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.
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