B, 0)
return eps, B
def distribute_to_columns(self, rho_mm, srcdescriptor):
redistributor = Redistributor(
self.block_comm, # XXX
srcdescriptor,
self.mM_unique_descriptor)
rho_mM = redistributor.redistribute(rho_mm)
if self.gd.rank != 0:
rho_mM = self.mMdescriptor.zeros(dtype=rho_mm.dtype)
self.gd.comm.broadcast(rho_mM, 0)
return rho_mM
def initialize(self, paw, hamiltonian=None):
LCAOPropagator.initialize(self, paw)
if hamiltonian is not None:
self.hamiltonian = hamiltonian
ksl = self.wfs.ksl
self.blacs = ksl.using_blacs
if self.blacs:
from gpaw.blacs import Redistributor
self.log('BLACS Parallelization')
# Parallel grid descriptors
grid = ksl.blockgrid
assert grid.nprow * grid.npcol == ksl.block_comm.size
self.mm_block_descriptor = ksl.mmdescriptor
self.Cnm_block_descriptor = grid.new_descriptor(ksl.bd.nbands,
ksl.nao,
ksl.blocksize,
ksl.blocksize)
self.CnM_unique_descriptor = ksl.nM_unique_descriptor
# Redistributors
self.Cnm2nM = Redistributor(ksl.block_comm,
self.Cnm_block_descriptor,
self.CnM_unique_descriptor)
self.CnM2nm = Redistributor(ksl.block_comm,
self.CnM_unique_descriptor,
self.Cnm_block_descriptor)
if debug:
nao = ksl.nao
self.MM_descriptor = grid.new_descriptor(nao, nao, nao, nao)
self.mm2MM = Redistributor(ksl.block_comm,
self.mm_block_descriptor,
self.MM_descriptor)
self.MM2mm = Redistributor(ksl.block_comm,
self.MM_descriptor,
self.mm_block_descriptor)
for kpt in self.wfs.kpt_u:
scalapack_zero(self.mm_block_descriptor, kpt.S_MM, 'U')
scalapack_zero(self.mm_block_descriptor, kpt.T_MM, 'U')
def __init__(self,
gd,
bd,
block_comm,
dtype,
mcpus,
ncpus,
blocksize,
buffer_size=None,
timer=nulltimer):
BlacsLayouts.__init__(self, gd, bd, block_comm, dtype, mcpus, ncpus,
blocksize, timer)
self.buffer_size = buffer_size
nbands = bd.nbands
self.mynbands = mynbands = bd.mynbands
self.blocksize = blocksize
# 1D layout - columns
self.columngrid = BlacsGrid(self.column_comm, 1, bd.comm.size)
self.Nndescriptor = self.columngrid.new_descriptor(
nbands, nbands, nbands, mynbands)
# 2D layout
self.nndescriptor = self.blockgrid.new_descriptor(
nbands, nbands, blocksize, blocksize)
# 1D layout - rows
self.rowgrid = BlacsGrid(self.column_comm, bd.comm.size, 1)
self.nNdescriptor = self.rowgrid.new_descriptor(
nbands, nbands, mynbands, nbands)
# Only redistribute filled out half for Hermitian matrices
self.Nn2nn = Redistributor(self.block_comm, self.Nndescriptor,
self.nndescriptor)
#self.Nn2nn = Redistributor(self.block_comm, self.Nndescriptor,
# self.nndescriptor, 'L') #XXX faster but...
# Resulting matrix will be used in dgemm which is symmetry obvlious
self.nn2nN = Redistributor(self.block_comm, self.nndescriptor,
self.nNdescriptor)
def redistribute_H(self, H_sS):
g1 = BlacsGrid(world, size, 1)
g2 = BlacsGrid(world, 1, size)
N = self.nS
nndesc1 = g1.new_descriptor(N, N, self.nS_local, N)
nndesc2 = g2.new_descriptor(N, N, N, self.nS_local)
H_Ss = nndesc2.empty(dtype=H_sS.dtype)
redistributor = Redistributor(world, nndesc1, nndesc2)
redistributor.redistribute(H_sS, H_Ss)
return H_Ss
def distribute_MM(wfs, a_MM):
ksl = wfs.ksl
if not ksl.using_blacs:
return a_MM
dtype = a_MM.dtype
ksl_comm = ksl.block_comm
NM = ksl.nao
grid = BlacsGrid(ksl_comm, 1, 1)
MM_descriptor = grid.new_descriptor(NM, NM, NM, NM)
MM2mm = Redistributor(ksl_comm, MM_descriptor, ksl.mmdescriptor)
if ksl_comm.rank != 0:
a_MM = MM_descriptor.empty(dtype=dtype)
a_mm = ksl.mmdescriptor.empty(dtype=dtype)
MM2mm.redistribute(a_MM, a_mm)
return a_mm
def redistribute(self, in_wGG, out_x=None):
"""Redistribute array.
Switch between two kinds of parallel distributions:
1) parallel over G-vectors (second dimension of in_wGG)
2) parallel over frequency (first dimension of in_wGG)
Returns new array using the memory in the 1-d array out_x.
"""
comm = self.blockcomm
if comm.size == 1:
return in_wGG
nw = len(self.omega_w)
nG = in_wGG.shape[2]
mynw = (nw + comm.size - 1) // comm.size
mynG = (nG + comm.size - 1) // comm.size
bg1 = BlacsGrid(comm, comm.size, 1)
bg2 = BlacsGrid(comm, 1, comm.size)
md1 = BlacsDescriptor(bg1, nw, nG**2, mynw, nG**2)
md2 = BlacsDescriptor(bg2, nw, nG**2, nw, mynG * nG)
if len(in_wGG) == nw:
mdin = md2
mdout = md1
else:
mdin = md1
mdout = md2
r = Redistributor(comm, mdin, mdout)
outshape = (mdout.shape[0], mdout.shape[1] // nG, nG)
if out_x is None:
out_wGG = np.empty(outshape, complex)
else:
out_wGG = out_x[:np.product(outshape)].reshape(outshape)
r.redistribute(in_wGG.reshape(mdin.shape),
out_wGG.reshape(mdout.shape))
return out_wGG
def test(comm, M, N, mcpus, ncpus, mb, nb):
grid0 = BlacsGrid(comm, 1, 1)
desc0 = grid0.new_descriptor(M, N, M, N, 0, 0)
A_mn = desc0.zeros(dtype=float)
A_mn[:] = comm.size + 1
grid1 = BlacsGrid(comm, mcpus, ncpus)
desc1 = grid1.new_descriptor(M, N, mb, nb, 0, 0) # ???
B_mn = desc1.zeros(dtype=float)
B_mn[:] = comm.rank
if comm.rank == 0:
msg = 'Slices of global matrix indices by rank'
print(msg)
print('-' * len(msg))
for rank in range(comm.size):
comm.barrier()
if rank == comm.rank:
print('Rank %d:' % rank)
last_Mstart = -1
for Mstart, Mstop, Nstart, Nstop, block in desc1.my_blocks(B_mn):
if Mstart > last_Mstart and last_Mstart >= 0:
print()
print('[%3d:%3d, %3d:%3d]' % (Mstart, Mstop, Nstart, Nstop),
end=' ')
last_Mstart = Mstart
assert (block == comm.rank).all()
#print block
#print
print()
print()
comm.barrier()
redistributor = Redistributor(comm, desc1, desc0)
redistributor.redistribute(B_mn, A_mn)
if comm.rank == 0:
msg = 'Rank where each element of the global matrix is stored'
print(msg)
print('-' * len(msg))
print(A_mn)
def collect_wuMM(wfs, a_wuMM, w, s, k):
# This function is based on
# gpaw/wavefunctions/base.py: WaveFunctions.collect_auxiliary()
dtype = a_wuMM[0][0].dtype
ksl = wfs.ksl
NM = ksl.nao
kpt_rank, u = wfs.kd.get_rank_and_index(s, k)
ksl_comm = ksl.block_comm
if wfs.kd.comm.rank == kpt_rank:
a_MM = a_wuMM[w][u]
# Collect within blacs grid
if ksl.using_blacs:
a_mm = a_MM
grid = BlacsGrid(ksl_comm, 1, 1)
MM_descriptor = grid.new_descriptor(NM, NM, NM, NM)
mm2MM = Redistributor(ksl_comm, ksl.mmdescriptor, MM_descriptor)
a_MM = MM_descriptor.empty(dtype=dtype)
mm2MM.redistribute(a_mm, a_MM)
# KSL master send a_MM to the global master
if ksl_comm.rank == 0:
if kpt_rank == 0:
assert wfs.world.rank == 0
# I have it already
return a_MM
else:
wfs.kd.comm.send(a_MM, 0, 2017)
return None
elif ksl_comm.rank == 0 and kpt_rank != 0:
assert wfs.world.rank == 0
a_MM = np.empty((NM, NM), dtype=dtype)
wfs.kd.comm.receive(a_MM, kpt_rank, 2017)
return a_MM
def calculate_density_matrix(self, f_n, C_nM, rho_mM=None):
"""Calculate density matrix from occupations and coefficients.
Presently this function performs the usual scalapack 3-step trick:
redistribute-numbercrunching-backdistribute.
Notes on future performance improvement.
As per the current framework, C_nM exists as copies on each
domain, i.e. this is not parallel over domains. We'd like to
correct this and have an efficient distribution using e.g. the
block communicator.
The diagonalization routine and other parts of the code should
however be changed to accommodate the following scheme:
Keep coefficients in C_mm form after the diagonalization.
rho_mm can then be directly calculated from C_mm without
redistribution, after which we only need to redistribute
rho_mm across domains.
"""
dtype = C_nM.dtype
rho_mm = self.calculate_blocked_density_matrix(f_n, C_nM)
rback = Redistributor(self.block_comm, self.mmdescriptor,
self.mM_unique_descriptor)
rho1_mM = self.mM_unique_descriptor.zeros(dtype=dtype)
rback.redistribute(rho_mm, rho1_mM)
del rho_mm
if rho_mM is None:
if self.gd.rank == 0:
rho_mM = rho1_mM
else:
rho_mM = self.mMdescriptor.zeros(dtype=dtype)
self.gd.comm.broadcast(rho_mM, 0)
return rho_mM
def distribute_frequencies(self, chi0_wGG):
"""Distribute frequencies to all cores."""
world = self.world
comm = self.blockcomm
if world.size == 1:
return chi0_wGG
nw = len(self.omega_w)
nG = chi0_wGG.shape[2]
mynw = (nw + world.size - 1) // world.size
mynG = (nG + comm.size - 1) // comm.size
wa = min(world.rank * mynw, nw)
wb = min(wa + mynw, nw)
if self.blockcomm.size == 1:
return chi0_wGG[wa:wb].copy()
if self.kncomm.rank == 0:
bg1 = BlacsGrid(comm, 1, comm.size)
in_wGG = chi0_wGG.reshape((nw, -1))
else:
bg1 = DryRunBlacsGrid(mpi.serial_comm, 1, 1)
in_wGG = np.zeros((0, 0), complex)
md1 = BlacsDescriptor(bg1, nw, nG**2, nw, mynG * nG)
bg2 = BlacsGrid(world, world.size, 1)
md2 = BlacsDescriptor(bg2, nw, nG**2, mynw, nG**2)
r = Redistributor(world, md1, md2)
shape = (wb - wa, nG, nG)
out_wGG = np.empty(shape, complex)
r.redistribute(in_wGG, out_wGG.reshape((wb - wa, nG**2)))
return out_wGG
def tddft_init(self):
if not self.tddft_initialized:
if world.rank == 0:
print('Initializing real time LCAO TD-DFT calculation.')
print('XXX Warning: Array use not optimal for memory.')
print('XXX Taylor propagator probably doesn\'t work')
print('XXX ...and no arrays are listed in memory estimate yet.')
self.blacs = self.wfs.ksl.using_blacs
if self.blacs:
self.ksl = ksl = self.wfs.ksl
nao = ksl.nao
nbands = ksl.bd.nbands
mynbands = ksl.bd.mynbands
blocksize = ksl.blocksize
from gpaw.blacs import Redistributor
if world.rank == 0:
print('BLACS Parallelization')
# Parallel grid descriptors
self.MM_descriptor = ksl.blockgrid.new_descriptor(nao, nao, nao, nao) # FOR DEBUG
self.mm_block_descriptor = ksl.blockgrid.new_descriptor(nao, nao, blocksize, blocksize)
self.Cnm_block_descriptor = ksl.blockgrid.new_descriptor(nbands, nao, blocksize, blocksize)
#self.CnM_descriptor = ksl.blockgrid.new_descriptor(nbands, nao, mynbands, nao)
self.mM_column_descriptor = ksl.single_column_grid.new_descriptor(nao, nao, ksl.naoblocksize, nao)
self.CnM_unique_descriptor = ksl.single_column_grid.new_descriptor(nbands, nao, mynbands, nao)
# Redistributors
self.mm2MM = Redistributor(ksl.block_comm,
self.mm_block_descriptor,
self.MM_descriptor) # XXX FOR DEBUG
self.MM2mm = Redistributor(ksl.block_comm,
self.MM_descriptor,
self.mm_block_descriptor) # XXX FOR DEBUG
self.Cnm2nM = Redistributor(ksl.block_comm,
self.Cnm_block_descriptor,
self.CnM_unique_descriptor)
self.CnM2nm = Redistributor(ksl.block_comm,
self.CnM_unique_descriptor,
self.Cnm_block_descriptor)
self.mM2mm = Redistributor(ksl.block_comm,
self.mM_column_descriptor,
self.mm_block_descriptor)
for kpt in self.wfs.kpt_u:
scalapack_zero(self.mm_block_descriptor, kpt.S_MM,'U')
scalapack_zero(self.mm_block_descriptor, kpt.T_MM,'U')
# XXX to propagator class
if self.propagator == 'taylor' and self.blacs:
# cholS_mm = self.mm_block_descriptor.empty(dtype=complex)
for kpt in self.wfs.kpt_u:
kpt.invS_MM = kpt.S_MM.copy()
scalapack_inverse(self.mm_block_descriptor,
kpt.invS_MM, 'L')
if self.propagator_debug:
if world.rank == 0:
print('XXX Doing serial inversion of overlap matrix.')
self.timer.start('Invert overlap (serial)')
invS2_MM = self.MM_descriptor.empty(dtype=complex)
for kpt in self.wfs.kpt_u:
#kpt.S_MM[:] = 128.0*(2**world.rank)
self.mm2MM.redistribute(self.wfs.S_qMM[kpt.q], invS2_MM)
world.barrier()
if world.rank == 0:
tri2full(invS2_MM,'L')
invS2_MM[:] = inv(invS2_MM.copy())
self.invS2_MM = invS2_MM
kpt.invS2_MM = ksl.mmdescriptor.empty(dtype=complex)
self.MM2mm.redistribute(invS2_MM, kpt.invS2_MM)
verify(kpt.invS_MM, kpt.invS2_MM, 'overlap par. vs. serial', 'L')
self.timer.stop('Invert overlap (serial)')
if world.rank == 0:
print('XXX Overlap inverted.')
if self.propagator == 'taylor' and not self.blacs:
tmp = inv(self.wfs.kpt_u[0].S_MM)
self.wfs.kpt_u[0].invS = tmp
# Reset the density mixer
self.density.mixer = DummyMixer()
self.tddft_initialized = True
for k, kpt in enumerate(self.wfs.kpt_u):
kpt.C2_nM = kpt.C_nM.copy()
def main(M=160, N=120, K=140, seed=42, mprocs=2, nprocs=2, dtype=float):
gen = np.random.RandomState(seed)
grid = BlacsGrid(world, mprocs, nprocs)
if dtype == complex:
epsilon = 1.0j
else:
epsilon = 0.0
# Create descriptors for matrices on master:
globA = grid.new_descriptor(M, K, M, K)
globB = grid.new_descriptor(K, N, K, N)
globC = grid.new_descriptor(M, N, M, N)
globZ = grid.new_descriptor(K, K, K, K)
globX = grid.new_descriptor(K, 1, K, 1)
globY = grid.new_descriptor(M, 1, M, 1)
globD = grid.new_descriptor(M, K, M, K)
globS = grid.new_descriptor(M, M, M, M)
globU = grid.new_descriptor(M, M, M, M)
globHEC = grid.new_descriptor(K, K, K, K)
# print globA.asarray()
# Populate matrices local to master:
A0 = gen.rand(*globA.shape) + epsilon * gen.rand(*globA.shape)
B0 = gen.rand(*globB.shape) + epsilon * gen.rand(*globB.shape)
D0 = gen.rand(*globD.shape) + epsilon * gen.rand(*globD.shape)
X0 = gen.rand(*globX.shape) + epsilon * gen.rand(*globX.shape)
# HEC = HEA * B
HEA0 = gen.rand(*globHEC.shape) + epsilon * gen.rand(*globHEC.shape)
if world.rank == 0:
HEA0 = HEA0 + HEA0.T.conjugate() # Make H0 hermitean
HEA0 = np.ascontiguousarray(HEA0)
# Local result matrices
Y0 = globY.empty(dtype=dtype)
C0 = globC.zeros(dtype=dtype)
Z0 = globZ.zeros(dtype=dtype)
S0 = globS.zeros(dtype=dtype) # zeros needed for rank-updates
U0 = globU.zeros(dtype=dtype) # zeros needed for rank-updates
HEC0 = globB.zeros(dtype=dtype)
# Local reference matrix product:
if rank == 0:
# C0[:] = np.dot(A0, B0)
gemm(1.0, B0, A0, 0.0, C0)
# gemm(1.0, A0, A0, 0.0, Z0, transa='t')
print(A0.shape, Z0.shape)
Z0[:] = np.dot(A0.T, A0)
# Y0[:] = np.dot(A0, X0)
gemv(1.0, A0, X0.ravel(), 0.0, Y0.ravel())
r2k(1.0, A0, D0, 0.0, S0)
rk(1.0, A0, 0.0, U0)
HEC0[:] = np.dot(HEA0, B0)
sM, sN = HEA0.shape
# We don't use upper diagonal
for i in range(sM):
for j in range(sN):
if i < j:
HEA0[i][j] = 99999.0
if world.rank == 0:
print(HEA0)
assert globA.check(A0) and globB.check(B0) and globC.check(C0)
assert globX.check(X0) and globY.check(Y0)
assert globD.check(D0) and globS.check(S0) and globU.check(U0)
# Create distributed destriptors with various block sizes:
distA = grid.new_descriptor(M, K, 2, 2)
distB = grid.new_descriptor(K, N, 2, 4)
distC = grid.new_descriptor(M, N, 3, 2)
distZ = grid.new_descriptor(K, K, 5, 7)
distX = grid.new_descriptor(K, 1, 4, 1)
distY = grid.new_descriptor(M, 1, 3, 1)
distD = grid.new_descriptor(M, K, 2, 3)
distS = grid.new_descriptor(M, M, 2, 2)
distU = grid.new_descriptor(M, M, 2, 2)
distHE = grid.new_descriptor(K, K, 2, 4)
# Distributed matrices:
A = distA.empty(dtype=dtype)
B = distB.empty(dtype=dtype)
C = distC.empty(dtype=dtype)
Z = distZ.empty(dtype=dtype)
X = distX.empty(dtype=dtype)
Y = distY.empty(dtype=dtype)
D = distD.empty(dtype=dtype)
S = distS.zeros(dtype=dtype) # zeros needed for rank-updates
U = distU.zeros(dtype=dtype) # zeros needed for rank-updates
HEC = distB.zeros(dtype=dtype)
HEA = distHE.zeros(dtype=dtype)
Redistributor(world, globA, distA).redistribute(A0, A)
Redistributor(world, globB, distB).redistribute(B0, B)
Redistributor(world, globX, distX).redistribute(X0, X)
Redistributor(world, globD, distD).redistribute(D0, D)
Redistributor(world, globHEC, distHE).redistribute(HEA0, HEA)
pblas_simple_gemm(distA, distB, distC, A, B, C)
pblas_simple_gemm(distA, distA, distZ, A, A, Z, transa='T')
pblas_simple_gemv(distA, distX, distY, A, X, Y)
pblas_simple_r2k(distA, distD, distS, A, D, S)
pblas_simple_rk(distA, distU, A, U)
pblas_simple_hemm(distHE, distB, distB, HEA, B, HEC, uplo='L', side='L')
# Collect result back on master
C1 = globC.empty(dtype=dtype)
Y1 = globY.empty(dtype=dtype)
S1 = globS.zeros(dtype=dtype) # zeros needed for rank-updates
U1 = globU.zeros(dtype=dtype) # zeros needed for rank-updates
HEC1 = globB.zeros(dtype=dtype)
Redistributor(world, distC, globC).redistribute(C, C1)
Redistributor(world, distY, globY).redistribute(Y, Y1)
Redistributor(world, distS, globS).redistribute(S, S1)
Redistributor(world, distU, globU).redistribute(U, U1)
Redistributor(world, distB, globB).redistribute(HEC, HEC1)
if rank == 0:
gemm_err = abs(C1 - C0).max()
gemv_err = abs(Y1 - Y0).max()
r2k_err = abs(S1 - S0).max()
rk_err = abs(U1 - U0).max()
hemm_err = abs(HEC1 - HEC0).max()
print('gemm err', gemm_err)
print('gemv err', gemv_err)
print('r2k err', r2k_err)
print('rk_err', rk_err)
print('hemm_err', hemm_err)
else:
gemm_err = 0.0
gemv_err = 0.0
r2k_err = 0.0
rk_err = 0.0
hemm_err = 0.0
gemm_err = world.sum(gemm_err) # We don't like exceptions on only one cpu
gemv_err = world.sum(gemv_err)
r2k_err = world.sum(r2k_err)
rk_err = world.sum(rk_err)
hemm_err = world.sum(hemm_err)
equal(gemm_err, 0, tol)
equal(gemv_err, 0, tol)
equal(r2k_err, 0, tol)
equal(rk_err, 0, tol)
equal(hemm_err, 0, tol)
def calculate_rkernel(self):
gd = self.gd
ng_c = gd.N_c
cell_cv = gd.cell_cv
icell_cv = 2 * np.pi * np.linalg.inv(cell_cv)
vol = np.linalg.det(cell_cv)
ns = self.calc.wfs.nspins
n_g = self.n_g # density on rough grid
fx_g = ns * self.get_fxc_g(n_g) # local exchange kernel
qc_g = (-4 * np.pi * ns / fx_g)**0.5 # cutoff functional
flocal_g = qc_g**3 * fx_g / (6 * np.pi**2) # ren. x-kernel for r=r'
Vlocal_g = 2 * qc_g / np.pi # ren. Hartree kernel for r=r'
ng = np.prod(ng_c) # number of grid points
r_vg = gd.get_grid_point_coordinates()
rx_g = r_vg[0].flatten()
ry_g = r_vg[1].flatten()
rz_g = r_vg[2].flatten()
prnt(' %d grid points and %d plane waves at the Gamma point' %
(ng, self.pd.ngmax),
file=self.fd)
# Unit cells
R_Rv = []
weight_R = []
nR_v = self.unit_cells
nR = np.prod(nR_v)
for i in range(-nR_v[0] + 1, nR_v[0]):
for j in range(-nR_v[1] + 1, nR_v[1]):
for h in range(-nR_v[2] + 1, nR_v[2]):
R_Rv.append(i * cell_cv[0] + j * cell_cv[1] +
h * cell_cv[2])
weight_R.append((nR_v[0] - abs(i)) * (nR_v[1] - abs(j)) *
(nR_v[2] - abs(h)) / float(nR))
if nR > 1:
# with more than one unit cell only the exchange kernel is
# calculated on the grid. The bare Coulomb kernel is added
# in PW basis and Vlocal_g only the exchange part
dv = self.calc.density.gd.dv
gc = (3 * dv / 4 / np.pi)**(1 / 3.)
Vlocal_g -= 2 * np.pi * gc**2 / dv
prnt(' Lattice point sampling: ' + '(%s x %s x %s)^2 ' %
(nR_v[0], nR_v[1], nR_v[2]) +
' Reduced to %s lattice points' % len(R_Rv),
file=self.fd)
l_g_size = -(-ng // mpi.world.size)
l_g_range = range(mpi.world.rank * l_g_size,
min((mpi.world.rank + 1) * l_g_size, ng))
fhxc_qsGr = {}
for iq in range(len(self.ibzq_qc)):
fhxc_qsGr[iq] = np.zeros(
(ns, len(self.pd.G2_qG[iq]), len(l_g_range)), dtype=complex)
inv_error = np.seterr()
np.seterr(invalid='ignore')
np.seterr(divide='ignore')
t0 = time()
# Loop over Lattice points
for i, R_v in enumerate(R_Rv):
# Loop over r'. f_rr and V_rr are functions of r (dim. as r_vg[0])
if i == 1:
prnt(' Finished 1 cell in %s seconds' % int(time() - t0) +
' - estimated %s seconds left' % int(
(len(R_Rv) - 1) * (time() - t0)),
file=self.fd)
self.fd.flush()
if len(R_Rv) > 5:
if (i + 1) % (len(R_Rv) / 5 + 1) == 0:
prnt(' Finished %s cells in %s seconds' %
(i, int(time() - t0)) +
' - estimated %s seconds left' % int(
(len(R_Rv) - i) * (time() - t0) / i),
file=self.fd)
self.fd.flush()
for g in l_g_range:
rx = rx_g[g] + R_v[0]
ry = ry_g[g] + R_v[1]
rz = rz_g[g] + R_v[2]
# |r-r'-R_i|
rr = ((r_vg[0] - rx)**2 + (r_vg[1] - ry)**2 +
(r_vg[2] - rz)**2)**0.5
n_av = (n_g + n_g.flatten()[g]) / 2.
