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https://github.com/QuantumPackage/qp2.git
synced 2024-11-19 04:22:32 +01:00
working on pw integral converter
This commit is contained in:
Kevin Gasperich
parent
7b3b10e143
commit
1a9a6b240d
@ -22,12 +22,29 @@ import gzip
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#fname = sys.argv[1]
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#qph5name = sys.argv[2]
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def kconserv_p_from_qkk2_mk(qkk2,mk):
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nk, nk2 = qkk2.shape
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assert(nk == nk2)
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kcon_p = np.zeros((nk,nk,nk),dtype=int)
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for i in range(nk):
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for j in range(nk):
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for k in range(nk):
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kcon_p[i,j,k] = qkk2[mk[j],qkk2[k,i]]
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return kcon_p
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def get_full_path(file_path):
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file_path = os.path.expanduser(file_path)
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file_path = os.path.expandvars(file_path)
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# file_path = os.path.abspath(file_path)
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return file_path
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def make_reim_identity_kblocks(nk,nm,na=None):
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if na is None:
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na = nm
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single_block = np.eye(nm, na, dtype=np.complex128).view(dtype=np.float64).reshape((nm, na, 2))
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kblocks = np.tile(single_block,[nk, 1, 1, 1])
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return kblocks
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def flatten(l):
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res = []
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@ -174,7 +191,7 @@ def convert_mol(filename,qph5path):
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return
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def convert_kpts_cd(filename,qph5path,qmcpack=True):
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def convert_kpts_cd(filename,qph5path,qmcpack=True,is_ao=True):
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import json
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ezfio.set_file(filename)
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@ -186,20 +203,36 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
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ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
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with h5py.File(qph5path,'r') as qph5:
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kpt_num = qph5['Hamiltonian']['KPoints'].shape[0]
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elec_alpha_num = qph5['Hamiltonian']['dims'][4]
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elec_beta_num = qph5['Hamiltonian']['dims'][5]
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orb_num = qph5['Hamiltonian']['dims'][3]
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try:
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is_ao = json.loads(qph5['metadata'][()].decode("utf-8").replace("'",'"'))['ortho_ao']
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if is_ao:
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ao_num = orb_num
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elif is_ao ==False:
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mo_num = orb_num
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else:
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raise ValueError('Problem with ortho_ao key in metadata')
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except:
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raise UnicodeDecodeError('metadata not correctly parsed from HDF5 file')
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kpt_num = qph5['Hamiltonian/KPoints'][()].shape[0]
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ham_dims = qph5['Hamiltonian/dims'][()]
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NMOPerKP = qph5['Hamiltonian/NMOPerKP'][()]
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_, _, kpt_num, orb_num, elec_alpha_num_tot, elec_beta_num_tot, _, nchol_maybe = ham_dims
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#for now, all kpts must have same number of MOs
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for nmoi in NMOPerKP:
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if nmoi != NMOPerKP[0]:
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print("ERROR: all KPs must have same number of MOs")
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raise ValueError
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#TODO: fix na, nb in rmg
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assert(elec_alpha_num_tot % kpt_num == 0)
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assert(elec_beta_num_tot % kpt_num == 0)
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elec_alpha_num_per_kpt = elec_alpha_num_tot // kpt_num
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elec_beta_num_per_kpt = elec_beta_num_tot // kpt_num
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#elec_alpha_num_per_kpt = qph5['Hamiltonian']['dims'][4]
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#elec_beta_num_per_kpt = qph5['Hamiltonian']['dims'][5]
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#orb_num = qph5['Hamiltonian']['dims'][3]
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#try:
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# is_ao = json.loads(qph5['metadata'][()].decode("utf-8").replace("'",'"'))['ortho_ao']
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# if is_ao:
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# ao_num = orb_num
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# elif is_ao ==False:
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# mo_num = orb_num
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# else:
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# raise ValueError('Problem with ortho_ao key in metadata')
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#except:
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# raise UnicodeDecodeError('metadata not correctly parsed from HDF5 file')
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ezfio.set_nuclei_kpt_num(kpt_num)
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kpt_pair_num = (kpt_num*kpt_num + kpt_num)//2
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@ -210,12 +243,20 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
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# these are totals (kpt_num * num_per_kpt)
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# need to change if we want to truncate orbital space within pyscf
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_ao_basis_ao_num_per_kpt(ao_num//kpt_num)
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ezfio.set_mo_basis_mo_num_per_kpt(mo_num//kpt_num)
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ezfio.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_num
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#if is_ao:
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# ao_num = orb_num*kpt_num
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#TODO: fix this?
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ao_num_tot = orb_num
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ao_num_per_kpt = NMOPerKP[0]
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mo_num_tot = orb_num
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mo_num_per_kpt = NMOPerKP[0]
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#mo_num_per_kpt = ao_num_per_kpt
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ezfio.set_ao_basis_ao_num(ao_num_per_kpt * kpt_num)
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ezfio.set_mo_basis_mo_num(mo_num_per_kpt * kpt_num)
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ezfio.set_ao_basis_ao_num_per_kpt(ao_num_per_kpt)
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ezfio.set_mo_basis_mo_num_per_kpt(mo_num_per_kpt)
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ezfio.electrons_elec_alpha_num = elec_alpha_num_per_kpt * kpt_num
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ezfio.electrons_elec_beta_num = elec_beta_num_per_kpt * kpt_num
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##########################################
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# #
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# Basis #
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@ -228,13 +269,38 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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# #
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##########################################
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#TODO
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#coef_per_kpt = np.eye(mo_num_per_kpt, ao_num_per_kpt, dtype=np.complex128).view(dtype=np.float64).reshape((mo_num_per_kpt, ao_num_per_kpt, 2))
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#mo_coef_kpts = np.tile(coef_per_kpt,[kpt_num, 1, 1, 1])
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#qph5.create_dataset('mo_basis/mo_coef_kpts',data=make_reim_identity_kblocks(kpt_num, mo_num_per_kpt, ao_num_per_kpt))
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ezfio.set_mo_basis_mo_coef_kpts(make_reim_identity_kblocks(kpt_num, mo_num_per_kpt, ao_num_per_kpt))
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##########################################
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# #
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# Integrals Mono #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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# we don't have separate kinetic, nuc-elec, pseudo 1e ints, so just combine in nuc-elec and set rest to zero
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mono_ints_tot = np.zeros((kpt_num,ao_num_per_kpt,ao_num_per_kpt,2),dtype=np.float64)
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for i in range(kpt_num):
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mono_ints_tot[i] = qph5[f'Hamiltonian/H1_kp{i}'][()]
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ovlp_ao_reim = make_reim_identity_kblocks(kpt_num,ao_num_per_kpt,ao_num_per_kpt)
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kin_ao_reim = np.zeros((kpt_num,ao_num_per_kpt,ao_num_per_kpt,2),dtype=np.float64)
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ne_ao_reim = mono_ints_tot
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ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim)
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ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read')
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ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read')
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ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read')
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"""
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with h5py.File(qph5path,'r') as qph5:
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with h5py.File(qph5path,'r') as qph5:
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if is_ao:
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kin_ao_reim=
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ovlp_ao_reim=
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@ -267,16 +333,19 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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##########################################
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#TODO
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with h5py.File(qph5path,'r') as qph5:
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kconserv = qph5['nuclei/kconserv'][()].tolist()
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minusk = qph5['Hamiltonian']['MinusK'][:]+1
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QKTok2 = qph5['Hamiltonian']['QPTok2'][:]+1
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#kconserv = qph5['nuclei/kconserv'][()].tolist()
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#TODO: change this after rmg is fixed
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#minusk = qph5['Hamiltonian']['MinusK'][:]+1
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QKTok2 = qph5['Hamiltonian']['QKTok2'][:]+1
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minusk = QKTok2[:,0]
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kconserv = kconserv_p_from_qkk2_mk(QKTok2-1,minusk-1)+1
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unique_kpt_num = len(qph5['Hamiltonian']['KPFactorized'])
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unique_k_idx = []
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for i in qph5['Hamiltonian']['KPFactorized'].keys():
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unique_k_idx.append(int(i[1:])+1)
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kpt_sparse_map = np.zeros(kpt_num)
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for i in range(kpt_num):
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if i+1 in uniq_k_idx:
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if i+1 in unique_k_idx:
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kpt_sparse_map[i] = i+1
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else:
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kpt_sparse_map[i] = -minusk[i]
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@ -298,16 +367,18 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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# should this be in ao_basis? ao_two_e_ints?
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with h5py.File(qph5path,'r') as qph5:
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nchol_per_kpt = qph5['Hamiltonian']['NCholPerKP'][:]
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print(nchol_per_kpt)
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nchol_per_kpt = nchol_per_kpt[nchol_per_kpt != 0]
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print(nchol_per_kpt)
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nchol_per_kpt_max = max(nchol_per_kpt)
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ezfio.set_chol_num(nchol_per_kpt)
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ezfio.set_chol_num_max(nchol_per_kpt_max)
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ezfio.set_ao_two_e_ints_chol_num(nchol_per_kpt)
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ezfio.set_ao_two_e_ints_chol_num_max(nchol_per_kpt_max)
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if is_ao:
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ao_num_per_kpt = ao_num//kpt_num
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ezfio.set_io_chol_ao_integrals('Read')
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#ao_num_per_kpt = ao_num//kpt_num
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ezfio.set_ao_two_e_ints_io_chol_ao_integrals('Read')
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#ao_chol_two_e_ints = np.zeros((2, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max, kpt_num, len(nchol_per_kpt)))
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L_list = []
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for i in len(nchol_per_kpt):
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for i in range(len(nchol_per_kpt)):
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L = qph5['Hamiltonian']['KPFactorized'][f'L{i}'][:]
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L.reshape(kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt[i], 2)
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L = np.einsum("ijklm->ilkjm", A, B)
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@ -344,7 +415,7 @@ def convert_kpts_cd(filename,qph5path,qmcpack=True):
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ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
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ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
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"""
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mo_num_per_kpt = ao_num//kpt_num
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#mo_num_per_kpt = ao_num//kpt_num
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ezfio.set_io_chol_mo_integrals('Read')
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#ao_chol_two_e_ints = np.zeros((2, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max, kpt_num, len(nchol_per_kpt)))
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L_list = []
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