def load_mol(chkfile):
''' Load the mol from the chkfile.
See pyscf.lib.chkfile
'''
if mpi_helper.rank == 0:
mol = chkutil.load_mol(chkfile)
dumps = mol.dumps()
else:
dumps = None
mpi_helper.barrier()
dumps = mpi_helper.bcast_dict(dumps)
mol = gto.loads(dumps)
return mol
def load_mol(chkfile):
'''Load Mole object from chkfile.
The save_mol/load_mol operation can be used a serialization method for Mole object.
Args:
chkfile : str
Name of chkfile.
Returns:
A (initialized/built) Mole object
Examples:
>>> from pyscf import gto, lib
>>> mol = gto.M(atom='He 0 0 0')
>>> lib.chkfile.save_mol(mol, 'He.chk')
>>> lib.chkfile.load_mol('He.chk')
<pyscf.gto.mole.Mole object at 0x7fdcd94d7f50>
'''
from numpy import array
from pyscf import gto
try:
with h5py.File(chkfile, 'r') as fh5:
mol = gto.loads(fh5['mol'].value)
except:
# Compatibility to the old serialization format
# TODO: remove it in future release
with h5py.File(chkfile, 'r') as fh5:
mol = gto.Mole()
mol.output = '/dev/null'
moldic = eval(fh5['mol'].value)
for key in ('mass', 'grids', 'light_speed'):
if key in moldic:
del (moldic[key])
mol.build(False, False, **moldic)
return mol
def load_mol(chkfile):
'''Load Mole object from chkfile.
The save_mol/load_mol operation can be used a serialization method for Mole object.
Args:
chkfile : str
Name of chkfile.
Returns:
A (initialized/built) Mole object
Examples:
>>> from pyscf import gto, lib
>>> mol = gto.M(atom='He 0 0 0')
>>> lib.chkfile.save_mol(mol, 'He.chk')
>>> lib.chkfile.load_mol('He.chk')
<pyscf.gto.mole.Mole object at 0x7fdcd94d7f50>
'''
from numpy import array
from pyscf import gto
try:
with h5py.File(chkfile, 'r') as fh5:
mol = gto.loads(fh5['mol'].value)
except:
# Compatibility to the old serialization format
# TODO: remove it in future release
with h5py.File(chkfile, 'r') as fh5:
mol = gto.Mole()
mol.output = '/dev/null'
moldic = eval(fh5['mol'].value)
for key in ('mass', 'grids', 'light_speed'):
if key in moldic:
del(moldic[key])
mol.build(False, False, **moldic)
return mol
def _write_integral_file(mc_chkfile, nevpt_scratch, comm):
mpi_size = comm.Get_size()
rank = comm.Get_rank()
if rank == 0:
fh5 = h5py.File(mc_chkfile, 'r')
def load(key):
if key in fh5:
return comm.bcast(fh5[key][()])
else:
return comm.bcast([])
else:
def load(key):
return comm.bcast(None)
mol = gto.loads(load('mol'))
ncore = load('mc/ncore')
ncas = load('mc/ncas')
nvirt = load('mc/nvirt')
orbe = load('mc/orbe')
orbsym = list(load('mc/orbsym'))
nelecas = load('mc/nelecas')
h1e_Si = load('h1e_Si')
h1e_Sr = load('h1e_Sr')
h1e = load('h1e')
e_core = load('e_core')
h2e = load('h2e')
h2e_Si = load('h2e_Si')
h2e_Sr = load('h2e_Sr')
if rank == 0:
fh5.close()
if mol.symmetry and len(orbsym) > 0:
orbsym = orbsym[ncore:ncore + ncas] + orbsym[:ncore] + orbsym[ncore +
ncas:]
orbsym = dmrg_sym.convert_orbsym(mol.groupname, orbsym)
else:
orbsym = [1] * (ncore + ncas + nvirt)
partial_size = int(math.floor((ncore + nvirt) / float(mpi_size)))
num_of_orb_begin = min(rank * partial_size, ncore + nvirt)
num_of_orb_end = min((rank + 1) * partial_size, ncore + nvirt)
#Adjust the distrubution the non-active orbitals to make sure one processor has at most one more orbital than average.
