def load_from_pyscf_chk_mol(chkfile, base='scf'):
mol = load_mol(chkfile)
with h5py.File(chkfile, 'r') as fh5:
try:
hcore = fh5['/scf/hcore'][:]
except KeyError:
hcore = mol.intor_symmetric('int1e_nuc')
hcore += mol.intor_symmetric('int1e_kin')
if len(mol._ecpbas) > 0:
hcore += mol.intor_symmetric('ECPScalar')
try:
X = fh5['/scf/orthoAORot'][:]
except KeyError:
s1e = mol.intor('int1e_ovlp_sph')
X = get_ortho_ao_mol(s1e)
try:
df_ints = fh5['j3c'][:]
except KeyError:
df_ints = None
mo_occ = numpy.array(lib.chkfile.load(chkfile, base+'/mo_occ'))
mo_coeff = numpy.array(lib.chkfile.load(chkfile, base+'/mo_coeff'))
uhf = len(mo_coeff.shape) == 3
if mol.nelec[0] != mol.nelec[1] and not uhf:
rohf = True
else:
rohf = False
scf_data = {'mol': mol, 'mo_occ': mo_occ, 'hcore': hcore,
'X': X, 'mo_coeff': mo_coeff,
'isUHF': uhf, 'df_ints': df_ints,
'rohf': rohf}
return scf_data
def pyscf_from_file(chkfile):
mol = chk.load_mol(chkfile)
mf = RHF(mol)
mf.__dict__.update(chk.load(chkfile, 'scf'))
mc_dict = chk.load(chkfile, 'mcscf')
if mc_dict:
mc_dict['ci'] = chk.load(chkfile, 'ci')
mc_dict['nelecas'] = tuple(map(int, chk.load(chkfile, 'nelecas')))
mc = CASSCF(mf, 0, 0)
mc.__dict__.update(mc_dict)
else:
mc = None
return mf, mc
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 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 DMRG_COMPRESS_NEVPT(mc, maxM=500, root=0, nevptsolver=None, tol=1e-7):
if (isinstance(mc, str)):
mol = chkfile.load_mol(mc)
fh5 = h5py.File(mc, 'r')
ncas = fh5['mc/ncas'].value
ncore = fh5['mc/ncore'].value
nvirt = fh5['mc/nvirt'].value
nelecas = fh5['mc/nelecas'].value
nroots = fh5['mc/nroots'].value
wfnsym = fh5['mc/wfnsym'].value
fh5.close()
mc_chk = mc
else :
mol = mc.mol
ncas = mc.ncas
ncore = mc.ncore
nvirt = mc.mo_coeff.shape[1] - mc.ncas-mc.ncore
nelecas = mc.nelecas
nroots = mc.fcisolver.nroots
wfnsym = mc.fcisolver.wfnsym
mc_chk = 'nevpt_perturb_integral'
write_chk(mc, root, mc_chk)
if nevptsolver is None:
nevptsolver = default_nevpt_schedule(mol,maxM, tol)
nevptsolver.wfnsym = wfnsym
nevptsolver.block_extra_keyword = mc.fcisolver.block_extra_keyword
nevptsolver.nroots = nroots
from pyscf.dmrgscf import settings
nevptsolver.executable = settings.BLOCKEXE_COMPRESS_NEVPT
scratch = nevptsolver.scratchDirectory
nevptsolver.scratchDirectory = ''
dmrgci.writeDMRGConfFile(nevptsolver, nelecas, False, with_2pdm=False,
extraline=['fullrestart','nevpt_state_num %d'%root])
nevptsolver.scratchDirectory = scratch
if nevptsolver.verbose >= logger.DEBUG1:
inFile = os.path.join(nevptsolver.runtimeDir, nevptsolver.configFile)
logger.debug1(nevptsolver, 'Block Input conf')
logger.debug1(nevptsolver, open(inFile, 'r').read())
t0 = (time.clock(), time.time())
cmd = ' '.join((nevptsolver.mpiprefix,
'%s/nevpt_mpi.py' % os.path.dirname(os.path.realpath(__file__)),
mc_chk,
nevptsolver.executable,
os.path.join(nevptsolver.runtimeDir, nevptsolver.configFile),
nevptsolver.outputFile,
nevptsolver.scratchDirectory))
logger.debug(nevptsolver, 'DMRG_COMPRESS_NEVPT cmd %s', cmd)
try:
output = subprocess.check_call(cmd, shell=True)
except subprocess.CalledProcessError as err:
logger.error(nevptsolver, cmd)
raise err
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, open(os.path.join(nevptsolver.scratchDirectory, '0/dmrg.out')).read())
fh5 = h5py.File('Perturbation_%d'%root,'r')
Vi_e = fh5['Vi/energy'].value
Vr_e = fh5['Vr/energy'].value
fh5.close()
logger.note(nevptsolver,'Nevpt Energy:')
logger.note(nevptsolver,'Sr Subspace: E = %.14f'%( Vr_e))
logger.note(nevptsolver,'Si Subspace: E = %.14f'%( Vi_e))
logger.timer(nevptsolver,'MPS NEVPT calculation time', *t0)
from pyscf.lib import chkfile
#
# Check args
#
if len(sys.argv) != 2:
raise AssertionError("Incorrect # of args\n"
"Use like: python pt2.py 1\n"
"Where 1 is the root you want to target.")
