Diffusion based Fick's 1st and 2nd Laws can't handle concentration at pM ~fM range. #75513

New Issue

Gavin · 2020-04-08T06:53:15+02:00

Gavin commented

2020-04-08 06:53:15 +02:00

System Information
Operating system: windows 10
Graphics card: Geforece GTX 1070

Blender Version
Broken: Blender 2.79 Hash: 5bd8ac9 Cellblender: 1.2.0
(example: 2.79b release)
(example: 2.80, edbf15d3c044, blender2.8, 2018-11-28, as found on the splash screen)
Worked: typical parameter setting works well in term of molecule animation after simulation following the example on the web: the https://mcell.org/tutorials/ficks_laws.html#part-1-building-the-model-and-running-the-simulation.

Error: Once clamp concentration down to pM or less without changing other parameters, no molecule in animation bserved after simulation.

Exact steps for others to reproduce the error
Based on the default startup or an attached .blend file (as simple as possible).

**System Information** Operating system: windows 10 Graphics card: Geforece GTX 1070 **Blender Version** Broken: Blender 2.79 Hash: 5bd8ac9 Cellblender: 1.2.0 (example: 2.79b release) (example: 2.80, edbf15d3c044, blender2.8, 2018-11-28, as found on the splash screen) Worked: typical parameter setting works well in term of molecule animation after simulation following the example on the web: the https://mcell.org/tutorials/ficks_laws.html#part-1-building-the-model-and-running-the-simulation. Error: Once clamp concentration down to pM or less without changing other parameters, no molecule in animation bserved after simulation. **Exact steps for others to reproduce the error** Based on the default startup or an attached .blend file (as simple as possible).

Gavin commented

2020-04-08 06:53:15 +02:00

Added subscriber: @gavin_c

Philipp Oeser commented

2020-04-08 10:53:40 +02:00

Added subscriber: @lichtwerk

Philipp Oeser commented

2020-04-08 10:53:40 +02:00

Changed status from 'Needs Triage' to: 'Archived'

Philipp Oeser closed this issue

2020-04-08 10:53:40 +02:00

Philipp Oeser self-assigned this 2020-04-08 10:53:40 +02:00

Philipp Oeser commented

2020-04-08 10:53:40 +02:00

Cellblender is not maintained by blender.
Please report the issue to the original author(s) instead. [Not quite sure how to contact them tbh, but there is not much we can do here...]

Cellblender is not maintained by blender. Please report the issue to the original author(s) instead. [Not quite sure how to contact them tbh, but there is not much we can do here...]

Evan Wilson commented

2020-04-08 12:53:08 +02:00

Added subscriber: @EAW

Evan Wilson commented

2020-04-08 12:53:08 +02:00

Once clamp concentration down to pM or less without changing other parameters, no molecule in animation observed after simulation.

Just glancing at the tutorial out of curiosity, I wouldn't say this is something that you should report to the original developers as a bug.

The clamp concentration you are told to use is 2e-5. The example output plots shown all have results of 1400-1500 molecules at the end of the simulation. You scaled down the concentration, the input parameter of the simulation, to 1e-7 and then 1e-10 of the original given working value without compensating for this by changing the other parameters...

1500 molecules * 0.00000001 = ? molecules

> Once clamp concentration down to pM or less **without changing other parameters,** no molecule in animation observed after simulation. Just glancing at the tutorial out of curiosity, I wouldn't say this is something that you should report to the original developers as a bug. The clamp concentration you are told to use is `2e-5`. The example output plots shown all have results of 1400-1500 molecules at the end of the simulation. You scaled down the concentration, *the input parameter of the simulation*, to 1e-7 and then 1e-10 of the original given working value without compensating for this by changing the other parameters... 1500 molecules * 0.00000001 = ? molecules

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Diffusion based Fick's 1st and 2nd Laws can't handle concentration at pM ~fM range. #75513