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updated converter

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This commit is contained in:
Kevin Gasperich 2020-03-31 14:20:20 -05:00
parent 4a31254d6b
commit 1277f78d72
2 changed files with 53 additions and 36 deletions
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65
src/utils_complex/MolPyscfToQPkpts.py
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@ -553,14 +553,25 @@ def df_ao_to_mo_test(j3ao,mo_coef):
np.einsum('mij,ik,jl->mkl',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj]) np.einsum('mij,ik,jl->mkl',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj])
for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)]) for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)])
def pyscf2QP2_mo(cell,mf,kpts,kmesh=None,cas_idx=None, int_threshold = 1E-8,qph5path='qpdat.h5'):
pyscf2QP2(cell,mf,kpts,kmesh,cas_idx,int_threshold,qph5path,
print_ao_ints_df=False,
print_mo_ints_df=True,
print_ao_ints_mono=False,
print_mo_ints_mono=True)
return
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5path = 'qpdat.h5',
print_ao_ints_bi=False, print_ao_ints_bi=False,
print_mo_ints_bi=False, print_mo_ints_bi=False,
print_ao_ints_df=True, print_ao_ints_df=True,
print_mo_ints_df=False, print_mo_ints_df=False,
print_ao_ints_mono=True, print_ao_ints_mono=True,
print_mo_ints_mono=False): print_mo_ints_mono=False,
print_debug=False):
''' '''
kpts = List of kpoints coordinates. Cannot be null, for gamma is other script kpts = List of kpoints coordinates. Cannot be null, for gamma is other script
kmesh = Mesh of kpoints (optional) kmesh = Mesh of kpoints (optional)
@ -582,7 +593,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
thresh_mono = int_threshold thresh_mono = int_threshold
qph5path = 'qpdat.h5' # qph5path = 'qpdat.h5'
# create hdf5 file, delete old data if exists # create hdf5 file, delete old data if exists
with h5py.File(qph5path,'w') as qph5: with h5py.File(qph5path,'w') as qph5:
qph5.create_group('nuclei') qph5.create_group('nuclei')
@ -685,13 +696,14 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
mo_coef_f = np.array(mo_k.transpose((0,2,1)),order='c') mo_coef_f = np.array(mo_k.transpose((0,2,1)),order='c')
mo_coef_blocked=block_diag(*mo_k) mo_coef_blocked=block_diag(*mo_k)
mo_coef_blocked_f = block_diag(*mo_coef_f) mo_coef_blocked_f = block_diag(*mo_coef_f)
qph5.create_dataset('mo_basis/mo_coef_real',data=mo_coef_blocked.real) #qph5.create_dataset('mo_basis/mo_coef_real',data=mo_coef_blocked.real)
qph5.create_dataset('mo_basis/mo_coef_imag',data=mo_coef_blocked.imag) #qph5.create_dataset('mo_basis/mo_coef_imag',data=mo_coef_blocked.imag)
qph5.create_dataset('mo_basis/mo_coef_kpts_real',data=mo_k.real) #qph5.create_dataset('mo_basis/mo_coef_kpts_real',data=mo_k.real)
qph5.create_dataset('mo_basis/mo_coef_kpts_imag',data=mo_k.imag) #qph5.create_dataset('mo_basis/mo_coef_kpts_imag',data=mo_k.imag)
qph5.create_dataset('mo_basis/mo_coef_complex',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2))) qph5.create_dataset('mo_basis/mo_coef_complex',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2)))
qph5.create_dataset('mo_basis/mo_coef_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2))) qph5.create_dataset('mo_basis/mo_coef_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2)))
if print_debug:
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold) print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
########################################## ##########################################
@ -719,20 +731,21 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
ovlp_ao_blocked_f = block_diag(*ovlp_ao_f) ovlp_ao_blocked_f = block_diag(*ovlp_ao_f)
ne_ao_blocked_f = block_diag(*ne_ao_f) ne_ao_blocked_f = block_diag(*ne_ao_f)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_real',data=kin_ao_blocked.real) #qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_real',data=kin_ao_blocked.real)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao_blocked.imag) #qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao_blocked.imag)
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_real',data=ovlp_ao_blocked.real) #qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_real',data=ovlp_ao_blocked.real)
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao_blocked.imag) #qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao_blocked.imag)
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_real', data=ne_ao_blocked.real) #qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_real', data=ne_ao_blocked.real)
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=ne_ao_blocked.imag) #qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=ne_ao_blocked.imag)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic',data=kin_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2))) #qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic',data=kin_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap',data=ovlp_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2))) #qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap',data=ovlp_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e', data=ne_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2))) #qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e', data=ne_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_kpts',data=kin_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2))) qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_kpts',data=kin_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_kpts',data=ovlp_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2))) qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_kpts',data=ovlp_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_kpts', data=ne_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2))) qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_kpts', data=ne_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
