[cig-commits] commit: Merge in Underworld 1.4.1
Mercurial
hg at geodynamics.org
Tue Mar 23 10:35:27 PDT 2010
changeset: 601:b045449155c4
tag: tip
parent: 591:5579dd441349
parent: 600:c2cbeb437c52
user: Walter Landry <wlandry at caltech.edu>
date: Tue Mar 23 08:16:05 2010 -0700
files: Shape/src/BelowCosinePlane.meta Shape/src/Superellipsoid.meta Swarm/src/FileParticleLayout.c
description:
Merge in Underworld 1.4.1
diff -r 5579dd441349 -r b045449155c4 .hgtags
--- a/.hgtags Mon Mar 22 16:37:46 2010 -0700
+++ b/.hgtags Tue Mar 23 08:16:05 2010 -0700
@@ -1,1 +1,7 @@ 9d80e49b228982359893644281d42f53a40def8c
9d80e49b228982359893644281d42f53a40def8c v1.2.0
+09dd796686149cc49bdb98d4e713333575259523 1.4.0
+02f4b902987d154c41877d08bc0717f273d143d4 1.4.1
+02f4b902987d154c41877d08bc0717f273d143d4 1.4.1
+0000000000000000000000000000000000000000 1.4.1
+0000000000000000000000000000000000000000 1.4.1
+d0c52b4f028587261932dd435b070e52bcd04517 1.4.1
diff -r 5579dd441349 -r b045449155c4 Mesh/src/linearSpaceAdaptor.meta
--- a/Mesh/src/linearSpaceAdaptor.meta Mon Mar 22 16:37:46 2010 -0700
+++ b/Mesh/src/linearSpaceAdaptor.meta Tue Mar 23 08:16:05 2010 -0700
@@ -13,7 +13,7 @@
<param name="Parent">MeshAdaptor</param>
<param name="Reference">...</param>
<param name="Summary">Changes the mesh nodes location.</param>
-<param name="Description"> This adaptos takes a regular mesh and allows to change the position of the nodes without changing the connectivity of the elements. The node location is changed using a mapping function. There are two or three independent mapping functions $F_i$ one for each axis. The mapping function is defined as $F: [0,1]\rightarrow[0,1]$ and is described in the input xml by a series of linear segments. The function must be strictly increasing. \\Note 1: the mesh must be flagged as not regular (see example below).\\Note 2: optionally you can change the initial particle layout to have the same number of particles per element (see example below).\\Note 3: the mapping functions are defined by a series of points. The first point (0,0) is always implicit. The last point (1,1) must be present.</param>
+<param name="Description"> This adaptos takes a regular mesh and allows to change the position of the nodes without changing the connectivity of the elements. The node location is changed using a mapping function. There are two or three independent mapping functions $F_i$ one for each axis. The mapping function is defined as $F: [0,1]\rightarrow[0,1]$ and is described in the input xml by a series of linear segments. The function must be strictly increasing. \Note 1: the mesh must be flagged as not regular (see example below).\Note 2: optionally you can change the initial particle layout to have the same number of particles per element (see example below).\Note 3: the mapping functions are defined by a series of points. The first point (0,0) is always implicit. The last point (1,1) must be present.</param>
<list name="Params">
</list>
diff -r 5579dd441349 -r b045449155c4 Shape/src/BelowCosinePlane.meta
--- a/Shape/src/BelowCosinePlane.meta Mon Mar 22 16:37:46 2010 -0700
+++ b/Shape/src/BelowCosinePlane.meta Tue Mar 23 08:16:05 2010 -0700
@@ -14,7 +14,7 @@
<param name="Reference">...</param>
<param name="Summary">...</param>
<param name="Description">Defines a cosine shape, with the region less than the function included</param>
- <param name="Equation">$y \\leq a_0 + b_0sin( (2\\pi/T) x + \\phi)$ </param>
+ <param name="Equation">$y \leq a_0 + b_0sin( (2\pi/T) x + \phi)$ </param>
