April 2013 Commit Log

Number of Commits:
111
Number of Active Developers:
12
guilkey 2013-04-30 16:12 Rev.: 50194

A little less spew, please.

1 lines of code changed in 1 file:

guilkey 2013-04-30 15:15 Rev.: 50193

Include a multiplication by the deformation gradient in computing p.scaleFactor

8 lines of code changed in 1 file:

guilkey 2013-04-30 14:57 Rev.: 50192

Remove some pollution from scheduleTimeAdvance.

1 lines of code changed in 1 file:

tsaad 2013-04-30 14:09 Rev.: 50190

Replace StringNames with TagNames to simplify access to commonly used tags.

257 lines of code changed in 22 files:

tsaad 2013-04-30 12:10 Rev.: 50188

revert changes made to SimulationController.cc

2 lines of code changed in 1 file:

harman 2013-04-30 11:47 Rev.: 50187

changed from /bin/sh -> /bin/bash

Debian wheezy doesn't recognize this as a sh script.

1 lines of code changed in 1 file:

tsaad 2013-04-30 10:38 Rev.: 50186

This is a major Wasatch commit. First, the viscosity is removed from the stress tensor calculation so that it becomes a strain tensor. This separation helps us reuse the strain tensor in LES models yielding a noticeable speedup. Second, as the viscosity is moved into the momentum RHS calculation, one must exrapolate its values at all patch boundaries - this lead to the development of an extrapolant operator that takes care of this extrapolation. One could of course perform and MPI communication on the turbulent viscosity but this was twice as costly as the extrapolation. Furthermore, the extrapolant will be used in the dynamic smagorinsky model to fill in ghost-cell values before filtering operations. Finally, a few cosmetic changes here and there to make the code look nice. NOTE: this commit will break every Wasatch test that solves the momentum equations - as expected - due to the change in the algebraic operations order. All differences are of the order of machine precision except for the turbulence tests due to the extrapolation.

875 lines of code changed in 25 files:

harman 2013-04-26 12:27 Rev.: 50178

Added the todd1 option which performs 1st law analysis on the control volume.

379 lines of code changed in 8 files:

harman 2013-04-26 10:19 Rev.: 50177

if compare_uda fails execute
compute_Lnorms <uda1> <uda2>
and save the output to compare_sus_runs.txt


0 lines of code changed in 2 files:

jsutherland 2013-04-26 08:58 Rev.: 50176

Update due to changes in SpatialOps.

1 lines of code changed in 1 file:

jsutherland 2013-04-26 08:57 Rev.: 50175

minor cleanup.

3 lines of code changed in 1 file:

wyxpuma 2013-04-26 08:32 Rev.: 50174

to add the lower limit for char oxidation

10 lines of code changed in 2 files:

wyxpuma 2013-04-26 08:30 Rev.: 50173

to add the simplest method to DQMOM model

120 lines of code changed in 2 files:

awabboud 2013-04-25 15:57 Rev.: 50171

Add in surface energy variation due to the tolman length into the ostwald ripening term.

16 lines of code changed in 2 files:

awabboud 2013-04-25 14:01 Rev.: 50170

Make sure that zero values from embedded geometries don't give nan/inf for aggregation efficiency.

23 lines of code changed in 1 file:

harman 2013-04-25 12:47 Rev.: 50169

Added bulletproofing. A user must specify more than 1 max_levels if they're using
AMR and a regridder.

7 lines of code changed in 1 file:

harman 2013-04-24 10:21 Rev.: 50168

- using printSchedule and printTask()
- changed logic in doMPMOnLevel()
- on scheduleInitialize on the finest level.

17 lines of code changed in 1 file:

jthornoc 2013-04-23 21:37 Rev.: 50166

Should be checking the bounds on 1-eta for the denominator to get f.

10 lines of code changed in 1 file:

jthornoc 2013-04-23 21:13 Rev.: 50165

tolerance -> tol in the input.

