MRI-adaptivity #564

drreynolds · 2024-09-05T18:49:41Z

I think that this PR is now ready for full review.

Note: I removed all of the changesets that I'd pulled from @Steven-Roberts's PR #547 to simplify the review process for this PR.

…some issues

…ript on arXiv)

…o feature/mri-adaptivity

…eature/mri-adaptivity

… as its own inner stepper

…o feature/mri-adaptivity

I believe I addressed all requests, and none are visible on GitHub.

Steven-Roberts

Ok finished going through new changes and remaining files

doc/arkode/guide/source/Usage/MRIStep/MRIStepCoupling.rst

doc/arkode/guide/source/Usage/MRIStep/User_callable.rst

Steven-Roberts · 2024-10-03T23:21:19Z

doc/arkode/guide/source/Usage/MRIStep/MRIStepCoupling.rst


- **Arguments:**
- * ``method`` -- the coupling table identifier.
+ :return value: An :c:type:`MRIStepCoupling` structure if successful. A ``NULL``


Minor inconsistency between using :return value: vs :return: in the PR

I think that I made these consistent among files that I'd edited in this PR, but if you notice something that I missed, please let me know.

The (undocumented) style used elsewhere is to use :return: (or :returns:) when describing what a function returns and :retval <value>: for a list of error codes. Additionally, .. c:type:: does not work with these directives and generally looks bad (as I think was noted here and in other PRs). I've suggested edits to keep things generally more consistent and future PRs can address updating existing documentation. To help keep the style consistent in the future I've proposed a style guide for function documentation in #588.

include/arkode/arkode_mristep.h

test/unit_tests/arkode/CXX_serial/ark_test_accumerror_brusselator.cpp

Steven-Roberts · 2024-10-04T02:00:42Z

test/unit_tests/arkode/CXX_serial/ark_test_slowerror_brusselator.cpp

@@ -0,0 +1,611 @@
+/*-----------------------------------------------------------------


It would be nice to consolidate the common code among this and the other two Brusselator tests (possible a few other places too) into a shared file.

Perhaps, but based on the type of test (slow error, accumulated fast error, MRI adaptivity) I need to put different operators into the various RHS functions, so although the parameters and equations are shared, I worry that a common header file would have too many different permutations of RHS functions, potentially obfuscating what actually differentiates one test from another.

I started a directory (test/unit_test/problems) for doing this in #501. In that case there is a kpr.hpp file with different RHS functions for different splittings of the problem and it's used in the logging tests.

Steven-Roberts · 2024-10-04T02:15:07Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

@@ -0,0 +1,386 @@
+/* -----------------------------------------------------------------------------


I'm concerned about how much code is duplicated here with the corresponding arkstep version. Now that forcing is define at the ARKode level, I think we can have one test file that covers several steppers. I realize that's easier said than done and that it's probably not feasible to do now.

I'll give this some thought, since we might also want to eventually add a unit test for mristepsetforcing. However, I think that for now these can remain separate.

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

src/arkode/arkode_io.c

Co-authored-by: Steven Roberts <[email protected]>

…ARK_ERK22b (to match fixed-step default)

…caption?)

gardner48 · 2024-10-04T17:23:08Z

CHANGELOG.md

+Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep
+inner stepper object, `ARKodeCreateMRIStepInnerStepper`.


Suggested change

Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep

inner stepper object, `ARKodeCreateMRIStepInnerStepper`.

Added a utility routine to wrap any valid ARKODE integrator for use as an MRIStep

inner stepper object, `ARKodeCreateMRIStepInnerStepper`.

gardner48 · 2024-10-04T17:24:00Z

CHANGELOG.md

+Deprecated ARKStep-specific utility routine for wrapping as an MRIStep
+inner stepper object, `ARKStepCreateMRIStepInnerStepper`.


Suggested change

Deprecated ARKStep-specific utility routine for wrapping as an MRIStep

inner stepper object, `ARKStepCreateMRIStepInnerStepper`.

Deprecated the ARKStep-specific utility routine for wrapping an ARKStep instance

as an MRIStep inner stepper object, `ARKStepCreateMRIStepInnerStepper`. Use

`ARKodeCreateMRIStepInnerStepper` instead.

gardner48 · 2024-10-04T17:27:17Z

doc/shared/RecentChanges.rst

+Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep
+inner stepper object, :c:func:`ARKodeCreateMRIStepInnerStepper`.


Suggested change

Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep

inner stepper object, :c:func:`ARKodeCreateMRIStepInnerStepper`.

Added a utility routine to wrap any valid ARKODE integrator for use as an MRIStep

inner stepper object, :c:func:`ARKodeCreateMRIStepInnerStepper`.

gardner48 · 2024-10-04T17:28:30Z

doc/shared/RecentChanges.rst

+Deprecated ARKStep-specific utility routine for wrapping as an MRIStep
+inner stepper object, :c:func:`ARKStepCreateMRIStepInnerStepper`.


Suggested change

Deprecated ARKStep-specific utility routine for wrapping as an MRIStep

inner stepper object, :c:func:`ARKStepCreateMRIStepInnerStepper`.

Deprecated the ARKStep-specific utility routine for wrapping an ARKStep instance

as an MRIStep inner stepper object, :c:func:`ARKStepCreateMRIStepInnerStepper`. Use

:c:func:`ARKodeCreateMRIStepInnerStepper` instead.

gardner48 · 2024-10-04T21:07:18Z

doc/arkode/guide/source/Mathematics.rst

-solution are computed by solving an auxiliary ODE with a fast (inner) time
-integration method. This corresponds to the following algorithm for a single
-step:
+For cases with only a single slow right-hand side function (i.e., :math:`f^E


I took a pass at revising this section to clean up the formatting of the algorithm and add back some of the detail that was removed for IMEX-MRI-GARK methods (e.g., the description of "solve-decoupled") by adding a short subsection for each family. Please add some more detail to the IMEX-MRI-SR and MERK similar to the IMEX-MRI-GARK section (e.g., that some integrations are grouped).

gardner48 · 2024-10-18T20:52:22Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

+ * erkStep_SetInnerForcing is used to provide a polynomial forcing term in
+ * ERKStep when it is used as the inner integrator under MRIStep. To check that
+ * the forcing is computed and applied correctly we integrate an ODE in time
+ * with ERKStep where to RHS consists of only the polynomial forcing term. The


Suggested change

* with ERKStep where to RHS consists of only the polynomial forcing term. The

* with ERKStep where the RHS consists of only the polynomial forcing term. The

gardner48 · 2024-10-18T20:53:49Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

+#endif
+
+/* User-supplied Functions Called by the Solver */
+static int f(realtype t, N_Vector y, N_Vector ydot, void* user_data);


Update realtype to sunrealtype

gardner48 · 2024-10-18T20:58:47Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

+ tshift = (realtype)atof(argv[5]);
+ tscale = (realtype)atof(argv[6]);


Suggested change

tshift = (realtype)atof(argv[5]);

tscale = (realtype)atof(argv[6]);

tshift = SUNStrToReal(argv[5]);

tscale = SUNStrToReal(argv[6]);

gardner48 · 2024-10-18T20:59:43Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

+ T0 = (realtype)atof(argv[3]);
+ Tf = (realtype)atof(argv[4]);


Suggested change

T0 = (realtype)atof(argv[3]);

Tf = (realtype)atof(argv[4]);

T0 = SUNStrToReal(argv[3]);

Tf = SUNStrToReal(argv[4]);

gardner48 · 2024-10-18T21:00:30Z

test/unit_tests/arkode/C_serial/ark_test_erkstepsetforcing.c

+
+ if (argc > 2)
+ {
+ order = (int)atol(argv[2]);


Suggested change

order = (int)atol(argv[2]);

order = atoi(argv[2]);

drreynolds and others added 30 commits July 24, 2024 16:34

Initial merge with rebased 'develop' branch -- I'm still ironing out …

9951d88

…some issues

Fixed coefficients for MRI-GARK-ERK45a (from Sandu's corrected manusc…

faa4f91

…ript on arXiv)

Documentation updates

355b87a

Documentation updates

ce22dff

Documentation updates

c734e81

Documentation updates

8ce94ca

Renamed type enum for MRI coupling tables

7e5e60c

Documentation updates

a400707

Update default RK methods by order

f6ff36d

Merge branch 'develop' into feature/rk_defaults

198b442

Documentation updates

6152fce

Add 5th order ERK of Tsitouras

2bc4fb0

Add FSAL 2nd order Ralston method

6acabdc

Add Ralston to table in def file

c5aeea6

Update Fortran interfaces

609abba

Added documentation for MRIHTol controller

e76d939

Minor fix for default value

fa91d1d

Merge branch 'feature/mri-adaptivity' of github.com:LLNL/sundials int…

306d6db

…o feature/mri-adaptivity

Merge branch 'feature/rk_defaults' of github.com:LLNL/sundials into f…

bf47f53

…eature/mri-adaptivity

Added control over slow time scale adaptivity safety factor

2d8855a

Updated accuracy calculation for mri-adaptivity test problems.

b5fabd3

merged upstream changes

e2289a8

Removed logging from reference solver

2d1de72

Ran code formatter; added initial implementation for MRIStep to serve…

a104e7e

… as its own inner stepper

Minor cleanup

20593d6

Added nested MRI test

11f03d5

Updated double-step fast error accumulation formula

f83c2de

Merge branch 'feature/mri-adaptivity' of github.com:LLNL/sundials int…

263e4bf

…o feature/mri-adaptivity

Initial pass at removing MRI-Hh controllers

997964d

Fixed IMEX-MRI-SR method names

0e8e5c7

drreynolds added 4 commits October 1, 2024 13:30

Minor documentation fix

f0c53cb

formatting

3ac7812

Removed unused variables

2ecafeb

Removed unused variables

fbc48bd

drreynolds added 4 commits October 1, 2024 13:47

Table formatting fix

ed75b3e

Minor formatting fixes

f9886a2

Merge branch 'develop' into feature/mri-adaptivity

bba4dd8

Merge branch 'develop' into feature/mri-adaptivity

b1379e8

This was referenced Oct 2, 2024

SUNStepper basics based on MRIStepInnerStepper #463

Open

Feature: Logging Updates #501

Open

Merge branch 'develop' into feature/mri-adaptivity

5e576ee

Steven-Roberts reviewed Oct 4, 2024

View reviewed changes

Applied suggestions from code review

ffbe805

Steven-Roberts reviewed Oct 4, 2024

View reviewed changes

src/arkode/arkode_io.c Outdated Show resolved Hide resolved

drreynolds and others added 14 commits October 4, 2024 10:16

Apply suggestion from code review

c445608

Co-authored-by: Steven Roberts <[email protected]>

Fix formatting introduced in PR suggestion

a017c07

Updated answers repository commit

e5c2801

Added comment regarding order of MERK54 method

884b78d

Changed default embedded second-order MRI-GARK method to ARKODE_MRI_G…

bb0dc39

…ARK_ERK22b (to match fixed-step default)

Swig

cc2f2a2

Fixed docs build error (apparently, you cannot :cite: inside a table …

c4d0b27

…caption?)

revise MRIStep mathmatics section

af9205e

notational consistency

0419c3a

wrap long line

3e09545

Merge branch 'develop' into feature/mri-adaptivity

a32deb6

Merge branch 'develop' into feature/mri-adaptivity

99d76b7

Merge branch 'develop' into feature/mri-adaptivity

c05a779

Merged with upstream changes to develop

69b7e98

gardner48 requested changes Oct 18, 2024

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MRI-adaptivity #564

MRI-adaptivity #564

drreynolds commented Sep 5, 2024 •

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		@@ -0,0 +1,611 @@
		/*-----------------------------------------------------------------

		@@ -0,0 +1,386 @@
		/* -----------------------------------------------------------------------------

		Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep
		inner stepper object, `ARKodeCreateMRIStepInnerStepper`.

		Deprecated ARKStep-specific utility routine for wrapping as an MRIStep
		inner stepper object, `ARKStepCreateMRIStepInnerStepper`.

-Deprecated ARKStep-specific utility routine for wrapping as an MRIStep
-inner stepper object, `ARKStepCreateMRIStepInnerStepper`.
+Deprecated the ARKStep-specific utility routine for wrapping an ARKStep instance
+as an MRIStep inner stepper object, `ARKStepCreateMRIStepInnerStepper`. Use
+`ARKodeCreateMRIStepInnerStepper` instead.

		Added utility routine to wrap any valid ARKODE integrator for use as an MRIStep
		inner stepper object, :c:func:`ARKodeCreateMRIStepInnerStepper`.

		Deprecated ARKStep-specific utility routine for wrapping as an MRIStep
		inner stepper object, :c:func:`ARKStepCreateMRIStepInnerStepper`.

	* with ERKStep where to RHS consists of only the polynomial forcing term. The
	* with ERKStep where the RHS consists of only the polynomial forcing term. The

		tshift = (realtype)atof(argv[5]);
		tscale = (realtype)atof(argv[6]);

MRI-adaptivity #564

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MRI-adaptivity #564

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drreynolds commented Sep 5, 2024 •

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