June 2010 Commit Log

Number of Commits:
92
Number of Active Developers:
11
qymeng 2010-06-29 11:11 Rev.: 45785

Changed loops on vector varlist from int to iterator.

9 lines of code changed in 1 file:

luitjens 2010-06-28 11:22 Rev.: 45784

Changed a couple of size_t variables back to an int.

This is because Patch::selectType returns a fixedvector not a vector which is using a signed int parameter.
Also changed a couple of loops that loop backwards while >=0 back to a signed integer to avoid an underflow problem.

6 lines of code changed in 1 file:

jsutherland 2010-06-26 18:18 Rev.: 45783

- First cut at a general scalar transport equation. This is currently restricted to only diffusion.
- Add some input files into version control.
- Add TabProps interface.
- Add Doxygen configuration file to generate documentation for Wasatch.
- Add more documentation in source.

2374 lines of code changed in 20 files:

dav 2010-06-25 15:04 Rev.: 45781

#include vector in .h file to use vector. Add names to public function parameters (need to do this to all functions in .h file). Use std:: as necessary.

17 lines of code changed in 2 files:

luitjens 2010-06-25 08:33 Rev.: 45780

Use appropriate datatypes for STL containers.

int -> size_t
unsigned -> size_t


15 lines of code changed in 1 file:

jpeterson 2010-06-24 11:27 Rev.: 45777

Should fix memory leak. Code beautification.

491 lines of code changed in 2 files:

jmschrei 2010-06-24 10:49 Rev.: 45776

pass CXX and CXXFLAGS to cmake, so plugin is built with the same flags as everything else

1 lines of code changed in 1 file:

dav 2010-06-23 17:28 Rev.: 45775

The avtudaReaderMTMDFileFormat.C must be created (initially) before CMake is run... so I moved it up in the list of dependencies in the makefile. (This fixes the problem with just running 'make'... (Note, before 'make -j2' worked around the problem).) (This change is necessary due to the switch to CMake for the plugin (I think), and was not the case before CMake was used to build the plugin.) Also removed some unwanted tabs (be careful, some tabs (eg: the ones remaining) in makefiles are necessary).

7 lines of code changed in 1 file:

jpeterson 2010-06-23 17:02 Rev.: 45774

Implicit CNH now in UCNH. Will break RT because of round off errors on order of 1e-10 abs tolerance. GS will be replaced tomorrow morning

299 lines of code changed in 3 files:

dav 2010-06-23 15:05 Rev.: 45773

Added informational message to configure to let user know that check for VisIt is being run.

5 lines of code changed in 2 files:

dav 2010-06-23 15:00 Rev.: 45772

really fixed the configure check for cmake for VisIt

4 lines of code changed in 2 files:

dav 2010-06-23 14:40 Rev.: 45771

fixed the configure check for cmake for VisIt

2 lines of code changed in 2 files:

dav 2010-06-23 14:24 Rev.: 45770

configure check for cmake for VisIt

12 lines of code changed in 2 files:

guilkey 2010-06-23 13:47 Rev.: 45769

Fixed bug that was preventing cohesive zones from crossing patch boundaries.
Added a few comments, commented out an incorrect ASSERTRANGE.
Todd is the man.

18 lines of code changed in 1 file:

dav 2010-06-21 20:17 Rev.: 45767

Committing configure to go with previous commits configure.ac

28 lines of code changed in 1 file:

jsutherland 2010-06-21 20:16 Rev.: 45766

Minor changes to Wasatch:

- remove the HeatFlux expression and replace it by the more general
DiffusionFlux expression.

370 lines of code changed in 5 files:

dav 2010-06-21 20:16 Rev.: 45765

Fix error with mac fortran configure

4 lines of code changed in 1 file:

dav 2010-06-21 19:45 Rev.: 45764

Alphabetize lib list, which led to removing several duplicates. Added dependent OnTheFlyAnalysis lib (caught through Mac build).

0 lines of code changed in 2 files:

dav 2010-06-21 19:07 Rev.: 45763


Removing 'using namespace std;' from some .h files. This helps prevent
polluting the namespace.

