October 2012 Commit Log

Number of Commits:
139
Number of Active Developers:
17
tsaad 2012-10-31 22:40 Rev.: 49513

Resolve the issue of having different dependencies on different patches for a given task. The solution consists of exposing all additional dependencies across all patches.

103 lines of code changed in 14 files:

qymeng 2012-10-31 15:48 Rev.: 49512

fix a subscheduling related timing bug

0 lines of code changed in 2 files:

tsaad 2012-10-31 14:36 Rev.: 49511

Allow the pressure expression to set the filename of the Hypre solver output files. Append those output filenames with the simulation time, rkstage, and patch ID. Also allow the pressure to be cleaved from its children now that we fixed the timestep in the SetCurrentTime expression.

21 lines of code changed in 4 files:

jsutherland 2012-10-31 12:16 Rev.: 49510

Update to conform to modified ExprLib interface.

1 lines of code changed in 1 file:

qymeng 2012-10-30 11:01 Rev.: 49507

add ComponentTiming to environmentalFalgs.txt

0 lines of code changed in 2 files:

jthornoc 2012-10-30 10:50 Rev.: 49506

Updates to the inert mixing transform.
Change checkpoint output for coal_pipe_test to fix failing restart test.

0 lines of code changed in 2 files:

guilkey 2012-10-30 10:00 Rev.: 49505

Add requires for pParticleIDLabel

1 lines of code changed in 1 file:

jthornoc 2012-10-26 16:53 Rev.: 49504

EqnBase.h: Fix a bug in the initialization to use point->getCellPosition rather
than trying to compute it locally.

BCUtil: Fix a memory bug that showed up when doing strict memory
testing.

9 lines of code changed in 3 files:

harman 2012-10-26 16:20 Rev.: 49503

Script that extracts the hypre timer information over multiple timesteps
and computes the averages. It will also output 3 different files in
different formats that can be easily parsed in a scaling study.
This is basically John's extract script taken a step further.


313 lines of code changed in 1 file:

tsaad 2012-10-26 15:14 Rev.: 49502

forgot to remove a few cout comments.

0 lines of code changed in 2 files:

tsaad 2012-10-26 15:11 Rev.: 49501

fix a subtle bug in the recently committed fix for initializations with volumeFractions.

91 lines of code changed in 3 files:

harman 2012-10-26 07:27 Rev.: 49500

Fixed the calculation of FIRST_DAY. I have no idea why it just stopped working.

0 lines of code changed in 4 files:

tsaad 2012-10-25 20:49 Rev.: 49499

Allow users to specify a list of moments for initialization moment transport problems (QMOM) instead of creating a BasicExpression for each moment. This will reduce some production input files by hundreds of lines. Allow the transport equation base class to be aware of any volume fractions. If volume fractions exist, then automagically multiply the initial condition by the volume fraction. This will allow reduce clutter in the input file by avoiding the creation of ExprAlgebra as well as using force_on_graph. Update the QMOM input files to reflect those recent changes. cleanup some output information. Alex: you will need to update the mineralization input files.

85 lines of code changed in 5 files:

jthornoc 2012-10-25 17:21 Rev.: 49497

Some leftovers in TabPropsInterface.cc.

0 lines of code changed in 2 files:

jthornoc 2012-10-25 16:55 Rev.: 49496

** Big Changes **

1) Added more access function to BC data in BCUtil. This should help in determining if <value> is a double, string, or vector. I didn't see any previous method that provided this information.

2) ClassicTables now require explicit definitions of each independent variable, model, through either <TransportEqn> or <PropertyModel> definitions in the input file. (currently scalar variance is the one exception, where the old normalizedScalarVar can still be used).

3) Added a <PropertyModel> for heat_loss.

4) Transport equations can now have a "Tabulated" attribute spec for boundary conditions. The <value> should be specified as the string identifier for the dependent variable the user wants to use as the boundary condition. Note that this only works for Dirichlet conditions as Neumann conditions don't require a table lookup.

5) Transport equations can now be initialized to a tabulated dependent variable based on the initialized independent variable space.

6) Pulled some weeds, including removing the noSolve function. This is the beginning of complete removal of the dummySolve. Still has a lot more weeds to go.

