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qp2/bin/qp_convert_h5_to_ezfio

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added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
#!/usr/bin/env python3
"""
convert hdf5 output (e.g. from PySCF) to ezfio
Usage:
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
qp_convert_h5_to_ezfio [--noqmc] [-o EZFIO_DIR] FILE
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
Options:
-o --output=EZFIO_DIR Produced directory
by default is FILE.ezfio
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
--noqmc don't include basis, cell, etc. for QMCPACK
starting separate function with dummy atom
2022-05-03 18:23:51 +02:00
-cd h5 contains cholesky decomposition informatin, these h5 result from RMG and the pyscf AFQMC converter of QMCPACK.
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
"""
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)
fix for bytes/string conversion
2020-07-30 00:36:28 +02:00
if isinstance(nucl_label[0],bytes):
nucl_label = list(map(lambda x:x.decode(),nucl_label))
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
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
starting separate function with dummy atom
2022-05-03 18:23:51 +02:00
def convert_kpts_cd(filename,qph5path,qmcpack=True):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(True)
# Dummy atom since AFQMC h5 has no atom information
nucl_num = 1
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 )
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
with h5py.File(qph5path,'r') as qph5:
kpt_num = qph5['Hamiltonian']['KPoints'].shape[0]
elec_alpha_num = qph5['Hamiltonian']['dims'][4]
elec_beta_num = qph5['Hamiltonian']['dims'][5]
orb_num = qph5['Hamiltonian']['dims'][3]
try:
is_ao = json.loads(qph5['metadata'][()].decode("utf-8").replace("'",'"'))['ortho_ao']
if is_ao:
ao_num = orb_num
elif is_ao ==False:
mo_num = orb_num
else:
raise ValueError('Problem with ortho_ao key in metadata')
except:
raise UnicodeDecodeError('metadata not correctly parsed from HDF5 file')
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
##########################################
# #
# Basis #
# #
##########################################
#TODO
##########################################
# #
# MOCoeff #
# #
##########################################
#TODO
##########################################
# #
# Integrals Mono #
# #
##########################################
"""
with h5py.File(qph5path,'r') as qph5:
if is_ao:
kin_ao_reim=
ovlp_ao_reim=
ne_ao_reim=
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')
else:
kin_mo_reim=
ovlp_mo_reim=
ne_mo_reim=
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_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')
"""
##########################################
# #
# k-points #
# #
##########################################
#TODO
with h5py.File(qph5path,'r') as qph5:
kconserv = qph5['nuclei/kconserv'][()].tolist()
ezfio.set_nuclei_kconserv(kconserv)
ezfio.set_nuclei_io_kconserv('Read')
# qktok2
# minuxk
# kpt_sparse_map
# unique_kpt_num
# io_kpt_symm
##########################################
# #
# Integrals Bi #
# #
##########################################
# should this be in ao_basis? ao_two_e_ints?
with h5py.File(qph5path,'r') as qph5:
qph5[]
nchol_per_kpt = qph5['Hamiltonian']['NCholPerKP'][:]
nchol_per_kpt = nchol_per_kpt[nchol_per_kpt != 0]
Start ao chol ints
2022-05-04 22:03:11 +02:00
nchol_per_kpt_max = max(nchol_per_kpt)
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
ezfio.set_chol_num(nchol_per_kpt)
Start ao chol ints
2022-05-04 22:03:11 +02:00
ezfio.set_chol_num_max(nchol_per_kpt_max)
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
if is_ao:
Start ao chol ints
2022-05-04 22:03:11 +02:00
ao_num_per_kpt = ao_num//kpt_num
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
ezfio.set_io_chol_ao_integrals('Read')
Reordering indicies AO chol integrals
2022-05-04 22:49:05 +02:00
#ao_chol_two_e_ints = np.zeros((2, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max, kpt_num, len(nchol_per_kpt)))
L_list = []
Start ao chol ints
2022-05-04 22:03:11 +02:00
for i in len(nchol_per_kpt):
L = qph5['Hamiltonian']['KPFactorized'][f'L{i}'][:]
L.reshape(kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt[i], 2)
Reordering indicies AO chol integrals
2022-05-04 22:49:05 +02:00
L = np.einsum("ijklm->ilkjm", A, B)
L_list.append(L)
Start ao chol ints
2022-05-04 22:03:11 +02:00
#(6, 5184, 2)
Reordering indicies AO chol integrals
2022-05-04 22:49:05 +02:00
"""
Start ao chol ints
2022-05-04 22:03:11 +02:00
for cmplx in range(2):
for ao_idx_i in range(ao_num_per_kpt):
for ao_idx_j in range(ao_num_per_kpt):
for chol_idx in range(nchol_per_kpt[i]):
for kpt_idx in range(kpt_num):
Reordering indicies AO chol integrals
2022-05-04 22:49:05 +02:00
ao_chol_two_e_ints[cmplx][ao_idx_i][ao_idx_j][chol_idx][kpt_idx][i] = L[kpt_idx][ao_idx_i][ao_idx_j][chol_idx][cmplx]
"""
ao_chol_two_e_ints = np.vstack(L_list)
ao_chol_two_e_ints = ao_chol_two_e_ints.transpose()
ezfio.set_chol_ao_integrals_complex(ao_chol_two_e_ints)
Start ao chol ints
2022-05-04 22:03:11 +02:00
#(2,ao_basis.ao_num_per_kpt,ao_basis.ao_num_per_kpt,ao_two_e_ints.chol_num_max,nuclei.kpt_num,nuclei.unique_kpt_num#)
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
"""
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_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')
"""
else:
ezfio.set_io_chol_mo_integrals('Read')
"""
ezfio.set_io_chol_mo_integrals('Read')
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
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
starting separate function with dummy atom
2022-05-03 18:23:51 +02:00
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
def convert_kpts(filename,qph5path,qmcpack=True):
updated pyscf converter
2020-07-29 21:07:03 +02:00
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)
##########################################
# #
updated qmcpack converter
2020-09-01 17:13:04 +02:00
# Basis(Dummy) #
updated pyscf converter
2020-07-29 21:07:03 +02:00
# #
##########################################
updated qmcpack converter
2020-09-01 17:13:04 +02:00
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())
updated pyscf converter
2020-07-29 21:07:03 +02:00
#Just need one (can clean this up later)
updated qmcpack converter
2020-09-01 17:13:04 +02:00
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)
updated pyscf converter
2020-07-29 21:07:03 +02:00
updated qmcpack converter
2020-09-01 17:13:04 +02:00
###########################################
## #
## Pseudo #
## #
###########################################
#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())
AB update
2020-08-28 21:13:09 +02:00
##########################################
# #
updated qmcpack converter
2020-09-01 17:13:04 +02:00
# Basis(Dummy) #
AB update
2020-08-28 21:13:09 +02:00
# #
##########################################
updated qmcpack converter
2020-09-01 17:13:04 +02:00
#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())
AB update
2020-08-28 21:13:09 +02:00
updated qmcpack converter
2020-09-01 17:13:04 +02:00
##########################################
# #
# Basis(QMC) #
# #
##########################################
AB update
2020-08-28 21:13:09 +02:00
updated qmcpack converter
2020-09-01 17:13:04 +02:00
if qmcpack:
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
try:
with h5py.File(qph5path,'r') as qph5:
ezfio.set_qmcpack_qmc_nshell(qph5['qmcpack'].attrs['qmc_nshell'])
ezfio.set_qmcpack_qmc_prim_num_max(qph5['qmcpack'].attrs['qmc_prim_num_max'])
ezfio.set_qmcpack_qmc_nucl(qph5['qmcpack/qmc_nucl'][()].tolist())
ezfio.set_qmcpack_qmc_prim_num(qph5['qmcpack/qmc_prim_num'][()].tolist())
ezfio.set_qmcpack_qmc_lbas(qph5['qmcpack/qmc_lbas'][()].tolist())
ezfio.set_qmcpack_qmc_coef(qph5['qmcpack/qmc_coef'][()].tolist())
ezfio.set_qmcpack_qmc_expo(qph5['qmcpack/qmc_expo'][()].tolist())
ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
Update qp_convert_h5_to_ezfio add cart flag for qmc
2020-09-15 22:45:45 +02:00
ezfio.set_qmcpack_qmc_cart(qph5['qmcpack'].attrs['cart'])
Fixing converter for qmcpack and qp2 with pbc and excited states
2020-10-19 20:26:16 +02:00
ezfio.set_qmcpack_qmc_pseudo(qph5['qmcpack'].attrs['Pseudo'])
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist())
ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist())
Fixing converter for qmcpack and qp2 with pbc and excited states
2020-10-19 20:26:16 +02:00
ezfio.set_qmcpack_qmc_phase(qph5['qmcpack/qmc_phase'][()].tolist())
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist())
Fixing converter for qmcpack and qp2 with pbc and excited states
2020-10-19 20:26:16 +02:00
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
except AttributeError as err:
print("################################################")
print("# ERROR: problem copying QMCPACK data to ezfio #")
print("# make sure qmcpack plugin is built #")
print("################################################")
#print(f"AttributeError: {err}")
print("to create ezfio without qmcpack data, use 'qp_convert_h5_to_ezfio --noqmc'")
raise
AB update
2020-08-28 21:13:09 +02:00
updated pyscf converter
2020-07-29 21:07:03 +02:00
##########################################
# #
# 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 #
# #
##########################################
AB update
2020-08-28 21:13:09 +02:00
# 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)
##########################################
# #
# Basis #
# #
##########################################
updated pyscf converter
2020-07-29 21:07:03 +02:00
with h5py.File(qph5path,'r') as qph5:
AB update
2020-08-28 21:13:09 +02:00
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'][()]
updated pyscf converter
2020-07-29 21:07:03 +02:00
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
AB update
2020-08-28 21:13:09 +02:00
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())
updated pyscf converter
2020-07-29 21:07:03 +02:00
##########################################
# #
# 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
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
if __name__ == '__main__':
ARGUMENTS = docopt(__doc__)
FILE = get_full_path(ARGUMENTS['FILE'])
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
qmcpack = True
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
if ARGUMENTS["--output"]:
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
else:
EZFIO_FILE = "{0}.ezfio".format(FILE)
changed converter default behavior for qmc
2020-09-01 18:19:09 +02:00
if ARGUMENTS["--noqmc"]:
qmcpack = False
starting separate function with dummy atom
2022-05-03 18:23:51 +02:00
if ARGUMENTS["--rmg"]:
rmg = True
updated pyscf converter
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")
starting separate function with dummy atom
2022-05-03 18:23:51 +02:00
if cd:
print("Using RMG and AFQMC h5")
convert_kpts_cd(EZFIO_FILE,FILE,qmcpack)
else:
adding chol_num info and function framework
2022-05-04 21:14:04 +02:00
convert_kpts(EZFIO_FILE,FILE,qmcpack)
updated pyscf converter
2020-07-29 21:07:03 +02:00
else:
print("converting HDF5 to EZFIO for molecular system")
convert_mol(EZFIO_FILE,FILE)
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
updated pyscf converter
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).""")
added cleaner pyscf h5 converter
2020-07-29 19:14:14 +02:00
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