August 2012 Commit Log

Number of Commits:
113
Number of Active Developers:
16
jas 2012-08-31 21:39 Rev.: 49161

Squashed commit of the following:

commit dca53ea5fb64ef131903b5c0767c5ac71c85ab41
Author: John Schmidt <john.schmidt@utah.edu>
Date: Fri Aug 31 22:24:35 2012 -0600

Remove old $Id$ that tracked the svn revision.

0 lines of code changed in 3 files:

ahumphrey 2012-08-31 16:47 Rev.: 49160

Start adding GPU task queue locks in Unified Scheduler.

31 lines of code changed in 2 files:

ahumphrey 2012-08-31 16:10 Rev.: 49159

Fix SchedulerFactory so the Unified scheduler can be created (Corresponding info in ups_spec).
Also fix a debug stream issue in BoundCondReader (change std::cout to BCR_dbg).

6 lines of code changed in 4 files:

jas 2012-08-31 12:00 Rev.: 49158

Remove duplication of hypre_solver_structure, use the hypre data
structure from the HypreSolver include file.

10 lines of code changed in 3 files:

ahumphrey 2012-08-30 16:55 Rev.: 49156

Disengage Hypre includes in a few more spots.

8 lines of code changed in 2 files:

jas 2012-08-30 15:21 Rev.: 49155

Put HAVE_HYPRE guards around hypre specific calls.

23 lines of code changed in 3 files:

tsaad 2012-08-30 14:26 Rev.: 49154

add the Uintah boundary conditions name attribute to the BoundCondBase class so that we can access that along with the iterator. Jeremy and Todd you may now access this info within get_iter_bcval_bckind by calling getBCFaceName on the BoundCond or BoundCondBase objects. You can find my usage in Wasatch/BCHelperTools.cc, line 380. NOTE: I had preferred for this attribute to be called label instead of name - but I assumed that someone is using it somewhere. if there is absolutely no prior use of it, i'd like to change it to label for consistency reason. please let me know - if you happen to read these commits...

29 lines of code changed in 6 files:

jas 2012-08-30 13:18 Rev.: 49153

Turn off the hypre timing output.

1 lines of code changed in 1 file:

jthornoc 2012-08-30 10:49 Rev.: 49152

Now requiring a specification for the mass fraction which is computing
the stripping factor.

9 lines of code changed in 2 files:

jthornoc 2012-08-29 15:58 Rev.: 49150

Fix name in spec.

1 lines of code changed in 1 file:

awabboud 2012-08-29 15:57 Rev.: 49149

Update to using ostwald ripenign model, and reading in initial moments if embedded geometry is used.

43 lines of code changed in 3 files:

jthornoc 2012-08-29 15:25 Rev.: 49147

Adding a temperature clip to the rate term.

3 lines of code changed in 2 files:

tsaad 2012-08-29 13:57 Rev.: 49145

fix restart on MPMArches-Wasatch. This was a VERY BAD miss in MPMArches...

1 lines of code changed in 1 file:

tsaad 2012-08-28 14:47 Rev.: 49142

fix warches restart on parallel runs.

1 lines of code changed in 1 file:

jas 2012-08-28 13:47 Rev.: 49140

Fix memory leak by deleting solver parameters.

1 lines of code changed in 1 file:

tsaad 2012-08-28 10:45 Rev.: 49139

update dipole vortex formula to a simpler form which will match the one going into the Wasatch documentation.

6 lines of code changed in 1 file:

awabboud 2012-08-27 15:22 Rev.: 49138

Found a few typos in Wasatch PBE stuff.

5 lines of code changed in 2 files:

jthornoc 2012-08-27 14:45 Rev.: 49137

1) Fixing Martin's restart issue. Looks like the d_labelInit flag was
not being used correctly.

2) Adding post-mixing to the enthalpy calculation (for heat loss)

3) Removing the laminar_pr number option.

103 lines of code changed in 16 files:

tsaad 2012-08-25 14:58 Rev.: 49134

add Lamb's dipole (aka Chaplygin's dipole - first discovery) to our repertoire of initial conditions. this is a wonderful initial condition to test outflow boundary conditions. i'll commit the analytical solution to the Wasatch doc soon in case you want to check it out.

