May 2006 Commit Log

Number of Commits:
232
Number of Active Developers:
23
jeroen 2006-05-31 21:48 Rev.: 34371

Fix a stupid problem in get_faces, the orginal function querried an inverse face, however this was corrected with the overhead in the face_table_, with this removed this became a problem, but is fixed now

4 lines of code changed in 1 file:

jas 2006-05-31 20:58 Rev.: 34370

Eliminate the hard coding of the PetsSolver so that SimpleSolver can
be used even if petsc is installed.

87 lines of code changed in 41 files:

borodai 2006-05-31 15:16 Rev.: 34366

failsafe

2 lines of code changed in 1 file:

harman 2006-05-31 13:11 Rev.: 34364

removed
- <PhysicalBC>
- <MPM>
- </MPM>
- </PhysicalBC

from all inputs files and made <PhysicalBC> an optional input.

23 lines of code changed in 1 file:

jas 2006-05-31 12:19 Rev.: 34363

Use mpirun -np 1 for impm runs.

5 lines of code changed in 1 file:

jfsheph 2006-05-30 16:46 Rev.: 34362

fixing what appears to be an overlooked cut-and-paste error in a synchronization check.

1 lines of code changed in 1 file:

kuzimmer 2006-05-30 16:07 Rev.: 34361

comment out exhaustive search button since its not doing anything

0 lines of code changed in 2 files:

kuzimmer 2006-05-30 16:06 Rev.: 34360

update documentation

0 lines of code changed in 6 files:

kuzimmer 2006-05-30 15:23 Rev.: 34359

Fix the GUI so that it opens correctly, also made it so that it resizes to accomodate text based on the selection.

0 lines of code changed in 2 files:

callahan 2006-05-30 14:32 Rev.: 34358

Fix TetVolMesh::insert_node_in_elem memory corruption error.

73 lines of code changed in 1 file:

worthen 2006-05-30 14:21 Rev.: 34357

Add some memory-leak tracking functionality, add some scinews, and fix memory leak in impAMRICE's subscheduler

114 lines of code changed in 21 files:

callahan 2006-05-30 14:21 Rev.: 34356

Cleanup hash_edge, hash_face, remove_edge, remove_face functions.

62 lines of code changed in 1 file:

jeroen 2006-05-29 21:23 Rev.: 34352

Adding preparations for Regression testing: added comaprison functions for dataflow objects. Modified Dynamic compilation so it has an option to compile load and destroy the library, to prevent the on-the-fly-lib directory to grow out of control when testing whether dynamically compilled algorithms work. Fixed HexVolMesh to deal with degenerate meshes and started to better optimize this mesh to use less memory (still need to finish this as table sizes can be shrunk even more). Added a RegressionReporter to store all the information during regression testing. Fixed the Finite Element Code to deal with degenerate elements (Comparison with Tetsn and Prisms show that Hexahedral elements with degenerate nodes can act as tetrahedrals or prisms and still generate the proper stiffness matrix). Fixed the visualization so degenerate elements show upm properly (fixed the order of the faces of these degenerate elements so the three unique element nodes are always returned first when quering a face). Still need to upgrade the quadsurfmesh to also support degenerate elements. Field boundary now also supports degenerate elements as the number of faces returned per element can now vary with the actual number of faces. Next to do: generate degenerate meshes with tets, piramids, prisms and hexahedral and test which algorithms fail and fix those.

1552 lines of code changed in 35 files:

banerjee 2006-05-29 17:40 Rev.: 34351

Update. Added Exchange Coeffs. Converted from panels to frames.

3915 lines of code changed in 77 files:

kuzimmer 2006-05-29 15:01 Rev.: 34350

Removes a bug that occured when switching from a single level field to a multi-level field. tHandle->nlevels() depended upon the previous use of tHandle, but we ant to clear the texture bricks every time there is a multi-level field. If the previous use was a single level field, then the first build of a multi-level field would reuse a previous texture for level 0. Changing the if to mrvfld->nlevels() gives us the correct behavior.

0 lines of code changed in 2 files:

callahan 2006-05-26 14:57 Rev.: 34345

Add a PNG option to viewer save image.

24 lines of code changed in 2 files:

worthen 2006-05-26 08:33 Rev.: 34341

revert ShowDipoles from yesterday, and do a check on all calls to gl*Pointer before trying to dereference an empty vector

148 lines of code changed in 3 files:

dav 2006-05-25 15:58 Rev.: 34339

The current image is corrupted. This resurrects the most recent image that worked.

0 lines of code changed in 2 files:

spinti 2006-05-25 14:22 Rev.: 34338

Fixed soot factor for empirical soot model

1 lines of code changed in 1 file:

worthen 2006-05-25 14:02 Rev.: 34337

Only add GeomLines if you're going to add points to it (i.e., you need more than 2 points).

1 lines of code changed in 1 file:

mjc 2006-05-25 13:22 Rev.: 34336

change the default behavior to disabled for SCI_MALLOC, use --enable-sci-malloc if you want to enable SCI_MALLOC

150 lines of code changed in 3 files:

kuzimmer 2006-05-25 11:18 Rev.: 34335

added missing </p>

0 lines of code changed in 2 files:

allen 2006-05-24 18:21 Rev.: 34332

fixed global vars

128 lines of code changed in 3 files:

callahan 2006-05-24 17:11 Rev.: 34331

Add virtual destructor to SearchGridConstructor class.

12 lines of code changed in 2 files:

callahan 2006-05-24 16:25 Rev.: 34330

Synchronize FACES when extracting mesh in InsertField.

18 lines of code changed in 1 file:

dmw 2006-05-24 16:08 Rev.: 34329

- Fix typo

1 lines of code changed in 1 file:

worthen 2006-05-24 15:37 Rev.: 34328

Implement a version of McKay's Tcl{Set,Get}Var to be passed as a message via the experimental TCL thread.

126 lines of code changed in 3 files:

callahan 2006-05-24 15:19 Rev.: 34327

Synchronize locate

6 lines of code changed in 1 file:

callahan 2006-05-24 11:19 Rev.: 34323

Force insert_node_in_elem tets to always be positive.

89 lines of code changed in 1 file:

jfsheph 2006-05-24 10:36 Rev.: 34322

preventing a crash in MeshSmoother if no elements are passed in to smooth.

9 lines of code changed in 1 file:

harman 2006-05-24 10:19 Rev.: 34321

For single material problems you no longer need

<exchange_properties>
<exchange_coefficients>
<momentum> [] </momentum>
<heat> [] </heat>
</exchange_coefficients>
</exchange_properties>

in the input files.

55 lines of code changed in 5 files:

kuzimmer 2006-05-23 17:48 Rev.: 34320

Place a frame around the SCI Button Panel so that the window always expands to reveal it. Comment out or remove some debugging print statements.

203 lines of code changed in 47 files:

callahan 2006-05-23 16:28 Rev.: 34319

Faster insert_node_in_elem implementation.

146 lines of code changed in 2 files:

callahan 2006-05-23 15:23 Rev.: 34318

Make remove syncs from insert_node_in_face.

95 lines of code changed in 1 file:

callahan 2006-05-23 13:57 Rev.: 34317

Remove create_cell_syncinfo from add_tet.

7 lines of code changed in 1 file:

callahan 2006-05-23 13:37 Rev.: 34316

Remove tet orientation on Pio.

13 lines of code changed in 1 file:

callahan 2006-05-23 13:31 Rev.: 34315

Remove resynchronization from internal orient/pio reading functions for faster Pio.

21 lines of code changed in 1 file:

callahan 2006-05-23 11:29 Rev.: 34314

Use const references where applicable for PFace and PEdge, avoid copies.

3 lines of code changed in 1 file:

bigler 2006-05-23 11:03 Rev.: 34313

##
##
##
##
##

Core/ExternalUIInterface.h

Added virtual destructor to make GCC happy.

Core/Gui.cc
Core/Gui.h

Added ability to turn on "Frame for Frame" animations for
SelectableGroup classes.

Core/SelectableGroup.cc
Core/SelectableGroup.h

Added ability to animate frame for frame. Each animation call
explictly increments the animated frame without care of the
framerate.

0 lines of code changed in 10 files:

worthen 2006-05-22 20:28 Rev.: 34311

Fix level-based error message

0 lines of code changed in 2 files:

worthen 2006-05-22 18:54 Rev.: 34310

Fix MPM memory leak

6 lines of code changed in 3 files:

worthen 2006-05-22 18:07 Rev.: 34309

Make restart_merger only copy the checkpoints data on the last uda

10 lines of code changed in 3 files:

callahan 2006-05-22 17:22 Rev.: 34308

Remove redundant resync_cells function.

0 lines of code changed in 1 file:

bigler 2006-05-22 17:11 Rev.: 34307

Better linking for scene libraries.

0 lines of code changed in 2 files:

callahan 2006-05-22 15:35 Rev.: 34306

Minor cleanups to InsertField inserting edges into tets algorithm.

14 lines of code changed in 1 file:

callahan 2006-05-22 15:34 Rev.: 34305

Fix cell_epsilon race condition

4 lines of code changed in 2 files:

callahan 2006-05-22 12:06 Rev.: 34304

Add proper debugging asserts for TEXTURE_MAX_COMPONENTS.

18 lines of code changed in 4 files:

callahan 2006-05-22 11:49 Rev.: 34301

Add define for maximum number of components available and use it instead of hardcoding 2.

24 lines of code changed in 5 files:

worthen 2006-05-22 11:33 Rev.: 34300

Some fixes for win32 stack trace

Define EXPERIMENTAL_TCL_THREAD in NetworkEditor so ThreadLock doesn't crash at shutdown

Declare SCISHARE for a few Dynamic Compilation Makers

33 lines of code changed in 13 files:

worthen 2006-05-22 07:53 Rev.: 34298

Sync with ICE prototype

91 lines of code changed in 1 file:

banerjee 2006-05-21 19:04 Rev.: 34297

Some updates. Added hollow particle feature.

743 lines of code changed in 23 files:

worthen 2006-05-20 00:11 Rev.: 34296

Reorganize AMR input file and Regridder (most of these changes involve moving the time_refinement_ratio from Level to SimulationState). Also make error message in DataArchiver, usage in RestartMerger, and pids (for debugger attachment) more useful. Do implicit MPM TG compile once per outer level TG compile (and put Todd's for impICE how he likes it).

537 lines of code changed in 58 files:

banerjee 2006-05-19 16:50 Rev.: 34294

Updated layout and actions.

911 lines of code changed in 32 files:

borodai 2006-05-19 16:02 Rev.: 34292

Computing variance and reactive scalar is now fully controlled from CFD side,
not from table side, as it should be. Bogus multiple scalar support has been
removed.

