def par_write(filename, name, comm, chi0_wGG):
## support only world communicator at the moment
from gpaw.mpi import rank, size, world
from gpaw.io import open
assert comm.size == size
assert comm.rank == rank
Nw_local, npw, npw1 = chi0_wGG.shape
assert npw == npw1
Nw = Nw_local * size
if rank == 0:
w = open(filename, 'w', comm)
w.dimension('Nw', Nw)
w.dimension('npw', npw)
w.add(name, ('Nw', 'npw', 'npw'), dtype=complex)
tmp = np.zeros_like(chi0_wGG[0])
for iw in range(Nw):
irank = iw // Nw_local
if irank == 0:
if rank == 0:
w.fill(chi0_wGG[iw])
else:
if rank == irank:
world.send(chi0_wGG[iw - rank * Nw_local], 0, irank + 100)
if rank == 0:
world.receive(tmp, irank, irank + 100)
w.fill(tmp)
if rank == 0:
w.close()
world.barrier()
def par_save(self,filename, name, A_sS):
from gpaw.io import open
nS_local = self.nS_local
nS = self.nS
if rank == 0:
w = open(filename, 'w', world)
w.dimension('nS', nS)
if name == 'v_SS':
w.add('w_S', ('nS',), dtype=self.w_S.dtype)
w.fill(self.w_S)
w.add('rhoG0_S', ('nS',), dtype=complex)
w.fill(self.rhoG0_S)
w.add(name, ('nS', 'nS'), dtype=complex)
tmp = np.zeros_like(A_sS)
# Assumes that H_SS is written in order from rank 0 - rank N
for irank in range(size):
if irank == 0:
if rank == 0:
w.fill(A_sS)
else:
if rank == irank:
world.send(A_sS, 0, irank+100)
if rank == 0:
world.receive(tmp, irank, irank+100)
w.fill(tmp)
if rank == 0:
w.close()
world.barrier()
def par_write(filename, name, comm, chi0_wGG):
## support only world communicator at the moment
from gpaw.mpi import rank, size, world
from gpaw.io import open
assert comm.size == size
assert comm.rank == rank
Nw_local, npw, npw1 = chi0_wGG.shape
assert npw == npw1
Nw = Nw_local * size
w = open(filename, 'w', comm)
w.dimension('Nw', Nw)
w.dimension('npw', npw)
w.add(name, ('Nw', 'npw', 'npw'), dtype=complex)
if rank == 0:
tmp = np.zeros_like(chi0_wGG[0])
for iw in range(Nw):
irank = iw // Nw_local
if irank == 0:
if rank == 0:
w.fill(chi0_wGG[iw])
else:
if rank == irank:
world.send(chi0_wGG[iw-rank*Nw_local], 0, irank+100)
if rank == 0:
world.receive(tmp, irank, irank+100)
w.fill(tmp)
if rank == 0:
w.close()
world.barrier()
def par_save(self, filename, name, A_sS):
from gpaw.io import open
nS = self.nS
if rank == 0:
w = open(filename, 'w', world)
w.dimension('nS', nS)
if name == 'v_SS':
w.add('w_S', ('nS', ), dtype=self.w_S.dtype)
w.fill(self.w_S)
w.add('rhoG0_S', ('nS', ), dtype=complex)
w.fill(self.rhoG0_S)
w.add(name, ('nS', 'nS'), dtype=complex)
tmp = np.zeros_like(A_sS)
# Assumes that H_SS is written in order from rank 0 - rank N
for irank in range(size):
if irank == 0:
if rank == 0:
w.fill(A_sS)
else:
if rank == irank:
world.send(A_sS, 0, irank + 100)
if rank == 0:
world.receive(tmp, irank, irank + 100)
w.fill(tmp)
if rank == 0:
w.close()
world.barrier()
def get_wavefunction(self, ibzk, n, check_focc=True, spin=0):
if self.calc.wfs.kpt_comm.size != world.size or world.size == 1:
if check_focc == False:
return
else:
psit_G = self.calc.wfs.get_wave_function_array(n, ibzk, spin)
if self.calc.wfs.world.size == 1:
return np.complex128(psit_G)
if not self.calc.wfs.world.rank == 0:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype,
global_array=True)
self.calc.wfs.world.broadcast(psit_G, 0)
return np.complex128(psit_G)
else:
if self.nkpt % size != 0:
raise ValueError(
'The number of kpoints should be divided by the number of cpus for no wfs dumping mode ! '
)
# support ground state calculation with only kpoint parallelization
kpt_rank, u = self.calc.wfs.kd.get_rank_and_index(0, ibzk)
bzkpt_rank = rank
klist = np.array([kpt_rank, u, bzkpt_rank, n])
klist_kcomm = np.zeros((self.kcomm.size, 4), dtype=int)
self.kcomm.all_gather(klist, klist_kcomm)
check_focc_global = np.zeros(self.kcomm.size, dtype=bool)
self.kcomm.all_gather(np.array([check_focc]), check_focc_global)
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
for i in range(self.kcomm.size):
if check_focc_global[i] == True:
kpt_rank, u, bzkpt_rank, nlocal = klist_kcomm[i]
if kpt_rank == bzkpt_rank:
if rank == kpt_rank:
psit_G = self.calc.wfs.kpt_u[u].psit_nG[nlocal]
else:
if rank == kpt_rank:
world.send(self.calc.wfs.kpt_u[u].psit_nG[nlocal],
bzkpt_rank, 1300 + bzkpt_rank)
if rank == bzkpt_rank:
psit_G = self.calc.wfs.gd.empty(
dtype=self.calc.wfs.dtype)
world.receive(psit_G, kpt_rank, 1300 + bzkpt_rank)
self.wScomm.broadcast(psit_G, 0)
return psit_G
def get_wavefunction(self, ibzk, n, check_focc=True, spin=0):
if (self.calc.wfs.world.size == 1 or self.calc.wfs.gd.comm.size != 1
or self.calc.input_parameters['mode'] == 'lcao'):
if not check_focc:
return
else:
psit_G = self.calc.wfs.get_wave_function_array(n, ibzk, spin)
if self.calc.wfs.world.size == 1:
return np.complex128(psit_G)
if self.calc.wfs.world.rank != 0:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype,
global_array=True)
self.calc.wfs.world.broadcast(psit_G, 0)
return np.complex128(psit_G)
else:
# support ground state calculation with kpoint and band parallelization
# but domain decomposition must = 1
kpt_rank, u = self.calc.wfs.kd.get_rank_and_index(0, ibzk)
bzkpt_rank = self.kcomm.rank
band_rank, myn = self.calc.wfs.bd.who_has(n)
assert self.calc.wfs.gd.comm.size == 1
world_rank = (kpt_rank * self.calc.wfs.band_comm.size + band_rank)
# in the following, kpt_rank is assigned to world_rank
klist = np.array([world_rank, u, bzkpt_rank, myn])
klist_kcomm = np.zeros((self.kcomm.size, 4), dtype=int)
self.kcomm.all_gather(klist, klist_kcomm)
check_focc_global = np.zeros(self.kcomm.size, dtype=bool)
self.kcomm.all_gather(np.array([check_focc]), check_focc_global)
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
for i in range(self.kcomm.size):
if check_focc_global[i]:
kpt_rank, u, bzkpt_rank, nlocal = klist_kcomm[i]
if kpt_rank == bzkpt_rank:
if rank == kpt_rank:
psit_G = self.calc.wfs.kpt_u[u].psit_nG[nlocal]
else:
if rank == kpt_rank:
world.send(self.calc.wfs.kpt_u[u].psit_nG[nlocal],
bzkpt_rank, 1300 + bzkpt_rank)
if rank == bzkpt_rank:
psit_G = self.calc.wfs.gd.empty(
dtype=self.calc.wfs.dtype)
world.receive(psit_G, kpt_rank, 1300 + bzkpt_rank)
self.wScomm.broadcast(psit_G, 0)
return psit_G
def get_wavefunction(self, ibzk, n, check_focc=True, spin=0):
if (self.calc.wfs.world.size == 1 or self.calc.wfs.gd.comm.size != 1
or self.calc.input_parameters['mode'] == 'lcao'):
if not check_focc:
return
else:
psit_G = self.calc.wfs.get_wave_function_array(n, ibzk, spin)
if self.calc.wfs.world.size == 1:
return np.complex128(psit_G)
if self.calc.wfs.world.rank != 0:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype,
global_array=True)
self.calc.wfs.world.broadcast(psit_G, 0)
return np.complex128(psit_G)
else:
# support ground state calculation with kpoint and band parallelization
# but domain decomposition must = 1
kpt_rank, u = self.calc.wfs.kd.get_rank_and_index(0, ibzk)
