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https://github.com/QuantumPackage/qp2.git
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pyscf converter hdf5 arr
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85f4ca3121
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@ -560,19 +560,28 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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# _|
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# _|
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if mf.cell.pseudo:
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if mf.cell.pseudo:
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ao_n_e = np.reshape(mf.with_df.get_pp(kpts=kpts),(Nk,nao,nao))
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v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=kpts),(Nk,nao,nao))
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else:
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else:
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v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao))
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v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao))
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if len(cell._ecpbas) > 0:
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if len(cell._ecpbas) > 0:
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v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao))
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v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao))
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ne_ao = ('ne',v_kpts_ao,ne_threshold)
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ne_ao = ('V',v_kpts_ao,ne_threshold)
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ovlp_ao = ('overlap',np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao)),ovlp_threshold)
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ovlp_ao = ('S',np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao)),ovlp_threshold)
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kin_ao = ('kinetic',np.reshape(cell.pbc_intor('int1e_kin',1,1,kpts=kpts),(Nk,nao,nao)),kin_threshold)
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kin_ao = ('T',np.reshape(cell.pbc_intor('int1e_kin',1,1,kpts=kpts),(Nk,nao,nao)),kin_threshold)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic', data=kin_ao[1].real)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao[1].imag)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap', data=ovlp_ao[1].real)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao[1].imag)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e', data=v_kpts_ao.real)
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qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=v_kpts_ao.imag)
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for name, intval_kpts_ao, thresh in (ne_ao, ovlp_ao, kin_ao):
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for name, intval_kpts_ao, thresh in (ne_ao, ovlp_ao, kin_ao):
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if print_ao_ints_mono:
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if print_ao_ints_mono:
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with open('%s_ao_complex' % name,'w') as outfile:
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with open('%s.qp' % name,'w') as outfile:
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for ik in range(Nk):
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for ik in range(Nk):
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shift=ik*nao+1
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shift=ik*nao+1
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for i in range(nao):
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for i in range(nao):
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@ -582,7 +591,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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outfile.write('%s %s %s %s\n' % (i+shift, j+shift, int_ij.real, int_ij.imag))
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outfile.write('%s %s %s %s\n' % (i+shift, j+shift, int_ij.real, int_ij.imag))
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if print_mo_ints_mono:
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if print_mo_ints_mono:
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intval_kpts_mo = np.einsum('kim,kij,kjn->kmn',mo_k.conj(),intval_kpts_ao,mo_k)
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intval_kpts_mo = np.einsum('kim,kij,kjn->kmn',mo_k.conj(),intval_kpts_ao,mo_k)
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with open('%s_mo_complex' % name,'w') as outfile:
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with open('%s_mo.qp' % name,'w') as outfile:
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for ik in range(Nk):
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for ik in range(Nk):
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shift=ik*nmo+1
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shift=ik*nmo+1
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for i in range(nmo):
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for i in range(nmo):
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@ -598,8 +607,16 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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# _|
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# _|
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#
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#
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kconserv = tools.get_kconserv(cell, kpts)
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kconserv = tools.get_kconserv(cell, kpts)
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qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1)))
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kcon_test = np.zeros((Nk,Nk,Nk),dtype=int)
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for a in range(Nk):
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for b in range(Nk):
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for c in range(Nk):
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kcon_test[a,c,b] = kconserv[a,b,c]+1
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qph5.create_dataset('nuclei/kconserv_test',data=kcon_test)
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with open('kconserv_complex','w') as outfile:
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with open('K.qp','w') as outfile:
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for a in range(Nk):
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for a in range(Nk):
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for b in range(Nk):
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for b in range(Nk):
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for c in range(Nk):
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for c in range(Nk):
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@ -630,17 +647,22 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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j3arr=np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
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j3arr=np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
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nkpt_pairs = j3arr.shape[0]
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nkpt_pairs = j3arr.shape[0]
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df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
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if print_ao_ints_df:
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if print_ao_ints_df:
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with open('df_ao_integral_array','w') as outfile:
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with open('D.qp','w') as outfile:
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pass
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pass
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with open('df_ao_integral_array','a') as outfile:
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with open('D.qp','a') as outfile:
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for k,kpt_pair in enumerate(j3arr):
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for k,kpt_pair in enumerate(j3arr):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for i,i0 in enumerate(dfbasfunc):
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for i,i0 in enumerate(dfbasfunc):
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for j,v in enumerate(i0):
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for j,v in enumerate(i0):
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if (abs(v) > bielec_int_threshold):
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if (abs(v) > bielec_int_threshold):
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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df_ao_tmp[i,j,iaux,k]=v
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qph5.create_dataset('ao_two_e_ints/df_ao_array_real',data=df_ao_tmp.real)
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qph5.create_dataset('ao_two_e_ints/df_ao_array_imag',data=df_ao_tmp.imag)
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if print_mo_ints_df:
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if print_mo_ints_df:
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kpair_list=[]
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kpair_list=[]
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@ -649,15 +671,19 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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if(i>=j):
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if(i>=j):
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kpair_list.append((i,j,idx2_tri((i,j))))
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kpair_list.append((i,j,idx2_tri((i,j))))
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j3mo = np.array([np.einsum('mij,ik,jl->mkl',j3arr[kij],mo_k[ki].conj(),mo_k[kj]) for ki,kj,kij in kpair_list])
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j3mo = np.array([np.einsum('mij,ik,jl->mkl',j3arr[kij],mo_k[ki].conj(),mo_k[kj]) for ki,kj,kij in kpair_list])
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with open('df_mo_integral_array','w') as outfile:
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df_mo_tmp = np.zeros((nmo,nmo,naux,nkpt_pairs),dtype=np.complex128)
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with open('D_mo.qp','w') as outfile:
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pass
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pass
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with open('df_mo_integral_array','a') as outfile:
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with open('D_mo.qp','a') as outfile:
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for k,kpt_pair in enumerate(j3mo):
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for k,kpt_pair in enumerate(j3mo):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for i,i0 in enumerate(dfbasfunc):
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for i,i0 in enumerate(dfbasfunc):
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for j,v in enumerate(i0):
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for j,v in enumerate(i0):
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if (abs(v) > bielec_int_threshold):
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if (abs(v) > bielec_int_threshold):
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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df_mo_tmp[i,j,iaux,k]=v
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qph5.create_dataset('mo_two_e_ints/df_mo_array_real',data=df_mo_tmp.real)
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qph5.create_dataset('mo_two_e_ints/df_mo_array_imag',data=df_mo_tmp.imag)
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@ -681,10 +707,10 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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if (print_ao_ints_bi or print_mo_ints_bi):
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if (print_ao_ints_bi or print_mo_ints_bi):
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if print_ao_ints_bi:
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if print_ao_ints_bi:
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with open('bielec_ao_complex','w') as outfile:
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with open('W.qp','w') as outfile:
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pass
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pass
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if print_mo_ints_bi:
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if print_mo_ints_bi:
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with open('bielec_mo_complex','w') as outfile:
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with open('W_mo.qp','w') as outfile:
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pass
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pass
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for d, kd in enumerate(kpts):
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for d, kd in enumerate(kpts):
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for c, kc in enumerate(kpts):
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for c, kc in enumerate(kpts):
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@ -698,7 +724,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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ka = kpts[a]
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ka = kpts[a]
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if print_ao_ints_bi:
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if print_ao_ints_bi:
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with open('bielec_ao_complex','a') as outfile:
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with open('W.qp','a') as outfile:
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
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eri_4d_ao_kpt *= 1./Nk
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eri_4d_ao_kpt *= 1./Nk
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for l in range(nao):
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for l in range(nao):
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@ -719,7 +745,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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outfile.write('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
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outfile.write('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
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if print_mo_ints_bi:
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if print_mo_ints_bi:
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with open('bielec_mo_complex','a') as outfile:
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with open('W_mo.qp','a') as outfile:
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eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]],
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eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]],
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[ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
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[ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
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eri_4d_mo_kpt *= 1./Nk
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eri_4d_mo_kpt *= 1./Nk
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