M StandAlone/tools/dumpfields/FieldDumper.h
M StandAlone/tools/dumpfields/VectorDiags.h
M StandAlone/tools/dumpfields/ScalarDiags.h
M StandAlone/tools/dumpfields/TensorDiags.h
M Core/Containers/RunLengthEncoder.h

0 lines of code changed in 10 files:

dav 2010-06-21 19:02 Rev.: 45762


Fixing --without-fortran. (Some MPM optional fortran files weren't
being guarded.)

M include/sci_defs/uintah_testdefs.h.in

Added @DEF_NO_FORTRAN@ set to "#define NO_FORTRAN" if fortran disabled.
If you want to check for NO_FORTRAN, you need to

#include <sci_defs/uintah_defs.h> // For NO_FORTRAN

and then:

#if !defined(NO_FORTRAN)
...fortran code...
#endif

M CCA/Components/MPM/ConstitutiveModel/ConstitutiveModelFactory.cc
M CCA/Components/MPM/ConstitutiveModel/sub.mk

Turn off HypoElasticFortran, Kayenta, and Diamm (and fortran/ subdir)
if fortran disabled.

M configure.ac
M configure

- Added more specific build system variables for turning off fortran.
(Before, only needed to turn off all of Arches. Now need to turn off
parts of certain components (eg: MPM)).
- Clear out fortran build variables if fortran disabled.

M configVars.mk.in

Put NO_FORTRAN into Makefiles so it can be used to conditionally
build/not build fortran files as necessary.

10318 lines of code changed in 7 files:

jeff788 2010-06-21 17:27 Rev.: 45761

updated the README to reflect changes in the Kayenta source

0 lines of code changed in 2 files:

guilkey 2010-06-21 17:20 Rev.: 45760

For CohesiveZones:

1. Make failure in the shear direction symmetric.
2. Currently set failure criteria in the shear direction higher than will be
reached.
3. Make the cz.failed variable take on a value of 1 for normal failure, 2 for
shear failure.

12 lines of code changed in 1 file:

jpeterson 2010-06-21 11:12 Rev.: 45759

After checking differences in RT, failure was caused by roundoff error, Plasticity is now handled by UCNH

1 lines of code changed in 1 file:

jpeterson 2010-06-21 00:00 Rev.: 45758

Revert change that broke RT

1 lines of code changed in 1 file:

jpeterson 2010-06-20 18:18 Rev.: 45757

Fixed spelling of false

1 lines of code changed in 1 file:

jpeterson 2010-06-20 18:12 Rev.: 45756

Moved pressure stabilization outside particle subset loop so that original program excecution speed is matched

38 lines of code changed in 2 files:

harman 2010-06-17 13:56 Rev.: 45753

Label name change:
DDT(0/1)::onSurface -> onSurface
DDT(0/1)::surfaceTemp -> surfaceTemp

Scirun can't handle names with "::" in them.

15 lines of code changed in 2 files:

luitjens 2010-06-17 13:24 Rev.: 45752

Fixed another segfault in compare_uda.

1 lines of code changed in 1 file:

jpeterson 2010-06-17 10:59 Rev.: 45750

Fix memory leak that RT was picking up. Still need to replace Checkpoint files--this model saves bElBar labels while CompNeoHook did not originally

4 lines of code changed in 1 file:

luitjens 2010-06-17 08:23 Rev.: 45748

Verify that the number of variables is the same after removing ignored variables

6 lines of code changed in 1 file:

jsutherland 2010-06-16 17:33 Rev.: 45747

This checkin adds a new component (Wasatch) to Uintah. Wasatch uses
graph theory to automatically assemble algorithms from individual
"expressions." It also uses an operator approach to discrete field
operations, i.e. application of a gradient to a field. It provides
general wrapper capabilities for these "expression graphs" and exposes
them as Uintah tasks.

Currently Wasatch will not be built by default. This is to avoid
breaking other developers until we get the build system in shape.

Noteworthy changes outside of wasatch:

- the configure stuff was changed to allow Wasatch to be turned on
during configure. This required me to re-run autoconf, resulting
in numerous changes to configure since I was using a different
version of autoconf than was previously run.

- Modified the ups_spec.xml file to add a few more "common tags."
Dav is working on a better way to introduce these so that we don't
need to "pollute" this file.