360 lines of code changed in 34 files:

borodai 2006-05-19 11:50 Rev.: 34290

Fixed FPE

15 lines of code changed in 1 file:

harman 2006-05-19 11:24 Rev.: 34289

turn on scheduleInitialErrorEstimate()

- scheduleErrorEstimate() & errorEstimate()
During the initialization phase only require *_CC variables for ice_matls.
These variables are not available for mpm_matls.

77 lines of code changed in 1 file:

callahan 2006-05-19 10:12 Rev.: 34287

Cleanup code, fix comments, add some white space.

107 lines of code changed in 1 file:

callahan 2006-05-19 10:12 Rev.: 34286

Fix warning messages.

4 lines of code changed in 1 file:

jeroen 2006-05-18 21:34 Rev.: 34285

Fix the MatlabBundlesWriter so we have an option to write a strutured matrix or a numeric matrix. Fixed the StreamMatrix function to use weights for row vectors and added a few sanity checks in the function.

68 lines of code changed in 9 files:

callahan 2006-05-18 16:57 Rev.: 34284

Fix compilation warnings.

0 lines of code changed in 2 files:

callahan 2006-05-18 15:31 Rev.: 34283

Add a more thread safe add_raw_message to ProgressReporter and use it.

44 lines of code changed in 14 files:

callahan 2006-05-18 15:21 Rev.: 34282

Fix compiler warnings.

2 lines of code changed in 2 files:

jeroen 2006-05-18 15:06 Rev.: 34281

Adding functionality to stream time adaptive signals. TimeToWeights takes in a vector with times and creates the weights of the nearest timeframes and does a linear interpolation. This module serves as input for StreamMatrix which has a port with weights that describe how multiple columns or rows need to be combined into one. Note: the weights here are not compatible yet with MatrixSelectVector, that module uses a custom system to do a sparse matrix. StreamMatrix and TimeToWeights use the default sparse matrix to define weights.

653 lines of code changed in 11 files:

callahan 2006-05-18 14:06 Rev.: 34280

Clean up ProgressReporter functions in Module.cc to be less sensitive to threading issues.

20 lines of code changed in 1 file:

callahan 2006-05-18 11:03 Rev.: 34276

Remove post_message from Module and ProgressReporter interface. It's still accessible from the GuiInterface if needed.

14 lines of code changed in 6 files:

callahan 2006-05-18 11:01 Rev.: 34275

Fix compiler warnings.

28 lines of code changed in 3 files:

callahan 2006-05-18 10:18 Rev.: 34274

Fix various compiler warnings.

32 lines of code changed in 12 files:

kuzimmer 2006-05-17 20:46 Rev.: 34272

initial module documentation for Uintah release.

198 lines of code changed in 38 files:

banerjee 2006-05-17 17:13 Rev.: 34271

More stuff.

8327 lines of code changed in 33 files:

callahan 2006-05-17 16:10 Rev.: 34270

Fix compiler warnings.

2 lines of code changed in 3 files:

borodai 2006-05-17 15:52 Rev.: 34269

Made input tags more meaningful

20 lines of code changed in 9 files:

worthen 2006-05-17 15:09 Rev.: 34268

Get rid of dependency on external readdir, opendir, closedir (wrote out own)
Consolidate stack trace into one function, and make available to anywhere
Add a public domain utility for windows to do the stack trace

Parse filenames in ServiceDB for windows like we do in PackageDB (I.e., filenames can have colons in them.

1602 lines of code changed in 36 files:

worthen 2006-05-17 13:46 Rev.: 34265

Change constant value to something more reasonable

10 lines of code changed in 1 file:

worthen 2006-05-17 13:12 Rev.: 34260

Implement a Box difference algorithm, and use it to set the faces outside of the allocated patch region to an initialized bogus value Also fix a small bug in LocallyComputedPatchVarMap and start a process to get an arbitrary particleSubset with given low/high coordinates (necessary for any regridder with a non-determined lattice)

216 lines of code changed in 6 files:

borodai 2006-05-17 12:13 Rev.: 34258

Fixed reduction variable and post Bryan fix.

9 lines of code changed in 1 file:

jfsheph 2006-05-17 12:04 Rev.: 34257

adding some code for detecting non-manifold edges that Michael is going to help me with...

394 lines of code changed in 1 file:

kuzimmer 2006-05-17 10:32 Rev.: 34255

Fixed dynamic compilation with new compilers

0 lines of code changed in 2 files:

kuzimmer 2006-05-17 10:24 Rev.: 34254

These were supposed to have been checked in when 'varname' was changed to 'name' in the properties list with revision 33691

23 lines of code changed in 7 files:

harman 2006-05-17 10:09 Rev.: 34253

- removed <toughness> and <speed_of_sound> from all input files.

ICEMaterial.cc .h
We don't need to get the speed_of_sound from the input files

0 lines of code changed in 3 files:

guilkey 2006-05-17 09:29 Rev.: 34251

Nix the SCIRun in the include of SCIRun/Core/Util/Array3.h

1 lines of code changed in 1 file:

callahan 2006-05-16 18:21 Rev.: 34250

Fix timer issue, more code cleanups

135 lines of code changed in 1 file:

knolla 2006-05-16 17:33 Rev.: 34249

reverted Array3 back to correct state

0 lines of code changed in 1 file:

borodai 2006-05-16 17:15 Rev.: 34248

reverted back some garbage I accidentally commited on my previous commit

1 lines of code changed in 2 files:

knolla 2006-05-16 17:05 Rev.: 34247

added a safe lookup to Array3.h

20 lines of code changed in 1 file:

borodai 2006-05-16 17:04 Rev.: 34246

6 lines of code changed in 3 files:

borodai 2006-05-16 16:20 Rev.: 34245

Fixed uninitialized value. Cleaned up input files.

1 lines of code changed in 1 file:

borodai 2006-05-16 16:10 Rev.: 34244

cleanup

30 lines of code changed in 2 files:

borodai 2006-05-16 13:57 Rev.: 34243

Removed thermal NOx stuff

5 lines of code changed in 32 files:

kuzimmer 2006-05-16 13:08 Rev.: 34242

updateParticleFieldExtractor like it should have been on revision 34177

26 lines of code changed in 2 files:

cgribble 2006-05-16 12:48 Rev.: 34241

Added missing #include Assert.h>

0 lines of code changed in 2 files:

callahan 2006-05-16 11:34 Rev.: 34240

more code cleanups

99 lines of code changed in 1 file:

callahan 2006-05-16 10:51 Rev.: 34239

code cleanup

500 lines of code changed in 1 file:

borodai 2006-05-15 16:35 Rev.: 34236

removed nonworking eno and weno

41 lines of code changed in 18 files:

dav 2006-05-15 15:33 Rev.: 34235

These apps apparently need to link against the fortran library... at
least on my Mac... so I added it to their sub.mk files.

24 lines of code changed in 10 files:

callahan 2006-05-15 15:06 Rev.: 34234

Fix two insert_node_in_elem bugs. The volume checking code was too permissive allowing degenerate tets to be created rather than reusing existing nodes when the size was too small. Also fix the orientation of tets in the insert_node_in_edge helper function.

46 lines of code changed in 1 file:

jfsheph 2006-05-15 14:07 Rev.: 34232

adding a function to get all faces in a mesh connected to an edge. Thanks to Michael for the function...

34 lines of code changed in 1 file:

harman 2006-05-15 13:57 Rev.: 34231

user input "Max_iterations_equilibraton" is now optional, default set to 100
user input "solution technique" had been eliminated
user input "useCompatibleFluxes = true" is now the default, it can still be turned off.

24 lines of code changed in 2 files:

kuzimmer 2006-05-15 13:46 Rev.: 34230

Added include of Matrix3.h, so that dynamic compilation of TensorFieldExtractor works on gcc 4.0+ compilers

1 lines of code changed in 1 file:

jeroen 2006-05-15 11:34 Rev.: 34229

Adding a different stimulus model

1073 lines of code changed in 27 files:

callahan 2006-05-15 11:25 Rev.: 34228

Clean up compiler warnings.

0 lines of code changed in 4 files:

jeroen 2006-05-15 11:25 Rev.: 34227

Adding a plugin to matrix reader that reads Nrrd compatible files directly as matrices. This way the model creation effeort will not depend on anything in the Teem Package

170 lines of code changed in 5 files:

dgroulx 2006-05-15 10:43 Rev.: 34226

Added the SciMakeButtonPanel to the Uintah modules which did not have it yet.

73 lines of code changed in 14 files:

harman 2006-05-15 09:27 Rev.: 34224

added level index to "Mass gained by the models....." spew

1 lines of code changed in 1 file:

jeroen 2006-05-13 01:48 Rev.: 34223

updates

0 lines of code changed in 6 files:

jeroen 2006-05-13 01:47 Rev.: 34222

Updates to algorithms

352 lines of code changed in 10 files:

jfsheph 2006-05-12 16:32 Rev.: 34212

reducing the number of warning lines printed out when negative volume hexes are detected

0 lines of code changed in 2 files:

callahan 2006-05-12 16:12 Rev.: 34211

Fix bug in SearchGrid::min_distance_squared, compute distance to the cell rather than to the nearest cell corner.

14 lines of code changed in 1 file:

callahan 2006-05-12 16:02 Rev.: 34210

Add a SearchGridInfo module, outputs a LatVolField with the same geometry as the search grid for the input field. Primarily useful as a debugging tool.

222 lines of code changed in 3 files:

callahan 2006-05-12 15:54 Rev.: 34209

Undo accidental checkin. Add a get_search_grid_info function to TriSurfMesh.

6 lines of code changed in 1 file:

callahan 2006-05-12 15:52 Rev.: 34208

Skip floor call when converting from double to int, redundant.

30 lines of code changed in 3 files:

borodai 2006-05-12 15:28 Rev.: 34207

Delete geometry objects

63 lines of code changed in 2 files:

banerjee 2006-05-12 14:44 Rev.: 34206

A bit more stuff. More to go.

1879 lines of code changed in 5 files:

dgroulx 2006-05-11 15:01 Rev.: 34203

Added the endianess tag back to the main index file to not break the whole uintah toolchain.

1 lines of code changed in 1 file:

jfsheph 2006-05-11 12:00 Rev.: 34202

changing the output field type from the MeshQuality module to a constant basis, and storing the value of the scaled Jacobian metric for each element on the field. This enables me to better visualize all of the poor quality elements in a mesh.

46 lines of code changed in 1 file:

mjc 2006-05-11 11:08 Rev.: 34201

synchronize faces before iterating over them

1 lines of code changed in 1 file:

dav 2006-05-10 17:31 Rev.: 34198


Real change: 'buildLevel' changed to 'buildLevels' (added the 's').
This fixes a runtime error I was getting. I believe it is the correct
fix. Kurt?

Also, untabified, indented, standardized, etc.

309 lines of code changed in 1 file:

harman 2006-05-10 17:20 Rev.: 34197

No longer requiring reacted fraction from old_dw, AMR now runs.

