def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec // 2 + nelec % 2
nelecb = nelec - neleca
else:
neleca, nelecb = nelec
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
orbsym = numpy.asarray(
dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym))
pair_irrep = (orbsym.reshape(-1, 1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1, 1) != pair_irrep.ravel()
eri_cas = pyscf.ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
else:
orbsym = []
eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
pyscf.tools.fcidump.from_integrals(integralFile,
h1eff,
eri_cas,
ncas,
neleca + nelecb,
ecore,
ms=abs(neleca - nelecb),
orbsym=orbsym)
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec//2 + nelec%2
nelecb = nelec - neleca
else :
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
# First removing the symmetry forbidden integrals. This has been done using
# the pyscf internal irrep-IDs (stored in DMRGCI.orbsym)
orbsym = numpy.asarray(DMRGCI.orbsym) % 10
pair_irrep = (orbsym.reshape(-1,1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1,1) != pair_irrep.ravel()
eri_cas = ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = ao2mo.restore(8, eri_cas, ncas)
#orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym))
#eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
# Then convert the pyscf internal irrep-ID to molpro irrep-ID
orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, orbsym))
else:
orbsym = []
eri_cas = ao2mo.restore(8, eri_cas, ncas)
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
tools.fcidump.from_integrals(integralFile, h1eff, eri_cas, ncas,
neleca+nelecb, ecore, ms=abs(neleca-nelecb),
orbsym=orbsym)
return integralFile
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec//2 + nelec%2
nelecb = nelec - neleca
else :
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
# First removing the symmetry forbidden integrals. This has been done using
# the pyscf internal irrep-IDs (stored in DMRGCI.orbsym)
orbsym = numpy.asarray(DMRGCI.orbsym) % 10
pair_irrep = (orbsym.reshape(-1,1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1,1) != pair_irrep.ravel()
eri_cas = ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = ao2mo.restore(8, eri_cas, ncas)
#orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym))
#eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
# Then convert the pyscf internal irrep-ID to molpro irrep-ID
orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, orbsym))
else:
orbsym = []
eri_cas = ao2mo.restore(8, eri_cas, ncas)
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
tools.fcidump.from_integrals(integralFile, h1eff, eri_cas, ncas,
neleca+nelecb, ecore, ms=abs(neleca-nelecb),
orbsym=orbsym)
return integralFile
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec // 2 + nelec % 2
nelecb = nelec - neleca
else:
neleca, nelecb = nelec
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
orbsym = dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym)
else:
orbsym = []
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
pyscf.tools.fcidump.from_integrals(integralFile,
h1eff,
eri_cas,
ncas,
neleca + nelecb,
ecore,
ms=abs(neleca - nelecb),
orbsym=orbsym)
def writeIntegralFile(SHCI, h1eff, eri_cas, norb, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec // 2 + nelec % 2
nelecb = nelec - neleca
else:
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(SHCI.runtimeDir, SHCI.integralFile)
if not os.path.exists(SHCI.scratchDirectory):
os.makedirs(SHCI.scratchDirectory)
from pyscf import symm
from pyscf.dmrgscf import dmrg_sym
if (SHCI.groupname == 'Dooh'
or SHCI.groupname == 'Cooh') and SHCI.useExtraSymm:
eri_cas = pyscf.ao2mo.restore(1, eri_cas, norb)
coeffs, nRows, rowIndex, rowCoeffs, orbsym = D2htoDinfh(
SHCI, norb, nelec)
newintt = numpy.tensordot(coeffs.conj(), h1eff, axes=([1], [0]))
newint1 = numpy.tensordot(newintt, coeffs, axes=([1], [1]))
newint1r = numpy.zeros(shape=(norb, norb), order='C')
for i in range(norb):
for j in range(norb):
newint1r[i, j] = newint1[i, j].real
eri_cas = pyscf.ao2mo.restore(1, eri_cas, norb)
int2 = 1.0 * eri_cas
eri_cas = 0.0 * eri_cas
transformDinfh(norb, numpy.ascontiguousarray(nRows, numpy.int32),
numpy.ascontiguousarray(rowIndex, numpy.int32),
numpy.ascontiguousarray(rowCoeffs, numpy.float64),
numpy.ascontiguousarray(int2, numpy.float64),
numpy.ascontiguousarray(eri_cas, numpy.float64))
writeIntNoSymm(norb, numpy.ascontiguousarray(newint1r, numpy.float64),
numpy.ascontiguousarray(eri_cas, numpy.float64), ecore,
neleca + nelecb, numpy.asarray(orbsym,
dtype=numpy.int32))
else:
if SHCI.groupname is not None and SHCI.orbsym is not []:
orbsym = dmrg_sym.convert_orbsym(SHCI.groupname, SHCI.orbsym)
else:
eri_cas = pyscf.ao2mo.restore(8, eri_cas, norb)
orbsym = [1] * norb
eri_cas = pyscf.ao2mo.restore(8, eri_cas, norb)
