ECP_note

Q: Is it possible to calculate NPA charges with JANPA for heavy atoms, when effective core potentials (ECPs) are used?

A: The short answer is 'yes', it is possible to do NPA for heavy atoms with JANPA.
The longer answer is mainly about 'how'. So, there are two options.
The first one is to do a full-electron calculation (using one of relativistic Hamiltonians) and then process the output with JANPA as usual.
The second option is to use ECP, but then NPA method itself needs to be 'tweaked' in order to remove the electrons attributed to the 'effective core' from the so-called 'natural minimal basis' (NMB). This can be done in the 'pre-release' version of JANPA https://sourceforge.net/projects/janpa/files/V2.03%28pre-release%29/
However, running it requires the user to inform the program about the number and types of shells from which the electrons have been 'moved' into the effective core.
Appendix 1 below contains the documentation for the format in which the corresponding input should be given.
The good news is, however, that for the special case of Def2-basis sets the required input is available Def2_ECP_inps.txt in https://sourceforge.net/projects/janpa/files/utilities/
So, if the system was calculated with one of the Def2-basis sets using its set of ECPs, then the command line for calling JANPA
(not including the preparation of the input .molden file, which might need using molden2molden or other utilities) is

java -jar janpa.jar -i input.molden -NMBoverride def2_ECP_inps.txt > logfile.log

That beign said, I'd still encourage you to perform some test computations on some 'prototypical' system using both ways to check whether they give close results for the considered system.

Appendix 1. NMB-overriding file format
Each line in this file has the following stcuture:

a nS nP nD ...

where
a means a comment line if a=0 (i.e., if line starts with 0), or an atomic number within the input molecule or system if a>0 (note that 1-based atomic numbers are used), or, finally, it can be minus the number of the chemical element in periodic table of elements (aka Z) when a<0,
nS, nP, nD stand for the number constituting the NMB set functions with L=0, 1, 2, ... for a particular atom or element (if these numbers are non-negative), or (if they are negative) they represent a negative value which should be added to the previously defined (either by default settings within the program, or those set previously through their modification) number of NMB functions with certain L. That second kind of input is particularly convenient for ECP usecase.
Note that nX=0 sets the corresponding NMB number to zero, rather than preserves its default value.

The NMB-overriding file is parsed and applied line by line (i.e., next line can overwrite/modify the effect of any of the previous ones).

When JANPA starts, default values are assigned to number of NMB functions, just before the file is read. Moreover, if
the number of argumens (nS, nP, nD ...) is smaller than the maximum L, the remaining default values remain unchanged, i.e., kept with their default values.