PDE Petrinet models #77

danbryce · 2024-01-11T17:33:10Z

This directory includes subdirectories (noted below) for multiple PDE problems that are encoded as Petri nets.

halfar: ice dome model
advection: advection model for incompressible flows

The files in each subdirectory use the naming scheme, as follows:

{problem}_{derivative}_{dimensions}_{boundary_slope}_{num_disc}.json

where

problem: the name of the problem (e.g., advection)
derivative: the method used to compute spatial derivatives (e.g., forward, backward, and centered)
dimensions: the number of spatial dimensions (1, 2, or 3)
boundary_slope: the coefficient for boundary conditions, expressed as u(x, t) = kt, where k = boundary_slope, t is the time (relative to starting time at 0), u is a state variable, and x is a boundary position.
num_disc: the number of discrete points in each dimension (e.g., if dimension = 2 and num_disc = 5, then there will be 5^2 = 25 positions, not including boundaries).

The generator for these instances is currently available here, and a notebook illustrating the results of FUNMAN analyzing the models is available here.

Authored by dbryce@sift.net and dmosaphir@sift.net

djinnome · 2024-02-16T23:06:29Z

Hi @danbryce

I ran python model_inventory.py --format md ../petrinet/examples/pde/halfar/*.json in the validation directory, and there were no issues reported. Yay! :-)

However, when I ran python model_inventory.py --format md ../petrinet/examples/pde/advection/*.json I got the following results below. It appears that there are quite a few AMRs that do not have rate laws for all edges of the Petri net. Boo! :-(

source	parameter distribution exists	parameter dist/value set	rate laws present	rate law vars defined	initial values present
...ection_backward_1_0.01_10.json	True	True	True	True	True
...vection_backward_1_0.01_3.json	True	True	True	True	True
...vection_backward_1_0.01_5.json	True	True	True	True	True
...vection_backward_1_0.0_10.json	True	True	True	True	True
...dvection_backward_1_0.0_3.json	True	True	True	True	True
...dvection_backward_1_0.0_5.json	True	True	True	True	True
...vection_backward_1_0.1_10.json	True	True	True	True	True
...dvection_backward_1_0.1_3.json	True	True	True	True	True
...dvection_backward_1_0.1_5.json	True	True	True	True	True
...vection_backward_1_0.2_10.json	True	True	True	True	True
...dvection_backward_1_0.2_3.json	True	True	True	True	True
...dvection_backward_1_0.2_5.json	True	True	True	True	True
...ection_backward_2_0.01_10.json	True	True	True	True	True
...vection_backward_2_0.01_3.json	True	True	True	True	True
...vection_backward_2_0.01_5.json	True	True	True	True	True
...vection_backward_2_0.0_10.json	True	True	True	True	True
...dvection_backward_2_0.0_3.json	True	True	True	True	True
...dvection_backward_2_0.0_5.json	True	True	True	True	True
...vection_backward_2_0.1_10.json	True	True	True	True	True
...dvection_backward_2_0.1_3.json	True	True	True	True	True
...dvection_backward_2_0.1_5.json	True	True	True	True	True
...vection_backward_2_0.2_10.json	True	True	True	True	True
...dvection_backward_2_0.2_3.json	True	True	True	True	True
...dvection_backward_2_0.2_5.json	True	True	True	True	True
...ection_backward_3_0.01_10.json	True	True	True	True	True
...vection_backward_3_0.01_3.json	True	True	True	True	True
...vection_backward_3_0.01_5.json	True	True	True	True	True
...vection_backward_3_0.0_10.json	True	True	True	True	True
...dvection_backward_3_0.0_3.json	True	True	True	True	True
...dvection_backward_3_0.0_5.json	True	True	True	True	True
...vection_backward_3_0.1_10.json	True	True	True	True	True
...dvection_backward_3_0.1_3.json	True	True	True	True	True
...dvection_backward_3_0.1_5.json	True	True	True	True	True
...vection_backward_3_0.2_10.json	True	True	True	True	True
...dvection_backward_3_0.2_3.json	True	True	True	True	True
...dvection_backward_3_0.2_5.json	True	True	True	True	True
...ection_centered_1_0.01_10.json	True	True	True	False	True
...vection_centered_1_0.01_3.json	True	True	True	False	True
...vection_centered_1_0.01_5.json	True	True	True	False	True
...vection_centered_1_0.0_10.json	True	True	True	True	True
...dvection_centered_1_0.0_3.json	True	True	True	True	True
...dvection_centered_1_0.0_5.json	True	True	True	True	True
...vection_centered_1_0.1_10.json	True	True	True	False	True
...dvection_centered_1_0.1_3.json	True	True	True	False	True
...dvection_centered_1_0.1_5.json	True	True	True	False	True
...vection_centered_1_0.2_10.json	True	True	True	False	True
...dvection_centered_1_0.2_3.json	True	True	True	False	True
...dvection_centered_1_0.2_5.json	True	True	True	False	True
...ection_centered_2_0.01_10.json	True	True	True	False	True
...vection_centered_2_0.01_3.json	True	True	True	False	True
...vection_centered_2_0.01_5.json	True	True	True	False	True
...vection_centered_2_0.0_10.json	True	True	True	True	True
...dvection_centered_2_0.0_3.json	True	True	True	True	True
...dvection_centered_2_0.0_5.json	True	True	True	True	True
...vection_centered_2_0.1_10.json	True	True	True	False	True
...dvection_centered_2_0.1_3.json	True	True	True	False	True
...dvection_centered_2_0.1_5.json	True	True	True	False	True
...vection_centered_2_0.2_10.json	True	True	True	False	True
...dvection_centered_2_0.2_3.json	True	True	True	False	True
...dvection_centered_2_0.2_5.json	True	True	True	False	True
...ection_centered_3_0.01_10.json	True	True	True	False	True
...vection_centered_3_0.01_3.json	True	True	True	False	True
...vection_centered_3_0.01_5.json	True	True	True	False	True
...vection_centered_3_0.0_10.json	True	True	True	True	True
...dvection_centered_3_0.0_3.json	True	True	True	True	True
...dvection_centered_3_0.0_5.json	True	True	True	True	True
...vection_centered_3_0.1_10.json	True	True	True	False	True
...dvection_centered_3_0.1_3.json	True	True	True	False	True
...dvection_centered_3_0.1_5.json	True	True	True	False	True
...vection_centered_3_0.2_10.json	True	True	True	False	True
...dvection_centered_3_0.2_3.json	True	True	True	False	True
...dvection_centered_3_0.2_5.json	True	True	True	False	True
...vection_forward_1_0.01_10.json	True	True	True	False	True
...dvection_forward_1_0.01_3.json	True	True	True	False	True
...dvection_forward_1_0.01_5.json	True	True	True	False	True
...dvection_forward_1_0.0_10.json	True	True	True	True	True
...advection_forward_1_0.0_3.json	True	True	True	True	True
...advection_forward_1_0.0_5.json	True	True	True	True	True
...dvection_forward_1_0.1_10.json	True	True	True	False	True
...advection_forward_1_0.1_3.json	True	True	True	False	True
...advection_forward_1_0.1_5.json	True	True	True	False	True
...dvection_forward_1_0.2_10.json	True	True	True	False	True
...advection_forward_1_0.2_3.json	True	True	True	False	True
...advection_forward_1_0.2_5.json	True	True	True	False	True
...vection_forward_2_0.01_10.json	True	True	True	False	True
...dvection_forward_2_0.01_3.json	True	True	True	False	True
...dvection_forward_2_0.01_5.json	True	True	True	False	True
...dvection_forward_2_0.0_10.json	True	True	True	True	True
...advection_forward_2_0.0_3.json	True	True	True	True	True
...advection_forward_2_0.0_5.json	True	True	True	True	True
...dvection_forward_2_0.1_10.json	True	True	True	False	True
...advection_forward_2_0.1_3.json	True	True	True	False	True
...advection_forward_2_0.1_5.json	True	True	True	False	True
...dvection_forward_2_0.2_10.json	True	True	True	False	True
...advection_forward_2_0.2_3.json	True	True	True	False	True
...advection_forward_2_0.2_5.json	True	True	True	False	True
...vection_forward_3_0.01_10.json	True	True	True	False	True
...dvection_forward_3_0.01_3.json	True	True	True	False	True
...dvection_forward_3_0.01_5.json	True	True	True	False	True
...dvection_forward_3_0.0_10.json	True	True	True	True	True
...advection_forward_3_0.0_3.json	True	True	True	True	True
...advection_forward_3_0.0_5.json	True	True	True	True	True
...dvection_forward_3_0.1_10.json	True	True	True	False	True
...advection_forward_3_0.1_3.json	True	True	True	False	True
...advection_forward_3_0.1_5.json	True	True	True	False	True
...dvection_forward_3_0.2_10.json	True	True	True	False	True
...advection_forward_3_0.2_3.json	True	True	True	False	True
...advection_forward_3_0.2_5.json	True	True	True	False	True

PDE Petrinet models

81521f7

danbryce assigned bgyori and djinnome Jan 11, 2024

sabinala mentioned this pull request Jan 17, 2024

Solving pdes with petrinets ciemss/pyciemss#459

Closed

danbryce added 2 commits January 17, 2024 17:10

update pde amrs per @sabinala comments

23ccde1

misspelling

18390ca

danbryce mentioned this pull request Jan 17, 2024

AMR issues with pde petrinets #78

Open

4 tasks

update references to generator

7086b9d

sabinala mentioned this pull request Feb 21, 2024

Getting a RuntimeError when trying to sample a pde as petrinet ciemss/pyciemss#487

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

PDE Petrinet models #77

PDE Petrinet models #77

Uh oh!

danbryce commented Jan 11, 2024 •

edited

Loading

Uh oh!

djinnome commented Feb 16, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

PDE Petrinet models #77

Are you sure you want to change the base?

PDE Petrinet models #77

Uh oh!

Conversation

danbryce commented Jan 11, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

djinnome commented Feb 16, 2024

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

danbryce commented Jan 11, 2024 •

edited

Loading