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cleaning up converter

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This commit is contained in:
Kevin Gasperich 2020-03-10 18:10:55 -05:00
parent c5726abb13
commit 8411167e90
1 changed files with 207 additions and 66 deletions
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273
src/utils_complex/MolPyscfToQPkpts.py
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@ -509,8 +509,74 @@ def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E
v.real,v.imag)+'\n')
def print_kpts_unblocked(ints_k,outfilename,thresh):
'''
for ints_k of shape (Nk,n1,n2),
print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n2) in file
'''
Nk,n1,n2 = ints_k.shape
with open(outfilename,'w') as outfile:
for ik in range(Nk):
shift1 = ik*n1+1
shift2 = ik*n2+1
for i1 in range(n1):
for i2 in range(n2):
int_ij = ints_k[ik,i1,i2]
if abs(int_ij) > thresh:
outfile.write(stri2z(i1+shift1, i2+shift2, int_ij.real, int_ij.imag)+'\n')
return
def print_kpts_unblocked_upper(ints_k,outfilename,thresh):
'''
for hermitian ints_k of shape (Nk,n1,n1),
print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n1) in file
(only upper triangle is printed)
'''
Nk,n1,n2 = ints_k.shape
if (n1!=n2):
raise Exception('print_kpts_unblocked_upper called with non-square matrix')
with open(outfilename,'w') as outfile:
for ik in range(Nk):
shift = ik*n1+1
for i1 in range(n1):
for i2 in range(i1,n1):
int_ij = ints_k[ik,i1,i2]
if abs(int_ij) > thresh:
outfile.write(stri2z(i1+shift, i2+shift, int_ij.real, int_ij.imag)+'\n')
return
def get_kin_ao(mf):
nao = mf.cell.nao_nr()
Nk = len(mf.kpts)
return np.reshape(mf.cell.pbc_intor('int1e_kin',1,1,kpts=mf.kpts),(Nk,nao,nao))
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))
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))
else:
v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=kpts),(Nk,nao,nao))
if len(cell._ecpbas) > 0:
from pyscf.pbc.gto import ecp
v_kpts_ao += np.reshape(ecp.ecp_int(cell, 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 pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
print_ao_ints_bi=False,
print_mo_ints_bi=False,
@ -532,19 +598,23 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
import h5py
import scipy
qph5=h5py.File('qpdat.h5')
qph5.create_group('nuclei')
qph5.create_group('electrons')
qph5.create_group('ao_basis')
qph5.create_group('mo_basis')
mo_coef_threshold = int_threshold
ovlp_threshold = int_threshold
kin_threshold = int_threshold
ne_threshold = int_threshold
bielec_int_threshold = int_threshold
thresh_mono = int_threshold
qph5path = 'qpdat.h5'
# create hdf5 file, delete old data if exists
with h5py.File(qph5path,'w') as qph5:
qph5.create_group('nuclei')
qph5.create_group('electrons')
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
@ -573,18 +643,19 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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)
# 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']=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
# qph5['ao_two_e_ints'].attrs['df_num']=naux
qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
ao_nucl=[mf.cell.bas_atom(i)+1 for i in range(nao)]
@ -612,67 +683,52 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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)
with open('C.qp','w') as outfile:
c_kpts = np.reshape(mo_k,(Nk,nao,nmo))
for ik in range(Nk):
shift1=ik*nao+1
shift2=ik*nmo+1
for i in range(nao):
for j in range(nmo):
cij = c_kpts[ik,i,j]
if abs(cij) > mo_coef_threshold:
outfile.write(stri2z(i+shift1, j+shift2, cij.real, cij.imag)+'\n')
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
# ___
# | ._ _|_ _ _ ._ _. | _ |\/| _ ._ _
# _|_ | | |_ (/_ (_| | (_| | _> | | (_) | | (_)
# _|
if mf.cell.pseudo:
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 = ('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)
kin_ao_blocked=scipy.linalg.block_diag(*kin_ao[1])
ovlp_ao_blocked=scipy.linalg.block_diag(*ovlp_ao[1])
ne_ao_blocked=scipy.linalg.block_diag(*v_kpts_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)
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)
for name, intval_kpts_ao, thresh in (ne_ao, ovlp_ao, kin_ao):
if print_ao_ints_mono:
with open('%s.qp' % name,'w') as outfile:
for ik in range(Nk):
shift=ik*nao+1
for i in range(nao):
for j in range(i,nao):
int_ij = intval_kpts_ao[ik,i,j]
if abs(int_ij) > thresh:
outfile.write(stri2z(i+shift, j+shift, int_ij.real, int_ij.imag)+'\n')
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.qp' % name,'w') as outfile:
for ik in range(Nk):
shift=ik*nmo+1
for i in range(nmo):
for j in range(i,nmo):
int_ij = intval_kpts_mo[ik,i,j]
if abs(int_ij) > thresh:
outfile.write(stri2z(i+shift, j+shift, int_ij.real, int_ij.imag)+'\n')
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)):
print_kpts_unblocked_upper(ints,fname,thresh_mono)
if print_mo_ints_mono:
kin_mo = ao_to_mo_1e(kin_ao,mo_k)
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)
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)
# ___ _
@ -721,6 +777,9 @@ 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]
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)
if print_ao_ints_df:
@ -764,6 +823,88 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
if (print_mo_ints_bi):
print_mo_bi(mf,kconserv,'W.mo.qp',cas_idx,bielec_int_threshold)
def getj3ao(cell,mf, kpts, cas_idx=None, int_threshold = 1E-8):
'''
kpts = List of kpoints coordinates. Cannot be null, for gamma is other script
kmesh = Mesh of kpoints (optional)
cas_idx = List of active MOs. If not specified all MOs are actives
int_threshold = The integral will be not printed in they are bellow that
'''
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
mo_coef_threshold = int_threshold
ovlp_threshold = int_threshold
kin_threshold = int_threshold
ne_threshold = int_threshold
bielec_int_threshold = int_threshold
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)
with h5py.File(mf.with_df._cderi) as intfile:
# intfile=h5py.File(mf.with_df._cderi,'r')
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])
return j3arr
#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('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
#def testpyscf2QP(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8):