mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-06-26 15:12:19 +02:00
converter cleanup
This commit is contained in:
Kevin Gasperich
parent
8411167e90
commit
f07bdee9cd
|
|
@ -33,6 +33,9 @@ def idx40(i,j,k,l):
|
|||
def idx4(i,j,k,l):
|
||||
return idx2_tri((idx2_tri((i-1,k-1)),idx2_tri((j-1,l-1))))+1
|
||||
|
||||
def stri4(i,j,k,l):
|
||||
return (4*'{:5d}').format(i,j,k,l)
|
||||
|
||||
def stri4z(i,j,k,l,zr,zi):
|
||||
return (4*'{:5d}'+2*'{:25.16e}').format(i,j,k,l,zr,zi)
|
||||
|
||||
|
|
@ -509,6 +512,25 @@ def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E
|
|||
v.real,v.imag)+'\n')
|
||||
|
||||
|
||||
def print_kcon_chem_to_phys(kcon,fname):
|
||||
'''
|
||||
input: kconserv in chem notation kcon_c[a,b,c] = d
|
||||
where (ab|cd) is allowed by symmetry
|
||||
output: kconserv in phys notation kcon_p[i,j,k] = l
|
||||
where <ij|kl> is allowed by symmetry
|
||||
(printed to file)
|
||||
'''
|
||||
Nk,n2,n3 = kcon.shape
|
||||
if (n2!=n3 or Nk!=n2):
|
||||
raise Exception('print_kcon_chem_to_phys called with non-cubic array')
|
||||
|
||||
with open(fname,'w') as outfile:
|
||||
for a in range(Nk):
|
||||
for b in range(Nk):
|
||||
for c in range(Nk):
|
||||
d = kcon[a,b,c]
|
||||
outfile.write(stri4(a+1,c+1,b+1,d+1)+'\n')
|
||||
|
||||
def print_kpts_unblocked(ints_k,outfilename,thresh):
|
||||
'''
|
||||
for ints_k of shape (Nk,n1,n2),
|
||||
|
|
@ -556,26 +578,70 @@ def get_kin_ao(mf):
|
|||
def get_ovlp_ao(mf):
|
||||
nao = mf.cell.nao_nr()
|
||||
Nk = len(mf.kpts)
|
||||
return np.reshape(mf.get_ovlp(cell=cell,kpts=kpts),(Nk,nao,nao))
|
||||
return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
|
||||
|
||||
def get_pot_ao(mf):
|
||||
nao = mf.cell.nao_nr()
|
||||
Nk = len(mf.kpts)
|
||||
|
||||
if mf.cell.pseudo:
|
||||
v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=kpts),(Nk,nao,nao))
|
||||
v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=mf.kpts),(Nk,nao,nao))
|
||||
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=mf.kpts),(Nk,nao,nao))
|
||||
|
||||
if len(cell._ecpbas) > 0:
|
||||
if len(mf.cell._ecpbas) > 0:
|
||||
from pyscf.pbc.gto import ecp
|
||||
v_kpts_ao += np.reshape(ecp.ecp_int(cell, kpts),(Nk,nao,nao))
|
||||
v_kpts_ao += np.reshape(ecp.ecp_int(mf.cell, mf.kpts),(Nk,nao,nao))
|
||||
|
||||
return v_kpts_ao
|
||||
|
||||
def ao_to_mo_1e(ao_kpts,mo_coef):
|
||||
return np.einsum('kim,kij,kjn->kmn',mo_coef.conj(),ao_kpts_ao,mo_coef)
|
||||
|
||||
def get_j3ao(fname,nao,Nk):
|
||||
import h5py
|
||||
with h5py.File(fname,'r') as intfile:
|
||||
j3c = intfile.get('j3c')
|
||||
j3ckeys = list(j3c.keys())
|
||||
j3ckeys.sort(key=lambda strkey:int(strkey))
|
||||
|
||||
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
||||
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
||||
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
||||
j3clist = [j3c.get(i+'/0') for i in j3ckeys]
|
||||
#if j3clist==[None]*len(j3clist):
|
||||
if not(any(j3clist)):
|
||||
# if using older version, stop before last level
|
||||
j3clist = [j3c.get(i) for i in j3ckeys]
|
||||
|
||||
naosq = nao*nao
|
||||
naotri = (nao*(nao+1))//2
|
||||
nkinvsq = 1./np.sqrt(Nk)
|
||||
|
||||
# dimensions are (kikj,iaux,jao,kao), where kikj is compound index of kpts i and j
|
||||
# output dimensions should be reversed (nao, nao, naux, nkptpairs)
|
||||
return np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
|
||||
|
||||
def print_df(j3arr,fname,thresh):
|
||||
with open(fname,'w') 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) > thresh):
|
||||
outfile.write(stri4z(i+1,j+1,iaux+1,k+1,v.real,v.imag)+'\n')
