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mirror of https://github.com/QuantumPackage/qp2.git synced 2024-12-24 13:23:39 +01:00

converter cleanup

This commit is contained in:
Kevin Gasperich 2020-02-18 15:34:55 -06:00
parent b3390f2fa3
commit 1c09b7dcbc

View File

@ -27,6 +27,19 @@ def pad(arr_in,outshape):
arr_out[dataslice] = arr_in arr_out[dataslice] = arr_in
return arr_out 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): def makesq(vlist,n1,n2):
''' '''
make hermitian matrices of size (n2 x n2) from from lower triangles 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) # 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: def print_mo_bi(mf,kconserv=None,outfilename='W.mo.qp',cas_idx=None,bielec_int_threshold = 1E-8):
with open('bielec_ao_complex','w') as outfile:
pass cell = mf.cell
if print_mo_ints_bi: kpts = mf.kpts
with open('bielec_mo_complex','w') as outfile: #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 pass
for d, kd in enumerate(kpts): for d, kd in enumerate(kpts):
for c, kc in enumerate(kpts): for c, kc in enumerate(kpts):
if c > d: break if c > d: break
idx2_cd = idx2_tri((c,d)) #idx2_cd = idx2_tri((c,d))
for b, kb in enumerate(kpts): for b, kb in enumerate(kpts):
if b > d: break if b > d: break
a = kconserv[b,c,d] a = kconserv[b,c,d]
if idx2_tri((a,b)) > idx2_cd: continue if a > d: continue
if ((c==d) and (a>b)): continue #if idx2_tri((a,b)) > idx2_cd: continue
#if ((c==d) and (a>b)): continue
ka = kpts[a] ka = kpts[a]
with open(outfilename,'a') as outfile:
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:
eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]], 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) [ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
eri_4d_mo_kpt *= 1./Nk 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 if ((jj==ll) and (ii>kk)): break
v=eri_4d_mo_kpt[i,k,j,l] v=eri_4d_mo_kpt[i,k,j,l]
if (abs(v) > bielec_int_threshold): 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): def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_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 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 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) 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(outfilename,'w') as outfile:
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:
pass pass
for d, kd in enumerate(kpts): for d, kd in enumerate(kpts):
for c, kc in enumerate(kpts): for c, kc in enumerate(kpts):
if c > d: break if c > d: break
idx2_cd = idx2_tri((c,d)) #idx2_cd = idx2_tri((c,d))
for b, kb in enumerate(kpts): for b, kb in enumerate(kpts):
if b > d: break if b > d: break
a = kconserv[b,c,d] a = kconserv[b,c,d]
#if idx2_tri((a,b)) > idx2_cd: continue
if a > d: continue if a > d: continue
#if idx2_tri((a,b)) > idx2_cd: continue
#if ((c==d) and (a>b)): continue #if ((c==d) and (a>b)): continue
ka = kpts[a] 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 = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
eri_4d_ao_kpt *= 1./Nk eri_4d_ao_kpt *= 1./Nk
for l in range(nao): 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 if ((jj==ll) and (ii>kk)): break
v=eri_4d_ao_kpt[i,k,j,l] v=eri_4d_ao_kpt[i,k,j,l]
if (abs(v) > bielec_int_threshold): 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')