if rank < (ncore + nvirt - partial_size * mpi_size):
num_of_orb_begin += rank
num_of_orb_end += rank + 1
else:
num_of_orb_begin += ncore + nvirt - partial_size * mpi_size
num_of_orb_end += ncore + nvirt - partial_size * mpi_size
if num_of_orb_begin < ncore:
if num_of_orb_end < ncore:
h1e_Si = h1e_Si[:, num_of_orb_begin:num_of_orb_end]
h2e_Si = h2e_Si[:, num_of_orb_begin:num_of_orb_end, :, :]
h1e_Sr = []
h2e_Sr = []
# elif num_of_orb_end > ncore + nvirt :
# h1e_Si = h1e_Si[:,num_of_orb_begin:]
# h2e_Si = h2e_Si[:,num_of_orb_begin:,:,:]
# #h2e_Sr = []
# orbsym = orbsym[:ncas] + orbsym[num_of_orb_begin:]
# norb = ncas + ncore + nvirt - num_of_orb_begin
else:
h1e_Si = h1e_Si[:, num_of_orb_begin:]
h2e_Si = h2e_Si[:, num_of_orb_begin:, :, :]
h1e_Sr = h1e_Sr[:num_of_orb_end - ncore, :]
h2e_Sr = h2e_Sr[:num_of_orb_end - ncore, :, :, :]
elif num_of_orb_begin < ncore + nvirt:
if num_of_orb_end <= ncore + nvirt:
h1e_Si = []
h2e_Si = []
h1e_Sr = h1e_Sr[num_of_orb_begin - ncore:num_of_orb_end - ncore, :]
h2e_Sr = h2e_Sr[num_of_orb_begin - ncore:num_of_orb_end -
ncore, :, :, :]
# else :
# h1e_Si = []
# h2e_Si = []
# h1e_Sr = h1e_Sr[num_of_orb_begin - ncore:,:]
# h2e_Sr = h2e_Sr[num_of_orb_begin - ncore:,:,:,:]
# orbsym = orbsym[:ncas] + orbsym[ncas+num_of_orb_begin: ]
# norb = ncas + ncore + nvirt - num_of_orb_begin
else:
raise RuntimeError(
'No job for this processor. It may block MPI.COMM_WORLD.barrier')
norb = ncas + num_of_orb_end - num_of_orb_begin
orbsym = orbsym[:ncas] + orbsym[ncas + num_of_orb_begin:ncas +
num_of_orb_end]
if num_of_orb_begin >= ncore:
partial_core = 0
partial_virt = num_of_orb_end - num_of_orb_begin
else:
if num_of_orb_end >= ncore:
partial_core = ncore - num_of_orb_begin
partial_virt = num_of_orb_end - ncore
else:
partial_core = num_of_orb_end - num_of_orb_begin
partial_virt = 0
tol = float(1e-15)
f = open(os.path.join(nevpt_scratch, 'FCIDUMP'), 'w')
nelec = nelecas[0] + nelecas[1]
fcidump.write_head(f,
norb,
nelec,
ms=abs(nelecas[0] - nelecas[1]),
orbsym=orbsym)
#h2e in active space
writeh2e_sym(h2e, f, tol)
#h1e in active space
writeh1e_sym(h1e, f, tol)
orbe = list(orbe[:ncore]) + list(orbe[ncore + ncas:])
orbe = orbe[num_of_orb_begin:num_of_orb_end]
for i in range(len(orbe)):
f.write('% .16f %4d %4d %4d %4d\n' %
(orbe[i], i + 1 + ncas, i + 1 + ncas, 0, 0))
f.write('%.16f %4d %4d %4d %4d\n' % (e_core, 0, 0, 0, 0))
if (len(h2e_Sr)):
writeh2e(h2e_Sr, f, tol, shift0=ncas + partial_core + 1)
f.write('% 4d %4d %4d %4d %4d\n' % (0, 0, 0, 0, 0))
if (len(h2e_Si)):
writeh2e(h2e_Si, f, tol, shift1=ncas + 1)
f.write('% 4d %4d %4d %4d %4d\n' % (0, 0, 0, 0, 0))
if (len(h1e_Sr)):
writeh1e(h1e_Sr, f, tol, shift0=ncas + partial_core + 1)
f.write('% 4d %4d %4d %4d %4d\n' % (0, 0, 0, 0, 0))
if (len(h1e_Si)):
writeh1e(h1e_Si, f, tol, shift1=ncas + 1)
f.write('% 4d %4d %4d %4d %4d\n' % (0, 0, 0, 0, 0))
f.write('% 4d %4d %4d %4d %4d\n' % (0, 0, 0, 0, 0))
f.close()
return ncas, partial_core, partial_virt
import pickle
from pyscf import gto
'''
Serialize Mole object
Mole.pack function transform the Mole object to a Python dict. It can be
serialized using the standard serialization module in python, eg pickle.