if print_debug:
for fname,ints in zip(('S.qp','V.qp','T.qp'), for fname,ints in zip(('S.qp','V.qp','T.qp'),
(ovlp_ao, ne_ao, kin_ao)): (ovlp_ao, ne_ao, kin_ao)):
print_kpts_unblocked_upper(ints,fname,thresh_mono) print_kpts_unblocked_upper(ints,fname,thresh_mono)
@ -754,20 +767,21 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
kin_mo_blocked_f = block_diag(*kin_mo_f) kin_mo_blocked_f = block_diag(*kin_mo_f)
ovlp_mo_blocked_f = block_diag(*ovlp_mo_f) ovlp_mo_blocked_f = block_diag(*ovlp_mo_f)
ne_mo_blocked_f = block_diag(*ne_mo_f) ne_mo_blocked_f = block_diag(*ne_mo_f)
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_real',data=kin_mo_blocked.real) #qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_real',data=kin_mo_blocked.real)
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_imag',data=kin_mo_blocked.imag) #qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_imag',data=kin_mo_blocked.imag)
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_real',data=ovlp_mo_blocked.real) #qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_real',data=ovlp_mo_blocked.real)
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_imag',data=ovlp_mo_blocked.imag) #qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_imag',data=ovlp_mo_blocked.imag)
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_real', data=ne_mo_blocked.real) #qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_real', data=ne_mo_blocked.real)
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_imag', data=ne_mo_blocked.imag) #qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_imag', data=ne_mo_blocked.imag)
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic',data=kin_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2))) #qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic',data=kin_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2)))
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap',data=ovlp_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2))) #qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap',data=ovlp_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2)))
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e', data=ne_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2))) #qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e', data=ne_mo_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nmo,2)))
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_kpts',data=kin_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2))) qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_kpts',data=kin_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_kpts',data=ovlp_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2))) qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_kpts',data=ovlp_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_kpts', data=ne_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2))) qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_kpts', data=ne_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
if print_debug:
for fname,ints in zip(('S.mo.qp','V.mo.qp','T.mo.qp'), for fname,ints in zip(('S.mo.qp','V.mo.qp','T.mo.qp'),
(ovlp_mo, ne_mo, kin_mo)): (ovlp_mo, ne_mo, kin_mo)):
print_kpts_unblocked_upper(ints,fname,thresh_mono) print_kpts_unblocked_upper(ints,fname,thresh_mono)
@ -785,6 +799,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c') kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c')
qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1) qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1)
if print_debug:
print_kcon_chem_to_phys(kconserv,'K.qp') print_kcon_chem_to_phys(kconserv,'K.qp')
########################################## ##########################################
@ -805,6 +820,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
j3ao_new = get_j3ao_new(mf.with_df._cderi,nao,Nk) j3ao_new = get_j3ao_new(mf.with_df._cderi,nao,Nk)
if print_ao_ints_df: if print_ao_ints_df:
if print_debug:
print_df(j3arr,'D.qp',bielec_int_threshold) print_df(j3arr,'D.qp',bielec_int_threshold)
with h5py.File(qph5path,'a') as qph5: with h5py.File(qph5path,'a') as qph5:
@ -817,6 +833,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
j3mo = df_ao_to_mo(j3arr,mo_k) j3mo = df_ao_to_mo(j3arr,mo_k)
j3mo_new = df_ao_to_mo_new(j3ao_new,mo_k) j3mo_new = df_ao_to_mo_new(j3ao_new,mo_k)
if print_debug:
print_df(j3mo,'D.mo.qp',bielec_int_threshold) print_df(j3mo,'D.mo.qp',bielec_int_threshold)
with h5py.File(qph5path,'a') as qph5: with h5py.File(qph5path,'a') as qph5:

2
src/utils_complex/create_ezfio_complex_3idx.py
View File

@ -139,7 +139,7 @@ def convert_kpts(filename,qph5path):
with h5py.File(qph5path,'r') as qph5: with h5py.File(qph5path,'r') as qph5:
if 'mo_one_e_ints' in qph5.keys(): if 'mo_one_e_ints' in qph5.keys():
kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic_kpts'][()].tolist() kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic_kpts'][()].tolist()
ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap'][()].tolist() ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap_kpts'][()].tolist()
ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e_kpts'][()].tolist() ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e_kpts'][()].tolist()
ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim) ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim)