January 2011 Commit Log

Number of Commits:
79
Number of Active Developers:
8
harman 2011-01-31 15:28 Rev.: 46761

Code consolidation:
- moved common routines to PetscCommon.cc. You don't need 3 copies of the same
code.
Common routines:
PestcLocalToGlobalMapping()
PetscToUintah_Vectcor()
PetscLinearSolve()
FinalizePetscSolver()

Still need to consolidate a few more functions.
This shouldn't change the answers.

696 lines of code changed in 9 files:

tsaad 2011-01-31 12:52 Rev.: 46758

In this commit:
- Added parser for momentum transport equations.
- Added necessary expression registration in momentum transport equations.
- Pressure expression now compiles and has most of the ingredients for linear solve.
NOTE:THIS COMMIT DOES NOT SOLVE MOMENTUM EQUATIONS YET. WE STILL NEED TO GET THE SOLVER PORT INTO THE PRESSURE EXPRESSION.

367 lines of code changed in 8 files:

harman 2011-01-31 12:13 Rev.: 46757

fixed memory leak

2 lines of code changed in 1 file:

harman 2011-01-31 12:01 Rev.: 46756

added a test that exercises the petsc radiation solver.

8 lines of code changed in 1 file:

jsutherland 2011-01-29 08:21 Rev.: 46754

Fix include path for a SpatialOps file.

3 lines of code changed in 2 files:

guilkey 2011-01-28 16:45 Rev.: 46753

Spit out a bit more information when polar decomposition fails.

2 lines of code changed in 1 file:

guilkey 2011-01-27 18:02 Rev.: 46752

Add addInitialComputesAndRequires.

I owe Todd 5 Snickers bars...

12 lines of code changed in 2 files:

guilkey 2011-01-27 15:53 Rev.: 46751

Change NGP to NGN in scheduleIHR to be consistent with iHR itself.

2 lines of code changed in 1 file:

harman 2011-01-26 18:05 Rev.: 46749

code diet:
-replaced 7 duplicate IntVector statements with 1.

This will not change the answers.

28 lines of code changed in 1 file:

jthornoc 2011-01-26 15:59 Rev.: 46747

Conditional deletion of d_RMCRT object.
This will fix failing regression tests.

2 lines of code changed in 1 file:

harman 2011-01-26 11:32 Rev.: 46746

When finding the row of a failed test grep the first column for the row index.
Previously, if the test name contained the same number as row of the failed
test it would return the wrong test and component


5 lines of code changed in 1 file:

jas 2011-01-25 22:24 Rev.: 46745

Change the MCRT directory name to RMCRT and remove the ArchesRMCRT
directory.

2 lines of code changed in 1 file:

guilkey 2011-01-25 18:33 Rev.: 46742

Slight change to the way that erroneously fast particles are handled.

3 lines of code changed in 1 file:

guilkey 2011-01-25 17:55 Rev.: 46741

Now using a Mie-Gruneisen EOS for the fully compacted state. Replaced some
hardwired code with a general implementation, added a variable label to allow
for visualization of alpha.

78 lines of code changed in 2 files:

jthornoc 2011-01-25 16:03 Rev.: 46737

Initial commit of Isaac's ray tracer.
- Moved Paula's stuff to the attic
- Currently for this to work, needs to have DO radiation model turned on
- Ray.cc needs some cleaning up

25 lines of code changed in 6 files:

jsutherland 2011-01-24 21:58 Rev.: 46736

Rip out wasatch headers from expressions, relying directly on spatialops headers instead.

322 lines of code changed in 7 files:

jsutherland 2011-01-24 21:58 Rev.: 46735

More progress on momentum
- expression to calculate the RHS of the momentum
- expression to calculate the partial RHS of momentum for use in the poisson solver
- more work on momentum transport equation

442 lines of code changed in 7 files:

harman 2011-01-24 17:59 Rev.: 46734

Filter.cc .h
- moved applyFilter() from .cc to .h file and made it a templated function.
There were two versions of applyFilter with only 1 line different.

globally:
defined variable type when apply filter is being called.

This should not change the answers

248 lines of code changed in 9 files:

guilkey 2011-01-24 12:09 Rev.: 46733

1. Use polarDecompositionRMB in all instances (instead of polarDecomposition)

2. Compute rotation twice for each step. First compute the old rotation
(based on F^n) to unrotate stress to material coordinates, then compute new
rotation (based on F^(n+1) to rotate stress back to lab coordinates.

Once again, this change is likely to break the RT.