There is a hacky way to serialize the Mole object for broadcasting or saving.
Use format or str function to convert the Mole-python-dict to a string.
Later, use the built-in eval function and Mole.unpack function to restore the
Mole object.
'''
mol = gto.M(
atom='''
O 0 0. 0
H1 0 -2.757 2.587
H2 0 2.757 2.587''',
basis='ccpvdz',
)
# In Python pickled format
ar = pickle.dumps(format(mol.pack()))
mol1 = gto.unpack(eval(pickle.loads(ar)))
# In JSON format
ar = mol.dumps()
mol1 = gto.loads(ar)
from pyscf import gto
'''
Serialize Mole object
Mole.pack function transform the Mole object to a Python dict. It can be
serialized using the standard serialization module in python, eg pickle.
There is a hacky way to serialize the Mole object for broadcasting or saving.
Use format or str function to convert the Mole-python-dict to a string.
Later, use the built-in eval function and Mole.unpack function to restore the
Mole object.
'''
mol = gto.M(
atom = '''
O 0 0. 0
H1 0 -2.757 2.587
H2 0 2.757 2.587''',
basis = 'ccpvdz',
)
# In Python pickled format
ar = pickle.dumps(format(mol.pack()))
mol1 = gto.unpack(eval(pickle.loads(ar)))
# In JSON format
ar = mol.dumps()
mol1 = gto.loads(ar)
def _write_integral_file(mc_chkfile, nevpt_scratch, comm):
mpi_size = comm.Get_size()
rank = comm.Get_rank()
if rank == 0:
fh5 = h5py.File(mc_chkfile, 'r')
def load(key):
if key in fh5:
return comm.bcast(fh5[key].value)
else:
return comm.bcast([])
else:
def load(key):
return comm.bcast(None)
mol = gto.loads(load('mol'))
ncore = load('mc/ncore')
ncas = load('mc/ncas')
nvirt = load('mc/nvirt')
orbe = load('mc/orbe')
orbsym = list(load('mc/orbsym'))
nelecas = load('mc/nelecas')
h1e_Si = load('h1e_Si')
h1e_Sr = load('h1e_Sr')
h1e = load('h1e')
e_core = load('e_core')
h2e = load('h2e')
h2e_Si = load('h2e_Si')
h2e_Sr = load('h2e_Sr')
if rank == 0:
fh5.close()
if mol.symmetry and len(orbsym) > 0:
orbsym = orbsym[ncore:ncore+ncas] + orbsym[:ncore] + orbsym[ncore+ncas:]
orbsym = dmrg_sym.convert_orbsym(mol.groupname, orbsym)
else:
orbsym = [1] * (ncore+ncas+nvirt)
partial_size = int(math.floor((ncore+nvirt)/float(mpi_size)))
num_of_orb_begin = min(rank*partial_size, ncore+nvirt)
num_of_orb_end = min((rank+1)*partial_size, ncore+nvirt)
#Adjust the distrubution the non-active orbitals to make sure one processor has at most one more orbital than average.
