Genchiaki merge2 #143

genchiaki · 2023-03-23T13:17:47Z

This is a re-issue of PR #78 with many, but not all, upstream changes merged in. Gen has tested this extensively with results shown here.

Below is the original description from PR #78.

Metal/dust chemistry/cooling is included into grackle.
Each new feature can be switched on/off with corresponding parameters:

primordial_chemistry = 4
switch to solve chemistry for 3 extra primordial species (D-, HD+, and HeH+)
metal_chemistry
switch to solve metal chemistry
grain_growth
switch to solve the growth of dust grains
multi_metals
This switch enables to consider multiple metal sources (e.g. supernovae with different metal yields).
Now this version includes

  0. metal/dust abundances of local ISM (Pollack et al. 1994)
  1-4. Pop III normal core-collapse supernovae (Nozawa et al. 2007)
    with progenitor masses 13, 20, 25 and 30 Msun
  5-8. Pop III faint supernovae (Marassi et al. 2014)
    with progenitor masses 13, 50 and 80 Msun
  9-10. Pop III pair-instability supernovae (Nozawa et al. 2007)
    with progenitor masses 170 and 200 Msun
  11. simple dust model (only include silicate and graphite; Yajima et al. 2019)

metal_abundances
If multi_metals = 0, you can select a single metal/dust yield from the list above.
dust_species
You can consider multiple grain species

  1. enstatite + amorphous carbon
  2. + metallic silicon + metallic iron + forsterite + magnetite + silica + magnesia + troilite + alumina
  3. + water ice + volatile organics + refractory organics

dust_temperature_multi
switch to consider different dust temperature for each species if dust_species > 0
dust_sublimation
switch to include dust sublimation

Also photochemistry of metal species is included
radiative_transfer_HDI_diss
photodissociation of HD molecules
radiative_transfer_metal_ion
photoionization of C and O atoms
radiative_transfer_metal_diss
photodissociation of CO, OH and H2O molecules

…nchiaki_merge

…mmit) to initialize_rates.c

src/clib/grackle_chemistry_data.h

matthewturk · 2023-04-07T13:13:14Z

src/python/pygrackle/grackle_wrapper.pyx

@@ -594,60 +864,298 @@ cdef class chemistry_data:
            cdef double[:] memview = <double[:self.NumberOfTemperatureBins]>(<double*> self.rates.k58)
            return np.asarray(memview)

-    property h2dust:
+    property k125:


Did the return statement get lost here?

Thank you for the comment.
In addition to this bug, there are still many conflicts in pygrackle. I'll fix them in the later commit.

src/python/dist/pygrackle-0.1-py3.7-linux-x86_64.egg

src/clib/cool1d_multi_g.F

src/clib/initialize_chemistry_data.c

src/clib/initialize_rates.c

Co-authored-by: Matthew Abruzzo <[email protected]>

brittonsmith · 2023-06-07T15:23:55Z

src/clib/auto_get_version.c

@@ -0,0 +1,20 @@
+#include <stdio.h>


This file is automatically generated by the build system. Can you delete this file?

brittonsmith · 2023-06-07T15:45:05Z

src/clib/grackle_chemistry_data.h

+  int radiative_transfer_H2II_diss;
+  int radiative_transfer_HDI_diss;
+  int radiative_transfer_metal_ion;
+  int radiative_transfer_metal_diss;
+
+  /* flag to H2 self-shielding in hydro code */
+  int radiative_transfer_use_H2_shielding;


These parameters need defaults set in grackle_chemistry_data_fields.def.

brittonsmith · 2023-06-07T15:45:16Z

src/clib/grackle_chemistry_data.h

+  /* flags for alternative rate calculations */
+  int use_palla_salpeter_stahler_1983; //Alternative k13dd calculation scheme
+  int use_stancil_lepp_dalgarno_1998; //Alternative calculation scheme for k50-k56
+  int use_omukai_gas_grain; //Alternative calculation scheme for gas_grain
+  int use_uniform_grain_dist_gamma_isrf; //Alternative calculation scheme for gamma_isrf


These parameters need defaults set in grackle_chemistry_data_fields.def.

genchiaki and others added 30 commits June 22, 2020 17:01

Metal chemistry, grain growth

511a539

enable multi metals

bdfa14f

modify solver of grain temperature

88f7720

correct gasgr

eecb3ad

correct confliction of parameters

38116eb

more stable at high density and temperature

1d5c9e3

correct convergence criteria

f03bdf3

correct chunit

c2c344a

correct a fatal error in scale_fields_g (only for comoving)

8b6f008

correct for SMBH radiation problem

f3977a5

make consistency of dust density

62bfa64

for NAOJ

29d8998

correct chunit

973ba10

correct chunit for iexpand = 1 (final)

e21a272

comment out write statements

88ec27d

correct chunit for cosmology simulations

eb8f4ee

convergence criteria for imp_eng = 0

b833c9d

convergence criteria for imp_eng = 0 II

7afaa2e

convergence criteria for imp_eng = 0 III

0c24be5

multi metals

ef01ada

correct ceiling_species for multi_metals

6b79d74

correct error in ceiling_species

dd3c4e5

metal ionization/dissociation

fab8734

correction

6a4f1a9

Merge remote-tracking branch 'genchiaki/metal-dust-radiation' into ge…

2b233d9

…nchiaki_merge

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

7faef62

Added rates moved from calc_rates_g.F to rate_functions.c (in last co…

ea06a25

…mmit) to initialize_rates.c

Began pygrackle update for merge

56f04eb

Merged master into branch

29fe448

Fixing bugs in pygrackle merge

963961d

Ewan Jones and others added 3 commits November 14, 2022 11:14

Pygrackle wrapper now compiles. Ready for testing!

ae8cf65

modify several parts

c7ec575

tests cleared

4cce99f

mabruzzo reviewed Apr 5, 2023

View reviewed changes

src/clib/grackle_chemistry_data.h Outdated Show resolved Hide resolved

matthewturk reviewed Apr 7, 2023

View reviewed changes

src/python/dist/pygrackle-0.1-py3.7-linux-x86_64.egg Outdated Show resolved Hide resolved

mabruzzo reviewed Apr 7, 2023

View reviewed changes

src/clib/cool1d_multi_g.F Outdated Show resolved Hide resolved

mabruzzo reviewed Apr 7, 2023

View reviewed changes

src/clib/cool1d_multi_g.F Outdated Show resolved Hide resolved

mabruzzo reviewed Apr 7, 2023

View reviewed changes

src/clib/cool1d_multi_g.F Outdated Show resolved Hide resolved

mabruzzo reviewed Apr 7, 2023

View reviewed changes

src/clib/cool1d_multi_g.F Outdated Show resolved Hide resolved

mabruzzo reviewed Apr 8, 2023

View reviewed changes

src/clib/initialize_chemistry_data.c Show resolved Hide resolved

mabruzzo reviewed Apr 8, 2023

View reviewed changes

src/clib/initialize_rates.c Outdated Show resolved Hide resolved

brittonsmith added 2 commits April 18, 2023 13:48

Merging with main.

864ed4c

Merger remnants.

00bbbb0

brittonsmith added this to the 3.3 milestone May 1, 2023

genchiaki and others added 3 commits May 17, 2023 10:35

fix a conflict

7f7e08b

Merge branch 'main' into genchiaki_merge2

8eebcca

Revert changes to linux make file.

76a431b

brittonsmith mentioned this pull request May 22, 2023

Metal dust radiation #78

Closed

genchiaki and others added 2 commits May 27, 2023 11:11

Update src/clib/initialize_rates.c

a1e7588

Co-authored-by: Matthew Abruzzo <[email protected]>

answer to comments/questions

d289462

brittonsmith reviewed Jun 7, 2023

View reviewed changes

This was referenced Mar 1, 2024

Finalize Gen PR #177

Draft

Adding make files from PR #78 #178

Draft

brittonsmith removed this from the 3.3 milestone Apr 25, 2024

brittonsmith marked this pull request as draft June 5, 2024 13:27

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Genchiaki merge2 #143

Genchiaki merge2 #143

genchiaki commented Mar 23, 2023 •

edited by brittonsmith

Loading

matthewturk Apr 7, 2023

genchiaki Jun 5, 2023

brittonsmith Jun 7, 2023

brittonsmith Jun 7, 2023

brittonsmith Jun 7, 2023

Genchiaki merge2 #143

Are you sure you want to change the base?

Genchiaki merge2 #143

Conversation

genchiaki commented Mar 23, 2023 • edited by brittonsmith Loading

matthewturk Apr 7, 2023

Choose a reason for hiding this comment

genchiaki Jun 5, 2023

Choose a reason for hiding this comment

brittonsmith Jun 7, 2023

Choose a reason for hiding this comment

brittonsmith Jun 7, 2023

Choose a reason for hiding this comment

brittonsmith Jun 7, 2023

Choose a reason for hiding this comment

genchiaki commented Mar 23, 2023 •

edited by brittonsmith

Loading