April 2009 Commit Log

Number of Commits:
92
Number of Active Developers:
11
jthornoc 2009-04-30 17:26 Rev.: 44236

Adding a class that will encapsulate the discretization methods.

696 lines of code changed in 2 files:

charlesreid 2009-04-29 18:19 Rev.: 44235

Reverting to previous version of DQMOM class until I figure out what's wrong with new version

59 lines of code changed in 2 files:

harman 2009-04-29 15:31 Rev.: 44234

user can now input physical coordinates as opposed to cell coordinates

0 lines of code changed in 2 files:

charlesreid 2009-04-29 15:31 Rev.: 44233

Also updating LU solver for DQMOM

28 lines of code changed in 2 files:

charlesreid 2009-04-29 15:21 Rev.: 44232

Adding calculation of norm of the residual to DQMOM solver.

127 lines of code changed in 2 files:

harman 2009-04-29 14:57 Rev.: 44231

added option to input physical coordinates for the starting and ending pts.

I'm not completely happy with this. Computing the cell indicies from the input
points occurs _before_ any bullet proofing takes place. The bullet proofing
(do level exists for all time steps) should be placed immediately after parsing the
arguments.

37 lines of code changed in 1 file:

jthornoc 2009-04-29 14:19 Rev.: 44230

Initial import of the DQMOM solvers into Arches along with a few model terms.

6285 lines of code changed in 49 files:

jthornoc 2009-04-29 14:12 Rev.: 44229

Adding the LU solver.

282 lines of code changed in 2 files:

sshankar 2009-04-29 13:38 Rev.: 44228

Fixed particle data memory leaks

107 lines of code changed in 4 files:

dav 2009-04-29 11:41 Rev.: 44227

Added info about the combination of libraries.

0 lines of code changed in 4 files:

dav 2009-04-29 11:25 Rev.: 44226

Rearrange order of variable initialization to quiet compiler warning.

0 lines of code changed in 2 files:

harman 2009-04-28 17:32 Rev.: 44225

updated ups files to pass the ups_spec
- changed path to sus.

6 lines of code changed in 6 files:

gforgeadmin 2009-04-23 13:47 Rev.: 44213

added newline to test svn commit

0 lines of code changed in 2 files:

luitjens 2009-04-23 13:06 Rev.: 44212

Added the ability to turn on/off tile growth.

91 lines of code changed in 2 files:

luitjens 2009-04-23 13:05 Rev.: 44211

Added the ability to specify the collection of particles with the <collectParticles> tag. The patchFactorParticles algorithm is now obsolete but is included for backwards compatability. The same algorithm can now be achieved by using patchFactor with collectParticles turned on.

7 lines of code changed in 1 file:

luitjens 2009-04-18 10:34 Rev.: 44157

Factored out the multiply by the identity matrix. This saves a few floating point operations. This should not change the answers.

2 lines of code changed in 1 file:

harman 2009-04-17 11:08 Rev.: 44143

preprocess_Lodi_BCs()
getICEMaterials -> getMaterials
The user is inputting the material index not the index for just the ICE matls.
Confusing enough?

1 lines of code changed in 1 file:

sshankar 2009-04-17 10:59

Added partial code for preventing memory leak

413 lines of code changed in 6 files:

charlesreid 2009-04-17 01:48 Rev.: 44139

Adding another conditional to check for division by zero

22 lines of code changed in 1 file:

luitjens 2009-04-16 16:58 Rev.: 44136

Lowered the small number so that it is 5*machine precision. Eliminated a floating point division from the termination condition. Eliminated the iteration count and the corresponding termination condition. Terminate if the convergence has stopped.

0 lines of code changed in 2 files:

harman 2009-04-16 16:35 Rev.: 44135

eliminate excess chatter

0 lines of code changed in 2 files:

harman 2009-04-16 14:41 Rev.: 44131

octave script that computes the exact solution to the Couette-Poiseuille flow problem
and compares it to simulation data

201 lines of code changed in 1 file:

guilkey 2009-04-15 21:40 Rev.: 44123

Fix typo in the outputProblemSpec

1 lines of code changed in 1 file:

guilkey 2009-04-15 21:36 Rev.: 44122

Instead of just falling into the "weibull" option if nothing else fits,
use an "else if" to make sure that was what was intended.