245 lines of code changed in 2 files:

jas 2012-08-24 18:28 Rev.: 49133

Set the override flag for the hypre_solver_label.

4 lines of code changed in 1 file:

jas 2012-08-24 17:41 Rev.: 49132

Set the override flag for the hypre_solver_label.

9 lines of code changed in 3 files:

jas 2012-08-24 16:39

Set the modifies_hypre flag to false.

20 lines of code changed in 3 files:

jas 2012-08-24 14:34 Rev.: 49129

Update configure.

129 lines of code changed in 1 file:

jas 2012-08-24 14:27 Rev.: 49128

Use the DW to keep track of the HypreSolver data structures from one time
step to the next to avoid the setup costs that occur for doing very large
core count runs.

For smaller core counts, this does not affect the efficiency of the solver.

Answers should not change.


971 lines of code changed in 39 files:

jthornoc 2012-08-24 12:12 Rev.: 49127

Missing reassignment of the temp table value after the post comb.
mixing.

4 lines of code changed in 1 file:

guilkey 2012-08-24 09:34 Rev.: 49126

Comment out GUVShellGeometryPiece to see if anyone squawks before this is
deleted.

5 lines of code changed in 2 files:

awabboud 2012-08-23 12:44 Rev.: 49123

Fix memory leak

1 lines of code changed in 1 file:

banerjee 2012-08-22 19:02 Rev.: 49120

Arena added and JWLppMPM now gets density from matl.

18 lines of code changed in 3 files:

banerjee 2012-08-22 19:01 Rev.: 49119

Removed Arenisca_BB files.

0 lines of code changed in 4 files:

banerjee 2012-08-22 19:00 Rev.: 49118

Create the Arena model from Arenisca_BB.

3523 lines of code changed in 11 files:

awabboud 2012-08-22 12:56 Rev.: 49114

Fix to prevent memory leak in dbg build. Cleaning up compiler warnings.

12 lines of code changed in 2 files:

jthornoc 2012-08-22 12:49 Rev.: 49113

Better specification for this option. Input files updated accordingly.

1 lines of code changed in 1 file:

jthornoc 2012-08-22 12:49 Rev.: 49111

1) Update to documentation.
2) Added more flexibility for specifying the molecular diffusion coef.
for scalars
3) Turned on the option for using density_guess or actual density for
scalars.

Update 2) will change the answers.

472 lines of code changed in 5 files:

tsaad 2012-08-22 09:36 Rev.: 49110

add exponential vortex initialization to Arches. this is part of our recent efforts to develop a non-reflecting boundary condition for low-Mach combustion. The associated test illustrates the use of this vortex along with the exisiting outflow condition in Arches.

129 lines of code changed in 2 files:

jsutherland 2012-08-22 08:13 Rev.: 49109

Remove an unused variable.

0 lines of code changed in 1 file:

banerjee 2012-08-21 15:55 Rev.: 49107

Added another check to constrain the burn fraction. Why is 1 < 1 true?

12 lines of code changed in 1 file:

awabboud 2012-08-21 12:22 Rev.: 49104

Added line to RT script to test the digital filter.

3 lines of code changed in 1 file:

jsutherland 2012-08-21 08:32 Rev.: 49102

more dead code removal and warning cleanup

2 lines of code changed in 2 files:

jsutherland 2012-08-21 08:29 Rev.: 49101

1. remove some dead code.
2. silence a few warnings

12 lines of code changed in 2 files:

dav 2012-08-20 16:44 Rev.: 49100

Fix DigitalFilterGenerator build on Mac

3 lines of code changed in 1 file:

dav 2012-08-20 16:12 Rev.: 49099


Fix a couple of build problems (that occurs on various platforms but are exemplified in static builds.)

M StandAlone/sub.mk

Build the DigitalFilterGenerator (from CCA/Components/Arches) here as
I have direct access to the correct list of LIBS (both for static and
shared builds).

M CCA/Components/Arches/sub.mk

Don't specify the DigitalFilterGenerator build line here... it has been
moved to StandAlone/sub.mk (see above).


M StandAlone/tools/extractors/sub.mk

Fix the static build of this utility (need to actually link in the
tiff library)... Not sure why the RT (don't we have a static build
RT?) didn't catch this...

13 lines of code changed in 3 files:

awabboud 2012-08-20 14:40 Rev.: 49098

Implementation of Digital Filter inlet coniditons in Arches. These are read in through a table parser, generated with a stand alone executable.

1979 lines of code changed in 8 files:

banerjee 2012-08-17 19:17 Rev.: 49094

Now using incremental J for burn fraction subcycles.

29 lines of code changed in 2 files:

jsutherland 2012-08-17 13:46 Rev.: 49093

Fix another warning.

2 lines of code changed in 1 file:

jsutherland 2012-08-17 13:42 Rev.: 49092

Clean up a few warnings.

9 lines of code changed in 6 files:

harman 2012-08-17 12:06 Rev.: 49091

Delete VarLabel

1 lines of code changed in 1 file:

awabboud 2012-08-17 11:03 Rev.: 49090

Ripping out dependent logic of QMOM on the supersaturation ratio, which is specific to precipitation. The individual source terms for precipitation should have enough logic to maintain stability without this.

10 lines of code changed in 2 files:

tsaad 2012-08-17 08:41 Rev.: 49088

allow the exponential vortex expression to move in any direction, specified by user. This commit modifies the free stream by adding the transverse component. user now specifies both free stream velocities which then determines the advective direction of the vortex.

32 lines of code changed in 2 files:

jthornoc 2012-08-16 23:03 Rev.: 49087

Fixing a few memory cleanup issues with DQMOM.
Cleaning up some recompiling of the task graph for MPMArches. This is
no longer needed without the dummy solve.

28 lines of code changed in 5 files:

tsaad 2012-08-16 16:15 Rev.: 49085

add a vortex in a uniform stream initialization to start testing with non-reflecting boundary conditions. this expression corresponds to an exponential vortex superimposed on a uniform stream. the exponential vortex is an upgraded model of Rankine's vortex and provides a smooth transition for the tangential velocity at the vortex boundary. also add an example that uses this vortex.

215 lines of code changed in 2 files:

harman 2012-08-16 10:02 Rev.: 49081

Moved deletion of defState to fix memory leak.

1 lines of code changed in 1 file:

banerjee 2012-08-15 21:41 Rev.: 49079

Added a few more knobs for better control of algorithms.

68 lines of code changed in 2 files:

harman 2012-08-15 16:12 Rev.: 49077

added regression test for Scott.

34 lines of code changed in 1 file:

beckvermit 2012-08-15 10:45 Rev.: 49076

Fixed post processing script so it wont crash if burning stops or detonations occurs.

8 lines of code changed in 1 file:

harman 2012-08-15 10:35 Rev.: 49075

variable name change viscoElasticWorkInc -> viscoElasticWorkRate

ElasticPlasticHP()
corrected calculation of Tdot from viscoelasticity

updateInternalStresses()
- corrections to viscoElasticWorkRate calculations

18 lines of code changed in 3 files:

harman 2012-08-15 10:05 Rev.: 49074

Moved overrideVariableBehavior() call from

scheduleInitialize() -> scheduleDoAnalysis_preReloc()

so it will be called during a restart.

4 lines of code changed in 1 file:

harman 2012-08-15 09:30 Rev.: 49073

doAnalysis_preReloc()
- only transfer forward the file pointer if it exists in the old_dw.
The filePointerLabel is NOT saved in the checkpoints and so you can't
get it from the old_dw.

22 lines of code changed in 1 file:

harman 2012-08-15 08:55 Rev.: 49072

initialize()
- initialize the filePointer to null for all particles

doAnalysis()
- added global variable d_isDirCreated to detect if a directory already exists
- the function createFile() now opens the file pointer and passes it back


26 lines of code changed in 2 files:

banerjee 2012-08-14 23:03 Rev.: 49070

Full Backward Euler to compute stress. Hoping that this will fix collapse issue.

445 lines of code changed in 2 files:

harman 2012-08-14 16:00 Rev.: 49069

Global:
- added new particleVariable type <FILE*>
- added pre relocation data analysis task stub call.

