Refactor quadrature

- Use a separate TS for quadrature
- Initially focus on Theta and Beuler
- Tested on ex3opt and ex9opt
- RK support is not complete
- Fixed memory leak. log_view for ex3sa shows

Refactor quadrature

- Use a separate TS for quadrature
- Initially focus on Theta and Beuler
- Tested on ex3opt and ex9opt
- RK support is not complete
- Fixed memory leak. log_view for ex3sa shows that there is one matrix that is not destroyed.

Funded-by:
Project: FASTMath adjoint
Time: 9.0 hours
Reported-by:
Thanks-to:

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Add second-order adjoint for ERK

Funded-by:
Project: FASTMath adjoint
Time: 4.0 hours
Reported-by:
Thanks-to:

Add TLM ERK

Funded-by:
Project: FASTMATH adjoint
Time: 4.0 hours
Reported-by:
Thanks-to:

AdjointRK: bug fix for RKs with zeros in b

- One of the problems was caused by FASL
- The other problem was caused by zeros in the b vector. The stage sensitivity vector cannot be simply set to zero

AdjointRK: bug fix for RKs with zeros in b

- One of the problems was caused by FASL
- The other problem was caused by zeros in the b vector. The stage sensitivity vector cannot be simply set to zero when b[i] is zero.
- Before this fix, the adjoint of RK works for only some methods such as 2a,3,4; now it works for all RK methods

Funded-by:
Project: FASTMath adjoint
Time: 2.0 hours
Reported-by:
Thanks-to:

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Optimize adjoint ERK and prepare for 2nd-order adjoint

Funded-by:
Project: PETSc for Theta
Time: 2.0 hours
Reported-by:
Thanks-to:

Replace deprecated adjoint functions with new ones

Change y to U for consistency

Funded-by:
Project: FASTMATH adjoint
Time: 1.0 hours
Reported-by:
Thanks-to:

Add missing ;

RK: add missing PetscFunctionBegin

Funded-by:
Project: PETSc time integration
Time:
Reported-by:
Thanks-to:

Fix warnings from BSD build

Funded-by:
Project: PETSc time integration
Time:
Reported-by: nightly test
Thanks-to: Satish Balay

Add missing CHKERRQ()

Funded-by:
Project: PETSc time integration
Time:
Reported-by: nightly test
Thanks-to:

RK: fix warnings caused by commit 474dd77

Rename MRK to RK_Multirate

Funded-by:
Project: PETSc time integration
Time: 0.5 hours
Reported-by:
Thanks-to: Barry Smith

MRK: put in PetscTryMethod

Funded-by:
Project: PETSc time integration
Time: 1.0 hours
Reported-by:
Thanks-to:

Add option -ts_use_splitrhsfunction

This option is added at TS level so that all the multirate methods can use it.

Funded-by:
Project: PETSc time integration
Time: 8.0 hours
Reported-by:
Thanks-to:

MRK: bug fix for more than 2 partitions

- The implementation has been improved significantly (much easier to understand)
- At each level, the time integration of the fast components is viewed as a r

MRK: bug fix for more than 2 partitions

- The implementation has been improved significantly (much easier to understand)
- At each level, the time integration of the fast components is viewed as a refinement to the solution at previous level
- The refinement is done recursively

Funded-by:
Project:
Time: 30.0 hours
Reported-by:
Thanks-to:

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MRK: allow more than 2 paritions in the nonsplit version

MRK: add multirate suport for more than 2 partitions

The key idea is to allow for slow-fast paritioning recursively. For example, the first level could consist of a slow part and a fast part. Then t

MRK: add multirate suport for more than 2 partitions

The key idea is to allow for slow-fast paritioning recursively. For example, the first level could consist of a slow part and a fast part. Then the fast part can be futher split into a slow part and a fast part. Each subts has its own rk context, but share as many working vectors as possible.

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Move multirate implementation out of rk.c

Simplify the nonsplit version of MRK

- VecISCopy is more efficient
- EvaluateStep_Rk can be reused

Overhaul the MRK implementation using RHSSplit

add a dense output for tsrk5dp

add multirate method to rk

Also
- add partitioned RHS to mrk
- add command line option -ts_rk_multirate_type

Fixes for begining of users manual and a variety of webpages including manual pages

Commit-type: bug-fix, documentation

TSGetStages: make each return argument optional

Add if (*ierr) return checks for all Fortran stubs that utilize FREECHAR()

Otherwise the ierr is overwritten by the FREECHAR() thus returning a zero error code when it should not

Commit-type: bug-f

Add if (*ierr) return checks for all Fortran stubs that utilize FREECHAR()

Otherwise the ierr is overwritten by the FREECHAR() thus returning a zero error code when it should not

Commit-type: bug-fix
Reported-by: Tim Steinhoff <kandanovian@gmail.com>

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