mirror of
https://github.com/QuantumPackage/qp2.git
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updated pyscf converter
This commit is contained in:
Kevin Gasperich
parent
6512d3827f
commit
bd076b62a4
@ -135,6 +135,387 @@ def convert_mol(filename,qph5path):
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return
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def convert_kpts(filename,qph5path):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(True)
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with h5py.File(qph5path,'r') as qph5:
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kpt_num = qph5['nuclei'].attrs['kpt_num']
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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ao_num = qph5['ao_basis'].attrs['ao_num']
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mo_num = qph5['mo_basis'].attrs['mo_num']
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elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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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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ezfio.set_nuclei_kpt_pair_num(kpt_pair_num)
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# don't multiply nuclei by kpt_num
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# work in k-space, not in equivalent supercell
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nucl_num_per_kpt = nucl_num
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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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##ao_num = mo_num
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##Important !
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#import math
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#nelec_per_kpt = num_elec // n_kpts
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#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
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#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
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#
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#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
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#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
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#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
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#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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#ezfio.set_utils_num_kpts(n_kpts)
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#ezfio.set_integrals_bielec_df_num(n_aux)
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#(old)Important
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#ezfio.set_nuclei_nucl_num(nucl_num)
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#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
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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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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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if isinstance(nucl_label[0],bytes):
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nucl_label = list(map(lambda x:x.decode(),nucl_label))
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ezfio.set_nuclei_nucl_label(nucl_label)
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ezfio.set_nuclei_io_nuclear_repulsion('Read')
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#Just need one (can clean this up later)
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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##########################################
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# #
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# MO Coef #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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mo_coef_kpts = qph5['mo_basis/mo_coef_kpts'][()].tolist()
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mo_coef_cplx = qph5['mo_basis/mo_coef_complex'][()].tolist()
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ezfio.set_mo_basis_mo_coef_kpts(mo_coef_kpts)
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ezfio.set_mo_basis_mo_coef_complex(mo_coef_cplx)
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#maybe fix qp so we don't need this?
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#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
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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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if 'ao_one_e_ints' in qph5.keys():
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kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic_kpts'][()].tolist()
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ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap_kpts'][()].tolist()
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ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e_kpts'][()].tolist()
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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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with h5py.File(qph5path,'r') as qph5:
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if 'mo_one_e_ints' in qph5.keys():
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kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic_kpts'][()].tolist()
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ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap_kpts'][()].tolist()
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ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e_kpts'][()].tolist()
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ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim)
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ezfio.set_mo_one_e_ints_mo_integrals_overlap_kpts(ovlp_mo_reim)
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#ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
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ezfio.set_mo_one_e_ints_mo_integrals_n_e_kpts(ne_mo_reim)
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ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
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ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
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#ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
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ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
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##########################################
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# #
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# k-points #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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kconserv = qph5['nuclei/kconserv'][()].tolist()
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ezfio.set_nuclei_kconserv(kconserv)
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ezfio.set_nuclei_io_kconserv('Read')
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##########################################
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# #
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# Integrals Bi #
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# #
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##########################################
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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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if 'ao_two_e_ints' in qph5.keys():
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df_num = qph5['ao_two_e_ints'].attrs['df_num']
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ezfio.set_ao_two_e_ints_df_num(df_num)
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if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
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# dfao_re0=qph5['ao_two_e_ints/df_ao_integrals_real'][()].transpose((3,2,1,0))
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# dfao_im0=qph5['ao_two_e_ints/df_ao_integrals_imag'][()].transpose((3,2,1,0))
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# dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist()
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# ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0)
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dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
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ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
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ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
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if 'mo_two_e_ints' in qph5.keys():
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df_num = qph5['ao_two_e_ints'].attrs['df_num']
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ezfio.set_ao_two_e_ints_df_num(df_num)
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# dfmo_re0=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0))
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# dfmo_im0=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0))
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# dfmo_cmplx0 = np.stack((dfmo_re0,dfmo_im0),axis=-1).tolist()
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# ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_cmplx0)
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dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
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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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return
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def convert_cplx(filename,qph5path):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(True)
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with h5py.File(qph5path,'r') as qph5:
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kpt_num = qph5['nuclei'].attrs['kpt_num']
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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ao_num = qph5['ao_basis'].attrs['ao_num']
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mo_num = qph5['mo_basis'].attrs['mo_num']
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elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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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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ezfio.set_nuclei_kpt_pair_num(kpt_pair_num)
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# don't multiply nuclei by kpt_num
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# work in k-space, not in equivalent supercell
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nucl_num_per_kpt = nucl_num
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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.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_num
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##ao_num = mo_num
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##Important !
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#import math
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#nelec_per_kpt = num_elec // n_kpts
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#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
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#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
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#
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#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
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#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
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#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
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#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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#ezfio.set_utils_num_kpts(n_kpts)
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#ezfio.set_integrals_bielec_df_num(n_aux)
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#(old)Important
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#ezfio.set_nuclei_nucl_num(nucl_num)
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#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
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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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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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if isinstance(nucl_label[0],bytes):
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nucl_label = list(map(lambda x:x.decode(),nucl_label))
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ezfio.set_nuclei_nucl_label(nucl_label)
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ezfio.set_nuclei_io_nuclear_repulsion('Read')
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
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ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
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#Just need one (can clean this up later)
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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##########################################
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# #
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# MO Coef #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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mo_coef_reim = qph5['mo_basis/mo_coef_complex'][()].tolist()
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ezfio.set_mo_basis_mo_coef_complex(mo_coef_reim)
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#maybe fix qp so we don't need this?
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#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
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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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if 'ao_one_e_ints' in qph5.keys():
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kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic'][()].tolist()
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ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap'][()].tolist()
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ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e'][()].tolist()
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ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(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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with h5py.File(qph5path,'r') as qph5:
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if 'mo_one_e_ints' in qph5.keys():
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kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic'][()].tolist()
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#ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap'][()].tolist()
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ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e'][()].tolist()
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ezfio.set_mo_one_e_ints_mo_integrals_kinetic_complex(kin_mo_reim)
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#ezfio.set_mo_one_e_ints_mo_integrals_overlap_complex(ovlp_mo_reim)
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#ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
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ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
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ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
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#ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
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#ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
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ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
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##########################################
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# #
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# k-points #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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kconserv = qph5['nuclei/kconserv'][()].tolist()
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ezfio.set_nuclei_kconserv(kconserv)
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ezfio.set_nuclei_io_kconserv('Read')
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||||
##########################################
|
||||
# #
|
||||
# Integrals Bi #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
# should this be in ao_basis? ao_two_e_ints?
|
||||
with h5py.File(qph5path,'r') as qph5:
|
||||
if 'ao_two_e_ints' in qph5.keys():
|
||||
df_num = qph5['ao_two_e_ints'].attrs['df_num']
|
||||
ezfio.set_ao_two_e_ints_df_num(df_num)
|
||||
if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
|
||||
# dfao_re0=qph5['ao_two_e_ints/df_ao_integrals_real'][()].transpose((3,2,1,0))
|
||||
# dfao_im0=qph5['ao_two_e_ints/df_ao_integrals_imag'][()].transpose((3,2,1,0))
|
||||
# dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist()
|
||||
# ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0)
|
||||
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
|
||||
ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
|
||||
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
|
||||
|
||||
if 'mo_two_e_ints' in qph5.keys():
|
||||
df_num = qph5['ao_two_e_ints'].attrs['df_num']
|
||||
ezfio.set_ao_two_e_ints_df_num(df_num)
|
||||
# dfmo_re0=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0))
|
||||
# dfmo_im0=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0))
|
||||
# dfmo_cmplx0 = np.stack((dfmo_re0,dfmo_im0),axis=-1).tolist()
|
||||
# ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_cmplx0)
|
||||
dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
|
||||
ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
|
||||
ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
|
||||
|
||||
return
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
ARGUMENTS = docopt(__doc__)
|
||||
|
||||
@ -145,15 +526,21 @@ if __name__ == '__main__':
|
||||
else:
|
||||
EZFIO_FILE = "{0}.ezfio".format(FILE)
|
||||
|
||||
|
||||
convert_mol(EZFIO_FILE,FILE)
|
||||
with h5py.File(FILE,'r') as qph5:
|
||||
do_kpts = ('kconserv' in qph5['nuclei'].keys())
|
||||
if (do_kpts):
|
||||
print("converting HDF5 to EZFIO for periodic system")
|
||||
convert_kpts(EZFIO_FILE,FILE)
|
||||
else:
|
||||
print("converting HDF5 to EZFIO for molecular system")
|
||||
convert_mol(EZFIO_FILE,FILE)
|
||||
|
||||
sys.stdout.flush()
|
||||
if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
|
||||
print("""Warning: You need to run
|
||||
|
||||
qp run save_ortho_mos
|
||||
|
||||
to be sure your MOs will be orthogonal, which is not the case when
|
||||
the MOs are read from output files (not enough precision in output).""")
|
||||
# sys.stdout.flush()
|
||||
# if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
|
||||
# print("""Warning: You need to run
|
||||
#
|
||||
# qp run save_ortho_mos
|
||||
#
|
||||
#to be sure your MOs will be orthogonal, which is not the case when
|
||||
#the MOs are read from output files (not enough precision in output).""")
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user