|
||||
return
|
||||
|
||||
def df_pad_ref_test(j3arr,nao,naux,nkpt_pairs):
|
||||
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
|
||||
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):
|
||||
df_ao_tmp[i,j,iaux,k]=v
|
||||
return df_ao_tmp
|
||||
|
||||
|
||||
|
||||
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
||||
print_ao_ints_bi=False,
|
||||
|
|
@ -591,12 +657,11 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|||
int_threshold = The integral will be not printed in they are bellow that
|
||||
'''
|
||||
|
||||
from pyscf.pbc import ao2mo
|
||||
# from pyscf.pbc import ao2mo
|
||||
from pyscf.pbc import tools
|
||||
from pyscf.pbc.gto import ecp
|
||||
from pyscf.data import nist
|
||||
import h5py
|
||||
import scipy
|
||||
# import scipy
|
||||
from scipy.linalg import block_diag
|
||||
|
||||
mo_coef_threshold = int_threshold
|
||||
ovlp_threshold = int_threshold
|
||||
|
|
@ -614,98 +679,127 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|||
qph5.create_group('ao_basis')
|
||||
qph5.create_group('mo_basis')
|
||||
|
||||
qph5 = h5py.File(qph5path,'a')
|
||||
natom = cell.natm
|
||||
nelec = cell.nelectron
|
||||
neleca,nelecb = cell.nelec
|
||||
atom_xyz = mf.cell.atom_coords()
|
||||
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
|
||||
atom_xyz /= nist.BOHR # always convert to au
|
||||
|
||||
strtype=h5py.special_dtype(vlen=str)
|
||||
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
||||
for i in range(natom):
|
||||
atom_dset[i] = mf.cell.atom_pure_symbol(i)
|
||||
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
||||
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
|
||||
|
||||
|
||||
print('n_atom per kpt', natom)
|
||||
print('num_elec per kpt', nelec)
|
||||
|
||||
mo_coeff = mf.mo_coeff
|
||||
# Mo_coeff actif
|
||||
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
||||
e_k = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
||||
|
||||
Nk, nao, nmo = mo_k.shape
|
||||
|
||||
print("n Kpts", Nk)
|
||||
print("n active Mos per kpt", nmo)
|
||||
print("n AOs per kpt", nao)
|
||||
|
||||
# naux = mf.with_df.auxcell.nao
|
||||
# print("n df fitting functions", naux)
|
||||
|
||||
#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
|
||||
qph5['electrons'].attrs['elec_alpha_num']=neleca*Nk
|
||||
qph5['electrons'].attrs['elec_beta_num']=nelecb*Nk
|
||||
qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
||||
qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
||||
#qph5['nuclei'].attrs['nucl_num']=Nk*natom
|
||||
qph5['nuclei'].attrs['nucl_num']=natom
|
||||
qph5['nuclei'].attrs['kpt_num']=Nk
|
||||
qph5.create_group('ao_two_e_ints')
|
||||
# qph5['ao_two_e_ints'].attrs['df_num']=naux
|
||||
##########################################
|
||||
# #
|
||||
# Nuclei #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
||||
ao_nucl=[mf.cell.bas_atom(i)+1 for i in range(nao)]
|
||||
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
||||
natom = cell.natm
|
||||
print('n_atom per kpt', natom)
|
||||
|
||||
atom_xyz = mf.cell.atom_coords()
|
||||
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
|
||||
from pyscf.data.nist import BOHR
|
||||
atom_xyz /= BOHR # always convert to au
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5['nuclei'].attrs['kpt_num']=Nk
|
||||
qph5['nuclei'].attrs['nucl_num']=natom
|
||||
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
||||
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
|
||||
|
||||
strtype=h5py.special_dtype(vlen=str)
|
||||
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