1 lines of code changed in 1 file:

jthornoc 2013-04-23 15:39 Rev.: 50164

** Warning ** Monolithic commit **

1) Always recompile taskgraph on restart until restartInitialize lives up to its name.

2) Adding new variable transforms for the table lookup: rcce, rcce_fp, fcce_eta. These are still somewhat incomplete and should be used with caution.

3) Clipping on the RK averaging to actually allow variables to go to zero: This may change answers!!

4) In EmpSoot, make sure you specify the correct radiation model.

5) Some major reworking of the Westbrook dryer model. This should fix some of the mass balance issues seen in some cases.

6) Changed how the clipping is specified for some variables. Note that <small> was removed from the DQMOM option in favor of a more universal <tol>

489 lines of code changed in 14 files:

dav 2013-04-23 13:56 Rev.: 50163

Fix indentation, clean up, remove superfluous ';'s.

18 lines of code changed in 1 file:

dav 2013-04-23 13:52 Rev.: 50162

Remove tabs / fix indentation.

1 lines of code changed in 1 file:

dav 2013-04-23 13:51 Rev.: 50161

Fix missing 'std::' for the 2nd 'map' in typedef.

1 lines of code changed in 1 file:

harman 2013-04-23 12:51 Rev.: 50160

Spring Cleaning:
- removed tecplot and rtdata options. If anyone has used these in the last
5 years let me know.


2 lines of code changed in 7 files:

tsaad 2013-04-23 10:04 Rev.: 50159

warches fix to account for removing the Kolmogorov scale from Wasatch.

1 lines of code changed in 1 file:

tsaad 2013-04-23 09:23 Rev.: 50158

improve the stability of the dynamic coefficient calculation.

31 lines of code changed in 1 file:

tsaad 2013-04-22 15:07 Rev.: 50155

get rid of the Kolmogorov scale user input. Please revise your input files if you are using any of the Wasatch turbulence models by simply deleting the KolmogorovScale xml spec under the Turbulence block. Alternatively, you can use remove_xml_block for batch removal of xml blocks (see: inputs/Wasatch/remove_xml_block). This commit will break ALL WASATCH TURBULENCE regression tests.

5 lines of code changed in 4 files:

awabboud 2013-04-22 10:29 Rev.: 50153

Fix the logic in bulk diffusion growth with sBar. Update the multi-environment input file.

3 lines of code changed in 1 file:

tsaad 2013-04-22 07:47 Rev.: 50152

modify exception handling for the dynamic model

1 lines of code changed in 1 file:

tsaad 2013-04-21 16:43 Rev.: 50148

change performance tests on isotropic turbulence to regular tests. Those were not intended to be performance tests in the first place.

6 lines of code changed in 1 file:

tsaad 2013-04-21 14:00 Rev.: 50147

Add a dynamic Smagorinsky model to Wasatch. This model currently operates for constant density flows. variable density handling will be committed soon. Verificaiton and regression tests will also follow.

944 lines of code changed in 12 files:

tsaad 2013-04-20 20:02 Rev.: 50146

add regression tests for the turbulence verification cases in anticipation of the dynamic model commit. This will break the RT for tonight.

95 lines of code changed in 1 file:

harman 2013-04-19 17:54 Rev.: 50145

Added ability to output on multiple levels.

The user can specify
<analyze label="g.velocity" matl="0" level = "-1"/>
<analyze label="press_CC" matl="0" level = "0"/>

where -1 equals finest level. The default is to compute the min/max on all levels and all matls.

I'm now using a std::vector<struct >instead of several std::vectors to keep track of the
variable label, matl and level.

185 lines of code changed in 2 files:

awabboud 2013-04-19 15:25 Rev.: 50143

Add in a more complex homogenous nucleation term, add in a size-dependent surface energy term based on the Tolman length, and allow for the R-critical expression to allow for either constant or variable surface energy.

473 lines of code changed in 4 files:

jthornoc 2013-04-19 14:12 Rev.: 50142

Fixing a bug in how the rate is clipped.

2 lines of code changed in 1 file:

harman 2013-04-19 07:56 Rev.: 50141

outputInterval and Checkpoint Interval changes:

-added a reduction variable to log when the pressure threshold has been exceeded
or a detonation detected.
- changed logic. The pressure threshold must be exceeded before detonation.


59 lines of code changed in 2 files:

guilkey 2013-04-18 18:07 Rev.: 50140

1. Fixed a small bug in CBDI with Ali's help.
2. Better input labels in SmoothCylGeomPiece (Scott Bardenhagen)
3. Example input file of a pressurized cylinder using the smooth cylinder, cpdi and cbdi.

30 lines of code changed in 4 files:

guilkey 2013-04-18 15:04 Rev.: 50139

Remove the code associated with on the fly material addition.

0 lines of code changed in 2 files:

guilkey 2013-04-18 14:51 Rev.: 50138

Freshen up the SmoothCylinder code to be compatible with CPDI.
(Work done by Scott Bardenhagen.)

63 lines of code changed in 2 files:

guilkey 2013-04-18 11:56 Rev.: 50137

Stop compiling the fracture code. Next stop, SL County Landfill.
Remove unneeded include files (Node27 and NodeIterator) from several material
models.

2 lines of code changed in 32 files:

jthornoc 2013-04-17 22:57 Rev.: 50135

Adding radiation abskp calculation using Lyubima's code. This code still needs to be verified.

282 lines of code changed in 3 files:

wyxpuma 2013-04-17 16:22 Rev.: 50134

optimize the loops for coalgas*.cc to save 15% cpu times

0 lines of code changed in 8 files:

harman 2013-04-17 08:16 Rev.: 50133

Updated the gnuplot template for plotting scaling data.
Removed an dead matlab script

14 lines of code changed in 2 files:

wyxpuma 2013-04-16 16:00 Rev.: 50132

make the default of save_moments as false in order to save 10% cpu cost

1 lines of code changed in 1 file:

wyxpuma 2013-04-16 12:46 Rev.: 50131

add the time calculator for optimized solver and linear system construction

10 lines of code changed in 1 file:

qymeng 2013-04-16 09:38 Rev.: 50130

skip first timestep for checking output/checkpoint interval changes.

4 lines of code changed in 1 file:

harman 2013-04-15 17:09 Rev.: 50129

Turn off explode2D_AMR. The BNR regridder is no longer being used.

1 lines of code changed in 1 file:

harman 2013-04-15 16:05 Rev.: 50128

schedule_computerBurnLogic()
- only compute outputInterval or checkpointInterval IF
the user has requested in the input file.

8 lines of code changed in 1 file:

qymeng 2013-04-15 13:05 Rev.: 50127

For debug stream sendtiming recvtiming taskorder, only output on where rank id is half of the world size.

47 lines of code changed in 9 files:

qymeng 2013-04-15 09:57 Rev.: 50126

Make update output/checkpoint interval works with all schedulers.

27 lines of code changed in 1 file:

tsaad 2013-04-15 09:48 Rev.: 50125

update documentation for the strain tensor magnitude.

8 lines of code changed in 1 file:

ihunsaker 2013-04-12 14:47 Rev.: 50124

More intuitive variable names.
More reasonable default values.

15 lines of code changed in 3 files:

qymeng 2013-04-12 14:47 Rev.: 50123

Only change output/checkpoint interval when new value computed by simulation components

10 lines of code changed in 2 files:

harman 2013-04-11 15:08 Rev.: 50121

Added bulletproofing to AMRICE.

Input files:
Changed the regridder type from BNR or Hierarchical to the Tiled algorithm.
The tiled regridder is faster, scales better and the other regridders create patches that
are partially filled with old data. The refine() task was designed to work
over an entire patch and don't want to overwrite the old data, thus only use the tiled regridder.



33 lines of code changed in 2 files:

ihunsaker 2013-04-11 13:20 Rev.: 50119

Fixed an oops. Not sure how that made it
through my local RT.

