August 2010 Commit Log

Number of Commits:
116
Number of Active Developers:
12
luitjens 2010-08-31 22:40 Rev.: 46145

commit the MPI type

0 lines of code changed in 2 files:

luitjens 2010-08-31 09:40 Rev.: 46142

MallocTrace tags and indenting

20 lines of code changed in 1 file:

luitjens 2010-08-31 09:15 Rev.: 46141

Added some MallocTrace profiling.

Enabled parallel SFC generation. This was disabled when we ran into an allgatherv bug on Kraken which has now been fixed.

0 lines of code changed in 2 files:

luitjens 2010-08-31 09:13 Rev.: 46140

Added some MallocTrace tags

5 lines of code changed in 1 file:

harman 2010-08-30 17:40 Rev.: 46138

Turned on bulletproofing.
The number of cells a BC touches must = the number of cells on that boundary face.

240 lines of code changed in 14 files:

luitjens 2010-08-30 17:34

quiet some compiler warnings

8 lines of code changed in 3 files:

luitjens 2010-08-30 17:13 Rev.: 46135

Pass stl vectors by const reference instead of by value.

18 lines of code changed in 6 files:

jthornoc 2010-08-30 17:08 Rev.: 46134

mixMW wasn't being allocated in dummy solve.
ch4 label no longer required in tabulated stripping factor.

5 lines of code changed in 3 files:

kunkel 2010-08-30 16:22 Rev.: 46133

Added the Nodal Smoothed Volume Fraction Contact model to MPM.

375 lines of code changed in 6 files:

jsutherland 2010-08-30 15:37 Rev.: 46131

- Update Wasatch/FieldAdaptor.h due to upstream library changes in SpatialOps
- Fix a -I in Wasatch/sub.mk

4 lines of code changed in 2 files:

harman 2010-08-30 12:50 Rev.: 46130

added cleanVisIt
nukes <bin>/VisIt/udaReaderMTMD directory.

4 lines of code changed in 1 file:

jthornoc 2010-08-30 07:03 Rev.: 46129

Cleanup.

1 lines of code changed in 1 file:

jpeterson 2010-08-28 18:14 Rev.: 46127

Get rid of unused variable warning

1 lines of code changed in 1 file:

jpeterson 2010-08-28 17:59 Rev.: 46126

Added temperature dependent JWL to ComputePressEOSCM

142 lines of code changed in 2 files:

jpeterson 2010-08-28 15:51 Rev.: 46125

Finished infrastructure changes for temperatures in EOS

235 lines of code changed in 56 files:

jpeterson 2010-08-28 14:19 Rev.: 46122

Constitutive Models

Added cell temperature parameter to computePressEOSCM.
This will allow temperature dependent equations of state.


A StandAlone/inputs/MPM/insert.dat
A StandAlone/inputs/MPM/extrude.xml
A StandAlone/inputs/MPM/extrude.ups

Added example problem of particle insertion.


M CCA/Components/Models/HEChem/DDT1.cc
M CCA/Components/Models/HEChem/DDT1.h

Added line to prevent cracked burning in the cell ahead of front.

92 lines of code changed in 58 files:

guilkey 2010-08-27 15:52 Rev.: 46119

Minor housekeeping

1 lines of code changed in 1 file:

guilkey 2010-08-27 15:46 Rev.: 46118

Add rotation to the cohesive zone's normal and tangential direction.
--Ravi Bhide

41 lines of code changed in 1 file:

jpedel 2010-08-27 15:25 Rev.: 46117

Fixing a bug. First enthalpy was computed using incorrect adiabatic and sensible enthalpies. Adia. and sens. enthalpies were obtained in the table with zero values for both mixture fractions

2 lines of code changed in 1 file:

luitjens 2010-08-27 13:16 Rev.: 46115

Minor change to allow mallocTrace to better determine where memory usage came from

1 lines of code changed in 1 file:

luitjens 2010-08-26 14:46 Rev.: 46113

TAU fix

5 lines of code changed in 1 file:

luitjens 2010-08-26 14:04 Rev.: 46112

Possible fix for aliasing errors.

0 lines of code changed in 2 files:

luitjens 2010-08-26 12:35 Rev.: 46111

possible fixes for strict aliasing compiler warnings.

0 lines of code changed in 2 files:

jthornoc 2010-08-24 09:24 Rev.: 46110

Fixed a "bug" where the new scalar solver was not time averaging in a
consistent manner with the other (old) scalars. This was causing
general instabilities in certain cases where the new scalars were acting
as table parameters. To fix this I had to:

1) Separate out the time averaging in the scalar eqn and schedule it
later in the algorithm
2) Create a new timeAve procedure for equations that needed density
3) Turned off the density guess knob for scalar equations until the
algorithmic issues are settled.

146 lines of code changed in 10 files:

guilkey 2010-08-23 17:26

Cosmetic changes

17 lines of code changed in 2 files:

guilkey 2010-08-23 14:34 Rev.: 46106

Add particle deletion condition in momentum form code as well.

5 lines of code changed in 1 file:

jthornoc 2010-08-23 07:05 Rev.: 46104

Added scalar variance option for TabProps.

6 lines of code changed in 1 file:

guilkey 2010-08-21 14:08 Rev.: 46102

A little more information in the error message generated by a degenerate box.

0 lines of code changed in 2 files:

guilkey 2010-08-21 14:06 Rev.: 46101

Change the value for pLocalized that causes particles to be deleted from 2 to -999.

2 lines of code changed in 1 file:

jthornoc 2010-08-20 05:29 Rev.: 46100

More explicit error message in MomentumSolver.cc
Actually returning the source term type in SourceTermBase.h
Some minor bulletproofing in the initialization of transport equations.

6 lines of code changed in 5 files:

luitjens 2010-08-19 20:38 Rev.: 46099

Added const to size functions

0 lines of code changed in 12 files:

harman 2010-08-19 17:21 Rev.: 46098

added size

0 lines of code changed in 2 files:

guilkey 2010-08-19 09:55 Rev.: 46094

Fixing more warnings.

11 lines of code changed in 2 files:

jthornoc 2010-08-19 06:33 Rev.: 46093

Specified _src_type for each source.

69 lines of code changed in 21 files:

jthornoc 2010-08-19 06:15 Rev.: 46092

Added intrusion_inlet option to Arches.
Added spec for intrusion inlet.
Made generic the source addition in MomentumSolver.
Removed subequent weed from Source.cc.

101 lines of code changed in 9 files:

guilkey 2010-08-18 17:31 Rev.: 46090

Fix a warning.

0 lines of code changed in 2 files:

guilkey 2010-08-18 17:24 Rev.: 46089

Fix warning for uninitialized variable.

1 lines of code changed in 1 file:

guilkey 2010-08-18 17:14 Rev.: 46088

Clean up warnings in the MPM component.

15 lines of code changed in 7 files:

jpeterson 2010-08-18 14:45 Rev.: 46081

Moved initialization outside of loop

3 lines of code changed in 1 file:

jpeterson 2010-08-18 14:44 Rev.: 46080

Added JWL equation of state to ViscoScram. Made modifications to how Murnaghan EOS data is stored.

M CCA/Components/MPM/ConstitutiveModel/ViscoScram.h
M CCA/Components/MPM/ConstitutiveModel/ViscoScram.cc
M StandAlone/inputs/UPS_SPEC/constitutive_models.xml



Fixed compiler warnings about uninitialized IntVectors

M CCA/Components/MPM/ConstitutiveModel/UCNH.cc

194 lines of code changed in 3 files:

dav 2010-08-18 14:33 Rev.: 46079


M configure
M configure.ac

Test for floating point number precision issue now automatically adds
the compiler flag (instead of erroring out and asking the user to get
involved). Also, added a 'persistent' warning message array so that
important warning messages (generated during configure) can be
preserved and repeated at the end of configure in the hopes that the
user may actually see them.

91 lines of code changed in 2 files:

luitjens 2010-08-18 14:09 Rev.: 46078

Fixed a typo.

