December 2009 Commit Log

Number of Commits:
93
Number of Active Developers:
11
jthornoc 2009-12-30 00:32 Rev.: 45234

Adding some missing "VarLabel::destroy"s

0 lines of code changed in 6 files:

jthornoc 2009-12-28 14:51 Rev.: 45233

Added ability to initialize scalars in geometry obects.

0 lines of code changed in 4 files:

harman 2009-12-23 11:49 Rev.: 45232

Thrashing/hacking:

Added the idea of Levels and Patches in the initialization phase.


0 lines of code changed in 4 files:

jthornoc 2009-12-23 01:11 Rev.: 45231

Corrections to the boundary condition for setting the particle velocity to the gas velocity.

0 lines of code changed in 2 files:

jthornoc 2009-12-23 00:30 Rev.: 45230

Better logic for the new time integrator.

0 lines of code changed in 2 files:

jthornoc 2009-12-22 22:58 Rev.: 45229

Whoops. Forgot to add "if" on the delete.

5 lines of code changed in 1 file:

jthornoc 2009-12-22 19:08 Rev.: 45228

Hopefully cleaning up a few memory leaks.

16 lines of code changed in 8 files:

jthornoc 2009-12-22 17:08 Rev.: 45227

Deleting the boundary condition object.

0 lines of code changed in 2 files:

sshankar 2009-12-22 16:09 Rev.: 45226

Modified the sub.mk file to include xml2info

0 lines of code changed in 2 files:

harman 2009-12-22 13:38 Rev.: 45225

copied single level composite grid scripts to Multilevel directory.

1744 lines of code changed in 5 files:

luitjens 2009-12-22 13:29 Rev.: 45224

changed > to >=. This should fix an RT error that occurs when outputInitTimestep is enabled.

0 lines of code changed in 2 files:

harman 2009-12-22 11:31 Rev.: 45223

Initial commit for multilevel amrmpm
This is just a copy of amrmpm

734 lines of code changed in 1 file:

harman 2009-12-21 16:20 Rev.: 45221

pulled initialization functions out of AMRMPM.m and put them in
initializationFunctions.m


269 lines of code changed in 4 files:

harman 2009-12-21 16:19 Rev.: 45220

Changes so you can read in a file that contains the L2norm and maxError
to compute the order of accuracy

0 lines of code changed in 2 files:

sshankar 2009-12-21 15:52 Rev.: 45219

Changes to the molecule plot

91 lines of code changed in 9 files:

harman 2009-12-18 17:18 Rev.: 45218

added hack so you can skip sections of the computational domain.

0 lines of code changed in 2 files:

harman 2009-12-18 16:27 Rev.: 45217

2nd order accuracy for MMS problem
A = 0.05
t_initial = 0.0
t_final = wavelength
constant resolution

95 lines of code changed in 4 files:

guilkey 2009-12-18 13:46 Rev.: 45215

Add the ability to get out the reaction force experienced by the rigid object(s)
when specified contact is used. One needs to add:
<save label="RigidReactionForce"/>
to the DataArchive section of the input file to obtain this output in the form
of a .dat file.

0 lines of code changed in 6 files:

jthornoc 2009-12-18 12:24 Rev.: 45214

Turning on exactComparison for these tests.

0 lines of code changed in 2 files:

harman 2009-12-18 11:28 Rev.: 45213

order of accuracy result for the MMS problem, PPC:2, A = 0.001
NN = [22, 46, 64, 130, 262, 514]

9 lines of code changed in 1 file:

harman 2009-12-17 19:07 Rev.: 45212

Now using initializeRegions()

Took out most of the hard coded code. You should be able to switch between
plots of the linear & gimp functions by changing "interpolation"

added asci-art, hopefully it's a little clearer what is going on.

0 lines of code changed in 2 files:

harman 2009-12-17 19:02 Rev.: 45211

More informative error messages.

PositionToClosestNodes()
- Can now handle computational domains that have regions that are negative.

0 lines of code changed in 2 files:

harman 2009-12-17 19:00 Rev.: 45210

define a new region used specifically for plotShapeFunction.m

NN is now computed in initializeRegions.m

Define extra cells on the outermost regions (not used)

31 lines of code changed in 2 files:

jthornoc 2009-12-17 18:40 Rev.: 45209

MPMArches.cc:
Moved setAreaFraction from MPMArches.cc to ExplicitSolver.cc (with an "if d_MAlab" -- i.e., only called every time step if mpm is present.)

