Input File
The input file is a script in the LUA language (lua.org) lsms will read the input values from LUA variables or use default values when appropriate. Lines starting with – are comments.
Run Parameters
Let’s go through the different variables that need to be specified in the input file for the example system FeCo
systemid="FeCo"
system_title="Iron-Cobalt test for LSMS 3"
systemid is used to construct potential filenames.
system_title is an arbitrary text to describe the system.
pot_in_type=1
pot_out_type=0
pot_in_type and pot_out_type are the file formats for the potential files. There are three options available
...type=0- HDF5 binary file. Only one file is needed as input and only one file will be produced as output for the whole system....type=1- Text file. One file per atom is needed/produced. For eg, if there are 100 atoms in the system and type=1 is chosen, then 100 starting potential files are needed and 100 converged potential files will be produced....type=-1- No starting potential needed and no output potential file will be produced. The code will generate a starting potential.
num_atoms=2
nspin=3
nscf=10
num_atoms represents the number of atoms in the simulation cell.
nspin determines how magnetism is treated. There are three options
nspin=1: no spin polarizationnspin=2: collinear spinsnspin=3: non-collinear magnetism
nscf is the maximum number of self-consistent iterations.
mixing = { {quantity = "potential", algorithm = "broyden", mixing_parameter = 0.05} }
numberOfMixQuantities = 0
for k,v in pairs(mixing) do
numberOfMixQuantities = numberOfMixQuantities + 1
end
This sets the mixing of quantities during the self-consistent iterations, generally this does not need to be modified. The last four lines are boilerplate to count the number of quantities to be mixed.
energyContour = {npts=31, grid=2, ebot=-0.3, etop=0.0, eitop=0.825, eibot=0.0025}
This specifies the contour for integration of the Green’s function. npts is the number of grid points along the contour. ebot is the bottom of the contour, etop is the top of the contour which is always set to the Fermi energy (etop = 0). eitop and eibot are the imaginary parts of the energy at the top and end of the contour.
site_default = {lmax=3, rLIZ=13.5, rsteps={96.9, 97.9, 98.9, 99.9}}
lmax represents the angular momentum cutoff and rLIZ is the radius of the local interaction zone. Refer to the theory behind LSMS to know more about the local interaction zone.
Position Data
In lsms, the position data should be provided in the input file. The lattice vectors can be defined the following way
a = 5.218
bravais = {}
bravais[1]={a,0,0}
bravais[2]={0,a,0}
bravais[3]={0,0,a}
The units are Bohr radii, also known as atomic units (1 a.u. = 0.5291 angstrom). Then to setup the cell some boilerplate code is needed
site = {}
for i=1,num_atoms do site[i]={} end
After this the atoms have to be defined.
-- FIRST ATOM
site[1].pos={0,0,0}
site[1].evec={0,0,1}
site[1].pot_in_idx=0
site[1].atom="Fe"
site[1].Z=26
site[1].Zc=10
site[1].Zs=8
site[1].Zv=8
-- SECOND ATOM
site[2].pos={0.5*a,0.5*a,0.5*a}
site[2].evec={0,0,1}
site[2].pot_in_idx=1
site[2].atom="Co"
site[2].Z=27
site[2].Zc=10
site[2].Zs=8
site[2].Zv=9
Here are the definitions for the different keywords
posrepresents the position of the atom in atomic unitsevecsets the direction of the spin quantization axispot_in_idxis the index of the potential input file. Ifpot_in_idx=0, the input potential for that atom will be read from the file v_FeCo.0.atomis the name of the atomic speciesZis the atomic numberZc,ZsandZvare the number of core, semicore and valence electrons respectively. Note that these should sum toZ.
Finally some additional boilerplate code is needed to copy values defined in site_default into the atomic sites that have not defined them.
-- set site defaults
for i=1,num_atoms do
for k,v in pairs(site_default) do
if(site[i][k]==nil) then site[i][k]=v end
end
end
Reading from Position File
Alternatively, it is possible to create a separate position file and have the input file read from it. This is a more convenient option when the number of atoms is very large. the position file can be formatted in any way the user desires, there is no fixed way. Appropriate parsing code should then be provided in the input file. Additionally, the position file can also be given any file name. For example, consider the following format for the positions.
117.057267 0.0 0.0
0.0 117.057267 0.0
0.0 0.0 117.057267
Al 0.0 35.1171801 17.55859005
Al 87.79295024999999 11.7057267 58.5286335
Al 14.632158375 90.719381925 67.307928525
Al 11.7057267 23.4114534 76.08722355
Al 32.190748424999995 67.307928525 20.485021725
Al 58.5286335 11.7057267 87.79295024999999
...
...
...
The first three lines are the lattice vectors and subsequent lines are the atom species name and the position, expressed in Cartesian coordinates. Let’s call this file position.dat. To parse this, the following lines are added to the input file
posfile = io.open("position.dat")
bravais = {}
for i = 1, 3 do
l = next_line(posfile)
x, y, z = l:match("([+-]?%d*%.%d*)%s+([+-]?%d*%.%d*)%s+([+-]?%d*%.%d*)")
bravais[i] = {x, y, z}
end
for i = 1, num_atoms do
l = next_line(posfile)
at, x, y, z = l:match("(%a+)%s+([+-]?%d*%.%d*)%s+([+-]?%d*%.%d*)%s+([+-]?%d*%.%d*)")
print(l)
print(at, x, y, z)
site[i].atom = at
site[i].pos = {x, y, z}
end
posfile:close()
-- set atom types
for i = 1,num_atoms do
atom_name = site[i].atom
if(atom_name~=nil) then
for k,v in pairs(atom_type[atom_name]) do
site[i][k]=v
end
end
end
-- set site defaults
for i =1,num_atoms do
for k,v in pairs(site_default) do
if(site[i][k]==nil) then site[i][k]=v end
end
end
This type of procedure can be carried out for any position format.
Restarting Calculations
After a calculation is complete lsms will generate output potentials with filenames starting with w_ and the restart input file i_lsms.restart. To restart, copy the new potential to the old potential and run the new input file
cp w_FeCo v_FeCo
mpirun -np <number of MPI ranks> $LSMS_PATH/lsms i_lsms.restart