# Writes the FCIDUMP file using functions in SHCI_tools.cpp.
fcidumpFromIntegral(integralFile, h1eff, eri_cas, norb,
neleca + nelecb, ecore,
numpy.asarray(orbsym, dtype=numpy.int32),
abs(neleca - nelecb))
print "ECORE: ", ecore
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec // 2 + nelec % 2
nelecb = nelec - neleca
else:
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym is not []:
# First removing the symmetry forbidden integrals. This has been done using
# the pyscf internal irrep-IDs (stored in DMRGCI.orbsym)
orbsym = numpy.asarray(DMRGCI.orbsym) % 10
pair_irrep = (orbsym.reshape(-1, 1) ^ orbsym)[numpy.tril_indices(ncas)]
sym_forbid = pair_irrep.reshape(-1, 1) != pair_irrep.ravel()
eri_cas = ao2mo.restore(4, eri_cas, ncas)
eri_cas[sym_forbid] = 0
eri_cas = ao2mo.restore(8, eri_cas, ncas)
#orbsym = numpy.asarray(dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym))
#eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
# Then convert the pyscf internal irrep-ID to molpro irrep-ID
orbsym = numpy.asarray(
dmrg_sym.convert_orbsym(DMRGCI.groupname, orbsym))
else:
orbsym = []
eri_cas = ao2mo.restore(8, eri_cas, ncas)
# The following checks for scratch on node0 only but it can be missing on node1 etc.
# The previous WF could have been copied to node0.
# Comment out the if for now.
# if not os.path.exists(DMRGCI.scratchDirectory):
# os.makedirs(DMRGCI.scratchDirectory)
cmd = ' '.join((DMRGCI.mpiprefix, "mkdir -p", DMRGCI.scratchDirectory))
check_call(cmd, shell=True)
if not os.path.exists(DMRGCI.runtimeDir):
os.makedirs(DMRGCI.runtimeDir)
tools.fcidump.from_integrals(integralFile,
h1eff,
eri_cas,
ncas,
neleca + nelecb,
ecore,
ms=abs(neleca - nelecb),
orbsym=orbsym)
return integralFile
def writeIntegralFile(DMRGCI, h1eff, eri_cas, ncas, nelec):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec//2 + nelec%2
nelecb = nelec - neleca
else :
neleca, nelecb = nelec
integralFile = os.path.join(DMRGCI.runtimeDir, DMRGCI.integralFile)
if DMRGCI.groupname is not None and DMRGCI.orbsym:
orbsym = dmrg_sym.convert_orbsym(DMRGCI.groupname, DMRGCI.orbsym)
else:
orbsym = []
if not os.path.exists(DMRGCI.scratchDirectory):
os.makedirs(DMRGCI.scratchDirectory)
eri_cas = pyscf.ao2mo.restore(8, eri_cas, ncas)
pyscf.tools.fcidump.from_integrals(integralFile, h1eff, eri_cas, ncas,
neleca+nelecb, ms=abs(neleca-nelecb),
orbsym=orbsym)
def nevpt_integral_mpi(mc_chkfile,blockfile,dmrginp,dmrgout,scratch):
from mpi4py import MPI
comm = MPI.COMM_WORLD
mpi_size = MPI.COMM_WORLD.Get_size()
rank = comm.Get_rank()
if rank == 0:
mol = chkfile.load_mol(mc_chkfile)
fh5 = h5py.File(mc_chkfile,'r')
mo_coeff = fh5['mc/mo'].value
ncore = fh5['mc/ncore'].value
ncas = fh5['mc/ncas'].value
nvirt = fh5['mc/nvirt'].value
orbe = fh5['mc/orbe'].value
root = fh5['mc/root'].value
orbsym = list(fh5['mc/orbsym'].value)
nelecas = fh5['mc/nelecas'].value
h1e_Si = fh5['h1e_Si'].value
h1e_Sr = fh5['h1e_Sr'].value
h1e = fh5['h1e'].value
e_core = fh5['e_core'].value
h2e = fh5['h2e'].value
h2e_Si = fh5['h2e_Si'].value
h2e_Sr = fh5['h2e_Sr'].value
fh5.close()
headnode = MPI.Get_processor_name()
else:
mol = None
mo_coeff = None
ncore = None
ncas = None
nvirt = None
orbe = None
root = None
orbsym = None
nelecas = None
h1e_Si = None
h1e_Sr = None
h1e = None
e_core = None
h2e = None
h2e_Si = None
h2e_Sr = None
headnode = None
comm.barrier()
mol = comm.bcast(mol,root=0)
mo_coeff = comm.bcast(mo_coeff,root=0)
ncas = comm.bcast(ncas,root=0)
ncore = comm.bcast(ncore,root=0)
nvirt = comm.bcast(nvirt,root=0)
root = comm.bcast(root,root=0)
orbsym = comm.bcast(orbsym,root=0)
nelecas = comm.bcast(nelecas,root=0)
orbe = comm.bcast(orbe,root=0)
h1e_Si = comm.bcast(h1e_Si,root=0)
h1e_Sr = comm.bcast(h1e_Sr,root=0)
h1e = comm.bcast(h1e,root=0)
h2e = comm.bcast(h2e,root=0)
h2e_Si = comm.bcast(h2e_Si,root=0)
h2e_Sr = comm.bcast(h2e_Sr,root=0)
headnode = comm.bcast(headnode,root=0)
e_core = comm.bcast(e_core,root=0)
mo_core = mo_coeff[:,:ncore]
mo_cas = mo_coeff[:,ncore:ncore+ncas]
mo_virt = mo_coeff[:,ncore+ncas:]
nelec = nelecas[0] + nelecas[1]
if mol.symmetry and len(orbsym):
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
newscratch = os.path.join(os.path.abspath(scratch), str(rank))
if not os.path.exists('%s'%newscratch):
os.makedirs('%s'%newscratch)
os.makedirs('%s/node0'%newscratch)
nevptinp = os.path.join(newscratch, os.path.basename(dmrginp))
subprocess.check_call('cp %s %s'%(dmrginp,nevptinp),shell=True)
f = open(nevptinp, 'a')
f.write('restart_mps_nevpt %d %d %d \n'%(ncas,partial_core, partial_virt))
f.close()
tol = float(1e-15)
#from subprocess import Popen
#from subprocess import PIPE
#print 'scratch', scratch
##p1 = Popen(['cp %s/* %d/'%(scratch, rank)],shell=True,stderr=PIPE)
#p1 = Popen(['cp','%s/*'%scratch, '%d/'%rank],shell=True,stderr=PIPE)
#print p1.communicate()
#p2 = Popen(['cp %s/node0/* %d'%(scratch, rank)],shell=True,stderr=PIPE)
##p2 = Popen(['cp','%s/node0/*'%scratch, '%d/'%rank],shell=True,stderr=PIPE)
#print p2.communicate()
#call('cp %s/* %d/'%(scratch,rank),shell = True,stderr=os.devnull)
#call('cp %s/node0/* %d/'%(scratch,rank),shell = True,stderr=os.devnull)
# f1 =open(os.devnull,'w')
# if MPI.Get_processor_name() == headnode:
# subprocess.call('cp %s/* %s/'%(scratch,newscratch),stderr=f1,shell = True)
# subprocess.call('cp %s/node0/* %s/node0'%(scratch,newscratch),shell = True)
# else:
# subprocess.call('scp %s:%s/* %s/'%(headnode,scratch,newscratch),stderr=f1,shell = True)
# subprocess.call('scp %s:%s/node0/* %s/node0'%(headnode,scratch,newscratch),shell = True)
# f1.close()
#TODO
#Use mpi rather than scp to copy the file.
#To make the code robust.
if rank==0:
filenames = []
for fn in os.listdir('%s/node0'%scratch):
if fn== 'dmrg.e' or fn== 'statefile.0.tmp' or fn== 'RestartReorder.dat' or fn.startswith('wave') or fn.startswith('Rotation'):
filenames.append(fn)
else:
filenames = None
filenames = comm.bcast(filenames, root=0)
for i in range(len(filenames)):
if rank == 0:
with open('%s/node0/%s'%(scratch,filenames[i]),'rb') as f:
data = f.read()
else:
data = None
data = comm.bcast(data, root=0)
if data==None:
print 'empty file'
with open('%s/node0/%s'%(newscratch,filenames[i]),'wb') as f:
f.write(data)
f = open('%s/FCIDUMP'%newscratch,'w')
pyscf.tools.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()
current_path = os.getcwd()
os.chdir('%s'%newscratch)
env = os.environ
envnew = {}
for k in env:
if 'MPI' not in k and 'SLURM' not in k:
# remove PBS and SLURM environments to prevent Block running in MPI mode
envnew[k] = os.environ[k]
p = subprocess.Popen(['%s %s > %s'%(blockfile,nevptinp,dmrgout)], env=envnew, shell=True)
p.wait()
f = open('node0/Va_%d'%root,'r')
Vr_energy = float(f.readline())
Vr_norm = float(f.readline())
f.close()
f = open('node0/Vi_%d'%root,'r')
Vi_energy = float(f.readline())
Vi_norm = float(f.readline())
f.close()
comm.barrier()
#Vr_total = 0.0
#Vi_total = 0.0
Vi_total_e = comm.gather(Vi_energy,root=0)
Vi_total_norm = comm.gather(Vi_norm,root=0)
Vr_total_e = comm.gather(Vr_energy,root=0)
Vr_total_norm = comm.gather(Vr_norm,root=0)
#comm.Reduce(Vi_energy,Vi_total,op=MPI.SUM, root=0)
os.chdir('%s'%current_path)
if rank == 0:
fh5 = h5py.File('Perturbation_%d'%root,'w')
fh5['Vi/energy'] = sum(Vi_total_e)
fh5['Vi/norm'] = sum(Vi_total_norm)
fh5['Vr/energy'] = sum(Vr_total_e)
fh5['Vr/norm'] = sum(Vr_total_norm)
fh5.close()
def writeIntegralFile(SHCI, h1eff, eri_cas, norb, nelec, ecore=0):
if isinstance(nelec, (int, numpy.integer)):
neleca = nelec // 2 + nelec % 2
nelecb = nelec - neleca
else:
neleca, nelecb = nelec
# The name of the FCIDUMP file, default is "FCIDUMP".
integralFile = os.path.join(SHCI.runtimeDir, SHCI.integralFile)
from pyscf import symm
from pyscf.dmrgscf import dmrg_sym
if (SHCI.groupname == 'Dooh'
or SHCI.groupname == 'Coov') and SHCI.useExtraSymm:
coeffs, nRows, rowIndex, rowCoeffs, orbsym = D2htoDinfh(
SHCI, norb, nelec)
newintt = numpy.tensordot(coeffs.conj(), h1eff, axes=([1], [0]))
newint1 = numpy.tensordot(newintt, coeffs, axes=([1], [1]))
newint1r = numpy.zeros(shape=(norb, norb), order='C')
for i in range(norb):
for j in range(norb):
newint1r[i, j] = newint1[i, j].real
int2 = pyscf.ao2mo.restore(1, eri_cas, norb)
eri_cas = numpy.zeros_like(int2)
transformDinfh(norb, numpy.ascontiguousarray(nRows, numpy.int32),
numpy.ascontiguousarray(rowIndex, numpy.int32),
numpy.ascontiguousarray(rowCoeffs, numpy.float64),
numpy.ascontiguousarray(int2, numpy.float64),
numpy.ascontiguousarray(eri_cas, numpy.float64))
writeIntNoSymm(norb, numpy.ascontiguousarray(newint1r, numpy.float64),
numpy.ascontiguousarray(eri_cas, numpy.float64), ecore,
neleca + nelecb, numpy.asarray(orbsym,
dtype=numpy.int32))
else:
if SHCI.groupname is not None and SHCI.orbsym is not []:
orbsym = dmrg_sym.convert_orbsym(SHCI.groupname, SHCI.orbsym)
else:
orbsym = [1] * norb
eri_cas = pyscf.ao2mo.restore(8, eri_cas, norb)
# Writes the FCIDUMP file using functions in SHCI_tools.cpp.
integralFile = integralFile.encode(
) # .encode for python3 compatibility
fcidumpFromIntegral(integralFile, h1eff, eri_cas, norb,
neleca + nelecb, ecore,
numpy.asarray(orbsym, dtype=numpy.int32),
abs(neleca - nelecb))
# Fix possible errors in symmetry lables
if SHCI.groupname == 'Dooh' and SHCI.useExtraSymm:
# # these lines call the python program
# if os.path.isfile("FCIDUMP_new"):
# check_call('rm FCIDUMP_new', shell = True)
# check_call('python checkLz_fcidump.py FCIDUMP', shell=True)
# while os.path.isfile("FCIDUMP_new"):
# check_call('mv FCIDUMP_new FCIDUMP', shell = True)
# check_call('python checkLz_fcidump.py FCIDUMP', shell = True)
# these lines call the fortran program
check_call(SHCI.Lz_relabel + ' ' + integralFile + ' ' +
SHCI.pyscf_home,
shell=True)
orbsym = getorbsymfromFCIDUMP(norb)
def writeSHCIConfFile(SHCI, nelec, Restart):
confFile = os.path.join(SHCI.runtimeDir, SHCI.configFile)
f = open(confFile, 'w')
# Reference determinant section
f.write('nocc %i\n' % (nelec[0] + nelec[1]))
if SHCI.__class__.__name__ == 'FakeCISolver':
for i in range(nelec[0]):
f.write('%i ' % (2 * i))
for i in range(nelec[1]):
f.write('%i ' % (2 * i + 1))
else:
if SHCI.initialStates is not None:
for i in range(len(SHCI.initialStates)):
for j in SHCI.initialStates[i]:
f.write('%i ' % (j))
if (i != len(SHCI.initialStates) - 1):
f.write('\n')
elif SHCI.irrep_nelec is None:
for i in range(int(nelec[0])):
f.write('%i ' % (2 * i))
for i in range(int(nelec[1])):
f.write('%i ' % (2 * i + 1))
else:
from pyscf import symm
from pyscf.dmrgscf import dmrg_sym
from pyscf.symm.basis import DOOH_IRREP_ID_TABLE
if SHCI.groupname is not None and SHCI.orbsym is not []:
orbsym = dmrg_sym.convert_orbsym(SHCI.groupname, SHCI.orbsym)
else:
orbsym = [1] * norb
done = []
for k, v in SHCI.irrep_nelec.items():
irrep, nalpha, nbeta = [dmrg_sym.irrep_name2id(SHCI.groupname, k)],\
v[0], v[1]
for i in range(len(orbsym)): #loop over alpha electrons
if (orbsym[i] == irrep[0] and nalpha != 0
and i * 2 not in done):
done.append(i * 2)
f.write('%i ' % (i * 2))
nalpha -= 1
if (orbsym[i] == irrep[0] and nbeta != 0
and i * 2 + 1 not in done):
done.append(i * 2 + 1)
f.write('%i ' % (i * 2 + 1))
nbeta -= 1
if (nalpha != 0):
print("number of irreps %s in active space = %d" %
(k, v[0] - nalpha))
print("number of irreps %s alpha electrons = %d" %
(k, v[0]))
exit(1)
if (nbeta != 0):
print("number of irreps %s in active space = %d" %
(k, v[1] - nbeta))
print("number of irreps %s beta electrons = %d" %
(k, v[1]))
exit(1)
f.write('\nend\n')
f.write('nroots %r\n' % SHCI.nroots)
# Variational Keyword Section
if (not Restart):
schedStr = make_sched(SHCI)
f.write(schedStr)
else:
f.write('schedule\n')
f.write('%d %g\n' % (0, SHCI.sweep_epsilon[-1]))
f.write('end\n')
f.write('davidsonTol %g\n' % SHCI.davidsonTol)
f.write('dE %g\n' % SHCI.dE)
if (SHCI.DoRDM):
f.write('DoRDM\n')
# Perturbative Keyword Section
if (SHCI.stochastic == False):
f.write('deterministic \n')
else:
f.write('nPTiter %d\n' % SHCI.nPTiter)
f.write('epsilon2 %g\n' % SHCI.epsilon2)
f.write('epsilon2Large %g\n' % SHCI.epsilon2Large)
f.write('targetError %g\n' % SHCI.targetError)
f.write('sampleN %i\n' % SHCI.sampleN)
# Miscellaneous Keywords
f.write('noio \n')
if (SHCI.prefix != ""):
if not os.path.exists(SHCI.prefix):
os.makedirs(SHCI.prefix)
f.write('prefix %s\n' % (SHCI.prefix))
