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* ci: Building is passing locally Probably it is an issue with M1 silicon. * ci: export MACOSX_DEPLOYMENT_TARGET=11_0 As suggested by some good FOSS citizens. * fix: Support action 'trans' - Hide actions that were for internal use. - Added tests for setting actions. * chore: update to python classifiers Added Python3 only. * ci: glut search is failing on OSX in pipeline build: OPTION_STATIC is removed libsmoldyn_static is always built. Required for Python module. * ci: MACOSX_DEPLOYMENT_TARGET is set to 10.4 * ci: Trying with target 10.9
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Dilawar Singh
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Jan 11, 2022
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| Original file line number | Diff line number | Diff line change |
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| # Original author: Upinder Bhalla, NCBS Bangalore | ||
| # Modified by Dilawar Singh for smoldyn integration. | ||
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| import smoldyn | ||
| import random | ||
| import math | ||
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| def build_model(): | ||
| """ | ||
| Size of bouton: 1 cubic µm | ||
| diameter of Synaptic Vesicle (SV): 40 nm | ||
| Diff of SV: 0.024 um^2/s (2400 nm^2/s) | ||
| 1px = 1nm throughout. | ||
| """ | ||
| global r1_, bouton_ | ||
| s = smoldyn.Simulation(low=[-500, -500], high=[1500, 1500]) | ||
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| # a molecule that self-generate | ||
| sv = s.addSpecies( | ||
| "SV", difc=dict(all=2400, front=10), color="blue", display_size=10 | ||
| ) | ||
| sv.addToSolution(100, lowpos=(0, 0), highpos=(1000, 1000)) | ||
| s.addReaction("svgen", [sv], [sv, sv], rate=1e-6) | ||
| svFused = s.addSpecies("VSOpen", color="blue", display_size=10) | ||
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| # intermediate speficies with a lifetime. | ||
| B = s.addSpecies("B", color="red", difc=10000, display_size=2) | ||
| decay = s.addReaction("decay", subs=[B], prds=[], rate=math.log(2) / 20e-3) | ||
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| # A very non-interesting surface. | ||
| path = s.addPath2D((1000, 0), (1000, 1000), (0, 1000), (0, 0)) | ||
| bouton_ = s.addSurface("bouton", panels=path.panels) | ||
| bouton_.setStyle("both", color="blue") | ||
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| # try to add all actions. | ||
| bouton_.setAction("both", [sv], "reflect") | ||
| bouton_.setAction("both", [sv], "trans") | ||
| bouton_.setAction("back", [sv], "absorb") | ||
| bouton_.setAction("back", [sv], "jump") | ||
| bouton_.setAction("back", [sv], "port") | ||
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| # NOTE: action 'mult', 'no' and 'none' causes error here. | ||
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| # this is the bottom surface of bouton. This is sticky for synaptic | ||
| # vesciles | ||
| rect1 = smoldyn.Rectangle(corner=(0, 0), dimensions=[1000], axis="+y") | ||
| bottom = s.addSurface("boutonBottom", panels=[rect1]) | ||
| bottom.setStyle("both", color="red") | ||
| bottom.setAction("back", B, "reflect") | ||
| bottom.setAction("back", B, "trans") | ||
| bottom.setAction("back", B, "absorb") | ||
| bottom.setAction("back", B, "jump") | ||
| bottom.setAction("back", B, "port") | ||
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| return s | ||
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| def test_action(): | ||
| s = build_model() | ||
| print("[INFO] Starting simulation ...") | ||
| s.run(stop=20, dt=0.001) | ||
| print("Done") | ||
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| if __name__ == "__main__": | ||
| test_action() |