Dear all,
I am having trouble in understanding how the coordinates are defined/read when considering a periodic (3D) system.
By now I am defining the cartesian coordinates in the GEOMETRY block and the supercell lattice vectors inside the SIMULATION_CELL block, as follows:
geometry geometry units angstrom autosym noautoz
Si 5 5 5
Si 10 10 10
end
set geometry:actlist 2
nwpw
simulation_cell
lattice_vectors
10.20 0.00 0.00
-5.10 8.83 0.00
0.00 0.00 30.00
end
smear 0.001 fermi
xc pbe96-Grimme2
cutoff 20
energy_cutoff 120
monkhorst-pack 6 6 1
end
However in the output the coordinates are somehow scrambled:
Geometry "geometry" -> ""
-------------------------
Output coordinates in angstroms (scale by 1.889725989 to convert to a.u.)
No. Tag Charge X Y Z
---- ---------------- ---------- -------------- -------------- --------------
1 Si 14.0000 0.00000000 0.00000000 -4.33012702
2 Si 14.0000 0.00000000 0.00000000 4.33012702
I have also tried to input fractional coordinates, but the outcome is similar.
Regarding the GEOMETRY block I also have another question:
If I define the axes as follows:
system crystal
lat_a 10
lat_b 10
lat_c 20
alpha 90
beta 90
gamma 120
end
They are interpreted as:
a1=< 8.660 -5.000 0.000 >
a2=< 0.000 10.000 0.000 >
a3=< 0.000 0.000 20.000 >
a= 10.000 b= 10.000 c= 20.000
alpha= 90.000 beta= 90.000 gamma= 120.000
omega= 1732.1
but contrarily as I expected, the a1 axis in not aligned to the x direction.
Would please help me in clearing this step? And also, I am assuming the simulation_cell block uses the same units as defined in the geometry block, but I would like to be confirmed about it.
Thank you in advance,
Aldo
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