7) Changed some input files

** some tests ( methane_jet, heptane_pipe, coal_pipe) will fail and will need GS replacement because of the new heat loss calculation and the changes to the input files **

1072 lines of code changed in 33 files:

tsaad 2012-10-25 16:23 Rev.: 49495

allow getting only a subset of multiple_doubles from PorblemSpec::get

0 lines of code changed in 4 files:

tsaad 2012-10-25 12:18 Rev.: 49494

Fix a serious bug in ProblemSpec::get(vector<double>) and get(vector<string>). This is used when parsing MULTIPLE_DOUBLES. The current code assumes that the multiple doubles are surrounded by brackets [ ... ]. If the brackets are NOT provided, the last entry in the list of doubles is NOT returned. This requirement for the brackets is NOT enforced in the problemspecreader or in other parts of the code. In fact, different parts of the code use different techniques to parse the multiple doubles, hence the reason that this bug was able to slip through.

1 lines of code changed in 1 file:

guilkey 2012-10-24 15:28 Rev.: 49493

Change <= to <

0 lines of code changed in 2 files:

harman 2012-10-24 12:28 Rev.: 49492

added hypre style timers to the creation HA, HX & HB.

29 lines of code changed in 1 file:

jthornoc 2012-10-23 22:02 Rev.: 49491

Now building PCTransport. It still doesn't do anything.

196 lines of code changed in 4 files:

guilkey 2012-10-23 18:18 Rev.: 49490

Remove extra cbrt from each file.

6 lines of code changed in 5 files:

guilkey 2012-10-23 18:13 Rev.: 49489

Add subcycling to the computation of F, and remove an extra cbrt call that
wasn't needed.

20 lines of code changed in 1 file:

harman 2012-10-23 12:20 Rev.: 49488

Added a script to plot nodal variables for both single level and multi-level udas.
Useful tool to identify differences in solution at different timesteps.

187 lines of code changed in 1 file:

harman 2012-10-23 12:07 Rev.: 49487

Save the plot to a png file, not pipe it to the display.

3 lines of code changed in 3 files:

jas 2012-10-22 23:47 Rev.: 49484

Update the copyright notice to include the MIT License and fix the formatting
issues with the spurious "\".

11531 lines of code changed in 4495 files:

amir 2012-10-22 18:46 Rev.: 49480

Two fixes regarding to the changes in ExprAlgebra that Tony committed. We need to specify the density STATE in the initialization method of the solution variables (both the momentum and the scalar)

2 lines of code changed in 2 files:

harman 2012-10-22 16:53 Rev.: 49477

The user can now pass in multiple files.

0 lines of code changed in 2 files:

harman 2012-10-22 10:05 Rev.: 49473

If the "do_performance_test" flag is selected log the simulation
run time to a file and plot it. Make this plot accessible to
users via the web page.

Note you can't perform uda_comparisons and performance
tests together. With performance testing all file I/O is turned off.


115 lines of code changed in 25 files:

harman 2012-10-19 15:47 Rev.: 49472

gnuplot file for plotting the run time history.

86 lines of code changed in 1 file:

harman 2012-10-19 15:09 Rev.: 49471

The user now has the option to clear any logs (highwater memory or simulation run time (soon))
when they replace the gold standards.

0 lines of code changed in 4 files:

tsaad 2012-10-19 14:21 Rev.: 49470

simplify and expand the ParabolicBC specification. Now allow users to specify a parabola centered on a face by specifying the center, value at center, and height.

34 lines of code changed in 2 files:

tsaad 2012-10-19 13:58 Rev.: 49468

simplify and expand the interface of the ExprAlgebra interface. Allow an arbitrary number of expressions to be operated upon. The only caveat is that all source expressions have to be of the same field type, which is the case for the majority of problems. When this is not the case (see initialiation of momentu, density, and velocity), the InterpolateExpression can be used to move fileds around.

92 lines of code changed in 4 files:

tsaad 2012-10-19 12:57 Rev.: 49467

Remove an ambigious requirement to create a directory named 'output' in which hypre saves its data when PRINTSYSTEM is defined. This filename/directory should be set by the component.

3 lines of code changed in 1 file:

tsaad 2012-10-19 12:56 Rev.: 49466

fix hypre struct printout when using PRINTSYSTEM for the linear solver.

3 lines of code changed in 1 file:

guilkey 2012-10-18 18:06 Rev.: 49465

Implemented the Gershgorin circle theorem for finding bounds of eigenvalues.
Usage, e.g.:

double minB, maxB;
pStress.gershgorinBounds(minB,maxB);


25 lines of code changed in 2 files:

ahumphrey 2012-10-18 14:39 Rev.: 49464

Change hostname of GPU RT machine in runSusTests.py

2 lines of code changed in 1 file:

ahumphrey 2012-10-18 13:30 Rev.: 49463

Fix configure line in GPU RT scripts.