83 lines of code changed in 8 files:

tsaad 2011-01-22 13:30 Rev.: 46732

Fix cause of recent buildbot failure

1 lines of code changed in 1 file:

tsaad 2011-01-21 22:07 Rev.: 46730

1. Removed SuperBeeInterpolant and replaced it with a FluxLimiterInterpolant to handle a variety of convective flux limiters.
2. Added several flux limiters. These are defined in the ConvectiveInterpolationMethods.h
3. Cleaned up ScalarTransportEquation and ConvectiveFlux expression.

758 lines of code changed in 15 files:

jsutherland 2011-01-21 20:05 Rev.: 46729

First cut at defining an interface for the Pressure expression.
There is no way this will compile as of yet. Just committing it so that Tony can get going on the guts here and I can work on getting it plugged in to the momentum equation...

336 lines of code changed in 4 files:

jsutherland 2011-01-21 08:51 Rev.: 46727

cosmetic changes.

131 lines of code changed in 7 files:

jsutherland 2011-01-20 18:24 Rev.: 46726

Merge branch 'Momentum'

Conflicts:
src/StandAlone/inputs/UPS_SPEC/wasatch_spec.xml

507 lines of code changed in 4 files:

jsutherland 2011-01-20 18:21 Rev.: 46725

Cleanup. My last commit missed a few files.

12 lines of code changed in 4 files:

jsutherland 2011-01-20 18:16 Rev.: 46724

Add an error check.

6 lines of code changed in 1 file:

jsutherland 2011-01-20 14:28 Rev.: 46723

- fix convective flux compilation issues
- clean up other stuff associated with explicit template instantiation for convective fluxes.

109 lines of code changed in 3 files:

jsutherland 2011-01-20 14:28 Rev.: 46722

Oops - forgot to add the Stress implementation that was moved out of the header.

229 lines of code changed in 1 file:

jsutherland 2011-01-20 14:28 Rev.: 46721

Remove normal stess expression. This is now calculated as a specialized version of the Stress.

0 lines of code changed in 1 file:

jsutherland 2011-01-20 14:27 Rev.: 46720

Stress tensor expression modifications.

74 lines of code changed in 2 files:

jsutherland 2011-01-20 14:27 Rev.: 46719

Add an expression to calculate primitive variables from conserved variables, i.e. phi from rho*phi.

188 lines of code changed in 3 files:

jsutherland 2011-01-20 14:27 Rev.: 46718

Changes due to moving Operator type inference into SpatialOps.

75 lines of code changed in 5 files:

jsutherland 2011-01-20 14:27 Rev.: 46717

clean up some includes in ScalarTransportEquation

2 lines of code changed in 2 files:

jsutherland 2011-01-20 14:27 Rev.: 46716

remove some unnecessary explicit template instantiations.

0 lines of code changed in 1 file:

jsutherland 2011-01-20 14:26 Rev.: 46715

First pass at getting the stress tensor expressions in.

385 lines of code changed in 2 files:

harman 2011-01-20 14:07 Rev.: 46714

changed conditional test from ! -f $MALLOC_STATS.* -> ! -f $MALLOC_STATS.0

1 lines of code changed in 1 file:

jas 2011-01-20 13:12 Rev.: 46713

Add check for static option in xml2-config which is required for kraken and jaguar.

5553 lines of code changed in 2 files:

guilkey 2011-01-19 16:52 Rev.: 46710

Previously, the stress was unrotated at the beginning of a step using the new
value of R, and was rotated back at the end using the same value of R.
Now, unrotate using the old value of R, and rotate back using the new value.

5 lines of code changed in 1 file:

guilkey 2011-01-19 15:26 Rev.: 46709

Major revisions to MPM Boundary conditions. This is almost sure to break the
RT. Changes include:

Now do gimp, cpdi and 3rdOrderBSplines the exact same way. Previously,
3rdOrderBS had its own sections.

Setting extra node velocities using values one layer of nodes inside the
computational boundary. The normal component on the extra node is set to the
negative of the interior value. The tangential values are set to be the same
as the interior values.

Due to the second change above, the nodes on the faces are done for both the
minus and plus faces BEFORE doing the extra nodes for the minus and plus faces.
This is done to avoid problems with 2D simulations. By doing this, we avoid
setting the extra node values on one face to unset values on the opposite face.

98 lines of code changed in 1 file:

harman 2011-01-19 13:50 Rev.: 46708

Added ability for pseudo rays to be shot from a fine patch, leave that patch and continue across the domain
using coarser level data.

It works in serial on two levels

216 lines of code changed in 2 files:

tsaad 2011-01-19 10:36 Rev.: 46704

Repair counter in the z direction.

0 lines of code changed in 1 file:

tsaad 2011-01-18 22:00 Rev.: 46703

1. Added Superbee limiter for convective flux calculation.
2. Changed ConvectiveFluxUpwind to ConvectiveFluxLimiter. This is to be used with convective flux interpolants that are dependent on a velocity field including limiters.
3. Modified sub.mk to compile the new interpolant.

592 lines of code changed in 9 files:

jthornoc 2011-01-18 11:43 Rev.: 46702

Removing test commits.

0 lines of code changed in 1 file:

jthornoc 2011-01-18 11:35 Rev.: 46701

Another test.

1 lines of code changed in 1 file:

jthornoc 2011-01-18 11:35 Rev.: 46700

Testing a single commit.

1 lines of code changed in 1 file:

jsutherland 2011-01-17 13:39 Rev.: 46696

- Move some field type inference utilities to SpatialOps.
- Modify some header inclusions.

33 lines of code changed in 8 files:

guilkey 2011-01-14 19:13 Rev.: 46695

First cut at a P-alpha model for pressure in porous solids.

672 lines of code changed in 4 files:

harman 2011-01-14 13:44 Rev.: 46694

Now using 1 layer of ExtraCells

Working on 2 levels RR: 4, non-overlapping patches.

7 lines of code changed in 1 file:

jpeterson 2011-01-14 11:55 Rev.: 46692

You can now specify the image file base name, 'movie' is the default

14 lines of code changed in 1 file:

jsutherland 2011-01-14 11:52 Rev.: 46691

- Move some header stuff into a implementation file with explicit template instantiation
- Modify some documentation.
- minor changes to build system.

563 lines of code changed in 11 files:

guilkey 2011-01-14 11:11 Rev.: 46689

Move delete state to below last use of state.

2 lines of code changed in 1 file:

jas 2011-01-12 18:50 Rev.: 46688

Fix compiler warning.

1 lines of code changed in 1 file:

harman 2011-01-12 18:38 Rev.: 46687

Added coupling between the levels.
- pseudoCFD utilizes refined data from the shootRays task
- manually scheduling coarsen_Q and refineQ
- moved code from coarsen and refine to coarsen_Q and refine_Q.

shootRays()
- shoot "rays" from all cells in the patch, not just the middle cell.

Works for 2 levels, RR:1 , serial.

90 lines of code changed in 2 files:

jas 2011-01-12 18:17 Rev.: 46686

Fix some compiler warnings.

4 lines of code changed in 1 file:

harman 2011-01-12 17:11 Rev.: 46684

- deleted unused variables
- added pseudoCFD task
- added shootRays task
- added refineQ task

-scheduleTimeAdvance
added scheduling of pseudoCFD and shootRays task.

shootRays task can access data on another patch on the same level.
Levels are uncoupled

Still thrashing.

635 lines of code changed in 2 files:

dav 2011-01-12 17:10 Rev.: 46683

More executables that require the BLAS_LIBRARY to link on ember@chpc.

8 lines of code changed in 6 files:

jas 2011-01-12 14:51 Rev.: 46681

Remove the *.d files during make cleanreally.

1 lines of code changed in 1 file:

dav 2011-01-12 14:49 Rev.: 46680

The following (minor) updates are to fix issues or quite compiler
warnings when building under ICC on Ember@CHPC (thought they probably
apply to all ICC v12+ compilers.

M CCA/Components/Schedulers/MixedScheduler.h
M CCA/Components/Schedulers/MixedScheduler.cc

- Fix 'is virtual overloading intended' warning message. Signature of
child class function needs to match that of its parent.

M CCA/Components/Arches/CoalModels/ModelBase.h

- Cosmetics. White space is your friend.

M CCA/Components/Arches/CoalModels/HeatTransfer.h
M CCA/Components/Arches/CoalModels/SimpleHeatTransfer.h
M CCA/Components/Arches/TransportEqns/DQMOMEqnFactory.h
M CCA/Components/Arches/TransportEqns/EqnBase.h
M CCA/Components/Arches/TransportEqns/DQMOMEqn.h
M CCA/Components/Arches/LU.h

- Returning a 'const' non-pointer doesn't make sense... and causes ICC
to spew warnings all over the place.

M CCA/Components/Arches/DQMOM.cc

- Organize #includes alphabetically in order to understand what is
included more easily.

M CCA/Components/Arches/DQMOM.h

- Made weightedAbscissaModels into a vector of vectors of pointers.
ICC won't allow a vector of abstract classes... I'm actually not
quite sure how this variable is compiling or what it is used for, but
both ICC and GCC seem to be ok with the pointer version. It is possible
that this could cause an issue that I'm not immediately seeing, or cause
a memory leak. Perhaps someone familiar with this code could take a look?

M StandAlone/tools/pfs/sub.mk
M StandAlone/tools/puda/sub.mk
M StandAlone/tools/dumpfields/sub.mk
M StandAlone/tools/graphview/sub.mk
M StandAlone/tools/sub.mk
M StandAlone/Benchmarks/sub.mk
M testprograms/CubeRootTest/sub.mk

- These executables (at least when they use Ember's MPI) are required
to be linked against the thread library.

M Core/Containers/SuperBox.h

- There appears to be a 'hack' in our code that fixed an old problem with
ICC. However, it seems that icc 12.0.0 took care of the problem
and now our 'hack' doesn't compile. I've removed the hack and it
seems to be good now.
- Indentation... is your friend. (The comes under the whitespace category. ;)


69 lines of code changed in 20 files:

harman 2011-01-10 12:30 Rev.: 46679

Use different command line options for stat if using OSX.

Bulletproofing:
- if malloc_stats && malloc_stats.* don't exist then warn the user and
exit.

only concatenate the malloc_stats files together if there is more than 1.

More informative diagnostic messages.


28 lines of code changed in 1 file:

harman 2011-01-10 11:33 Rev.: 46678

auto size the dialog box so it won't throw an error on ancient version of dialog on OSX.

1 lines of code changed in 1 file:

guilkey 2011-01-08 13:43 Rev.: 46677

Delete z_matl, this should fix the memory leak.

3 lines of code changed in 1 file:

guilkey 2011-01-07 19:19 Rev.: 46676

Fix a minor error in the documentation

1 lines of code changed in 1 file:

guilkey 2011-01-07 16:30 Rev.: 46675

Added the option of applying a volume constraint to simulations involving
SpecifiedBody (Rigid) contact. Syntax is the same as friction contact:
<volume_constraint>X.YZ</volume_constraint>, where X.YZ is a number in the
range [0-1].

43 lines of code changed in 2 files:

harman 2011-01-06 09:33 Rev.: 46673

Removed an environmental variable that isn't needed and is confusing. When memory tests are performed
set the environmental variable MALLOC_STRICT.

5 lines of code changed in 3 files:

jsutherland 2011-01-05 13:17 Rev.: 46672

remove an unused variable.

0 lines of code changed in 1 file:

jsutherland 2011-01-05 12:40 Rev.: 46671

destroy some VarLabels that are being created.

21 lines of code changed in 4 files:

jsutherland 2011-01-05 12:39 Rev.: 46670

- use StringNames to define strings associated with coordinates.

68 lines of code changed in 6 files:

jsutherland 2011-01-05 11:00 Rev.: 46669

Okay - my compiler must have been throwing stdio in for me. Let's try this again and see if the buildbot is happy now.

4 lines of code changed in 1 file:

jsutherland 2011-01-05 10:53 Rev.: 46668

Not sure why this slipped through on my machine but killed the buildbot. This should compile now.

2 lines of code changed in 1 file:

jsutherland 2011-01-05 10:40 Rev.: 46667

This checkin may break something if I was not able to build it. I will clean it up if that happens...

- removing "using" standard namespace stuff from headers. This is really bad practice, and anyone doing it should be flogged. Opening up a namespace in a header file defeats the purpose of namespaces because all downstream inclusions of the header file will also result in that namespace opening up. This can lead to inadvertent name clashes, etc. Only open a namespace in an implementation file!

- put the SymmMatrix3 implementation in the Uintah namespace to be consistent with its declaration.

1018 lines of code changed in 66 files:

jsutherland 2011-01-05 09:08 Rev.: 46665

Forbid specification of extraCells in Wasatch.

35 lines of code changed in 1 file:

harman 2011-01-03 15:28 Rev.: 46663

User can either manually specify a multilevel grid or specify geometry objects
that will be refined.

- cleaned out unused code.
- runs without crashing on 2 levels, with a manually specified grid
- Doesn't run with the regridder turned on

Still thrashing....

218 lines of code changed in 2 files:

tsaad 2011-01-03 06:58 Rev.: 46661

Cleanup and documentation for boundary conditions treatment.

60 lines of code changed in 2 files:

harman 2011-01-02 17:04 Rev.: 46660

New component, a sandbox for testing ideas associated with multi-level RMCRT

750 lines of code changed in 4 files:

harman 2011-01-01 19:02 Rev.: 46659

advect_3L_3D: skip the restarts tests. The restart tests don't compare and I don't
have time to look at it.

2 lines of code changed in 1 file:

harman 2011-01-01 18:46 Rev.: 46658

added level index to the output.

1 lines of code changed in 1 file:

harman 2011-01-01 14:08 Rev.: 46657

removed AMRMPM test advect_3L_3D.
The script is trying to run this serial problem with 27 procs.

1 lines of code changed in 1 file:

harman 2011-01-01 13:21 Rev.: 46656

fixed memory leak

2 lines of code changed in 1 file:

harman 2011-01-01 12:28 Rev.: 46654

syntax error

4 lines of code changed in 1 file:

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