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pyscf converter hdf5 arr

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This commit is contained in:
Kevin Gasperich 2020-02-10 15:21:41 -06:00
parent 85f4ca3121
commit c4154c10ea
1 changed files with 41 additions and 15 deletions
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56
src/utils_periodic/MolPyscfToQPkpts.py
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@ -560,19 +560,28 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
# _| # _|
if mf.cell.pseudo: 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: else:
v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao)) v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao))
if len(cell._ecpbas) > 0: if len(cell._ecpbas) > 0:
v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao)) v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao))
ne_ao = ('ne',v_kpts_ao,ne_threshold) ne_ao = ('V',v_kpts_ao,ne_threshold)
ovlp_ao = ('overlap',np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao)),ovlp_threshold) ovlp_ao = ('S',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) 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): for name, intval_kpts_ao, thresh in (ne_ao, ovlp_ao, kin_ao):
if print_ao_ints_mono: 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): for ik in range(Nk):
shift=ik*nao+1 shift=ik*nao+1
for i in range(nao): 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)) outfile.write('%s %s %s %s\n' % (i+shift, j+shift, int_ij.real, int_ij.imag))
if print_mo_ints_mono: if print_mo_ints_mono:
intval_kpts_mo = np.einsum('kim,kij,kjn->kmn',mo_k.conj(),intval_kpts_ao,mo_k) 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): for ik in range(Nk):
shift=ik*nmo+1 shift=ik*nmo+1
for i in range(nmo): 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) 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 a in range(Nk):
for b in range(Nk): for b in range(Nk):
for c 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]) 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] nkpt_pairs = j3arr.shape[0]
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
if print_ao_ints_df: if print_ao_ints_df:
with open('df_ao_integral_array','w') as outfile: with open('D.qp','w') as outfile:
pass 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 k,kpt_pair in enumerate(j3arr):
for iaux,dfbasfunc in enumerate(kpt_pair): for iaux,dfbasfunc in enumerate(kpt_pair):
for i,i0 in enumerate(dfbasfunc): for i,i0 in enumerate(dfbasfunc):
for j,v in enumerate(i0): for j,v in enumerate(i0):
if (abs(v) > bielec_int_threshold): 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)) 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: if print_mo_ints_df:
kpair_list=[] kpair_list=[]
@ -649,15 +671,19 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
if(i>=j): if(i>=j):
kpair_list.append((i,j,idx2_tri((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]) 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 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 k,kpt_pair in enumerate(j3mo):
for iaux,dfbasfunc in enumerate(kpt_pair): for iaux,dfbasfunc in enumerate(kpt_pair):
for i,i0 in enumerate(dfbasfunc): for i,i0 in enumerate(dfbasfunc):
for j,v in enumerate(i0): for j,v in enumerate(i0):
if (abs(v) > bielec_int_threshold): 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)) 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 or print_mo_ints_bi):
if print_ao_ints_bi: if print_ao_ints_bi:
with open('bielec_ao_complex','w') as outfile: with open('W.qp','w') as outfile:
pass pass
if print_mo_ints_bi: if print_mo_ints_bi:
with open('bielec_mo_complex','w') as outfile: with open('W_mo.qp','w') as outfile:
pass pass
for d, kd in enumerate(kpts): for d, kd in enumerate(kpts):
for c, kc 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] ka = kpts[a]
if print_ao_ints_bi: 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 = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
eri_4d_ao_kpt *= 1./Nk eri_4d_ao_kpt *= 1./Nk
for l in range(nao): 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)) 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: 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]], 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) [ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
eri_4d_mo_kpt *= 1./Nk eri_4d_mo_kpt *= 1./Nk