1 lines of code changed in 1 file:

luitjens 2010-08-18 14:05 Rev.: 46077

Added a mallocTrace tag

1 lines of code changed in 1 file:

jthornoc 2010-08-18 12:21 Rev.: 46076

* Added a new source term that will inject source terms as inlet
* conditions normal to specified solid geometry.
* Fixed a warning in LaminarPrNo
* Fixed a warning in TabStripFactor
* Fixed notation in Inject
* Modified the SourceTemplatedTemplate
* Fixed a warning in Discretization_new
* Added spec for IntrusionInlets

374 lines of code changed in 9 files:

jthornoc 2010-08-18 12:20 Rev.: 46075

Added source term templates and updated the property template.

565 lines of code changed in 8 files:

guilkey 2010-08-18 11:44 Rev.: 46074

Fix warnings.

0 lines of code changed in 2 files:

luitjens 2010-08-18 11:15 Rev.: 46071

quiet some uninitialized variable warning messages on older compilers (the variables actually were not uninitialized).

7 lines of code changed in 1 file:

luitjens 2010-08-18 11:04 Rev.: 46070

Removed unused variable

1 lines of code changed in 1 file:

dav 2010-08-17 20:46 Rev.: 46069


Fix a problem with Parallelpiped (aka NaaBoxGeometryPiece). The
problem was that the bounding box was being set to the 1st and
(calculated) last point of the parallelpiped being created.
Unfortunately, the bounding box must have p1 < p2 (ie, all components
of the 1st point must be smaller than the corresponding last point).
I now check for this case and fix it automatically in the
NaaBoxGeometryPiece.

M Grid/Box.h
M Grid/Box.cc

- Added fixBoundingBox() to update (rearrange) the bounding box of a 'Box'.

M GeometryPiece/NaaBoxGeometryPiece.cc

- Set the name of the NaaBoxGeometryPiece correctly.
- Fix the bounding box if necessary, or die (informatively) while trying.

M ProblemSpec/ProblemSpec.h

- Fix function doc to be explict as to what happens if an attribute is
not found.

46 lines of code changed in 7 files:

dav 2010-08-17 18:15 Rev.: 46068

Make warning/error message stand out a little better.

9 lines of code changed in 2 files:

dav 2010-08-17 18:04 Rev.: 46067

Add floating point register size check. Check some VisIt stuff before checking for CMake.

126 lines of code changed in 2 files:

harman 2010-08-17 16:50 Rev.: 46066

inFluxOutFluxVolume()
- if a timestep is going to be restarted as a result of the
outflux vol > cell volume then dump out all of the face flux data
for the bad cells.
- removed the progressive warning, it only masks the problem.

0 lines of code changed in 8 files:

jpeterson 2010-08-17 14:52 Rev.: 46064

Fix last commit

0 lines of code changed in 1 file:

jpeterson 2010-08-17 14:32 Rev.: 46062

New CPDI interpolator with performance enhancements

265 lines of code changed in 2 files:

jthornoc 2010-08-17 13:12 Rev.: 46060

Boolean needed initialization for the tabulated stripping factor.
Logic for the cell iterator in Inject.h was incorrect.

7 lines of code changed in 2 files:

jthornoc 2010-08-17 13:12 Rev.: 46059

Bug fix in computeFirstEnthalpy.
Changed naming convention to be consistent with TabProps.
Added some debugging print statements.

12 lines of code changed in 1 file:

jthornoc 2010-08-16 20:27 Rev.: 46057

Addition of new property models:
ExtentRxn: Computes the extent of reaction given a grid resolved
variable.
ScalarDiss: Computes the scalar dissipation rate (currently a constant)
TabStripFactor: Back calculates a stripping factor based on local
tabulated CO2
Also added a source term -- TabRxnRate, for user specified reaction
rates.
Updated spec for models and sources.
Arches, MixingRxnModel, ExplicitSolver were all changed to accomidate
these models.

1233 lines of code changed in 17 files:

jsutherland 2010-08-16 17:33 Rev.: 46056

- Modify ScalarTransportEquation constructor to eliminate parser as an argument.
- add some comments to Wasatch.cc to indicate work to be done.

71 lines of code changed in 4 files:

harman 2010-08-16 16:09 Rev.: 46055

updated comment

0 lines of code changed in 2 files:

qymeng 2010-08-16 15:11 Rev.: 46050

Fixed a problem that caused MPI dynamic scheduler to deadlock when scheduling non-local OncePerProc tasks.

