OpenFreeEnergy / OpenFreeEnergy/openfe

Time reporting has float error

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Python
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Description

Hello, I'm running the development version.
The reported time presents variations in small decimal numbers, I'm wondering if that is the real time of the simulation or if it is a floating point approximation. I imagine the latter since the timestep is an integer number.

Versions:
openfe 0.15.0+315.g60a5eca
openfe-analysis 0.2.0
gufe 0.10.0+25.g6475936

#"Step","Time (ps)","Potential Energy (kJ/mole)","Kinetic Energy (kJ/mole)","Total Energy (kJ/mole)","Temperature (K)","Box Volume (nm^3)","Density (g/mL)","Speed (ns/day)"
275250,1101.0000000016123,-1513177.195653773,281099.61265226157,-1232077.5830015114,300.53213164335966,1110.8722854062532,1.0113971314879227,0
275500,1102.0000000015887,-1514694.6284266198,281524.2596771021,-1233170.3687495177,300.986134672276,1111.351750001563,1.0109607897839161,62.5
275750,1103.000000001565,-1516134.323078569,281896.2790246153,-1234238.0440539536,301.383871853291,1111.5121505590835,1.0108148996339694,63.1
276000,1104.0000000015414,-1515533.9000263875,281266.84228145867,-1234267.0577449289,300.7109219179614,1111.7632311723871,1.0105866171923306,63.1

The script I'm running:

protein = openfe.ProteinComponent.from_pdb_file(protein_file)
solv = openfe.SolventComponent(ion_concentration=0.15 * unit.molar)
simulation_system = ChemicalSystem({"solvent": solv, "protein": protein})
md_settings = PlainMDProtocol.default_settings()
protocol = PlainMDProtocol(md_settings)
dag = protocol._create(
    stateA=simulation_system, stateB=simulation_system, mapping=None
)
protocolRunner = dag[0]
result = protocolRunner.run()

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  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by tracing the time values produced after PlainMDProtocol.default_settings(), protocol._create(), and protocolRunner.run(). Compare the reported timestep and time calculations with the displayed CSV values, then determine whether the observed floating-point variation is expected or indicates a reporting bug.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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