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Progress and notes:
DataFrame
.Observable
andSimulation
objects from user input (100% done)solid_density
orliquid_density
Observable
class needs to pass some information to theSimulation
. Need to figure out how to do this right.eq_steps
,md_steps
,timestep
).get_timeseries()
frommolecular_dynamics()
(60% done)DataFrame
.md_chain.py
(i.e. a chain of simulations for a particular index), ormd_one.py
(i.e. independent simulations) (50% done)npt.py
andnpt_lipid.py
md_chain.py
andmd_one.py
use the same file and directory structure? Need to make sure output frommd_one.py
is properly named - or put results frommd_one.py
into different folders.Target
anyway.targets/target_name/system_index/simulation_name_#.[gro|pdb|xyz]
numbered from 1. Multiple files are best because PDB format often doesn't update the periodic box across different structures._#
not needed.md_one.py
andmd_chain.py
should have ways to calculate all observables that they are able to calculate (as an additional way to check consistency)