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https://github.com/QuantumPackage/qp2.git
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156 lines
5.4 KiB
Python
Executable File
156 lines
5.4 KiB
Python
Executable File
#!/usr/bin/env python
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from ezfio import ezfio
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import h5py
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import sys
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import numpy as np
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filename = sys.argv[1]
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h5filename = sys.argv[2]
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#num_elec, nucl_num, mo_num = map(int,sys.argv[2:5])
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#nuclear_repulsion = float(sys.argv[5])
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#ao_num = int(sys.argv[6])
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#n_kpts = int(sys.argv[7])
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#n_aux = int(sys.argv[8])
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ezfio.set_file(filename)
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qph5=h5py.File(h5filename,'r')
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kpt_num = qph5['nuclei'].attrs['kpt_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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# should this be in ao_basis? ao_two_e_ints?
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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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# 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.electrons_elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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nucl_num_per_kpt = nucl_num // kpt_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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ezfio.set_mo_basis_mo_num(mo_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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ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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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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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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# Ao num
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#ao_num = mo_num
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#ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
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ezfio.set_ao_basis_ao_num(ao_num)
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#ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
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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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ezfio.set_mo_basis_mo_num(mo_num)
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#c_mo = [[1 if i==j else 0 for i in range(mo_num)] for j in range(ao_num)]
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#ezfio.set_mo_basis_mo_coef([ [0]*mo_num] * ao_num)
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##ezfio.set_mo_basis_mo_coef_real(c_mo)
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mo_coef_re0 = qph5['mo_basis/mo_coef_real'][()].T
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mo_coef_im0 = qph5['mo_basis/mo_coef_imag'][()].T
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mo_coef_cmplx0 = np.stack((mo_coef_re0,mo_coef_im0),axis=-1).tolist()
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#ezfio.set_mo_basis_mo_coef_real(qph5['mo_basis/mo_coef_real'][()].tolist())
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#ezfio.set_mo_basis_mo_coef_imag(qph5['mo_basis/mo_coef_imag'][()].tolist())
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ezfio.set_mo_basis_mo_coef_complex(mo_coef_cmplx0)
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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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ezfio.set_nuclei_is_complex(True)
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# fortran-ordered re,im parts
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kin_ao_re0=qph5['ao_one_e_ints/ao_integrals_kinetic_real'][()].T
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kin_ao_im0=qph5['ao_one_e_ints/ao_integrals_kinetic_imag'][()].T
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#test where to stack? (axis=0 or -1?)
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kin_ao_cmplx0=np.stack((kin_ao_re0,kin_ao_im0),axis=-1).tolist()
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ovlp_ao_re0=qph5['ao_one_e_ints/ao_integrals_overlap_real'][()].T
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ovlp_ao_im0=qph5['ao_one_e_ints/ao_integrals_overlap_imag'][()].T
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#test where to stack? (axis=0 or -1?)
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ovlp_ao_cmplx0=np.stack((ovlp_ao_re0,ovlp_ao_im0),axis=-1).tolist()
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ne_ao_re0=qph5['ao_one_e_ints/ao_integrals_n_e_real'][()].T
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ne_ao_im0=qph5['ao_one_e_ints/ao_integrals_n_e_imag'][()].T
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#test where to stack? (axis=0 or -1?)
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ne_ao_cmplx0=np.stack((ne_ao_re0,ne_ao_im0),axis=-1).tolist()
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ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_cmplx0)
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ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_cmplx0)
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ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(ne_ao_cmplx0)
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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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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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#ezfio.set_ao_two_e_ints_df_ao_integrals_real(dfao_re.tolist())
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#ezfio.set_ao_two_e_ints_df_ao_integrals_imag(dfao_im.tolist())
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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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ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
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#TODO: add check and only do this if ints exist
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#dfmo_re=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0)).tolist()
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#dfmo_im=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0)).tolist()
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#ezfio.set_mo_two_e_ints_df_mo_integrals_real(dfmo_re)
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#ezfio.set_mo_two_e_ints_df_mo_integrals_imag(dfmo_im)
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