Import heterogeneous particles

[DaveOri]

I have started trying to import partially melted snowflakes and I am constatly getting segfault.

First memory corruption I have identified in the algorithm that parses the constituents. The algorithm consider the vector of particle constituents to be long: Ndipole*Nmaterials instead of Ndipoles. I have started implementing a solution in branch https://github.com/rhoneyager/libicedb/tree/heterogeneous_particles but I hesitate to pull-request because:

1. We need to discuss a little bit more on how we store the constituents informations (at the moment it is not clear to me and I might have resolved the issue in the wrong way)
2. There is a check in Shapes.cpp that prevents to write files with more than one constituent without specifying constituent_names

Thanks to answers to #15 I know the second point has some hdf I/O issues as well. We might want to fix those before making additional progress

[rhoneyager]

Could you provide an example code to show where you are getting the segfault?

[DaveOri]

I have added also some 2-components shapefiles to the folder samplefiles.
After the recent changes to the master branch I do not get segmentation faults anymore.
However if I do

icedb-3d_structures_singlethreaded --from ../samplefiles/ddscat6melting.dat --to melt.hdf5

I get Abort message.
That is due to lines 149-152 of Shapes.cpp that check if the number of constituents names is equal to the number of particle constituents. Fine, I comment that check and try to run again obtaining my first 2-components shape database.

Now looking to the content it seems that components are just randomly assigned.
I think that is related to how particle_scattering_element_composition_whole is filled in shapeIOtextParsers2.cpp

There that variable is treated as it is Ndipole*Nmaterials long whereas it is actually just Ndipole long (different sizing of the variables may "erroneously" compensate for the diverse memory allocations).

I do not think it is urgent to fix this. It is much more important to agree on the standard first. I thought we were looking to include just particle_scattering_element_composition_fractional to simplify the standard (at the cost of trivial floating point storage), but I might be wrong.