2 lines of code changed in 1 file:

harman 2010-08-16 11:45 Rev.: 46045


Nightly_order_accuracy
-added command "make uintah"

masterScript
- Each component can specify a path in which symbolic links will be made to that
path. For example inside of whatToRun.xml:

<symbolicLinks>
/.../src/scripts/ /.../StandAlone/inputs
</symbolicLinks>

Lodi.tst, Lodi_pulse.ups, ICE/whatToRun
- added parameter study of speed of sound knob with Lodi BCs.

Added post processing script movie_lineExtract.csh. This script
produces a line plot for each output timestep and then glues them together
with ppm_To_mpeg.




439 lines of code changed in 12 files:

jpeterson 2010-08-16 11:35 Rev.: 46044

Add in initialization that was nuked in creation of UCNH. Wasn't noticed because bug only occurs when pressure stabilization is used

1 lines of code changed in 1 file:

luitjens 2010-08-16 10:23 Rev.: 46042

Handle std::runtime_error

6 lines of code changed in 1 file:

luitjens 2010-08-16 09:39 Rev.: 46040

Moved the Crashpad messages to earlier. For some reason they don't print later.

Justin

0 lines of code changed in 2 files:

jthornoc 2010-08-16 05:10 Rev.: 46039

Added the name check for "MixtureFraction" to the tabprops interface.
Fixed two warnings.

3 lines of code changed in 3 files:

guilkey 2010-08-15 18:06 Rev.: 46038

Add UsePressureStabilization option to CompMooneyRivlin.

52 lines of code changed in 1 file:

guilkey 2010-08-15 17:36 Rev.: 46037

Moved an unused CM to the unusedCM directory.

1580 lines of code changed in 2 files:

guilkey 2010-08-15 17:28 Rev.: 46036

Add calls for contact and boundary conditions for the momentum form version of
the code.

6 lines of code changed in 1 file:

guilkey 2010-08-15 16:05 Rev.: 46035

Remove #define for USL and MOM_FORM from SerialMPM, now a run time option.

20 lines of code changed in 3 files:

jas 2010-08-13 16:42 Rev.: 46034

Fix doxygen errors.

46 lines of code changed in 20 files:

jthornoc 2010-08-13 12:20 Rev.: 46029

Added boolean for determining if the model should be evaluated before
or after the table lookup.
Updated template examples with Boolean.
Updated current property models with new boolean.
Added scalar dissipation rate handle in TabProps interface.

61 lines of code changed in 12 files:

luitjens 2010-08-13 11:05 Rev.: 46028

Moved crashpad to Core/Thread to avoid linking issues in static builds

123 lines of code changed in 9 files:

luitjens 2010-08-13 10:43 Rev.: 46027

Addd a new debugging utility called CrashPad. This
utility allows you to insert strings into a database
which will be output if the system crashes (and our
signal handler is called). This will help debug
crashes on machines like Kraken where we are running
with too many processors to output data while running
and where we cannot attach a debugger.

To use it:

#include <CrashPad.h>

To add a message:

CrashPad::addMessage("Insert diagnostic message here\n");

To clear all messages:

CrashPadd::clearMessages();



127 lines of code changed in 4 files:

guilkey 2010-08-12 11:35 Rev.: 46021

Add a missing requires in some of the MOM_FORM code.

4 lines of code changed in 1 file:

guilkey 2010-08-12 11:11 Rev.: 46020

Add reduction variables to the MOM_FORM sections of the code.

14 lines of code changed in 1 file:

jas 2010-08-11 20:35 Rev.: 46018

Update copyright date.

381 lines of code changed in 714 files:

harman 2010-08-11 17:57 Rev.: 46017

implicitPressureSolver()
- using proc0cout instead of cout with a bunch of conditionals
- fixed a bug that if one of the subschedule task requested a timestep
then restart the timestep. Previous it didn't restart the timestep
until the max iterations was reached.

11 lines of code changed in 1 file:

guilkey 2010-08-11 17:20 Rev.: 46016

Add capability to put pressure BCs on cylinder ends.

14 lines of code changed in 1 file:

harman 2010-08-11 09:11 Rev.: 46014

cerr -> cout so you can redirect to an output file.

5 lines of code changed in 3 files:

jthornoc 2010-08-11 06:13 Rev.: 46013

Got too agressive with the comments...this should compile now.

1 lines of code changed in 1 file:

jthornoc 2010-08-11 06:07 Rev.: 46012

Fixed warning.

2 lines of code changed in 1 file:

harman 2010-08-10 17:59 Rev.: 46011

customInitialize.cc.h
added
bool doesComputePressure
to each of the different initialization routings.

ICE.cc
problemSetup()
- if the user selects a custom initialization that does compute the pressure
field don't wipe it out with an EOS evaluation.

20 lines of code changed in 5 files:

jthornoc 2010-08-10 16:55 Rev.: 46009

Pulled a new weed. TabProps will take care of cold flow mixing rather than having a separate model for it.

0 lines of code changed in 4 files:

jthornoc 2010-08-10 16:51 Rev.: 46008

Scalar equation can now handle a variable Pr number.
Overloaded the diffusion calculation to handle variable Pr numbers.
Removed calculation of diffusion coefficient in LaminarPrNo as it is not needed.

424 lines of code changed in 11 files:

luitjens 2010-08-10 15:42 Rev.: 46006

Don't call MPI functions when only using a single processor.

0 lines of code changed in 2 files:

luitjens 2010-08-10 14:30 Rev.: 46005

If the iterator high and low points are reversed return 0 cells for the size.

12 lines of code changed in 3 files:

luitjens 2010-08-10 13:31 Rev.: 46004

Added a size() operator to the iterator classes.

45 lines of code changed in 6 files:

harman 2010-08-09 17:11 Rev.: 46002

Added new custom initialization code for a counterflow in the x-y plane.

Usage:
</ICE>
<customInitialization>
<counterflow>
<strainRate> 2000 </strainRate>
<referenceCell> [0,0,0] </referenceCell>
</counterflow>
</customInitialization>
</ICE>

This is useful since it generates larges transverse gradients at the
boundaries.

66 lines of code changed in 3 files:

eldredge 2010-08-09 14:46 Rev.: 46000

FIxed some bugs in the viscosity and diffusivity routines in
LaminarPrNo.h. Weston Eldrege Aug 9, 2010

14 lines of code changed in 2 files:

jthornoc 2010-08-09 13:15 Rev.: 45999

Forgot to add new mixing model.

338 lines of code changed in 3 files:

jthornoc 2010-08-09 13:08 Rev.: 45998

Arches: Added the option for laminar Pr. number.
LaminarPrNo: More doxygen comments.

32 lines of code changed in 2 files:

eldredge 2010-08-09 12:14 Rev.: 45997

Added some comments related to the LaminarPr class.
Weston Eldredge, Aug 8, 2010.

55 lines of code changed in 1 file:

jthornoc 2010-08-09 10:57 Rev.: 45996

Updated doxygen comments.

20 lines of code changed in 1 file:

luitjens 2010-08-09 10:56 Rev.: 45995

Removed the special scrubbing logic for simulations with a dynamic load balancer.

0 lines of code changed in 2 files:

luitjens 2010-08-09 10:48 Rev.: 45994

Initilize the scrubbing mode to ScrubNone, previously this variable was uninitialized leading to undefined behavior.


2 lines of code changed in 1 file:

jthornoc 2010-08-09 10:42 Rev.: 45992

Updated the problemSetup.
Defaulted to binary for now.
Removed the air_b boolean.
Spacing, tabs, etc...

83 lines of code changed in 2 files:

luitjens 2010-08-08 11:58 Rev.: 45991

Another weed.

0 lines of code changed in 2 files:

luitjens 2010-08-08 10:17 Rev.: 45990

Pulled a weed.

1 lines of code changed in 1 file:

luitjens 2010-08-08 10:13 Rev.: 45989

Small cleanup of code that deletes from some STL containers

0 lines of code changed in 2 files:

harman 2010-08-06 15:21 Rev.: 45985

Changed hard coded paths from inputs/ICE/Scripts to scripts/ICE -Jake Padawan

24 lines of code changed in 13 files:

harman 2010-08-06 14:58 Rev.: 45983

added macro to make a symbolic link to src/scripts in the Standalone/

8 lines of code changed in 1 file:

eldredge 2010-08-06 14:13 Rev.: 45982

This commit includes some changes to calculate prandlt numbers
in arches for laminar flows. Weston Eldredge, Aug 06, 2010

156 lines of code changed in 2 files:

jthornoc 2010-08-06 10:45 Rev.: 45980

Updates to the Laminar Pr number to include more (any) functionality. Details of the actual calculation to be added later.

