DMAdaptor: Refine viewing

DMAdaptor:
- Added sequential adaptation
- Added DMAdaptorGet/SetSequenceLength()
- Use AdaptationCriterion now
- Added untested unstructured interpolation

DMAdaptor: Now I have AdaptationStrategy and AdaptationCriterion
- Fixed some docs

DMAdaptor: Now adaptation can change the DM and solution Vec
- Use the DS exact solution if available to reinitialize on the new grid (need to get real interpolation working)
- Starting to flesh out

DMAdaptor: Now adaptation can change the DM and solution Vec
- Use the DS exact solution if available to reinitialize on the new grid (need to get real interpolation working)
- Starting to flesh out adaptation types

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DMAdaptor: Allow user to set function for solution transfer

DMAdapt: Thanks to Nicolas, this is now working
- Obviously, much cleanup to be done

DM: Added DMAdaptor
- The idea here is to package up the control flow for adaptation, so that a user can do it with no code changes
- The mesh manipulation is still done by DMAdaptMetric() and DMAdap

DM: Added DMAdaptor
- The idea here is to package up the control flow for adaptation, so that a user can do it with no code changes
- The mesh manipulation is still done by DMAdaptMetric() and DMAdaptLabel()

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configure: add option --with-fortran-bindings

Now one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly
[for externalpacakge use - for eg: scalapack] but avoid

configure: add option --with-fortran-bindings

Now one can use --with-fc=gfortran --with-fortran-bindings=0 to detect fortran compiler properly
[for externalpacakge use - for eg: scalapack] but avoid building PETSc fortran bindings in library and modules.

Also disable sowing when with-fortran-bindings is disabled

Fix makefiles (corresponding to fortran bindings) to consistantly use PETSC_HAVE_FORTRAN

Also remove unused PETSC_USE_FORTRAN_DATATYPES flag
Reported-by: Patrick Farrell <patrick.farrell@maths.ox.ac.uk>

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always need to caste PetscReal variables to (double) in print statements

Commit-type: portability-fix

fix: use %g - and fix corresponding output logs

Thanks-to: Barry Smith <bsmith@mcs.anl.gov>

ConvEst: Restore the SNES to the original condition after estimation

ConvEst: Discretization can change, so move name extraction into loop

ConvEst: Initialize variables

ConvEst: Fixed spelling, fixed type

ConvEst: Fixing LAPACK type

PetscConvEst: Added an object which estimates the convergence rate of a discretization

Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finit

Merge branch 'tisaac/feature-plex-tests-new'

This merge changes PetscSpace and PetscQuadrature to have a number of
components, so that vector-valued functionals can be defined for
non-Lagrange finite elements. Along the way, this branch also converts
the regression tests related to DMPlex that were in config/builder.py to
the new test harness, and makes lots of changes necessary for them to
be portable tests.

* tisaac/feature-plex-tests-new: (263 commits)
TS tutorials ex11: remove unused functions
DMPlex: missed viewer change in synchronized output
TS tutorials ex11: make work with complex scalars
TS ex18: Fix initializer
TS ex11: Fix M_PI
Plex ex1f90: FUCK FORTRAN
TS tutorials ex11: use a union when punning
silence compiler warnings
SNES tutorials ex56: set partitioner from options
Plex: once again, MPI_Barrier() can't be used to synch output
windows compile fixes balay@ps4 ~/petsc/src/ts/examples/tutorials $ make PETSC_DIR=$HOME/petsc ex11 /home/balay/petsc/bin/win32fe/win32fe cl -o ex11.o -c -MD -wd4996 -Z7 -I/home/balay/petsc/include -I/home/balay/petsc/arch-mswin-uni/include -I/home/balay/petsc/include/petsc/mpiuni `pwd`/ex11.c ex11.c C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(300): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(301): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(370): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(463): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(505): error C2229: struct '<unnamed-tag>' has an illegal zero-sized array C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(724): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(728): warning C4113: 'void (__cdecl *)()' differs in parameter lists from 'void (__cdecl *)(void)' C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1179): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1184): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1191): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1194): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1383): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1521): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1522): warning C4090: 'function': different 'const' qualifiers C:\cygwin64\home\balay\petsc\src\ts\examples\TUTORI~1\ex11.c(1523): warning C4090: 'function': different 'const' qualifiers
PetscMath: check for math functions by function pointer resolvability
another windows fix for log2() C:\cygwin64\home\petsc\PETSC~1.CLO\include\petscmath.h(28): warning C4273: 'log2': inconsistent dll linkage C:\Program Files (x86)\Windows Kits\10\include\10.0.10240.0\ucrt\../ucrt/math.h(506): note: see previous definition of 'log2'
fix log2() compile error on windows /home/petsc/petsc.clone-4/include/petscmath.h:28:8: error: expected ‘)’ before ‘/’ token double log2(double); ^
SNES tutorials ex12: turn off complex for restart test
Add empty file to silence warnings
TS tutorials ex46: make output match floating point filter
TS tutorials ex18: remove unused flags
SNES tutorials ex69: use end of line anchor instead of word boundary
SNES tutorials ex69: portable word boundary regex
...

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DMPlexSNES: double formatting of printfs

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to s

Merge branch 'knepley/feature-plex-tests-new' into knepley/feature-fe-dual-apply

* knepley/feature-plex-tests-new: (73 commits)
Plex: Fix overeager protection of function
Travis-CI: Attempt to solve issues with gfortran
Travis-CI: Use newer macOS image
clarify damping and other issues related to SNESLINESEARCHBASIC
change example in new harness to use simple partitioner so gets consistent output on all systems
remove unused function from test file
cleanup formatting in example, plus myrank not rank
all requires need to go on the same line in test definition otherwise they are skipped
missing - makes the manual page formatting wrong
The developer manual clearly states that MPI_Comm_size() returns size it doesn't return numProcs or other nonsense. Pretty soon you'll start using mype instead of rank?
fix typo and cut and paste error in docs
bugfix for !HYPRE
fix warning for ';;'
may switch to scalable only when B->cmap->N > 100000
MatLRC: store in the context the parallel matrices rather than the sequential ones
Bib: Add ref
set default algorithm based on B->cmap->N for MatMatMult_MPIAIJ_MPIAIJ()
Error in VecScatterView_MPI() had the meaning of from and to backwards
fix build warning as reported by the nightly tests
Update alquimia.py to use Glenn's branch that updates alquimia for pflotran xsdk
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PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
-

PetscFE+FV: Now discretization can be vector spaces
- Space and DualSpace have a number of components
- Now the dimension of a space incorporates the components, so all size determinations changed
- The default is to form direct sums of scalar spaces, e.g. for constants (1, 0) and (0, 1) so every
basis vector is a vector with only one component nonzero
- DualSpaceApply() is now handled by the implementation
- FE now uses numDof directly from the DualSpace
- Changed SpaceDG --> SpacePoint
- Updated ex3 tests (DA and p4est is still broken)

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