3 lines of code changed in 1 file:

banerjee 2006-05-10 17:04 Rev.: 34196

First cut beginner's UI for creating a Uintah input ups file. Uses
JDK 1.4.2 and Swing.

7745 lines of code changed in 23 files:

harman 2006-05-10 17:00 Rev.: 34195

get_rho_micro()

commented out code that doesn't work with AMR. The refine/setBC_fineLevel
task only refines ICE matls, thus you don't have access to sp_vol_mpm

6 lines of code changed in 1 file:

jfsheph 2006-05-10 16:57 Rev.: 34194

couple of updates

33 lines of code changed in 1 file:

jfsheph 2006-05-10 16:56 Rev.: 34193

adding a couple of translators to make it easier for me to go back and forth between SCIRun and CUBIT.

439 lines of code changed in 3 files:

sachse 2006-05-10 16:31 Rev.: 34192

bug fix

0 lines of code changed in 2 files:

dav 2006-05-10 13:50 Rev.: 34185

Added newline to end of file.

0 lines of code changed in 2 files:

sachse 2006-05-10 13:50 Rev.: 34184

bug fix

0 lines of code changed in 2 files:

worthen 2006-05-10 12:25 Rev.: 34183

Get rid of extra output

0 lines of code changed in 1 file:

worthen 2006-05-10 12:23 Rev.: 34182

Latest wave of windows fixes.

28 lines of code changed in 9 files:

kuzimmer 2006-05-10 09:02 Rev.: 34177

Fix oddities with multi-resolution data, only allow users to pick level with particles on it for vis

63 lines of code changed in 2 files:

kuzimmer 2006-05-10 09:01 Rev.: 34176

add error messages when a scalarParticleField is either empty or not hooked up, remove some debugging statments

4 lines of code changed in 3 files:

callahan 2006-05-09 16:20 Rev.: 34173

Temporary fix for SetupFEMatrix crash bug until code rewrite is completed.

5 lines of code changed in 1 file:

harman 2006-05-09 13:46 Rev.: 34172

The AMR refinement threshold criteria is now associated with each material
Here's an example of how to specify it
<Refinement_Criteria_Thresholds>
<Variable name = "rho_CC" value = "1e3" matl = "all" />
<Variable name = "vol_frac_CC" value = "10" matl = "1" />
<Variable name = "vol_frac_CC" value = "5" matl = "3" />
<Variable name = "press_CC" value = "100" matl = "0" />
</Refinement_Criteria_Thresholds>

Eliminated regridderTest code and ups file, no longer used.

103 lines of code changed in 2 files:

harman 2006-05-09 09:38 Rev.: 34171

delete table VarLabels

4 lines of code changed in 1 file:

jeroen 2006-05-08 17:08 Rev.: 34169

Merge my algorithms from the ModelCreation package to Core/Algorithms so they are available for everyone. I added four directories to Core/Algorithms: Math for mathematical operations (mirrors Math in module tree), this currently has the FE code, Fields: my version of the field algorithms, these contain new ones and old ones with bug fixes to get my CardioWave stuff to work, Converter: Converter algorithms a series of converters to deal with conversion between Matrices, Nrrds and Fields, DataIO: gui less version for writing and reading in SCIRun files using PersistentIO or the Plug-ins. All the algorithms are grouped into libraries with one main header file: Algorithms/Math/MathAlgo.h Algorithms/Fields/FieldsAlgo.h Algorithms/DataIO/DataIOAlgo.h Algorithms/Converter/ConverterAlgo.h. Each library needs to be initialised with the ProgressReporter after which all the dynamic compilation is hidden from the user. I put all the algorithms in a separate namespace call SCIRunAlgo to avoid possible conflicts between class names. Similarly all the dynamic files will start with the word ALGO, to avoid duplication of filenames created by the current set of modules. --Jeroen

13371 lines of code changed in 308 files:

dav 2006-05-08 16:39 Rev.: 34168


Real change: Looks like Arches now depends on the OnTheFlyAnalysis
component (library). Added this dependency so OSX build would
completed.

And... removed Tabs, indented, cleaned up.

47 lines of code changed in 1 file:

dgroulx 2006-05-08 16:14 Rev.: 34167

Now outputs endianess information per timestep.

9 lines of code changed in 1 file:

harman 2006-05-08 15:07 Rev.: 34164

added AMR errorEstimate task.

108 lines of code changed in 2 files:

jeroen 2006-05-08 14:42 Rev.: 34163

Fix the compilation of RenderField.h for the MaskedLatVolMesh. I still need to fix the algorithm to do the topology for the mesh, but it will now use the old renderer again for this mesh.

23 lines of code changed in 3 files:

callahan 2006-05-08 14:01 Rev.: 34162

Fix Number of processor selection for SetupFEMatrix

0 lines of code changed in 2 files:

callahan 2006-05-08 13:39 Rev.: 34161

Fix bad grid_ copy in the mesh copy constructors.

34 lines of code changed in 8 files:

worthen 2006-05-08 13:30 Rev.: 34160

Fix restart_merger

1 lines of code changed in 1 file:

jas 2006-05-08 13:22 Rev.: 34158

Reduce the size of the DIAG_MAX and ONNZ_MAX if those values are greater
than then numlcolumns.

6 lines of code changed in 1 file:

jas 2006-05-08 13:08 Rev.: 34157

Add virtual destructor so compiler won't complain.

2 lines of code changed in 1 file:

jas 2006-05-08 12:58 Rev.: 34156

Fix warnings comparing unsigned int to int.