2 lines of code changed in 1 file:

ahumphrey 2012-10-18 13:25 Rev.: 49462

Add in new host name for GPU tester. There are two possible right now (albion & kaibab), soon only one though.

6 lines of code changed in 4 files:

jthornoc 2012-10-18 12:13 Rev.: 49461

Rm'ing another unused property model.

Printing more information regarding the choice of turbulence model.

Somehow, CompDynamicProcedure didn't get all the PetscFilter ifdef's
cleaned up. This will change the answers as the previous RT results
which used this model essentially didn't have a turbulent viscosity.

2 lines of code changed in 5 files:

harman 2012-10-18 08:24 Rev.: 49460

deleted relic scripts that are no longer used or have been replaced by something better


moved removeBraces -> src/scripts
Updated all references to removeBraces


31 lines of code changed in 15 files:

harman 2012-10-17 16:25 Rev.: 49459

Another AMRMPM sanity check. Passing particles through the edges of the coarse
fine interface along all edges. The particles have with equal and opposite velocities
so the total momentum is 0,0,0.

1 lines of code changed in 1 file:

jthornoc 2012-10-17 16:04 Rev.: 49458

RM'ing an old, unused property model.
Adding a filter to the scalar variance model.
Fixing a warning.

9 lines of code changed in 6 files:

jthornoc 2012-10-17 16:04 Rev.: 49457

Deleting unused model.

0 lines of code changed in 3 files:

harman 2012-10-17 09:42 Rev.: 49456

advect_3L_3D.ups:
reduced size of computational domain and number of timesteps.
reduced size of sphere.

compare_uda:
- increased number of significant digits output when there's a failure.

1 lines of code changed in 1 file:

jsutherland 2012-10-17 08:11 Rev.: 49455

Fix an ordering issue with setting the time and time step in the time integrator.

10 lines of code changed in 1 file:

ahumphrey 2012-10-16 15:42 Rev.: 49454

Fix leftover escape characters in LICENSE file.

0 lines of code changed in 2 files:

tsaad 2012-10-16 15:08 Rev.: 49453

Reduce the amount of BC processing (and code) using an elegant way for setting BC values for staggered fields. Also cleanup some cout statements and obsolete comments.

40 lines of code changed in 6 files:

jsutherland 2012-10-16 14:29 Rev.: 49452

temporary fix to get the 2-level test working again. There are bugs lurking here...

5 lines of code changed in 1 file:

jsutherland 2012-10-16 14:02 Rev.: 49451

move some code around to clarify use of compiler directives.

10 lines of code changed in 1 file:

jsutherland 2012-10-16 14:02 Rev.: 49450

Resolve a linker problem (thanks Dav!) that cropped up on newer versions of boost when Arches pulls in wasatch or tabprops.

3 lines of code changed in 2 files:

jsutherland 2012-10-16 14:02 Rev.: 49449

- Set time and time step value on each patch. Still tracking a bug here, but this will make it a bit easier.
- lots of code cleanup to remove some now obsolete methods and also remove some un-needed includes

90 lines of code changed in 4 files:

austin 2012-10-16 13:23 Rev.: 49448

Commiting J. Colovos's changes to Arenisca.
-D. Austin

1725 lines of code changed in 2 files:

harman 2012-10-16 13:06 Rev.: 49447

remove commented out lines from tst files before processing them.
ignore blank lines.

0 lines of code changed in 4 files:

jthornoc 2012-10-16 12:34 Rev.: 49446

Should not be deleting this array here.

0 lines of code changed in 1 file:

jsutherland 2012-10-16 10:53 Rev.: 49445

Initialization doesn't really need a nonzero time step, so relax an assertion a bit.

1 lines of code changed in 1 file:

jsutherland 2012-10-16 08:51 Rev.: 49444

Rework SetCurrentTime a bit to remove SimulationState from it. TimeStepper now holds a pointer to the SimulationState so that it can set appropriate values in SetCurrentTime.

48 lines of code changed in 5 files:

jthornoc 2012-10-15 15:19 Rev.: 49443

Initializing mass_flow_rate to zero for walls.
Adding some print statments at startup to show explicit details of
boundary condition information.

7 lines of code changed in 1 file:

harman 2012-10-15 14:51 Rev.: 49442

computeAndIntegrateAcceleration()
- rearrange gacceleration calc.

applyExternalLoads()
- added computeExternalForceForMMS()

setGridBoundaryConditions()
- removed second expression from conditional. setBCs if the patch has a boundary face.

interpolateToParticles and Update()
- no longer modifying pvolume. This will be added when burning particles is added.

# This WILL change all the AMRMPM answers.

33 lines of code changed in 1 file:

beckvermit 2012-10-15 14:48 Rev.: 49441

Corrected error so simulations can be run without using crack model

4 lines of code changed in 1 file:

jthornoc 2012-10-15 13:43 Rev.: 49440

1) Trimming some dead wood. Unused files have been boxed and moved to the Attic/ for future reference.
2) Removing petsc completely from Filter.cc. This trimmed down the file considerably and removed the extra dangly bits among several files as a result.
3) Removing the #ifdef PetscFilter
4) Now allowing for no <Turbulence> spec -- defaults to "none".
5) All turbulence models now have a common problemSetup (problemSetupCommon) located in the base class definition.
6) Removed large sections of code in the turbulence models that dealt with #ifndef PetscFilter. It looks like the new filter, without petsc, should cover this scenario just fine.
7) Added scale-similarity scalar variance model. This isn't complete yet.

My local RT is messed up but I don't believe answers will change. Will review after the changes are submitted to ensure any changes are valid.

470 lines of code changed in 23 files:

jthornoc 2012-10-15 13:43 Rev.: 49439

Converting IncDynamicProcedure to the new filter. Next step is to
remove the #ifdef PETSC_FILTER for good.

Removing CompLocalDynamicProcedure. Looks to be out of date and never
used.

27 lines of code changed in 6 files:

jthornoc 2012-10-15 13:43 Rev.: 49438

Simplifying the filter interface a bit in preparation of getting rid of
the PETSC filter.

Adding a scale-similarity, scalar variance model.

79 lines of code changed in 6 files:

jthornoc 2012-10-15 13:43 Rev.: 49437

Actually add the files this time for the algebraic scalar dissipation
rate.

295 lines of code changed in 2 files:

jthornoc 2012-10-15 13:43 Rev.: 49436

Adding an algebraic expression for the scalar dissipation rate.

9 lines of code changed in 2 files:

jthornoc 2012-10-15 13:43 Rev.: 49435

Adding empty functions for the PC model.

192 lines of code changed in 2 files:

jthornoc 2012-10-15 13:43 Rev.: 49433

1) Setting the density guess = true for table mixture fractions.
Note that this only applies to mixture fractions identified in the table header and
enthalpy. It doesn't apply for any other transported quantity that might require
density guess = true.

2) Adding a variable transformation for "inert mixing", wherein inert streams may be
mixed into the tabulated state-space ex post facto when using the LES constrained rate
model. This required a dynamic_cast which wasn't as elegant as I would have liked. May need to
review this later.

413 lines of code changed in 4 files:

jpeterson 2012-10-15 09:59 Rev.: 49432

Updated license to conform to new standard.

32 lines of code changed in 2 files:

harman 2012-10-15 09:19 Rev.: 49431

pulled tab weeds.

applyExternalLoads()
- formatting, 2 space indentation.

46 lines of code changed in 1 file:

harman 2012-10-15 08:35 Rev.: 49430

disks_AMR_*: deleted redundant input files.

MPM.py: using 4 procs/cores for advect_3L_3D test.

advect_3L_3D.ups: increased particle resolution to avoid crappy numerics
with linear shape function. Saving less data.



1 lines of code changed in 1 file:

harman 2012-10-15 08:28 Rev.: 49429

turn advect_3L_3D back on. Using exact comparisons

1 lines of code changed in 1 file:

harman 2012-10-15 08:24 Rev.: 49428

coarsenNodalData_CFI(), coarsenNodalData_CFI2(), interoplateToParticlesAndUpdate_CFI()
- using getRegion() instead of get() to pull variables from the dw. On multiprocessor
runs get() throws an assert, even though getRegion() and get() are
equivalent in this case.

* this should not change the answers.

34 lines of code changed in 1 file:

jas 2012-10-15 08:13 Rev.: 49427

Change the bigmac fix to mac_zlib_fix.

0 lines of code changed in 2 files:

harman 2012-10-15 07:31 Rev.: 49426

Removed tests with resolution > 32^3. All tests are now serial.
Linear only works with A = 0.001

0 lines of code changed in 8 files:

harman 2012-10-15 07:26 Rev.: 49425

missing comma

1 lines of code changed in 1 file:

jpeterson 2012-10-14 11:32 Rev.: 49424

Mesoscale burn model.

1123 lines of code changed in 4 files:

tsaad 2012-10-14 01:50 Rev.: 49423

fix typo in Wasatch's RT test.

2 lines of code changed in 1 file:

tsaad 2012-10-13 23:14 Rev.: 49422

add regression test for using the same modifier expression on multiple faces (same normal) on a single patch.

2 lines of code changed in 1 file:

tsaad 2012-10-13 21:51 Rev.: 49420

rename bigmac_hack to a more generic name. This script fixes the problem with the zlib path when macports is used on a mac.

31 lines of code changed in 2 files:

tsaad 2012-10-13 21:48 Rev.: 49419

Allow BoundaryCondition expressions to handle multiple pointfields so that we can avoid duplicating expressions (i.e. unique nametags) on same patches.

7 lines of code changed in 1 file:

tsaad 2012-10-13 16:16 Rev.: 49418

fix bug in realizable qmom (based on discussions with Alex). change nomenclature also.

28 lines of code changed in 1 file:

tsaad 2012-10-13 14:39 Rev.: 49417

a few fixes to the Warches turbulence model interface. Remove redundant multiplication of density since wasatch is using the Arches density now. Also allow Warches to run with Arches-proper turbulence models.

10 lines of code changed in 3 files:

tsaad 2012-10-13 14:34 Rev.: 49416

enforce realizability on Vreman model when using embedded boundaries. This is much more efficient than multiplying with a volume fraction (which increases dependencies and number of operations).

13 lines of code changed in 2 files:

tsaad 2012-10-13 08:42 Rev.: 49415

Allow ProblemSpec to identify scientific notation as a NumberType. credit: Dav.

1 lines of code changed in 1 file:

jas 2012-10-12 16:59 Rev.: 49413

Squashed commit of the following:

commit a1e8c675d139003247378067ec0431806029cb14
Merge: 5e29398 49ca967
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:36:18 2012 +0000

Update branch with latest changes from trunk.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49412 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 5e293985e95fc70fd682fbf31fb93d7b72f1108e
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:36:07 2012 +0000

Fix missing slash in installation guide.

Refactor the boost discovery mechanism in configure.ac.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49411 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit dd2caee9921c7d89791d866bccc1adbddf967f04
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:35:56 2012 +0000

Update build instructions for petsc and hypre for Fedora and CentOS.

Add BASE_LIB_DIR to the Boost section in configure.ac.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49410 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit c211e5394202174e69c4781b1bfd937e6a4e9e70
Merge: 425f4ca 6255204
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:35:14 2012 +0000

Update the release branch with changes from master.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49409 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 425f4caed59a4864374dbed64d46ade4d5fa5eee
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:33:39 2012 +0000

Remove all remaining pieces of the Angio component.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49408 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 5a92abece778059b6a1765ebd971b71744f64793
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:33:24 2012 +0000

Remove the Angio component.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49407 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 78e24afb3a187a45cf3669ff4588d096c8d38b8f
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:33:11 2012 +0000

Remove the Dan_files/ from the StandAlone/inputs/UintahRelease/.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49406 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit a938560edb0607e2e4aa63cb742b4b55b7f62cd7
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:33:01 2012 +0000

Notes about compiling boost and cmake and changes to the Centos section.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49405 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 0c7aa437777c336f92dd8be971c1e1a1cf01c367
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:32:53 2012 +0000

Add wasatch build dependences for opensuse.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49404 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 23b71be7d9ffd177b81f64498411584c055504e1
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:32:46 2012 +0000

Update dependencies for CentOS for building Wasatch.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49403 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 5b99e25a6306b02cc8ecb9baad84fa3d470e194f
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Oct 12 23:32:38 2012 +0000

Update packages necessary for compiling Wasatch.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49402 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit add8b7cbd6668abbe4f57f584dab24c8552b6da8
Author: tsaad <tsaad@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Tue Oct 2 20:36:32 2012 +0000

remove obsolete input files.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49330 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit f7ac87d4fd61d896eb1ba9f52a0b6cd2970783e5
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sun Sep 30 02:11:34 2012 +0000

Use the 1.5.0 git branch for the various Wasatch3P libraries.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49311 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 25156c6ba612634f5d66a5fb1be670fd5a82a23b
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sat Sep 29 03:41:39 2012 +0000

Remove the release file in the build_scripts/.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49308 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 94b484f3b209b8b5d8ee73bae0f9ba54c91592ef
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sat Sep 29 03:41:31 2012 +0000

Change == to = in all "test statements".