SerialMPM & MPMICE
- added scheduling for a data analysis pre relocation task

particleExtract
- now storing file pointers in the data warehouse for the particle data.
The file pointers are treated just like the other particle data.
This should handle when particles move off of a patch to another
processor, and be be much faster than opening and closing the files.

Still testing.

Qingyu & Todd

163 lines of code changed in 13 files:

harman 2012-08-14 15:11 Rev.: 49068

global:
- updated prototype for updateInternalStresses()
- added viscoElasticWorkInc to deformation state

HypoViscoElasticDevStress:
- updateInternalStress()
added computation for viscoElasticWorkIncrement

ElasticPlasticHP
- added T dot equation from viscoelasticity.

* This should not change the answers -Todd & Scott

20 lines of code changed in 7 files:

banerjee 2012-08-13 22:47 Rev.: 49067

Corrected initialization of pLocalized_new. Was causing wierd behavior across patches.

17 lines of code changed in 1 file:

amir 2012-08-13 18:42 Rev.: 49066

Turbulent scalar closure model. The verification test case is not included. It will be added after getting LES model verification test case. The plus shape profile is committed for initial condition purposes as well.

593 lines of code changed in 17 files:

harman 2012-08-13 16:23 Rev.: 49065

computeStressTensorImplicit()
- adced the update to internal Cauchy stresses, viscoelasticity only. Now
consistent with explicit computeStressTensor. -Scott

8 lines of code changed in 1 file:

harman 2012-08-13 10:34 Rev.: 49063

now using a globally defined set to keep track if a directory has been
previously been opened. This should be quicker that a system call.

5 lines of code changed in 2 files:

beckvermit 2012-08-11 10:12 Rev.: 49061

Split Comopute ModelSources into two tasks to allow for stencil operations -Jacqueline

620 lines of code changed in 2 files:

harman 2012-08-10 15:52 Rev.: 49060

ElasticPlasticHP.cc
computeStressTensor()
-Update internal Cauchy stresses (only for viscoelasticity) --Scott

HypoViscoElasticDevStress::updateInternalStresses()
- now using:
sigmaDev_new = sigmaDev + ........
instead of
sigmaDev_new += ...........

8 lines of code changed in 2 files:

tsaad 2012-08-10 10:48 Rev.: 49059

minor cleanup of comments in qmom.

8 lines of code changed in 1 file:

beckvermit 2012-08-10 10:45 Rev.: 49058

Added a simulation to the nightly regression test. The simulation looks at convective burning in a material. -Jacqueline

4 lines of code changed in 1 file:

jthornoc 2012-08-09 16:50 Rev.: 49056

Now storing the turbulence closure without the molecular viscosity.

54 lines of code changed in 7 files:

harman 2012-08-09 15:22 Rev.: 49054

changed proc0cout to a DebugStream

13 lines of code changed in 1 file:

jthornoc 2012-08-09 15:04 Rev.: 49053

Add missing dt and V to mass source term for pressure equation.

4 lines of code changed in 1 file:

tsaad 2012-08-09 11:46 Rev.: 49052

use field_max_interior now that the buga now that the bugn now that the bugd now that the bug now that the bug is fixed in spatialops. also fix the input file for readfromfile expression as it was failing the RT due to a typo in the checkpoint interval. finally, add that test to the RT.

10 lines of code changed in 2 files:

jsutherland 2012-08-09 10:52 Rev.: 49051

Eliminate support for staggered scalar fields and diffusive fluxes.

49 lines of code changed in 7 files:

jsutherland 2012-08-09 10:52 Rev.: 49050

rip out some dead code.

0 lines of code changed in 1 file:

tsaad 2012-08-09 10:40 Rev.: 49049

rip out all staggered-scalar tests from Wasatch. Wasatch will no longer support staggered scalars which will help us reduce the number of initialized fields which in turn improves the Wasatch performance. This commit will break the RT and I will update the GS tomorrow morning. James will follow that with a commit to rip out the Wasatch code that handles staggered scalars.\n

2 lines of code changed in 2 files:

beckvermit 2012-08-09 08:25 Rev.: 49048

MIN_MASS_IN_A_CELL is now initialized. -Jacqueline

1 lines of code changed in 1 file:

banerjee 2012-08-08 17:04 Rev.: 49047

Removed kappa>0 checks.

