missed one of the renames in uda2nrrd
2 lines of code changed in 1 file:
added comments and moved cullIntersection, nodePostion, and cellPosition
to the completed section.
updated getBox and getInteriorBox to the new interface, renamed them to
getExtraBox and getBox.
renamed neighborsLow to noNeighborsLow and neighborsHigh to
noNeighborsHigh. This follows the logic that 1 is true and 0 is false.
170 lines of code changed in 29 files:
Reworked some code to be more clear and concise.
216 lines of code changed in 5 files:
Hopefully last compile fix.
4 lines of code changed in 1 file:
Missed a function, not sure why my build is building.
4 lines of code changed in 1 file:
Missed a file when renaming functions.
18 lines of code changed in 1 file:
Renamed the get*Index(basis) functions to be inline with naming
convention.
115 lines of code changed in 15 files:
Migrated the get*Index(basis) functions to the new interface.
Added asserts to make sure boundaryLayers and extraCells are not used at
the same time.
128 lines of code changed in 2 files:
Need #include <algorithm> (for 'find()') for pedantic IBM compiler...
3 lines of code changed in 1 file:
Store the BCData as a pointer that will only be allocated on patches owned
by processors.
40 lines of code changed in 3 files:
Made superbox functions private and made superbox classes friends of the
patch class. This is to ensure that the infastructure is using the more
descriptive interfaces than the generic ones required by superbox.
Also updated the dynamic load balancer to use a more descriptive
interface.
48 lines of code changed in 2 files:
Fix closedir of null.
10 lines of code changed in 1 file:
Added comments that describe the mapping of functions that need to
replaced.
1627 lines of code changed in 1 file:
Converted the following to the new interface:
getCellIterator(Box b)
getNodeIterator(Box b)
getCellCenterIterator(Box b)
These need to be renamed sometime in the future to include 'Extra' as
they all involve extra cells.
Deleted getExtraCellIterator(Box b) it isn't used and its name doesn't
match what it does. The only difference between this function and
getCellIterator(Box b) appears to be that this function is not inclusive
on the plus face.
Rearranged the header slightly.
Made some spacing changes.
1624 lines of code changed in 2 files:
fixed restart bug created by d_computeNodalHeatFlux
16 lines of code changed in 1 file:
A few more small changes to the way the grid is stored in the patch
class.
Factored out d_level.
43 lines of code changed in 7 files:
use patch->findClosestNode instead of the old stale code I ripped off from
pre-Justin patch.h
2 lines of code changed in 1 file:
Use the command (whoami) instead of the environmental variable USER (wiped out
at the beginning of the script) to decipher who is running the script.
Note only csafe-tester can update the svn_revision log.
1 lines of code changed in 1 file:
Include tag name in more validation error messages.
27 lines of code changed in 2 files:
Slightly changed the way Patch stores the grid.
33 lines of code changed in 8 files:
Added new task (turned off by default) to compute the nodal heat flux.
To turn it on, add either:
<save label = "g.HeatFlux"/>
or
<DataAnalysis>
<Module name="flatPlate_heatFlux">
<snip>
</DataAnalysis>
to the ups file.
190 lines of code changed in 10 files:
added gHeatFlux label
0 lines of code changed in 4 files:
Reimplemented findClosestNode using the new interface. The new
implementation has a slightly different footprint than the old one. It
now returns the node instead of taking it as a reference parameter. It
also no longer computes or returns the relative node index.
21 lines of code changed in 1 file:
New analysis module that computes the total heat rate through a user
specified plane. Ups usage:
<DataAnalysis>
<Module name="flatPlate_heatFlux">
<material>0</material>
<plane>
<startingPt> [0.00, 0.005, 0.000] </startingPt>
<endingPt> [0.01, 0.005, 0.01] </endingPt>
</plane>
</Module>
</DataAnalysis>
Currently, only setup for a single plane but could be easily extended to
multiple planes.
451 lines of code changed in 4 files:
Fixed the boundary source terms to work on multiple patches.
236 lines of code changed in 5 files:
Changed to new iterators
6 lines of code changed in 2 files:
pulled out dav's changes to SimulationTime until a more complete patch
can be made. This appears to fix the RT.
8 lines of code changed in 1 file:
Replaced tabs with spaces... purely cosmetic.
33 lines of code changed in 1 file:
Slightly cleaner (more concise) output
0 lines of code changed in 2 files:
Added some tabs... testing new diff -b functionality
49 lines of code changed in 1 file:
hack to remove word 'exception' from output.
