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converter cleanup

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This commit is contained in:
Kevin Gasperich 2020-02-18 15:34:55 -06:00
parent b3390f2fa3
commit 1c09b7dcbc
1 changed files with 101 additions and 238 deletions
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339
src/utils_complex/MolPyscfToQPkpts.py
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@ -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
@ -409,260 +422,110 @@ 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):
if (print_ao_ints_bi or print_mo_ints_bi): print_ao_bi(mf,kconserv,'bielec_ao_complex',bielec_int_threshold)
if print_ao_ints_bi: if (print_mo_ints_bi):
with open('bielec_ao_complex','w') as outfile: print_mo_bi(mf,kconserv,'bielec_mo_complex',cas_idx,bielec_int_threshold)
pass
if print_mo_ints_bi:
with open('bielec_mo_complex','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))
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]
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]],
[ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
eri_4d_mo_kpt *= 1./Nk
for l in range(nmo):
ll=l+d*nmo
for j in range(nmo):
jj=j+c*nmo
if jj>ll: break
idx2_jjll = idx2_tri((jj,ll))
for k in range(nmo):
kk=k+b*nmo
if kk>ll: break
for i in range(nmo):
ii=i+a*nmo
if idx2_tri((ii,kk)) > idx2_jjll: break
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))
def testprintbi(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8): def print_mo_bi(mf,kconserv=None,outfilename='W.mo.qp',cas_idx=None,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
from pyscf.pbc import tools
from pyscf.pbc.gto import ecp
from pyscf.data import nist
import h5py
import scipy
cell = mf.cell
kpts = mf.kpts
#nao = mf.cell.nao
#Nk = kpts.shape[0]
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 = mf.mo_coeff
# Mo_coeff actif # Mo_coeff actif
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff) 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 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 if (kconserv is None):
print("n df fitting functions", naux) from pyscf.pbc import tools
kconserv = tools.get_kconserv(cell, kpts)
#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
with open(outfilename,'w') as outfile:
# ___ _ pass
# | ._ _|_ _ _ ._ _. | _ |_) o for d, kd in enumerate(kpts):
# _|_ | | |_ (/_ (_| | (_| | _> |_) | for c, kc in enumerate(kpts):
# _| if c > d: break
# #idx2_cd = idx2_tri((c,d))
kconserv = tools.get_kconserv(cell, kpts) for b, kb in enumerate(kpts):
qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1))) if b > d: break
kcon_test = np.zeros((Nk,Nk,Nk),dtype=int) a = kconserv[b,c,d]
for a in range(Nk): if a > d: continue
for b in range(Nk): #if idx2_tri((a,b)) > idx2_cd: continue
for c in range(Nk): #if ((c==d) and (a>b)): continue
kcon_test[a,c,b] = kconserv[a,b,c]+1 ka = kpts[a]
qph5.create_dataset('nuclei/kconserv_test',data=kcon_test) 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)
with open('K.qp','w') as outfile: eri_4d_mo_kpt *= 1./Nk
for a in range(Nk): for l in range(nmo):
for b in range(Nk): ll=l+d*nmo
for c in range(Nk): for j in range(nmo):
d = kconserv[a,b,c] jj=j+c*nmo
outfile.write('%s %s %s %s\n' % (a+1,c+1,b+1,d+1)) if jj>ll: break
idx2_jjll = idx2_tri((jj,ll))
for k in range(nmo):
intfile=h5py.File(mf.with_df._cderi,'r') kk=k+b*nmo
if kk>ll: break
j3c = intfile.get('j3c') for i in range(nmo):
naosq = nao*nao ii=i+a*nmo
naotri = (nao*(nao+1))//2 if idx2_tri((ii,kk)) > idx2_jjll: break
j3ckeys = list(j3c.keys()) if ((jj==ll) and (ii>kk)): break
j3ckeys.sort(key=lambda strkey:int(strkey)) v=eri_4d_mo_kpt[i,k,j,l]
if (abs(v) > bielec_int_threshold):
# in new(?) version of PySCF, there is an extra layer of groups before the datasets outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,v.real,v.imag)+'\n')
# 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)
def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E-8):
# eri_4d_ao = np.zeros((Nk,nao,Nk,nao,Nk,nao,Nk,nao), dtype=np.complex) cell = mf.cell
# for d, kd in enumerate(kpts): kpts = mf.kpts
# for c, kc in enumerate(kpts): nao = mf.cell.nao
# if c > d: break Nk = kpts.shape[0]
# idx2_cd = idx2_tri(c,d)
# for b, kb in enumerate(kpts): if (kconserv is None):
# if b > d: break from pyscf.pbc import tools
# a = kconserv[b,c,d] kconserv = tools.get_kconserv(cell, kpts)
# if idx2_tri(a,b) > idx2_cd: continue
# if ((c==d) and (a>b)): continue with open(outfilename,'w') as outfile:
# ka = kpts[a] pass
# v = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4) for d, kd in enumerate(kpts):
# v *= 1./Nk for c, kc in enumerate(kpts):
# eri_4d_ao[a,:,b,:,c,:,d] = v if c > d: break
# #idx2_cd = idx2_tri((c,d))
# eri_4d_ao = eri_4d_ao.reshape([Nk*nao]*4) 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 ((c==d) and (a>b)): continue
ka = kpts[a]
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):
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(stri4z(ii+1,jj+1,kk+1,ll+1,v.real,v.imag)+'\n')
with open('W.qp','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))
for b, kb in enumerate(kpts):
if b > d: break
a = kconserv[b,c,d]
#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:
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))
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8, def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,