Code

Finalize Gen PR#177

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brittonsmith wants to merge 173 commits intograckle-project:maingrackle-project/grackle:mainfrom brittonsmith:gen2024brittonsmith/grackle:gen2024Copy head branch name to clipboard

+19,327-918

Commits

Commits on Jun 22, 2020

• Metal chemistry, grain growth

  genchiaki

  committed
  511a539

Commits on Jun 29, 2020

• enable multi metals

  genchiaki

  committed
  bdfa14f

Commits on Jul 10, 2020

• modify solver of grain temperature

  genchiaki

  committed
  88f7720

• correct gasgr

  genchiaki

  committed
  eecb3ad

Commits on Jul 17, 2020

• correct confliction of parameters

  genchiaki

  committed
  38116eb

Commits on Jul 25, 2020

• more stable at high density and temperature

  genchiaki

  committed
  1d5c9e3

Commits on Jul 26, 2020

• correct convergence criteria

  genchiaki

  committed
  f03bdf3

Commits on Jul 27, 2020

• correct chunit

  genchiaki

  committed
  c2c344a

Commits on Jul 28, 2020

• correct a fatal error in scale_fields_g (only for comoving)

  genchiaki

  committed
  8b6f008

Commits on Jul 29, 2020

• correct for SMBH radiation problem

  genchiaki

  committed
  f3977a5

Commits on Jul 31, 2020

• make consistency of dust density

  genchiaki

  committed
  62bfa64

Commits on Aug 4, 2020

• for NAOJ

  genchiaki

  committed
  29d8998

Commits on Aug 5, 2020

• correct chunit

  genchiaki

  committed
  973ba10

Commits on Aug 6, 2020

• correct chunit for iexpand = 1 (final)

  genchiaki

  committed
  e21a272

• comment out write statements

  genchiaki

  committed
  88ec27d

Commits on Aug 11, 2020

• correct chunit for cosmology simulations

  genchiaki

  committed
  eb8f4ee

Commits on Aug 13, 2020

• convergence criteria for imp_eng = 0

  genchiaki

  committed
  b833c9d

• convergence criteria for imp_eng = 0 II

  genchiaki

  committed
  7afaa2e

Commits on Aug 20, 2020

• convergence criteria for imp_eng = 0 III

  genchiaki

  committed
  0c24be5

Commits on Aug 31, 2020

• multi metals

  genchiaki

  committed
  ef01ada

Commits on Sep 8, 2020

• correct ceiling_species for multi_metals

  genchiaki

  committed
  6b79d74

Commits on Sep 14, 2020

• correct error in ceiling_species

  genchiaki

  committed
  dd3c4e5

Commits on Jan 17, 2021

• metal ionization/dissociation

  genchiaki

  committed
  fab8734

Commits on Apr 12, 2021

• correction

  genchiaki

  committed
  6a4f1a9

Commits on Sep 22, 2022

• Merge remote-tracking branch 'genchiaki/metal-dust-radiation' into genchiaki_merge

  EwanBJones98

  committed
  2b233d9

• Merged genchiaki's pull request into master. Not yet compiled or tested.

  EwanBJones98

  committed
  7faef62

Commits on Oct 2, 2022

• Added rates moved from calc_rates_g.F to rate_functions.c (in last commit) to initialize_rates.c

  

  Ewan Jones

  committed
  ea06a25

Commits on Nov 10, 2022

• Began pygrackle update for merge

  

  Ewan Jones

  committed
  56f04eb

• Merged master into branch

  

  Ewan Jones

  committed
  29fe448

Commits on Nov 11, 2022

• Fixing bugs in pygrackle merge

  

  Ewan Jones

  committed
  963961d

Commits on Nov 14, 2022

• Pygrackle wrapper now compiles. Ready for testing!

  

  Ewan Jones

  committed
  ae8cf65

Commits on Mar 23, 2023

• modify several parts

  genchiaki

  committed
  c7ec575

• tests cleared

  genchiaki

  committed
  4cce99f

Commits on Apr 18, 2023

• Merging with main.

  brittonsmith

  committed
  864ed4c

• Merger remnants.

  brittonsmith

  committed
  00bbbb0

Commits on May 17, 2023

• fix a conflict

  genchiaki

  committed
  7f7e08b

Commits on May 19, 2023

• Merge branch 'main' into genchiaki_merge2

  brittonsmith

  committed
  8eebcca

Commits on May 22, 2023

• Revert changes to linux make file.

  brittonsmith

  committed
  76a431b

Commits on May 27, 2023

• Update src/clib/initialize_rates.c

  Show description for a1e7588
  

  genchiaki

  and

  mabruzzo

  authored
  a1e7588

Commits on Jun 5, 2023

• answer to comments/questions

  genchiaki

  committed
  d289462

Commits on Jun 8, 2023

• Reset pygrackle cython files to main.

  brittonsmith

  committed
  1db890f

• Add metal_chemistry parameter with default value.

  brittonsmith

  committed
  220462e

• Add new primordial chemistry and metal chemistry fields to python wrapper.

  brittonsmith

  committed
  016ffad

• Add metal chemistry fields to fluid container

  brittonsmith

  committed
  369fde9

• Add new primordial chemistry fields to free fall example.

  brittonsmith

  committed
  e95fb89

Commits on Mar 1, 2024

• Stop tracking auto generated file.

  brittonsmith

  committed
  ac4666a

• Remove machine make files.

  brittonsmith

  committed
  05803f3

• Revert gitignore change.

  brittonsmith

  committed
  4390636

Commits on Mar 7, 2024

• Add pc=4 species in pygrackle.

  brittonsmith

  committed
  8827fd6

• Fix HDI contribution to nH and include primorridal_chemistry 3 terms in mean molecular weight.

  brittonsmith

  committed
  ae1fc85

• Add HDII to nH calculation.

  brittonsmith

  committed
  d4628f3

Commits on Mar 8, 2024

• Add free script using metal chemistry.

  brittonsmith

  committed
  855d461

• Do proper metallicity scaling.

  brittonsmith

  committed
  df5cb31

Commits on Mar 19, 2024

• Remove deprecated internal functions.

  brittonsmith

  committed
  209ae66

• Remove OTHER_DEFINES from make file.

  brittonsmith

  committed
  a9a9220

Commits on Mar 20, 2024

• Merging with main, first day of spring 2024.

  brittonsmith

  committed
  6fa0a00

• Fix wild, loose commas.

  brittonsmith

  committed
  3ad0254

• Make commas consistent in c files.

  brittonsmith

  committed
  b2ff6c1

Commits on Mar 22, 2024

• Initialize some size pointers we always need.

  brittonsmith

  committed
  d19dc62

• Always initialize primordial opacity.

  brittonsmith

  committed
  14c4996

• Fix linting errors, just want to see tests run.

  brittonsmith

  committed
  e6dbd1c

Commits on Mar 26, 2024

• Remove unused parameter.

  brittonsmith

  committed
  2f2a25a

• Remove unused grain opacity variables.

  brittonsmith

  committed
  e0eb543

Commits on Aug 20, 2024

• Merging with main.

  brittonsmith

  committed
  4b3b412

• Update cmake build.

  brittonsmith

  committed
  361a679

• Merging with gtest.

  brittonsmith

  committed
  b6ae5a3

• Fix merge typo.

  brittonsmith

  committed
  818afde

• Add atomic data.

  brittonsmith

  committed
  1919643

• Add metal_chemistry support in setup_fluid_container.

  brittonsmith

  committed
  7a0b2a3

• Remove freefall script copy.

  brittonsmith

  committed
  7c09fe2

Commits on Aug 21, 2024

• Add support for multi_metals and metal_abundances fields and rename for consistency.

  brittonsmith

  committed
  cb84275

• Add dust_species support and rename fields for consistency.

  brittonsmith

  committed
  acea316

• Add support for multiple dust temperatures.

  brittonsmith

  committed
  ab2a6de

• Add dust sublimation support.

