mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-12-23 21:03:49 +01:00
469df719e7
Dev pbc config
904 lines
38 KiB
Python
Executable File
904 lines
38 KiB
Python
Executable File
#!/usr/bin/env python3
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"""
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convert hdf5 output (e.g. from PySCF) to ezfio
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Usage:
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qp_convert_h5_to_ezfio [--noqmc] [-o EZFIO_DIR] FILE
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Options:
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-o --output=EZFIO_DIR Produced directory
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by default is FILE.ezfio
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--noqmc don't include basis, cell, etc. for QMCPACK
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-cd h5 contains cholesky decomposition informatin, these h5 result from RMG and the pyscf AFQMC converter of QMCPACK.
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"""
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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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import os
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from docopt import docopt
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import gzip
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#fname = sys.argv[1]
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#qph5name = sys.argv[2]
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def get_full_path(file_path):
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file_path = os.path.expanduser(file_path)
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file_path = os.path.expandvars(file_path)
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# file_path = os.path.abspath(file_path)
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return file_path
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def flatten(l):
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res = []
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for i in l:
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if hasattr(i, "__iter__") and not isinstance(i, str):
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res.extend(flatten(i))
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else:
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res.append(i)
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return res
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def save_array_do(ezfioname,subdir,data,chunksize=16384):
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dims = list(reversed(data.shape))
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rank = len(dims)
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flatdata = data.reshape(-1)
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dim_max = 1
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for i in dims:
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dim_max *= i
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with gzip.open(os.path.join(ezfioname,subdir)+'.gz','wb') as f:
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f.write(f'{rank:3d}\n'.encode())
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for d in dims:
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f.write(f'{d:20d} '.encode())
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f.write("\n".encode())
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fmtstring = chunksize*'{:24.15E}\n'
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for i in range(dim_max//chunksize):
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#f.write((chunksize*'{:24.15E}\n').format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
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#f.write(fmtstring.format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
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f.write((''.join("%24.15E\n" % xi for xi in flatdata[i*chunksize:(i+1)*chunksize])).encode())
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print(f'{100.*i/(dim_max//chunksize):7.3f}% complete')
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rem = dim_max%chunksize
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if rem:
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f.write((rem*'{:24.15E}\n').format(*flatdata[-rem:]).encode())
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return
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def convert_mol(filename,qph5path):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(False)
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with h5py.File(qph5path,'r') as qph5:
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nucl_num = qph5['nuclei'].attrs['nucl_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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elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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ezfio.set_nuclei_nucl_num(nucl_num)
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_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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with h5py.File(qph5path,'r') as qph5:
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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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if isinstance(nucl_label[0],bytes):
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nucl_label = list(map(lambda x:x.decode(),nucl_label))
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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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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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ezfio.set_pseudo_do_pseudo(do_pseudo)
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if (do_pseudo):
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ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
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ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
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ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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#coeftmp = qph5['ao_basis/ao_coef'][()]
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#expotmp = qph5['ao_basis/ao_expo'][()]
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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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ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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##########################################
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# #
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# MO Coef #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
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ezfio.set_mo_basis_mo_coef(mo_coef)
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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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return
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def convert_kpts_cd(filename,qph5path,qmcpack=True):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(True)
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# Dummy atom since AFQMC h5 has no atom information
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nucl_num = 1
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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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with h5py.File(qph5path,'r') as qph5:
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kpt_num = qph5['Hamiltonian']['KPoints'].shape[0]
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elec_alpha_num = qph5['Hamiltonian']['dims'][4]
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elec_beta_num = qph5['Hamiltonian']['dims'][5]
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orb_num = qph5['Hamiltonian']['dims'][3]
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try:
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is_ao = json.loads(qph5['metadata'][()].decode("utf-8").replace("'",'"'))['ortho_ao']
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if is_ao:
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ao_num = orb_num
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elif is_ao ==False:
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mo_num = orb_num
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else:
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raise ValueError('Problem with ortho_ao key in metadata')
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except:
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raise UnicodeDecodeError('metadata not correctly parsed from HDF5 file')
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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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# don't multiply nuclei by kpt_num
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# work in k-space, not in equivalent supercell
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nucl_num_per_kpt = nucl_num
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ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
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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.set_ao_basis_ao_num(ao_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_ao_basis_ao_num_per_kpt(ao_num//kpt_num)
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ezfio.set_mo_basis_mo_num_per_kpt(mo_num//kpt_num)
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ezfio.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_num
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##########################################
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# #
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# Basis #
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# #
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##########################################
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#TODO
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##########################################
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# #
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# MOCoeff #
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# #
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##########################################
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#TODO
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##########################################
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# #
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# Integrals Mono #
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# #
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##########################################
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"""
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with h5py.File(qph5path,'r') as qph5:
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if is_ao:
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kin_ao_reim=
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ovlp_ao_reim=
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ne_ao_reim=
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ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim)
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ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim)
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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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else:
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kin_mo_reim=
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ovlp_mo_reim=
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ne_mo_reim=
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ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim)
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ezfio.set_mo_one_e_ints_mo_integrals_overlap_kpts(ovlp_mo_reim)
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ezfio.set_mo_one_e_ints_mo_integrals_n_e_kpts(ne_mo_reim)
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ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
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ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
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ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
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"""
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##########################################
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# #
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# k-points #
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# #
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##########################################
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#TODO
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with h5py.File(qph5path,'r') as qph5:
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kconserv = qph5['nuclei/kconserv'][()].tolist()
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minusk = qph5['Hamiltonian']['MinusK'][:]+1
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QKTok2 = qph5['Hamiltonian']['QPTok2'][:]+1
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unique_kpt_num = len(qph5['Hamiltonian']['KPFactorized'])
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unique_k_idx = []
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for i in qph5['Hamiltonian']['KPFactorized'].keys():
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unique_k_idx.append(int(i[1:])+1)
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kpt_sparse_map = np.zeros(kpt_num)
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for i in range(kpt_num):
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if i+1 is in uniq_k_idx:
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kpt_sparse_map[i] = i+1
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else:
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kpt_sparse_map[i] = -minusk[i]
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ezfio.set_nuclei_kconserv(kconserv)
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ezfio.set_nuclei_io_kconserv('Read')
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ezfio.set_nuclei_minusk(minusk)
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ezfio.set_nuclei_qktok2(QKTok2)
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ezfio.set_nuclei_kpt_sparse_map(kpt_sparse_map)
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ezfio.set_nuclei_unique_kpt_num(unique_kpt_num)
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# kpt_sparse_map
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# unique_kpt_num
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# io_kpt_symm
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##########################################
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# #
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# Integrals Bi #
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# #
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##########################################
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# should this be in ao_basis? ao_two_e_ints?
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with h5py.File(qph5path,'r') as qph5:
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nchol_per_kpt = qph5['Hamiltonian']['NCholPerKP'][:]
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nchol_per_kpt = nchol_per_kpt[nchol_per_kpt != 0]
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nchol_per_kpt_max = max(nchol_per_kpt)
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ezfio.set_chol_num(nchol_per_kpt)
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ezfio.set_chol_num_max(nchol_per_kpt_max)
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if is_ao:
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ao_num_per_kpt = ao_num//kpt_num
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ezfio.set_io_chol_ao_integrals('Read')
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#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)))
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L_list = []
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for i in len(nchol_per_kpt):
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L = qph5['Hamiltonian']['KPFactorized'][f'L{i}'][:]
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L.reshape(kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt[i], 2)
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L = np.einsum("ijklm->ilkjm", A, B)
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L_list.append(L)
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#(6, 5184, 2)
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"""
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for cmplx in range(2):
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for ao_idx_i in range(ao_num_per_kpt):
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for ao_idx_j in range(ao_num_per_kpt):
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for chol_idx in range(nchol_per_kpt[i]):
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for kpt_idx in range(kpt_num):
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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]
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"""
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ao_chol_two_e_ints = np.vstack(L_list)
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ao_chol_two_e_ints = ao_chol_two_e_ints.transpose()
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ezfio.set_chol_ao_integrals_complex(ao_chol_two_e_ints)
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#(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#)
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"""
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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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if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
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dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
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ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
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ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
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"""
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else:
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"""
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ezfio.set_io_chol_mo_integrals('Read')
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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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dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
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ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
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ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
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"""
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mo_num_per_kpt = ao_num//kpt_num
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ezfio.set_io_chol_mo_integrals('Read')
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#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)))
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L_list = []
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for i in len(nchol_per_kpt):
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L = qph5['Hamiltonian']['KPFactorized'][f'L{i}'][:]
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L.reshape(kpt_num, mo_num_per_kpt, mo_num_per_kpt, nchol_per_kpt[i], 2)
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L = np.einsum("ijklm->ilkjm", A, B)
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L_list.append(L)
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#(6, 5184, 2)
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"""
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for cmplx in range(2):
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for ao_idx_i in range(ao_num_per_kpt):
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for ao_idx_j in range(ao_num_per_kpt):
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for chol_idx in range(nchol_per_kpt[i]):
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for kpt_idx in range(kpt_num):
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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]
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"""
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mo_chol_two_e_ints = np.vstack(L_list)
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mo_chol_two_e_ints = mo_chol_two_e_ints.transpose()
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ezfio.set_chol_mo_integrals_complex(mo_chol_two_e_ints)
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return
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def convert_kpts(filename,qph5path,qmcpack=True):
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ezfio.set_file(filename)
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ezfio.set_nuclei_is_complex(True)
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with h5py.File(qph5path,'r') as qph5:
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kpt_num = qph5['nuclei'].attrs['kpt_num']
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nucl_num = qph5['nuclei'].attrs['nucl_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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elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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elec_beta_num = qph5['electrons'].attrs['elec_beta_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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# don't multiply nuclei by kpt_num
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# work in k-space, not in equivalent supercell
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nucl_num_per_kpt = nucl_num
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ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
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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.set_ao_basis_ao_num(ao_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_ao_basis_ao_num_per_kpt(ao_num//kpt_num)
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ezfio.set_mo_basis_mo_num_per_kpt(mo_num//kpt_num)
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ezfio.electrons_elec_alpha_num = elec_alpha_num
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ezfio.electrons_elec_beta_num = elec_beta_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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with h5py.File(qph5path,'r') as qph5:
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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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if isinstance(nucl_label[0],bytes):
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nucl_label = list(map(lambda x:x.decode(),nucl_label))
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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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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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##########################################
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# #
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# Basis(Dummy) #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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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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###########################################
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## #
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## Pseudo #
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## #
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###########################################
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|
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#with h5py.File(qph5path,'r') as qph5:
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# do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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# ezfio.set_pseudo_do_pseudo(do_pseudo)
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# if (do_pseudo):
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# ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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# ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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# ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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# ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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# ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
|
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# ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
|
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# ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
|
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# ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
|
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# 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(Dummy) #
|
|
# #
|
|
##########################################
|
|
|
|
#with h5py.File(qph5path,'r') as qph5:
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# coeftmp = qph5['ao_basis/ao_coef'][()]
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|
# expotmp = qph5['ao_basis/ao_expo'][()]
|
|
# 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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# ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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# ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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|
# ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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# ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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|
|
|
|
|
##########################################
|
|
# #
|
|
# Basis(QMC) #
|
|
# #
|
|
##########################################
|
|
|
|
if qmcpack:
|
|
try:
|
|
with h5py.File(qph5path,'r') as qph5:
|
|
ezfio.set_qmcpack_qmc_nshell(qph5['qmcpack'].attrs['qmc_nshell'])
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|
ezfio.set_qmcpack_qmc_prim_num_max(qph5['qmcpack'].attrs['qmc_prim_num_max'])
|
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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())
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|
|
|
ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
|
|
ezfio.set_qmcpack_qmc_cart(qph5['qmcpack'].attrs['cart'])
|
|
ezfio.set_qmcpack_qmc_pseudo(qph5['qmcpack'].attrs['Pseudo'])
|
|
ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist())
|
|
ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist())
|
|
ezfio.set_qmcpack_qmc_phase(qph5['qmcpack/qmc_phase'][()].tolist())
|
|
ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist())
|
|
|
|
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
|
|
|
|
|
|
|
|
##########################################
|
|
# #
|
|
# 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])
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|
|
|
|
|
##########################################
|
|
# #
|
|
# 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()
|
|
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()]
|
|
save_array_do(filename,'ao_two_e_ints/df_ao_integrals_complex',dfao_reim)
|
|
#ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
|
|
#dfao_dims = list(reversed(dfao_reim.shape))
|
|
#test_write_df_ao(,5,dfao_dims,dfao_reim.size,dfao_reim.ravel())
|
|
|
|
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())
|
|
#
|
|
#
|
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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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#
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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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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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do_pseudo = qph5['pseudo'].attrs['do_pseudo']
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ezfio.set_pseudo_do_pseudo(do_pseudo)
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if (do_pseudo):
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ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
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ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
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ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
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ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
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ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
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ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
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ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
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ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
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##########################################
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# #
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# Basis #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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coeftmp = qph5['ao_basis/ao_coef'][()]
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expotmp = qph5['ao_basis/ao_expo'][()]
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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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ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
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ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
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ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
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ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
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##########################################
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# #
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# MO Coef #
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# #
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##########################################
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with h5py.File(qph5path,'r') as qph5:
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mo_coef_reim = qph5['mo_basis/mo_coef_complex'][()].tolist()
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ezfio.set_mo_basis_mo_coef_complex(mo_coef_reim)
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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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|
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##########################################
|
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# #
|
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# Integrals Mono #
|
|
# #
|
|
##########################################
|
|
|
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with h5py.File(qph5path,'r') as qph5:
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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
|
|
|
|
|
|
if __name__ == '__main__':
|
|
ARGUMENTS = docopt(__doc__)
|
|
|
|
FILE = get_full_path(ARGUMENTS['FILE'])
|
|
qmcpack = True
|
|
if ARGUMENTS["--output"]:
|
|
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
|
|
else:
|
|
EZFIO_FILE = "{0}.ezfio".format(FILE)
|
|
|
|
if ARGUMENTS["--noqmc"]:
|
|
qmcpack = False
|
|
if ARGUMENTS["--rmg"]:
|
|
rmg = True
|
|
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")
|
|
if cd:
|
|
print("Using RMG and AFQMC h5")
|
|
convert_kpts_cd(EZFIO_FILE,FILE,qmcpack)
|
|
else:
|
|
convert_kpts(EZFIO_FILE,FILE,qmcpack)
|
|
else:
|
|
print("converting HDF5 to EZFIO for molecular system")
|
|
convert_mol(EZFIO_FILE,FILE)
|
|
|
|
# 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).""")
|