Improvements needed for io.lammps.data

[adengz]

A few issues with the current implementation I would like to discuss with whoever involved in this module.

• A list of lists of floats is now used as the data structure for each long section like "atoms", "bonds", etc. Since each column has its specific meaning, can we store the data using a list of dicts instead? Though this means more efforts in refactoring the parser, it will make formatting (e.g., float rounding) a lot easier. The current code after last time fix will output integers with 6 digits after the decimal point as well, which is ridiculous.
• With the dict setting above, the "atoms" section can be formatted according to an external variable atom_style.
• Is it possible to merge the two objects? The parent class LammpsData is a special case where only "atoms" is required.

[shyuep]

Go ahead and make the changes.

[adengz]

After struggling for weeks, here I will list a few upcoming major changes to the entire io.lammps package. Yes it will certainly break some code, but I don't see many API usage depending on methods or attributes of LammpsData or LammpsForceFieldData.

1. LammpsData and LammpsForceFieldData will be merged into one class LammpsData, where force field and topology sections are optional. write_file and from_file will be the only methods of LammpsData, and it will have no dependency on any subclass of SiteCollection. As LAMMPS data file may carry a lot more information than other geometry input files (like POSCAR), it might not be suitable for LammpsData to take in or export any types of molecule or structure directly.
2. Though LammpsData will become kinda independent, there would be supporting classes/methods to help generate all kinds of data. For instance, getting Atoms section data from any SiteCollection, labeling atoms or topologies from ForceField, and automatically determining bonding topologies. These would be in module io.lammps.data or a separate module, say io.lammps.data_utils. ForceField and Topology are now in separate modules, though both of them only serve LammpsForceFieldData.

I would like to hear some feedbacks from users of this package, especially @matk86

[shyuep]

Just go ahead and make the changes.