||||
for i in range(natom):
|
||||
atom_dset[i] = mf.cell.atom_pure_symbol(i)
|
||||
|
||||
##########################################
|
||||
# #
|
||||
# Basis #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
# nucleus on which each AO is centered
|
||||
ao_nucl=[i[0] for i in mf.cell.ao_labels(fmt=False,base=1)]
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
||||
qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
||||
|
||||
qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
||||
|
||||
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
||||
|
||||
##########################################
|
||||
# #
|
||||
# Electrons #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
nelec = cell.nelectron
|
||||
neleca,nelecb = cell.nelec
|
||||
|
||||
print('num_elec per kpt', nelec)
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
|
||||
qph5['electrons'].attrs['elec_alpha_num']=neleca*Nk
|
||||
qph5['electrons'].attrs['elec_beta_num']=nelecb*Nk
|
||||
|
||||
##########################################
|
||||
# #
|
||||
# Nuclear Repulsion #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
# _
|
||||
# |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._
|
||||
# | \| |_| (_ | (/_ (_| | | \ (/_ |_) |_| | _> | (_) | |
|
||||
# |
|
||||
|
||||
#Total energy shift due to Ewald probe charge = -1/2 * Nelec*madelung/cell.vol =
|
||||
shift = tools.pbc.madelung(cell, kpts)*cell.nelectron * -.5
|
||||
e_nuc = (cell.energy_nuc() + shift)*Nk
|
||||
|
||||
print('nucl_repul', e_nuc)
|
||||
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
||||
|
||||
# __ __ _
|
||||
# |\/| | | | _ _ |_ _
|
||||
# | | |__| |__ (_) (/_ | _>
|
||||
#
|
||||
mo_coef_blocked=scipy.linalg.block_diag(*mo_k)
|
||||
qph5.create_dataset('mo_basis/mo_coef_real',data=mo_coef_blocked.real)
|
||||
qph5.create_dataset('mo_basis/mo_coef_imag',data=mo_coef_blocked.imag)
|
||||
qph5.create_dataset('mo_basis/mo_coef_kpts_real',data=mo_k.real)
|
||||
qph5.create_dataset('mo_basis/mo_coef_kpts_imag',data=mo_k.imag)
|
||||
##########################################
|
||||
# #
|
||||
# MO Coef #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
mo_coef_blocked=block_diag(*mo_k)
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('mo_basis/mo_coef_real',data=mo_coef_blocked.real)
|
||||
qph5.create_dataset('mo_basis/mo_coef_imag',data=mo_coef_blocked.imag)
|
||||
qph5.create_dataset('mo_basis/mo_coef_kpts_real',data=mo_k.real)
|
||||
qph5.create_dataset('mo_basis/mo_coef_kpts_imag',data=mo_k.imag)
|
||||
|
||||
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
|
||||
|
||||
# ___
|
||||
# | ._ _|_ _ _ ._ _. | _ |\/| _ ._ _
|
||||
# _|_ | | |_ (/_ (_| | (_| | _> | | (_) | | (_)
|
||||
# _|
|
||||
##########################################
|
||||
# #
|
||||
# Integrals Mono #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
ne_ao = get_pot_ao(mf)
|
||||
kin_ao = get_kin_ao(mf)
|
||||
ovlp_ao = get_ovlp_ao(mf)
|
||||
|
||||
if print_ao_ints_mono:
|
||||
kin_ao_blocked=scipy.linalg.block_diag(*kin_ao)
|
||||
ovlp_ao_blocked=scipy.linalg.block_diag(*ovlp_ao)
|
||||
ne_ao_blocked=scipy.linalg.block_diag(*ne_ao)
|
||||
kin_ao_blocked=block_diag(*kin_ao)
|
||||
ovlp_ao_blocked=block_diag(*ovlp_ao)
|
||||
ne_ao_blocked=block_diag(*ne_ao)
|
||||
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_real',data=kin_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao_blocked.imag)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_real',data=ovlp_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao_blocked.imag)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_real', data=ne_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=ne_ao_blocked.imag)
