mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-06-28 08:02:33 +02:00
converter cleanup
This commit is contained in:
Kevin Gasperich
parent
b3390f2fa3
commit
1c09b7dcbc
|
|
@ -27,6 +27,19 @@ def pad(arr_in,outshape):
|
|||
arr_out[dataslice] = arr_in
|
||||
return arr_out
|
||||
|
||||
def idx40(i,j,k,l):
|
||||
return idx2_tri((idx2_tri((i,k)),idx2_tri((j,l))))
|
||||
|
||||
def idx4(i,j,k,l):
|
||||
return idx2_tri((idx2_tri((i-1,k-1)),idx2_tri((j-1,l-1))))+1
|
||||
|
||||
def stri4z(i,j,k,l,zr,zi):
|
||||
return (4*'{:5d}'+2*'{:25.16e}').format(i,j,k,l,zr,zi)
|
||||
|
||||
def strijklikjli4z(i,j,k,l,zr,zi):
|
||||
return ('{:10d}'+ 2*'{:8d}'+4*'{:5d}'+2*'{:25.16e}').format(idx4(i,j,k,l),idx2_tri((i-1,k-1))+1,idx2_tri((j-1,l-1))+1,i,j,k,l,zr,zi)
|
||||
|
||||
|
||||
def makesq(vlist,n1,n2):
|
||||
'''
|
||||
make hermitian matrices of size (n2 x n2) from from lower triangles
|
||||
|
|
@ -409,48 +422,43 @@ def pyscf2QP(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|||
#
|
||||
# eri_4d_ao = eri_4d_ao.reshape([Nk*nao]*4)
|
||||
|
||||
if (print_ao_ints_bi):
|
||||
print_ao_bi(mf,kconserv,'bielec_ao_complex',bielec_int_threshold)
|
||||
if (print_mo_ints_bi):
|
||||
print_mo_bi(mf,kconserv,'bielec_mo_complex',cas_idx,bielec_int_threshold)
|
||||
|
||||
if (print_ao_ints_bi or print_mo_ints_bi):
|
||||
if print_ao_ints_bi:
|
||||
with open('bielec_ao_complex','w') as outfile:
|
||||
pass
|
||||
if print_mo_ints_bi:
|
||||
with open('bielec_mo_complex','w') as outfile:
|
||||
|
||||
def print_mo_bi(mf,kconserv=None,outfilename='W.mo.qp',cas_idx=None,bielec_int_threshold = 1E-8):
|
||||
|
||||
cell = mf.cell
|
||||
kpts = mf.kpts
|
||||
#nao = mf.cell.nao
|
||||
#Nk = kpts.shape[0]
|
||||
|
||||
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)
|
||||
|
||||
Nk, nao, nmo = mo_k.shape
|
||||
|
||||
if (kconserv is None):
|
||||
from pyscf.pbc import tools
|
||||
kconserv = tools.get_kconserv(cell, kpts)
|
||||
|
||||
with open(outfilename,'w') as outfile:
|
||||
pass
|
||||
for d, kd in enumerate(kpts):
|
||||
for c, kc in enumerate(kpts):
|
||||
if c > d: break
|
||||
idx2_cd = idx2_tri((c,d))
|
||||
#idx2_cd = idx2_tri((c,d))
|
||||
for b, kb in enumerate(kpts):
|
||||
if b > d: break
|
||||
a = kconserv[b,c,d]
|
||||
if idx2_tri((a,b)) > idx2_cd: continue
|
||||
if ((c==d) and (a>b)): continue
|
||||
if a > d: continue
|
||||
#if idx2_tri((a,b)) > idx2_cd: continue
|
||||
#if ((c==d) and (a>b)): continue
|
||||
ka = kpts[a]
|
||||
|
||||
if print_ao_ints_bi:
|
||||
with open('bielec_ao_complex','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 *= 1./Nk
|
||||
for l in range(nao):
|
||||
ll=l+d*nao
|
||||
for j in range(nao):
|
||||
jj=j+c*nao
|
||||
if jj>ll: break
|
||||
idx2_jjll = idx2_tri((jj,ll))
|
||||
for k in range(nao):
|
||||
kk=k+b*nao
|
||||
if kk>ll: break
|
||||
for i in range(nao):
|
||||
ii=i+a*nao
|
||||
if idx2_tri((ii,kk)) > idx2_jjll: break
|
||||
if ((jj==ll) and (ii>kk)): break
|
||||
v=eri_4d_ao_kpt[i,k,j,l]
|
||||
if (abs(v) > bielec_int_threshold):
|
||||
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:
|
||||
with open('bielec_mo_complex','a') as outfile:
|
||||
with open(outfilename,'a') as outfile:
|
||||
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)
|
||||
eri_4d_mo_kpt *= 1./Nk
|
||||
|
|
@ -469,181 +477,35 @@ def pyscf2QP(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|||
if ((jj==ll) and (ii>kk)): break
