OpenFreeEnergy / OpenFreeEnergy/openfe
Time reporting has float error
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- Dominant language
- Python
- Stars
- 331
- Forks
- 56
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 13
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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First steps
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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