Monomers ports #1
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Mostly minor comments, everything looks great. Just a couple questions: is SimulariumEmitter no longer used anywhere? Is there a corresponding SimulariumFilamentEmitter to the SimulariumMonomerEmitter? I think we should aim for a general SimulariumEmitter, so that it can handle all possible cases -- if we use only emitters that are specialized for a single data type, the simulation won't be able to stream the other data types that might be available.
| } | ||
| }, | ||
| } | ||
| return monomer_ports_schema |
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nice, I like this reuse of schema.
| self.system.potentials.add_harmonic_repulsion( | ||
| type1, | ||
| type2, | ||
| force_constant=self.parameters["force_constant"], | ||
| interaction_distance=( | ||
| self.parameters["particle_radii"][type1] | ||
| + self.parameters["particle_radii"][type2] | ||
| self.parameters["particle_radii"].get(type1, 1.0) |
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maybe this should use a default size set in self.parameters instead of a hardcoded 1.0?
| import numpy as np | ||
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| monomer_ports_schema = { |
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I would name this file schema.py instead of utils. It seems like a file that could be expanded upon with more schemas for reuse.
Problem
We're working on visualizing a simple ReaDDy model (simularium/vivarium-models#19) in Simularium as it calculates live, and we need updates to the ports structure and emitter in order to convert data for SImularium in the same way we visualize actin models from ReaDDy.
Solution
Updated the ports structure to match other ReaDDy processes, made implementation more general wrt scale and system, and updated the emitter accordingly.
Type of change
Change summary: