March 2009 Commit Log

Number of Commits:
185
Number of Active Developers:
11
jthornoc 2009-03-31 10:21 Rev.: 43937

Don't change 8 patch test simulation time.

1 lines of code changed in 1 file:

dav 2009-03-30 17:55 Rev.: 43932

M CCA/Components/ProblemSpecification/ProblemSpecReader.cc

Make vector verificaiton a tad bit better.

M Core/Containers/StringUtil.h
M Core/Containers/StringUtil.cc

Added count_substrs().

M StandAlone/inputs/UPS_SPEC/ups_spec.xml

Updated <dbg_[Begin|End]Index> to use MULTIPLE_VECTORS (instead of string).

21 lines of code changed in 5 files:

luitjens 2009-03-30 17:36 Rev.: 43930

Added some grid bulletproofing.

28 lines of code changed in 2 files:

jthornoc 2009-03-30 17:08 Rev.: 43926

Some bug fixes.

147 lines of code changed in 6 files:

dav 2009-03-30 17:04 Rev.: 43925


M CCA/Components/ProblemSpecification/ProblemSpecReader.cc

Update ups_spec to allow for validating MULTIPLE_VECTORS.

M StandAlone/inputs/UPS_SPEC/ups_spec.xml

Use MULTIPLE_VECTORS for <min_patch_size>

M Core/Containers/StringUtil.h
M Core/Containers/StringUtil.cc
M Core/Util/FileUtils.cc

Clean up StringUtil functions.


79 lines of code changed in 5 files:

harman 2009-03-30 14:41 Rev.: 43924

with -gridstats option dump out the refinement ratio for each level.

4 lines of code changed in 1 file:

charlesreid 2009-03-27 23:41 Rev.: 43912

Updating UPS spec to include <Moment> tag for DQMOM, and updating SpatialOps class to recognize all available model types when registering models

13 lines of code changed in 1 file:

charlesreid 2009-03-27 20:06 Rev.: 43911

Adding call to DQMOM linear solver to end of SpatialOps::scheduleTimeAdvance

8 lines of code changed in 1 file:

charlesreid 2009-03-27 19:15 Rev.: 43910

Commenting out unused variables; implementing machinery to differentiate between different internal coordinates for Kobayashi-Sarofim model

140 lines of code changed in 18 files:

charlesreid 2009-03-27 17:15 Rev.: 43909

Forgot a [c]

1 lines of code changed in 1 file:

charlesreid 2009-03-27 17:12 Rev.: 43908

Removing comments

2 lines of code changed in 1 file:

dav 2009-03-27 16:51 Rev.: 43907


M CoalModels/KobayashiSarofimDevol.cc

- Fix most of this to compile... But Charles/Jeremey, y'all are going
to need to go over this function. If nothing else, the commented
out FIXME at the end (looks like there was already a comment there
about work that needs to be done...).

8 lines of code changed in 1 file:

dav 2009-03-27 16:40 Rev.: 43906

Fix forward declarations.

0 lines of code changed in 2 files:

dav 2009-03-27 16:32 Rev.: 43904

M CCA/Components/SpatialOps/CoalModels/ModelFactory.h

- Reorder constructor initialization of variables to match order that
they are declared in the file. (This removes a compiler warning.)
- Added some cosmetic whitespace.

M CCA/Components/SpatialOps/DQMOM.h

- N_xi and N appear to be (and are used as) unsigned ints, so I made
them unsigned ints.
- Also, couldn't search for 'N' in the file, so I updated it to the
coding standard and named it N_.
- Can't (shouldn't?) put "DQMOM::" in front of function names in the
DQMOM class. (Fixes linux compiler error.)

M CCA/Components/SpatialOps/DQMOM.cc

- Removed "std::" as it is not necessary (using namespace std;).
- Used "unsigned int" as loop var for some N_'s (for consistency and to silence compiler warning).
- Commented out unused variable to silence compiler warning.

M CCA/Components/SpatialOps/SpatialOps.cc

- Commented out unused variable to silence compiler warning.

45 lines of code changed in 4 files:

dav 2009-03-27 16:20 Rev.: 43902

M CoalModels/BadHawkDevol.cc
M CoalModels/ConstantModel.h
M CoalModels/BadHawkDevol.h
M CoalModels/KobayashiSarofimDevol.h
M CoalModels/ModelFactory.h
M CoalModels/ConstantModel.cc

- Fix compilation errors. Clean up code formatting. Pass arguments
using const and reference to make code faster/cleaner.
- Match 'modelName' parameter's name in both .h and .cc files.
- Some of the parameters appeared to be in a different order from
other files, so made them consistent.
- Don't need ';' in .h files after {} for constructors/destructors.

M CoalModels/KobayashiSarofimDevol.cc

- Seems like there are a lot of compilation problems in this file, so
just commented them out. I'll take another pass in a minute.

59 lines of code changed in 7 files:

jthornoc 2009-03-27 16:17 Rev.: 43901

Fixed initialization to loop over factories rather than the generic labelMap list.

52 lines of code changed in 1 file:

charlesreid 2009-03-27 16:06 Rev.: 43900

Accidentally removed Jeremy's changes to CoalModel's sub.mk...

1 lines of code changed in 1 file:

charlesreid 2009-03-27 15:46 Rev.: 43899

Adding DQMOM & LU classes to sub.mk file, adding Kobayashi-Sarofim model to sub.mk file, and adding Constant Model class for constant model source terms.

224 lines of code changed in 9 files:

dav 2009-03-27 15:33 Rev.: 43898

Mac/OSX linking fixes.

0 lines of code changed in 4 files:

jthornoc 2009-03-27 14:06 Rev.: 43897

Whoops! Forgot to actually add the model to the tree for the particle velocities.

229 lines of code changed in 3 files:

jthornoc 2009-03-27 13:54 Rev.: 43896

Added a model for the particle velocities

76 lines of code changed in 13 files:

charlesreid 2009-03-27 12:14 Rev.: 43895

Adding/updating coal models and model factory to accept field labels, and adding correct Taylor-Green velocity field to SpatialOps.cc

210 lines of code changed in 8 files:

jas 2009-03-27 10:45 Rev.: 43894

Initialize values.

0 lines of code changed in 2 files:

jas 2009-03-27 10:44 Rev.: 43893

Remove sgi woff ifdefs.

9 lines of code changed in 136 files:

harman 2009-03-27 10:40 Rev.: 43892

parseAndLookupMaterial()
- for single material problems return matl 0
- for multi material problems return user specified matl.

14 lines of code changed in 1 file:

charlesreid 2009-03-26 19:59 Rev.: 43890

Fixing how DQMOM accesses variables from the data warehouse

30 lines of code changed in 1 file:

charlesreid 2009-03-26 19:58 Rev.: 43889

Adding gas phase temperature to SpatialOps' Fields class

19 lines of code changed in 4 files:

guilkey 2009-03-26 17:11 Rev.: 43888

Make a Weibull distribution of the failure stress (or strain) an option.

17 lines of code changed in 2 files:

guilkey 2009-03-26 17:03 Rev.: 43886

Adding a Weibull distribution, so that material properties in MPM can now be
assigned according to either this or a normal (Gaussian) distribution.

137 lines of code changed in 3 files:

charlesreid 2009-03-26 16:40 Rev.: 43885

Undoing changes (for real this time)

3 lines of code changed in 4 files:

charlesreid 2009-03-26 16:12 Rev.: 43883

Undoing ModelBase changes

4 lines of code changed in 6 files:

harman 2009-03-26 15:37 Rev.: 43877

MPMICE:
- moved scheduleDoAnalysis after scheduleParticlePrelocate
SerialMPM:
- added ability to call dataAnalysis modules

61 lines of code changed in 3 files:

charlesreid 2009-03-26 15:21 Rev.: 43876

Committed incorrect versions of DQMOM.h and DQMOM.cc... committing correct versions this time.

232 lines of code changed in 2 files:

charlesreid 2009-03-26 15:19 Rev.: 43875

Two major updates:
1) adding DQMOM class and LU solver class into code
2) modifying ModelBase and model classes to take Fields* as arguments in constructors, and adding Kobayashi Sarofim devolatilization model

However, there are a few issues still remaining with the Kobayashi Sarofim model; those will be fixed shortly.

827 lines of code changed in 10 files:

guilkey 2009-03-26 15:11 Rev.: 43873

John, Justin Siddarth and I tracked down some unitialized variables in the code that deals with particle variables that were causing the code to crash on
optimized 32 bit build, e.g. on my VMware installation.

7 lines of code changed in 3 files:

harman 2009-03-26 15:04 Rev.: 43872

only schedule doAnalysis if on the finest level

27 lines of code changed in 3 files:

dav 2009-03-26 14:45 Rev.: 43871


M DataArchiver.cc

- Initialize d_writeMeta to false. This fixes a bug that occurred
when the <DataArchiver> was told not to save data
(<outputTimestepInterval> == 0). In this case, no new uda directory
is created. However, if d_writeMeta is true (or uninitialized as in
this case) then the DataArchiver tries to write files to a directory
that was never created.

- Some cosmetic white space fixes. Only this line is a real update:

+ d_writeMeta = false;

77 lines of code changed in 1 file:

dav 2009-03-26 14:40 Rev.: 43870

Fix a couple compiler warnings.

2 lines of code changed in 1 file:

harman 2009-03-26 12:59 Rev.: 43869

-formating
-added bulletproofing
-added ability to extract Matrix3 variables
-Only extract particles that are above a user defined colorThreshold

86 lines of code changed in 2 files:

harman 2009-03-26 10:12 Rev.: 43864

The user needs to input a string for the material "name", not an integer, or blank
when a model is used. This eliminates the models from throwing a cryptic
exception when the user forgets to associate a Model/analysis tool
with a material.

5 lines of code changed in 1 file:

jthornoc 2009-03-25 22:00 Rev.: 43863

Changed the source term access in DQMOMEqn and initialized source terms in SpatialOps.cc

26 lines of code changed in 2 files:

harman 2009-03-25 17:28 Rev.: 43861

initial commit for on-the-fly analysis module particleExract.
- it basically works for int, double, Vectors variables
- needs to be further refined and tested

626 lines of code changed in 5 files:

burghard 2009-03-25 16:29 Rev.: 43860

fixed the index on internal state variable array

1 lines of code changed in 1 file:

jas 2009-03-25 08:30 Rev.: 43854

Remove 'spatial ops materials' debug output.

2 lines of code changed in 1 file:

jas 2009-03-24 15:50 Rev.: 43846

Add malloc trace library to sci_try_link for hypre and petsc.

8 lines of code changed in 3 files:

guilkey 2009-03-24 15:45 Rev.: 43845

Add two additional requires to scheduleApplyExternalLoads.

3 lines of code changed in 1 file:

jas 2009-03-24 14:32 Rev.: 43844

Test for the existance of a non-zero size leak file.

1 lines of code changed in 1 file:

jas 2009-03-24 14:32 Rev.: 43843

Only run memory leak check if sus was successfully run.

15 lines of code changed in 1 file:

jas 2009-03-24 14:32 Rev.: 43842

Added memory leak testing in the regression_tester script.

Broke out the MallocTrace library into a mpi and non-mpi version when
including it into the MPI_LIBRARY flag in configure.ac.

Changed various sub.mk to include the MPI_LIBRARY in the testprograms
directory.

36 lines of code changed in 9 files:

sshankar 2009-03-24 13:31

Fixed issues with contouring. Added ghost cells to patches.

993 lines of code changed in 4 files:

harman 2009-03-24 12:30 Rev.: 43839

update inputfile name

3 lines of code changed in 3 files:

dav 2009-03-24 11:08 Rev.: 43837

Fix memory leak.

2 lines of code changed in 1 file:

jthornoc 2009-03-24 10:06 Rev.: 43835

Changed directory name in the ARCHES tester to match the change made yesterday.

2 lines of code changed in 1 file:

jthornoc 2009-03-23 18:55 Rev.: 43829

Corrected path for new inut spec.
Cleaned up EqnBase.h

10 lines of code changed in 3 files:

jas 2009-03-23 17:29 Rev.: 43828

Check for a clean shutdown of sus instead of looking for return code from sus.
This should fix issues with our error handling when using mpi.

10 lines of code changed in 1 file:

jthornoc 2009-03-23 17:04 Rev.: 43827

Added spatialOps spec.
Moved specialization of the DQMOM functonality back into the DQMOM class and used dynamic_cast in spatialOps.cc

41 lines of code changed in 3 files:

dav 2009-03-23 16:57 Rev.: 43826

Fix filesytem check when input file is bad. Fix a couple of compiler warnings.

7 lines of code changed in 1 file:

guilkey 2009-03-23 16:43 Rev.: 43825

Add the additional input arguments to the appendElements list.

22 lines of code changed in 1 file:

dav 2009-03-23 15:51 Rev.: 43824


- Updated the ups validation code.
- Split the ups_spec into several different files.
- Added -do_not_validate flag.

See below for details:

D StandAlone/inputs/ups_spec.xml
A StandAlone/inputs/UPS_SPEC
AM + StandAlone/inputs/UPS_SPEC/ups_spec.xml
A StandAlone/inputs/UPS_SPEC/constitutive_models.xml
A StandAlone/inputs/UPS_SPEC/mpm_spec.xml
A StandAlone/inputs/UPS_SPEC/ice_spec.xml
A StandAlone/inputs/UPS_SPEC/arches_spec.xml

- Moved the ups_spec.xml file into UPS_SPEC and broke out pieces of it into separate files.
More pieces can probably be broken out and/or other files created for those pieces.
- Note, a lot of changes were made to the .ups spec (by other people) while I was doing this.
I tried to incorporate those changes, but might have misses a few. If so, I apologize.

M CCA/Components/ProblemSpecification/ProblemSpecReader.cc

- Added the ups_spec child requirement ALL_OR_NONE_OF and fixed the
ONE_OF. Added some bulletproofing to make sure that specified
children/attributes actually exist.
- Fixed a number of error statements to be more clear.
- Updated the <include> directive to allow for specifying a section of
a file.

M Core/ProblemSpec/ProblemSpec.h
M Core/ProblemSpec/ProblemSpec.cc

- getAttribute() functions should be 'const'.

M StandAlone/inputs/Models/Radiation/impHotBlob_Container.ups

- Removed 2nd <absorbingSolid>... Todd/Jeremy, is this right?

M StandAlone/inputs/MPMICE/grainSlice_noReact.ups

- Cosmetic cleanup. Don't need an explicit </end_tag> if the tag doesn't have children.

M StandAlone/inputs/MPMICE/LODI_BUG.ups

- The <union> tag had only one child, so I removed it...
- Spaced out some input values to make it easier to see them.