17 lines of code changed in 2 files:

tsaad 2012-08-08 15:35 Rev.: 49046

remove the read from file test from the RT in anticipation of its failure... again for a reason that may be realted to extra/ghost cells. the input file should contain interior data only...

0 lines of code changed in 1 file:

tsaad 2012-08-08 10:23 Rev.: 49045

add regression test for the ReadFromFile expression.

2 lines of code changed in 1 file:

harman 2012-08-08 10:12 Rev.: 49044

more formating
name changes
begin_ -> d_begin
pField2 -> field2 <consistent with field>

57 lines of code changed in 1 file:

harman 2012-08-08 09:36 Rev.: 49043

variable name changes
var_ -> d_var



47 lines of code changed in 1 file:

harman 2012-08-08 09:00 Rev.: 49042

Added d_ to the global variables names.


65 lines of code changed in 1 file:

harman 2012-08-08 08:43 Rev.: 49041

formatting:
- added vertical & horziontal spaces
- aligment
- 2 space indentation
- no longer using archaic 80 column wrap rule. Monitors are bigger these days.

268 lines of code changed in 1 file:

tsaad 2012-08-07 20:42 Rev.: 49040

initialize a few temporary fields to clear the RT error. Will still need to update those gold standards tomorrow mornin.

12 lines of code changed in 1 file:

banerjee 2012-08-07 20:21 Rev.: 49039

Patch communication error fixed.

241 lines of code changed in 3 files:

banerjee 2012-08-07 18:09 Rev.: 49037

1) Added series expansioon for computing deformation gradient.
2) Move datawarehouse updates back to calling routines. Some
strange miscommunication between patches continues.

220 lines of code changed in 8 files:

harman 2012-08-07 16:04 Rev.: 49036

doAnalysis()
Open the file pointer only once and store it.

6 lines of code changed in 2 files:

tsaad 2012-08-07 14:17 Rev.: 49035

clean up some obsolete comments.

13 lines of code changed in 1 file:

sadeghirad 2012-08-07 14:06 Rev.: 49034

added the affine transformation to make particle distributions suitable for conforming CPDI simulations

63 lines of code changed in 3 files:

tsaad 2012-08-07 10:30 Rev.: 49033

comment some obsolete code that I forgot to merge in my recent commit.

12 lines of code changed in 1 file:

banerjee 2012-08-06 21:04 Rev.: 49031

Added possibility of using Arenisca_BB. The new version does not pass some of the
verification tests.

3 lines of code changed in 1 file:

tsaad 2012-08-06 19:30 Rev.: 49029

use the new BC operators that were recently added to SpatialOps. This commit also brings significant memory usage improvements to Wasatch and should fix the RT-increased-memory-usage error.\n

99 lines of code changed in 1 file:

banerjee 2012-08-06 18:00 Rev.: 49028

Corrected spelling of PrescribedDeformationFile tag.

2 lines of code changed in 1 file:

banerjee 2012-08-05 23:37 Rev.: 49027

Some more floating point checks.

35 lines of code changed in 2 files:

banerjee 2012-08-05 20:41 Rev.: 49026

1) Correct Newton iteration checks.
2) Added checks to see that the function X1 actually has zeroes.
3) Need to rerun verification to check everything still OK.

159 lines of code changed in 3 files:

banerjee 2012-08-03 23:18 Rev.: 49025

Added new Arenisca-type model for testing purposes.

3109 lines of code changed in 15 files:

ihunsaker 2012-08-03 13:54 Rev.: 49024

Allow for scattering/ non-scattering cases
via compiler directive in configure line.
Added error handling for scattering.

37 lines of code changed in 2 files:

harman 2012-08-03 08:03 Rev.: 49023

Only run explode2D_amr with optimized code.

1 lines of code changed in 1 file:

dav 2012-08-02 15:35 Rev.: 49022

Fix compilation on some pedantic platforms...

2 lines of code changed in 1 file:

dav 2012-08-02 15:29 Rev.: 49021

Allow for turning on ray scattering (for Isaac Hunsaker).