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49307 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit daeab4316362d0081fb8a66832734a3ffdfbff1f
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sat Sep 29 03:41:23 2012 +0000

Update to version 1.5.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49306 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit e3d51281308a5fbbde3f097e5826e85686fe9254
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sat Sep 29 03:41:15 2012 +0000

Update release files to include Wasatch component.

Add option to build Wasatch3P libraries for a particular hash tag.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49305 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 9a8451d8a5b1fbf36626b3727dad48d7184b5e6d
Merge: 984d356 0a25aa2
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Sat Sep 29 03:38:16 2012 +0000

Update copyright notice.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49304 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 984d3566f78e7e1c2b2c29ea0368451ae768119a
Author: jas <jas@aee3fe44-4ef4-0310-ac56-cc817e9d0e43>
Date: Fri Sep 28 18:39:29 2012 +0000

Uintah 1.5.0 Branch.

git-svn-id: https://gforge.sci.utah.edu/svn/uintah/branches/UintahRelease_1_5_0@49299 aee3fe44-4ef4-0310-ac56-cc817e9d0e43

commit 0a25aa2731b9c75fcf609f70093484af5be5f23a
Author: John Schmidt <john.schmidt@utah.edu>
Date: Thu Sep 27 01:50:47 2012 -0600

Updated copyright header.

46328 lines of code changed in 2254 files:

dav 2012-10-11 15:11 Rev.: 49401

Fix compiler warning: BurningCriteria is an array of integers, not floats.

1 lines of code changed in 1 file:

harman 2012-10-11 07:01 Rev.: 49400

advect_2L_Slabs: ignore restart tests until we figure out why answers are different.

1 lines of code changed in 1 file:

dav 2012-10-10 16:17 Rev.: 49399

Fix compiler warnings.

9 lines of code changed in 1 file:

tsaad 2012-10-10 09:51 Rev.: 49397

use std::fill to reduce code clutter when setting values for some vectors.

7 lines of code changed in 1 file:

harman 2012-10-09 16:52 Rev.: 49396

added sanity check for amrmpm.

2 lines of code changed in 1 file:

harman 2012-10-09 15:26 Rev.: 49395

Final touches on high water memory usage plots.
Saving the actual highwater usage in the goldStandards directories

plotMemUsage.gp
using 1024 instead of 1000 in converionn of bytes -> Kilobytes.

13 lines of code changed in 5 files:

tsaad 2012-10-09 13:49 Rev.: 49394

Allow arches to run without a turbulence model.

16 lines of code changed in 2 files:

tsaad 2012-10-09 13:48 Rev.: 49393

add regression test for realizable qmom. make some cosmetic changes to qmom.h \n

15 lines of code changed in 2 files:

harman 2012-10-09 13:21 Rev.: 49392

Only process plots nFoundPlots > 0.

Corrected paths in url links.
Polished and added comments.


28 lines of code changed in 1 file:

tsaad 2012-10-09 12:56 Rev.: 49391

Rework the QMOM interface. make it simpler and implement a more efficient realizable QMOM.

187 lines of code changed in 2 files:

qymeng 2012-10-09 11:01 Rev.: 49390

Bug fix: passing coarsestLevelwithParticles from scheduler instead of getting from local patches.

32 lines of code changed in 5 files:

awabboud 2012-10-09 10:14 Rev.: 49389

Small fix to digital filter generator to prevent nans from showing up in table sometimes.

7 lines of code changed in 1 file:

jthornoc 2012-10-08 18:56 Rev.: 49388

An ifdef in the wrong spot.

1 lines of code changed in 1 file:

jthornoc 2012-10-08 17:39 Rev.: 49387

Adding ifdefs back in until the filter can be completely petsc-free.

20 lines of code changed in 1 file:

harman 2012-10-08 17:24 Rev.: 49386

create a separate web page for each component's memory usage. There's already
enough text on the existing page.

Not working, but close....

11 lines of code changed in 1 file:

harman 2012-10-08 16:35 Rev.: 49385

Added date to memory plot

Copy memory plots to the public.html directory
Adding links to the plots on the web page.


23 lines of code changed in 2 files:

ihunsaker 2012-10-08 15:17 Rev.: 49384

Remove compiler warnings.