M StandAlone/inputs/IS/ArchesHeatUpExplosion/HTContainer_arches_mpmice.ups

- <DataArchiver> requires an <outputInterval>.

M StandAlone/sus.cc

- Added a '-do_not_validate' flag to sus to turn off .ups validation.
I highly suggest not using it. ;) A warning is displayed on the screen if you do.

M CCA/Components/DataArchiver/DataArchiver.cc

- Just some cosmetic cleanups.

283 lines of code changed in 5 files:

jthornoc 2009-03-23 15:18 Rev.: 43822

Fixed an uninitialized variable.

1 lines of code changed in 1 file:

jthornoc 2009-03-23 12:35 Rev.: 43818

Removed some more ancient input files.
Removed the required tag <probe_data> and made d_probe_data true if the <ProbePoints> exists.

3 lines of code changed in 2 files:

jthornoc 2009-03-22 00:11 Rev.: 43807

Added beginings of the time advance for DQMOM equations.
Fixed bug with a couple of access functions for DQMOM eqns.

43 lines of code changed in 4 files:

luitjens 2009-03-21 15:30 Rev.: 43806

Fixed ASSERT bug with rewindow in uda2nrrd that was also in uda2vis

1 lines of code changed in 1 file:

luitjens 2009-03-21 12:07 Rev.: 43805

Modified the WAIT_FOR_DEBUGGER macro so that it is now a function call. This is nicer in gdb.


16 lines of code changed in 3 files:

luitjens 2009-03-21 12:04 Rev.: 43804

Don't place an ASSERT around the rewindow. Doing this will causes the rewindow to only happen in debug builds.

3 lines of code changed in 1 file:

jthornoc 2009-03-21 02:07 Rev.: 43803

Fixed the way we handle extra scalar input.
Changed input files to conform.

90 lines of code changed in 2 files:

jthornoc 2009-03-20 14:18 Rev.: 43792

Changed "requiredLabels" to "ICLabels".

23 lines of code changed in 5 files:

jthornoc 2009-03-20 00:06 Rev.: 43786

Now using new_dw->exists rather than my own boolean. (thanks Dav!)
Also added the BadHawkDevol builder to the model registration.

13 lines of code changed in 8 files:

jthornoc 2009-03-19 23:50 Rev.: 43785

Added the beginings of the Badzioch and Hawksley devol. model.
Added quadrature node to the modelBase.
Removed a SourceTerm reference (rather than SourceTermBase) in ConstSrcTerm...Don't know how that got in there.

185 lines of code changed in 8 files:

jas 2009-03-19 16:44 Rev.: 43782

Added input_file.sh which validates a directory or all input files.

Input file fixes.

24 lines of code changed in 1 file:

jthornoc 2009-03-19 15:38 Rev.: 43781

Added interface to model factory.
Now each DQMOM transport equation holds a list of models.

126 lines of code changed in 4 files:

jas 2009-03-18 23:33 Rev.: 43774

Use findBlockWithOutAttributes() when searching for MaterialProperties
to avoid finding the MaterialProperties add=true node.

This is second part of the changes needed to replace the
AddMaterialProperties with attribute add=true for MaterialProperties.

69 lines of code changed in 24 files:

jas 2009-03-18 23:33 Rev.: 43773

Check if the MaterialProperties tag has an attribute.

5 lines of code changed in 1 file:

jas 2009-03-18 23:33 Rev.: 43772

Remove the <AddMaterialProperties> tag and replace it with the
<MaterialProperties add="true">.

Add the function ProblemSpec::findBlockWithAttribute('name','attr') which
finds a block with an attribute used for the change in the MaterialProperties
tag.

Change input files to use the new MaterialProperties tag when adding a
material.

Eliminate from the ups_spec.xml all references to AddMaterialProperties.

67 lines of code changed in 4 files:

jthornoc 2009-03-18 16:11 Rev.: 43767

Added a DQMOM eqn factory.
Added a mechanism for creating DQMOM equations on the fly.
Added interface to DQMOM section of the input file.

305 lines of code changed in 9 files:

harman 2009-03-18 08:55 Rev.: 43754

Now using the correct path for svnStat & svnDiff

1 lines of code changed in 1 file:

luitjens 2009-03-17 18:38 Rev.: 43751

only use export on files, for directories use checkout.

0 lines of code changed in 2 files:

luitjens 2009-03-17 17:41 Rev.: 43750

Don't allow tile sizes to grow if doing so would violate alignment constraints

2 lines of code changed in 1 file:

luitjens 2009-03-17 17:05 Rev.: 43749

use export instead of checkout so that it works on a single file.

4 lines of code changed in 1 file:

harman 2009-03-17 15:23 Rev.: 43746

Changes so ups_spec passes. This input file crashes on the first timestep.

46 lines of code changed in 1 file:

qymeng 2009-03-17 15:05 Rev.: 43745

Fixed a bug which passed wrong size to MPI_Allgatherv()

1 lines of code changed in 1 file:

jthornoc 2009-03-17 14:44 Rev.: 43744

Returned a reference rather than a copy.


2 lines of code changed in 2 files:

jthornoc 2009-03-17 14:34 Rev.: 43743

Added a way to access all equations at once in factory.
Changed the way spatialops was looping over the solution to the equations by using eqn map rather than a looking up each equation individually.
Added an access function to get an eqn's name.

17 lines of code changed in 3 files:

jas 2009-03-17 12:59 Rev.: 43738

Add check for --with-teem when using --with-visit.

5148 lines of code changed in 2 files:

dav 2009-03-17 12:27 Rev.: 43737

Combined Core/Math, Core/Disclosure, and Core/Geometry into one
library (with respect to linking (at least for now)) in order to get
around the circular dependency problem we are having under OSX... (and
on any other machine where we need to build static libraries.) Had to
add Core/Math to the PSELIBS line of a number of sub.mk files.

Currently all the files are compiled into the Core/Math library (but
still exist in their original locations). I created dummy.cc files to
allow me to still create the Core/Disclosure and Core/Geometry
libraries (which are now basically empty) so that I didn't have to
update all the sub.mk files to remove these references. However, at
some point in the near future, this needs to be cleaned up.

M Core/Persistent/Persistent.cc

For some reason Persistent.cc was #including <Endian.cc> which caused
symbols to appear twice. I changed this to #include the .h file.
This shouldn't be an issue... and may have only shown up (now, instead
of years ago) because I don't have TEEM turned on right now (TEEM used
to be on by default). (With TEEM turned on, Persistent.cc uses nrrd.h
for endian stuff.)

M CCA/Components/Arches/MCRT/ArchesRMCRT/RMCRTRRSDStratified.cc

Replaced 100000000000000000 with DBL_MAX, so that compilations on 32
bit machines don't error out.

143 lines of code changed in 35 files:

harman 2009-03-16 17:21 Rev.: 43727

massMomEng_src.cc: Material->material
massX.ups: now uses massMomEng model
impAdvect-SineLodi.ups: debug->Debug
ups_spec.xml: Adding more

1 lines of code changed in 1 file:

jthornoc 2009-03-16 16:30 Rev.: 43723

- Moved d_labalMap into Fields.h
- Created a DQMOM type equation.

673 lines of code changed in 7 files:

harman 2009-03-16 16:28 Rev.: 43722

-removed xml tags that didn't belong.
-updated the ups_spec
-cleaned up the .ups files

27 lines of code changed in 1 file:

luitjens 2009-03-16 15:56 Rev.: 43721

Reworked the svn revert script. It no longer uses merge and shouldn't have any problems with Packages/Uintah.

The script creates a 'Packages/Uintah' symbolic link which points to source.

The script then deletes the revert target and then checks out the revision requested.

To undo changes by this script use 'svn up' (this has to be done twice).

39 lines of code changed in 1 file:

luitjens 2009-03-16 11:18 Rev.: 43707

Fixed a bug in svn_revert.

1 lines of code changed in 1 file:

charlesreid 2009-03-16 00:06 Rev.: 43705

Adding access methods to Transport Equation object classes; one is an access function to access the transported variable's label (d_transportVarLabel), one is to access the (string) list of sources (d_sources), and one is to access the (string) list of models (d_models)

9 lines of code changed in 2 files:

dav 2009-03-13 18:54 Rev.: 43702


Fixes to the code that broke when I fixed the checkForInputError()
code.

M Grid/BoundaryConditions/BoundCondFactory.cc

Clean up the Boundary Condition input code. Not sure if we really
should use the try/catch mechanism to determine if the BC is a double
or a vector... but perhaps there isn't any other choice. However, I
think the <BCType> tag should be fixed... perhaps add an attribute
that specifies what type it really is instead of relying on the
string in the <value> tag...?

M ProblemSpec/ProblemSpec.h

Update the documentation on get() to be more accurate.

M ProblemSpec/ProblemSpec.cc

* Fix indentation of #includes.
* Remove old SGI pragmas.
* use namespace std
* Fix checkForInputError() error strings.
* Use {} for if statement.

59 lines of code changed in 4 files:

dav 2009-03-13 17:30 Rev.: 43700

Exposed checkForInputError() as it might be useful in other locations. Also fixed it to use a 'enum' instead of a 'string' (sigh). BTW, all the checks for the validity of 'double' before hand were actually not doing anything as only "int" and "float" were being tested. (Note, with respect to a 'string', doubles and floats are the same thing.)

5 lines of code changed in 1 file:

dav 2009-03-13 17:23 Rev.: 43699

Exposed checkForInputError() as it might be useful in other locations. Also fixed it to use a 'enum' instead of a 'string' (sigh). BTW, all the checks for the validity of 'double' before hand were actually not doing anything as only 'int' and 'float' were being tested. (Note, with respect to a 'string', doubles and floats are the same thing.)

52 lines of code changed in 1 file:

dav 2009-03-13 17:19 Rev.: 43698

Deleted VisIt/UdaReader as this was old code and is not needed anymore...

0 lines of code changed in 1 file:

guilkey 2009-03-13 16:42 Rev.: 43697

Change the usage to not lead the user to believe that iend and istart are comma delimited integers.

2 lines of code changed in 1 file:

jas 2009-03-13 15:27 Rev.: 43694

fix bug --with-libxml2 specification

1 lines of code changed in 1 file:

jas 2009-03-13 15:25 Rev.: 43693

fix bug with --with-libxml2 specification

5 lines of code changed in 1 file:

dav 2009-03-12 19:49 Rev.: 43685

Trying to restore log history of these files.

1996 lines of code changed in 8 files:

dav 2009-03-12 19:23 Rev.: 43684

Reverting previous Core/Datatypes commit as this broke VisIt plugin. Will fix VisIt plugin and then recommit this.

3675 lines of code changed in 69 files:

dav 2009-03-12 17:54 Rev.: 43678

Removed Persistent from Datatypes.. Am going to remove all the Datatypes next, but just in case wanted to hold onto this update.

35 lines of code changed in 41 files:

luitjens 2009-03-12 16:44 Rev.: 43673

Initial commit for a script which hopefully will safely revert code over the code restructure using svn merge. This script is designed to only go one way as it is meant for testing old code only. To undo changes made by this script use `svn revert target`. This script should probalby only be applied to a clean tree.

Usage: svn_revert -r revision# //applies the merges to the current directory
svn_revert -r revision# target //applies the merges to the target

This script does not merge any changes that occured during the restructure.

97 lines of code changed in 1 file:

jthornoc 2009-03-12 12:59 Rev.: 43670

Missed a class.

0 lines of code changed in 2 files:

jthornoc 2009-03-12 12:58 Rev.: 43669

Made some subfolders for better organization.

1772 lines of code changed in 35 files:

jthornoc 2009-03-12 11:49 Rev.: 43667

Removing unnecessary code.

0 lines of code changed in 2 files:

harman 2009-03-12 10:49 Rev.: 43665

test of email messages

1 lines of code changed in 1 file:

luitjens 2009-03-11 16:31 Rev.: 43613

use ASSERT instead of assert

0 lines of code changed in 3 files:

luitjens 2009-03-11 16:31 Rev.: 43612

Don't set non virtual functions equal to 0.

0 lines of code changed in 1 file:

jthornoc 2009-03-11 14:55 Rev.: 43603

Deleting a swp file.

0 lines of code changed in 1 file:

jthornoc 2009-03-11 14:53 Rev.: 43602

Whoops. Forgot to actually add the component.

3089 lines of code changed in 31 files:

jthornoc 2009-03-11 14:52 Rev.: 43601

Adding the spatialOps Component.

46 lines of code changed in 5 files:

harman 2009-03-10 18:04 Rev.: 43557

moved radiatingGas tag into the RadiationModel tag.

12 lines of code changed in 1 file:

guilkey 2009-03-10 17:31 Rev.: 43555

Combine solveEquationsMotion and integrateAcceleration into one task,
computeAndIntegrateAcceleration. This should provide a modest performance
improvement, and an overall reduction in lines of code.

Also, stripped out the damping rate calculation code. This code was fairly
indefensible and pretty much never used. The d_dampingCoefficient flag is
still in place, and it can now used in computing the acceleration. This is
similar to code that has been in place, but commented out, for a long time.
The damping force is now -d_dampingCoefficient*velocity.

Added a cut off mass for computing the acceleration. If the nodal masses are
below this cut off value, then that node's acceleration will be zero. This is
definitely a hack, but it is easy to defend based on the numerics of MPM.

These changes didn't affect the results for the MPM, MPMArches or MPMICE
regression tests.

264 lines of code changed in 18 files:

jas 2009-03-10 16:21 Rev.: 43549

Add math library to link line for teem check.

3 lines of code changed in 2 files:

jas 2009-03-10 13:20 Rev.: 43545

Add (Z_LIBRARY) to sub.mk line.

9 lines of code changed in 9 files:

csafe-tester 2009-03-10 10:30 Rev.: 43544

Modified doxygen scripts to account for new tree structure.

0 lines of code changed in 2 files:

luitjens 2009-03-10 10:26 Rev.: 43543

Added a missing #ifndef

0 lines of code changed in 2 files:

luitjens 2009-03-10 10:12 Rev.: 43542

updates to the RT scripts and doxygen scripts.

23 lines of code changed in 3 files:

jas 2009-03-09 21:43 Rev.: 43540

Change configure lines and remove Packages/Uintah.

68 lines of code changed in 1 file:

jas 2009-03-09 21:38 Rev.: 43539

Only compile if both teem and visit are defined.

3 lines of code changed in 1 file:

jas 2009-03-09 21:20 Rev.: 43538

Change the location of the src/StandAlone/inputs.

0 lines of code changed in 2 files:

jas 2009-03-09 20:55 Rev.: 43537

Only compile if Teem is defined.

11 lines of code changed in 5 files:

jas 2009-03-09 20:36 Rev.: 43536

Remove Packages/Uintah

2 lines of code changed in 1 file:

jas 2009-03-09 20:15 Rev.: 43535

Add cstdlib.

0 lines of code changed in 2 files:

jas 2009-03-09 20:02 Rev.: 43534

Conditional compile if visit is specified.

8 lines of code changed in 3 files:

jas 2009-03-09 18:48 Rev.: 43533

Remove unused SCIRun checks

355 lines of code changed in 4 files:

jas 2009-03-09 18:48 Rev.: 43532

Remove Packages/Uintah

2 lines of code changed in 2 files:

jas 2009-03-09 18:00 Rev.: 43530

Remove Core/XMLUtil in LIBS

7 lines of code changed in 7 files:

jas 2009-03-09 17:59

Add PatchToField.h

130 lines of code changed in 3 files:

jas 2009-03-09 17:56 Rev.: 43527

Use UintahMiscMath.h for getNan()

1 lines of code changed in 1 file:

jas 2009-03-09 17:54

Change to_char_ptr to (const char *) to eliminate requirement of XMLUtil.h

36 lines of code changed in 7 files:

jas 2009-03-09 17:51 Rev.: 43524

Remove unused files.

0 lines of code changed in 8 files:

jas 2009-03-09 17:45 Rev.: 43523

Remove Teem Dataflow items

0 lines of code changed in 12 files:

jas 2009-03-09 17:05 Rev.: 43522

Delete GUI/. Modify Core libraries to include.

3 lines of code changed in 11 files:

jas 2009-03-09 16:43 Rev.: 43521

Remove sgi_stl_warnings include line

1725 lines of code changed in 610 files:

jas 2009-03-09 16:38 Rev.: 43519

Remove SCIRun packages and dependencies.

131 lines of code changed in 4 files:

jas 2009-03-09 16:37 Rev.: 43518

Formatting changes.

5 lines of code changed in 1 file:

jas 2009-03-09 16:37 Rev.: 43517

Remove Packages/Uintah.

4 lines of code changed in 4 files:

jas 2009-03-09 16:35 Rev.: 43516

Remove Packages from sub.mks.

18 lines of code changed in 24 files:

jas 2009-03-09 15:44 Rev.: 43514

Remove Packages/Uintah.

16 lines of code changed in 9 files:

jas 2009-03-09 15:37 Rev.: 43513

Remove the Packages/Uintah/

45 lines of code changed in 39 files:

jas 2009-03-09 15:29

Remove the Packages/Uintah/

5503 lines of code changed in 1463 files:

jas 2009-03-09 15:23

Remove the Packages/Uintah/

1816 lines of code changed in 461 files:

jas 2009-03-09 15:18 Rev.: 43505

Add in Uintah/Core directories

0 lines of code changed in 2 files:

jas 2009-03-09 15:15 Rev.: 43504

Remove Packages/

0 lines of code changed in 2352 files:

jas 2009-03-09 15:14 Rev.: 43503

Move Uintah/Core/Util to Core/Util/

667 lines of code changed in 13 files:

jas 2009-03-09 15:11 Rev.: 43501

Add Uintah/Core/Math files

21 lines of code changed in 1 file:

jas 2009-03-09 15:09 Rev.: 43500

Move Uintah/Core/Math to Core/Math

5558 lines of code changed in 55 files:

jas 2009-03-09 15:08 Rev.: 43499

Rename MiscMath.h

0 lines of code changed in 2 files:

jas 2009-03-09 15:04 Rev.: 43495

Move Uintah/Core/Exceptions to src/Core/Exceptions

1394 lines of code changed in 39 files:

jas 2009-03-09 15:00 Rev.: 43493

Add in Uintah Datatypes.

19 lines of code changed in 1 file:

jas 2009-03-09 14:54

Move Uintah/Core/Datatypes to src/Core/Datatypes

2160 lines of code changed in 26 files:

jas 2009-03-09 14:52 Rev.: 43489

Move Uintah/Core/Datatypes to src/Core/Datatypes.

2320 lines of code changed in 30 files:

jas 2009-03-09 14:37 Rev.: 43486

Move Uintah/tools to src/tools

948 lines of code changed in 11 files:

jas 2009-03-09 14:33 Rev.: 43484

Add in Uintah testprograms

31 lines of code changed in 1 file:

jas 2009-03-09 14:30 Rev.: 43483

Move Packages/Uintah/testprograms to src/testprograms

388 lines of code changed in 4 files:

jas 2009-03-09 14:24 Rev.: 43482

Remove SCIRun/testprograms/Component

0 lines of code changed in 24 files:

jas 2009-03-09 14:20 Rev.: 43479

Move Uintah TODO

126 lines of code changed in 1 file:

jas 2009-03-09 14:08 Rev.: 43473

Delete main/

0 lines of code changed in 1 file:

jas 2009-03-09 14:07 Rev.: 43472

Delete nets/

0 lines of code changed in 1 file:

jas 2009-03-09 14:07 Rev.: 43471

Delete pixmaps scirunrc Packages/Uintah/Dataflow.
Rename src/scripts to src/buildscripts.
Move Packages/Uintah/CCA src/CCA.

0 lines of code changed in 2 files:

jas 2009-03-09 14:01 Rev.: 43470

Delete CCA/ Comm Geom GeomInterface/ globus_threads/ GuiInterface/ GuiInterface/ ICom/ ImportExport/ Init/ ParticleSystem/ Services/ SystemCall/ TkExtensions/ Volume/ Winfix/ XMLUtil/

0 lines of code changed in 26 files:

jas 2009-03-09 13:59 Rev.: 43469

Remove Algorithms/ Babel/ Bundle/

0 lines of code changed in 11 files:

jas 2009-03-09 13:54 Rev.: 43468

Remove CMakeLists.txt

0 lines of code changed in 10 files:

jas 2009-03-09 13:47 Rev.: 43466

Delete main SCIRun directories

0 lines of code changed in 45 files:

luitjens 2009-03-06 17:15 Rev.: 43449

Now checking the absolute memory increase in addition to the percent. For RT to fail the memory must increase by both 10% or more and 1 MB or more.

0 lines of code changed in 4 files:

luitjens 2009-03-06 15:20 Rev.: 43446

Fixed a few initilization problems.

0 lines of code changed in 2 files:

guilkey 2009-03-05 17:37 Rev.: 43432

Cleaning this new model up a bit.

0 lines of code changed in 2 files:

luitjens 2009-03-05 16:23 Rev.: 43428

Modified the debug output to hopefully reduce message interleaving on ranger.

13 lines of code changed in 1 file:

luitjens 2009-03-05 15:29 Rev.: 43426

Modified some debugging output.

102 lines of code changed in 3 files:

guilkey 2009-03-05 15:11 Rev.: 43424

Adding the previously neglected AA_MMS.h file.

0 lines of code changed in 3 files:

guilkey 2009-03-05 13:48 Rev.: 43420

Adding a puda option to compute the L-infinity error for the 3D axis aligned
problem. Todd will consider this pollution of puda, but will be wise to keep
that opinion to himself, as he has been nagging me to get an MMS solution into
MPM for a long time, and this is a start.

97 lines of code changed in 7 files:

luitjens 2009-03-05 13:39 Rev.: 43419

Commented out some debugging spew that was having problems on mac.

0 lines of code changed in 2 files:

guilkey 2009-03-04 20:54 Rev.: 43412

Add simplified neo-hookean model used in Phil's MMS simulations.

561 lines of code changed in 6 files:

dav 2009-03-04 14:21 Rev.: 43398

M StandAlone/sus.cc

Don't show a stack trace if a ProblemSetupException is caught. (In
these cases, the stack trace does not provide any helpful
information.)

M CCA/Components/ProblemSpecification/ProblemSpecReader.cc

When a tag is missing, there is not xml node from which to extract
a line number, so don't try to do it.

0 lines of code changed in 4 files:

harman 2009-03-03 19:16 Rev.: 43389

-removed command line component options
-compliance with ups_spec (getting closer)

0 lines of code changed in 18 files:

dav 2009-03-03 17:24 Rev.: 43384

Fix error (file/line#) reporting for xml parsing errors.

23 lines of code changed in 1 file:

guilkey 2009-03-03 17:21 Rev.: 43383

Added code to do prescribed homogeneous deformations, which basically means
overwriting the solution of the momentum equation with a prescribed deformation.

0 lines of code changed in 8 files:

jthornoc 2009-03-03 15:36 Rev.: 43381

Fixed a bug with prefill that was committed yesterday.

Also, commented out a couple of variables that were causing warnings because they were unused.

0 lines of code changed in 2 files:

jas 2009-03-03 14:48 Rev.: 43380

Fix bug when a sus fails but the return code indicated it passed.

Remove some commented out code and put some code into functions.

0 lines of code changed in 2 files:

luitjens 2009-03-03 12:08 Rev.: 43377

Fixed a couple of bugs which could lead to invalid profile data.

47 lines of code changed in 1 file:

jthornoc 2009-03-03 11:45 Rev.: 43376

Missed a boolean check for extra scalars.

13 lines of code changed in 1 file:

luitjens 2009-03-02 14:47 Rev.: 43368

Added a few debug streams. No longer profile fine tasks seperately from regular tasks.

308 lines of code changed in 21 files:

jthornoc 2009-03-02 14:34 Rev.: 43367

- Added whitespace
- Removed the extra loop for extra scalars and put it in the main loop
- Added comments
- Changed the way we were checking to see if a point was inside the geometry
- Commented out the call to get_ramping_factor (wasn't being used)

No change in answers expected.

58 lines of code changed in 1 file:

luitjens 2009-03-01 13:11 Rev.: 43363

Don't schedule data checkpointing if checkpointing is disabled.

0 lines of code changed in 2 files:

February 2009 »

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