- Modified CCA/Components/Parent/ComponentFactory.cc to plug Wasatch
in. In doing this, I moved a header file inclusion up a bit so
that the appropriate #define were available when including header
files.

- Changes to the appropriate sub.mk files to plug in the new component.

8878 lines of code changed in 46 files:

harman 2010-06-16 16:27 Rev.: 45746

ProblemSetup()
removed commented out code
actuallyInitialize()
- output the material indices and the names of the materials. For example:

Materials Indicies: MPM [Matls: {{0,1}}] ICE[Matls: {{2}}]
Material Names: 0) Steel Ring 1) Reactant 2) Product


20 lines of code changed in 1 file:

jpeterson 2010-06-16 16:25 Rev.: 45745

To see if the regression tester passes with UCNH

946 lines of code changed in 3 files:

jpeterson 2010-06-16 14:17 Rev.: 45744

Y and Z rotation were not correct previously. Fixed rotation and Error handling

0 lines of code changed in 2 files:

harman 2010-06-16 13:52 Rev.: 45743

added the conditional statement:
if (flags->d_reductionVars->accStrainEnergy ||
flags->d_reductionVars->strainEnergy) {

around all of the computes and puts for StrainEnergyLabel, yuck.

Will not change answers

311 lines of code changed in 31 files:

luitjens 2010-06-16 12:10 Rev.: 45740

Adjusted where the weighting functions are applied.

3 lines of code changed in 1 file:

luitjens 2010-06-16 11:24 Rev.: 45739

Moved some debug code into an assertion

2 lines of code changed in 1 file:

guilkey 2010-06-15 17:21 Rev.: 45737

Move the calculation of TotalMass and TotalVolume to
interpolateToParticlesAndUpdate to be correct and consistent with the other
reduction quantities.

19 lines of code changed in 1 file:

jpeterson 2010-06-15 15:18 Rev.: 45736

Moved angle calculation to setup to reduce time spent in inside()

53 lines of code changed in 3 files:

jpeterson 2010-06-15 14:08 Rev.: 45735

Removed debug output and added some example problems

0 lines of code changed in 1 file:

jpeterson 2010-06-15 13:23 Rev.: 45732

Ellipsoid geometry piece

485 lines of code changed in 6 files:

luitjens 2010-06-15 12:19 Rev.: 45731

Added the ability to weight particles or cells when partitioning the patches into particle or cell patches.

9 lines of code changed in 3 files:

harman 2010-06-15 09:57 Rev.: 45728

Being a little smarter.

Removed the d_AccStrainEnergy flag from input files and code. Added the flag
in d_reductionVars struct. To save the accumulated strain energy the user
needs to add:

<save label = "AccStrainEnergy"/>

to the ups file

24 lines of code changed in 5 files:

harman 2010-06-14 18:15 Rev.: 45727

ICE.h
added mass to the conservationTest_flags struct.

ICE.cc
ProblemSetup()
- instead of parsing the input file to determine if a reduction variable is being
saved used the dataArchiver::isLabelSaved()

scheduleTestConservation()
- placed condititional statements around each of the computes

testConservation()
- Computing the conserved quantities over all the patches in the subset before
putting them in the DW.
- placed condititional statements around each of the put statements
- totalMass is no longer always computed.

66 lines of code changed in 2 files:

harman 2010-06-14 16:38 Rev.: 45726

Put conditional statements around reduction variables.

SerialMPM.cc
- For the following reduction variables:
TotalMass
TotalMomentum
KineticEnenergy
ThermalEnergy
CenterOfMassPosition
TotalVolumeDeformed
placed the computes and put statements inside conditional statements. For example

if(flags->d_reductionVars->BananaNutBread){
t->computes(lb->BananaNutBreadLabel);
}


MPMFlags.cc/h
- added struct (reductionVars) that contains the various flags
- now passing dataArchive into readMPMFlags.

ImpMPMFlags.cc & AMRMPM.cc
- updated argument list to readMPMFlags()

134 lines of code changed in 9 files:

luitjens 2010-06-14 13:41 Rev.: 45725

Added the SCI_DEBUG ReductionTasks which outputs whenever a reduction task is ran.

