Remember to set the required environment variables (see Installation).
xmolecule is called by providing an input file:
xmolecule input_file
Any parameters can be set using command line arguments as "-arg1=value" or you can alternatively add the options in the input file with a line "arg1=value"
The input file specifies the molecular geometry. This is done in xyz format.
Atoms: Specify each atom in a line:
AtomType1 x1 y1 z1
AtomType2 x2 y2 z2
...
where AtomType is the label of the atomic element, e.g., "H","He","Li","B","C","N","O","F", ...
x, y, z are the cartesian positions (by default in atomic units)
If you use a numerical atomic orbitals, you can specify the specific radial basis function.
AtomType x y z basisString basisFile
basisString is a string like '3s2p', specifying the number of radial functions per angular momentum l.
Point charges: To incorporate point charges to the calculation add lines with atom type "X"
X x y z charge
where charge is the charge value (float) of the point charge.
Gaussian charge distribution: To incorporate spatially spreaded charge distribution to the calculation, add lines with an atom type "XG"
XG x y z charge zeta
where charge is the integrated charge value (float), and zeta (float) is the exponent of the Gaussian.
The radial values for numberical atomic orbitals are saved in a .nao file format. Numerical atomic orbitals are generated via xatom
xatom -s ATOMTYPE -conf ATOMIC_CONFIGURATION -silent -nev NEV \
-lmax LMAX -latter off -rm RMTHRESHOLD -N NGRID -rmax RMAX \
-nao yes -file_nao ATOMTYPE.nao \
-transition auger -file_auger ATOMTYPE.auger \
-transition transitiondipole -file_tdipole ATOMTYPE.tdipole \
-PE_start PESTART -PE_end PEEND -dE PESTEP
Parameters:
specifies the atomic configuration for which the numerical atomic orbital is built. Example: 1s2_2s2_2p2 for neutral carbon.
specifies the number of radial functions for each angular momentum. Example: NEV=2 for a minimal basis set for carbon
specifies the maximum angular momentum Example: lmax=1 for a minimal basis set for carbon
The bound radial wavefunction should be smaller than this at the maximum radial grid point Example: 1e-6
Numer of radial grid points. Example: 30
Maximum radial grid point in a.u. Example: 50.0
Lowest considered photoelectron energy for photoionization in eV. Example: 1000
Highest considered photoelectron energy for photoionization in eV. Example: 5000
Step with which to scan the photoelectron energy in eV. Example: 1.0