10 lines of code changed in 1 file:

jas 2006-05-08 12:44 Rev.: 34155

Use PCFactorSetFill instead of PCILUSetFill for petsc-2.3.1.

6 lines of code changed in 1 file:

jas 2006-05-08 12:17 Rev.: 34154

Add exact solution formulation.

52 lines of code changed in 1 file:

dgroulx 2006-05-08 11:54 Rev.: 34153

Added MPI, blas, and lapack libs to the dependencies so it builds on non-linux.

1 lines of code changed in 1 file:

worthen 2006-05-08 11:52 Rev.: 34152

Only 'create' a new PerProc patchset when necessary, and not just whenever called

181 lines of code changed in 27 files:

sachse 2006-05-08 11:26 Rev.: 34151

bug fix

0 lines of code changed in 2 files:

jeroen 2006-05-07 16:47 Rev.: 34150

Added a mode to display the data contained in the cells of volumetric meshes using two-sided triangles and quadrilaterals. For shared faces each side is given the color representing the data in the cell, for outward facing faces they are colored on both sides with the color, the one of the cell they are bordering. This way one can use the clipping planes to check segmentations of unstructured mesh, without the need of doing a full volume rendering.

122 lines of code changed in 1 file:

jeroen 2006-05-07 16:43 Rev.: 34149

Adding new Geometry objects to deal with faces that are colored different in the front and the back. The current implementation uses culling to first draw the front of all the faces in the object and then draw the back of the objects. This way in between we can switch dataset and color both faces differently. This functionality is intended to display data located at cells. As each part of the face is part of a different cell they get colored differently.

863 lines of code changed in 9 files:

jeroen 2006-05-07 16:39 Rev.: 34148

Fix a bug: Standalone uses integers that are not typed Node::index_type, which is causing problems when I added additional functionality to get_elems().

0 lines of code changed in 2 files:

jeroen 2006-05-07 16:37 Rev.: 34147

Adding functions to find element indices based on the Edge of Face index. This functionality is needed for volumetric meshes to find the colors that are assigned in the renderer to faces when assuming constant data on the elements. Fixed or added these functions to all mesh classes (still need to complete TriSurfmesh and QuadSurfMesh).

257 lines of code changed in 14 files:

sachse 2006-05-06 10:41 Rev.: 34146

bug fixes

20 lines of code changed in 1 file:

sachse 2006-05-06 09:45 Rev.: 34145

bug fixes

45 lines of code changed in 1 file:

worthen 2006-05-05 22:57 Rev.: 34144

Turn off dlb test so the rest of RT will pass, hopefully to be fixed on Monday

0 lines of code changed in 2 files:

jeroen 2006-05-05 19:21 Rev.: 34143

Fixes to do deal with changes in Core

4 lines of code changed in 2 files:

jeroen 2006-05-05 19:20 Rev.: 34142

Add a new package to help with the needs of Alexey Zaitsev, a collaborator at CVRTI. These tools include reconstructions and visualizations of phase of the cardiac cycle as a function of time

1347 lines of code changed in 20 files:

jeroen 2006-05-05 19:18 Rev.: 34141

Updates to fix the changes I made in Core/Algorithms. Renamed a couple of modules to better represent the functionality. Remove Cardiac Visualization tools developed for CVRTI.

3888 lines of code changed in 107 files:

jeroen 2006-05-05 19:17 Rev.: 34140

Change Numeric into Math to better represent the tree we have as module names in the dataflow system. And a few fixes to FieldInformation class

2022 lines of code changed in 16 files:

sachse 2006-05-05 17:33 Rev.: 34139

bug fix

0 lines of code changed in 2 files:

sbrown 2006-05-05 16:08 Rev.: 34138

Beginnings of support for OnTheFlyAnalysis. Not ready for primetime yet.

41 lines of code changed in 2 files:

dav 2006-05-05 16:05 Rev.: 34137

M Modules/Operators/CompareMMS.cc

Use field property 'name' (was 'varname', but this was changed in
FieldExtractor.)

M GUI/VariablePlotter.tcl

Turn off spew.

3 lines of code changed in 2 files:

dgroulx 2006-05-05 12:24 Rev.: 34136

Now propery handles underscores for fortran symbols on OS X.

2 lines of code changed in 2 files:

sachse 2006-05-05 11:35 Rev.: 34135

bug fix

0 lines of code changed in 2 files:

ayla 2006-05-04 20:40 Rev.: 34133

Ptolemy package Comm does not depend on Java.

2 lines of code changed in 1 file:

jfsheph 2006-05-04 17:07 Rev.: 34132

continuing progress and updates to the InsertHexSheet module. Still not complete, but a substantial amount of capability has been added since my last update, and I wanted to back it up...

306 lines of code changed in 4 files:

sachse 2006-05-04 16:04 Rev.: 34131

Performance fix

0 lines of code changed in 2 files:

worthen 2006-05-04 15:40 Rev.: 34130

1) Create 1 patch group per level instead of 1 per variable per level
2) AMRInterpolate coarse range high fix
3) Fix (hopefully the right thing) refined variable for a 3+ level mpmice problem

76 lines of code changed in 8 files:

borodai 2006-05-04 15:37 Rev.: 34129

More cleanup

31 lines of code changed in 17 files:

worthen 2006-05-04 15:26 Rev.: 34128

revive ARCHES tests

0 lines of code changed in 2 files:

sachse 2006-05-04 14:36 Rev.: 34126

Optimization for locate functions

0 lines of code changed in 4 files:

borodai 2006-05-04 13:35 Rev.: 34121

Forgot to add a replacement for RBGS solver.

356 lines of code changed in 2 files:

borodai 2006-05-04 13:33 Rev.: 34120

Clean up

96 lines of code changed in 55 files:

harman 2006-05-03 17:16 Rev.: 34119

use level->getIndex() instead of getID()

19 lines of code changed in 1 file:

harman 2006-05-03 17:02 Rev.: 34118

added comments for getID and getIndex

6 lines of code changed in 1 file:

harman 2006-05-03 16:01 Rev.: 34117

Eliminated unused code and general cleanup.

8 lines of code changed in 3 files:

callahan 2006-05-03 15:56 Rev.: 34116

Fix minor lock issue in copy constructor.

3 lines of code changed in 1 file:

callahan 2006-05-03 15:55 Rev.: 34115

Use bigger default stack size on 64 bit machines

0 lines of code changed in 2 files:

harman 2006-05-03 15:51 Rev.: 34114

general cleanup, comments and formatting

21 lines of code changed in 5 files:

harman 2006-05-03 15:23 Rev.: 34113

-General cleanup, formatting and comments
-Put cout_dbg on a strict diet.
-Eliminated extra layer of abstraction for getSolution() makeLinearSystem(),

47 lines of code changed in 2 files:

harman 2006-05-03 15:19 Rev.: 34112

General cleanup, formatting, comments

Simplification: eliminated special cases for SFC(x,y,z)Variables and NC variables
(We only need CCVariables)

20 lines of code changed in 2 files:

borodai 2006-05-03 14:47 Rev.: 34111

Fixed hypre solver for DO radiation, if it has to work for spherical harmonics
as well , look in Models/Radiation to see how to do that. Spherical harmonics
is disabled now (it does not run in parallel) so having solvers work for it
is not required.

1 lines of code changed in 2 files:

borodai 2006-05-03 14:00 Rev.: 34110

Petsc solver cleanup for radiation. Results seem to deviate
too fast for hypre and petsc

104 lines of code changed in 9 files:

harman 2006-05-03 13:38 Rev.: 34109

Simplify: if it's not currently or ever going to be used, it's not needed.
- nuked getSolution_(SFC(x,y,z), NC)
- nuked makeLinearSystem_(SFC(x,y,z), NC)

19 lines of code changed in 2 files:

kuzimmer 2006-05-03 13:21 Rev.: 34108

Added a Matrix port for transforming particle locations in ParticleVis

28 lines of code changed in 4 files:

sbrown 2006-05-03 13:17 Rev.: 34107

Adding some diagnostics to trace excessive heat loss to a certain cell.

26 lines of code changed in 4 files:

callahan 2006-05-03 11:59 Rev.: 34106

More code cleanups, identify class variables.

68 lines of code changed in 1 file:

callahan 2006-05-03 11:38 Rev.: 34105

Fix compiler warnings, minor cleanup

56 lines of code changed in 1 file:

callahan 2006-05-03 11:27 Rev.: 34104

Cleaner insert_node_in_face implementation, remove unused insert_node function.

14 lines of code changed in 1 file:

harman 2006-05-03 10:58 Rev.: 34102

Intermediate commit:
complete overhaul of makeGraphConnections() and makeConnection()
Status:
-now runs with on 1 processor with various patch configurations, not thoroughly tested.
-multi-processor multi-patch problems don't work.
-debugging spew turned on.

235 lines of code changed in 1 file:

mjc 2006-05-03 08:15 Rev.: 34101

fix bug with setting extended viewwindow option variables

2 lines of code changed in 1 file:

callahan 2006-05-02 18:09 Rev.: 34100

Make sure TetVolMesh::insert_node_in_face preserves the tet orientation.

38 lines of code changed in 1 file:

dmw 2006-05-02 15:46 Rev.: 34099

- Tweaking default scales for nodes, edges, and dipoles

3 lines of code changed in 2 files:

callahan 2006-05-02 15:33 Rev.: 34098

Clean up TetVolMesh::insert_node_in_elem code, make auxiliary functions protected.

38 lines of code changed in 2 files:

banerjee 2006-05-02 14:45 Rev.: 34097

Added option for arc start position. Angles are always counterclockwise.

15 lines of code changed in 3 files:

dmw 2006-05-02 14:42 Rev.: 34096

- Dataflow/Network now depends on Core/Geometry -- fixes Mac build

0 lines of code changed in 2 files:

dmw 2006-05-02 14:40 Rev.: 34095

- Make ApplyFEMCurrentSource module work with source/sink configuration again. - No longer split the output Matrix in build-fem-elem-leadfield network

6 lines of code changed in 3 files:

mjc 2006-05-02 14:25 Rev.: 34094

if SCIRUN_USE_DEFAULT_SETTINGS is true, add a callback that will resize the dipole widgets based on the view bounds

35 lines of code changed in 1 file:

mjc 2006-05-02 14:24 Rev.: 34093

provide functinality to get the view bounding box from a geometry port

25 lines of code changed in 7 files:

jas 2006-05-02 13:08 Rev.: 34092

Use PCFactorSetFill instead of PCILUSetFill if using petsc 2.3.1 (latest
version).


12 lines of code changed in 2 files:

callahan 2006-05-02 12:18 Rev.: 34091

Fix sync_on_execute deadlock while making movies, bug 2849.

11 lines of code changed in 1 file:

callahan 2006-05-02 12:03 Rev.: 34090

Fix flipped PNG movie image, bug 2848.