Updating template and removing an extra "if" statement.

115 lines of code changed in 4 files:

harman 2010-08-06 10:22 Rev.: 45979

switched from naming convention from expoential to gaussian initial temperature distribution,

39 lines of code changed in 2 files:

jthornoc 2010-08-06 08:22 Rev.: 45978

Adding Laminar Pr number property calculator and fixing a bug in the templates.


272 lines of code changed in 5 files:

jthornoc 2010-08-06 08:10 Rev.: 45977

Adding some generic classes for developers of new property models. This gives developers a generic template as a starting point
for adding both assumed CCVariable<double> properties and templated property models.

820 lines of code changed in 4 files:

jthornoc 2010-08-06 07:03 Rev.: 45976

Boolean was missing initialization which caused the variable to not be computed.

9 lines of code changed in 8 files:

jthornoc 2010-08-05 09:47 Rev.: 45971

PropertyModelBase.h:
Now destroying the VarLabel in the base class.
ConstProperty.cc, .h:
A little better strategy for the cell iterator.
SourceTerms/*:
Formatting. Moved the builder class into the source term class.
Arches.cc:
The source term registration is now consistent with the new sourcetermbase.

691 lines of code changed in 35 files:

harman 2010-08-04 15:33 Rev.: 45970

FaceVel_LODI()
- removed some old debugging code that ignored what was computed by the
LODI relationships. This should have never been committed.

1 lines of code changed in 1 file:

harman 2010-08-04 15:28 Rev.: 45969

customInitialization:exponentialTemperature profile
added ability to initialize the domain with a smooth
temperature peak in the domain. Currently, only works for 1matl ICE problems.
Usage:

<ICE>
<customInitialization>
<exponentialTemperature>
<direction> [1,0,0] </direction>
<coefficient> 10 </coefficient>
<minPoint> [0.25, 0, 0] </minPoint>
<maxPoint> [1.0, 0, 0] </maxPoint>
</exponentialTemperature>
</customInitialization>
</ICE>

Added Lodi_pulse.ups
1 matl ICE problem with a smooth temperature peak in the domain and LODI BCs.
This is used to identify symmetry errors from the reflecting waves resulting
from the boundary conditions.

49 lines of code changed in 2 files:

harman 2010-08-04 13:48 Rev.: 45968

matlab script to plot the exponential temperature profile used in the
custom initialization routine

21 lines of code changed in 1 file:

jthornoc 2010-08-04 11:05 Rev.: 45965

Missing an include.

1 lines of code changed in 1 file:

jthornoc 2010-08-04 10:48 Rev.: 45964

Adding the property model factory and base class property model.
This will allow for easy addition of "stand-alone" property models.

Also added an example constant property model.

717 lines of code changed in 16 files:

luitjens 2010-08-04 09:38 Rev.: 45963

Reenabled scrubbing for most problems.

1 lines of code changed in 1 file:

harman 2010-08-02 17:33 Rev.: 45961

BCDataArray.cc()
-revert back to r45926. In r45927 there was a bug.
45926: in multi-patch problems with jets a boundary face there were multiple children
even when there was not jet on the patch's face.

45927: in multi-patch problems with jets the boundary face there was only 1 child, even
if there was a jet on the patch's face.


BoundaryCondtion.cc/.h
-global
comment out all exception throws and output only the exception message. This
will generate a tremendous amount of output for any problems with multiple
geom objects on the boundary faces.

-getIteratorBCValuesBCKind()
deleted exception to catch if the iterator is size 0

This commit is to get the RT running.

25 lines of code changed in 3 files:

harman 2010-08-02 09:34 Rev.: 45960

operator: <<

if the the iterator has 0 elements or is done then indicate so and don't crash.

5 lines of code changed in 1 file:

July 2010 »

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