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add converter changes from @anbenali

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This commit is contained in:
Kevin Gasperich 2020-11-05 13:11:19 -06:00
parent 0d9879dcb1
commit fc71c0efcc
1 changed files with 13 additions and 8 deletions
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21
src/utils_complex/MolPyscfToQPkpts.py
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@ -440,10 +440,10 @@ def get_j3ao_new(fname,nao,Nk):
# 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, ...]
#keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
#naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
naux = max(map(lambda k: j3c[k]['0'].shape[0],j3c.keys()))
naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
#naux = max(map(lambda k: j3c[k]['0'].shape[0],j3c.keys()))
naosq = nao*nao
naotri = (nao*(nao+1))//2
@ -452,12 +452,15 @@ def get_j3ao_new(fname,nao,Nk):
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
for i,kpair in enumerate(j3ckeys):
tmpdat = np.concatenate([j3c[kpair][ii][()] for ii in j3c[kpair]],axis=1)
iaux,dim2 = tmpdat.shape
iaux,dim2 = j3c[kpair+keysub].shape
#tmpdat = np.concatenate([j3c[kpair][ii][()] for ii in j3c[kpair]],axis=1)
#iaux,dim2 = tmpdat.shape
if (dim2==naosq):
j3arr[i,:iaux,:,:] = tmpdat.reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
#j3arr[i,:iaux,:,:] = tmpdat.reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
else:
j3arr[i,:iaux,:,:] = makesq3(tmpdat.conj(),nao) * nkinvsq
j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
#j3arr[i,:iaux,:,:] = makesq3(tmpdat.conj(),nao) * nkinvsq
return j3arr
@ -586,12 +589,14 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
print('n_atom per kpt', natom)
#BY DEFAULT SEEMS TO BE IN BOHR
atom_xyz = mf.cell.atom_coords()
unit_bohr=1.0
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
from pyscf.data.nist import BOHR
atom_xyz /= BOHR # always convert to au
# atom_xyz *= BOHR # always convert to au
# atom_xyz /= BOHR # always convert to au
unit_bohr=BOHR
with h5py.File(qph5path,'a') as qph5: