[newchem-cpp] transcribe calc_grain_size_increment_species_1d by ChristopherBignamini · Pull Request #507 · grackle-project/grackle

ChristopherBignamini · 2026-02-16T11:49:38Z

This PR requires some additional work to fix a numerical issue which occurs in a call with j=k=0 and first iteration of i-loop (j=k=1 in Fortran), when coef3 is equal to zero. I temporarily added a line to skip the cubic equation solution in this case and we need to find a final fix.

…ion interface/name

…transcribe_calc_grain_size_increment_species_1d

ChristopherBignamini · 2026-02-16T11:57:11Z

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brittonsmith · 2026-05-07T16:10:12Z

@ChristopherBignamini, I'm not able to push to your branch to update this PR. Can you merge in the latest changes to newchem-cpp and update this? While you are at it, can you do the same for PR #519 and #520?

…transcribe_calc_grain_size_increment_species_1d

ChristopherBignamini · 2026-05-07T17:44:59Z

@brittonsmith sure, done! The failure with Pygrackle test suite is due to the missing gold-standard-nccv8 tag

brittonsmith · 2026-05-08T09:39:34Z

@brittonsmith sure, done! The failure with Pygrackle test suite is due to the missing gold-standard-nccv8 tag

Oops, thought I pushed that. I've done it now and restarted the tests.

brittonsmith · 2026-05-08T12:44:47Z

@ChristopherBignamini, @mabruzzo I've take a closer look at the failed tests and the differences are significant for most of the ionic and molecular species, but even the dust temperature is different from the first iteration. I think we'll need a closer look here.

ChristopherBignamini · 2026-05-08T15:23:44Z

@brittonsmith @mabruzzo it could be my fault, there is a TODO in calc_grain_size_increment_species_1d concerning a manual assignment of the first element of drsp for a specific entry of input the indexes: I added that assignment when I was comparing the numerical values of the various steps with the Fortran version and I found a discrepancy due to that first element, most likely because of the different handling of NaN between C++ and Fortran. By manually setting to zero that element in both the C++ and Fortran versions of the subroutine the numerical results were identical. I tried now to remove that assignment and re-run the pygrackle suite: it still fails but I'm not sure the errors are now acceptable. My apologies.

brittonsmith · 2026-05-11T09:59:42Z

@ChristopherBignamini, ok the agreement is much better now, on the level of what I see for PRs #519 and #520. I think this would be acceptable for merging.

mabruzzo

I started to look this over. I hope to circle back and finish up later today, but I wanted to post what I had so far.

I feel pretty strongly that we should rename alsp_data to kappa_data. You can totally feel free to punt on renaming all of the other variables (maybe open an issue to record some of those renaming ideas?)

mabruzzo · 2026-05-14T13:58:22Z

somehow, the comments that apply here, were made on PR #519

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ChristopherBignamini · 2026-05-15T08:32:19Z

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mabruzzo · 2026-05-28T13:25:28Z

+
+namespace grackle::impl {


Suggested change

namespace grackle::impl {

#include "support/config.hpp"

namespace GRIMPL_NAMESPACE_DECL {

I'm porting over this suggestion from #519 (I fixed the error in the suggestion)

mabruzzo · 2026-05-28T13:25:56Z

+    double* SN_r0sp_data, double bulk_density, double* sigma_per_gas_mass,
+    double* kappa_data, int* gr_N, const double* opac_coef_table_data);
+
+}  // namespace grackle::impl


Suggested change

} // namespace grackle::impl

} // namespace GRIMPL_NAMESPACE_DECL

mabruzzo · 2026-05-28T13:26:40Z

I think we need to remove this subroutine now that it has been transcribed

mabruzzo · 2026-05-28T13:27:44Z

+
+#include "calc_grain_size_increment_species_1d.hpp"
+
+void grackle::impl::calc_grain_size_increment_species_1d(


Suggested change

void grackle::impl::calc_grain_size_increment_species_1d(

namespace GRIMPL_NAMESPACE_DECL {

void calc_grain_size_increment_species_1d(

mabruzzo · 2026-05-28T13:28:02Z

+  }
+
+  return;
+}


Suggested change

}

}

} // namespace GRIMPL_NAMESPACE_DECL

mabruzzo · 2026-05-28T13:29:19Z

+///
+/// @par History
+/// modified: February, 2026 by Christopher Bignamini & Matthew Abruzzo; port to
+/// C++


Suggested change

/// C++

/// C++

///

mabruzzo · 2026-05-28T13:35:33Z

+    gr_float* selected_inj_path_metal_densities, const double* SN_fsp,
+    double* SN_r0sp_data, double bulk_density, double* sigma_per_gas_mass,


can you make double* SN_r0sp_data into const double* SN_r0sp_data?

It might also be nice to rename SN_fsp to initial_species_yield and SN_r0sp_data to initial_size_distribution_moments. But, maybe just making a todo note is adequate? Longer term, I want us to just be able to directly pass in the entire struct of size moment data rather than needing to repack it.

…age update

ChristopherBignamini · 2026-05-28T14:15:06Z

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Update gold standard for PR #507.

ChristopherBignamini added 6 commits February 14, 2026 10:41

calc_grain_size_increment_species_1d C++ version created

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calc_grain_size_increment_1d translation WIP

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Code cleanup and documentation added

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Debugging code added

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Call to calc_grain_size_increment_species_1d aligned to updated funct…

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…ion interface/name

Unused wrapper removed

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ChristopherBignamini changed the title ~~Newchem cpp transcribe calc grain size increment species 1d~~ [newchem-cpp] transcribe calc_grain_size_increment_species 1d Feb 16, 2026

Merge remote-tracking branch 'upstream/newchem-cpp' into newchem-cpp_…

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…transcribe_calc_grain_size_increment_species_1d

ChristopherBignamini changed the title ~~[newchem-cpp] transcribe calc_grain_size_increment_species 1d~~ [newchem-cpp] transcribe calc_grain_size_increment_species_1d Feb 16, 2026

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ChristopherBignamini mentioned this pull request Mar 28, 2026

[newchem-cpp] Transcribe solve_cubic_equation #520

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ChristopherBignamini added 2 commits April 19, 2026 16:57

Merge remote-tracking branch 'upstream/newchem-cpp' into newchem-cpp_…

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mabruzzo reviewed May 11, 2026

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[newchem-cpp] Transcribe calc_gr_balance_g #519

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ChristopherBignamini added 8 commits May 15, 2026 00:53

File path update

60863bc

Include path update

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SN0_N renamed as n_inj_pathways

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in, jn, kn replaced with a 3 element array

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in, jn, kn replaced with a 3 element array

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Old declaration removed

13bc712

Cleanup and adoption of new calc_grain_size_increment_species_1d sign…

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…ature

gr_Size removed from function signature and internally calculated

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mabruzzo reviewed May 28, 2026

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ChristopherBignamini added 3 commits May 28, 2026 16:10

Old fortran implementation removed

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brittonsmith merged commit 255eec6 into grackle-project:newchem-cpp Jun 11, 2026
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brittonsmith added a commit that referenced this pull request Jun 11, 2026

Update gold standard for PR #507.

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brittonsmith added a commit that referenced this pull request Jun 11, 2026

Merge pull request #556 from brittonsmith/nccv11

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Update gold standard for PR #507.

-namespace grackle::impl {
+#include "support/config.hpp"
+namespace GRIMPL_NAMESPACE_DECL {

	} // namespace grackle::impl
	} // namespace GRIMPL_NAMESPACE_DECL


		#include "calc_grain_size_increment_species_1d.hpp"

		void grackle::impl::calc_grain_size_increment_species_1d(

+                }
+                return;
+              }

-}
+}
+}  // namespace GRIMPL_NAMESPACE_DECL

		gr_float* selected_inj_path_metal_densities, const double* SN_fsp,
		double* SN_r0sp_data, double bulk_density, double* sigma_per_gas_mass,

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ChristopherBignamini commented May 28, 2026

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mabruzzo commented May 14, 2026 •

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