PetscDS: accept null objective and riemann solver

PetscDS+FE: Added dynamic Jacobian, dF/du_t, to DS and FE
- Added PetscFEJacobianType
- PetscFEIntegrateJacobian() now uses PetscFEJacobianType

PetscFV: Disable Fortran interfaces for functions with strings

PetscFV: Added PetscDualSpaceApplyFVM() where the quadrature points are the centroids

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with t

Merge branch 'master' into tisaac/dmforest

* master: (136 commits)
Make error message specific to exactly what matrix is supported
Prevent fblaslapack or f2cblaslapack from being compiled with the -no-prec-dev Intel compiler option since it can produce incorrect results
Fix for PCReset_HYPRE to make it reentrant.
replace default superlu_dist '-mat_superlu_dist_colperm METIS_AT_PLUS_A' with MMD_ATA to avoid different random numbers for nightly tests
fixes for merge from maint patch
Added PCReset_HYPRE() so it may be used with SNESVI solvers
remove Microsoft compiler message for paste macros used for handling Blas/Lapack macro name mangling for example
Increase the number of PetscViewerPushFormat() possible to 25 and use a macro PETSCVIEWERFORMATPUSHESMAX for the value
Configure: Remove redundant logging
Bib: Added ref
nightlybuids: fix permissions of script
MatRegisterDestroy() does not exist but it is listed in manual pages
externalpackages-git: save local changes if any - in git stash - before 'git checkout -f' Useful incase --with-package-commit=HEAD option was msissing [perhaps due to a typo]
nightlybuilds: add xsdk builds
Add architectures for testing xsdk package downloads (Trilinos, Hypre, SuperLU)
create another version of TurnForward() for adaptive time stepping specifically
Configure: Give proper default if HOME is missing from the environment
fix abbreviation
allow zeropivot for MatSOR_SeqAIJ_Inode, node size=1
add test case using adpative time stepping for checkpointing type 'NONE'
...

show more ...

PetscFV: added PetscFVGet/SetComponentName()

The problem right now is that fields that would be separate under
PetscFE are joined into one PetscFV field, because they are handled
together in RHS eva

PetscFV: added PetscFVGet/SetComponentName()

The problem right now is that fields that would be separate under
PetscFE are joined into one PetscFV field, because they are handled
together in RHS evaluation. Maybe that can be changed in the future,
but for right now it makes sense to allow for components of FV fields to
have separate names. I put this in the VTU viewer, but it wasn't
obvious how to do it for the VTK viewer, so I didn't do it.

show more ...

fixed up formatting of references in manualpages to consistent style

References:
+ 1. - ref1
. 2. - ref2
- 3. - ref3

previously the formatting was varied and ugly

FE: Now we can form either the Jacobian or the Jacobian preconditioned matrix using a flag

DS: Now have point wise function slots for the Jacobian preconditioned matrix
- This will allow us to form the "right" operator for preconditioning, like M in the (2,2) block for Stokes

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fie

Merge branch 'master' into knepley/feature-plex-add-time

* master: (57 commits)
add fortran stub for TSMonitorLGSetTransform() and fix TSMonitorLG for multiple fields but no names provided for fields
add -binary_write_double so __float128 precision can save as double to binary files
TSClone() did not clone Fortran function pointers hence some TS methods would fail if functions provided in Fortan
petsc4py: update to snapshot with 'barry/petscoptions-object' changes
fix bad merge that introduced 2 copies of the MPI_Comm_free()
update example to use MAT_INPLACE_MATRIX, not REUSE
incorrect addition of float to PetscInt
update for new PetscOptions API
Function now takes PetscOptions as first argument, this was missed during the first round of updates
bugfix for MatSetOption_Elemental()
fix test example no change output that was missing a line
fixes for new PetscOptions.. API that are needed based on problems with nightly build
mark variable as unused so compiler doesn't warn about unused value
configure: use 'git cat-file -e' to check for existance of a commit in localrepo. ['git rev-parse' does not give error for a hash thats not in repo]
petsc4py: revert to manually syncing petsc4py with petsc master changes
configure: revert gitcommit default value to Null. If a pacakge using giturl does not change this value - raise an error
fix: revert change in a44bcdf that breaks with pgf90
update test output for fixed to hypre interface that now actually pass the interp vectors to BoomerAMG
fixes for merge from Jed's branch that should have been merged into master months ago!
Add to changes dev.html file the change to the PetscOptions routines
...

show more ...

Function now takes PetscOptions as first argument, this was missed during the first round of updates

Plex+SNES+TS: Changed all of the callback function to take time as an argument

Merge branch 'jed/process-options-handler' into barry/petscoptions-object

Begin renaming the PetscOptions objects for the future where PetscOptions will not be a singleton

B[] can compute to -0 resulting in difference in test output even though its values is actually 0

Merge branch 'master' into barry/always-mark-floats

Needed to merge in master to resolve conflicts that will appear when this branch is merged with master