GitHub / uw-comphys/openccm / commits
OpenCCM is a CFD-based compartment modelling software package. It is primarily intended for convection dominated reactive flows which feature a weak or one-way coupling between the reactive species and the carrier fluid, i.e. the reaction does not substantially influence the fluid flow over the course of the simulation.
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| a695827a | FIX: Change `final` parameter in the connecting compartments function to a 3 ... | Alex Vasile <4****e@u****m> | about 2 years ago | |
| b5110835 | NEW: Output velocity and direction vector for OpenFOAM input | Alex Vasile <4****e@u****m> | about 2 years ago | |
| f14774a3 | FIX: Disable networkX usage by default since it's an optional dependency | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 3197186d | FIX: Change assert to fix off-by-one | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 9c4ec259 | FORMAT: Document loop checks | Alex Vasile <4****e@u****m> | about 2 years ago | |
| cdd41551 | FIX: Correct bug in moving of domain boundary connections | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 73f4f0a1 | merge Merge pull request #36 from Alex-Vasile/cleanup |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
about 2 years ago | |
| 151471f7 | NEW: Check for disconnected subgraphs | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 0f6db91a | FIX: Better network visualization for small domains | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 52d03a41 | NEW: Check that each connection is used at least once. | Alex Vasile <4****e@u****m> | about 2 years ago | |
| ca6caa72 | FIX: Correctly checking that each connection is used properly. | Alex Vasile <4****e@u****m> | about 2 years ago | |
| ad5c4d4f | FIX: Correct parameter name for connections_and_flows | Alex Vasile <4****e@u****m> | about 2 years ago | |
| eff9e2a1 | FIX: Added missing else-statement | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 36844465 | FIX: Let user specify which OpenFOAM time-step results to use | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 3b9011a7 | FIX: Indexing error in `needs_merging` | Alex Vasile <4****e@u****m> | about 2 years ago | |
| df231ad9 | FORMAT: Change intra-compartment flowrate variable name to be more descriptive | Alex Vasile <4****e@u****m> | about 2 years ago | |
| 2d986c40 | NEW: Save CSTR- and PFR-based compartment networks as differently named files... | Alex Vasile <4****e@u****m> | about 2 years ago | |
| bd95e05f | FIX: Change PFR example to have less aggresive ramping in order for adaptive ... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| d0b63575 | NEW: Spatially varying initial conditions | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 44624f92 | FIX: Change get_item to no longer split on ',' so that entries can have commas. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| bfbd4316 | FORMAT: Change `solve_system` to take CMesh as an argument instead of GroupedBCs | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 7b330134 | NEW: Check BC and variable names against reserved keywords. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 355643ad | NEW: Simplify label_elements_openfoam | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 87577c40 | NEW: Handle OpenFOAM visulzation for both PFR- and CSTR-based CMs with the sa... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 4f6aa688 | FORMAT: Stop returning compartments from connect_pfr_compartments making it l... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| acc1dc34 | NEW: Model ID and DOF visualization for OpenFOAM | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 78c1dd7d | NEW: Support OpenFOAM visualization output for PFR-based CMs | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 84806268 | NEW: Mapping each element to distance along PFR (or CSTR). | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 8bb6638d | FORMAT: Change return type of connect_pfr_compartments to clean up call-sites. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| ff85c03b | NEW: Add element centroid to CMesh | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 65abdf21 | FIX: Corrected off-by-one bug in connecting PFRs during simulation. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| d88e220a | NEW: Closed system example (OpenCMP) | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 8e74ccea | NEW: Handle compartmentalizing closed systems with PFRs | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 1df90046 | FORMAT: Cleanup type hints | Alex Vasile <4****e@u****m> | over 2 years ago | |
| f3987c58 | merge Merge pull request #35 from Alex-Vasile/bug-fixes |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 39b5a746 | FIX: Change merge_illformed_compartments to use same criteria and selection a... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 2ef5a7e8 | NEW: Consider flowrate when identifying compartments to merge | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 06ace9a8 | FIX: Ensure that compartments have at least 2 connections after flow threshol... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 3be1bf6b | FORMAT: Introduce sub-function to clean-up _merge_two_compartments | Alex Vasile <4****e@u****m> | over 2 years ago | |
| fadffcf4 | FORMAT: Minor readability cleanup | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 4521c55d | FIX: Correctly identify and merge compartments with only one neighbour | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 25b40e90 | FIX: Correctly merge in connection_pairing when a compartment has a connectio... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| ace4bc08 | NEW: Using facet velocities instead of cell-centered velocities. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| cb9733fd | FIX: _check_flow_requirement was being passed n_vec instead of v_vec. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 3513611d | FIX: Check against flow threshold in connect_cstr_compartments only on final ... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 2c271c09 | NEW: Include check on absolute tolerance. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 88ba0a14 | FIX: Correctly calculate # of net-outflow compartments in tweak_compartment_f... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 5dfb7cfc | FIX: Merging two compartments sometimes grabbed wrong ID | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 05ffe0de | FIX: Correctly export compartment labels pre- and post- merging on subsequent... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 2b67739b | NEW: Added check for connect_cstr_compartments to disable asserts when runnin... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 8c63ac78 | FIX: Check to avoid warning about invalid values in division. There can be in... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| c756af33 | merge Merge pull request #34 from Alex-Vasile/upwinding |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| cf531ce4 | merge Merge pull request #33 from Alex-Vasile/flow-optimization-fix |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| b15ef13b | merge Merge pull request #32 from Alex-Vasile/static-cmesh |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 38181116 | merge Merge pull request #31 from Alex-Vasile/better-merging |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| aee4b209 | FIX: Flow threshold value for 2d flow in pipe | Alex Vasile <4****e@u****m> | over 2 years ago | |
| f6521a75 | Change `tweak_compartment_flows` to correctly impose atol_opt on the optimiza... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 69b344f9 | Rewrite flow optimization to not require rtol_opt. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| c7c25ce3 | Change flowrate through surface calculations to use velocity upwind of the fa... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 04017979 | Stop modifying facet_to_bc_map in an unnecessary way. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 06078306 | Changed compartments_to_pfrs' signature to not require compartment_network, m... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| e48cb01c | Add immutable flags to CMesh's numpy objects | Alex Vasile <4****e@u****m> | over 2 years ago | |
| e7d814bd | Skip attempting to merge compartments only connected to domain boundaries (e.... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 1b0ed3d5 | Bypass connections which have already been evaluated but rejected. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| cd275726 | merge Merge pull request #30 from Alex-Vasile/merging-fix |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| de846a51 | merge Merge pull request #29 from Alex-Vasile/faster-compartmentalize |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 75c61098 | Changing how merging of compartments functions in order to prevent cstr compa... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 4930deed | Restructure merging of compartments. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 532a0f9d | NEW: Add the newest examples to pytest file | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 7bb3b4d7 | Fixed a bug with how the average compartment direction was calculated | Alex Vasile <4****e@u****m> | over 2 years ago | |
| be5f5b39 | Switch element_connectivity to immutable since it's no longer changed. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| b46c409b | Simplified run.py based on unmodified CMesh | Alex Vasile <4****e@u****m> | over 2 years ago | |
| fcf39e8d | Stop modifying CMesh as part of the compartmentalization. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 36556e26 | merge Merge pull request #28 from Alex-Vasile/simplify-heaviside |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| fedad46b | merge Merge pull request #27 from Alex-Vasile/specify-t_eval |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 302c85c1 | merge Merge pull request #26 from Alex-Vasile/merge-warning |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 041809d9 | merge Merge pull request #25 from Alex-Vasile/linprog-fix |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| bbec2eb0 | merge Merge pull request #24 from mptino/main |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 5c79a700 | Switching out list for OrderedDict | Alex Vasile <4****e@u****m> | over 2 years ago | |
| b405c274 | Add entry in example config file | Alex Vasile <4****e@u****m> | over 2 years ago | |
| db645246 | Simplify the smoothed heaviside function | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 68f4e0ff | Added warning to compartmentalization and merging steps if too many compartme... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| b0de2c2f | Added test which runs all of the examples to ensure they pass their asserts. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 7ec3b185 | Fix integrality parameter, wrong value provided. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 17e28a85 | minor docstring change | Matthew Peres Tino <m****o@u****a> | over 2 years ago | |
| dce6a913 | Split parser function into two for readability | Matthew Peres Tino <m****o@u****a> | over 2 years ago | |
| 75a640ca | merge Merge pull request #22 from Alex-Vasile/speedup-cmesh |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 4eca7061 | merge Merge pull request #21 from Alex-Vasile/no_bc |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| af213a88 | Cleanup (#20) |
Alex Vasile <4****e@u****m>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| e0aae7f2 | Added support for use of alphanumeric specie names | Matthew Peres Tino <m****o@u****a> | over 2 years ago | |
| 3a226fad | Update CMesh documentation | Alex Vasile <4****e@u****m> | over 2 years ago | |
| d3b0f0e9 | Implemented specifying of t_eval for solve_ivp. | Alex Vasile <4****e@u****m> | over 2 years ago | |
| ab25f0b7 | Change facet_to_bc_map to store ints (as it should have been doing) | Alex Vasile <4****e@u****m> | over 2 years ago | |
| c00179cc | Allow for simulation to be run without any boundary conditions (other than no... | Alex Vasile <4****e@u****m> | over 2 years ago | |
| e5286a7b | Significantly speed up _calculate_facet_normals and _calculate_facet_sizes | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 1b943998 | NEW: Add .gitignore | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 98f24acc | - corrected DOIs in JOSS submission bib file | Nasser Mohieddin Abukhdeir <n****r@u****a> | over 2 years ago | |
| e02dd15e | merge Merge pull request #18 from Alex-Vasile/manuscript-touchup |
nasserma <n****r@u****a>
Committed by: GitHub <n****y@g****m> |
over 2 years ago | |
| 216004d9 | Minor changes | Alex Vasile <4****e@u****m> | over 2 years ago | |
| 88284760 | Added tag v0.9 for changeset ede5284b2b73 | Nasser M. Abukhdeir <n****r@u****a> | over 2 years ago |