fix warnings on bsd/single-precision/clang
Merge from doc-fixes branch
Fixes for doctext update
Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new formsReplace a couple multi-mallocs with a single mallocReplace backwards loops in MatSetValues_*()
Add PetscArraycmp(), PetscArraycpy(), PetscArrayzero(), PetscArraymove(), update code to use new formsReplace a couple multi-mallocs with a single mallocReplace backwards loops in MatSetValues_*() with PetscArraymove()Commit-type: style-fix, feature
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Fixed inconsistent naming with CG methods for TRSome of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx nameThe KSPCGXXX was used for KSPCreate_CGXXX() but the
Fixed inconsistent naming with CG methods for TRSome of the KSPXXX macros for xxx had an inconsisten KSPCGXXX that was not in the string xxx nameThe KSPCGXXX was used for KSPCreate_CGXXX() but the other method functions were missing the CG, for example, KSPSolve_XXX() (these meant using tags to find functions was cumbersome due to the special cases)Missing Fortran macroRemoved the extraneous CG from the macros and the function usage; now all macros and functions have consistent PETSc style usage that match the string namesAdded deprecation messages for out-dated useAdded new configure check for PETSC_DEPRECATED_MACROI decided to remove the CG from the KSPCGXXX instead of adding a cg to the string name because 1) it was not possible to deprecatethe string names at compile time, we would have to have runtime warnings. 2) the string names are shorter, 3) the stcg alreadyhad a cg (at the end and not the beginning) and that would have to be removed or we'd have the absurd cgstcg. If starting fromsratch today not worrying about legacy I would have all the string names begin with cg consistently (and naturally the KSPXXX wouldhave them as well), but for legacy reasons we have the current naming which is not ideal because it does not clearlyindicate which methods are CG methods. (We have this problem with other subclasses in PETSc also).Commit-type: style-fix
TAONM: increment interation
TAONTR: minor fix to code style
Tao: PETSc does not print warnings
TAOSetUpdate: change the Update callbackIn SNES, the update function does not uses contexts, and thus it does not appear in the callback prototypeWith TAO, since we are explcitily passing the ctx
TAOSetUpdate: change the Update callbackIn SNES, the update function does not uses contexts, and thus it does not appear in the callback prototypeWith TAO, since we are explcitily passing the ctx via TAOSetUpdate, we have to give it back to the user when performing the call
TaoCreate_XYZ() docstring updates
Merge branch 'denera/tao-nls-ntr-ksp-tag-fix' [PR #1174]* denera/tao-nls-ntr-ksp-tag-fix:Tao: NLS, NTR and NTL options and doc cleanup
defunct options removed from options database comments
code style fixes
replacing strlcat calls with KSP prefix API
Tao KSP prefixes fixed to account for multiple Tao solvers with their own prefixes
KSP prefix updated for unconstrained Newton solvers
Regularization changed to x-x_old, user hook added into optimization loops, eliminated explicit MatTransposeMatMult option in Hessian computation
reverting back to using shared MatSolve interface
Custom solve function for LMVM matrices, disconnected from the common MatSolve interface
fixes for code style and single/double/quad builds
fixing output files
curvature check updated
removed diagonal Broyden matrix and buried it into SymBrdn as a scaling option
Added diagonal Broyden scaling and preconditioning to BQNK algorithms
LMVM matrices can now define J0 with another LMVM matrix, and DiagBrdn scaling implemented for relevant TAO algorithms
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