gmso

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GMSO needs some optimization

2

My water example is extra slow in the atomtyping step (cell 8). Some optimization is necessary to scale up to a reasonably sized system (10000 water molecules). https://gist.github.com/uppittu11/c421280913edee7e3a56ce09a7d3c2d3 Related to...

uppittu11

Might be worth stealing this code (which involves copying the license over) or doing our own version of it, if we want different requirements https://github.com/mdtraj/mdtraj/blob/4709b085f2454764111bccbe3eee46782ab032e9/tests/test_docstrings.py

mattwthompson

Atomtypes parameters needs some Unit love

2

For our charges, etc. in an atomtype, we do not support setting the `mass`, `charge`, etc of an atomtype on an `atomtype` by `atomtype` basis. We support setting these in...

justinGilmer

Add XML for 3 body potential

1

Add a simple XML file for a mW water. This is to make sure GMSO can handle 3-body potentials internally. At this stage I don't imagine implementing a SW writer...

rsdefever

Possible starting points for new contributors

1

I wanted to point to a few ideas that would involve useful, but relatively small, changes to the codebase that would be good for new users to * Add unit...

mattwthompson

ForceField XML Files and Future Spirints for ForceField Class

3

Now #186 is merged, the next step would be collect as many XML Files as possible. Infact, the next step should be the ability to convert standard XML files from...

umesh-timalsina

1. Add a `FENEBondedPotential` or something like that as a `PotentialTemplate` here: https://github.com/mosdef-hub/gmso/blob/f2e6fbb28d408254d3aa99266cdb29ae1b9e7df0/gmso/lib/potential_templates.py 2. Add support for writing FENE potentials to the LAMMPS data writer somewhere in here: https://github.com/mosdef-hub/gmso/blob/f2e6fbb28d408254d3aa99266cdb29ae1b9e7df0/gmso/formats/lammpsdata.py It...

mattwthompson

Handle Default Units and Redefine Schema in **GMSO**. Related to #310( Broader Issue)

umesh-timalsina

Currently we are _very_ verbose in our XMLs. Which is very useful, but also a bit difficult to parse. Possible defining a unit system within the xml itself would be...

justinGilmer

How would we handle multibody potentials? For example: https://lammps.sandia.gov/doc/pair_polymorphic.html Probably another potential class

justinGilmer