  brittonsmith

  committed
  bf70b13

• Add grain_growth support.

  brittonsmith

  committed
  0ba3589

• Remove unused radiative_transfer_H2II_diss parameter.

  brittonsmith

  committed
  58ada3e

• Add radiation transter flags and fields and rename for consistency.

  brittonsmith

  committed
  e94ec46

Commits on Aug 22, 2024

• Add the last of the new parameters.

  brittonsmith

  committed
  5bf449c

Commits on Aug 23, 2024

• Move calc_rates functions to initialize_rates.

  brittonsmith

  committed
  62ceb75

• Move calc dust rates functions inside calc_rates_dust and rename for consistency.

  brittonsmith

  committed
  2c6291b

• Remove unused variables and includes.

  brittonsmith

  committed
  bbcb4de

• Add function to free dust yield data.

  brittonsmith

  committed
  a1f58a2

Commits on Aug 25, 2024

• Remove unused variables and fix error messages for metal chemistry rates.

  brittonsmith

  committed
  1c035a0

• Move Chiaki primordial rates to initialize_rates.

  brittonsmith

  committed
  abdca6e

• Merge branch 'main' into gen2024

  brittonsmith

  committed
  66020ea

Commits on Aug 26, 2024

• Merging data file repo with main.

  brittonsmith

  committed
  59c9e73

• Refactor metal cooling rates initializer and add associated cleanup function.

  brittonsmith

  committed
  5dbb21f

• Update NULL/0 initialization for all chemistry_data_storage members.

  brittonsmith

  committed
  10a7e25

• Fix a few more in the initialization.

  brittonsmith

  committed
  e72ebed

• Fix some allocation and freeing issues and thread in all metal field initialization in setup_fluid_container.

  brittonsmith

  committed
  40c4bfb

Commits on Aug 27, 2024

• Fix flake8 error.

  brittonsmith

  committed
  6b79b40

• Allow initialize_metal_chemistry_rates to run based on primordial_chemistry setting since it still has primordial chemistry rates.

  brittonsmith

  committed
  5a323f0

Commits on Aug 28, 2024

• Reorganize fields struct and grackle_wrapper to make it clearer that they match.

  brittonsmith

  committed
  5b1eae8

Commits on Aug 30, 2024

• Rename individual dust temperature fields and allow them to be calculated in FluidContainer.

  brittonsmith

  committed
  0176cd2

• Put primordial continuum opacity inside runtime parameter.

  brittonsmith

  committed
  41ed4bb

Commits on Sep 2, 2024

• Add missing arguments to cool1d_multi call.

  brittonsmith

  committed
  756c7ea

• Always calculate metallicity and use it in place of metal divided by density to avoid segfaults.

  brittonsmith

  committed
  5abc24f

• Move some rates into the correct if statement.

  brittonsmith

  committed
  3d9d098

• Add h2_cooling_rate runtime parameter to choose H2 cooling rates.

  brittonsmith

  committed
  d579b3c

• Implement H2 cooling rate runtime parameter.

  brittonsmith

  committed
  4b7b100

• Add hd_cooling_rate runtime parameter for HD cooling rate selection.

  brittonsmith

  committed
  8ea49e7

• Implement hd cooling rate runtime option.

  brittonsmith

  committed
  760c558

Commits on Sep 3, 2024

• Add runtime option to cie_cooling parameter to use Yoshida 2006 rates.

  brittonsmith

  committed
  b6fe1bf

• Use float variable for toggling H2 cooling with ih2co parameter.

  brittonsmith

  committed
  6ebd34b

• Flesh out comments for parameters in headers.

  brittonsmith

  committed
  dec7ddd

Commits on Sep 5, 2024

• Merge branch 'main' into gen2024

  brittonsmith

  committed
  5e5e6a7

• Change use_stancil_lepp_dalgarno_1998 parameter to hd_reaction_rates.

  brittonsmith

  committed
  0692eaa

• Change use_omukai_gas_grain parameter to gas_grain_cooling_rate.

  brittonsmith

  committed
  5400f61

• Change use_uniform_grain_dist_gamma_isrf parameter to uniform_grain_isrf_heating_rate.

  brittonsmith

  committed
  bcae634

• Update fdatamembers.

  brittonsmith

  committed
  c4ee340

• Update fortran interface.

  brittonsmith

  committed
  4bb9d75

Commits on Sep 10, 2024

• Remove old test_data directory.

  brittonsmith

  committed
  2dc06d4

• Output all fields that fail in code examples tests.

  brittonsmith

  committed
  d18c8b0

• Output all fields that fail in code examples tests.

  brittonsmith

  committed
  0ac411b

Commits on Sep 11, 2024

• Standardize code examples and add calculate calls both before and after a solve_chemistry call.

  brittonsmith

  committed
  4ca4b3c

• Update code examples test to get before and after results.

  brittonsmith

  committed
  e325e64

• Merge with codetest branch.

  brittonsmith

  committed
  147444b

Commits on Sep 13, 2024

• Fix indent for clarify.

  brittonsmith

  committed
  4c0484c

• Add standalone scale_fields subroutine.

  brittonsmith

  committed
  971a499

• Use standalone scale_fields in solve_rate_cool.

  brittonsmith

  committed
  84c0b3e

Commits on Sep 18, 2024

• Make sure dust cooling is additive when dust_species > 0.

  brittonsmith

  committed
  3de14ae

• Add tabulated_cooling_minimum_temperature to supplement metal chemistry with tabulated cooling.

  brittonsmith

  committed
  2682bf6

• Implement temperature threshold for supplementing metal chemistry with tabulated cooling.

  brittonsmith

  committed
  70eac5c

Commits on Sep 19, 2024

• Remove unnecessary variable initialization and optimize some arithmetic.

  brittonsmith

  committed
  7acc064

• Remove some commented out debugging print.

  brittonsmith

  committed
  f433acb

Commits on Sep 20, 2024

• Make velocity unit fix consistent with main.

  brittonsmith

  committed
  c04b201

Commits on Oct 17, 2024

• Simplify itmask_metal calculation and limit to one place.

  brittonsmith

  committed
  44a5c19

• Fix compiler warning.

  brittonsmith

  committed
  16b61d4

• Add some local variables to simplify if statements.

  brittonsmith

  committed
  b70e94c

• Remove some old debug printing.

  brittonsmith

  committed
  25f252b

Commits on Oct 18, 2024

• Remove commented out debugging code.

  brittonsmith

  committed
  f2ecabb

Commits on Oct 20, 2024

• Change types of the d_N and d_Size variables inside of lookup_cool_rates1d_g from integer (presumably it defaults to integer*4) to integer*8.

  Show description for ce881e9
  mabruzzo

  committed
  ce881e9

• fix a minor formatting error that causes CI to fail.

  mabruzzo

  committed
  d5da3fb

• replaced int8(arg) with int(arg, 8) 4 times

  mabruzzo

  committed
  395d207

• replace int8(arg) with int(arg) throughout cool1d_multi_g.F

  mabruzzo

  committed
  7fb933a

Commits on Oct 21, 2024

• Remove where clause from itmask_metal calc

  Show description for b89b1d3
  mabruzzo

  committed
  b89b1d3

Commits on Oct 22, 2024

• Merge pull request #3 from mabruzzo/gen2024-fix-flake8-complaint

  Show description for 017d82a
  brittonsmith

  authored
  017d82a

• Merge pull request #4 from mabruzzo/gen2024-removing-int8-casts

  Show description for 6c7564a
  brittonsmith

  authored
  6c7564a

• Merge pull request #5 from mabruzzo/gen2024-removing-where-clause

  Show description for c3c0734
  brittonsmith

  authored
  c3c0734

• Fix tabbing for readability.

  brittonsmith

  committed
  40d5eb2

• Merge branch 'gen2024' of github.com:brittonsmith/grackle into gen2024

  brittonsmith

  committed
  6737286

• Add comment.

  brittonsmith

  committed
  1ebc512

• Standardize parameter declaration

  Show description for 24cfbc5
  mabruzzo

  committed
  24cfbc5

• standardized the format of precision-dependent tolerance

  mabruzzo

  committed
  21fb999

Commits on Oct 27, 2024

• adding include-directive for the sake of consistency.

  mabruzzo

  committed
  3f747da

Commits on Oct 29, 2024

• Convert most logicals to MASK_TYPE

  Show description for ed05328
  mabruzzo

  committed
  ed05328

• minor refactoring of cool1d_multi_g so that it is easier to transcribe

  mabruzzo

  committed
  2d24754

• fixing a type declaration.

  mabruzzo

  committed
  0de37a1

Commits on Dec 4, 2024

• reformatted some lines into a more-friendly format for transcription.

  mabruzzo

  committed
  ecc61f2

• Removed unused argument from lookup_cool_rates0d

  mabruzzo

  committed
  db6d0dd

• Define dummy_iter_arg within cool_multi_time_g

  Show description for a0f244c
  mabruzzo

  committed
  a0f244c

• reformatted some lines into a more-friendly format for transcription.

  mabruzzo

  committed
  6c7e1b9

• Removed unused argument from lookup_cool_rates0d

  mabruzzo

  committed
  09f10cf

• Define dummy_iter_arg within cool_multi_time_g

  Show description for a9ac1ab
  mabruzzo

  committed
  a9ac1ab

• update readme for this special development branch

  mabruzzo

  committed
  2916da1

• Minor tweaks to improve transcription

  Show description for 234a676
  mabruzzo

  committed
  234a676

• Minor tweaks to improve transcription

  Show description for 37838a4
  mabruzzo

  committed
  37838a4

Commits on Dec 11, 2024

• Porting over various physical constants defined in the Fortran

  Show description for c175cdb
  mabruzzo

  committed
  c175cdb

Commits on Dec 16, 2024

• Merge pull request #6 from mabruzzo/gen2024-standardize-parameter-decl

  Show description for 45fcf22
  brittonsmith

  authored
  45fcf22

• Merge pull request #8 from mabruzzo/gen2024-misc

  Show description for 55d9519
  brittonsmith

  authored
  55d9519

• Merge pull request #9 from mabruzzo/gen2024-constants

  Show description for 370b7bd
  brittonsmith

  authored
  370b7bd

Commits on Dec 17, 2024

• Merge remote-tracking branch 'origin/gen2024-dev' into gen2024-step_rate_newton_raphson_v2

  mabruzzo

  committed
  eae0850

• Initial attempt at extracting newtonraphson

  Show description for 4a71873
  mabruzzo

  committed
  4a71873

• attempt to remove some unneeded local variables from solve_rate_cool (these are used internally by step_rate_newton_raphson)

  mabruzzo

  committed
  89a8bf3

• convert itr_time into a local variable of step_rate_newton_raphson

  mabruzzo

  committed
  c65665e

• convert nsp, isp, jsp, id into local variables of step_rate_newton_raphson

  mabruzzo

  committed
  0d322fa

• converting a bunch more variables so that they are local variables of step_rate_newton_raphson.F

  mabruzzo

  committed
  ac1be72

• fixing a few bugs related to inconsistent array shapes.

  mabruzzo

  committed
  41645e3

• Correct the declaration of regra in cool_multi_time_g

  Show description for da4c3b5
  mabruzzo

  committed
  da4c3b5

Commits on Dec 18, 2024

• Merge pull request #7 from mabruzzo/gen2024-dev

  Show description for 185635a
  brittonsmith

  authored
  185635a

• Merge branch 'main' into gen2024

  brittonsmith

  committed
  1bd31a9

• Merge pull request #10 from mabruzzo/gen2024-step_rate_newton_raphson

  Show description for 60a389e
  brittonsmith

  authored
  60a389e

• Merge pull request #11 from mabruzzo/gen2024-rank-errors

  Show description for 001f509
  brittonsmith

  authored
  001f509