updates for display solution in particular cells

Begin work on simple TChem example that solves reactions in each cell on a one dimensional field

Merge branch 'master' into shri/adjoints-and-events

Need to update the branch to get the changes made by Hong to the adjoint code.

ADJOINTS+EVENTS: Initialize TSEvent at the beginning of each TSSolve.

ADJOINTS+EVENTS: The cost function and the sensitivity matches for the example with events (ex3adj_events) compared with the original adjoint example (ex3adj)

i) Added TSAdjointEventMonitor that si

ADJOINTS+EVENTS: The cost function and the sensitivity matches for the example with events (ex3adj_events) compared with the original adjoint example (ex3adj)

i) Added TSAdjointEventMonitor that simply checks if an event had occured in the forward solve at the current time. If true, calls the user postevent routine with the forwardsolve flag set to FALSE.
ii) Added stepnum field in event recorder
iii) Fixed the time interval of the disturbance in ex3adj.
iv) PostStepFunction in ex3adj_events (also added to ex3adj) displays value of delta after every time-step.
v) PostEventFunction in ex3adj_events now handles both the forward and the adjoint solve.
vi) Have commented out TSPostStep() from TSAdjointSolve as we don't need it in the adjoint solve (I think).

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merge with master to get all the latest great stuff in master

Merge branch 'master' into jed/chem
Note merging a branch with good stuff in it for a year and a half is insane!

Conflicts:
src/ts/examples/tutorials/makefile
src/ts/interface/ts.c

removed vector array arguments from TSAdjointSetCostIntegrand() since they can be created automatically inside TSAdjointSetUp()

ADJOINTS+EVENTS: Save TS trajectory only when the step is not being rolled back.

ADJOINTS+EVENTS: Added a flag called 'steprollback' to indicate that the previous step was rollbacked and the current step is being reevaluated possibly with a different timestep.

ts->steprollback i

ADJOINTS+EVENTS: Added a flag called 'steprollback' to indicate that the previous step was rollbacked and the current step is being reevaluated possibly with a different timestep.

ts->steprollback is set to FALSE after every succesful step in TSStep()
The flag is raised whenever TSRollBack() is called.
Modified TSSolve() to call TSPostStep() only if the previous step was not rollbacked.
TSMonitorDefault displays "(r)" for the step that's been reevaluated.

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TSSetSaveTrajectory() must set a default trajectory type otherwise if TSSetFromOptions() is not called no type is set so crashes with TSTrajectorySet()

updates to TSAdjoint users manual documentation and related manual pages
to make things more consistently and clearer

cleanup of TSAdjoint manual pages and notation for function arguments

improve docs for TSSetFromOptions

TS: Added -ts_fd_color to compute an IJacobian with coloring

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in pr

Merge branch 'master' into knepley/feature-harmonic-advection

* master: (205 commits)
Bib: Added bio refs
Don't print SAWs URL since it disturbs all the test output
missing (double) cast in print statement
don't output to test file all 12 digits of values
fixes and additions to SNESQM manual pages
PetscViewerBinaryGetDescriptor() is now a collective and must be treated as such fixed some calls to PetscViewerBinarySetUseMPIIO() removed some test runs that take too long
removed dead routine
ViennaCL: Added MCS download mirror URL for version 1.6.2
shift order of processing options for TS to be compatiable with SAWs Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing
remove some dead code for AD and old AMS java and Matlab utilities
add missing PetscFunctionBegin; that messed up displaying of stack
Viewer: Fixed PetscViewerBinarySetUseMPIIO() in some examples
removed unused variables, removed dead code from AMS
git is so freaking annoying I accidently made a bunch of updates in next which I pushed lets see if this diff makes the same changes in my branch Why can't git just forbid me to make changes or next or set up some utility to prevent it!
moved saws directory to proper share directory location updated source to point to it.
rm checkboxes at top of pcoptions.html (ugly and not useful) and centered display of solver
PetscOptionsObject->prefix was freed before using in SAWs post processing hence SAWs was unable to change any type which had a prefix
display URL to point to to access SAWs server
missing break in case for handling string arguments better description for Options database option handling
removed extern PC_CLASSID and KSP_CLASSID that don't belong in petscoptions.h
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TS: In order to make things work with Vec viewers in TS monitors, I needed to set the initial sequence number

Merge branch 'barry/saws-options-merge-master'

removed dead routine

Merge branch 'master' into stefano_zampini/pcbddc-adaptive-selection

Conflicts:
src/ksp/pc/impls/bddc/bddcprivate.c

shift order of processing options for TS to be compatiable with SAWs
Fix options handling for SAWs to duplicate array that previously was deleted too soon for SAWs processing

Merge branch 'maint'

Merge branch 'pr257/petsc/dalcinl/fix-draw/maint' into maint

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c

Merge branch 'master' into barry/saws-options-merge-master

Totally confusing manual merge, could be wrong

Conflicts:
include/petscoptions.h
src/dm/impls/da/dacreate.c
src/sys/objects/aoptions.c
src/sys/threadcomm/interface/threadcomm.c

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