fx_g = ns * self.get_fxc_g(n_av, index=g)
qc_g = (-4 * np.pi * ns / fx_g)**0.5
x = qc_g * rr
osc_x = np.sin(x) - x * np.cos(x)
f_rr = fx_g * osc_x / (2 * np.pi**2 * rr**3)
if nR > 1: # include only exchange part of the kernel here
V_rr = (sici(x)[0] * 2 / np.pi - 1) / rr
else: # include the full kernel (also hartree part)
V_rr = (sici(x)[0] * 2 / np.pi) / rr
# Terms with r = r'
if (np.abs(R_v) < 0.001).all():
tmp_flat = f_rr.flatten()
tmp_flat[g] = flocal_g.flatten()[g]
f_rr = tmp_flat.reshape(ng_c)
tmp_flat = V_rr.flatten()
tmp_flat[g] = Vlocal_g.flatten()[g]
V_rr = tmp_flat.reshape(ng_c)
del tmp_flat
f_rr[np.where(n_av < self.density_cut)] = 0.0
V_rr[np.where(n_av < self.density_cut)] = 0.0
f_rr *= weight_R[i]
V_rr *= weight_R[i]
# r-r'-R_i
r_r = np.array([r_vg[0] - rx, r_vg[1] - ry, r_vg[2] - rz])
# Fourier transform of r
for iq, q in enumerate(self.ibzq_qc):
q_v = np.dot(q, icell_cv)
e_q = np.exp(-1j * gemmdot(q_v, r_r, beta=0.0))
f_q = self.pd.fft((f_rr + V_rr) * e_q, iq) * vol / ng
fhxc_qsGr[iq][0, :, g - l_g_range[0]] += f_q
if ns == 2:
f_q = self.pd.fft(V_rr * e_q, iq) * vol / ng
fhxc_qsGr[iq][1, :, g - l_g_range[0]] += f_q
mpi.world.barrier()
np.seterr(**inv_error)
for iq, q in enumerate(self.ibzq_qc):
npw = len(self.pd.G2_qG[iq])
fhxc_sGsG = np.zeros((ns * npw, ns * npw), complex)
l_pw_size = -(-npw // mpi.world.size) # parallelize over PW below
l_pw_range = range(mpi.world.rank * l_pw_size,
min((mpi.world.rank + 1) * l_pw_size, npw))
if mpi.world.size > 1:
# redistribute grid and plane waves in fhxc_qsGr[iq]
bg1 = BlacsGrid(mpi.world, 1, mpi.world.size)
bg2 = BlacsGrid(mpi.world, mpi.world.size, 1)
bd1 = bg1.new_descriptor(npw, ng, npw, -(-ng / mpi.world.size))
bd2 = bg2.new_descriptor(npw, ng, -(-npw / mpi.world.size), ng)
fhxc_Glr = np.zeros((len(l_pw_range), ng), dtype=complex)
if ns == 2:
Koff_Glr = np.zeros((len(l_pw_range), ng), dtype=complex)
r = Redistributor(bg1.comm, bd1, bd2)
r.redistribute(fhxc_qsGr[iq][0], fhxc_Glr, npw, ng)
if ns == 2:
r.redistribute(fhxc_qsGr[iq][1], Koff_Glr, npw, ng)
else:
fhxc_Glr = fhxc_qsGr[iq][0]
if ns == 2:
Koff_Glr = fhxc_qsGr[iq][1]
# Fourier transform of r'
for iG in range(len(l_pw_range)):
f_g = fhxc_Glr[iG].reshape(ng_c)
f_G = self.pd.fft(f_g.conj(), iq) * vol / ng
fhxc_sGsG[l_pw_range[0] + iG, :npw] = f_G.conj()
if ns == 2:
v_g = Koff_Glr[iG].reshape(ng_c)
v_G = self.pd.fft(v_g.conj(), iq) * vol / ng
fhxc_sGsG[npw + l_pw_range[0] + iG, :npw] = v_G.conj()
if ns == 2: # f_00 = f_11 and f_01 = f_10
fhxc_sGsG[:npw, npw:] = fhxc_sGsG[npw:, :npw]
fhxc_sGsG[npw:, npw:] = fhxc_sGsG[:npw, :npw]
mpi.world.sum(fhxc_sGsG)
fhxc_sGsG /= vol
if mpi.rank == 0:
w = Writer('fhxc_%s_%s_%s_%s.gpw' %
(self.tag, self.xc, self.ecut, iq))
w.dimension('sG', ns * npw)
w.add('fhxc_sGsG', ('sG', 'sG'), dtype=complex)
if nR > 1: # add Hartree kernel evaluated in PW basis
Gq2_G = self.pd.G2_qG[iq]
if (q == 0).all():
Gq2_G[0] = 1.
vq_G = 4 * np.pi / Gq2_G
fhxc_sGsG += np.tile(np.eye(npw) * vq_G, (ns, ns))
w.fill(fhxc_sGsG)
w.close()
mpi.world.barrier()
prnt(file=self.fd)
def main(N=72, seed=42, mprocs=2, nprocs=2, dtype=float):
gen = np.random.RandomState(seed)
grid = BlacsGrid(world, mprocs, nprocs)
if (dtype == complex):
epsilon = 1.0j
else:
epsilon = 0.0
# Create descriptors for matrices on master:
glob = grid.new_descriptor(N, N, N, N)
# print globA.asarray()
# Populate matrices local to master:
H0 = glob.zeros(dtype=dtype) + gen.rand(*glob.shape)
S0 = glob.zeros(dtype=dtype) + gen.rand(*glob.shape)
C0 = glob.empty(dtype=dtype)
if rank == 0:
# Complex case must have real numbers on the diagonal.
# We make a simple complex Hermitian matrix below.
H0 = H0 + epsilon * (0.1 * np.tri(N, N, k=-N // nprocs) +
0.3 * np.tri(N, N, k=-1))
S0 = S0 + epsilon * (0.2 * np.tri(N, N, k=-N // nprocs) +
0.4 * np.tri(N, N, k=-1))
# Make matrices symmetric
rk(1.0, H0.copy(), 0.0, H0)
rk(1.0, S0.copy(), 0.0, S0)
# Overlap matrix must be semi-positive definite
S0 = S0 + 50.0 * np.eye(N, N, 0)
# Hamiltonian is usually diagonally dominant
H0 = H0 + 75.0 * np.eye(N, N, 0)
C0 = S0.copy()
S0_inv = S0.copy()
# Local result matrices
W0 = np.empty((N), dtype=float)
W0_g = np.empty((N), dtype=float)
# Calculate eigenvalues / other serial results
if rank == 0:
diagonalize(H0.copy(), W0)
general_diagonalize(H0.copy(), W0_g, S0.copy())
inverse_cholesky(C0) # result returned in lower triangle
tri2full(S0_inv, 'L')
S0_inv = inv(S0_inv)
# tri2full(C0) # symmetrize
assert glob.check(H0) and glob.check(S0) and glob.check(C0)
# Create distributed destriptors with various block sizes:
dist = grid.new_descriptor(N, N, 8, 8)
# Distributed matrices:
# We can use empty here, but end up with garbage on
# on the other half of the triangle when we redistribute.
# This is fine because ScaLAPACK does not care.
H = dist.empty(dtype=dtype)
S = dist.empty(dtype=dtype)
Sinv = dist.empty(dtype=dtype)
Z = dist.empty(dtype=dtype)
C = dist.empty(dtype=dtype)
Sinv = dist.empty(dtype=dtype)
# Eigenvalues are non-BLACS matrices
W = np.empty((N), dtype=float)
W_dc = np.empty((N), dtype=float)
W_mr3 = np.empty((N), dtype=float)
W_g = np.empty((N), dtype=float)
W_g_dc = np.empty((N), dtype=float)
W_g_mr3 = np.empty((N), dtype=float)
Glob2dist = Redistributor(world, glob, dist)
Glob2dist.redistribute(H0, H, uplo='L')
Glob2dist.redistribute(S0, S, uplo='L')
Glob2dist.redistribute(S0, C, uplo='L') # C0 was previously overwritten
Glob2dist.redistribute(S0, Sinv, uplo='L')
# we don't test the expert drivers anymore since there
# might be a buffer overflow error
## scalapack_diagonalize_ex(dist, H.copy(), Z, W, 'L')
scalapack_diagonalize_dc(dist, H.copy(), Z, W_dc, 'L')
## scalapack_diagonalize_mr3(dist, H.copy(), Z, W_mr3, 'L')
## scalapack_general_diagonalize_ex(dist, H.copy(), S.copy(), Z, W_g, 'L')
scalapack_general_diagonalize_dc(dist, H.copy(), S.copy(), Z, W_g_dc, 'L')
## scalapack_general_diagonalize_mr3(dist, H.copy(), S.copy(), Z, W_g_mr3, 'L')
scalapack_inverse_cholesky(dist, C, 'L')
if dtype == complex: # Only supported for complex for now
scalapack_inverse(dist, Sinv, 'L')
# Undo redistribute
C_test = glob.empty(dtype=dtype)
Sinv_test = glob.empty(dtype=dtype)
Dist2glob = Redistributor(world, dist, glob)
Dist2glob.redistribute(C, C_test)
Dist2glob.redistribute(Sinv, Sinv_test)
if rank == 0:
## diag_ex_err = abs(W - W0).max()
diag_dc_err = abs(W_dc - W0).max()
## diag_mr3_err = abs(W_mr3 - W0).max()
## general_diag_ex_err = abs(W_g - W0_g).max()
general_diag_dc_err = abs(W_g_dc - W0_g).max()
## general_diag_mr3_err = abs(W_g_mr3 - W0_g).max()
inverse_chol_err = abs(C_test - C0).max()
tri2full(Sinv_test, 'L')
inverse_err = abs(Sinv_test - S0_inv).max()
## print 'diagonalize ex err', diag_ex_err
print('diagonalize dc err', diag_dc_err)
## print 'diagonalize mr3 err', diag_mr3_err
## print 'general diagonalize ex err', general_diag_ex_err
print('general diagonalize dc err', general_diag_dc_err)
## print 'general diagonalize mr3 err', general_diag_mr3_err
print('inverse chol err', inverse_chol_err)
if dtype == complex:
print('inverse err', inverse_err)
else:
## diag_ex_err = 0.0
diag_dc_err = 0.0
## diag_mr3_err = 0.0
## general_diag_ex_err = 0.0
general_diag_dc_err = 0.0
## general_diag_mr3_err = 0.0
inverse_chol_err = 0.0
inverse_err = 0.0
# We don't like exceptions on only one cpu
## diag_ex_err = world.sum(diag_ex_err)
diag_dc_err = world.sum(diag_dc_err)
## diag_mr3_err = world.sum(diag_mr3_err)
## general_diag_ex_err = world.sum(general_diag_ex_err)
general_diag_dc_err = world.sum(general_diag_dc_err)
## general_diag_mr3_err = world.sum(general_diag_mr3_err)
inverse_chol_err = world.sum(inverse_chol_err)
inverse_err = world.sum(inverse_err)
## assert diag_ex_err < tol
assert diag_dc_err < tol
## assert diag_mr3_err < tol
## assert general_diag_ex_err < tol
assert general_diag_dc_err < tol
## assert general_diag_mr3_err < tol
assert inverse_chol_err < tol
if dtype == complex:
assert inverse_err < tol
def diagonalize_full_hamiltonian(self, ham, atoms, occupations, txt,
nbands=None, scalapack=None, expert=False):
assert self.dtype == complex
if nbands is None:
nbands = self.pd.ngmin // self.bd.comm.size * self.bd.comm.size
else:
assert nbands <= self.pd.ngmin
if expert:
iu = nbands
else:
iu = None
self.bd = bd = BandDescriptor(nbands, self.bd.comm)
p = functools.partial(print, file=txt)
p('Diagonalizing full Hamiltonian ({0} lowest bands)'.format(nbands))
p('Matrix size (min, max): {0}, {1}'.format(self.pd.ngmin,
self.pd.ngmax))
mem = 3 * self.pd.ngmax**2 * 16 / bd.comm.size / 1024**2
p('Approximate memory usage per core: {0:.3f} MB'.format(mem))
if bd.comm.size > 1:
if isinstance(scalapack, (list, tuple)):
nprow, npcol, b = scalapack
else:
nprow = int(round(bd.comm.size**0.5))
while bd.comm.size % nprow != 0:
nprow -= 1
npcol = bd.comm.size // nprow
b = 64
p('ScaLapack grid: {0}x{1},'.format(nprow, npcol),
'block-size:', b)
bg = BlacsGrid(bd.comm, bd.comm.size, 1)
bg2 = BlacsGrid(bd.comm, nprow, npcol)
scalapack = True
else:
nprow = npcol = 1
scalapack = False
self.pt.set_positions(atoms.get_scaled_positions())
self.kpt_u[0].P_ani = None
self.allocate_arrays_for_projections(self.pt.my_atom_indices)
myslice = bd.get_slice()
pb = ProgressBar(txt)
nkpt = len(self.kpt_u)
for u, kpt in enumerate(self.kpt_u):
pb.update(u / nkpt)
npw = len(self.pd.Q_qG[kpt.q])
if scalapack:
mynpw = -(-npw // bd.comm.size)
md = BlacsDescriptor(bg, npw, npw, mynpw, npw)
md2 = BlacsDescriptor(bg2, npw, npw, b, b)
else:
md = md2 = MatrixDescriptor(npw, npw)
with self.timer('Build H and S'):
H_GG, S_GG = self.hs(ham, kpt.q, kpt.s, md)
if scalapack:
r = Redistributor(bd.comm, md, md2)
H_GG = r.redistribute(H_GG)
S_GG = r.redistribute(S_GG)
psit_nG = md2.empty(dtype=complex)
eps_n = np.empty(npw)
with self.timer('Diagonalize'):
if not scalapack:
md2.general_diagonalize_dc(H_GG, S_GG, psit_nG, eps_n,
iu=iu)
else:
md2.general_diagonalize_dc(H_GG, S_GG, psit_nG, eps_n)
del H_GG, S_GG
kpt.eps_n = eps_n[myslice].copy()
if scalapack:
md3 = BlacsDescriptor(bg, npw, npw, bd.mynbands, npw)
r = Redistributor(bd.comm, md2, md3)
psit_nG = r.redistribute(psit_nG)
kpt.psit_nG = psit_nG[:bd.mynbands].copy()
del psit_nG
with self.timer('Projections'):
self.pt.integrate(kpt.psit_nG, kpt.P_ani, kpt.q)
kpt.f_n = None
pb.finish()
occupations.calculate(self)
def calculate_forces(self, hamiltonian, F_av):
self.timer.start('LCAO forces')
spos_ac = self.tci.atoms.get_scaled_positions() % 1.0
ksl = self.ksl
nao = ksl.nao
mynao = ksl.mynao
nq = len(self.kd.ibzk_qc)
dtype = self.dtype
tci = self.tci
gd = self.gd
bfs = self.basis_functions
Mstart = ksl.Mstart
Mstop = ksl.Mstop
from gpaw.kohnsham_layouts import BlacsOrbitalLayouts
isblacs = isinstance(ksl, BlacsOrbitalLayouts) # XXX
if not isblacs:
self.timer.start('TCI derivative')
dThetadR_qvMM = np.empty((nq, 3, mynao, nao), dtype)
dTdR_qvMM = np.empty((nq, 3, mynao, nao), dtype)
dPdR_aqvMi = {}
for a in self.basis_functions.my_atom_indices:
ni = self.setups[a].ni
dPdR_aqvMi[a] = np.empty((nq, 3, nao, ni), dtype)
tci.calculate_derivative(spos_ac, dThetadR_qvMM, dTdR_qvMM,
dPdR_aqvMi)
gd.comm.sum(dThetadR_qvMM)
gd.comm.sum(dTdR_qvMM)
self.timer.stop('TCI derivative')
my_atom_indices = bfs.my_atom_indices
atom_indices = bfs.atom_indices
def _slices(indices):
for a in indices:
M1 = bfs.M_a[a] - Mstart
M2 = M1 + self.setups[a].nao
if M2 > 0:
yield a, max(0, M1), M2
def slices():
return _slices(atom_indices)
def my_slices():
return _slices(my_atom_indices)
#
# ----- -----
# \ -1 \ *
# E = ) S H rho = ) c eps f c
# mu nu / mu x x z z nu / n mu n n n nu
# ----- -----
# x z n
#
# We use the transpose of that matrix. The first form is used
# if rho is given, otherwise the coefficients are used.
self.timer.start('Initial')
rhoT_uMM = []
ET_uMM = []
if not isblacs:
if self.kpt_u[0].rho_MM is None:
self.timer.start('Get density matrix')
for kpt in self.kpt_u:
rhoT_MM = ksl.get_transposed_density_matrix(
kpt.f_n, kpt.C_nM)
rhoT_uMM.append(rhoT_MM)
ET_MM = ksl.get_transposed_density_matrix(
kpt.f_n * kpt.eps_n, kpt.C_nM)
ET_uMM.append(ET_MM)
if hasattr(kpt, 'c_on'):
# XXX does this work with BLACS/non-BLACS/etc.?
assert self.bd.comm.size == 1
d_nn = np.zeros((self.bd.mynbands, self.bd.mynbands),
dtype=kpt.C_nM.dtype)
for ne, c_n in zip(kpt.ne_o, kpt.c_on):
d_nn += ne * np.outer(c_n.conj(), c_n)
rhoT_MM += ksl.get_transposed_density_matrix_delta(\
d_nn, kpt.C_nM)
ET_MM += ksl.get_transposed_density_matrix_delta(\
d_nn * kpt.eps_n, kpt.C_nM)
self.timer.stop('Get density matrix')
else:
rhoT_uMM = []
ET_uMM = []
for kpt in self.kpt_u:
H_MM = self.eigensolver.calculate_hamiltonian_matrix(\
hamiltonian, self, kpt)
tri2full(H_MM)
S_MM = kpt.S_MM.copy()
tri2full(S_MM)
ET_MM = np.linalg.solve(S_MM,
gemmdot(H_MM,
kpt.rho_MM)).T.copy()
del S_MM, H_MM
rhoT_MM = kpt.rho_MM.T.copy()
rhoT_uMM.append(rhoT_MM)
ET_uMM.append(ET_MM)
self.timer.stop('Initial')
if isblacs: # XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
from gpaw.blacs import BlacsGrid, Redistributor
def get_density_matrix(f_n, C_nM, redistributor):
rho1_mm = ksl.calculate_blocked_density_matrix(f_n,
C_nM).conj()
rho_mm = redistributor.redistribute(rho1_mm)
return rho_mm
pcutoff_a = [
max([pt.get_cutoff() for pt in setup.pt_j])
for setup in self.setups
]
phicutoff_a = [
max([phit.get_cutoff() for phit in setup.phit_j])
for setup in self.setups
]
# XXX should probably use bdsize x gdsize instead
# That would be consistent with some existing grids
grid = BlacsGrid(ksl.block_comm, self.gd.comm.size,
self.bd.comm.size)
blocksize1 = -(-nao // grid.nprow)
blocksize2 = -(-nao // grid.npcol)
# XXX what are rows and columns actually?
desc = grid.new_descriptor(nao, nao, blocksize1, blocksize2)
rhoT_umm = []
ET_umm = []
redistributor = Redistributor(grid.comm, ksl.mmdescriptor, desc)
Fpot_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
self.timer.start('Get density matrix')
rhoT_mm = get_density_matrix(kpt.f_n, kpt.C_nM, redistributor)
rhoT_umm.append(rhoT_mm)
self.timer.stop('Get density matrix')
self.timer.start('Potential')
rhoT_mM = ksl.distribute_to_columns(rhoT_mm, desc)
vt_G = hamiltonian.vt_sG[kpt.s]
Fpot_av += bfs.calculate_force_contribution(
vt_G, rhoT_mM, kpt.q)
del rhoT_mM
self.timer.stop('Potential')
self.timer.start('Get density matrix')
for kpt in self.kpt_u:
ET_mm = get_density_matrix(kpt.f_n * kpt.eps_n, kpt.C_nM,
redistributor)
ET_umm.append(ET_mm)
self.timer.stop('Get density matrix')
M1start = blocksize1 * grid.myrow
M2start = blocksize2 * grid.mycol
M1stop = min(M1start + blocksize1, nao)
M2stop = min(M2start + blocksize2, nao)
m1max = M1stop - M1start
m2max = M2stop - M2start
if not isblacs:
# Kinetic energy contribution
#
# ----- d T
# a \ mu nu
# F += 2 Re ) -------- rho
# / d R nu mu
# ----- mu nu
# mu in a; nu
#
Fkin_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
dEdTrhoT_vMM = (dTdR_qvMM[kpt.q] *
rhoT_uMM[u][np.newaxis]).real
for a, M1, M2 in my_slices():
Fkin_av[a, :] += \
2.0 * dEdTrhoT_vMM[:, M1:M2].sum(-1).sum(-1)
del dEdTrhoT_vMM
# Density matrix contribution due to basis overlap
#
# ----- d Theta
# a \ mu nu
# F += -2 Re ) ------------ E
# / d R nu mu
# ----- mu nu
# mu in a; nu
#
Ftheta_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
dThetadRE_vMM = (dThetadR_qvMM[kpt.q] *
ET_uMM[u][np.newaxis]).real
for a, M1, M2 in my_slices():
Ftheta_av[a, :] += \
-2.0 * dThetadRE_vMM[:, M1:M2].sum(-1).sum(-1)
del dThetadRE_vMM
if isblacs:
from gpaw.lcao.overlap import TwoCenterIntegralCalculator
self.timer.start('Prepare TCI loop')
M_a = bfs.M_a
Fkin2_av = np.zeros_like(F_av)
Ftheta2_av = np.zeros_like(F_av)
cell_cv = tci.atoms.cell
spos_ac = tci.atoms.get_scaled_positions() % 1.0
overlapcalc = TwoCenterIntegralCalculator(self.kd.ibzk_qc,
derivative=False)
# XXX this is not parallel *AT ALL*.
self.timer.start('Get neighbors')
nl = tci.atompairs.pairs.neighbors
r_and_offset_aao = get_r_and_offsets(nl, spos_ac, cell_cv)
atompairs = r_and_offset_aao.keys()
atompairs.sort()
self.timer.stop('Get neighbors')
T_expansions = tci.T_expansions
Theta_expansions = tci.Theta_expansions
P_expansions = tci.P_expansions
nq = len(self.kd.ibzk_qc)
dH_asp = hamiltonian.dH_asp
self.timer.start('broadcast dH')
alldH_asp = {}
for a in range(len(self.setups)):
gdrank = bfs.sphere_a[a].rank
if gdrank == gd.rank:
dH_sp = dH_asp[a]
else:
ni = self.setups[a].ni
dH_sp = np.empty((self.nspins, ni * (ni + 1) // 2))
gd.comm.broadcast(dH_sp, gdrank)
# okay, now everyone gets copies of dH_sp
alldH_asp[a] = dH_sp
self.timer.stop('broadcast dH')
# This will get sort of hairy. We need to account for some
# three-center overlaps, such as:
#
# a1
# Phi ~a3 a3 ~a3 a2 a2,a1
# < ---- |p > dH <p |Phi > rho
# dR
#
# To this end we will loop over all pairs of atoms (a1, a3),
# and then a sub-loop over (a3, a2).
from gpaw.lcao.overlap import DerivativeAtomicDisplacement
class Displacement(DerivativeAtomicDisplacement):
def __init__(self, a1, a2, R_c, offset):
phases = overlapcalc.phaseclass(overlapcalc.ibzk_qc,
offset)
DerivativeAtomicDisplacement.__init__(
self, None, a1, a2, R_c, offset, phases)
# Cache of Displacement objects with spherical harmonics with
# evaluated spherical harmonics.
disp_aao = {}
def get_displacements(a1, a2, maxdistance):
# XXX the way maxdistance is handled it can lead to
# bad caching when different maxdistances are passed
# to subsequent calls with same pair of atoms
disp_o = disp_aao.get((a1, a2))
if disp_o is None:
disp_o = []
for R_c, offset in r_and_offset_aao[(a1, a2)]:
if np.linalg.norm(R_c) > maxdistance:
continue
disp = Displacement(a1, a2, R_c, offset)
disp_o.append(disp)
disp_aao[(a1, a2)] = disp_o
return [disp for disp in disp_o if disp.r < maxdistance]
self.timer.stop('Prepare TCI loop')
self.timer.start('Not so complicated loop')
for (a1, a2) in atompairs:
if a1 >= a2:
# Actually this leads to bad load balance.
# We should take a1 > a2 or a1 < a2 equally many times.
# Maybe decide which of these choices
# depending on whether a2 % 1 == 0
continue
m1start = M_a[a1] - M1start
m2start = M_a[a2] - M2start
if m1start >= blocksize1 or m2start >= blocksize2:
continue # (we have only one block per CPU)
T_expansion = T_expansions.get(a1, a2)
Theta_expansion = Theta_expansions.get(a1, a2)
#P_expansion = P_expansions.get(a1, a2)
nm1, nm2 = T_expansion.shape
m1stop = min(m1start + nm1, m1max)
m2stop = min(m2start + nm2, m2max)
if m1stop <= 0 or m2stop <= 0:
continue
m1start = max(m1start, 0)
m2start = max(m2start, 0)
J1start = max(0, M1start - M_a[a1])
J2start = max(0, M2start - M_a[a2])
M1stop = J1start + m1stop - m1start
J2stop = J2start + m2stop - m2start
dTdR_qvmm = T_expansion.zeros((nq, 3), dtype=dtype)
dThetadR_qvmm = Theta_expansion.zeros((nq, 3), dtype=dtype)
disp_o = get_displacements(a1, a2,
phicutoff_a[a1] + phicutoff_a[a2])
for disp in disp_o:
disp.evaluate_overlap(T_expansion, dTdR_qvmm)
disp.evaluate_overlap(Theta_expansion, dThetadR_qvmm)
for u, kpt in enumerate(self.kpt_u):
rhoT_mm = rhoT_umm[u][m1start:m1stop, m2start:m2stop]
ET_mm = ET_umm[u][m1start:m1stop, m2start:m2stop]
Fkin_v = 2.0 * (
dTdR_qvmm[kpt.q][:, J1start:M1stop, J2start:J2stop] *
rhoT_mm[np.newaxis]).real.sum(-1).sum(-1)
Ftheta_v = 2.0 * (dThetadR_qvmm[kpt.q][:, J1start:M1stop,
J2start:J2stop] *
ET_mm[np.newaxis]).real.sum(-1).sum(-1)
Fkin2_av[a1] += Fkin_v
Fkin2_av[a2] -= Fkin_v
Ftheta2_av[a1] -= Ftheta_v
Ftheta2_av[a2] += Ftheta_v
Fkin_av = Fkin2_av
Ftheta_av = Ftheta2_av
self.timer.stop('Not so complicated loop')
dHP_and_dSP_aauim = {}
a2values = {}
for (a2, a3) in atompairs:
if not a3 in a2values:
a2values[a3] = []
a2values[a3].append(a2)
Fatom_av = np.zeros_like(F_av)
Frho_av = np.zeros_like(F_av)
self.timer.start('Complicated loop')
for a1, a3 in atompairs:
if a1 == a3:
# Functions reside on same atom, so their overlap
# does not change when atom is displaced
continue
m1start = M_a[a1] - M1start
if m1start >= blocksize1:
continue
P_expansion = P_expansions.get(a1, a3)
nm1 = P_expansion.shape[0]
m1stop = min(m1start + nm1, m1max)
if m1stop <= 0:
continue
m1start = max(m1start, 0)
J1start = max(0, M1start - M_a[a1])
J1stop = J1start + m1stop - m1start
disp_o = get_displacements(a1, a3,
phicutoff_a[a1] + pcutoff_a[a3])