4 lines of code changed in 1 file:
M CCA/Ports/ProblemSpecInterface.h
M CCA/Components/ProblemSpecification/ProblemSpecReader.h
M CCA/Components/ProblemSpecification/ProblemSpecReader.cc
* Only validate when told too.. currently only sus.cc tells the reader
to validate.
* Default dbg spew to off.
M CCA/Components/Schedulers/SchedulerCommon.cc
Turn off memory use dbg spew.
M StandAlone/sus.cc
Turn on reader validation.
M StandAlone/compare_uda.cc
Purely cosmetic update. Removed tabs, and indented.
M CCA/Components/LoadBalancers/DynamicLoadBalancer.cc
M StandAlone/tools/compare_mms/ExpMMS.h
M StandAlone/tools/compare_mms/SineMMS.h
M StandAlone/tools/compare_mms/MMS.h
M StandAlone/tools/compare_mms/compare_mms.cc
M StandAlone/tools/compare_mms/LinearMMS.h
Fixed compiler warnings.
561 lines of code changed in 17 files:
Fix compiler warnings/errors that didn't show up on the Mac.
34 lines of code changed in 2 files:
Quiet compiler warnings.
3 lines of code changed in 1 file:
Fixed bug in MPI_Request buffer.
6 lines of code changed in 1 file:
Adding in problem spec (.ups) validation. It will only produce
warnings for now... but soon it will kill the run with an
exception... so fix your .ups files. You can use use sus to validate
your .ups file by doing the following (note, you only need one
processor to do this):
> sus -validate simulation.ups
This will do the validation and then quit sus.
WARNING... if you run sus from anywhere but its build directory (or if
the build dir does not have a symbolic link to the inputs/ dir),
validation will not take place because the code will not be able to
find the ups_spec.xml file... I'll try to come up with a fix for this
soon.
M Core/Containers/StringUtil.h
M Core/Containers/StringUtil.cc
Updated split_string to allow multiple separator characters.
M Core/Init/init.cc
M Core/Util/FileUtils.cc
Use new split_string.
M Packages/Uintah/CCA/Components/ProblemSpecification/sub.mk
Need Core/Containers for StringUtil.
M Packages/Uintah/CCA/Components/ProblemSpecification/ProblemSpecReader.h
M Packages/Uintah/CCA/Components/ProblemSpecification/ProblemSpecReader.cc
Validate the .ups file passed in. Uses the inputs/ups_spec.xml file
for the validation. Still needs some work to handle "children"
elements in ups_spec.xml... This element will specify how children
relate to each other, but hasn't been completely thought through yet.
(For example, it could specify that all children tags are necessary,
or that only one of two tags is valid, but not both... etc.)
M Packages/Uintah/StandAlone/sus.cc
* Added some blank lines around exception prints to make them MUCH
easier to see in the output.
* Added -validate flag to only validate .ups file and quit.
M Packages/Uintah/Core/Grid/SimulationTime.cc
Made the naming consistent for the tags in the Time block... all now
start with a lowercase letter, followed by capital letters for each
new word... (instead of using '_'). I know, I know, but I couldn't
help myself... at least I didn't change every single tag in all the
.ups files to be consistent.
M Packages/Uintah/Core/ProblemSpec/sub.mk
Cosmetic fix.
M Packages/Uintah/StandAlone/inputs/*/*.ups
Fixed Time block to use new (old/consistent) naming standard.
M Packages/Uintah/StandAlone/inputs/ups_spec.xml
Added a common tags section so that they can be reused in the spec
without having to write them out every time. Added a few example
"children" elements, but they aren't used yet.
1063 lines of code changed in 14 files:
Don't p2p from same proc to same proc... perhaps this will fix the problem on Ranger.
10 lines of code changed in 1 file:
Fix linking (added Core/OS) on Mac OSX for last commit.
3 lines of code changed in 1 file:
Allow for very verbosity... :)
15 lines of code changed in 1 file:
quiet compiler warning
2 lines of code changed in 1 file:
Added support for visualizing vectors on both particle and volume data. Also, corrected the centering of variables in meshes.
190 lines of code changed in 1 file:
Major updates:
* Memory checking moved into the Scheduler... currently it is 'turned
off' and thus still only checks memory at the end of a
timestep.. However, we can easily now turn on checking after every
task. Note, this only catches slightly more memory use then
before... what we need to do is have each (some?) task make the memory
tracking call explicitly at a point where the author thinks that the
most memory is being used. The implementation of this isn't yet clear
as the tasks don't have a pointer to the scheduler... Still thinking
on the best way to do this.
