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https://github.com/QuantumPackage/qp2.git
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working on complex converter
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@ -18,3 +18,8 @@ interface: ezfio,provider,ocaml
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default: False
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default: False
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ezfio_name: direct
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ezfio_name: direct
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[df_num]
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type: integer
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doc: Size of df basis
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interface: ezfio, provider
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@ -1,17 +1,18 @@
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#!/bin/bash
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#!/bin/bash
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ezfio=$1
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ezfio=$1
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h5file=$2
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# Create the integral
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# Create the integral
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echo 'Create Integral'
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echo 'Create Integral'
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echo 'Create EZFIO'
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echo 'Create EZFIO'
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read nel nmo natom <<< $(cat param)
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#read nel nmo natom <<< $(cat param)
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read e_nucl <<< $(cat e_nuc)
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#read e_nucl <<< $(cat e_nuc)
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read nao <<< $(cat num_ao)
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#read nao <<< $(cat num_ao)
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read nkpts <<< $(cat num_kpts)
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#read nkpts <<< $(cat num_kpts)
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read ndf <<< $(cat num_df)
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#read ndf <<< $(cat num_df)
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#./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts
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##./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts
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./create_ezfio_complex_3idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts $ndf
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./create_ezfio_complex_3idx.py $ezfio $h5file #$nel $natom $nmo $e_nucl $nao $nkpts $ndf
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#Handle the orbital consitensy check
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#Handle the orbital consitensy check
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qp_edit -c $ezfio &> /dev/null
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qp_edit -c $ezfio &> /dev/null
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cp $ezfio/{ao,mo}_basis/ao_md5
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cp $ezfio/{ao,mo}_basis/ao_md5
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@ -23,7 +24,7 @@ echo 'Read Integral'
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################################################
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################################################
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## using AO mono, 4-idx from pyscf ##
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## using AO mono, 4-idx from pyscf ##
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################################################
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################################################
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qp_run import_integrals_ao_periodic $ezfio
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#qp_run import_integrals_ao_periodic $ezfio
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################################################
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################################################
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@ -489,6 +489,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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from pyscf.pbc import ao2mo
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from pyscf.pbc import ao2mo
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from pyscf.pbc import tools
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from pyscf.pbc import tools
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from pyscf.pbc.gto import ecp
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from pyscf.pbc.gto import ecp
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from pyscf.data import nist
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import h5py
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import h5py
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import scipy
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import scipy
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@ -507,6 +508,18 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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natom = cell.natm
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natom = cell.natm
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nelec = cell.nelectron
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nelec = cell.nelectron
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atom_xyz = mf.cell.atom_coords()
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if not(mf.cell.unit.startswith(('B','b','au','AU'))):
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atom_xyz /= nist.BOHR # always convert to au
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strtype=h5py.special_dtype(vlen=str)
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atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
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for i in range(natom):
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atom_dset[i] = mf.cell.atom_pure_symbol(i)
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qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
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qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
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print('n_atom per kpt', natom)
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print('n_atom per kpt', natom)
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print('num_elec per kpt', nelec)
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print('num_elec per kpt', nelec)
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@ -523,14 +536,20 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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naux = mf.with_df.auxcell.nao
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naux = mf.with_df.auxcell.nao
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print("n df fitting functions", naux)
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print("n df fitting functions", naux)
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#in old version: param < nelec*Nk, nmo*Nk, natom*Nk
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#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
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qph5['electrons'].attrs['elec_alpha_num']=nelec*Nk
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qph5['electrons'].attrs['elec_alpha_num']=nelec*Nk
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qph5['electrons'].attrs['elec_beta_num']=nelec*Nk
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qph5['electrons'].attrs['elec_beta_num']=nelec*Nk
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qph5['mo_basis'].attrs['mo_num']=Nk*nmo
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qph5['mo_basis'].attrs['mo_num']=Nk*nmo
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qph5['ao_basis'].attrs['ao_num']=Nk*nao
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qph5['ao_basis'].attrs['ao_num']=Nk*nao
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qph5['nuclei'].attrs['nucl_num']=Nk*natom
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qph5['nuclei'].attrs['nucl_num']=Nk*natom
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qph5['nuclei'].attrs['kpt_num']=Nk
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qph5['nuclei'].attrs['kpt_num']=Nk
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qph5['ao_basis'].attrs['df_num']=naux
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qph5.create_group('ao_two_e_ints')
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qph5['ao_two_e_ints'].attrs['df_num']=naux
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qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
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ao_nucl=[mf.cell.bas_atom(i)+1 for i in range(nao)]
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qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
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# _
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# _
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# |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._
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# |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._
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@ -12,28 +12,38 @@ h5filename = sys.argv[2]
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#n_kpts = int(sys.argv[7])
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#n_kpts = int(sys.argv[7])
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#n_aux = int(sys.argv[8])
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#n_aux = int(sys.argv[8])
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ezfio.set_file(filename)
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ezfio.set_file(filename)
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qph5=h5py.File(h5filename.'r')
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qph5=h5py.File(h5filename,'r')
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kpt_num = qph5['nuclei'].attrs['kpt_num']
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ezfio.set_nuclei_kpt_num(kpt_num)
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# should this be in ao_basis? ao_two_e_ints?
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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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# 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.electrons_elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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ezfio.electrons_elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
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ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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nucl_num = qph5['nuclei'].attrs['nucl_num']
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kpt_num = qph5['nuclei'].attrs['kpt_num']
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nucl_num_per_kpt = nucl_num // kpt_num
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df_num = qph5['ao_basis'].attrs['df_num']
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ao_num = qph5['ao_basis'].attrs['ao_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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mo_num = qph5['mo_basis'].attrs['mo_num']
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_mo_basis_mo_num(mo_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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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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##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_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.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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@ -41,13 +51,26 @@ ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
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#ezfio.set_utils_num_kpts(n_kpts)
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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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#ezfio.set_integrals_bielec_df_num(n_aux)
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#Important
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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_num(nucl_num)
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ezfio.set_nuclei_nucl_charge([0.]*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_coord( [ [0.], [0.], [0.] ]*nucl_num )
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ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
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#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
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ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
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nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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ezfio.set_nuclei_nucl_charge(nucl_charge)
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nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
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ezfio.set_nuclei_nucl_coord(nucl_coord)
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nucl_label=qph5['nuclei/nucl_label'][()].tolist()
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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_io_nuclear_repulsion('Read')
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nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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# Ao num
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# Ao num
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@ -56,7 +79,11 @@ ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
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ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
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#Just need one
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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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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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d = [ [0] *ao_prim_num_max]*ao_num
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@ -72,8 +99,15 @@ ezfio.set_mo_basis_ao_md5(ao_md5)
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ezfio.set_mo_basis_mo_num(mo_num)
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ezfio.set_mo_basis_mo_num(mo_num)
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c_mo = [[1 if i==j else 0 for i in range(mo_num)] for j in range(ao_num)]
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#c_mo = [[1 if i==j else 0 for i in range(mo_num)] for j in range(ao_num)]
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ezfio.set_mo_basis_mo_coef([ [0]*mo_num] * ao_num)
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#ezfio.set_mo_basis_mo_coef([ [0]*mo_num] * ao_num)
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#ezfio.set_mo_basis_mo_coef_real(c_mo)
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##ezfio.set_mo_basis_mo_coef_real(c_mo)
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ezfio.set_mo_basis_mo_coef_real(qph5['mo_basis/mo_coef_real'][()].tolist())
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ezfio.set_mo_basis_mo_coef_imag(qph5['mo_basis/mo_coef_imag'][()].tolist())
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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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ezfio.set_nuclei_is_periodic(True)
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ezfio.set_nuclei_is_periodic(True)
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