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added pbc basis and lattice info from Anouar

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This commit is contained in:
Kevin Gasperich 2020-08-18 15:51:37 -05:00 committed by Kevin Gasperich
parent 43c7696001
commit 6444cde88b
1 changed files with 86 additions and 4 deletions
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90
src/utils_complex/MolPyscfToQPkpts.py
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@ -564,7 +564,7 @@ def pyscf2QP2_mo(cell,mf,kpts,kmesh=None,cas_idx=None, int_threshold = 1E-8,qph5
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5path = 'qpdat.h5',
qph5path = 'qpdat.h5', sp_twist=None,
print_ao_ints_bi=False,
print_mo_ints_bi=False,
print_ao_ints_df=True,
@ -600,6 +600,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5.create_group('electrons')
qph5.create_group('ao_basis')
qph5.create_group('mo_basis')
qph5.create_group('PBC_DATA')
mo_coeff = mf.mo_coeff
# Mo_coeff actif
@ -646,14 +647,69 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
# nucleus on which each AO is centered
ao_nucl=[i[0] for i in mf.cell.ao_labels(fmt=False,base=1)]
nprim_max = 0
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
for ib in range(sh0,sh1): # sets of contracted exponents
nprim = cell.bas_nprim(ib)
if (nprim > nprim_max):
nprim_max = nprim
qp_prim_num = np.zeros((nao),dtype=int)
qp_coef = np.zeros((nao,nprim_max))
qp_expo = np.zeros((nao,nprim_max))
qp_nucl = np.zeros((nao),dtype=int)
qp_pwr = np.zeros((nao,3),dtype=int)
clabels = cell.cart_labels(fmt=False)
tmp_idx=0
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
# shell start,end; AO start,end (sph or cart) for each atom
for ib in range(sh0,sh1): # sets of contracted exponents
l = cell.bas_angular(ib) # angular momentum
if ( cell.cart==True):
representation=((l+1)*(l+2))//2
else:
representation=2*l-1
nprim = cell.bas_nprim(ib) # numer of primitives
es = cell.bas_exp(ib) # exponents
cs = cell.bas_ctr_coeff(ib) # coeffs
nctr = cell.bas_nctr(ib) # number of contractions
print(iatom,ib,l,nprim,nctr,tmp_idx)
for ic in range(nctr): # sets of contraction coeffs
# for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
# for nfunc in range(2*l-1):
for nfunc in range(representation):
qp_expo[tmp_idx,:nprim] = es[:]
qp_coef[tmp_idx,:nprim] = cs[:,ic]
qp_nucl[tmp_idx] = iatom + 1
qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
qp_prim_num[tmp_idx] = nprim
tmp_idx += 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['mo_basis'].attrs['mo_num']=nmo
qph5['ao_basis'].attrs['ao_num']=nao
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
qph5.create_dataset('ao_basis/ao_nucl',data=qp_nucl)
qph5.create_dataset('ao_basis/ao_prim_num',data=qp_prim_num)
qph5.create_dataset('ao_basis/ao_expo',data=qp_expo.T)
qph5.create_dataset('ao_basis/ao_coef',data=qp_coef.T)
qph5.create_dataset('ao_basis/ao_power',data=qp_pwr.T)
# 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['ao_basis'].attrs['ao_basis']="dummy basis"
#
# qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
##########################################
# #
@ -800,8 +856,34 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
print_ao_bi(mf,kconserv,'W.qp',bielec_int_threshold)
if (print_mo_ints_bi):
print_mo_bi(mf,kconserv,'W.mo.qp',cas_idx,bielec_int_threshold)
##########################################
# #
# PBC DATA To transfer to qmc #
# #
##########################################
if len(kpts)== 0:
sp_twist=[0.0,0.0,0.0]
with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('PBC_DATA/PBE',(1,),dtype="b1",data=True)
qph5.create_dataset('PBC_DATA/Super_Twist',(1,3),dtype="f8",data=sp_twist)
qph5.create_dataset('PBC_DATA/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
qph5.create_dataset('PBC_DATA/eigenval',(1,nmo),dtype="f8",data=mf.mo_energy)
return
def xyzcount(s):
return list(map(s.count,['x','y','z']))
def xyzcount(s):
return list(map(s.count,['x','y','z']))