Atoms missing from the geometry.


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Here is a sample input file for a simulation I'm running. (Never mind the fact that the lattice parameters aren't right.)
title "Lithium--H_2 adsorption site optimization"
echo

permanent_dir .
scratch_dir   .

start lithium

memory 2500 mb

nwpw
  simulation_cell
    ngrid 32 32 128
  end
  mult 2
  ewald_rcut 3.0
  ewald_ncut 8
  xc pbesol
end

set nwpw:minimizer     2       # Grassman LMBFGS minimizer
set nwpw:cif_filename   li.opt  # create a CIF file containing optimization history
set nwpw:lcao_skip      .true.
set nwpw:kbpp_ray       .true.
set nwpw:kbpp_filter    .true.

geometry        center  noautosym       noautoz print
        system  crystal
                lat_a   7.01000
                lat_b   4.95682
                lat_c   39.91364
                alpha   90.0d0
                beta    90.0d0
                gamma   90.0d0
        end
        Li1     0.25000 0.00000 0.50000
        Li2     0.00000 0.50000 0.50000
        Li3     0.25000 0.50000 0.56209
        Li4     0.00000 0.00000 0.56209
        Li5     0.25000 0.00000 0.62419
        Li6     0.00000 0.50000 0.62419
        Li7     0.75000 0.00000 0.50000
        Li8     0.50000 0.50000 0.50000
        Li9     0.75000 0.50000 0.56209
        Li10    0.50000 0.00000 0.56209
        Li11    0.75000 0.00000 0.62419
        Li12    0.50000 0.50000 0.62419
        H1      0.25000 0.00000 0.65000
        H2      0.25000 0.74300 0.65000
end
task band energy ignore

The problem I am consistently running into is that when the geometry block is read, the first hydrogen atom is dropped out!
...
                             Geometry "geometry" -> ""
                             -------------------------
 
 Output coordinates in angstroms (scale by  1.889725989 to convert to a.u.)
 
  No.       Tag          Charge          X              Y              Z
 ---- ---------------- ---------- -------------- -------------- --------------
    1 Li1                  3.0000     1.75250000     0.00000000    19.95682000
    2 Li2                  3.0000     0.00000000     2.47841000    19.95682000
    3 Li3                  3.0000     1.75250000     2.47841000    22.43505791
    4 Li4                  3.0000     0.00000000     0.00000000    22.43505791
    5 Li5                  3.0000     1.75250000     0.00000000    24.91369495
    6 Li6                  3.0000     0.00000000     2.47841000    24.91369495
    7 Li7                  3.0000     5.25750000     0.00000000    19.95682000
    8 Li8                  3.0000     3.50500000     2.47841000    19.95682000
    9 Li9                  3.0000     5.25750000     2.47841000    22.43505791
   10 Li10                 3.0000     3.50500000     0.00000000    22.43505791
   11 Li11                 3.0000     5.25750000     0.00000000    24.91369495
   12 Li12                 3.0000     3.50500000     2.47841000    24.91369495
   13 H2                   1.0000     1.75250000     3.68291726    25.94386600
 
      Lattice Parameters 
...

Obviously, the simulation requires all the input atoms. How can I ensure that this atom isn't missing from the database? Thanks.