#!/usr/bin/env python from ezfio import ezfio import h5py import sys import numpy as np fname = sys.argv[1] qph5name = sys.argv[2] #qph5=h5py.File(qph5path,'r') def convert_kpts(filename,qph5path): ezfio.set_file(filename) ezfio.set_nuclei_is_complex(True) with h5py.File(qph5path,'r') as qph5: kpt_num = qph5['nuclei'].attrs['kpt_num'] nucl_num = qph5['nuclei'].attrs['nucl_num'] ao_num = qph5['ao_basis'].attrs['ao_num'] mo_num = qph5['mo_basis'].attrs['mo_num'] elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num'] elec_beta_num = qph5['electrons'].attrs['elec_beta_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) # don't multiply nuclei by kpt_num # work in k-space, not in equivalent supercell nucl_num_per_kpt = nucl_num ezfio.set_nuclei_nucl_num(nucl_num_per_kpt) # these are totals (kpt_num * num_per_kpt) # need to change if we want to truncate orbital space within pyscf ezfio.set_ao_basis_ao_num(ao_num) ezfio.set_mo_basis_mo_num(mo_num) ezfio.set_ao_basis_ao_num_per_kpt(ao_num//kpt_num) ezfio.set_mo_basis_mo_num_per_kpt(mo_num//kpt_num) ezfio.electrons_elec_alpha_num = elec_alpha_num ezfio.electrons_elec_beta_num = elec_beta_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 ) with h5py.File(qph5path,'r') as qph5: nucl_charge=qph5['nuclei/nucl_charge'][()].tolist() nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist() nucl_label=qph5['nuclei/nucl_label'][()].tolist() nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion'] ezfio.set_nuclei_nucl_charge(nucl_charge) ezfio.set_nuclei_nucl_coord(nucl_coord) if isinstance(nucl_label[0],bytes): nucl_label = list(map(lambda x:x.decode(),nucl_label)) ezfio.set_nuclei_nucl_label(nucl_label) ezfio.set_nuclei_io_nuclear_repulsion('Read') ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion) ########################################## # # # Basis # # # ########################################## with h5py.File(qph5path,'r') as qph5: 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) ########################################## # # # MO Coef # # # ########################################## with h5py.File(qph5path,'r') as qph5: mo_coef_kpts = qph5['mo_basis/mo_coef_kpts'][()].tolist() mo_coef_cplx = qph5['mo_basis/mo_coef_complex'][()].tolist() ezfio.set_mo_basis_mo_coef_kpts(mo_coef_kpts) ezfio.set_mo_basis_mo_coef_complex(mo_coef_cplx) #maybe fix qp so we don't need this? #ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num]) ########################################## # # # Integrals Mono # # # ########################################## with h5py.File(qph5path,'r') as qph5: if 'ao_one_e_ints' in qph5.keys(): kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic_kpts'][()].tolist() ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap_kpts'][()].tolist() ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e_kpts'][()].tolist() ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim) ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim) ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim) 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') with h5py.File(qph5path,'r') as qph5: if 'mo_one_e_ints' in qph5.keys(): kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic_kpts'][()].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() ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim) ezfio.set_mo_one_e_ints_mo_integrals_overlap_kpts(ovlp_mo_reim) #ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim) ezfio.set_mo_one_e_ints_mo_integrals_n_e_kpts(ne_mo_reim) ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read') ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read') #ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read') ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read') ########################################## # # # k-points # # # ########################################## with h5py.File(qph5path,'r') as qph5: kconserv = qph5['nuclei/kconserv'][()].tolist() ezfio.set_nuclei_kconserv(kconserv) ezfio.set_nuclei_io_kconserv('Read') ########################################## # # # 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 def convert_cplx(filename,qph5path): ezfio.set_file(filename) ezfio.set_nuclei_is_complex(True) with h5py.File(qph5path,'r') as qph5: kpt_num = qph5['nuclei'].attrs['kpt_num'] nucl_num = qph5['nuclei'].attrs['nucl_num'] ao_num = qph5['ao_basis'].attrs['ao_num'] mo_num = qph5['mo_basis'].attrs['mo_num'] elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num'] elec_beta_num = qph5['electrons'].attrs['elec_beta_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) # don't multiply nuclei by kpt_num # work in k-space, not in equivalent supercell nucl_num_per_kpt = nucl_num ezfio.set_nuclei_nucl_num(nucl_num_per_kpt) # these are totals (kpt_num * num_per_kpt) # need to change if we want to truncate orbital space within pyscf ezfio.set_ao_basis_ao_num(ao_num) ezfio.set_mo_basis_mo_num(mo_num) ezfio.electrons_elec_alpha_num = elec_alpha_num ezfio.electrons_elec_beta_num = elec_beta_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 ) with h5py.File(qph5path,'r') as qph5: nucl_charge=qph5['nuclei/nucl_charge'][()].tolist() nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist() nucl_label=qph5['nuclei/nucl_label'][()].tolist() nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion'] ezfio.set_nuclei_nucl_charge(nucl_charge) ezfio.set_nuclei_nucl_coord(nucl_coord) if isinstance(nucl_label[0],bytes): nucl_label = list(map(lambda x:x.decode(),nucl_label)) ezfio.set_nuclei_nucl_label(nucl_label) ezfio.set_nuclei_io_nuclear_repulsion('Read') ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion) ########################################## # # # Basis # # # ########################################## with h5py.File(qph5path,'r') as qph5: 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) ########################################## # # # MO Coef # # # ########################################## with h5py.File(qph5path,'r') as qph5: mo_coef_reim = qph5['mo_basis/mo_coef_complex'][()].tolist() ezfio.set_mo_basis_mo_coef_complex(mo_coef_reim) #maybe fix qp so we don't need this? #ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num]) ########################################## # # # Integrals Mono # # # ########################################## with h5py.File(qph5path,'r') as qph5: if 'ao_one_e_ints' in qph5.keys(): kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic'][()].tolist() ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap'][()].tolist() ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e'][()].tolist() ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_reim) ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_reim) ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(ne_ao_reim) 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') with h5py.File(qph5path,'r') as qph5: if 'mo_one_e_ints' in qph5.keys(): kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic'][()].tolist() #ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap'][()].tolist() ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e'][()].tolist() ezfio.set_mo_one_e_ints_mo_integrals_kinetic_complex(kin_mo_reim) #ezfio.set_mo_one_e_ints_mo_integrals_overlap_complex(ovlp_mo_reim) #ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim) ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim) ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read') #ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read') #ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read') ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read') ########################################## # # # k-points # # # ########################################## with h5py.File(qph5path,'r') as qph5: kconserv = qph5['nuclei/kconserv'][()].tolist() ezfio.set_nuclei_kconserv(kconserv) ezfio.set_nuclei_io_kconserv('Read') ########################################## # # # 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 #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) convert_kpts(fname,qph5name)