bzkpt_rank = self.kcomm.rank
band_rank, myn = self.calc.wfs.bd.who_has(n)
assert self.calc.wfs.gd.comm.size == 1
world_rank = (kpt_rank * self.calc.wfs.band_comm.size + band_rank)
# in the following, kpt_rank is assigned to world_rank
klist = np.array([world_rank, u, bzkpt_rank, myn])
klist_kcomm = np.zeros((self.kcomm.size, 4), dtype=int)
self.kcomm.all_gather(klist, klist_kcomm)
check_focc_global = np.zeros(self.kcomm.size, dtype=bool)
self.kcomm.all_gather(np.array([check_focc]), check_focc_global)
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
for i in range(self.kcomm.size):
if check_focc_global[i]:
kpt_rank, u, bzkpt_rank, nlocal = klist_kcomm[i]
if kpt_rank == bzkpt_rank:
if rank == kpt_rank:
psit_G = self.calc.wfs.kpt_u[u].psit_nG[nlocal]
else:
if rank == kpt_rank:
world.send(self.calc.wfs.kpt_u[u].psit_nG[nlocal],
bzkpt_rank, 1300+bzkpt_rank)
if rank == bzkpt_rank:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
world.receive(psit_G, kpt_rank, 1300+bzkpt_rank)
self.wScomm.broadcast(psit_G, 0)
return psit_G
def get_wavefunction(self, ibzk, n, check_focc=True, spin=0):
if self.calc.wfs.kpt_comm.size != world.size or world.size == 1:
if check_focc == False:
return
else:
psit_G = self.calc.wfs.get_wave_function_array(n, ibzk, spin)
if self.calc.wfs.world.size == 1:
return np.complex128(psit_G)
if not self.calc.wfs.world.rank == 0:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype,
global_array=True)
self.calc.wfs.world.broadcast(psit_G, 0)
return np.complex128(psit_G)
else:
if self.nkpt % size != 0:
raise ValueError('The number of kpoints should be divided by the number of cpus for no wfs dumping mode ! ')
# support ground state calculation with only kpoint parallelization
kpt_rank, u = self.calc.wfs.kd.get_rank_and_index(0, ibzk)
bzkpt_rank = rank
klist = np.array([kpt_rank, u, bzkpt_rank, n])
klist_kcomm = np.zeros((self.kcomm.size, 4), dtype=int)
self.kcomm.all_gather(klist, klist_kcomm)
check_focc_global = np.zeros(self.kcomm.size, dtype=bool)
self.kcomm.all_gather(np.array([check_focc]), check_focc_global)
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
for i in range(self.kcomm.size):
if check_focc_global[i] == True:
kpt_rank, u, bzkpt_rank, nlocal = klist_kcomm[i]
if kpt_rank == bzkpt_rank:
if rank == kpt_rank:
psit_G = self.calc.wfs.kpt_u[u].psit_nG[nlocal]
else:
if rank == kpt_rank:
world.send(self.calc.wfs.kpt_u[u].psit_nG[nlocal],
bzkpt_rank, 1300+bzkpt_rank)
if rank == bzkpt_rank:
psit_G = self.calc.wfs.gd.empty(dtype=self.calc.wfs.dtype)
world.receive(psit_G, kpt_rank, 1300+bzkpt_rank)
self.wScomm.broadcast(psit_G, 0)
return psit_G
def update_references(self, kpt_u, rank_a):
requests = []
kpt_comm, band_comm, domain_comm = self.kd_old.comm, self.bd.comm, self.gd.comm
for u in range(self.kd_old.nks):
kpt_rank, myu = self.kd_old.who_has(u)
for n in range(self.bd.nbands):
band_rank, myn = self.bd.who_has(n)
for a in range(self.natoms):
domain_rank = rank_a[a]
if kpt_comm.rank == kpt_rank and \
band_comm.rank == band_rank and \
domain_comm.rank == domain_rank:
kpt = kpt_u[myu]
chk = md5_array(kpt.P_ani[a][myn], numeric=True)
if world.rank == 0:
self.chk_una[u, n, a] = chk
else:
requests.append(world.send(np.array([chk], \
dtype=np.int64), 0, 1303+a, block=False))
elif world.rank == 0:
world_rank = rank_a[a] + \
band_rank * domain_comm.size + \
kpt_rank * domain_comm.size * band_comm.size
chk = self.chk_una[u, n,
a:a + 1] #XXX hack to get pointer
requests.append(world.receive(chk, world_rank, \
1303+a, block=False))
world.waitall(requests)
world.broadcast(self.chk_una, 0)
def update_references(self, kpt_u, rank_a):
requests = []
kpt_comm, band_comm, domain_comm = self.kd_old.comm, self.bd.comm, self.gd.comm
for u in range(self.kd_old.nks):
kpt_rank, myu = self.kd_old.who_has(u)
for n in range(self.bd.nbands):
band_rank, myn = self.bd.who_has(n)
for a in range(self.natoms):
domain_rank = rank_a[a]
if kpt_comm.rank == kpt_rank and \
band_comm.rank == band_rank and \
domain_comm.rank == domain_rank:
kpt = kpt_u[myu]
chk = md5_array(kpt.P_ani[a][myn], numeric=True)
if world.rank == 0:
self.chk_una[u,n,a] = chk
else:
requests.append(world.send(np.array([chk], \
dtype=np.int64), 0, 1303+a, block=False))
elif world.rank == 0:
world_rank = rank_a[a] + \
band_rank * domain_comm.size + \
kpt_rank * domain_comm.size * band_comm.size
chk = self.chk_una[u,n,a:a+1] #XXX hack to get pointer
requests.append(world.receive(chk, world_rank, \
1303+a, block=False))
world.waitall(requests)
world.broadcast(self.chk_una, 0)
def collect_A_SS(self, A_sS):
if world.rank == 0:
A_SS = np.zeros((self.nS, self.nS), dtype=complex)
A_SS[:len(A_sS)] = A_sS
Ntot = len(A_sS)
for rank in range(1, world.size):
nkr, nk, ns = self.parallelisation_sizes(rank)
buf = np.empty((ns, self.nS), dtype=complex)
world.receive(buf, rank, tag=123)
A_SS[Ntot:Ntot + ns] = buf
Ntot += ns
else:
world.send(A_sS, 0, tag=123)
world.barrier()
if world.rank == 0:
return A_SS
def distribute_A_SS(self, A_SS, transpose=False):
if world.rank == 0:
for rank in range(0, world.size):
nkr, nk, ns = self.parallelisation_sizes(rank)
if rank == 0:
A_sS = A_SS[0:ns]
Ntot = ns
else:
world.send(A_SS[Ntot:Ntot + ns], rank, tag=123)
Ntot += ns
else:
nkr, nk, ns = self.parallelisation_sizes()
A_sS = np.empty((ns, self.nS), dtype=complex)
world.receive(A_sS, 0, tag=123)
world.barrier()
if transpose:
A_sS = A_sS.T
return A_sS
cell.shape = (3, 3)
positions.shape = (natoms, 3)
atomic_symbols = ''.join(
[ase.chemical_symbols[int(i)] for i in atomic_numbers])
atoms = ase.Atoms(atomic_symbols,
positions=positions,
cell=cell,
pbc=pbc)
calc = create_gpaw(my_comm)
atoms.set_calculator(calc)
else:
atoms.set_positions(positions)
calculation_failed = numpy.array((0, ), 'i')
try:
f1 = atoms.get_forces()
e1 = atoms.get_potential_energy()
e1 = numpy.array([
e1,
])
except gpaw.KohnShamConvergenceError:
calculation_failed = numpy.array(1, 'i')
if my_comm.rank == 0:
world.send(calculation_failed, my_client_rank, tag=0)
if not calculation_failed:
world.send(e1, my_client_rank, tag=0)
world.send(f1, my_client_rank, tag=0)
if first_time:
atomic_symbols = ''.join([ ase.chemical_symbols[int(i)] for i in atomic_numbers])
atoms = ase.Atoms(atomic_symbols, positions=positions, cell=cell, pbc=pbc)
calc = create_gpaw(my_comm)
atoms.set_calculator(calc)
first_time = False
else:
atoms.set_positions(positions)
logfile = os.path.join(logdir, "gpaw_%i.txt"%nforce_calls)
calc.set(txt=logfile)
calculation_failed = numpy.array((0,),'i')
try:
f1 = atoms.get_forces()
e1 = atoms.get_potential_energy()
e1 = numpy.array([e1,])
except gpaw.KohnShamConvergenceError:
calculation_failed = numpy.array(1,'i')
t1 = time.time()
