From c4154c10ea57f530659f4970fa61c83a2f0c0d7f Mon Sep 17 00:00:00 2001 From: Kevin Gasperich Date: Mon, 10 Feb 2020 15:21:41 -0600 Subject: [PATCH] pyscf converter hdf5 arr --- src/utils_periodic/MolPyscfToQPkpts.py | 56 +++++++++++++++++++------- 1 file changed, 41 insertions(+), 15 deletions(-) diff --git a/src/utils_periodic/MolPyscfToQPkpts.py b/src/utils_periodic/MolPyscfToQPkpts.py index 1f72788e..86db7285 100644 --- a/src/utils_periodic/MolPyscfToQPkpts.py +++ b/src/utils_periodic/MolPyscfToQPkpts.py @@ -560,19 +560,28 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, # _| if mf.cell.pseudo: - ao_n_e = np.reshape(mf.with_df.get_pp(kpts=kpts),(Nk,nao,nao)) + v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=kpts),(Nk,nao,nao)) else: v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao)) if len(cell._ecpbas) > 0: v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao)) - ne_ao = ('ne',v_kpts_ao,ne_threshold) - ovlp_ao = ('overlap',np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao)),ovlp_threshold) - kin_ao = ('kinetic',np.reshape(cell.pbc_intor('int1e_kin',1,1,kpts=kpts),(Nk,nao,nao)),kin_threshold) + ne_ao = ('V',v_kpts_ao,ne_threshold) + ovlp_ao = ('S',np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao)),ovlp_threshold) + kin_ao = ('T',np.reshape(cell.pbc_intor('int1e_kin',1,1,kpts=kpts),(Nk,nao,nao)),kin_threshold) + + qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic', data=kin_ao[1].real) + qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao[1].imag) + qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap', data=ovlp_ao[1].real) + qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao[1].imag) + qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e', data=v_kpts_ao.real) + qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=v_kpts_ao.imag) + + for name, intval_kpts_ao, thresh in (ne_ao, ovlp_ao, kin_ao): if print_ao_ints_mono: - with open('%s_ao_complex' % name,'w') as outfile: + with open('%s.qp' % name,'w') as outfile: for ik in range(Nk): shift=ik*nao+1 for i in range(nao): @@ -582,7 +591,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, outfile.write('%s %s %s %s\n' % (i+shift, j+shift, int_ij.real, int_ij.imag)) if print_mo_ints_mono: intval_kpts_mo = np.einsum('kim,kij,kjn->kmn',mo_k.conj(),intval_kpts_ao,mo_k) - with open('%s_mo_complex' % name,'w') as outfile: + with open('%s_mo.qp' % name,'w') as outfile: for ik in range(Nk): shift=ik*nmo+1 for i in range(nmo): @@ -598,8 +607,16 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, # _| # kconserv = tools.get_kconserv(cell, kpts) + qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1))) + kcon_test = np.zeros((Nk,Nk,Nk),dtype=int) + for a in range(Nk): + for b in range(Nk): + for c in range(Nk): + kcon_test[a,c,b] = kconserv[a,b,c]+1 + qph5.create_dataset('nuclei/kconserv_test',data=kcon_test) - with open('kconserv_complex','w') as outfile: + + with open('K.qp','w') as outfile: for a in range(Nk): for b in range(Nk): for c in range(Nk): @@ -630,17 +647,22 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, j3arr=np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist]) nkpt_pairs = j3arr.shape[0] + df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128) if print_ao_ints_df: - with open('df_ao_integral_array','w') as outfile: + with open('D.qp','w') as outfile: pass - with open('df_ao_integral_array','a') as outfile: + with open('D.qp','a') as outfile: for k,kpt_pair in enumerate(j3arr): for iaux,dfbasfunc in enumerate(kpt_pair): for i,i0 in enumerate(dfbasfunc): for j,v in enumerate(i0): if (abs(v) > bielec_int_threshold): outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag)) + df_ao_tmp[i,j,iaux,k]=v + + qph5.create_dataset('ao_two_e_ints/df_ao_array_real',data=df_ao_tmp.real) + qph5.create_dataset('ao_two_e_ints/df_ao_array_imag',data=df_ao_tmp.imag) if print_mo_ints_df: kpair_list=[] @@ -649,15 +671,19 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, if(i>=j): kpair_list.append((i,j,idx2_tri((i,j)))) 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]) - with open('df_mo_integral_array','w') as outfile: + df_mo_tmp = np.zeros((nmo,nmo,naux,nkpt_pairs),dtype=np.complex128) + with open('D_mo.qp','w') as outfile: pass - with open('df_mo_integral_array','a') as outfile: + with open('D_mo.qp','a') as outfile: for k,kpt_pair in enumerate(j3mo): for iaux,dfbasfunc in enumerate(kpt_pair): for i,i0 in enumerate(dfbasfunc): for j,v in enumerate(i0): if (abs(v) > bielec_int_threshold): outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag)) + df_mo_tmp[i,j,iaux,k]=v + qph5.create_dataset('mo_two_e_ints/df_mo_array_real',data=df_mo_tmp.real) + qph5.create_dataset('mo_two_e_ints/df_mo_array_imag',data=df_mo_tmp.imag) @@ -681,10 +707,10 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, if (print_ao_ints_bi or print_mo_ints_bi): if print_ao_ints_bi: - with open('bielec_ao_complex','w') as outfile: + with open('W.qp','w') as outfile: pass if print_mo_ints_bi: - with open('bielec_mo_complex','w') as outfile: + with open('W_mo.qp','w') as outfile: pass for d, kd in enumerate(kpts): for c, kc in enumerate(kpts): @@ -698,7 +724,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, ka = kpts[a] if print_ao_ints_bi: - with open('bielec_ao_complex','a') as outfile: + with open('W.qp','a') as outfile: eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4) eri_4d_ao_kpt *= 1./Nk for l in range(nao): @@ -719,7 +745,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, outfile.write('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag)) if print_mo_ints_bi: - with open('bielec_mo_complex','a') as outfile: + with open('W_mo.qp','a') as outfile: eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]], [ka,kb,kc,kd],compact=False).reshape((nmo,)*4) eri_4d_mo_kpt *= 1./Nk