if len(disp_o) == 0:
continue
dPdR_qvmi = P_expansion.zeros((nq, 3), dtype=dtype)
for disp in disp_o:
disp.evaluate_overlap(P_expansion, dPdR_qvmi)
dPdR_qvmi = dPdR_qvmi[:, :, J1start:J1stop, :].copy()
for a2 in a2values[a3]:
m2start = M_a[a2] - M2start
if m2start >= blocksize2:
continue
P_expansion2 = P_expansions.get(a2, a3)
nm2 = P_expansion2.shape[0]
m2stop = min(m2start + nm2, m2max)
if m2stop <= 0:
continue
disp_o = get_displacements(a2, a3,
phicutoff_a[a2] + pcutoff_a[a3])
if len(disp_o) == 0:
continue
m2start = max(m2start, 0)
J2start = max(0, M2start - M_a[a2])
J2stop = J2start + m2stop - m2start
if (a2, a3) in dHP_and_dSP_aauim:
dHP_uim, dSP_uim = dHP_and_dSP_aauim[(a2, a3)]
else:
P_qmi = P_expansion2.zeros((nq, ), dtype=dtype)
for disp in disp_o:
disp.evaluate_direct(P_expansion2, P_qmi)
P_qmi = P_qmi[:, J2start:J2stop].copy()
dH_sp = alldH_asp[a3]
dS_ii = self.setups[a3].dO_ii
dHP_uim = []
dSP_uim = []
for u, kpt in enumerate(self.kpt_u):
dH_ii = unpack(dH_sp[kpt.s])
dHP_im = np.dot(P_qmi[kpt.q], dH_ii).T.conj()
# XXX only need nq of these
dSP_im = np.dot(P_qmi[kpt.q], dS_ii).T.conj()
dHP_uim.append(dHP_im)
dSP_uim.append(dSP_im)
dHP_and_dSP_aauim[(a2, a3)] = dHP_uim, dSP_uim
for u, kpt in enumerate(self.kpt_u):
rhoT_mm = rhoT_umm[u][m1start:m1stop, m2start:m2stop]
ET_mm = ET_umm[u][m1start:m1stop, m2start:m2stop]
dPdRdHP_vmm = np.dot(dPdR_qvmi[kpt.q], dHP_uim[u])
dPdRdSP_vmm = np.dot(dPdR_qvmi[kpt.q], dSP_uim[u])
Fatom_c = 2.0 * (dPdRdHP_vmm *
rhoT_mm).real.sum(-1).sum(-1)
Frho_c = 2.0 * (dPdRdSP_vmm *
ET_mm).real.sum(-1).sum(-1)
Fatom_av[a1] += Fatom_c
Fatom_av[a3] -= Fatom_c
Frho_av[a1] -= Frho_c
Frho_av[a3] += Frho_c
self.timer.stop('Complicated loop')
if not isblacs:
# Potential contribution
#
# ----- / d Phi (r)
# a \ | mu ~
# F += -2 Re ) | ---------- v (r) Phi (r) dr rho
# / | d R nu nu mu
# ----- / a
# mu in a; nu
#
self.timer.start('Potential')
Fpot_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
vt_G = hamiltonian.vt_sG[kpt.s]
Fpot_av += bfs.calculate_force_contribution(
vt_G, rhoT_uMM[u], kpt.q)
self.timer.stop('Potential')
# Density matrix contribution from PAW correction
#
# ----- -----
# a \ a \ b
# F += 2 Re ) Z E - 2 Re ) Z E
# / mu nu nu mu / mu nu nu mu
# ----- -----
# mu nu b; mu in a; nu
#
# with
# b*
# ----- dP
# b \ i mu b b
# Z = ) -------- dS P
# mu nu / dR ij j nu
# ----- b mu
# ij
#
self.timer.start('Paw correction')
Frho_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
work_MM = np.zeros((mynao, nao), dtype)
ZE_MM = None
for b in my_atom_indices:
setup = self.setups[b]
dO_ii = np.asarray(setup.dO_ii, dtype)
dOP_iM = np.zeros((setup.ni, nao), dtype)
gemm(1.0, self.P_aqMi[b][kpt.q], dO_ii, 0.0, dOP_iM, 'c')
for v in range(3):
gemm(1.0, dOP_iM,
dPdR_aqvMi[b][kpt.q][v][Mstart:Mstop], 0.0,
work_MM, 'n')
ZE_MM = (work_MM * ET_uMM[u]).real
for a, M1, M2 in slices():
dE = 2 * ZE_MM[M1:M2].sum()
Frho_av[a, v] -= dE # the "b; mu in a; nu" term
Frho_av[b, v] += dE # the "mu nu" term
del work_MM, ZE_MM
self.timer.stop('Paw correction')
# Atomic density contribution
# ----- -----
# a \ a \ b
# F += -2 Re ) A rho + 2 Re ) A rho
# / mu nu nu mu / mu nu nu mu
# ----- -----
# mu nu b; mu in a; nu
#
# b*
# ----- d P
# b \ i mu b b
# A = ) ------- dH P
# mu nu / d R ij j nu
# ----- b mu
# ij
#
self.timer.start('Atomic Hamiltonian force')
Fatom_av = np.zeros_like(F_av)
for u, kpt in enumerate(self.kpt_u):
for b in my_atom_indices:
H_ii = np.asarray(unpack(hamiltonian.dH_asp[b][kpt.s]),
dtype)
HP_iM = gemmdot(
H_ii,
np.ascontiguousarray(self.P_aqMi[b][kpt.q].T.conj()))
for v in range(3):
dPdR_Mi = dPdR_aqvMi[b][kpt.q][v][Mstart:Mstop]
ArhoT_MM = (gemmdot(dPdR_Mi, HP_iM) * rhoT_uMM[u]).real
for a, M1, M2 in slices():
dE = 2 * ArhoT_MM[M1:M2].sum()
Fatom_av[a, v] += dE # the "b; mu in a; nu" term
Fatom_av[b, v] -= dE # the "mu nu" term
self.timer.stop('Atomic Hamiltonian force')
F_av += Fkin_av + Fpot_av + Ftheta_av + Frho_av + Fatom_av
self.timer.start('Wait for sum')
ksl.orbital_comm.sum(F_av)
if self.bd.comm.rank == 0:
self.kd.comm.sum(F_av, 0)
self.timer.stop('Wait for sum')
self.timer.stop('LCAO forces')
def __init__(self, sl_lrtddft, nrows, lr_comms):
self.mprocs, self.nprocs, self.block_size = tuple(sl_lrtddft)
self.lr_comms = lr_comms
# for SCALAPACK we need TRANSPOSED MATRIX (and vector)
#
# -----------------------------------------------------------------
# matrix
# original grid, ie, how matrix is stored
self.orig_matrix_grid = BlacsGrid(self.lr_comms.parent_comm,
self.lr_comms.dd_comm.size,
self.lr_comms.eh_comm.size)
# solve grid
self.solve_matrix_grid = BlacsGrid(self.lr_comms.parent_comm,
self.mprocs, self.nprocs)
# M = rows, N = cols
M = nrows * 4
N = nrows * 4
mb = 4
nb = 4
self.orig_matrix_descr = self.orig_matrix_grid.new_descriptor(
N, M, nb, mb)
bs = self.block_size
self.solve_matrix_descr = self.solve_matrix_grid.new_descriptor(
N, M, bs, bs)
self.matrix_in_redist = Redistributor(self.lr_comms.parent_comm,
self.orig_matrix_descr,
self.solve_matrix_descr)
# -----------------------------------------------------------------
# vector
# original grid, ie, how vector is stored
self.orig_vector_grid = BlacsGrid(
self.lr_comms.parent_comm, 1,
(self.lr_comms.dd_comm.size * self.lr_comms.eh_comm.size))
# solve grid
#self.solve_vector_grid = BlacsGrid(self.lr_comms.parent_comm, self.mprocs, self.nprocs)
# M = rows, N = cols
M = nrows * 4
Nrhs = 1
mb = 4
nb = 1
self.orig_vector_descr = self.orig_vector_grid.new_descriptor(
Nrhs, M, nb, mb)
bs = self.block_size
self.solve_vector_descr = self.solve_matrix_grid.new_descriptor(
Nrhs, M, 1, bs)
self.vector_in_redist = Redistributor(self.lr_comms.parent_comm,
self.orig_vector_descr,
self.solve_vector_descr)
self.vector_out_redist = Redistributor(self.lr_comms.parent_comm,
self.solve_vector_descr,
self.orig_vector_descr)
def __init__(self, sl_lrtddft, nkq, dd_comm, eh_comm):
mcpus, ncpus, blocksize = tuple(sl_lrtddft)
self.world = eh_comm.parent
self.dd_comm = dd_comm
if self.world is None:
self.world = self.dd_comm
# All the ranks within domain communicator contain the omega matrix
# construct new communicator only on domain masters
eh_ranks = np.arange(eh_comm.size) * dd_comm.size
self.eh_comm2 = self.world.new_communicator(eh_ranks)
self.eh_grid = BlacsGrid(self.eh_comm2, eh_comm.size, 1)
self.eh_descr = self.eh_grid.new_descriptor(nkq, nkq, 1, nkq)
self.diag_grid = BlacsGrid(self.world, mcpus, ncpus)
self.diag_descr = self.diag_grid.new_descriptor(
nkq, nkq, blocksize, blocksize)
self.redistributor_in = Redistributor(self.world, self.eh_descr,
self.diag_descr)
self.redistributor_out = Redistributor(self.world, self.diag_descr,
self.eh_descr)
"""
# -----------------------------------------------------------------
# for SCALAPACK we need TRANSPOSED MATRIX (and vector)
# -----------------------------------------------------------------
# M = rows, N = cols
M = nkq*4; N = nkq*4; mb = nkq*4; nb = 4; Nrhs = 1
# Matrix, mp=1, np=eh_comm.size
self.eh_grid2a = BlacsGrid(self.eh_comm2, eh_comm.size, 1)
# Vector, mp=eh_comm.size, np=1
self.eh_grid2b = BlacsGrid(self.eh_comm2, 1, eh_comm.size)
self.eh_descr2a = self.eh_grid2a.new_descriptor(N, M, nb, mb)
self.eh_descr2b = self.eh_grid2b.new_descriptor(Nrhs, N, 1, nb)
self.solve_descr2a =self.diag_grid.new_descriptor(N, M,
blocksize, blocksize)
self.solve_descr2b =self.diag_grid.new_descriptor(Nrhs, N,
1, blocksize)
self.redist_solve_in_2a = Redistributor(self.world,
self.eh_descr2a,
self.solve_descr2a)
self.redist_solve_in_2b = Redistributor(self.world,
self.eh_descr2b,
self.solve_descr2b)
self.redist_solve_out_2a = Redistributor(self.world,
self.solve_descr2a,
self.eh_descr2a)
self.redist_solve_out_2b = Redistributor(self.world,
self.solve_descr2b,
self.eh_descr2b)
"""
# -----------------------------------------------------------------
# for SCALAPACK we need TRANSPOSED MATRIX (and vector)
# -----------------------------------------------------------------
# M = rows, N = cols
M = nkq * 4
N = nkq * 4
mb = 4
nb = 4
Nrhs = 1
# Matrix, mp=1, np=eh_comm.size
self.eh_grid2a = BlacsGrid(self.world, dd_comm.size, eh_comm.size)
# Vector, mp=eh_comm.size, np=1
self.eh_grid2b = BlacsGrid(self.world, 1, dd_comm.size * eh_comm.size)
self.eh_descr2a = self.eh_grid2a.new_descriptor(N, M, nb, mb)
self.eh_descr2b = self.eh_grid2b.new_descriptor(Nrhs, N, Nrhs, nb)
self.solve_descr2a = self.diag_grid.new_descriptor(
N, M, blocksize, blocksize)
self.solve_descr2b = self.diag_grid.new_descriptor(
Nrhs, N, Nrhs, blocksize)
self.redist_solve_in_2a = Redistributor(self.world, self.eh_descr2a,
self.solve_descr2a)
self.redist_solve_in_2b = Redistributor(self.world, self.eh_descr2b,
self.solve_descr2b)
self.redist_solve_out_2a = Redistributor(self.world,
self.solve_descr2a,
self.eh_descr2a)
self.redist_solve_out_2b = Redistributor(self.world,
self.solve_descr2b,
self.eh_descr2b)
def calculate_blocked_density_matrix(self, f_n, C_nM):
nbands = self.bd.nbands
nao = self.nao
dtype = C_nM.dtype
self.nMdescriptor.checkassert(C_nM)
if self.gd.rank == 0:
Cf_nM = (C_nM * f_n[:, None])
else:
C_nM = self.nM_unique_descriptor.zeros(dtype=dtype)
Cf_nM = self.nM_unique_descriptor.zeros(dtype=dtype)
r = Redistributor(self.block_comm, self.nM_unique_descriptor,
self.mmdescriptor)
Cf_mm = self.mmdescriptor.zeros(dtype=dtype)
r.redistribute(Cf_nM, Cf_mm, nbands, nao)
del Cf_nM
C_mm = self.mmdescriptor.zeros(dtype=dtype)
r.redistribute(C_nM, C_mm, nbands, nao)
# no use to delete C_nM as it's in the input...
rho_mm = self.mmdescriptor.zeros(dtype=dtype)
if 1: # if self.libelpa is None:
pblas_simple_gemm(self.mmdescriptor,
self.mmdescriptor,
self.mmdescriptor,
Cf_mm,
C_mm,
rho_mm,
transa='C')
else:
# elpa_hermitian_multiply was not faster than the ordinary
# multiplication in the test. The way we have things distributed,
# we need to transpose things at the moment.
#
# Rather than enabling this, we should store the coefficients
# in an appropriate 2D block cyclic format (c_nm) and not the
# current C_nM format. This makes it possible to avoid
# redistributing the coefficients at all. But we don't have time
# to implement this at the moment.
mul = self.libelpa.hermitian_multiply
desc = self.mmdescriptor
from gpaw.utilities.scalapack import pblas_tran
def T(array):
tmp = array.copy()
pblas_tran(alpha=1.0,
a_MN=tmp,
beta=0.0,
c_NM=array,
desca=desc,
descc=desc)
T(C_mm)
T(Cf_mm)
mul(C_mm, Cf_mm, rho_mm, desc, desc, desc, uplo_a='X', uplo_c='X')
return rho_mm
def tddft_init(self):
if self.tddft_initialized:
return
self.blacs = self.wfs.ksl.using_blacs
if self.blacs:
self.ksl = ksl = self.wfs.ksl
nao = ksl.nao
nbands = ksl.bd.nbands
mynbands = ksl.bd.mynbands
blocksize = ksl.blocksize
from gpaw.blacs import Redistributor
if self.wfs.world.rank == 0:
print('BLACS Parallelization')
# Parallel grid descriptors
grid = ksl.blockgrid
assert grid.nprow * grid.npcol == self.wfs.ksl.block_comm.size
# FOR DEBUG
self.MM_descriptor = grid.new_descriptor(nao, nao, nao, nao)
self.mm_block_descriptor = grid.new_descriptor(
nao, nao, blocksize, blocksize)
self.Cnm_block_descriptor = grid.new_descriptor(
nbands, nao, blocksize, blocksize)
# self.CnM_descriptor = ksl.blockgrid.new_descriptor(nbands,
# nao, mynbands, nao)
self.mM_column_descriptor = ksl.single_column_grid.new_descriptor(
nao, nao, ksl.naoblocksize, nao)
self.CnM_unique_descriptor = ksl.single_column_grid.new_descriptor(
nbands, nao, mynbands, nao)
# Redistributors
self.mm2MM = Redistributor(ksl.block_comm,
self.mm_block_descriptor,
self.MM_descriptor) # XXX FOR DEBUG
self.MM2mm = Redistributor(ksl.block_comm, self.MM_descriptor,
self.mm_block_descriptor) # FOR DEBUG
self.Cnm2nM = Redistributor(ksl.block_comm,
self.Cnm_block_descriptor,
self.CnM_unique_descriptor)
self.CnM2nm = Redistributor(ksl.block_comm,
self.CnM_unique_descriptor,
self.Cnm_block_descriptor)
self.mM2mm = Redistributor(ksl.block_comm,
self.mM_column_descriptor,
self.mm_block_descriptor)
for kpt in self.wfs.kpt_u:
scalapack_zero(self.mm_block_descriptor, kpt.S_MM, 'U')
scalapack_zero(self.mm_block_descriptor, kpt.T_MM, 'U')
# XXX to propagator class
if self.propagator == 'taylor' and self.blacs:
# cholS_mm = self.mm_block_descriptor.empty(dtype=complex)
for kpt in self.wfs.kpt_u:
kpt.invS_MM = kpt.S_MM.copy()
scalapack_inverse(self.mm_block_descriptor, kpt.invS_MM,
'L')
if self.propagator == 'taylor' and not self.blacs:
tmp = inv(self.wfs.kpt_u[0].S_MM)
self.wfs.kpt_u[0].invS = tmp
# Reset the density mixer
self.density.set_mixer(DummyMixer())
self.tddft_initialized = True
for k, kpt in enumerate(self.wfs.kpt_u):
kpt.C2_nM = kpt.C_nM.copy()
from gpaw.blacs import BlacsGrid, Redistributor
if world.size < 2:
raise ValueError('Runs on two or more processors')
grid = BlacsGrid(world, 2, world.size // 2)
desc = grid.new_descriptor(12, 8, 2, 3)
a = desc.zeros()
a[:] = world.rank
subdesc = grid.new_descriptor(7, 7, 2, 2)
b = subdesc.zeros()
r = Redistributor(grid.comm, desc, subdesc, uplo='G')
ia = 3
ja = 2
ib = 1
jb = 1
M = 4
N = 5
r.redistribute(a, b, M, N, ia, ja, ib, jb)
a0 = desc.collect_on_master(a)
b0 = subdesc.collect_on_master(b)
if world.rank == 0:
print a0
print b0