|
||||
v=eri_4d_mo_kpt[i,k,j,l]
|
||||
if (abs(v) > bielec_int_threshold):
|
||||
outfile.write('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
|
||||
outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,v.real,v.imag)+'\n')
|
||||
|
||||
|
||||
def testprintbi(cell,mf, kpts, kmesh=None, 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
|
||||
'''
|
||||
def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E-8):
|
||||
|
||||
from pyscf.pbc import ao2mo
|
||||
cell = mf.cell
|
||||
kpts = mf.kpts
|
||||
nao = mf.cell.nao
|
||||
Nk = kpts.shape[0]
|
||||
|
||||
if (kconserv is None):
|
||||
from pyscf.pbc import tools
|
||||
from pyscf.pbc.gto import ecp
|
||||
from pyscf.data import nist
|
||||
import h5py
|
||||
import scipy
|
||||
|
||||
|
||||
bielec_int_threshold = int_threshold
|
||||
|
||||
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
|
||||
|
||||
|
||||
|
||||
# ___ _
|
||||
# | ._ _|_ _ _ ._ _. | _ |_) o
|
||||
# _|_ | | |_ (/_ (_| | (_| | _> |_) |
|
||||
# _|
|
||||
#
|
||||
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('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))
|
||||
|
||||
|
||||
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])
|
||||
|
||||
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('%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_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))))
|
||||
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])
|
||||
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('%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_integrals_real',data=df_mo_tmp.real)
|
||||
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=df_mo_tmp.imag)
|
||||
|
||||
|
||||
|
||||
# eri_4d_ao = np.zeros((Nk,nao,Nk,nao,Nk,nao,Nk,nao), dtype=np.complex)
|
||||
# for d, kd in enumerate(kpts):
|
||||
# for c, kc in enumerate(kpts):
|
||||
# if c > d: break
|
||||
# idx2_cd = idx2_tri(c,d)
|
||||
# for b, kb in enumerate(kpts):
|
||||
# if b > d: break
|
||||
# a = kconserv[b,c,d]
|
||||
# if idx2_tri(a,b) > idx2_cd: continue
|
||||
# if ((c==d) and (a>b)): continue
|
||||
# ka = kpts[a]
|
||||
# v = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
|
||||
# v *= 1./Nk
|
||||
# eri_4d_ao[a,:,b,:,c,:,d] = v
|
||||
#
|
||||
# eri_4d_ao = eri_4d_ao.reshape([Nk*nao]*4)
|
||||
|
||||
|
||||
with open('W.qp','w') as outfile:
|
||||
with open(outfilename,'w') as outfile:
|
||||
pass
|
||||
for d, kd in enumerate(kpts):
|
||||
for c, kc in enumerate(kpts):
|
||||
if c > d: break
|
||||
idx2_cd = idx2_tri((c,d))
|
||||
#idx2_cd = idx2_tri((c,d))
|
||||
for b, kb in enumerate(kpts):
|
||||
if b > d: break
|
||||
a = kconserv[b,c,d]
|
||||
if a > d: continue
|
||||
#if idx2_tri((a,b)) > idx2_cd: continue
|
||||
if a>d: continue
|
||||
#if ((c==d) and (a>b)): continue
|
||||
ka = kpts[a]
|
||||
|
||||
with open('W.qp','a') as outfile:
|
||||
with open(outfilename,'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 *= 1./Nk
|
||||
for l in range(nao):
|
||||
|
|
@ -661,7 +523,8 @@ def testprintbi(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8):
|
|||
if ((jj==ll) and (ii>kk)): break
|
||||
v=eri_4d_ao_kpt[i,k,j,l]
|
||||
if (abs(v) > bielec_int_threshold):
|
||||
outfile.write('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
|
||||
outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,v.real,v.imag)+'\n')
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user