Arches.cc:
Added WestbrookDryer.h
Added initialization for "extra local labels" for source terms
Added some print statements for the header of the output stream
Added WestbrookDryer model registration

ArchesLabel.cc and .h:
Added a new label for mixture molecular weight (from Table)

BoundaryCond_new.cc:
Fixed a bug with the material index

ExplicitSolver.cc:
Added the setAreaFraction call that was moved from MPMArches

ExplicitTimeInt.h:
Added a check for zero density (inside a wall). I am planning on moving this division by density out of the time integrator and into the scalar eqn where it belongs. More to come...

Properties.cc, NewStaticMixingTable.*, Stream.h:
Added the mixture molecular weight and access to it

SourceTerms/:
Added a new Source Term (WestbrookDryer)
Added a virtual function for initializing the sources and any local dependent functions the source might require
Added "extraLocalLabel" vector for the sources in the base class.

ScalarEqn.cc:
Names the "old" transport label with the correct name.
Initialized Conv and Diff at the start of a time step to zero.
Added the clipping function at the end of the averaging.
Added dummyInit of RHS, FCONV, FDIFF
Grabbing the right old variable for copying in the dummyInit

DQMOMEqn.cc:
Passing in a modifieable weight into getICVariables...we may want to handle the cutoff differently
Initializing Fconv and Fdiff to zero at the start of every t_step.

PartVel.cc:
Changed the default behavior of the particle velocities on the boundary to require (user specified) values from the input file.

700 lines of code changed in 48 files:

guilkey 2009-12-17 15:26 Rev.: 45208

Add new User Inputs (UIs) to the outputProblemSpec code.

0 lines of code changed in 2 files:

leavy 2009-12-16 20:54 Rev.: 45207

Fix accidentally committed bug.

1 lines of code changed in 1 file:

leavy 2009-12-16 20:40 Rev.: 45206

Modifications to accomodate new release of Kayenta.

189 lines of code changed in 5 files:

leavy 2009-12-16 19:35 Rev.: 45205

Add requires for delT in setPrescribedMotion.

0 lines of code changed in 2 files:

harman 2009-12-16 17:56 Rev.: 45204

pulled out all of the shape functions and placed them in a separate .m file.

Something is not working correctly with plotShapeFunctions.

495 lines of code changed in 3 files:

harman 2009-12-16 16:05 Rev.: 45203

The initial time is now a variable, t_initial.

Removed sections of debugging plots.

20 lines of code changed in 1 file:

harman 2009-12-16 15:54 Rev.: 45202

added debugging functions
MMS_acceleration()
MMS_dFdx()
MMS_divergenceStress()

44 lines of code changed in 1 file:

harman 2009-12-16 13:38 Rev.: 45201

script that generates an index.xml from a collection of udas. It warns the user
if the variable list is not the same amoung all the udas.

usage: makeMasterUda < list of uda files >

How to use:

mkdir <masterUda>
cd <masterUda>
makeMasterUda ../uda.000 ../uda.001 ../uda.00N

This should have been checkedin years ago

110 lines of code changed in 1 file:

harman 2009-12-15 17:11 Rev.: 45200

SerialMPM: errorEstimate()
MPMICE: coarsenDriver_std()
MPMICE: coarsenDriver_massWeighted()
ICE: fineToCoarseOperator()

Added logic to prevent trying to access data that is not available.

This should not change the answers.

46 lines of code changed in 7 files:

guilkey 2009-12-14 19:16 Rev.: 45199

Fix the surface normal calculation. Previously, there was an implicit
assumption that the cell size was the same in all directions.

0 lines of code changed in 4 files:

dav 2009-12-14 15:03 Rev.: 45198

Fix static build.

0 lines of code changed in 2 files:

jthornoc 2009-12-13 19:36 Rev.: 45196

Fixing a bug in the boundary check. I believe this only affected the super_bee scheme.

0 lines of code changed in 2 files:

charlesreid 2009-12-12 19:14 Rev.: 45195

Memory fix

0 lines of code changed in 2 files:

jas 2009-12-11 16:27 Rev.: 45193

Compiler warnings.

0 lines of code changed in 4 files:

harman 2009-12-10 17:07 Rev.: 45192

Restructuring:
- extForceP -> accl_extForceP
- moved all MMS related functions to MMS.m, and using function handles.

- use structures to minimize the function call lengths.

211 lines of code changed in 2 files:

dav 2009-12-09 18:29 Rev.: 45191

Fix display of multi-level global min/max. Fix error message when requested timestep out of bounds.

0 lines of code changed in 4 files:

harman 2009-12-09 17:57 Rev.: 45190

MMS_displacment()
MMS_deformationGradient()
MMS_velocity()
MMS_bodyForce
-Now dividing all trigometric functions by h or bar_length.
- dividing h in leading equation terms.

Pull out multiplcation of the bodyForce by massP to be consistent with
interpolate particles to grid section.

This shouldn't change the answers

62 lines of code changed in 1 file:

harman 2009-12-09 14:51 Rev.: 45189

Added initialCondition function.

Order of analysis for Matlab:ICE is now working for Toro's test1 problem.


96 lines of code changed in 10 files:

harman 2009-12-09 12:29 Rev.: 45188

Added matlab scripts/functions to compute the order of accuracy of
the matlab version of ice.

80% working

196 lines of code changed in 3 files:

harman 2009-12-08 18:47 Rev.: 45187

changes so ice can be called from an order of accurary script.

18 lines of code changed in 2 files:

harman 2009-12-08 18:37 Rev.: 45186

remove the temporary files

0 lines of code changed in 2 files:

harman 2009-12-08 18:36 Rev.: 45185

increase the array allocatio of gradLim and grad_x so you can plot
these variables against x_CC

0 lines of code changed in 4 files:

harman 2009-12-08 18:35 Rev.: 45184

dust this script off.

0 lines of code changed in 2 files:

harman 2009-12-07 19:02 Rev.: 45183

matlab script that plots matlab and uintah results.

88 lines of code changed in 1 file:

harman 2009-12-07 19:01 Rev.: 45182

- fixed x_FC calculation
- removed 1e-7 timestep hardcoding
- now writing CC and FC data to separate files on the final timestep

Matlab results compare pretty close to uintah result for first order advection
scheme. 2nd order hasn't been tested.


96 lines of code changed in 2 files:

harman 2009-12-07 18:57 Rev.: 45181

load face centered data
cosmetics

12 lines of code changed in 1 file:

dav 2009-12-07 18:15 Rev.: 45180

M ComponentFactory.cc

Make 'unknown component' error message a little more clear.

0 lines of code changed in 2 files:

dav 2009-12-07 17:42 Rev.: 45179


Fix the _static_ build when ARCHES is turned off (ie, when configure'd
with USE_ARCHES=no). Mostly this has to do with also disabling the
SpatialOps component when ARCHES is off.

M CCA/Components/Parent/sub.mk
M CCA/Components/Parent/ComponentFactory.cc
M CCA/Components/sub.mk

- Don't use SpatialOps if Arches is turned off.

M StandAlone/sub.mk

- Don't use SpatialOps if Arches is turned off.
- For some reason libraries were listed as CCA_Components_Parent
(using '_'s...) not sure how this works (perhaps the '/' that is
supposed to be there is replaced by the build system with '_'?)
Anyway, changed this (back?) to the standard/consistent way (using
'/').

77 lines of code changed in 7 files:

jas 2009-12-07 17:11 Rev.: 45178

Compiler warning.

0 lines of code changed in 2 files:

jas 2009-12-07 17:08 Rev.: 45177

Compiler warnings.

0 lines of code changed in 2 files:

jas 2009-12-07 16:55 Rev.: 45176

Compiler warning.

0 lines of code changed in 2 files:

jas 2009-12-07 16:29 Rev.: 45175

Fix compiler warnings.

0 lines of code changed in 2 files:

jas 2009-12-07 16:15 Rev.: 45174

Add virtual destructor.

1 lines of code changed in 1 file:

jas 2009-12-07 15:54 Rev.: 45173

Add virtual destructor.

