Code

ReactDiff#165

Code

Merged

ajnonaka merged 44 commits intomainAMReX-FHD/FHDeX:mainfrom reactDiffAMReX-FHD/FHDeX:reactDiffCopy head branch name to clipboardSep 10, 2024

+2,438-14

Commits

Commits on Aug 21, 2024

• reactDiff shell

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  fba95df

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• Merge branch 'main' into reactDiff

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  1533f0f

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• build chemistry namespace

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  c8befe2

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Commits on Aug 22, 2024

• chemistry functions

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  4e59a7a

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• namelist

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• reactDiff namespace

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Commits on Aug 23, 2024

• setup preliminaries

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  9576543

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• diffusion outline

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  9bf6d2c

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Commits on Aug 24, 2024

• build diffusion operator for explicit

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  3f4d752

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Commits on Aug 26, 2024

• more work

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  fcbe57b

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• more work

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  497c984

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• Merge branch 'main' into reactDiff

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  99f5b28

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• lots of more work

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  ff6d8e1

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• outline for reactions

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  9c3c7fe

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Commits on Aug 27, 2024

• more chemistry routines

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  62f6d3d

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• more chemistry routines

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  1e9b93d

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• starting the testing/debugging

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  01194aa

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• more debugging

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  5dcd786

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• bugfix

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  a3d7bb2

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• chemistry loop bugfix

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  786028e

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• sign fix

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  09f563c

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Commits on Aug 28, 2024

• cleanup, added several reactDiff_diffusion_types

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  020e76e

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• second-order split scheme chemistry

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  0b86555

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• implemented both strang splitting schemes

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• incorporate include_discrete_LMA_correction option

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Commits on Aug 29, 2024

• stochastic diffusion work

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  17be21c

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• unsplit integrator shell

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  1193194

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• fix first order unsplit integrator

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  1c46839

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• diffusive noise

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  ce9414b

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• paper setup

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  67ea8d5

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Commits on Sep 4, 2024

• paper setups

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  c9076f3

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• fine tuning of 3d setup. still needs work for larger time steps

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• implicit diffusion module, incorporated crank-nicolson strang option

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• add integer populations option

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  8b6539d

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Commits on Sep 5, 2024

• CLE and tau leaping implemented

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Commits on Sep 6, 2024

• implement midpoint_stoch_flux_type for split integrators

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  93bc070

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• split out GenerateStochasticFluxdivCorrector for split and unsplit algorithms to use

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  b13a58e

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• explicit midpoint (non-SSA) written

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Commits on Sep 7, 2024

• implicit midpoint (non-SSA) unsplit

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• match paper

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Commits on Sep 9, 2024

• SSA attempt

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  32f6395

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• ssa bugfix

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  fb97cf3

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• unsplit SSA schemes

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  e95745c

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• structure factor implemented

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  ddcf0bf

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