4 lines of code changed in 1 file:

harman 2012-10-08 12:19 Rev.: 49383

plotMemUsage.gp
- now plotting 1week, 2weeks, 1month, 3months, 6months and 1years worth of data

Added switch to control plotting. Don't plot unless it's a nightly RT test.

78 lines of code changed in 3 files:

harman 2012-10-08 12:16 Rev.: 49382

removed scirun from variable names

5 lines of code changed in 1 file:

jthornoc 2012-10-08 10:56 Rev.: 49381

Cleaning up warnings.

2 lines of code changed in 4 files:

jthornoc 2012-10-08 10:40 Rev.: 49380

Update to the new, non-PETSC based filter.

Switching compDynamicProcedure to use the new filter. This will change
the answers as the new filter is not switching to a box filter at
corners, unlike the old filter. I *believe* this filter to be more
consistent. Note that the default filter behavior near boundaries is to
renomalize the weights, like the PETSC filter. However, one can turn
off this behavior in the input file using the "new" filter.

126 lines of code changed in 7 files:

tsaad 2012-10-07 19:07 Rev.: 49379

help bigmac's buildbot by removing an include to a fortran file.

1 lines of code changed in 1 file:

kamojjala 2012-10-07 18:58 Rev.: 49378

Updated the AxisAligned MMS as there was mismatch for amplitude values while computing the exact solution and numerical solution

8 lines of code changed in 4 files:

tsaad 2012-10-07 18:34 Rev.: 49376

Allow Arches to use Wasatch's turbulence models. There is some work to be done here regarding the density. Currently, the turbulent viscosity will be multiplied by Arche's density, so make sure to specify a density of 1 in Wasatch. This will NOT pose a problem for Wasatch-in-Arches graphs that do not require density (i.e. mineralization project) << std::endl;

501 lines of code changed in 5 files:

tsaad 2012-10-06 22:45 Rev.: 49375

update taskinterface call for WARCHES to reflect recent changes in Wasatch.

0 lines of code changed in 1 file:

tsaad 2012-10-06 20:13 Rev.: 49374

turns out problemspecp->require (or get) does not parse space separated strings. revert back to local parsing. also add test for modifier expressions with parabolic bc.

7 lines of code changed in 1 file:

tsaad 2012-10-06 13:35 Rev.: 49372

Allow ProblemSpec to return a string vector from getAttribute. Use that to parse a list of tasks in Wasatch's forceongraph to reduce clutter in input files. test that with one of the existing input files.

63 lines of code changed in 4 files:

tsaad 2012-10-05 20:52 Rev.: 49371

turns out ProblemSpec can parse a list of strings so use that instead of doing it locally.

5 lines of code changed in 1 file:

harman 2012-10-05 17:09 Rev.: 49370

The y-axis is now in KBytes not Bytes.

Each test is generating a plot.

Still need to decide on a home for the memoryHistory files.

18 lines of code changed in 2 files:

harman 2012-10-05 16:43 Rev.: 49369

Added pieces to plot the highwater memory usage of every test.

83 lines of code changed in 3 files:

tsaad 2012-10-05 15:45 Rev.: 49367

add linearBC function. Also allow multiple tasklists in the BCExpression. This seems to reduce the amount of expressions in the input file significantly. This will be adopted by other expressions as well soon.

139 lines of code changed in 2 files:

jthornoc 2012-10-05 11:05 Rev.: 49366

Changing a bad naming convention for the turbulent viscosity.

49 lines of code changed in 8 files:

jthornoc 2012-10-05 10:08 Rev.: 49365

Moving Martin's water property code to the Arches directory.

1002 lines of code changed in 4 files:

wyxpuma 2012-10-04 18:59 Rev.: 49364

add the water properties calculation in StandAlone/water/

0 lines of code changed in 2 files:

jthornoc 2012-10-04 16:15 Rev.: 49363

Cleaning up some warnings after being notified by the warning-police.

0 lines of code changed in 8 files:

jthornoc 2012-10-04 15:44 Rev.: 49362

Zeroing out the fluxes at each DOM solve.

7 lines of code changed in 1 file:

dav 2012-10-03 15:09 Rev.: 49357

Fix compilation error... I assume this was just an oversight by whoever checked in the .cc file...

0 lines of code changed in 1 file:

ihunsaker 2012-10-03 14:48 Rev.: 49355

Made cellType general and dynamic, whereas before
the values of cellType that were recognized as walls
were hard coded.

10 lines of code changed in 1 file:

harman 2012-10-03 14:23 Rev.: 49352

Backed out previous commit which was causing explode2D_amr to hang.

5 lines of code changed in 1 file:

ihunsaker 2012-10-03 13:57 Rev.: 49347

Added benchmark testing for fluxes.

29 lines of code changed in 1 file:

harman 2012-10-03 09:57 Rev.: 49344

using 4 processors on HePlume test
nuked darwin test.

2 lines of code changed in 1 file:

awabboud 2012-10-03 09:13 Rev.: 49341

Fix turbulent inlet test to be multi-patch and decrease timesteps to speed up RT.

2 lines of code changed in 1 file:

tsaad 2012-10-02 18:15 Rev.: 49338

Graph-based boundary conditions are ready. There are some issues with boundary conditions that depend on coordinates due to Uintah's inability to handle different number of tasks on different patches.

375 lines of code changed in 6 files:

guilkey 2012-10-02 16:38 Rev.: 49335

Removing the Angio component from Uintah.

4 lines of code changed in 20 files:

harman 2012-10-02 14:25 Rev.: 49333

Kill a test if it exceeds the maximum allowable run time (dbg: 30min, opt: 15min)
We'll dial those numbers back once the RT running properly.

22 lines of code changed in 1 file:

tsaad 2012-10-02 10:49 Rev.: 49329

make the vreman and wale models more robust by proper handling of cases with zero denominators. This will break WALE wasatch test.

9 lines of code changed in 2 files:

tsaad 2012-10-02 08:47 Rev.: 49328

Change the way <value> is parsed in BoundCondFactory. Previous behavior used a try, catch statement assuming doubles otherwise a vector. This was modified to be more robust. Also add a functor_name option to allow developers to use functor on boundary conditions. This is simply a string value that may be obtained from bc objects.

76 lines of code changed in 5 files:

harman 2012-10-01 15:50 Rev.: 49327

interpolateParticlesToGrid_CFI() & computeInternalForce_CFI()
- expand the number of particles that are pulled from the coarse level
IF there is a neighboring low patch. Since the patch owns the low nodes
you must get coarse level particles further away from the low nodes at the CFI.
If you don't then the gAcceleration and gVelocity are not symmetrical
at patch boundaries on the CFI for a perfectly symmetric problem, advect_2L_3D_slabs.ups.

I can't wait for gimp.......

39 lines of code changed in 2 files:

dav 2012-10-01 15:40 Rev.: 49326


The Uintah Homebrew development team decided to remove the built in
(Unix file) permissions setting code in favor that the code would use
a users default permissions when it creates new UDA directories.
(This also means that the automatic setting of unix group has been
removed.)

A user is not in charge of their own permissions. If they would like
UDAs to be created such that other members of a specific group can
automatically see/read those files, then the user should do these things:

Set their umask to 022, and make sure the group set id bit is set for
the parent directory. You may want to set the umask in your dot login
script. Here is an example of the commands you might want to run:

umask 022
chmod g+s <data directory>

This gives: drwxr-sr-x

If, however, you want the data to be private, you might want to do the
following:

umask 077

This gives: drwx------

M CCA/Components/DataArchiver/DataArchiver.cc
M StandAlone/sus.cc

Removed the umask permission and group changing lines.

0 lines of code changed in 2 files:

harman 2012-10-01 14:36 Rev.: 49325

exchangeParticles() & relocateParticles()
patches->get(0)->getLevel() does not return the coarsest level!
Now using grid->getLevel(0). This fixes a multi-processor, multipatch, disappearing
particles bug

* This should not change the answers on 1L problems.

8 lines of code changed in 1 file:

guilkey 2012-10-01 13:17 Rev.: 49323

For axisymmetry, the nodal volume is not constant and needs to be computed
for each node.

14 lines of code changed in 1 file:

beckvermit 2012-10-01 11:16 Rev.: 49322

Modified JWL equation of state corrected. K0 was being initiallized twice so calculated value wasnt being used

2 lines of code changed in 1 file:

ahumphrey 2012-10-01 10:55 Rev.: 49321

Run with same # threads as decentralized CPU scheduler.

1 lines of code changed in 1 file:

guilkey 2012-10-01 10:31 Rev.: 49320

Fix memory leak introduced by Ali's CBDI commit on Friday.

2 lines of code changed in 1 file:

ahumphrey 2012-10-01 07:24 Rev.: 49317

Fix typo in environmentalFlags.txt for scheduler debug stream description.

1 lines of code changed in 1 file:

September 2012 »

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