target_state = int(sys.argv[-1])
#
# Load MF orbitals
#
chkname = "_chk/pp_dz_b3lyp.chk"
mol = chkfile.load_mol(chkname)
mol.max_memory = int(1e5) # memory in MB 1e6 -> 1 TB
mf = dft.RKS(mol)
mf.__dict__.update(chkfile.load(chkname, "scf"))
#
# Load SA-MCSCF
#
nelecas, ncas = (4, 4)
n_states = 3
weights = np.ones(n_states) / n_states
mc0 = mcscf.CASSCF(mf, ncas, nelecas).state_average_(weights)
mc0.fix_spin(ss=0)
mc0.chkfile = "_chk/pp_dz_cas_4e_4o.chk"
mc0.__dict__.update(chkfile.load(mc0.chkfile, "mcscf"))
def load_scf(chkfile):
return load_mol(chkfile), load(chkfile, 'scf')
def load_mcscf(chkfile):
return load_mol(chkfile), load(chkfile, 'mcscf')
def DMRG_COMPRESS_NEVPT(mc,
maxM=500,
root=0,
nevptsolver=None,
tol=1e-7,
nevpt_integral=None):
if isinstance(nevpt_integral, str) and h5py.is_hdf5(nevpt_integral):
nevpt_integral_file = os.path.abspath(nevpt_integral)
mol = chkfile.load_mol(nevpt_integral_file)
fh5 = h5py.File(nevpt_integral_file, 'r')
ncas = fh5['mc/ncas'][()]
ncore = fh5['mc/ncore'][()]
nvirt = fh5['mc/nvirt'][()]
nelecas = fh5['mc/nelecas'][()]
nroots = fh5['mc/nroots'][()]
wfnsym = fh5['mc/wfnsym'][()]
fh5.close()
else:
mol = mc.mol
ncas = mc.ncas
ncore = mc.ncore
nvirt = mc.mo_coeff.shape[1] - mc.ncas - mc.ncore
nelecas = mc.nelecas
nroots = mc.fcisolver.nroots
wfnsym = mc.fcisolver.wfnsym
nevpt_integral_file = None
if nevptsolver is None:
nevptsolver = default_nevpt_schedule(mc.fcisolver, maxM, tol)
#nevptsolver.__dict__.update(mc.fcisolver.__dict__)
nevptsolver.wfnsym = wfnsym
nevptsolver.block_extra_keyword = mc.fcisolver.block_extra_keyword
nevptsolver.nroots = nroots
nevptsolver.executable = settings.BLOCKEXE_COMPRESS_NEVPT
if nevptsolver.executable == getattr(mc.fcisolver, 'executable', None):
logger.warn(
mc, 'DMRG executable file for nevptsolver is the same '
'to the executable file for DMRG solver. If they are '
'both compiled by MPI compilers, they may cause error or '
'random results in DMRG-NEVPT calculation.')
nevpt_scratch = os.path.abspath(nevptsolver.scratchDirectory)
dmrg_scratch = os.path.abspath(mc.fcisolver.scratchDirectory)
# Integrals are not given by the kwarg nevpt_integral
if nevpt_integral_file is None:
nevpt_integral_file = os.path.join(nevpt_scratch,
'nevpt_perturb_integral')
write_chk(mc, root, nevpt_integral_file)
conf = dmrgci.writeDMRGConfFile(
nevptsolver,
nelecas,
False,
with_2pdm=False,
extraline=['fullrestart', 'nevpt_state_num %d' % root])
with open(conf, 'r') as f:
block_conf = f.readlines()
block_conf = [l for l in block_conf if 'prefix' not in l]
block_conf = ''.join(block_conf)
with h5py.File(nevpt_integral_file, 'a') as fh5:
if 'dmrg.conf' in fh5:
del (fh5['dmrg.conf'])
fh5['dmrg.conf'] = block_conf
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, 'Block Input conf')
logger.debug1(nevptsolver, block_conf)
t0 = (time.clock(), time.time())
# function nevpt_integral_mpi is called in this cmd
cmd = ' '.join(
(nevptsolver.mpiprefix,
os.path.realpath(os.path.join(__file__, '..',
'nevpt_mpi.py')), nevpt_integral_file,
nevptsolver.executable, dmrg_scratch, nevpt_scratch))
logger.debug(nevptsolver, 'DMRG_COMPRESS_NEVPT cmd %s', cmd)
try:
output = subprocess.check_call(cmd, shell=True)
except subprocess.CalledProcessError as err:
logger.error(nevptsolver, cmd)
raise err
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(
nevptsolver,
open(os.path.join(nevpt_scratch, '0', 'dmrg.out')).read())
perturb_file = os.path.join(nevpt_scratch, '0', 'Perturbation_%d' % root)
fh5 = h5py.File(perturb_file, 'r')
Vi_e = fh5['Vi/energy'][()]
Vr_e = fh5['Vr/energy'][()]
fh5.close()
logger.note(nevptsolver, 'Nevpt Energy:')
logger.note(nevptsolver, 'Sr Subspace: E = %.14f' % (Vr_e))
logger.note(nevptsolver, 'Si Subspace: E = %.14f' % (Vi_e))
logger.timer(nevptsolver, 'MPS NEVPT calculation time', *t0)
return perturb_file
mf.run()
print('E(HF) = %s' % mf.e_tot)
scf_result_dic = chkfile.load('example.chk', 'scf')
mf_new = scf.RHF(mol)
mf_new.__dict__.update(scf_result_dic)
print('E(HF) from chkfile = %s' % mf.e_tot)
myci = ci.CISD(mf).run()
myci.dump_chk()
print('E(CISD) = %s' % myci.e_tot)
cisd_result_dic = chkfile.load('example.chk', 'cisd')
myci_new = ci.CISD(mf_new)
myci_new.__dict__.update(cisd_result_dic)
print('E(CISD) from chkfile = %s' % myci_new.e_tot)
mol_new = chkfile.load_mol('example.chk')
print(numpy.allclose(mol.atom_coords(), mol_new.atom_coords()))
print(numpy.allclose(mol.atom_charges(), mol_new.atom_charges()))
with h5py.File('example.chk') as f:
print('\nCheckpoint file is a HDF5 file. data are stored in file/directory structure.')
print('/', f.keys())
print('/scf', f['scf'].keys())
print('/scf/mo_occ', f['scf/mo_occ'].value)
print('/cisd', f['cisd'].keys())
print('\nMolecular object (mol) is seriealized to json format and stored')
print('/mol: %s ...' % f['mol'].value[:20])
def DMRG_COMPRESS_NEVPT(mc,
maxM=500,
root=0,
nevptsolver=None,
tol=1e-7,
nevpt_integral=None):
if nevpt_integral:
mol = chkfile.load_mol(nevpt_integral)
fh5 = h5py.File(nevpt_integral, 'r')
ncas = fh5['mc/ncas'].value
ncore = fh5['mc/ncore'].value
nvirt = fh5['mc/nvirt'].value
nelecas = fh5['mc/nelecas'].value
nroots = fh5['mc/nroots'].value
wfnsym = fh5['mc/wfnsym'].value
fh5.close()
else:
mol = mc.mol
ncas = mc.ncas
ncore = mc.ncore
nvirt = mc.mo_coeff.shape[1] - mc.ncas - mc.ncore
nelecas = mc.nelecas
nroots = mc.fcisolver.nroots
wfnsym = mc.fcisolver.wfnsym
nevpt_integral_file = 'nevpt_perturb_integral'
write_chk(mc, root, nevpt_integral_file)
if nevptsolver is None:
nevptsolver = default_nevpt_schedule(mol, maxM, tol)
nevptsolver.__dict__.update(mc.fcisolver.__dict__)
nevptsolver.wfnsym = wfnsym
nevptsolver.block_extra_keyword = mc.fcisolver.block_extra_keyword
nevptsolver.nroots = nroots
nevptsolver.executable = settings.BLOCKEXE_COMPRESS_NEVPT
conf = dmrgci.writeDMRGConfFile(
nevptsolver,
nelecas,
False,
with_2pdm=False,
extraline=['fullrestart', 'nevpt_state_num %d' % root])
with open(conf, 'r') as f:
block_conf = f.readlines()
block_conf = [l for l in block_conf if 'prefix' not in l]
block_conf = '\n'.join(block_conf)
with h5py.File(nevpt_integral_file) as fh5:
if 'dmrg.conf' in fh5:
del (fh5['dmrg.conf'])
fh5['dmrg.conf'] = block_conf
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, 'Block Input conf')
logger.debug1(nevptsolver, block_conf)
t0 = (time.clock(), time.time())
cmd = ' '.join(
(nevptsolver.mpiprefix,
os.path.realpath(os.path.join(__file__, '..', 'nevpt_mpi.py')),
nevpt_integral_file, nevptsolver.executable,
mc.fcisolver.scratchDirectory, nevptsolver.scratchDirectory))
logger.debug(nevptsolver, 'DMRG_COMPRESS_NEVPT cmd %s', cmd)
try:
output = subprocess.check_call(cmd, shell=True)
except subprocess.CalledProcessError as err:
logger.error(nevptsolver, cmd)
raise err
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(
nevptsolver,
open(os.path.join(nevptsolver.scratchDirectory,
'0/dmrg.out')).read())
fh5 = h5py.File('Perturbation_%d' % root, 'r')
Vi_e = fh5['Vi/energy'].value
Vr_e = fh5['Vr/energy'].value
fh5.close()
logger.note(nevptsolver, 'Nevpt Energy:')
logger.note(nevptsolver, 'Sr Subspace: E = %.14f' % (Vr_e))
logger.note(nevptsolver, 'Si Subspace: E = %.14f' % (Vi_e))
logger.timer(nevptsolver, 'MPS NEVPT calculation time', *t0)
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 DMRG_COMPRESS_NEVPT(mc, maxM=500, root=0, nevptsolver=None, tol=1e-7):
if (isinstance(mc, str)):
mol = chkfile.load_mol(mc)
fh5 = h5py.File(mc, 'r')
ncas = fh5['mc/ncas'].value
ncore = fh5['mc/ncore'].value
nvirt = fh5['mc/nvirt'].value
nelecas = fh5['mc/nelecas'].value
nroots = fh5['mc/nroots'].value
wfnsym = fh5['mc/wfnsym'].value
fh5.close()
mc_chk = mc
else :
mol = mc.mol
ncas = mc.ncas
ncore = mc.ncore
nvirt = mc.mo_coeff.shape[1] - mc.ncas-mc.ncore
nelecas = mc.nelecas
nroots = mc.fcisolver.nroots
wfnsym = mc.fcisolver.wfnsym
mc_chk = 'nevpt_perturb_integral'
write_chk(mc, root, mc_chk)
if nevptsolver is None:
nevptsolver = default_nevpt_schedule(mol,maxM, tol)
nevptsolver.wfnsym = wfnsym
nevptsolver.block_extra_keyword = mc.fcisolver.block_extra_keyword
nevptsolver.nroots = nroots
from pyscf.dmrgscf import settings
nevptsolver.executable = settings.BLOCKEXE_COMPRESS_NEVPT
scratch = nevptsolver.scratchDirectory
nevptsolver.scratchDirectory = ''
dmrgci.writeDMRGConfFile(nevptsolver, nelecas, False, with_2pdm=False,
extraline=['fullrestart','nevpt_state_num %d'%root])
nevptsolver.scratchDirectory = scratch
if nevptsolver.verbose >= logger.DEBUG1:
inFile = os.path.join(nevptsolver.runtimeDir, nevptsolver.configFile)
logger.debug1(nevptsolver, 'Block Input conf')
logger.debug1(nevptsolver, open(inFile, 'r').read())
t0 = (time.clock(), time.time())
cmd = ' '.join((nevptsolver.mpiprefix,
'%s/nevpt_mpi.py' % os.path.dirname(os.path.realpath(__file__)),
mc_chk,
nevptsolver.executable,
nevptsolver.configFile,
nevptsolver.outputFile,
nevptsolver.scratchDirectory))
logger.debug(nevptsolver, 'DMRG_COMPRESS_NEVPT cmd %s', cmd)
try:
output = subprocess.check_call(cmd, shell=True)
except subprocess.CalledProcessError as err:
logger.error(nevptsolver, cmd)
raise err
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, open(os.path.join(nevptsolver.scratchDirectory, '0/dmrg.out')).read())
fh5 = h5py.File('Perturbation_%d'%root,'r')
Vi_e = fh5['Vi/energy'].value
Vr_e = fh5['Vr/energy'].value
fh5.close()
logger.note(nevptsolver,'Nevpt Energy:')
logger.note(nevptsolver,'Sr Subspace: E = %.14f'%( Vr_e))
logger.note(nevptsolver,'Si Subspace: E = %.14f'%( Vi_e))
logger.timer(nevptsolver,'MPS NEVPT calculation time', *t0)
def DMRG_COMPRESS_NEVPT(mc, maxM=500, root=0, nevptsolver=None, tol=1e-7,
nevpt_integral=None):
if isinstance(nevpt_integral, str) and h5py.is_hdf5(nevpt_integral):
nevpt_integral_file = os.path.abspath(nevpt_integral)
mol = chkfile.load_mol(nevpt_integral_file)
fh5 = h5py.File(nevpt_integral_file, 'r')
ncas = fh5['mc/ncas'].value
ncore = fh5['mc/ncore'].value
nvirt = fh5['mc/nvirt'].value
nelecas = fh5['mc/nelecas'].value
nroots = fh5['mc/nroots'].value
wfnsym = fh5['mc/wfnsym'].value
fh5.close()
else :
mol = mc.mol
ncas = mc.ncas
ncore = mc.ncore
nvirt = mc.mo_coeff.shape[1] - mc.ncas-mc.ncore
nelecas = mc.nelecas
nroots = mc.fcisolver.nroots
wfnsym = mc.fcisolver.wfnsym
nevpt_integral_file = None
if nevptsolver is None:
nevptsolver = default_nevpt_schedule(mc.fcisolver, maxM, tol)
#nevptsolver.__dict__.update(mc.fcisolver.__dict__)
nevptsolver.wfnsym = wfnsym
nevptsolver.block_extra_keyword = mc.fcisolver.block_extra_keyword
nevptsolver.nroots = nroots
nevptsolver.executable = settings.BLOCKEXE_COMPRESS_NEVPT
if nevptsolver.executable == getattr(mc.fcisolver, 'executable', None):
logger.warn(mc, 'DMRG executable file for nevptsolver %s is the same '
'to the executable file for DMRG solver %s. If they are '
'both compiled by MPI compilers, they may cause error or '
'random results in DMRG-NEVPT calculation.')
nevpt_scratch = os.path.abspath(nevptsolver.scratchDirectory)
dmrg_scratch = os.path.abspath(mc.fcisolver.scratchDirectory)
# Integrals are not given by the kwarg nevpt_integral
if nevpt_integral_file is None:
nevpt_integral_file = os.path.join(nevpt_scratch, 'nevpt_perturb_integral')
write_chk(mc, root, nevpt_integral_file)
conf = dmrgci.writeDMRGConfFile(nevptsolver, nelecas, False, with_2pdm=False,
extraline=['fullrestart','nevpt_state_num %d'%root])
with open(conf, 'r') as f:
block_conf = f.readlines()
block_conf = [l for l in block_conf if 'prefix' not in l]
block_conf = ''.join(block_conf)
with h5py.File(nevpt_integral_file) as fh5:
if 'dmrg.conf' in fh5:
del(fh5['dmrg.conf'])
fh5['dmrg.conf'] = block_conf
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, 'Block Input conf')
logger.debug1(nevptsolver, block_conf)
t0 = (time.clock(), time.time())
# function nevpt_integral_mpi is called in this cmd
cmd = ' '.join((nevptsolver.mpiprefix,
os.path.realpath(os.path.join(__file__, '..', 'nevpt_mpi.py')),
nevpt_integral_file,
nevptsolver.executable,
dmrg_scratch, nevpt_scratch))
logger.debug(nevptsolver, 'DMRG_COMPRESS_NEVPT cmd %s', cmd)
try:
output = subprocess.check_call(cmd, shell=True)
except subprocess.CalledProcessError as err:
logger.error(nevptsolver, cmd)
raise err
if nevptsolver.verbose >= logger.DEBUG1:
logger.debug1(nevptsolver, open(os.path.join(nevpt_scratch, '0', 'dmrg.out')).read())
perturb_file = os.path.join(nevpt_scratch, '0', 'Perturbation_%d'%root)
fh5 = h5py.File(perturb_file, 'r')
Vi_e = fh5['Vi/energy'].value
Vr_e = fh5['Vr/energy'].value
fh5.close()
logger.note(nevptsolver,'Nevpt Energy:')
logger.note(nevptsolver,'Sr Subspace: E = %.14f'%( Vr_e))
logger.note(nevptsolver,'Si Subspace: E = %.14f'%( Vi_e))
logger.timer(nevptsolver,'MPS NEVPT calculation time', *t0)
return perturb_file
