def test_self_consistent(): #pmDMET mol, mf, mydft, impClusters = test_makemole1() symmetry = None #or [0]*5, takes longer time solverlist = 'CASCI' #['RHF', 'CASCI', 'CASCI', 'CASCI', 'CASCI'] runDMET = dmet.DMET(mf, impClusters, symmetry, orthogonalize_method = 'overlap', schmidt_decomposition_method = 'OED', OEH_type = 'FOCK', SC_CFtype = 'F', solver = solverlist) #runDMET.CAS = [[4,4]] runDMET.SC_canonical = True time1 = time.time() runDMET.self_consistent() time2 = time.time() time_pmDMET = time2 - time1 #QC-DMET myInts = localintegrals.localintegrals( mf, range( mol.nao_nr() ), 'meta_lowdin' ) myInts.TI_OK = False method = 'CASSCF' SCmethod = 'BFGS' #Don't do it self-consistently TI = False theDMET = qc_dmet.dmet( myInts, impClusters, TI, method, SCmethod ) theDMET.impCAS = (4,4) time1 = time.time() theDMET.doselfconsistent() time2 = time.time() time_QCDMET = time2 - time1 return runDMET.Energy_total, time_pmDMET, time_QCDMET
def test_1rdm_response():
mol, mf, impClusters = test_makemole1()
#symmetry = [0, 1, 2, 1, 0]
#runDMET = dmet.DMET(mf, impClusters, symmetry, orthogonalize_method = 'overlap', schmidt_decomposition_method = 'OED', OEH_type = 'FOCK', SC_CFtype = 'FB', solver = 'RHF')
#runDMET.one_shot()
umat = np.zeros((mol.nao_nr(), mol.nao_nr()))
#QC-DMET
myInts = localintegrals.localintegrals(mf, range(mol.nao_nr()),
'meta_lowdin')
myInts.TI_OK = True
method = 'ED'
SCmethod = 'LSTSQ' #Don't do it self-consistently
TI = True
theDMET = qc_dmet.dmet(myInts, impClusters, TI, method, SCmethod)
RDMderivs_rot = theDMET.helper.construct1RDM_response(False, umat, None)
Norb = theDMET.helper.locints.Norbs
Nterms = theDMET.helper.Nterms
numPairs = theDMET.helper.numPairs
inH1start = theDMET.helper.H1start
inH1row = theDMET.helper.H1row
inH1col = theDMET.helper.H1col
inH0 = theDMET.helper.locints.loc_rhf_fock() #+ umat
RDMderivs_libdmet = libdmet.rhf_response(Norb, Nterms, numPairs, inH1start,
inH1row, inH1col, inH0)
inH0 = np.array(inH0.reshape((10 * 10)), dtype=ctypes.c_double)
assert np.abs((RDMderivs_rot - RDMderivs_libdmet)).sum() < 1e-8
return RDMderivs_rot, RDMderivs_libdmet
def test_costfunction():
#pmDMET
mol, mf, impClusters = test_makemole1()
symmetry = None #or [0]*5, takes longer time
runDMET = dmet.DMET(mf,
impClusters,
symmetry,
orthogonalize_method='meta_lowdin',
schmidt_decomposition_method='OED',
OEH_type='FOCK',
SC_CFtype='FB',
solver='RHF')
runDMET.one_shot()
#QC-DMET
myInts = localintegrals.localintegrals(mf, range(mol.nao_nr()),
'meta_lowdin')
myInts.TI_OK = False
method = 'RHF'
SCmethod = 'NONE' #Don't do it self-consistently
TI = False
theDMET = qc_dmet.dmet(myInts, impClusters, TI, method, SCmethod)
theDMET.doselfconsistent()
uvec_size = runDMET.uvec.size
uvec = np.random.rand(uvec_size)
umat = runDMET.uvec2umat(uvec)
CF_pmDMET = runDMET.costfunction(uvec)
CF_QCDMET = theDMET.costfunction(uvec)
CF_deriv_pmDMET = runDMET.costfunction_gradient(uvec)
CF_deriv_QCDMET = theDMET.costfunction_derivative(uvec)
assert np.isclose((CF_QCDMET - CF_pmDMET).sum(), 0)
assert np.isclose((CF_deriv_QCDMET - CF_deriv_pmDMET).sum(), 0)
def test_1RDM_response():
#pmDMET
mol, mf, impClusters = test_makemole1()
symmetry = [0] * 5 #or 'Translation'
runDMET = dmet.DMET(mf,
impClusters,
symmetry,
orthogonalize_method='meta_lowdin',
schmidt_decomposition_method='OED',
OEH_type='FOCK',
SC_CFtype='FB',
solver='RHF')
#QC-DMET
myInts = localintegrals.localintegrals(mf, range(mol.nao_nr()),
'meta_lowdin')
myInts.TI_OK = True
method = 'ED'
SCmethod = 'LSTSQ' #Don't do it self-consistently
TI = True
theDMET = qc_dmet.dmet(myInts, impClusters, TI, method, SCmethod)
uvec_size = runDMET.uvec.size
uvec = np.zeros(uvec_size)
umat = runDMET.uvec2umat(uvec)
RDMderivs_QCDMET = theDMET.helper.construct1RDM_response(False, umat, None)
RDMderivs_pDMET = runDMET.construct_1RDM_response(uvec)
diff = np.abs((RDMderivs_QCDMET - RDMderivs_pDMET)).sum()
assert np.isclose(RDMderivs_QCDMET.size, RDMderivs_pDMET.size)
assert np.isclose(diff, 0)
def test_make_H1():
#pmDMET
mol, mf, impClusters = test_makemole1()
symmetry = [0] * 5 #or 'Translation'
runDMET = dmet.DMET(mf,
impClusters,
symmetry,
orthogonalize_method='overlap',
schmidt_decomposition_method='OED',
OEH_type='FOCK',
SC_CFtype='FB',
solver='RHF')
H1start, H1row, H1col = runDMET.make_H1()[1:]
#QC-DMET
myInts = localintegrals.localintegrals(mf, range(mol.nao_nr()),
'meta_lowdin')
myInts.TI_OK = True
method = 'ED'
SCmethod = 'LSTSQ' #Don't do it self-consistently
TI = True
theDMET = qc_dmet.dmet(myInts, impClusters, TI, method, SCmethod)
H1start = theDMET.helper.H1start - H1start
H1row = theDMET.helper.H1row - H1row
H1col = theDMET.helper.H1col - H1col
assert H1start.sum() == 0
assert H1row.sum() == 0
assert H1col.sum() == 0
# Order of AO: 3s 2p 1d
rotation[ offset+3:offset+6, offset+3:offset+6 ] = ringhelper.p_functions( theta )
rotation[ offset+6:offset+9, offset+6:offset+9 ] = ringhelper.p_functions( theta )
rotation[ offset+9:offset+14, offset+9:offset+14 ] = ringhelper.d_functions( theta )
assert( np.linalg.norm( np.dot( rotation, rotation.T ) - np.eye( rotation.shape[0] ) ) < 1e-6 )
myInts = localintegrals.localintegrals( mf, range( mol.nao_nr() ), localization_type, rotation )
if (( localization_type == 'meta_lowdin' ) or ( localization_type == 'iao' )):
myInts.TI_OK = True
myInts.molden( 'Be-loc.molden' )
atoms_per_imp = 1 # Impurity size = 1/2/4 Be atoms
assert ( nat % atoms_per_imp == 0 )
orbs_per_imp = myInts.Norbs * atoms_per_imp / nat
impurityClusters = []
for cluster in range( nat / atoms_per_imp ):
impurities = np.zeros( [ myInts.Norbs ], dtype=int )
for orb in range( orbs_per_imp ):
impurities[ orbs_per_imp*cluster + orb ] = 1
impurityClusters.append( impurities )
if (( localization_type == 'meta_lowdin' ) or ( localization_type == 'iao' )):
isTranslationInvariant = True
else:
isTranslationInvariant = False # Boys TI is not OK
method = 'CC'
SCmethod = 'NONE' # NONE or LSTSQ for no self-consistency or least-squares fitting of the u-matrix, respectively
theDMET = dmet.dmet( myInts, impurityClusters, isTranslationInvariant, method, SCmethod )
theDMET.doselfconsistent()
#theDMET.dump_bath_orbs( 'Be-bathorbs.molden' )
def DMET_wrap(atoms, basis, charge, spin, fragments, fragment_spins, shells,
nfreeze, method, thresh, parallel):
mol = pyscf.gto.Mole()
mol.verbose = 4
mol.output = 'Mole'
mol.atom = atoms
mol.charge = charge
mol.spin = spin
mol.basis = basis
mol.symmetry = False
mol.ecp = None
mol.build()
from pyscf import scf
verbose = False
if (parallel):
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = MPI.COMM_WORLD.Get_rank()
size = MPI.COMM_WORLD.Get_size()
if (rank == 0): verbose = True
else:
verbose = True
Cf_core, Cf_vale, Cf_virt = orbital_partitioning(mol, fragments, shells,
verbose)
Cf = RHF_calculation(mol, verbose)
iAO_loc, Cf_core, Cf_x = build_iAO_basis(mol, Cf, Cf_core, Cf_vale,
nfreeze)
Cf_virt = virtual_orbitals(mol, Cf_core, Cf_vale, Cf_virt, iAO_loc)
#print("cf core",Cf_core)
if (Cf_core is not None):
nb = Cf_core.shape[0]
FrozenPot = numpy.zeros((nb, nb))
else:
nfreeze = 0
nb = mol.nao_nr()
FrozenPot = numpy.zeros((nb, nb))
e_core = 0.0
if (nfreeze > 0):
import numpy as np
from pyscf import scf
Hc = mol.intor_symmetric('cint1e_kin_sph') \
+ mol.intor_symmetric('cint1e_nuc_sph')
dm_core = np.dot(Cf_core, Cf_core.T) * 2
jk_core = scf.hf.get_veff(mol, dm_core)
e_core = np.trace(np.dot(Hc, dm_core)) \
+ 0.5*np.trace(np.dot(jk_core, dm_core))
FrozenPot = jk_core
Cf_core = None
mol.nelectron -= 2 * nfreeze
print(nfreeze)
idx_core = None
if (Cf_core is not None): idx_core = atom_to_orb_mapping(mol, Cf_core)
idx_vale = atom_to_orb_mapping(mol, Cf_vale)
idx_virt = atom_to_orb_mapping(mol, Cf_virt)
ximp_at = atom_to_frg_mapping(fragments)
print("idx core", idx_core)
print("idx_vale", idx_vale)
print("idx_virt", idx_virt)
print("ximp-at", ximp_at)
print("aio_loc", iAO_loc.shape)
if (parallel):
from mpi4py import MPI
comm = MPI.COMM_WORLD
rank = MPI.COMM_WORLD.Get_rank()
size = MPI.COMM_WORLD.Get_size()
assert (len(fragments) == size)
Cf_x = comm.bcast(Cf_x, root=0)
iAO_loc = comm.bcast(iAO_loc, root=0)
idx_vale = comm.bcast(idx_vale, root=0)
Cf_core = comm.bcast(Cf_core, root=0)
idx_core = comm.bcast(idx_core, root=0)
Cf_virt = comm.bcast(Cf_virt, root=0)
idx_virt = comm.bcast(idx_virt, root=0)
ximp_at = comm.bcast(ximp_at, root=0)
import time
start = time.time()
print("Starting the clock for solver")
mf_tot = scf.RHF(
mol).density_fit() # this was moved from dfmp2_testing solver
mf_tot.with_df._cderi_to_save = 'saved_cderi.h5' # rank-3 decomposition
mf_tot.kernel()
#print("shape of cderi", mf_tot.with_df._cderi.shape)
#TODO: make this ^ conditional, use saved eri
dmet_ = dmet.dmet(mol, Cf_x, ximp_at, \
iAO_loc, idx_vale, method=method, thresh=thresh, \
A_core = Cf_core, at_core = idx_core, \
A_virt = Cf_virt, at_virt = idx_virt, \
imp_atx = ximp_at, parallel = parallel, e_core=e_core,\
FrozenPot=FrozenPot, mf_tot = mf_tot)
dmet_.eval()
done = time.time()
elapsed = done - start
print("Total Time in Solver", elapsed)
if (True):
myInts = localintegrals.localintegrals(mf2, range(mol2.nao_nr()), 'iao')
myInts.molden('emft-loc.molden')
unit_sizes = None
if ((thebasis1 == 'cc-pvdz') and (thebasis2 == 'aug-cc-pvdz')):
if (thestructure == 'reactants'): # 1-chlorodecane
unit_sizes = np.array([27, 24, 24, 24, 24, 24, 24, 24, 24, 24,
29]) # Cl, 9xCH2, CH3 (272 orbs total)
if (thestructure == 'products'): # 1-decanol
unit_sizes = np.array([28, 24, 24, 24, 24, 24, 24, 24, 24, 24,
29]) # OH, 9xCH2, CH3 (273 orbs total)
assert (np.sum(unit_sizes) == mol2.nao_nr())
for carbons_in_cluster in range(0, 5): # 0, 1, 2, 3, 4
orbs_in_imp = np.sum(unit_sizes[0:carbons_in_cluster + 1])
impurityClusters = []
impurities = np.zeros([mol.nao_nr()], dtype=int)
impurities[0:orbs_in_imp] = 1
impurityClusters.append(impurities)
theDMET = dmet.dmet(myInts,
impurityClusters,
isTranslationInvariant=False,
method='CC',
SCmethod='NONE')
theDMET.CC_E_TYPE = 'CASCI'
the_energy = theDMET.doselfconsistent()
print "###### DMET(", carbons_in_cluster, "C , CCSD ) /", thebasis1, "/", thebasis2, " =", the_energy + ECCSD2
for carbons_in_cluster in cluster_sizes:
impurityClusters = []
if ( single_impurity == True ): # Do only 1 impurity at the edge
num_orb_in_imp = np.sum( unit_sizes[ 0 : carbons_in_cluster ] )
impurity_orbitals = np.zeros( [ mol.nao_nr() ], dtype=int )
impurity_orbitals[ 0 : num_orb_in_imp ] = 1
impurityClusters.append( impurity_orbitals )
else: # Partition
atoms_passed = 0
jump = 0
while ( atoms_passed < len( unit_sizes ) ):
num_carb_in_imp = min( carbons_in_cluster, len( unit_sizes ) - atoms_passed )
num_orb_in_imp = np.sum( unit_sizes[ atoms_passed : atoms_passed + num_carb_in_imp ] )
impurity_orbitals = np.zeros( [ mol.nao_nr() ], dtype=int )
impurity_orbitals[ jump : jump + num_orb_in_imp ] = 1
impurityClusters.append( impurity_orbitals )
atoms_passed += num_carb_in_imp
jump += num_orb_in_imp
theDMET = dmet.dmet( myInts, impurityClusters, isTranslationInvariant=False, method='CC', SCmethod='NONE' )
if ( casci_energy_formula == True ):
theDMET.CC_E_TYPE = 'CASCI'
if ( one_bath_orb_per_bond == True ):
theDMET.BATH_ORBS = 2 * np.ones( [ len(impurityClusters) ], dtype=int )
theDMET.BATH_ORBS[ 0 ] = 1
theDMET.BATH_ORBS[ len(impurityClusters) - 1 ] = 1
the_energy = theDMET.doselfconsistent()
print "###### DMET(", carbons_in_cluster,"C , CCSD ) /", thebasis1, "/", thebasis2, " =", the_energy
impurity_orbitals = np.zeros([mol.nao_nr()], dtype=int)
num_orb_in_imp = unit_sizes[fragment]
if (fragment > 0):
impurity_orbitals[jump:jump + num_orb_in_imp] = -1
else:
impurity_orbitals[jump:jump + num_orb_in_imp] = 1
impurityClusters.append(impurity_orbitals)
jump += num_orb_in_imp
isTranslationInvariant = False
method = 'CASSCF'
SCmethod = 'BFGS'
theDMET = dmet.dmet(myInts,
impurityClusters,
isTranslationInvariant,
method,
SCmethod,
fitImpBath=True,
doDET=False)
theDMET.impCAS = (2, 2)
theDMET.CASlist = [19, 21]
theDMET.CC_E_TYPE = 'CASCI'
the_energy = theDMET.doselfconsistent()
'''X1 = theDMET.ao2loc
X2 = theDMET.loc2dmet
#PRINT RHF in embedding space
for mo in range(10,40):
mo_coeff = reduce(np.dot,(X1,X2[:,:40], theDMET.MOmf))[:,mo].reshape(mol.nao_nr())
name = 'MO_nat_casdmet44_' + str(mo) + '.cube'
id = mo + 1
mocube.mo(mol, name, id, mo_coeff, nx=60, ny=60, nz=60)'''
