Note: If you work with the flexible-tip=PP-AFM adjust the geometry into the necessary box for the force-field calculations. Don't forget to put the top-most atoms above 0.0, but lower part of the box in the z direction.

At the moment the PP-STM code can read inputs from following DFT codes:

Fireball

http://www.fireball-dft.org

Official version of FireballTG can write out input files now.

A working executable for creation of necessary input files is also at: /storage/praha1/home/krejcio/bin_fireball_stable/fireball.x

Input files can computed with McWEDA functional as well as with computing XC on a grid. Cluster systems as well as systems with Periodic Boundary Conditions (PBC) can be computed. A fireball.in file for calculations with McWEDA: 

&OPTION
basisfile =     'answer.bas'
lvsfile =       'input.lvs'
kptpreference = 'input.kpts'    ! only gamma point-calculations work at the moment
nstepf     = 1
icluster   = 0     ! 0 for PBC / 1 for cluster calculation
itdse      = 0
iqout      = 1
ifixcharge = 1     ! 0 if you don't have pre-calculated atomic charges in CHARGES
iquench    = -1
&END

&OUTPUT
iwrtcdcoefs = -2   ! print the important files
&END

A fireball.in file for calculations with XC on a grid computations: 

&OPTION
basisfile     = 'answer.bas'
lvsfile       = 'input.lvs'
kptpreference = 'samplek.kpts'
nstepf     = 1
icluster   = 0      ! 0 for PBC / 1 for cluster calculation
itdse      = 0
iqout      = 1
ifixcharge = 0
dt         = 0.5
iquench    = -1
iks        = 1
imcweda    = 0
idogs      = 0
bmix       = 0.05
&END

&OUTPUT
iwrtcdcoefs =  -2
&END

In case of PBC calculations phik_0001_s.dat, phik_0001_py.dat, … files are produced by the Fireball. In case of cluster calculations phik_s.dat, phik_py.dat, … are outputs of the Fireball calculations. They serve as inputs for the PP-STM calculations. Inside they look like: 

      38     280     -5.37896401                                                          Number of atoms   Number of states (Molecular orbitals)   The Fermi Level
 -27.58251      -0.00004   0.00000      -0.00006   0.00000       0.00002   0.00000   ...  Eigen-energy of the 1st state  Real & Imaginary part for the LCAO coeficient for 1st state 1st atom for (s, py ... depending on the name of file) etc.
 -27.58139       0.02716   0.00000       0.04766   0.00000       0.00660   0.00000   ...  eigen-energy of the 2nd state  Real & Imaginary part for the LCAO coeficient for 2nd state 1st atom for (s, py ... depending on the name of file) etc.
 ...
GPAW

http://wiki.fysik.dtu.dk/gpaw/

Even though the GPAW is mainly used for representing the wave-function on a grid it can work in LCAO mode as well. For the purpose of making inputs for the PP-STM calculations the LCAO mode is necessary. Both - default or double-zeta (basis='dzp'; for more information look at the GPAW web page http://wiki.fysik.dtu.dk/gpaw/) - basis sets can be used. The PP-STM code reads the stored *.gpw binary produced by the GPAW calculations. Here is an example of some GPAW script for the calculations of the input: 

from ase import *
from ase.visualize import *
from ase.io import*
from gpaw import *
import numpy as npy

mol = read('input.xyz')                                       # xyz geometry of the sample
cell = npy.loadtxt('input.lvs')                               # cell in which a sample is
mol.set_cell(cell)
mol.set_pbc(False)                                            # cluster calculation, but PBC can be used as well: mol.set_pbc(True)
mol.center()
xc='LDA'                                                      # other XC like PBE, RPBE, PW91, BLYP can be used, too.
calc = GPAW(txt='out_LCAO.txt',xc=xc,mode='lcao',basis='dzp')
mol.set_calculator(calc)
en = mol.get_potential_energy()
print en
calc.write('out_LCAO_'+xc+'.gpw',mode='all')                  # saves the calculation into binary 'out_LCAO_LDA.gpw' file

The results of the GPAW calculations is stored in binary file 'out_LCAO_LDA.gpw'

FHI-aims

http://aimsclub.fhi-berlin.mpg.de/

Works for PBC calculations serial or parallel (mpi.scalapack) version. Ideally with the final geometry run a single point calculation with the following outputs added to your control.in: 

output eigenvectors
output band 0 0 0 0.5 0.5 0.0 2 G K
    KS_method lapack_fast  # for mpi-version (mpi.scalapack): The error message with HDF5 is not true in the aims output; use this keywords instead of recompilation #

See the CuPc example

In the case of hybrid functionals (B3LYP, PBE0, HSE) add also: 

exx_band_structure_version 1 ## for hybrid functionals only; both options 1 and 2 are working (1 takes more memory) ##

into your control.in file.

The calculations produces: KS_eigenvectors.band_1.kpt_1.out for spin-restricted calculations or KS_eigenvectors_dn.band_1.kpt_1.out & KS_eigenvectors_up.band_1.kpt_1.out in the case of spin-polarized calculations. You will also need geometry.in in the same directory. All of these files are supposed to be easily read by the PPSTM_simple.py script or within GUI.py.

Note: Under normal conditions, please use PBC calculations, Just adjust the geometry.in with a suitable lattice_vectors (for small molecules 30.0 30.0 30.0 box is enough). There is a possibility to run strict cluster calculations, but additional parsing through Mathematica scripts (and some additional outputs) have to be used for creating PP-STM inputs.

CP2K

http://www.cp2k.org/

into your input file YOUR_INPUT_FILE.inp into FORCE_EVAL → DFT → PRINT section add: 

    &MO ON
      EIGVECS
      CARTESIAN
      FILENAME cartesian-mos
      &EACH
        QS_SCF 0
      &END EACH
    &END MO

Examples of input (and output) files can be found in the code in examples/ 4N-coronene/ CuPc/ and TOAT/ .

Note: CP2K reading procedure was mainly written by Ole Schütt, those days working at EMPA, Switzerland.