* Updated VarTracker code to be a little better with respect to
letting the user know what is going on.
M CCA/Components/SimulationController/SimulationController.h
M CCA/Components/SimulationController/SimulationController.cc
Moved the memory tracking code to the Scheduler.
M CCA/Components/Schedulers/SendState.h
M CCA/Components/Schedulers/SendState.cc
Purely cosmetic (white space, use "{}") changes.
M CCA/Components/Schedulers/OnDemandDataWarehouse.h
setRestarted() is a virtual function.
M CCA/Components/Schedulers/OnDemandDataWarehouse.cc
Purely cosmetic (white space, use "{}") changes. Long lines are ok,
extremely long lines are too much.
M CCA/Components/Schedulers/MPIScheduler.cc
Added /* commented out */ section that will check memory use after each task.
M CCA/Components/Schedulers/SchedulerCommon.h
M CCA/Components/Schedulers/SchedulerCommon.cc
* Moved memory tracking code here.
* Expanded the VarTracker code to be more verbose and to give more
info, check error conditions, etc.
* Indented.
M CCA/Components/Arches/Mixing/NewStaticMixingTable.cc
Only print out the mixing table info on proc 0... makes it much easier to read.
M CCA/Ports/Scheduler.h
Moved memory tracking into Scheduler.
M Core/Grid/Variables/ReductionVariable.h
Cosmetics.
M Core/Grid/Variables/ReductionVariableBase.h
print() is a const function.
M StandAlone/sus.cc
Updates for mem tracking move to scheduler.
440 lines of code changed in 18 files:
clean up indentation
47 lines of code changed in 1 file:
cleaning up, fix poisson1 test... i think
16 lines of code changed in 1 file:
Reenabled getNodeIterator(Box b)
1 lines of code changed in 2 files:
More accurate info displayed to user. input.dtd and chem.bin aren't used anymore...
19 lines of code changed in 1 file:
Removed code accidently checked in last patch.
2 lines of code changed in 2 files:
Rolled back 40802. This code was used in some of the SCIRun modules.
Justin
51 lines of code changed in 2 files:
Replaced old iterator calls with __New() ones.
5 lines of code changed in 1 file:
old and very stale nets.
0 lines of code changed in 1 file:
Deleted some unused functions
0 lines of code changed in 2 files:
Converted the containsXXXXXX functions to the new interface
68 lines of code changed in 1 file:
made findCellsFromNode and findNodesFromCell static.
6 lines of code changed in 2 files:
Converted findCell, findCellsFromNode, and findNodesFromCell to new
interface.
Removed unused function findClosestNode.
54 lines of code changed in 2 files:
Accidently removed some code that was not ready to be removed yet.
22 lines of code changed in 1 file:
missed some code when removing getCoarseFineInterfaces.
0 lines of code changed in 1 file:
Removed getCoarseFineInterfaceFaces and related code.
0 lines of code changed in 2 files:
Remove unused SFC iterators.
49 lines of code changed in 14 files:
Improve the speed of sound calculation to hopefully improve stability.
3 lines of code changed in 1 file:
mplemented the following for the new interface:
getLevel__New()
getNodePosition()
getCellPosition()
containsPoint__New()
containsPointInExtraCells()
Updated the following to use the new interface:
findCellNodes()
findCellNodes27()
dCell()
140 lines of code changed in 2 files:
Delete unused class.
0 lines of code changed in 1 file:
Changed:
hasCoarseFineInterfaceFaces->hasCoarseFaces
getCoarseFineInterfaceFaces->getCoarseFaces
55 lines of code changed in 8 files:
Implemented the following:
getNeighborFaces
hasNeighborFaces
hasBoundaryFaces
hasCoarseFaces
62 lines of code changed in 1 file:
Removed the old interface for getBoundaryFaces and getCornerCells along
with all related code.
3 lines of code changed in 2 files:
Removed compiler warning. (Dd)
2 lines of code changed in 1 file:
Be more verbose. (Dd)
0 lines of code changed in 2 files:
need unistd.h
0 lines of code changed in 2 files:
Need #include <unistd.h>... strange that other compilers didn't pick up on this...
6 lines of code changed in 2 files:
Fix split to not return empty pieces.
3 lines of code changed in 1 file:
Added support for materials on both particle and volume data
150 lines of code changed in 3 files:
allow root and csafe-tester to update the svn_revison file
4 lines of code changed in 1 file:
Migrated last getBoundaryFaces to new interface.
