for atom1, [sp1, rv1, s1, f1] in enumerate(
zip(sv.atom2sp, sv.atom2coord, atom2s, atom2s[1:])):
for atom2, [sp2, rv2, s2, f2] in enumerate(
zip(sv.atom2sp, sv.atom2coord, atom2s, atom2s[1:])):
oo2f = funct(me, sp1, rv1, sp2, rv2, **kvargs)
res[s1:f1, s2:f2] = oo2f[:, :]
#np.savetxt("kernel_pyscf_dens.txt", res)
#print("sum(kernel) = ", np.sum(abs(res)))
#import sys
#sys.exit()
return res
#
#
#
if __name__ == '__main__':
from pyscf.nao.m_comp_coulomb_den import comp_coulomb_den
from pyscf.nao.m_comp_overlap_coo import comp_overlap_coo
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_overlap_am import overlap_am
sv = system_vars_c(label='siesta')
over_coo = comp_overlap_coo(sv, funct=overlap_am).toarray()
over_den = comp_coulomb_den(sv, funct=overlap_am)
print(np.allclose(over_coo, over_den)) # must be always true
irow,icol,data = zeros(nnz, dtype=int64),zeros(nnz, dtype=int64),zeros(nnz) # Start to construct coo matrix
inz=-1
for atom1,[sp1,rv1,s1,f1] in enumerate(zip(sv.atom2sp,sv.atom2coord,atom2s,atom2s[1:])):
for atom2,[sp2,rv2,s2,f2] in enumerate(zip(sv.atom2sp,sv.atom2coord,atom2s,atom2s[1:])):
if (sp2rcut[sp1]+sp2rcut[sp2])**2<=sum((rv1-rv2)**2) : continue
oo = funct(me,sp1,rv1,sp2,rv2,**kvargs)
for o1 in range(s1,f1):
for o2 in range(s2,f2):
inz = inz+1
irow[inz],icol[inz],data[inz] = o1,o2,oo[o1-s1,o2-s2]
norbs = atom2s[-1]
return coo_matrix((data, (irow, icol)), shape=(norbs, norbs))
#
#
#
if __name__=='__main__':
from pyscf.nao.m_comp_overlap_coo import comp_overlap_coo
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_overlap_am import overlap_am
from pyscf.nao.m_overlap_ni import overlap_ni
sv = system_vars_c(label='siesta')
over = comp_overlap_coo(sv, funct=overlap_ni, level=7).tocsr()
diff = (sv.hsx.s4_csr-over).sum()
summ = (sv.hsx.s4_csr+over).sum()
print(diff/summ, diff/over.size)
res = np.zeros((norbs,norbs), dtype=dtype)
for atom1,[sp1,rv1,s1,f1] in enumerate(zip(sv.atom2sp,sv.atom2coord,atom2s,atom2s[1:])):
for atom2,[sp2,rv2,s2,f2] in enumerate(zip(sv.atom2sp,sv.atom2coord,atom2s,atom2s[1:])):
oo2f = funct(me,sp1,rv1,sp2,rv2,**kvargs)
res[s1:f1,s2:f2] = oo2f[:,:]
#np.savetxt("kernel_pyscf_dens.txt", res)
#print("sum(kernel) = ", np.sum(abs(res)))
#import sys
#sys.exit()
return res
#
#
#
if __name__=='__main__':
from pyscf.nao.m_comp_coulomb_den import comp_coulomb_den
from pyscf.nao.m_comp_overlap_coo import comp_overlap_coo
from pyscf.nao.m_system_vars import system_vars_c
from pyscf.nao.m_overlap_am import overlap_am
sv = system_vars_c(label='siesta')
over_coo = comp_overlap_coo(sv, funct=overlap_am).toarray()
over_den = comp_coulomb_den(sv, funct=overlap_am)
print(np.allclose(over_coo, over_den)) # must be always true