if my_comm.rank == 0:
performance_log = os.path.join(logdir, "performance.txt")
fperformance = open(performance_log, "a+")
fperformance.write("%i %.3f\n" % (nforce_calls, (t1-t0)))
fperformance.close()
world.send(calculation_failed, my_client_rank, tag=0)
if not calculation_failed:
world.send(e1, my_client_rank, tag=0)
world.send(f1, my_client_rank, tag=0)
def get_phi_qaGp(self):
N1_max = 0
N2_max = 0
natoms = len(self.calc.wfs.setups)
for id in range(natoms):
N1 = self.npw
N2 = self.calc.wfs.setups[id].ni**2
if N1 > N1_max:
N1_max = N1
if N2 > N2_max:
N2_max = N2
nbzq = self.kd.nbzkpts
nbzq, nq_local, q_start, q_end = parallel_partition(
nbzq, world.rank, world.size, reshape=False)
phimax_qaGp = np.zeros((nq_local, natoms, N1_max, N2_max), dtype=complex)
#phimax_qaGp = np.zeros((nbzq, natoms, N1_max, N2_max), dtype=complex)
t0 = time()
for iq in range(nq_local):
q_c = self.bzq_qc[iq + q_start]
tmp_aGp = self.get_phi_aGp(q_c, parallel=False)
for id in range(natoms):
N1, N2 = tmp_aGp[id].shape
phimax_qaGp[iq, id, :N1, :N2] = tmp_aGp[id]
self.timing(iq*world.size, t0, nq_local, 'iq')
world.barrier()
# Write to disk
filename = 'phi_qaGp'
if world.rank == 0:
w = Writer(filename)
w.dimension('nbzq', nbzq)
w.dimension('natoms', natoms)
w.dimension('nG', N1_max)
w.dimension('nii', N2_max)
w.add('phi_qaGp', ('nbzq', 'natoms', 'nG', 'nii',), dtype=complex)
for q in range(nbzq):
residual = nbzq % size
N_local = nbzq // size
if q < residual * (N_local + 1):
qrank = q // (N_local + 1)
else:
qrank = (q - residual * (N_local + 1)) // N_local + residual
if qrank == 0:
if world.rank == 0:
phi_aGp = phimax_qaGp[q - q_start]
else:
if world.rank == qrank:
phi_aGp = phimax_qaGp[q - q_start]
world.send(phi_aGp, 0, q)
elif world.rank == 0:
world.receive(phi_aGp, qrank, q)
if world.rank == 0:
w.fill(phi_aGp)
world.barrier()
if world.rank == 0:
w.close()
return
def get_phi_qaGp(self):
N1_max = 0
N2_max = 0
natoms = len(self.calc.wfs.setups)
for id in range(natoms):
N1 = self.npw
N2 = self.calc.wfs.setups[id].ni**2
if N1 > N1_max:
N1_max = N1
if N2 > N2_max:
N2_max = N2
nbzq = self.kd.nbzkpts
nbzq, nq_local, q_start, q_end = parallel_partition(nbzq,
world.rank,
world.size,
reshape=False)
phimax_qaGp = np.zeros((nq_local, natoms, N1_max, N2_max),
dtype=complex)
#phimax_qaGp = np.zeros((nbzq, natoms, N1_max, N2_max), dtype=complex)
t0 = time()
for iq in range(nq_local):
q_c = self.bzq_qc[iq + q_start]
tmp_aGp = self.get_phi_aGp(q_c, parallel=False)
for id in range(natoms):
N1, N2 = tmp_aGp[id].shape
phimax_qaGp[iq, id, :N1, :N2] = tmp_aGp[id]
self.timing(iq * world.size, t0, nq_local, 'iq')
world.barrier()
# Write to disk
filename = 'phi_qaGp'
if world.rank == 0:
w = Writer(filename)
w.dimension('nbzq', nbzq)
w.dimension('natoms', natoms)
w.dimension('nG', N1_max)
w.dimension('nii', N2_max)
w.add('phi_qaGp', (
'nbzq',
'natoms',
'nG',
'nii',
), dtype=complex)
for q in range(nbzq):
residual = nbzq % size
N_local = nbzq // size
if q < residual * (N_local + 1):
qrank = q // (N_local + 1)
else:
qrank = (q - residual * (N_local + 1)) // N_local + residual
if qrank == 0:
if world.rank == 0:
phi_aGp = phimax_qaGp[q - q_start]
else:
if world.rank == qrank:
phi_aGp = phimax_qaGp[q - q_start]
world.send(phi_aGp, 0, q)
elif world.rank == 0:
world.receive(phi_aGp, qrank, q)
if world.rank == 0:
w.fill(phi_aGp)
if world.rank == 0:
w.close()
world.barrier()