0 lines of code changed in 2 files:

jas 2009-12-07 15:46 Rev.: 45172

Fix bug in CNHDamage.cc which initialized the seed data with the wrong data.

Fix compiler warnings.

3 lines of code changed in 3 files:

charlesreid 2009-12-07 00:57 Rev.: 45170

Changing delete's to delete[]'s

4 lines of code changed in 1 file:

charlesreid 2009-12-05 22:42 Rev.: 45169

Fixing one more compiler warning

1 lines of code changed in 1 file:

jas 2009-12-05 22:18 Rev.: 45168

The 4.2 compiler will not trigger a build unless the 4.1 compiler succeeds.

0 lines of code changed in 2 files:

jas 2009-12-05 22:10 Rev.: 45167

Add debug builds for 4.1 and 4.2 compilers on inferno.

78 lines of code changed in 1 file:

jas 2009-12-05 21:50 Rev.: 45166

If compile fails, try again.

0 lines of code changed in 2 files:

jas 2009-12-05 21:39 Rev.: 45165

Add option to change compiler version. Defaults to g++.

7 lines of code changed in 1 file:

charlesreid 2009-12-04 16:01 Rev.: 45164

Fixing compiler warning

18 lines of code changed in 1 file:

jpeterson 2009-12-04 15:16 Rev.: 45163

Another stupid mistake--fixed variable name

0 lines of code changed in 2 files:

jpeterson 2009-12-04 15:13 Rev.: 45162

Forgot a comma

1 lines of code changed in 1 file:

jpeterson 2009-12-04 15:09 Rev.: 45161

Add MPM version of Murnahan EOS via Constitutive Model.

586 lines of code changed in 6 files:

luitjens 2009-12-04 11:08 Rev.: 45160

Null constructor...

0 lines of code changed in 2 files:

luitjens 2009-12-04 11:01 Rev.: 45159

Avoid another null constructor

1 lines of code changed in 1 file:

luitjens 2009-12-04 10:50 Rev.: 45158

Avoid calling the null constructor for a varDBType iterator. This seems to cause problems in gcc4.1.

2 lines of code changed in 1 file:

harman 2009-12-03 18:16 Rev.: 45157

-cosmetics
-changes for direct comparison with uintah code.

I haven't found where the discrepency is between the two codes.

63 lines of code changed in 2 files:

harman 2009-12-03 18:14 Rev.: 45156

changes so we can directly compare uintah results with matlab results.

- fixed the timestep 1e-7 and only take 3 timesteps
- fixed error in the initialization code

13 lines of code changed in 1 file:

harman 2009-12-03 12:27 Rev.: 45155

Cosmetics- indentation

117 lines of code changed in 1 file:

harman 2009-12-03 12:23 Rev.: 45154

Added plotInterval variable.

MMS: L2norm & maxError are computed on every timestep

Added vertical lines at the node locations in two of the plots.

Current answers:
[L2_norm, maxError, NN, NP]=amrmpm('mms',0.1,22)
L2_norm = 7.5877320255472670E-04
maxError = 1.0740790335386496E-03


62 lines of code changed in 1 file:

jthornoc 2009-12-02 20:09 Rev.: 45152

Moved the diffusion calculation to the discretization class and removed all traces from DQMOMeqn and CCScalarEqn.
Also added doxygen comments to Discretization_new.h.

181 lines of code changed in 7 files:

dav 2009-12-02 16:32 Rev.: 45151


Updates to puda to display global min/max on a per timestep basis and
to add the '-brief' option to only show the global min/max info.

M puda/puda.h
M puda/puda.cc

- Added 'be_brief' and did some white space cleaning.
- Don't display global min/max in puda.cc as we need to do it in varsummary so we can display
them on a per timestep basis.

M puda/varsummary.h
M puda/varsummary.cc

- Implement the 'be_brief'
- Show global min/max each timestep.


140 lines of code changed in 7 files:

harman 2009-12-02 15:32 Rev.: 45150

Previous commit was only a partial commit.

moved computeDeformationGradient() & computeStress() to
just above project changes back to particles.


9 lines of code changed in 2 files:

harman 2009-12-02 14:43 Rev.: 45149

moved computeDeformationGradient() & computeStress() to
just above project changes back to particles.