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_real',data=kin_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao_blocked.imag)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_real',data=ovlp_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_imag',data=ovlp_ao_blocked.imag)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_real', data=ne_ao_blocked.real)
|
||||
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=ne_ao_blocked.imag)
|
||||
|
||||
for fname,ints in zip(('S.qp','V.qp','T.qp'),
|
||||
(ovlp_ao, ne_ao, kin_ao)):
|
||||
|
|
@ -716,107 +810,91 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|||
ovlp_mo = ao_to_mo_1e(ovlp_ao,mo_k)
|
||||
ne_mo = ao_to_mo_1e(ne_ao,mo_k)
|
||||
|
||||
kin_mo_blocked=scipy.linalg.block_diag(*kin_mo)
|
||||
ovlp_mo_blocked=scipy.linalg.block_diag(*ovlp_mo)
|
||||
ne_mo_blocked=scipy.linalg.block_diag(*ne_mo)
|
||||
kin_mo_blocked=block_diag(*kin_mo)
|
||||
ovlp_mo_blocked=block_diag(*ovlp_mo)
|
||||
ne_mo_blocked=block_diag(*ne_mo)
|
||||
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_real',data=kin_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_imag',data=kin_mo_blocked.imag)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_real',data=ovlp_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_imag',data=ovlp_mo_blocked.imag)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_real', data=ne_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_imag', data=ne_mo_blocked.imag)
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_real',data=kin_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_imag',data=kin_mo_blocked.imag)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_real',data=ovlp_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_imag',data=ovlp_mo_blocked.imag)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_real', data=ne_mo_blocked.real)
|
||||
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_imag', data=ne_mo_blocked.imag)
|
||||
for fname,ints in zip(('S.mo.qp','V.mo.qp','T.mo.qp'),
|
||||
(ovlp_mo, ne_mo, kin_mo)):
|
||||
print_kpts_unblocked_upper(ints,fname,thresh_mono)
|
||||
|
||||
|
||||
# ___ _
|
||||
# | ._ _|_ _ _ ._ _. | _ |_) o
|
||||
# _|_ | | |_ (/_ (_| | (_| | _> |_) |
|
||||
# _|
|
||||
#
|
||||
##########################################
|
||||
# #
|
||||
# k-points #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
kconserv = tools.get_kconserv(cell, kpts)
|
||||
qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1)))
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
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 h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('nuclei/kconserv_test',data=kcon_test)
|
||||
|
||||
|
||||
with open('K.qp','w') as outfile:
|
||||
for a in range(Nk):
|
||||
for b in range(Nk):
|
||||
for c in range(Nk):
|
||||
d = kconserv[a,b,c]
|
||||
outfile.write('%s %s %s %s\n' % (a+1,c+1,b+1,d+1))
|
||||
|
||||
print_kcon_chem_to_phys(kconserv,'K.qp')
|
||||
|
||||
##########################################
|
||||
# #
|
||||
# Integrals Bi #
|
||||
# #
|
||||
##########################################
|
||||
|
||||
intfile=h5py.File(mf.with_df._cderi,'r')
|
||||
# qph5['ao_two_e_ints'].attrs['df_num']=naux
|
||||
|
||||
j3c = intfile.get('j3c')
|
||||
naosq = nao*nao
|
||||
naotri = (nao*(nao+1))//2
|
||||
j3ckeys = list(j3c.keys())
|
||||
j3ckeys.sort(key=lambda strkey:int(strkey))
|
||||
|
||||
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