5 lines of code changed in 2 files:

luitjens 2010-06-14 13:31 Rev.: 45724

Added the ability to query the data archive to see if a label is being saved. This will always return false if the output has been disabled by setting the output frequency to 0.


18 lines of code changed in 5 files:

luitjens 2010-06-14 13:08 Rev.: 45723

fixed indenting

288 lines of code changed in 1 file:

jas 2010-06-14 10:55 Rev.: 45722

Fix compiler warning.

1 lines of code changed in 1 file:

jpeterson 2010-06-13 19:57 Rev.: 45721

1) Fixed indexing error in pressure get and require in DDT1 2) Changed fromMaterial and removed malformed comments from PBX Array files

13 lines of code changed in 1 file:

jas 2010-06-10 15:12 Rev.: 45719

Add in some functions for probing particle data.

23 lines of code changed in 1 file:

harman 2010-06-10 09:52 Rev.: 45718

Back to 4.2 for now.

3 lines of code changed in 1 file:

harman 2010-06-10 09:21 Rev.: 45716

Switch from 4.2 to 4.3 compiler libraries

3 lines of code changed in 1 file:

jmschrei 2010-06-09 17:50 Rev.: 45715

removing old uda2nrrd files from uda2vis that aren't used, renaming what's left to be more consistent

2058 lines of code changed in 27 files:

jmschrei 2010-06-09 17:20 Rev.: 45714

removing dependency on teem from uda2vis

2 lines of code changed in 2 files:

jmschrei 2010-06-09 16:58 Rev.: 45713

adding proc_id variable to show which processor a patch was assigned to

4770 lines of code changed in 3 files:

jeff788 2010-06-09 14:04 Rev.: 45712

added the diamm material model

4451 lines of code changed in 6 files:

guilkey 2010-06-08 17:23 Rev.: 45710

Ooops, flags should have been flag

2 lines of code changed in 2 files:

guilkey 2010-06-08 17:19 Rev.: 45709

Correct the NGN/NGP for the d_8or27=64 cases.

5 lines of code changed in 5 files:

jmschrei 2010-06-08 15:06 Rev.: 45708

fixing include directories

4 lines of code changed in 3 files:

guilkey 2010-06-07 17:40 Rev.: 45707

Correct name of model in outputProblemSpec so I can restart.

0 lines of code changed in 2 files:

harman 2010-06-07 15:30 Rev.: 45706

To keep the UPS spec file tractable the user must have

<Models>
<Model type = "SimpleRxn">
<SimpleRxn> <<<<< new
.
.
.
</SimpleRxn>
</Model>
<Models>

The rest of the models should be converted.

2 lines of code changed in 1 file:

harman 2010-06-07 15:10 Rev.: 45704

LODI2.cc
read_LODI_BC_inputs()
- the user must now input the name of the ICE material not the index. Previously,
the user could apply the LODI BCs to a mpm matl.

- Added more bulletproofing to the user input section.

addRequires_Lodi():implicitPressureSolve section
- added requires statements for variables.

LODI2.h/ICE.cc
updated read_LODI_BC_inputs() prototype.

59 lines of code changed in 3 files:

harman 2010-06-07 13:32 Rev.: 45703

removed: lastProbeDumpTimeLabel

1 lines of code changed in 3 files:

harman 2010-06-07 13:26 Rev.: 45702

Backed out changes that shouldn't have been committed.

1 lines of code changed in 1 file:

harman 2010-06-07 13:15 Rev.: 45701

If using the MPMICE component the dataAnalysis module is created, called and destroyed
from withing mpmice. This prevents the module from being created twice. ICE/MPM will now complete the
problemSetup task before d_analysis->problemSetup is run.

73 lines of code changed in 5 files:

jpeterson 2010-06-07 10:55 Rev.: 45700

Added label destroy statments

2 lines of code changed in 1 file:

harman 2010-06-07 10:50 Rev.: 45699

removed more probePt code.

0 lines of code changed in 1 file:

luitjens 2010-06-07 10:45 Rev.: 45698

Updated WaitTimes:+ to output per processor to a unique file

22 lines of code changed in 2 files:

harman 2010-06-07 10:19 Rev.: 45697

removed probePoints machinery. The user should be using LineExtract instead since
it does the same thing.

1 lines of code changed in 2 files:

jpeterson 2010-06-07 01:04 Rev.: 45696

Fixed double include

0 lines of code changed in 1 file:

jpeterson 2010-06-04 17:16 Rev.: 45694

Fix to last commit

1973 lines of code changed in 4 files:

jpeterson 2010-06-04 16:58 Rev.: 45693

First stab at UCNH. Implicit and solver based ComputeStressTensor functions only support Damage at the moment

1233 lines of code changed in 4 files:

dav 2010-06-04 15:14 Rev.: 45690


M ConstitutiveModel/MPMMaterial.h

Updated comment about #includ'ing things from other components. Note,
if Constitutive model was ever made into a separate library (it is
part of MPM now), then you would not be able to #include from MPM
itself (as MPM #include's from ConstitutiveModel. If you did so, a
circular dependency would be created. However, since this is all one
shared library, everything is fine.)


0 lines of code changed in 2 files:

guilkey 2010-06-04 11:01 Rev.: 45689

Add capability for Cohesive Zones to fail upon exceeding currently hardwired
values of their normal and tangential displacements, relative to the
characteristic values of each.

37 lines of code changed in 7 files:

harman 2010-06-04 10:36 Rev.: 45688

zeroModelSources()
- For each transported variable schedule the allocateAndPut for the
tvars material, NOT all matls.

18 lines of code changed in 1 file:

harman 2010-06-04 09:31 Rev.: 45685

Only output warning on processor 0. Updated the warning message.

3 lines of code changed in 1 file:

guilkey 2010-06-03 17:41 Rev.: 45684

HeatConduction.cc and ConstitutiveModel.cc
Set NGN and NGP in cases where d_8or27==64.
SoilFoam.cc and CompMooneyRivlin.cc
Cosmetic changes.

3 lines of code changed in 4 files:

harman 2010-06-03 17:24 Rev.: 45683

added command line option (transfer entire uda (y/n))
If the user says no then they can edit the directories they don't want.
This option will allow us to nuke pscp.

0 lines of code changed in 2 files:

luitjens 2010-06-03 16:14 Rev.: 45682

fixed a typo

1 lines of code changed in 1 file:

luitjens 2010-06-03 16:10 Rev.: 45681

Trying once again to make pscp2 shell independent

12 lines of code changed in 1 file:

jas 2010-06-03 15:14 Rev.: 45680

Fix multi-patch index space calculations.

31 lines of code changed in 2 files:

harman 2010-06-03 14:22 Rev.: 45679

updated svn line

0 lines of code changed in 2 files:

jthornoc 2010-06-03 12:46 Rev.: 45678

Fixing molecular weight for O2.

1 lines of code changed in 1 file:

jas 2010-06-03 08:32 Rev.: 45677

Python script that reads an uda file and can be used to convert to vtk
data format for use in Paraview.

592 lines of code changed in 1 file:

harman 2010-06-02 16:24 Rev.: 45675

added {} around conditionals

22 lines of code changed in 1 file:

harman 2010-06-02 09:45 Rev.: 45673

prototypes for counting particles.

14 lines of code changed in 1 file:

harman 2010-06-02 09:40 Rev.: 45672

added tasks to count total number of particles in the domain.

moved computation of the total mass of particles from
interpolateParticlesToGrid() -> interpolateToParticlesAndUpdate()

61 lines of code changed in 1 file:

jthornoc 2010-06-02 04:30 Rev.: 45671

logic was not correct.

1 lines of code changed in 1 file:

jmschrei 2010-06-01 17:51 Rev.: 45670

Updating uda reader plugin and installation guide to compile against the official 2.0 VisIt release.

76 lines of code changed in 11 files:

guilkey 2010-06-01 15:07 Rev.: 45669

Initializing ISVs based on RINIT value from KMMRXV (Yeah, I barely know what
that means myself...).

6 lines of code changed in 2 files:

jthornoc 2010-06-01 09:17 Rev.: 45668

Initialize dependent variables to zero.

1 lines of code changed in 1 file:

May 2010 »

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