1 lines of code changed in 1 file:

ihunsaker 2013-04-11 12:15 Rev.: 50117

Deleted comments. Moved check for negative
mole fractions to RadPropertyCalculator.


2 lines of code changed in 2 files:

dav 2013-04-10 17:09 Rev.: 50115


Updated configure to handle a newer layout (naming of libraries) of
libmkl (the IBM blas library) found on Yellowstone. Cleaned up the way
we check for multiple possible libs. This new approach should
eventually migrate to all of our configure tests for multiple
different possible layouts for libraries. This _should_ work for all
machines using mkl, but I haven't tried them... -Dav

47 lines of code changed in 2 files:

harman 2013-04-10 16:15 Rev.: 50114

No longer carry forward the outputInterval and checkpointInverval. Only put them
in the datawarehouse when they change.


12 lines of code changed in 1 file:

ihunsaker 2013-04-10 15:50 Rev.: 50113

Commenting out the changes in the Classic table
interface that broke the two regression tests
yesterday. When I figure out why this broke
the test, I'll put the changes back in.

15 lines of code changed in 1 file:

guilkey 2013-04-10 12:00 Rev.: 50112

Pass the cell size in for smooth geometry pieces. Quiet some errors in AMRMPM.

21 lines of code changed in 6 files:

guilkey 2013-04-09 16:31 Rev.: 50111

Progress towards getting the size initialized correctly for the SmoothCylinders.

21 lines of code changed in 3 files:

harman 2013-04-09 16:00 Rev.: 50110

problemSetup_BulletProofing()
- Only enter bulletproofing if the AMR xml tag exists.


12 lines of code changed in 1 file:

harman 2013-04-09 15:48 Rev.: 50109

- Added scheduleRefine() to the ModelInterface
- Adde a call to scheduleRefine in AMRICE
- Defined the refine task for the DDT1 burn model

142 lines of code changed in 7 files:

ahumphrey 2013-04-09 13:49 Rev.: 50107

Add declarations for extern C DQMOM kernel launch functions.

10 lines of code changed in 1 file:

ihunsaker 2013-04-09 12:28 Rev.: 50106

Made ray tracing capable of handling intrusion.

Bug fix in radprops interface. This fixes
the problem of negative mole fractions.

I have changed the input files for the RMCRT
regression tests, but the answers should
remain unchanged.

40 lines of code changed in 7 files:

ahumphrey 2013-04-08 22:30 Rev.: 50104

CPU optimizations in DQMOM::constructLinearSystem(). These changes yield a 5x speedup.

81 lines of code changed in 1 file:

tsaad 2013-04-08 16:54 Rev.: 50088

inline a few more expressions.

97 lines of code changed in 4 files:

guilkey 2013-04-08 16:14 Rev.: 50087

Add computes and allocates of pVelGradLabel for (schedule)Refine

3 lines of code changed in 1 file:

tsaad 2013-04-08 13:49 Rev.: 50086

Enforce staggered BCs to be applied on staggered fields using the value specified by the input file (or the bc expression) instead of using the averaging formula. This is the key to start ripping out some initializations for temporary fields in many of the Wasatch expressions. The behavior here is that, without the temporary field initializations, we were getting inf/nan values in the extra cells which in turn is infecting the staggered boundary cells because those were using the averaging formula.

28 lines of code changed in 3 files:

harman 2013-04-08 12:45 Rev.: 50085

BoundCondFactory.cc
- create()
The boundary condition is considered an integer if the attribute
'type = "int"' is included. If the attribute isn't there it will default
to a double.


Ray.cc/h
The user can now specify boundary conditions for the cellType. Use:

<BCType id = "0" label = "cellType" var = "Dirichlet" type = "int">
<value> 8 </value> ^^^^^^^^^^^^
</BCType>

31 lines of code changed in 3 files:

harman 2013-04-08 12:04 Rev.: 50084

Removed some old rotted out plumbing:
- scheduleCheckNeedAddMaterial()
- activateModel()

This idea died and blew away years ago.

* should not change answers

155 lines of code changed in 20 files:

tsaad 2013-04-08 11:01 Rev.: 50083

start inlining key Wasatch expressions. This should NOT break the regression tester. There is a very small memory overhead (<0.9% on cases tested). Hopefully, that will not cause the memory tests to fail.

127 lines of code changed in 4 files:

harman 2013-04-08 07:58 Rev.: 50082

delete a couple of structs to clean up a memory leak.

2 lines of code changed in 1 file:

qymeng 2013-04-07 11:50 Rev.: 50081

Use override in Simulation Controller when write into old DW.

2 lines of code changed in 1 file:

tsaad 2013-04-06 19:51 Rev.: 50080

add and report mean solver time when using hypre.

7 lines of code changed in 1 file:

tsaad 2013-04-06 19:48 Rev.: 50079

enable convection for scalability transport equations.

1 lines of code changed in 1 file:

harman 2013-04-06 12:22 Rev.: 50077

Added ability to update outputInterval and checkpointInterval if a detonation is detected
or if the pressure in the domain exceeds a user defined threshold. Needs further testing.

* should not change the answers

127 lines of code changed in 2 files:

guilkey 2013-04-05 22:21 Rev.: 50076

Add a computes for pVelGrad to actuallyInitialize.

1 lines of code changed in 1 file:

harman 2013-04-05 17:27 Rev.: 50075

include matls in debugging output.

0 lines of code changed in 2 files:

guilkey 2013-04-05 13:56 Rev.: 50074

Minor formatting.

3 lines of code changed in 1 file:

guilkey 2013-04-05 11:40 Rev.: 50072

Correct the error message, the user inputs angles in degrees, not radians.

1 lines of code changed in 1 file:

harman 2013-04-05 10:03 Rev.: 50071

fixed syntax error

1 lines of code changed in 1 file:

guilkey 2013-04-05 09:45 Rev.: 50070

replaced /2.0 with *0.5. Rename some variables for better formatting.

15 lines of code changed in 1 file:

ahumphrey 2013-04-05 09:36 Rev.: 50069

Add stubs for DQMOM GPU kernels.

0 lines of code changed in 2 files:

ahumphrey 2013-04-05 09:16 Rev.: 50068

Add in ARCHES-related DQMOM kernel source files (sub.mk) for compilation when CUDA is enabled.

5 lines of code changed in 1 file:

guilkey 2013-04-04 22:37 Rev.: 50067

Put the velGrad stuff inside a conditional so it only applies to explicit
calculations.

6 lines of code changed in 1 file:

jsutherland 2013-04-04 20:00 Rev.: 50066

Don't build the TabProps tests. This will cut down on build time a little bit.

1 lines of code changed in 1 file:

qymeng 2013-04-04 16:23 Rev.: 50065

Check chages on output interval after task graph compiling

27 lines of code changed in 1 file:

ahumphrey 2013-04-04 13:49 Rev.: 50063

ARCHES: FakeRadPetscSolver and RadPetscSolver need to have the same method headers for radLinearSolve() and setMatrix().

13 lines of code changed in 1 file:

qymeng 2013-04-04 12:21 Rev.: 50062

Better way to output task execution scheduled order debug info.
Get task static order from taskgraph instead of run once with Static MPI scheduler.

13 lines of code changed in 5 files:

qymeng 2013-04-04 12:21 Rev.: 50061

Fix a AMR hang.
Shouldn't skip the whole reduce sysvar task if no patches on a MPI Rank.

19 lines of code changed in 1 file:

harman 2013-04-04 10:08 Rev.: 50060

Put a loop around the svn checkout command that will try to checkout 10 times and sleep for a minute between tries.

