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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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[WIP] Migrate to forcetype attributes in place of force inheritance. #250

Closed ctk3b closed 8 years ago

ctk3b commented 9 years ago

GROMACS <-> GROMACS changes are in place for bonds/angles/dihedrals.

Still need to port some changes over for LAMMPS writing but it's basically done and the reading shouldn't be much harder. I won't have time to finish this before Monday.

I can take a crack at Desmond on Monday as well and let you know if/when I get stuck, @mrshirts.

mrshirts commented 9 years ago

Sounds like a good plan.

mrshirts commented 8 years ago

Just to check on this: is it correct to state that the changes are more or less implemented in the desmond code, but not functioning correctly?

ctk3b commented 8 years ago

Ok lots of things coming together here with @mrshirts amber conversion. Haven't quite got it working yet but hopefully early tomorrow morning.

mrshirts commented 8 years ago

Can you take a look at lammps_parser.py, line 1260? When I go through with test_all.py -t unit -p amber, I get an error with mol_type_j.angle_forces not existing. It shows up in the 'abs' test.

mrshirts commented 8 years ago

I see that desmond has been partially updated

mrshirts commented 8 years ago

It looks like the desmond code path has been partially converted. Can you give a brief explanation of what still remains (or point me to the commit where it is documented).

mrshirts commented 8 years ago

OK. if we can resolve/document these things, then it will be ready to merge.

ctk3b commented 8 years ago

Sorry, somehow missed your comments here. I'll go over a few now and some more later.

ctk3b commented 8 years ago

Looks like I got to making sure Desmond would write without throwing errors for most unit tests. Reading still causes some problems.

This was my first pass through the desmond file so you can sort of get an idea for how this proceeded.

Will have more time tomorrow morning to go over desmond.

Shall we go ahead and merge so it will be a bit easier to incrementally fix things from here?