1 lines of code changed in 1 file:

guilkey 2009-04-15 21:23 Rev.: 44120

Make alpha an optional input with default 0. I don't think I've ever
not given it a value of 0 in the input file.

1 lines of code changed in 1 file:

harman 2009-04-15 17:42 Rev.: 44117

fixed a parsing bug for the domain length. You can't delete the letter 'e' from
values that have exponents in them.

0 lines of code changed in 2 files:

harman 2009-04-15 13:09 Rev.: 44114

Variable name change that should have been committed a long time ago.
centerOfMass -> TotalMomentum

1 lines of code changed in 1 file:

harman 2009-04-15 12:20 Rev.: 44110

problemSetup
- added bulletproofing so the user can't apply LODI bcs to "all" materials

addRequires()
- require gammaLabel in CC_exchange portion

preprocess_Lodi_BCs()
- corrected how we determine the material index. This bug surfaced when we switch the
location of the ICE and MPM material sections in the ups file.

8 lines of code changed in 1 file:

luitjens 2009-04-15 10:12 Rev.: 44108

raised the convergence criteria to 10x machine precision.

1 lines of code changed in 1 file:

luitjens 2009-04-14 15:55 Rev.: 44100

increased the convergence criteria.

1 lines of code changed in 1 file:

luitjens 2009-04-14 15:43 Rev.: 44099

Fixed a couple bugs in the cubeRoot function.

Wrote a CurbeRootTest program which compares the time and accuracy to pow.


139 lines of code changed in 4 files:

guilkey 2009-04-13 23:48 Rev.: 44092

Update the code to reflect the changes that Cherie made to the input files
yesterday. d_adiabaticHeating is no longer a supported option. If one wishes
to turn off conduction, use
<DoExplicitHeatConduction>false</doExplicitHeatCondcution>

2 lines of code changed in 4 files:

sshankar 2009-04-13 19:23 Rev.: 44089

Some changes for periodic NC datasets

29 lines of code changed in 1 file:

sshankar 2009-04-13 17:34

Added changes for periodic and no extraCell datasets

582 lines of code changed in 3 files:

dav 2009-04-13 16:25 Rev.: 44084

Quiet compiler warning... #if 0 code that doesn't do anything.

2 lines of code changed in 1 file:

dav 2009-04-13 16:25 Rev.: 44083

Fixed compiler warning (put unsued var inside #if). Cosmetics... white space, coding standard...

24 lines of code changed in 1 file:

dav 2009-04-13 16:20 Rev.: 44082

Commit of configure that corresponds to new configure.ac

1 lines of code changed in 2 files:

dav 2009-04-13 16:18 Rev.: 44081

Cleaning up more of the Uintah tree.

Don't need/use ogl stuff anymore. Don't need the osx/ directory as
the hack isn't necessary anymore (We are 2 major OS versions past it).

1 lines of code changed in 6 files:

charlesreid 2009-04-13 15:34 Rev.: 44078

Fixing the driver so that it uses a set of moments that works OK

0 lines of code changed in 2 files:

charlesreid 2009-04-13 15:21 Rev.: 44077

Updating DQMOM matlab routines

185 lines of code changed in 5 files:

charlesreid 2009-04-13 02:39 Rev.: 44073

Fixing some indexing problems

15 lines of code changed in 1 file:

charlesreid 2009-04-13 00:00 Rev.: 44072

Fixing a model source term bug - don't accumulate model terms...

2 lines of code changed in 1 file:

luitjens 2009-04-11 10:52 Rev.: 44066

Combined the two cubeRoot functions into one function with a default parameter. This eliminates some code duplication.

11 lines of code changed in 3 files:

luitjens 2009-04-11 10:51 Rev.: 44065

Undid last patch and implemented it a better way.

2 lines of code changed in 1 file:

luitjens 2009-04-11 10:22 Rev.: 44064

Don't output the AMR overhead on non-AMR problems.

5 lines of code changed in 1 file:

guilkey 2009-04-10 16:20 Rev.: 44051

Getting rid of NormalForceBC from PhysicalBCs. I wrote it, I can't figure
out what I was thinking, so I can't document it, it isn't used. Outta here!

2 lines of code changed in 6 files:

luitjens 2009-04-10 13:59 Rev.: 44047

Added new cubeRoot functions for quickly computing the cubedRoot of a double.

87 lines of code changed in 2 files:

qymeng 2009-04-09 20:51 Rev.: 44043

Removed >= <= operators in IntVector.h.
Changed the order of foreign Grid variable link list in DW.

39 lines of code changed in 4 files:

charlesreid 2009-04-09 19:29 Rev.: 44039

Fixing a negative sign; also adding print statements for A, B, and X matrices for debugging purposes

27 lines of code changed in 1 file:

charlesreid 2009-04-09 19:02 Rev.: 44038

Adding a method to get the quadrature node associated with a DQMOM equation

0 lines of code changed in 4 files:

charlesreid 2009-04-09 19:01 Rev.: 44037

Adding LU decomposition solver (Crout.m) to compare Crout's method to Matlab's A^-1*B solver

156 lines of code changed in 3 files:

jas 2009-04-09 15:54 Rev.: 44032

Remove MALLOC_TRACE_TAG committed earlier.

0 lines of code changed in 2 files:

jas 2009-04-09 15:51 Rev.: 44031

More robust checking if we are using petsc version 2.3.

18 lines of code changed in 2 files:

jas 2009-04-09 15:51 Rev.: 44030

Use the MallocTrace library.

70 lines of code changed in 2 files:

qymeng 2009-04-09 15:08 Rev.: 44027

M Core/Grid/Variables/Variable.h
M Core/Grid/Variables/Variable.cc
M Core/Geometry/IntVector.h
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc

Add a next pointer for vars in DataWarehouse.
This linked list of vars is to store foreign Grid Variables received from same patch but with different range.
We need multiple ranges(windows) of data under same label for reordering task executions and MPI receives.

M CCA/Components/Schedulers/MPIScheduler.cc
M StandAlone/inputs/UPS_SPEC/ups_spec.xml
MPI queued task scheduler works now and can be turned on by tag <useExternalQueue_>.
Default is still the old fix-order scheduler.

117 lines of code changed in 5 files:

dav 2009-04-09 14:42 Rev.: 44025

Quiet debug spamming...

0 lines of code changed in 1 file:

dav 2009-04-09 14:24 Rev.: 44024


Merged LICENSE and LICENSE_CSAFE into one file (LICENSE).

0 lines of code changed in 3 files:

charlesreid 2009-04-08 23:06 Rev.: 44016

1) fixing bug in LU solver related to vector access
2) adding check in DQMOM problem setup for moment index size and number of indices
3) from SpatialOps.cc, removing initialization of weights/weighted abscissas in half the domain to be 0 (so we don't get a bunch of messages about A being singular)

38 lines of code changed in 3 files:

jthornoc 2009-04-08 12:44 Rev.: 44006

No longer passing in the varLabel into the transport equation. This should simplify things a bit.

23 lines of code changed in 14 files:

charlesreid 2009-04-08 03:04 Rev.: 44002

Fixing a bug in DQMOM class related to order of construction of A and B in AX=B solver

20 lines of code changed in 1 file:

charlesreid 2009-04-08 02:26 Rev.: 44001

- Fixing some major problems with the AX=B construction process
- Adding ability to incorporate phase-space diffusion in B matrix

121 lines of code changed in 2 files:

charlesreid 2009-04-07 19:07 Rev.: 43999

Fixing bug in source term calculation

1 lines of code changed in 1 file:

charlesreid 2009-04-07 18:42 Rev.: 43998

Adding "DQMOM sandbox" matlab script to SpatialOps

337 lines of code changed in 2 files:

jthornoc 2009-04-07 17:23 Rev.: 43994

Dd: On Macs, it isn't '.so', it is '.dylib' (so use generic var created for this).

1 lines of code changed in 1 file:

jthornoc 2009-04-07 17:12 Rev.: 43993

Removed Tabs (Dd)

4 lines of code changed in 1 file:

sshankar 2009-04-07 15:41

Fixed issues with multi-level NC data. Some memory clean up also done.

600 lines of code changed in 3 files:

dav 2009-04-07 15:23 Rev.: 43990

Fix max link.

0 lines of code changed in 2 files:

harman 2009-04-07 15:09 Rev.: 43989

contents moved to doc/ice.tex

0 lines of code changed in 1 file:

charlesreid 2009-04-07 13:25 Rev.: 43987

Fixing major sign error

1 lines of code changed in 1 file:

jthornoc 2009-04-06 18:08 Rev.: 43984

1) Fixed bugs in Ax=b solver.
2) Fixed sign error in DQMOMEqn.cc
3) Fixed src*vol in DQMOMEqn.cc

56 lines of code changed in 6 files:

charlesreid 2009-04-06 15:28 Rev.: 43982

Adding the missing weights assignment

5 lines of code changed in 1 file:

jthornoc 2009-04-06 15:08 Rev.: 43981

Source term wasn't being retrieved properly for higher order time stepping.

Also, there is missing code in DQMOM.cc. The source term for the weight equations are not being filled in.

50 lines of code changed in 7 files:

jthornoc 2009-04-05 23:05 Rev.: 43977

1) Fixed a bug in the multi-step time integrator. Now using old RK values rather than old_dw values in the intermediate steps.
2) Now passing in the ExplicitTimeIntegrator into the builder and then into the actual equation class rather than trying to set it afterwards.

283 lines of code changed in 10 files:

jthornoc 2009-04-04 09:56 Rev.: 43976

M CoalModels/PartVel.cc
M CoalModels/PartVel.h
- Fixed some bugs in the Particle velocity model. The model is adding to the magnitude of velocity...do we want to try adding to the components?

M TransportEqns/ScalarEqn.h
- Passing the timesubStep into the task properly.

M TransportEqns/EqnBase.cc
M TransportEqns/EqnBase.h
- Added a mechanism for storing initial conditions (still need to allow for reading in from the input file).
- Added an "old" transport varLabel for the RK time stepping.

M TransportEqns/DQMOMEqn.cc
M TransportEqns/DQMOMEqn.h
- Added upwind and super_bee convection schemes.
- Passing the timesubstep properly now.
- Fixed a sign error in the convection scheme addition to the RHS.
- Perform data copy after a RK step.

M TransportEqns/ScalarEqn.cc
- Passing the timesubstep properly now.
- Added an "if" statement to the sched_initialize (only perform when timesubstep = 0)
- Note: Still need to add flux limiters here.

M ExplicitTimeInt.h
- Now passing alpha and beta into the time averaging method. I was having some weirdness here that should be revisited (potential memory bug?).

M SpatialOps.cc
- Now setting the time integrator for the DQMOM equations. Don't ask me how this actually worked before :p
- Initializing particle velocities in actuallyInitialize.
- Right now there is a bunch of problem specific initialization going on that we will want to generalize in the future.
- Computing stable time step using a convective CFL. Will want to refine this (perhaps a different norm? Add diffusive CFL) soon.

M SourceTerms/SourceTermBase.h
- Passing timesubstep properly now and storing it in the base class.

M SourceTerms/ConstSrcTerm.cc
M SourceTerms/ConstSrcTerm.h
- Adusting to changes made in the base class.

M StandAlone/inputs/UPS_SPEC/spatialops_spec.xml
- Added more spec for the particle velocity model.

439 lines of code changed in 18 files:

dav 2009-04-03 16:54 Rev.: 43975

Fix to my bad merge from previous version.

0 lines of code changed in 2 files:

charlesreid 2009-04-03 15:30 Rev.: 43974

Adding ability to grab moments from input file for DQMOM; also updating SpatialOps input file to include particle velocity and moment specifications.

9 lines of code changed in 1 file:

dav 2009-04-03 15:26 Rev.: 43973

M CCA/Components/OnTheFlyAnalysis/particleExtract.cc

- Fixed compiler warnings. Use "()" around portions of if statements
to make them more clear (make explicit order of evaluation).
- Added 'default' to switch statement to quiet compiler complaint that some
options were not handled.

M CCA/Components/ICE/CustomBCs/LODI2.cc

- Fixed compiler warnings. Use "()" around portions of if statements
to make them more clear (make explicit order of evaluation).

M CCA/Components/Arches/Properties.cc

- Indented and added "{}" around some if statements. Quiets compiler
warnings and makes code easier to follow.

M CCA/Components/Arches/MCRT/ArchesRMCRT/RMCRTRadiationModel.h

- Added "{}" around some if statements. Quiets compiler warnings and
makes code easier to follow.