28 lines of code changed in 1 file:

tsaad 2013-04-04 09:33 Rev.: 50059

Add d_momentum/dt to the pressure RHS. This will enforce mass conservation on problems with time-dependent inlets (i.e. turbulent inlet). This will also (hopefully) help in reducing reflections at outflow boundaries. Developers have the option of disabling this term from the input file. Note that one regression test is expected to fail. Other regression tests would have reported failure not because of differences, but because of additional variables saved in checkpoints (old vars...). To avoid this, I disabled this new term in all those other tests.

173 lines of code changed in 5 files:

jthornoc 2013-04-04 09:19 Rev.: 50058

Refomatted the print statements for Radiation.

50 lines of code changed in 8 files:

qymeng 2013-04-03 19:29 Rev.: 50057

Bug fixes of recent added debug streams.

15 lines of code changed in 5 files:

harman 2013-04-03 17:17 Rev.: 50055

ComputeBurnLogic()
-removed requires and get of BurningCriterialLabel, it's never used.

1 lines of code changed in 1 file:

guilkey 2013-04-03 16:35 Rev.: 50054

Paving the way for "smooth" geometry pieces to have their "size" variables
created correctly. This commit is ~1/2 of the needed changes.

36 lines of code changed in 4 files:

qymeng 2013-04-03 14:01 Rev.: 50053

Add a debugstream TaskOrder. When set in SCI_DEBUG,
remember static order in static MPI scheduler on timestep 1
print out real execution order in dynamic/thread/unified scheduler.

65 lines of code changed in 6 files:

kamojjala 2013-04-03 09:20 Rev.: 50051

Changing the polar decomposition to polardecompositionRMB in the wrapper

ine, and those below, will be ignored--

M ConstitutiveModel/Kayenta.cc

0 lines of code changed in 2 files:

kamojjala 2013-04-03 09:14 Rev.: 50050

Updating the L consistent with F for pressure smoothing

3 lines of code changed in 1 file:

guilkey 2013-04-02 17:25 Rev.: 50048

Add gradient enhanced velocity projection, currently inside of an
inactive #ifdef. Also, comment out some warning inducing code.

30 lines of code changed in 3 files:

qymeng 2013-04-02 16:36 Rev.: 50047

put checkpoint/output interval value from ups file into the dw
if the variable doest not exsit, such as during the init timestep.

24 lines of code changed in 3 files:

tsaad 2013-04-02 14:46 Rev.: 50046

add interpolation to turbulent inlet boundary condition. Output the spacing between the turbulent data points from the digital filter generator.

52 lines of code changed in 4 files:

jthornoc 2013-04-02 13:53 Rev.: 50045

Using the geometric information a little better to determine the
iterators.

65 lines of code changed in 2 files:

jthornoc 2013-04-02 13:40 Rev.: 50044

Changing the way the pilot is turned on/off.

2 lines of code changed in 2 files:

qymeng 2013-04-01 20:55 Rev.: 50043

add debug stream SendTiming to print when MPI messages are send from DW.

31 lines of code changed in 3 files:

qymeng 2013-04-01 20:32 Rev.: 50041

add debug stream RecvTiming to print when MPI messages received to DW.

13 lines of code changed in 1 file:

harman 2013-04-01 15:54 Rev.: 50039

flush the file pointer. Some machines need a good kick in the pants
before they'll write the data.

2 lines of code changed in 1 file:

jsutherland 2013-04-01 15:49 Rev.: 50038

Modify the task list category parse tool interface to return the Category rather than the GraphHelper object. This will make it more generally useful.

26 lines of code changed in 5 files:

harman 2013-04-01 15:07 Rev.: 50037

More descriptive variable names
outputInv -> outputInterval
checkpointInv -> checkpointInterval

updateCheckpointInterval()
using d_checkpointInterval instead of d_outputInterval in conditional

48 lines of code changed in 6 files:

awabboud 2013-04-01 12:42 Rev.: 50035

Add in a size and growth dependent collision efficiency kernal to the aggregation.

534 lines of code changed in 4 files:

March 2013 »

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