||||
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
||||
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
||||
j3clist = [j3c.get(i+'/0') for i in j3ckeys]
|
||||
if j3clist==[None]*len(j3clist):
|
||||
# if using older version, stop before last level
|
||||
j3clist = [j3c.get(i) for i in j3ckeys]
|
||||
|
||||
nkinvsq = 1./np.sqrt(Nk)
|
||||
|
||||
# dimensions are (kikj,iaux,jao,kao), where kikj is compound index of kpts i and j
|
||||
# output dimensions should be reversed (nao, nao, naux, nkptpairs)
|
||||
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 = get_j3ao(mf.with_df._cderi,nao,Nk)
|
||||
|
||||
nkpt_pairs = j3arr.shape[0]
|
||||
naux = max(i.shape[0] for i in j3arr)
|
||||
print("n df fitting functions", naux)
|
||||
qph5['ao_two_e_ints'].attrs['df_num']=naux
|
||||
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_group('ao_two_e_ints')
|
||||
qph5['ao_two_e_ints'].attrs['df_num']=naux
|
||||
|
||||
if print_ao_ints_df:
|
||||
with open('D.qp','w') as outfile:
|
||||
pass
|
||||
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(stri4z(i+1,j+1,iaux+1,k+1,v.real,v.imag)+'\n')
|
||||
df_ao_tmp[i,j,iaux,k]=v
|
||||
print_df(j3arr,'D.qp',bielec_int_threshold)
|
||||
|
||||
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
|
||||
for i,di in enumerate(j3arr):
|
||||
df_ao_tmp[:,:,:di.shape[0],i] = np.transpose(di,(1,2,0))
|
||||
|
||||
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_real',data=df_ao_tmp.real)
|
||||
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_imag',data=df_ao_tmp.imag)
|
||||
#df_ao_old = df_pad_ref_test(j3arr,nao,naux,nkpt_pairs)
|
||||
#assert(abs(df_ao_tmp - df_ao_old).max() <= 1e-12)
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_real',data=df_ao_tmp.real)
|
||||
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_imag',data=df_ao_tmp.imag)
|
||||
|
||||
if print_mo_ints_df:
|
||||
kpair_list=[]
|
||||
for i in range(Nk):
|
||||
for j in range(Nk):
|
||||
if(i>=j):
|
||||
kpair_list.append((i,j,idx2_tri((i,j))))
|
||||
from itertools import product
|
||||
# WARNING: this is a generator, not a list; don't use it more than once
|
||||
kpair_list = ((i,j,idx2_tri((i,j))) for (i,j) in product(range(Nk),repeat=2) if (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])
|
||||
print_df(j3mo,'D.mo.qp',bielec_int_threshold)
|
||||
|
||||
df_mo_tmp = np.zeros((nmo,nmo,naux,nkpt_pairs),dtype=np.complex128)
|
||||
with open('D_mo.qp','w') as outfile:
|
||||
pass
|
||||
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(stri4z(i+1,j+1,iaux+1,k+1,v.real,v.imag)+'\n')
|
||||
df_mo_tmp[i,j,iaux,k]=v
|
||||
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_real',data=df_mo_tmp.real)
|
||||
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=df_mo_tmp.imag)
|
||||
for i,di in enumerate(j3mo):
|
||||
df_mo_tmp[:,:,:di.shape[0],i] = np.transpose(di,(1,2,0))
|
||||
|
||||
#df_mo_old = df_pad_ref_test(j3mo,nmo,naux,nkpt_pairs)
|
||||
#assert(abs(df_mo_tmp - df_mo_old).max() <= 1e-12)
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_real',data=df_mo_tmp.real)
|
||||
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=df_mo_tmp.imag)
|
||||
|
||||
if (print_ao_ints_bi):
|
||||
print_ao_bi(mf,kconserv,'W.qp',bielec_int_threshold)
|
||||
|
|
@ -835,7 +913,6 @@ def getj3ao(cell,mf, kpts, cas_idx=None, int_threshold = 1E-8):
|
|||
from pyscf.pbc import ao2mo
|
||||
from pyscf.pbc import tools
|
||||
from pyscf.pbc.gto import ecp
|
||||
from pyscf.data import nist
|
||||
import h5py
|
||||
import scipy
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user