1 lines of code changed in 1 file:
Changed the order that getBoundaryFaces and getCoarseFaces returns
faces.
It now returns the faces in order of xminus, xplus, yminus, yplus,
zminus, zplus.
4 lines of code changed in 1 file:
Reads in sulfur balance logical for the extra scalar.
1 lines of code changed in 1 file:
Missed this file in the previous commit.
3 lines of code changed in 1 file:
Converted all but 1 instance of getBoundaryFaces to the new interface.
The remaining one produces different results when the boundary faces are
returned in a different order.
Converted all instances of getCornerCells over to the new interface.
94 lines of code changed in 11 files:
Added another source term and the corresponding mechanisms for computing so2 efficiency.
371 lines of code changed in 18 files:
ImplicitMatrixBC()
-fixed debugging cout statement
1 lines of code changed in 1 file:
Should have fixed a case where you can do a timestep restart with particles (broken in my December commit)
13 lines of code changed in 3 files:
Cleaned up source term by removing the use of fortran indices and +='ed the calculation.
7 lines of code changed in 1 file:
- tabs
- 2 space indentation
- removed code related to IRIX
- added -mfpmath=sse to linux optimized configure line
- removed James & Bryan from the email list
- changed SCRIPT_DIR to /home/csafe/csafe-tester/scripts
180 lines of code changed in 1 file:
cosmetics
9 lines of code changed in 3 files:
Added collapse() function.
35 lines of code changed in 2 files:
Added a header to replace_gold_standard... Todd/someone please update the header with complete and accurate info...
17 lines of code changed in 1 file:
MPMF : on Darwin tests don't check the answers
MPMICE: spaces
9 lines of code changed in 2 files:
The user can now add a comment to the replaceLog file when replacing the goldStandard
5 lines of code changed in 1 file:
Fix SCI_MAKE_BE_QUIET for the rest of the depend modes
21 lines of code changed in 1 file:
Now passing myworld into NewStaticMixingTable for debugging.
33 lines of code changed in 5 files:
Initial uda file plugin for VisIt. Please read readme.txt before you proceed.
1333 lines of code changed in 9 files:
Rolled back changes in 40683, 40653, and 40651. These changes are
suspect to what is changing the answers.
This appears to fix the Models tests but does not fix the MPMICE tests.
253 lines of code changed in 11 files:
Fix positionToIndex for streched grids.
21 lines of code changed in 1 file:
More specific error message.
0 lines of code changed in 2 files:
Make print() output just a little cleaner
3 lines of code changed in 1 file:
Added a few cosmetic comments.
6 lines of code changed in 1 file:
M Util/ProgressiveWarning.h
Added some documentation as to what I think this class does...
M Util/ProgressiveWarning.cc
If multiplier is set to 1, an infinite loop occurs... Catch this case and change the multiplier to 2...
0 lines of code changed in 4 files:
Removed the boundary faces and corner cells vectors from Patch.
0 lines of code changed in 2 files:
Fixed a sign error
1 lines of code changed in 1 file:
turn back on all raid disk checks on inferno.
42 lines of code changed in 1 file:
Made an error message more descriptive.
3 lines of code changed in 1 file:
The static grid was not set with the queryGrid function which is used in
compare_uda. This caused compare_uda to fail some assertions.
1 lines of code changed in 1 file:
Updated the crontabs to run the scripts from /home/csafe/csafe-tester/scripts
2 lines of code changed in 3 files:
deleted spew
0 lines of code changed in 1 file:
Deleted the NirvanaLoadBalancer. This allowed us to remove an IntVector
from patch.
2 lines of code changed in 8 files:
Patch now contains the old and new grids as static members. This allows
us to remove level pointer from the patch class. Right now there is a
limit of 8 levels (3 bits) of refinement but this can easily be increased in the
future. Asserts that verify the correctness of this implementation have
been added.
5 lines of code changed in 2 files:
Progress twoard factoring out the level pointers from the patch class
58 lines of code changed in 5 files:
Fixed some errors in the last patch.
4 lines of code changed in 1 file:
Initial commit for factoring out the level pointer from the grid.
37 lines of code changed in 2 files:
Added asserts to compare getCoarseFaces and getCoarseFineInterfaceFaces
18 lines of code changed in 1 file:
Added function getCoarseFaces which returns a vector that contains all
of the coarse faces.
21 lines of code changed in 1 file:
Changed the for loops to be on 1 line...
24 lines of code changed in 9 files:
Accidently commited 2 files i didn't want to
1 lines of code changed in 1 file:
The code is now using the new versions of getCornerCells and
getBoundaryFaces. If these pass regressions tests then the old code
will be removed and a couple vectors will be removed from the patch
class.
126 lines of code changed in 12 files:
added const to some functions
17 lines of code changed in 1 file:
Use getNumCells instead of getInteriorVolume
1 lines of code changed in 1 file:
Enabled some exceptions for when bad parameters are passed to some of
the new patch functions.
4 lines of code changed in 1 file:
Renamed some of the options concerning face cells to be more
descriptive.
84 lines of code changed in 2 files:
Reenabled the asserts for getEdgeCellIterator when extraCells is
(1,1,1). The fix to getCornerCells fixed this function.
Optimized getFaceAxes and moved it to the verified section of the patch
class.
Moved the getFaceName function to the verified section of the patch.
Commented out a few unused functions.
55 lines of code changed in 2 files:
Rearrange initialization to remove compiler warnings.
6 lines of code changed in 1 file:
Asserts for getBoundaryFaceIterator when using NC_vars are now only done
when extraCells is (1,1,1). There was a bug in the original call which
returned an incorrect iterator when extraCells wasn't (1,1,1).
Fixed a bug in getCornerCells where in some cases some corner cells would not
be returned. Reenabled asserts for this call. This bug is also likely
part of the bug in getEdgeCellIterator.
30 lines of code changed in 1 file:
saved as unix file instead of dos file
now supporting CCVariable<int, double, Vector>, SFC(X,Y,Z)<double>
The file header is now sorted by variable type and subtype.
Data is written out by variable type and subtype.
632 lines of code changed in 3 files:
malloc.cc updates for memory initialization
11 lines of code changed in 3 files:
Forgot to commit configure controlled .h file for memory initialization code.
19 lines of code changed in 1 file:
M configure
M configure.ac
Added a configure flag (--enable-memory-initialization[=8_bit_number])
that turns on the memory initialization code that Justin wrote. If
8_bit_number is not specified, it defaults to 127. If the flag is not
specified, then memory initialization is turned off. This should only
effect new.cc, so via configure, you can toggle it back and forth
without having to worry about compiling lots of files.
M Core/Malloc/new.cc
Removed Todd's (bad :P) influence on Justin and renamed the flags to
be something meaningful. ;)
80 lines of code changed in 3 files:
Created a postfix ++ operator for the enum FaceType.
This allows us to do loops like the following:
for(FaceType face=startFace;face<numFaces;face++)
{
}
5 lines of code changed in 1 file:
Disabled asserts for getBoundaryFaceIterator with NC_vars because the
old version appears to be bugged.
Implemented getBoundaryCornerCells__New. Asserts for this function are
disabled because the old version appears to be bugged.
The RT should now work again
163 lines of code changed in 2 files:
Added the ability to initialize variables to "bad" numbers. To turn
this on add the following lines to "include/sci_defs/malloc_defs.h"
within your build directory.
//========================================
#define INITIALIZE_EVIL
#define EVIL_NUM 127
//========================================
Evil num specifies the bit pattern for each allocated byte.
If you set EIL_NUM to 127 both floats and ints will be initalized to
very large numbers. If you set to 255 you will initalize floating point
numbers to nan and signed integers to -1.
This will provide a mechinism to help tracking down uninitialized
variables. This should work with both SCI_MALLOC on and off.
90 lines of code changed in 2 files:
Previous patch implemented getBoundaryFaces__New()
This patch fixed a bug in that implementation and added asserts to
verify correctness.
40 lines of code changed in 2 files:
Added a private structure named PatchState. This structure will tightly
store data that the patch needs like its boundary conditions, its level,
etc. Each element in this struct will only use the necessary amount of
bits allowing us to greatly decrease the memory requirement for this
state. Currently only boundary conditions are in this struct.
Updated the BCs to use this struct.
143 lines of code changed in 2 files:
added mpmice component
2 lines of code changed in 1 file:
ooops
0 lines of code changed in 1 file:
added mpmice rayleigh problem. This runs however the order-of-accuracy is wrong
329 lines of code changed in 5 files:
Simplified the logic in getBoundaryFaceCellIterator. Which hopefully has
fixed a bug in it.
16 lines of code changed in 1 file:
Implemented getBoundaryEdgeCellIterator. Asserts have not been added
because original one appeared to be bugged.
Implemented getNumCells, getNumNodes, getNumExtraCells, getNumExtraCells
168 lines of code changed in 2 files: