Python comp_overlap_coo Examples

Example #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:])):
            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

Example #2

File: m_overlap_coo.py Project: NuturesH/pyscf-1

  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)

Example #3

File: m_comp_coulomb_den.py Project: chrinide/pyscf

  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