#!/usr/bin/env python from ezfio import ezfio import h5py import sys import numpy as np filename = sys.argv[1] h5filename = sys.argv[2] #num_elec, nucl_num, mo_num = map(int,sys.argv[2:5]) #nuclear_repulsion = float(sys.argv[5]) #ao_num = int(sys.argv[6]) #n_kpts = int(sys.argv[7]) #n_aux = int(sys.argv[8]) ezfio.set_file(filename) qph5=h5py.File(h5filename,'r') kpt_num = qph5['nuclei'].attrs['kpt_num'] ezfio.set_nuclei_kpt_num(kpt_num) kpt_pair_num = (kpt_num*kpt_num + kpt_num)//2 ezfio.set_nuclei_kpt_pair_num(kpt_pair_num) # should this be in ao_basis? ao_two_e_ints? df_num = qph5['ao_two_e_ints'].attrs['df_num'] ezfio.set_ao_two_e_ints_df_num(df_num) # these are totals (kpt_num * num_per_kpt) # need to change if we want to truncate orbital space within pyscf ezfio.electrons_elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num'] ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num'] nucl_num = qph5['nuclei'].attrs['nucl_num'] nucl_num_per_kpt = nucl_num // kpt_num ao_num = qph5['ao_basis'].attrs['ao_num'] mo_num = qph5['mo_basis'].attrs['mo_num'] ezfio.set_mo_basis_mo_num(mo_num) ##ao_num = mo_num ##Important ! #import math #nelec_per_kpt = num_elec // n_kpts #nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.)) #nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.)) # #ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts) #ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts) #ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.)) #ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.)) #ezfio.set_utils_num_kpts(n_kpts) #ezfio.set_integrals_bielec_df_num(n_aux) #(old)Important #ezfio.set_nuclei_nucl_num(nucl_num) #ezfio.set_nuclei_nucl_charge([0.]*nucl_num) #ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num ) #ezfio.set_nuclei_nucl_label( ['He'] * nucl_num ) ezfio.set_nuclei_nucl_num(nucl_num_per_kpt) nucl_charge=qph5['nuclei/nucl_charge'][()].tolist() ezfio.set_nuclei_nucl_charge(nucl_charge) nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist() ezfio.set_nuclei_nucl_coord(nucl_coord) nucl_label=qph5['nuclei/nucl_label'][()].tolist() ezfio.set_nuclei_nucl_label(nucl_label) ezfio.set_nuclei_io_nuclear_repulsion('Read') nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion'] ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion) # Ao num #ao_num = mo_num #ezfio.set_ao_basis_ao_basis("Dummy one. We read MO") ezfio.set_ao_basis_ao_num(ao_num) #ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis']) ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist()) #Just need one (can clean this up later) ao_prim_num_max = 5 d = [ [0] *ao_prim_num_max]*ao_num ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num) ezfio.set_ao_basis_ao_power(d) ezfio.set_ao_basis_ao_coef(d) ezfio.set_ao_basis_ao_expo(d) ezfio.set_mo_basis_mo_num(mo_num) #c_mo = [[1 if i==j else 0 for i in range(mo_num)] for j in range(ao_num)] #ezfio.set_mo_basis_mo_coef([ [0]*mo_num] * ao_num) ##ezfio.set_mo_basis_mo_coef_real(c_mo) mo_coef_re0 = qph5['mo_basis/mo_coef_real'][()].T mo_coef_im0 = qph5['mo_basis/mo_coef_imag'][()].T mo_coef_cmplx0 = np.stack((mo_coef_re0,mo_coef_im0),axis=-1).tolist() #ezfio.set_mo_basis_mo_coef_real(qph5['mo_basis/mo_coef_real'][()].tolist()) #ezfio.set_mo_basis_mo_coef_imag(qph5['mo_basis/mo_coef_imag'][()].tolist()) ezfio.set_mo_basis_mo_coef_complex(mo_coef_cmplx0) #maybe fix qp so we don't need this? #ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num]) ezfio.set_nuclei_is_complex(True) # fortran-ordered re,im parts kin_ao_re0=qph5['ao_one_e_ints/ao_integrals_kinetic_real'][()].T kin_ao_im0=qph5['ao_one_e_ints/ao_integrals_kinetic_imag'][()].T #test where to stack? (axis=0 or -1?) kin_ao_cmplx0=np.stack((kin_ao_re0,kin_ao_im0),axis=-1).tolist() ovlp_ao_re0=qph5['ao_one_e_ints/ao_integrals_overlap_real'][()].T ovlp_ao_im0=qph5['ao_one_e_ints/ao_integrals_overlap_imag'][()].T #test where to stack? (axis=0 or -1?) ovlp_ao_cmplx0=np.stack((ovlp_ao_re0,ovlp_ao_im0),axis=-1).tolist() ne_ao_re0=qph5['ao_one_e_ints/ao_integrals_n_e_real'][()].T ne_ao_im0=qph5['ao_one_e_ints/ao_integrals_n_e_imag'][()].T #test where to stack? (axis=0 or -1?) ne_ao_cmplx0=np.stack((ne_ao_re0,ne_ao_im0),axis=-1).tolist() ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_cmplx0) ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_cmplx0) ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(ne_ao_cmplx0) ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read') ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read') ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read') 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)) #ezfio.set_ao_two_e_ints_df_ao_integrals_real(dfao_re.tolist()) #ezfio.set_ao_two_e_ints_df_ao_integrals_imag(dfao_im.tolist()) dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist() ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0) ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read') #TODO: add check and only do this if ints exist #dfmo_re=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0)).tolist() #dfmo_im=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0)).tolist() #ezfio.set_mo_two_e_ints_df_mo_integrals_real(dfmo_re) #ezfio.set_mo_two_e_ints_df_mo_integrals_imag(dfmo_im)