Fixes for doctext update

Update the use of Collective on in the manual pages to reflect the new style

Commit-type: style-fix, documentation
Thanks-to: Patrick Sanan <patrick.sanan@gmail.com>

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be unif

Man pages: remove .keywords: fields

This field is recognized by doctext from Sowing (http://wgropp.cs.illinois.edu/projects/software/sowing/doctext/node20.htm#Node20),
but it doesn't seem to be uniformly used or maintained.

Thus, remove all .keywords: fields, and a following blank line, if present.

This is accomplished with GNU sed (gsed on OS X), with the following commands.
*Warning* that this type of command can corrupt a .git directory,
so be cautious in reusing or modifying these commands. They first look
for and delete matching lines with a following line consisting of only whitespace,
and then delete any remaining matching lines.

find src/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find src/ -type f -exec gsed -i '/keywords:/d' {} +
find include/ -type f -exec gsed -i '/keywords:/ {N; /\n\s*$/d}' {} +
find include/ -type f -exec gsed -i '/keywords:/d' {} +

Hints on the sed command obtained from: https://unix.stackexchange.com/questions/100754/how-to-delete-a-specific-line-and-the-following-blank-line-using-gnu-sed

show more ...

Fix the deprecations for some TSAdjoint functions

Funded-by:
Project: FASTMath adjoint
Time: 1.0 hours
Reported-by: Barry Smith <bsmith@mcs.anl.gov>
Thanks-to:

TSAdjoint: set TSTrajectory not to use TSHistory

Funded-by:
Project: FASTMath adjoint
Time: 0.5 hours
Reported-by:
Thanks-to:

Add object reference for JacobianP

- Move the setup from TSAdjont and TSForward to TS.
- TSSetRHSJacobianP has to be called before TSSetUp.

Funded-by:
Project: FASTMath adjoint
Time: 1.5 hours
Repo

Add object reference for JacobianP

- Move the setup from TSAdjont and TSForward to TS.
- TSSetRHSJacobianP has to be called before TSSetUp.

Funded-by:
Project: FASTMath adjoint
Time: 1.5 hours
Reported-by: Stefano Zampini
Thanks-to:

show more ...

Change names for Hessian functions

Funded-by:
Project: FASTMath adjoint
Time: 0.5 hours
Reported-by:
Thanks-to:

Add notes for Hessian callbacks

Funded-by:
Project: FASTMath adjoint
Time: 0.5 hours
Reported-by:
Thanks-to:

Replace PetscStrcmp with PetscObjectTypeCompare

Funded-by:
Project: FASTMath adjoint
Time:
Reported-by: Stefano Zampini
Thanks-to:

TSAdjoint: add check for checkpointing settings

- Error out when -ts_trajectory_type basic and -ts_trajectory_solution_only are used together
- The basic type simply saves everything to disk and doe

TSAdjoint: add check for checkpointing settings

- Error out when -ts_trajectory_type basic and -ts_trajectory_solution_only are used together
- The basic type simply saves everything to disk and does not recompute stage values needed by TSAdjoint
- Ugly workaround. Erroring out from TSTrajectory could be better

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

show more ...

Use TS communicator instead of PETSC_COMM_WORLD

Funded-by:
Project: FASTMath adjoint
Time: 0.5 hours
Reported-by: Barry Smith
Thanks-to:

Add TSAdjointSetForward and TSAdjointResetForward

Use quadrature ts to hold tlm sensitivities

- Need guards for integral sensitivity
- Remove unneeded check since TLM of quadrature TS use a different TS

Funded-by:
Project: FASTMath adjoint
Time: 6

Use quadrature ts to hold tlm sensitivities

- Need guards for integral sensitivity
- Remove unneeded check since TLM of quadrature TS use a different TS

Funded-by:
Project: FASTMath adjoint
Time: 6.0 hours
Reported-by:
Thanks-to:

show more ...

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:

show more ...

Add second-order adjoint for ERK

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

TSTheta: hack Hessian computation for explicit ODE

The adjoint of Theta methods does not work if users provide callbacks for an explicit ODE (RHSFunction,RHSJacobian,RHSHessian,etc.).
TSComputeXXX h

TSTheta: hack Hessian computation for explicit ODE

The adjoint of Theta methods does not work if users provide callbacks for an explicit ODE (RHSFunction,RHSJacobian,RHSHessian,etc.).
TSComputeXXX handles the conversion implicitly, which is convoluted.

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

show more ...

Refactor TSAdjoint

- Add TSComputeIJacobianP() and TSSetIJacobianP() to pave the way for IMEX adjoint.
- Working on the second-order adjoint to compute parametric sensitivities using backward Euler.

Refactor TSAdjoint

- Add TSComputeIJacobianP() and TSSetIJacobianP() to pave the way for IMEX adjoint.
- Working on the second-order adjoint to compute parametric sensitivities using backward Euler.
- Remove redundant code in TSReset_Theta. TSReset_Theta should not do what TSForwardReset_Theta or TSAdjointReset_Theta do

Funded-by:
Project: FASTMath adjoint
Time: 7.0 hours
Reported-by:
Thanks-to:

Fix TSAdjointInitializeForward for second-order adjoint

To calculate second-order parametric sensitivity, the TLM variable should be initialized as 2*dIdP*dir.

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

show more ...

TSView should not be called in TSAdjointStep

Funded-by:
Project: FASTMATH adjoint
Time: 0.2 hours
Reported-by:
Thanks-to:

Add check for convergence in adjoint run

Funded-by:
Project: FASTMATH adjoint
Time: 0.5 hours
Reported-by:
Thanks-to:

Add a switch for second-order adjoint

One can pass NULL to TSSetCostHessianProducts() for the 3rd argument lambda2 to disable second-order adjoint while not resetting the TSAdjoint context

Funded-b

Add a switch for second-order adjoint

One can pass NULL to TSSetCostHessianProducts() for the 3rd argument lambda2 to disable second-order adjoint while not resetting the TSAdjoint context

Funded-by:
Project: FASTMATH adjoint
Time: 0.5 hours
Reported-by:
Thanks-to:

show more ...

Separate TSReset(),TSForwardReset() and TSAdjointReset()

Allows the TLM and adjoint context to be removed from the TS context. Use cases are when one wants to disable sensitivity analysis while reus

Separate TSReset(),TSForwardReset() and TSAdjointReset()

Allows the TLM and adjoint context to be removed from the TS context. Use cases are when one wants to disable sensitivity analysis while reusing TS for the simulation.

Funded-by:
Project: FASTMath adjoint
Time: 0.2 hours
Reported-by:
Thanks-to:

show more ...

Add reset function for TSForward

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

Add reset function for TSAdjoint

This allows TSAdjoint to be turned on/off between different runs using the same TS

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

Checkpoint the TLM sensitivity for second-order adjoint

Add TSForwardGetStages to acces the stage values for TLM sensitivities

Funded-by:
Project: FASTMath adjoint
Time: 8 hours
Reported-by:
Thanks

Checkpoint the TLM sensitivity for second-order adjoint

Add TSForwardGetStages to acces the stage values for TLM sensitivities

Funded-by:
Project: FASTMath adjoint
Time: 8 hours
Reported-by:
Thanks-to:

show more ...

Add second-order adjoint backbone

Compiles, but not tested

Funded-by:
Project: FASTMath adjoint
Time: 10.0 hours
Reported-by:
Thanks-to:

Fix the forward setup for endpoint=0 case

Funded-by:
Proje

Add second-order adjoint backbone

Compiles, but not tested

Funded-by:
Project: FASTMath adjoint
Time: 10.0 hours
Reported-by:
Thanks-to:

Fix the forward setup for endpoint=0 case

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

show more ...