36 lines of code changed in 3 files:

dav 2012-08-02 14:32 Rev.: 49020

Look first for mt version of boost_serialization

2 lines of code changed in 2 files:

dav 2012-08-02 14:24 Rev.: 49019

Fix to find even newer versions of OSX correctly.

2 lines of code changed in 2 files:

jpeterson 2012-08-02 13:03 Rev.: 49017

Modifications to plug specific heat models in.
M CCA/Components/ICE/sub.mk
M CCA/Components/ICE/ICE.cc
M CCA/Components/ICE/ICEMaterial.cc
M CCA/Components/ICE/ICEMaterial.h

New specific heat models.
A CCA/Components/ICE/SpecificHeatModel
A CCA/Components/ICE/SpecificHeatModel/sub.mk
A CCA/Components/ICE/SpecificHeatModel/SpecificHeatFactory.cc
A CCA/Components/ICE/SpecificHeatModel/SpecificHeatFactory.h
A CCA/Components/ICE/SpecificHeatModel/Component.cc
A CCA/Components/ICE/SpecificHeatModel/Polynomial.cc
A CCA/Components/ICE/SpecificHeatModel/Component.h
A CCA/Components/ICE/SpecificHeatModel/Polynomial.h
A CCA/Components/ICE/SpecificHeatModel/SpecificHeat.cc
A CCA/Components/ICE/SpecificHeatModel/Debye.cc
A CCA/Components/ICE/SpecificHeatModel/SpecificHeat.h
A CCA/Components/ICE/SpecificHeatModel/Debye.h
M StandAlone/inputs/UPS_SPEC/ice_spec.xml


Example files for the new specific heat model.

A StandAlone/inputs/ICE/EOSData/HMXProductCv.xml
A StandAlone/inputs/ICE/EOSData/RDXProductCv.xml
A StandAlone/inputs/ICE/EOSData/NGProductCv.xml
A StandAlone/inputs/ICE/EOSData/TNTProductCv.xml
A StandAlone/inputs/ICE/EOSData/PETNProductCv.xml
A StandAlone/inputs/ICE/EOSData/NMProductCv.xml
A StandAlone/inputs/ICE/EOSData/CL-20ProductCv.xml

1010 lines of code changed in 15 files:

tsaad 2012-08-02 11:51 Rev.: 49015

rip out some redundant regression tests.

0 lines of code changed in 1 file:

jsutherland 2012-08-02 11:19 Rev.: 49014

silence some compiler warnings.

18 lines of code changed in 4 files:

tsaad 2012-08-02 10:42 Rev.: 49013

move a typedef outside a couple of if-statements for aesthetic reasons.

1 lines of code changed in 1 file:

tsaad 2012-08-02 10:30 Rev.: 49012

Throw an exception when wasatch-in-arches is enabled and the input file is missing extraCells.

12 lines of code changed in 1 file:

qymeng 2012-08-02 09:54 Rev.: 49011

Skip MPI Sends/Recvs for notCopyData Variables.

16 lines of code changed in 5 files:

tsaad 2012-08-02 09:20 Rev.: 49010

register Arches velocities with STATE_NONE. This will allow Wasatch to access arches velocities from either old or new datawarehouses.

24 lines of code changed in 1 file:

tsaad 2012-08-02 09:17 Rev.: 49009

fix subtle bug in the calculation of the convective flux and associated flux limiters. Previously, we were upwinding at both physical and processor boundaries. This introduced a spurious effect at the boundary and had the effect of a larger convective flux at the boundary. This fix will use central discretization at physical boundaries while staying with upwind at processor boundaries. NOTE: this fix will not work with staggered scalars. I will be changing to using memory windows in the flux limiter to avoid the complicated counters that cause problems with staggered scalars. This will break some convection regression tests as expected.

247 lines of code changed in 4 files:

ihunsaker 2012-08-01 14:32 Rev.: 49008

Scattering. This version has been verified against a
benchmark case described by R. Siegel. Documentation
and regression test to come shortly.

165 lines of code changed in 2 files:

harman 2012-08-01 07:48 Rev.: 49007

added "." to the path so it will find the doComponentTests scripts.

1 lines of code changed in 1 file:

July 2012 »

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