1 lines of code changed in 1 file:

worthen 2006-05-02 11:50 Rev.: 34089

Have ProgressiveWarning respond to a DebugStream so you can turn them off

0 lines of code changed in 2 files:

harman 2006-05-02 11:39 Rev.: 34088

filled in outputProblemSpec so restarting works

24 lines of code changed in 3 files:

harman 2006-05-02 11:05 Rev.: 34087

removed excess spew

0 lines of code changed in 4 files:

jas 2006-05-02 10:54 Rev.: 34086

Remove unused tags <sphere> and <shell>.

0 lines of code changed in 2 files:

jas 2006-05-02 10:40 Rev.: 34085

Remove unused tags <plane> and <shell>.

0 lines of code changed in 2 files:

oscar 2006-05-01 18:23 Rev.: 34084

updated to fix some more errors causes by changes elsewhere

0 lines of code changed in 2 files:

oscar 2006-05-01 18:10 Rev.: 34083

updated to fix some more errors causes by changes elsewhere

8 lines of code changed in 1 file:

oscar 2006-05-01 17:07 Rev.: 34082

updated to fix places where changes elsewhere broke the code

6 lines of code changed in 5 files:

oscar 2006-05-01 16:54 Rev.: 34081

Forgot to update package check for Ptolemy (ayla).

9 lines of code changed in 2 files:

borodai 2006-05-01 16:33 Rev.: 34080

Removed outdated ARCHES_DEBUG impementation. New implementation is
needed if somebody requires it.

961 lines of code changed in 24 files:

oscar 2006-05-01 15:49 Rev.: 34079

changed to work with the new way to access the gui

2 lines of code changed in 1 file:

oscar 2006-05-01 15:48 Rev.: 34078

Fixed broken code to start the Ptolemy server

3 lines of code changed in 1 file:

oscar 2006-05-01 15:47 Rev.: 34077

Updated for ptolemy package when building ptolemy server

1 lines of code changed in 1 file:

oscar 2006-05-01 15:44 Rev.: 34076

Fix including ptolemy server library (ayla).

295 lines of code changed in 4 files:

borodai 2006-05-01 15:35 Rev.: 34075

cleanup

3 lines of code changed in 30 files:

worthen 2006-05-01 14:13 Rev.: 34072

Fix ML-task copy data, coarsening getRegion, and rerun DLB after a restart

18 lines of code changed in 3 files:

sbrown 2006-05-01 13:36 Rev.: 34071

Cleaned out some more mixing garbage, hopefully the last. If sus won't compile, you'll have to make cleanreally or /scripts/repair.sh for each file it complains about.

0 lines of code changed in 19 files:

borodai 2006-05-01 13:23 Rev.: 34070

cleanup

0 lines of code changed in 82 files:

dav 2006-05-01 12:15 Rev.: 34068

M GUI/TimestepSelector.tcl

Set default max_time to 0 (there aren't any timesteps to begin with).
Make status frame larger so you can actually see most of the message.
Allow the arrow keys to inc/dec time based on the 'tinc' setting.

M Modules/DataIO/ArchiveReader.cc

Reformatted a little... but the real/only change is to add a warning
message that is displayed when the module has no file specified.

M Modules/Selectors/TimestepSelector.cc

Stop animating if there is not data. Only get the outPorts if there
is input.

45 lines of code changed in 4 files:

dav 2006-05-01 12:08 Rev.: 34067

Fixed a comment. This doesn't change configure, so I've not updated
configure at this time.

1 lines of code changed in 1 file:

dav 2006-05-01 12:06 Rev.: 34066

M Viewer.tcl

Renamed 'message' to more explicit 'movieMessage'.

M ClipLattice.tcl

Reformatted the GUI to use less space. Added the requisite sci button pannel.

M CreateMesh.tcl

Added the requisite sci button pannel.

14 lines of code changed in 5 files:

sbrown 2006-05-01 12:06 Rev.: 34065

As per Jennifer's requests, removed the rest of the old mixing table code, including the really old fortran interfaces. Email me if you still need these.

2 lines of code changed in 19 files:

dav 2006-05-01 11:59 Rev.: 34063

Proper indention. Removed superfluous ';'

10 lines of code changed in 1 file:

mjc 2006-05-01 11:01 Rev.: 34062

comment out tests that crash

0 lines of code changed in 2 files:

mjc 2006-05-01 10:53 Rev.: 34061

compilation fix

0 lines of code changed in 4 files:

mjc 2006-05-01 10:52 Rev.: 34060

partial fixes for bring VS up to date with fields/basis changes

0 lines of code changed in 16 files:

mjc 2006-05-01 10:46 Rev.: 34059

make hex vol order match hex basis order

47 lines of code changed in 5 files:

jeroen 2006-05-01 01:37 Rev.: 34058

Remove old unused modules in an effort to clean up this Package.

1 lines of code changed in 34 files:

jeroen 2006-05-01 01:23 Rev.: 34057

Interface modules for continuous bidomain

2578 lines of code changed in 41 files:

jeroen 2006-05-01 01:17 Rev.: 34056

Renamed CompartmentBoundary into DomainBoundary for more consistent naming, added framework for datastreaming (needs to be finished) add two modules for doing operations on a matrix on a row or column basis. Updated some of the module descriptions and various bug fixes.

2295 lines of code changed in 41 files:

jeroen 2006-05-01 01:10 Rev.: 34055

Added new functions to do row and column operations on matrices

0 lines of code changed in 4 files:

April 2006 »

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