12 lines of code changed in 1 file:

harman 2009-12-02 14:04 Rev.: 45148

fixed copy-paste error

0 lines of code changed in 2 files:

harman 2009-12-02 11:54 Rev.: 45147

split computeStressFromVelocity function into

computeDeformationGradient()
computeStress()

in preparation for reordering the timestep (USL)

16 lines of code changed in 1 file:

harman 2009-12-02 11:23 Rev.: 45146

Cleanup
- moved initialization of the regions to a separate function
- removed all the debugging output for that advect problem.

188 lines of code changed in 2 files:

charlesreid 2009-12-01 20:46 Rev.: 45144

Removing debug print statement

0 lines of code changed in 1 file:

charlesreid 2009-12-01 20:41 Rev.: 45143

M CCA/Components/Arches/sub.mk
Fixing duplicate line added in a previous commit

M CCA/Components/Arches/DQMOM.h
M CCA/Components/Arches/DQMOM.cc
Adding a <calcConditionNumber> tag - this will be useful and necessary if we want condition numbers but the solver isn't doing an SVD to solve AX=B
Clarifying names of solvers:
- "Lapack-invert" uses a Lapack decomposition and inversion (dgetrf and dgetri)
- "Lapack-svd" uses a Lapack singular value decomposition to solve AX=B (eliminated the "SVD" solver type)
- "LU" uses Crout's Method with partial pivoting
Fixing up the DEBUG_MATRICES blocks
Adding a maximum condition number solver constraint

M StandAlone/inputs/UPS_SPEC/arches_spec.xml
Updating tags corresponding to clarified linear solver names

M StandAlone/inputs/ARCHES/DQMOM_regression/dqmom-scalar_test2c.ups
This test was redundant, but it's now testing the "Lapack-invert" solver

M StandAlone/inputs/ARCHES/DQMOM_regression/dqmom-scalar_test3.ups
M StandAlone/inputs/ARCHES/DQMOM_regression/test_descriptions.lyx
The "SVD" solver is now the "Lapack-svd" solver; test 2c is now testing the "Lapack-invert" solver

255 lines of code changed in 5 files:

jthornoc 2009-12-01 19:08 Rev.: 45142

1) Added the setAreaFraction method to MPMArches.
2) Added new input files for DQMOM regression testing.
3) Added new tests for DQMOM/Scalar transport to the regression test.
4) Fixed an error in the methane_1m.ups file
5) Added central_limiter option to spec for Enthalpy_solver for consistency

9 lines of code changed in 2 files:

jthornoc 2009-12-01 17:27 Rev.: 45141

Added a solver option: Lapack-svd
which uses svd to estimate a condition number (not to be confused with the SVD solver option).

3 lines of code changed in 1 file:

harman 2009-12-01 17:16 Rev.: 45140

Moved all matlab scripts into a Matlab directory

Added script that computes the order of accuracy by calling amrmpm()


2584 lines of code changed in 5 files:

harman 2009-12-01 13:25 Rev.: 45139

Now passing lp out of computeStressFromVelocity(). Previously it was computed in
the function but never passed out.

MMS problem: particle velocity field no longer goes unstable.

0 lines of code changed in 2 files:

jpedel 2009-12-01 13:03 Rev.: 45138

Adding SVD solver capability in DQMOM.cc using LAPACK and DenseMatrix classes

63 lines of code changed in 8 files:

harman 2009-12-01 10:03 Rev.: 45137

initialize lp, vol and xp.

changed the variable that is used for the x axis in plotting.

Currently setup for 1 timestep and direct comparison of particle variables
with M. Stefen's 1D code.

The MMS problem runs and gives reasonable results for the particle displacement,
jowever, the particle velocity goes unstable. We suspect that the stress
calculations needs to be moved in order to match the results of M. Steffen and
Uintah code.

36 lines of code changed in 1 file:

charlesreid 2009-12-01 01:28 Rev.: 45136

Accidentally uncommented a directive in my last commit

0 lines of code changed in 2 files:

charlesreid 2009-12-01 01:27 Rev.: 45135

M Directives.h
Making comments more user-friendly

M CoalModels/HeatTransfer.cc
Fixing a problem with unfound tags

13 lines of code changed in 3 files:

November 2009 »

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