Add the shift variable to the TSTheta context

So the shift can be changed dynamically for SNES function and Jacobian evaluations. Previously it is fixed.

Funded-by:
Project: FASTMath adjoint
Time:

Add the shift variable to the TSTheta context

So the shift can be changed dynamically for SNES function and Jacobian evaluations. Previously it is fixed.

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

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Initial attempt to use FD Jacobian in adjoint BEuler

-snes_fd_color has more aggressive performance optimizations than -snes_fd; it takes advantage of the fact that a base vector may be ready before

Initial attempt to use FD Jacobian in adjoint BEuler

-snes_fd_color has more aggressive performance optimizations than -snes_fd; it takes advantage of the fact that a base vector may be ready before the Jacobian evaluation and the function evaluation can be skipped for the base vector. This commit makes -snes_fd_colr work for BEuler.

Funded-by:
Project: FASTMath adjoint
Time: 4.0 hours
Reported-by:
Thanks-to: Barry Smith <bsmith@mcs.anl.gov>

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Performance improvement for adjoint BEuler

Adjoint BEuler can use one Jacobian evaluatation per adjoint time step instead of two for explicit ODEs. But the equation type needs to be set by the user.

Performance improvement for adjoint BEuler

Adjoint BEuler can use one Jacobian evaluatation per adjoint time step instead of two for explicit ODEs. But the equation type needs to be set by the user.

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

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Merge branch 'maint'

typo in fixing __PETSCSUNDIALS guard

Commit-type: portability-fix, style-fix
Reported-by: nightly tests

Remove use of _ and __ in front of PETSc include guards. Reason: C99 Reserved Identifiers

Commit-type: portability-fix

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some Pets

Non-numeric optimizations focused on AIJ, MatFDColoring, and DMCreateMatrix_DA_*AIJ, looking to improve performance in GPU environments

1) PetscCalloc*() now uses system calloc()
2) Merged some PetscMalloc*()
3) Eliminated unneeded PetscCalloc*()
4) Removed some memory allocations and copies in MatFDColoringSetUp(), added local variables for better compiler optimization
5) Added MatSetValues_SeqAIJ_SortedFull(), added MatSetOption(MAT_SORTED_FULL)
6) Optimized DMCreateMatrix_DA_*AIJ for nonperiodic case to automatically have sorted columns (faster MatSetValues() times)
7) Eliminated call to PetscMemzero() in PetscFree()

Commit-type: style-fix, feature

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Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*()

Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new forms

Replace a couple multi-mallocs with a single malloc
Replace backwards loops in MatSetValues_*() with PetscArraymove()

Commit-type: style-fix, feature

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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

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