# Sets maxiter to 6 more than the last iter in sweep_iter[] if restarted.
if (not Restart):
f.write('maxiter %i\n' % (SHCI.sweep_iter[-1] + 6))
else:
f.write('maxiter 6\n')
f.write('fullrestart\n')
f.write('\n') # SHCI requires that there is an extra line.
f.write('%s\n' % (SHCI.extraline))
f.close()
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
def nevpt_integral_mpi(mc_chkfile,blockfile,dmrginp,dmrgout,scratch):
from mpi4py import MPI
comm = MPI.COMM_WORLD
mpi_size = MPI.COMM_WORLD.Get_size()
rank = comm.Get_rank()
if rank == 0:
mol = chkfile.load_mol(mc_chkfile)
fh5 = h5py.File(mc_chkfile,'r')
mo_coeff = fh5['mc/mo'].value
ncore = fh5['mc/ncore'].value
ncas = fh5['mc/ncas'].value
nvirt = fh5['mc/nvirt'].value
orbe = fh5['mc/orbe'].value
root = fh5['mc/root'].value
orbsym = list(fh5['mc/orbsym'].value)
nelecas = fh5['mc/nelecas'].value
h1e_Si = fh5['h1e_Si'].value
h1e_Sr = fh5['h1e_Sr'].value
h1e = fh5['h1e'].value
e_core = fh5['e_core'].value
h2e = fh5['h2e'].value
h2e_Si = fh5['h2e_Si'].value
h2e_Sr = fh5['h2e_Sr'].value
fh5.close()
headnode = MPI.Get_processor_name()
else:
mol = None
mo_coeff = None
ncore = None
ncas = None
nvirt = None
orbe = None
root = None
orbsym = None
nelecas = None
h1e_Si = None
h1e_Sr = None
h1e = None
e_core = None
h2e = None
h2e_Si = None
h2e_Sr = None
headnode = None
comm.barrier()
mol = comm.bcast(mol,root=0)
mo_coeff = comm.bcast(mo_coeff,root=0)
ncas = comm.bcast(ncas,root=0)
ncore = comm.bcast(ncore,root=0)
nvirt = comm.bcast(nvirt,root=0)
root = comm.bcast(root,root=0)
orbsym = comm.bcast(orbsym,root=0)
nelecas = comm.bcast(nelecas,root=0)
orbe = comm.bcast(orbe,root=0)
h1e_Si = comm.bcast(h1e_Si,root=0)
h1e_Sr = comm.bcast(h1e_Sr,root=0)
h1e = comm.bcast(h1e,root=0)
h2e = comm.bcast(h2e,root=0)
h2e_Si = comm.bcast(h2e_Si,root=0)
h2e_Sr = comm.bcast(h2e_Sr,root=0)
headnode = comm.bcast(headnode,root=0)
e_core = comm.bcast(e_core,root=0)
mo_core = mo_coeff[:,:ncore]
mo_cas = mo_coeff[:,ncore:ncore+ncas]
mo_virt = mo_coeff[:,ncore+ncas:]
nelec = nelecas[0] + nelecas[1]
if mol.symmetry and len(orbsym):
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
newscratch = os.path.join(scratch, str(rank))
if not os.path.exists('%s'%newscratch):
os.makedirs('%s'%newscratch)
os.makedirs('%s/node0'%newscratch)
subprocess.check_call('cp %s %s/%s'%(dmrginp,newscratch,dmrginp),shell=True)
f = open('%s/%s'%(newscratch,dmrginp), 'a')
f.write('restart_mps_nevpt %d %d %d \n'%(ncas,partial_core, partial_virt))
f.close()
tol = float(1e-15)
#from subprocess import Popen
#from subprocess import PIPE
#print 'scratch', scratch
##p1 = Popen(['cp %s/* %d/'%(scratch, rank)],shell=True,stderr=PIPE)
#p1 = Popen(['cp','%s/*'%scratch, '%d/'%rank],shell=True,stderr=PIPE)
#print p1.communicate()
#p2 = Popen(['cp %s/node0/* %d'%(scratch, rank)],shell=True,stderr=PIPE)
##p2 = Popen(['cp','%s/node0/*'%scratch, '%d/'%rank],shell=True,stderr=PIPE)
#print p2.communicate()
#call('cp %s/* %d/'%(scratch,rank),shell = True,stderr=os.devnull)
#call('cp %s/node0/* %d/'%(scratch,rank),shell = True,stderr=os.devnull)
# f1 =open(os.devnull,'w')
# if MPI.Get_processor_name() == headnode:
# subprocess.call('cp %s/* %s/'%(scratch,newscratch),stderr=f1,shell = True)
# subprocess.call('cp %s/node0/* %s/node0'%(scratch,newscratch),shell = True)
# else:
# subprocess.call('scp %s:%s/* %s/'%(headnode,scratch,newscratch),stderr=f1,shell = True)
# subprocess.call('scp %s:%s/node0/* %s/node0'%(headnode,scratch,newscratch),shell = True)
# f1.close()
#TODO
#Use mpi rather than scp to copy the file.
#To make the code robust.
if rank==0:
filenames = []
for fn in os.listdir('%s/node0'%scratch):
if fn== 'dmrg.e' or fn== 'statefile.0.tmp' or fn== 'RestartReorder.dat' or fn.startswith('wave') or fn.startswith('Rotation'):
filenames.append(fn)
else:
filenames = None
filenames = comm.bcast(filenames, root=0)
for i in range(len(filenames)):
if rank == 0:
with open('%s/node0/%s'%(scratch,filenames[i]),'rb') as f:
data = f.read()
else:
data = None
data = comm.bcast(data, root=0)
if data==None:
print 'empty file'
with open('%s/node0/%s'%(newscratch,filenames[i]),'wb') as f:
f.write(data)
f = open('%s/FCIDUMP'%newscratch,'w')
pyscf.tools.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()
current_path = os.getcwd()
os.chdir('%s'%newscratch)
env = os.environ
envnew = {}
for k in env:
if 'MPI' not in k and 'SLURM' not in k:
# remove PBS and SLURM environments to prevent Block running in MPI mode
envnew[k] = os.environ[k]
p = subprocess.Popen(['%s %s > %s'%(blockfile,dmrginp,dmrgout)], env=envnew, shell=True)
p.wait()
f = open('node0/Va_%d'%root,'r')
Vr_energy = float(f.readline())
Vr_norm = float(f.readline())
f.close()
f = open('node0/Vi_%d'%root,'r')
Vi_energy = float(f.readline())
Vi_norm = float(f.readline())
f.close()
comm.barrier()
#Vr_total = 0.0
#Vi_total = 0.0
Vi_total_e = comm.gather(Vi_energy,root=0)
Vi_total_norm = comm.gather(Vi_norm,root=0)
Vr_total_e = comm.gather(Vr_energy,root=0)
Vr_total_norm = comm.gather(Vr_norm,root=0)
#comm.Reduce(Vi_energy,Vi_total,op=MPI.SUM, root=0)
os.chdir('%s'%current_path)
if rank == 0:
fh5 = h5py.File('Perturbation_%d'%root,'w')
fh5['Vi/energy'] = sum(Vi_total_e)
fh5['Vi/norm'] = sum(Vi_total_norm)
fh5['Vr/energy'] = sum(Vr_total_e)
fh5['Vr/norm'] = sum(Vr_total_norm)
fh5.close()
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
