5.4 Keywords of file tcontrol

All keywords (tags) of tcontrol file begin with a special symbol $. Lines starting from # are comment lines. All lines after a keyword $end are ignored.

On output, the (energy dependent) density of states of the system is projected onto atomic orbitals of atoms marked by the same chemical symbols and is redirected to corresponding files, which have the self-explanatory names, e.g. ldos.au.dat, ldos.c.dat, ldos.h.dat and ldos.s.dat in the case of benzene-dithiol molecular junction shown in Fig. 5.1. For example, the file ldos.c.dat would contain LDoS summed up over all six C atoms of the molecule. Furthermore, only LDoS projected onto those electrodes’ atoms of the “extended molecule” which are not part of the interfaces to the reservoirs (shown in grey color in Fig. 5.1) is redirected to the file ldos.au.dat.

Data in the output files are arranged in columns as indicated in the file’s header, namely: energy in Hartree (atomic) units; energy in eV units given with respect to the Fermi energy; LDoS (in 1/eV units) in the $\alpha$ spin channel; if open shell calculation is chosen, next column contains LDoS (in 1/eV units) in the $\beta$ spin channel; last column contains LDoS summed up over two spin channels.

There is a possibility to arrange atoms having the same chemical symbol in groups by using the sixth field of the line staring from ’atom’ as appears, e.g., in the geometry.in file (see also a keyword $coord). For example, LDoS projected on the two Au atoms indicated by the mask ’apex’ as shown in the example below,

 atom    0.1424445    0.1134435    4.4557346    Au   apex
 ...
 atom   -0.1689195    0.0042317   -4.4601905    Au   apex
 

would appear in the file ldos.au_apex.dat. Caution: maximum 16 characters can be used to designate a group of atoms.

A specified file should be present in your directory. The whole string, file=geo-filename, should not contain any spacings.

A specified file should be present in your directory. The string file=basis-filename should not contain spacings.

A specified file should be present in your directory. The string file=basis-filename should not contain spacings.

A specified file should be present in your directory. The string file=mos-filename should not contain spacings.

Specified files should be present in your directory. The strings file=alpha-filename and file=beta-filename should not contain spacings.

In that case, exploiting Green’s function formalism, "core" electronic states of atoms with $Z\ge 19$ are integrated out and projected on a subspace of the remaining ("valence") electronic states. Thus, dimension of the effective Hilbert space of the "extended molecule" is reduced (see $valence_electrons), and only valence states are coupled to macroscopic reservoirs via model self-energies. For atoms from the $n$-th period of the periodic table, core states are associated with those "atomic" basis functions, which have the principle quantum numbers up to $n-2$.

An integer number ${\mathrm{N}}_{\mathrm{a}}$ should be taken from a header line of library files for Au electrodes which are placed in electrodes.library/ directory.

When using tcontrol.aims.x, the number $N_a$ is passed to a script by the option: -nlayers $N_a$.

Default values of leakage rates for Au clusters, written by the script tcontrol.aims.x to the file tcontrol, reflect a gradual switching of perturbation and are given by: ${\eta }_1=0.1$ for the outermost atomic layer of the “extended molecule” (see Fig. 5.1 for details); ${\eta }_2=0.05$ for the next-to-the-outermost atomic layer; and ${\eta }_3=0.025$ for the rest of atomic layers within the interface regions of the “extended molecule”.

See also a keyword $self_energy.

Disclaimer: ’Black-box’-users of aitranss are strongly advised to work with the Au-electrodes listed in the library and use default parameters for the self-energy, only. The transport code will print out a warning message if other chemical elements are employed as electrodes material. Unexpected modification of electrodes or self-energy settings will, in general, lead to misleading or incorrect scientific results.

If any of above mentioned keywords is missing, only conductance at the Fermi energy is calculated.

If a keyword $self_energy is present in tcontrol, the diagonal elements of the self-energy matrix are read from the referenced file. In that case, parameters and values given by keywords $lsurc, $lsurx, $lsury, $rsurc, $rsurx, $rsury, $nlayers, $s1i, $s2i, and $s3i do not have an effect.

If flag is set to on, several internal checks are performed to insure that employed numerical procedures give correct results, e.g.: (i) eigenvalues of the reconstructed Kohn-Sham Hamiltonian $H$ coincide with values stored in files mos.aims, alpha.aims or beta.aims, and eigenvectors of $H$ are orthogonal to each other; (ii) eigenvalues of the overlap matrix are positive, and the square-root of the overlap matrix multiplied by itself gives back the overlap matrix; (iii) a matrix $B$ of eigenvectors of the complex valued operator $H+\mathrm{\Sigma }$ multiplied by the inverse $B^{-1}$ gives a unitary matrix, $B{B}^{-1}=1$, etc. Furthermore, there appear many .tmp files: one of them called zmos.tmp (or zalpha.tmp and zbeta.tmp) contains information on the complex poles $E_n={\epsilon }_n-i{\delta }_n$ of the Green’s function $G^{-1}(E)=E-H-\mathrm{\Sigma }$.

Acknowledgment: A. Bagrets and F. Evers acknowledge the help of Richard Korytár in writing a manual on aitranss.