2020-07-29 19:14:14 +02:00
|
|
|
#!/usr/bin/env python3
|
|
|
|
|
"""
|
|
|
|
|
convert hdf5 output (e.g. from PySCF) to ezfio
|
|
|
|
|
|
|
|
|
|
Usage:
|
|
|
|
|
qp_convert_h5_to_ezfio [-o EZFIO_DIR] FILE
|
|
|
|
|
|
|
|
|
|
Options:
|
|
|
|
|
-o --output=EZFIO_DIR Produced directory
|
|
|
|
|
by default is FILE.ezfio
|
|
|
|
|
|
|
|
|
|
"""
|
|
|
|
|
from ezfio import ezfio
|
|
|
|
|
import h5py
|
|
|
|
|
import sys
|
|
|
|
|
import numpy as np
|
|
|
|
|
import os
|
|
|
|
|
from docopt import docopt
|
|
|
|
|
#fname = sys.argv[1]
|
|
|
|
|
#qph5name = sys.argv[2]
|
|
|
|
|
|
|
|
|
|
def get_full_path(file_path):
|
|
|
|
|
file_path = os.path.expanduser(file_path)
|
|
|
|
|
file_path = os.path.expandvars(file_path)
|
|
|
|
|
# file_path = os.path.abspath(file_path)
|
|
|
|
|
return file_path
|
|
|
|
|
|
|
|
|
|
def convert_mol(filename,qph5path):
|
|
|
|
|
ezfio.set_file(filename)
|
|
|
|
|
ezfio.set_nuclei_is_complex(False)
|
|
|
|
|
|
|
|
|
|
with h5py.File(qph5path,'r') as qph5:
|
|
|
|
|
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_nucl_num(nucl_num)
|
|
|
|
|
|
|
|
|
|
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)
|
|
|
|
|
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:
|
|
|
|
|
do_pseudo = qph5['pseudo'].attrs['do_pseudo']
|
|
|
|
|
ezfio.set_pseudo_do_pseudo(do_pseudo)
|
|
|
|
|
if (do_pseudo):
|
|
|
|
|
ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
|
|
|
|
|
ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
|
|
|
|
|
ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
|
|
|
|
|
ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
|
|
|
|
|
ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
|
|
|
|
|
|
|
|
|
|
##########################################
|
|
|
|
|
# #
|
|
|
|
|
# Basis #
|
|
|
|
|
# #
|
|
|
|
|
##########################################
|
|
|
|
|
|
|
|
|
|
with h5py.File(qph5path,'r') as qph5:
|
|
|
|
|
#coeftmp = qph5['ao_basis/ao_coef'][()]
|
|
|
|
|
#expotmp = qph5['ao_basis/ao_expo'][()]
|
|
|
|
|
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
|
|
|
|
|
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
|
|
|
|
|
ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
|
|
|
|
|
ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
|
|
|
|
|
ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
|
|
|
|
|
ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
##########################################
|
|
|
|
|
# #
|
|
|
|
|
# MO Coef #
|
|
|
|
|
# #
|
|
|
|
|
##########################################
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
with h5py.File(qph5path,'r') as qph5:
|
|
|
|
|
mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
|
|
|
|
|
ezfio.set_mo_basis_mo_coef(mo_coef)
|
|
|
|
|
#maybe fix qp so we don't need this?
|
|
|
|
|
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
|
|
|
|
|
|
|
|
|
|
return
|
|
|
|
|
|
2020-07-29 21:07:03 +02:00
|
|
|
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
|
|
|
|
|
|
|
|
|
|
|
2020-07-29 19:14:14 +02:00
|
|
|
if __name__ == '__main__':
|
|
|
|
|
ARGUMENTS = docopt(__doc__)
|
|
|
|
|
|
|
|
|
|
FILE = get_full_path(ARGUMENTS['FILE'])
|
|
|
|
|
|
|
|
|
|
if ARGUMENTS["--output"]:
|
|
|
|
|
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
|
|
|
|
|
else:
|
|
|
|
|
EZFIO_FILE = "{0}.ezfio".format(FILE)
|
|
|
|
|
|
2020-07-29 21:07:03 +02:00
|
|
|
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)
|
2020-07-29 19:14:14 +02:00
|
|
|
|
2020-07-29 21:07:03 +02:00
|
|
|
# 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).""")
|
2020-07-29 19:14:14 +02:00
|
|
|
|