M Core/Grid/Variables/constVariable.h
M Core/Grid/Variables/constVariableBase.h

- Make getBaseRep() const. This allows for making a vector of
constVariable pointers like this:

constCCVariable<int> testCC;
vector<const constCCVariable<int>*> vCCVars;

// Get the testCC variable.
new_dw->get( testCC, lb->partCountLabel, 0, patch, Ghost::None, 0 );

// Create an empty constCCVariable.
constCCVariable<int> * testCCp = scinew constCCVariable<int>();

// Copy the pointer to the data (testCC) into our new variable.
testCCp->copyPointer( testCC );

// Save the new variable in a vector for future use.
vCCVars.push_back( testCCp );

- Commented out duplicate(ish) copyPointer() that can't be used anyway
because the compiler complains that it is ambiguous with the other
version of copyPointer(). (The parameters Variable& and
VariableBase& can't be distinguished.)

116 lines of code changed in 8 files:

charlesreid 2009-04-03 00:10 Rev.: 43971

Adding a more robust LU decomposition solver/routine; also, a little cleaup of the DQMOM class.

176 lines of code changed in 4 files:

dav 2009-04-02 16:38 Rev.: 43966

Without SCIRun, we don't need on-the-fly-libs anymore...

0 lines of code changed in 3 files:

sbrown 2009-04-02 16:34 Rev.: 43965

Only fail test 6 if datafiles are gzip-compressed.

0 lines of code changed in 2 files:

dav 2009-04-02 16:09 Rev.: 43964

Need teem (and png) lib to link.

53 lines of code changed in 13 files:

dav 2009-04-02 15:52 Rev.: 43963

Don't use Packages anymore.

2 lines of code changed in 1 file:

dav 2009-04-02 15:49 Rev.: 43962

Still need Dynamic compilation stuff (until Fields go away (shortly)). Putting it back.

2472 lines of code changed in 5 files:

dav 2009-04-02 15:37 Rev.: 43961


D DynamicLoader.cc
D DynamicLoader.h
M sub.mk
D DynamicCompilation.cc
D DynamicCompilation.h

- New 'Uintah' does not use dynamic compilation... so removing associated files.

M Environment.cc

- Don't use ITCL, LOAD_PACKAGE, THIRDPARTY anymore.

0 lines of code changed in 7 files:

dav 2009-04-02 15:26 Rev.: 43960

Removed references to SCIRun 'Packages' as they don't exist anymore.

M configure.ac
M configure

- Require autoconf 2.63 to maintain consistency on the 'configure' file.
- Add "--with-teem" arg specification. (Removes configure complaint when using --with-teem.)
- AC_SUBST( name ) (in autoconf 2.63?) puts 'name ' (space at end) so use (name).

- NOTE: turned off svn property svn:eol-style because it was causing svn to have
a conniption fit, due to, I believe, the fact that autoconf 2.63 adds a ^M
into configure (so it can test for the end of line character). Unfortunately,
svn isn't smart enough to handle this correctly, so it just gives errors... sigh.

M aclocal.m4
M include/sci_defs/environment_testdefs.h.in

240 lines of code changed in 5 files:

charlesreid 2009-04-01 17:41 Rev.: 43955

Fixing a bug and adding a moment that won't confuse the LU solver

15 lines of code changed in 1 file:

dav 2009-04-01 17:17 Rev.: 43954

All these files are empty... I think they were consolidated in to GridVariableBase, but not deleted...

0 lines of code changed in 10 files:

dav 2009-04-01 16:59 Rev.: 43953

M ScalarSolver.cc

- Fixed compiler warnings:
-- Commented out unused variables.
-- Use () around ?: notation... Also I assume this code needs 'boolean
or' ("||") and not 'binary (bitwise) or' ("|")... Please verify.

5 lines of code changed in 1 file:

harman 2009-04-01 16:31 Rev.: 43952

using package setspace instead of doublespace

0 lines of code changed in 17 files:

jthornoc 2009-04-01 15:13 Rev.: 43951

Divide the weighted abscissa with the weight to get the right length.

38 lines of code changed in 1 file:

charlesreid 2009-04-01 15:00 Rev.: 43950

Modifying the way DQMOM.cc stores weights and weighted abscissas

72 lines of code changed in 1 file:

sshankar 2009-04-01 14:58

Fixes for node centered data

387 lines of code changed in 3 files:

March 2009 »

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