Fix issues that occured when running ppafm-generate-elff with tip's density

[yakutovicha]

fixes #312

blocked by this.

[NikoOinonen]

I think I see where the segfault is coming from. The first two commands use the --energy option which sets the pointer for the energy array on the C++ side. The third command (dftd3) does not have the option, but the pointer still remains even though it might not be valid anymore. A stopgap fix is to simply add the --energy option also to the dftd3 command.

[NikoOinonen]

For the -E argument issue, change this line :

ppafm/ppafm/common.py

Line 323 in 12a9034

arg_dict = self.cli_args[name]

into this:

import copy
arg_dict = copy.deepcopy(self.cli_args[name])

[yakutovicha]

I think I see where the segfault is coming from. The first two commands use the --energy option which sets the pointer for the energy array on the C++ side. The third command (dftd3) does not have the option, but the pointer still remains even though it might not be valid anymore. A stopgap fix is to simply add the --energy option also to the dftd3 command.

It's working! 👍