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Add initial species in core before seed mechanism #2382

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Add initial species in core before seed mechanism #2382

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hwpang
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@hwpang hwpang commented Mar 2, 2023

Motivation or Problem

The current initialization would fail if one uses a pyrms-based reactor with seed mechanism and the seed mechanism contains species that are the initial species. It would fail with an error related to the initial species not in the phase.names.

Description of Changes

I moved the code block for initializing the bath gases and the initial species in front of the seed mechanism code block.

@hwpang hwpang self-assigned this Mar 2, 2023
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hwpang commented Mar 2, 2023 •
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A bit more detailed explanation for future reference. Currently, when RMG tries to add pressure dependent reactions from the seed mechanism to core that are pressure dependent on the initial species, the code crashes when it tries to make the corresponding core phase(s). This is because the core phase tries to get the index of that initial species from phase.names, but initial species are not yet in the core phase.

@mjohnson541 mjohnson541 force-pushed the debug_seed_mechanism_phase_names branch from 8574d62 to 74ba2bd Compare March 2, 2023 19:40
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mjohnson541 previously approved these changes Mar 2, 2023
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Rebasing with updated CI

@JacksonBurns JacksonBurns force-pushed the debug_seed_mechanism_phase_names branch from 74ba2bd to 0835cbf Compare April 16, 2023 00:14
@hwpang hwpang force-pushed the debug_seed_mechanism_phase_names branch from 0835cbf to d5334ac Compare June 9, 2023 18:45
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github-actions bot commented Sep 8, 2023

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Sep 8, 2023
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@hwpang this looks simple enough - want to try and revive this one?

@github-actions github-actions bot removed the stale stale issue/PR as determined by actions bot label Sep 10, 2023
@hwpang hwpang force-pushed the debug_seed_mechanism_phase_names branch from d5334ac to da00ae8 Compare September 12, 2023 17:24
@hwpang
add initial species in core before seed mechanism to make sure initia…
54775a8 
…l species in phase.names
@hwpang
Move library to edge before adding initial species to core to make su…
b772183 
…re library reactions get move to core if all reactants and products are in initial species
@hwpang hwpang force-pushed the debug_seed_mechanism_phase_names branch from da00ae8 to b772183 Compare September 12, 2023 21:08
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hwpang commented Sep 13, 2023

I will close this PR for now as I don't have time to work on it.

@hwpang hwpang closed this Sep 13, 2023
@JacksonBurns JacksonBurns reopened this Sep 19, 2023
@sevyharris sevyharris self-assigned this Sep 19, 2023
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Blocked by #2514

@JacksonBurns JacksonBurns linked an issue Dec 12, 2023 that may be closed by this pull request
AssertionError during an RMG job run #2578
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This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

@github-actions github-actions bot added the stale stale issue/PR as determined by actions bot label Jan 23, 2024
@github-actions github-actions bot added the abandoned abandoned issue/PR as determined by actions bot label Feb 23, 2024
@github-actions github-actions bot closed this Feb 23, 2024
@JacksonBurns JacksonBurns removed stale stale issue/PR as determined by actions bot abandoned abandoned issue/PR as determined by actions bot labels Feb 26, 2024
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AssertionError during an RMG job run
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