if rank < (ncore+nvirt - partial_size*mpi_size):
num_of_orb_begin += rank
num_of_orb_end += rank + 1
else :
num_of_orb_begin += ncore+nvirt - partial_size*mpi_size
num_of_orb_end += ncore+nvirt - partial_size*mpi_size
if num_of_orb_begin < ncore:
if num_of_orb_end < ncore:
h1e_Si = h1e_Si[:,num_of_orb_begin:num_of_orb_end]
h2e_Si = h2e_Si[:,num_of_orb_begin:num_of_orb_end,:,:]
h1e_Sr = []
h2e_Sr = []
# elif num_of_orb_end > ncore + nvirt :
# h1e_Si = h1e_Si[:,num_of_orb_begin:]
# h2e_Si = h2e_Si[:,num_of_orb_begin:,:,:]
# #h2e_Sr = []
# orbsym = orbsym[:ncas] + orbsym[num_of_orb_begin:]
# norb = ncas + ncore + nvirt - num_of_orb_begin
else :
h1e_Si = h1e_Si[:,num_of_orb_begin:]
h2e_Si = h2e_Si[:,num_of_orb_begin:,:,:]
h1e_Sr = h1e_Sr[:num_of_orb_end - ncore,:]
h2e_Sr = h2e_Sr[:num_of_orb_end - ncore,:,:,:]
elif num_of_orb_begin < ncore + nvirt :
if num_of_orb_end <= ncore + nvirt:
h1e_Si = []
h2e_Si = []
h1e_Sr = h1e_Sr[num_of_orb_begin - ncore:num_of_orb_end - ncore,:]
h2e_Sr = h2e_Sr[num_of_orb_begin - ncore:num_of_orb_end - ncore,:,:,:]
# else :
# h1e_Si = []
# h2e_Si = []
# h1e_Sr = h1e_Sr[num_of_orb_begin - ncore:,:]
# h2e_Sr = h2e_Sr[num_of_orb_begin - ncore:,:,:,:]
# orbsym = orbsym[:ncas] + orbsym[ncas+num_of_orb_begin: ]
# norb = ncas + ncore + nvirt - num_of_orb_begin
else :
raise RuntimeError('No job for this processor. It may block MPI.COMM_WORLD.barrier')
norb = ncas + num_of_orb_end - num_of_orb_begin
orbsym = orbsym[:ncas] + orbsym[ncas + num_of_orb_begin:ncas + num_of_orb_end]
if num_of_orb_begin >= ncore:
partial_core = 0
partial_virt = num_of_orb_end - num_of_orb_begin
else:
if num_of_orb_end >= ncore:
partial_core = ncore -num_of_orb_begin
partial_virt = num_of_orb_end - ncore
else:
partial_core = num_of_orb_end -num_of_orb_begin
partial_virt = 0
tol = float(1e-15)
f = open(os.path.join(nevpt_scratch, 'FCIDUMP'), 'w')
nelec = nelecas[0] + nelecas[1]
fcidump.write_head(f,norb, nelec, ms=abs(nelecas[0]-nelecas[1]), orbsym=orbsym)
#h2e in active space
writeh2e_sym(h2e,f,tol)
#h1e in active space
writeh1e_sym(h1e,f,tol)
orbe =list(orbe[:ncore]) + list(orbe[ncore+ncas:])
orbe = orbe[num_of_orb_begin:num_of_orb_end]
for i in range(len(orbe)):
f.write('% .16f %4d %4d %4d %4d\n'%(orbe[i],i+1+ncas,i+1+ncas,0,0))
f.write('%.16f %4d %4d %4d %4d\n'%(e_core,0,0,0,0))
if (len(h2e_Sr)):
writeh2e(h2e_Sr,f,tol, shift0 = ncas + partial_core+1)
f.write('% 4d %4d %4d %4d %4d\n'%(0,0,0,0,0))
if (len(h2e_Si)):
writeh2e(h2e_Si,f,tol, shift1 = ncas+1)
f.write('% 4d %4d %4d %4d %4d\n'%(0,0,0,0,0))
if (len(h1e_Sr)):
writeh1e(h1e_Sr,f,tol, shift0 = ncas + partial_core+1)
f.write('% 4d %4d %4d %4d %4d\n'%(0,0,0,0,0))
if (len(h1e_Si)):
writeh1e(h1e_Si,f,tol, shift1 = ncas+1)
f.write('% 4d %4d %4d %4d %4d\n'%(0,0,0,0,0))
f.write('% 4d %4d %4d %4d %4d\n'%(0,0,0,0,0))
f.close()
return ncas, partial_core, partial_virt