<!--Now the interesting stuff-->
@@ -35,7 +35,7 @@
<param name="Name">phase</param>
<param name="Type">Double</param>
<param name="Default">0.0</param>
- <param name="Description">$ \\phi $ in the equation</param>
+ <param name="Description">$ \phi $ in the equation</param>
</struct>
</list>
diff -r 5579dd441349 -r b045449155c4 Shape/src/Superellipsoid.meta
--- a/Shape/src/Superellipsoid.meta Mon Mar 22 16:37:46 2010 -0700
+++ b/Shape/src/Superellipsoid.meta Tue Mar 23 08:16:05 2010 -0700
@@ -14,7 +14,7 @@
<param name="Reference">...</param>
<param name="Summary">...</param>
<param name="Description">This creates a superellipsoid shape given in the equation. </param>
-<param name="Equation">$ f(x,y,z) = \\Big\\lbrace (\\frac{x}{r_x})^{\\frac{1}{e_1}} + (\\frac{y}{r_y})^{\\frac{1}{e_1}}$ in 2D, $\\left[(\\frac{x}{r_x})^{\\frac{1}{e_2}} + (\\frac{y}{r_y})^{\\frac{1}{e_2}}\\right]^{\\frac{e_2}{e_1}} +(\\frac{z}{r_z})^{\\frac{1}{e_1}}$ in 3D. $\\Big\\rbrace$ A point is deemed inside the shape if $f \\leq 1$</param>
+ <param name="Equation">$ f(x,y,z) = \Big\lbrace (\frac{x}{r_x})^{\frac{1}{e_1}} + (\frac{y}{r_y})^{\frac{1}{e_1}}$ in 2D, $\left[(\frac{x}{r_x})^{\frac{1}{e_2}} + (\frac{y}{r_y})^{\frac{1}{e_2}}\right]^{\frac{e_2}{e_1}} +(\frac{z}{r_z})^{\frac{1}{e_1}}$ in 3D. $\Big\rbrace$ A point is deemed inside the shape if $f \leq 1$</param>
<!--Now the interesting stuff-->
<list name="Params">
diff -r 5579dd441349 -r b045449155c4 Swarm/src/FileParticleLayout.c
--- a/Swarm/src/FileParticleLayout.c Mon Mar 22 16:37:46 2010 -0700
+++ b/Swarm/src/FileParticleLayout.c Tue Mar 23 08:16:05 2010 -0700
@@ -400,7 +400,29 @@ void _FileParticleLayout_InitialiseParti
#else
self->fileData[swarmVar_I][ii-1] = H5Dopen2( file[ii-1], dataSpaceName, H5P_DEFAULT );
#endif
- self->fileSpace[swarmVar_I][ii-1] = H5Dget_space( self->fileData[swarmVar_I][ii-1] );
+ /* if we cannot find the specified dataSpace, try again using the old naming convention */
+ if(self->fileData[swarmVar_I][ii-1] < 0){
+ sprintf( dataSpaceName, "/%s", swarmVar->name );
+
+ #if H5_VERS_MAJOR == 1 && H5_VERS_MINOR < 8
+ self->fileData[swarmVar_I][ii-1] = H5Dopen( file[ii-1], dataSpaceName );
+ #else
+ self->fileData[swarmVar_I][ii-1] = H5Dopen2( file[ii-1], dataSpaceName, H5P_DEFAULT );
+ #endif
+ }
+ /* if we still cannot find the specified dataSpace, there is a problem */
+ if(self->fileData[swarmVar_I][ii-1] < 0)
+ Journal_Firewall(
+ NULL,
+ self->errorStream,
+ "\n\nError in %s for %s '%s' \n Cannot open dataSpace for checkpointed swarmvariable (%s) that requries reloading.\n Checkpoint files may be invalid.\n\n",
+ __func__,
+ self->type,
+ self->name,
+ swarmVar->name );
+
+
+ self->fileSpace[swarmVar_I][ii-1] = H5Dget_space( self->fileData[swarmVar_I][ii-1] );
Variable_Update( swarmVar->variable );
}
diff -r 5579dd441349 -r b045449155c4 Swarm/src/GlobalParticleLayout.c
--- a/Swarm/src/GlobalParticleLayout.c Mon Mar 22 16:37:46 2010 -0700
+++ b/Swarm/src/GlobalParticleLayout.c Tue Mar 23 08:16:05 2010 -0700
@@ -311,11 +311,14 @@ void _GlobalParticleLayout_InitialisePar
MPI_Allreduce( &swarm->particleLocalCount, &globalParticlesInitialisedCount, 1, MPI_UNSIGNED, MPI_SUM, swarm->comm );
Journal_Firewall( globalParticlesInitialisedCount == self->totalInitialParticles, errorStream,
"Error - in %s() - for GlobalParticleLayout \"%s\", of type %s: after initialising particles, "
- "actual global count of particles initialised was %u, whereas requested global total "
- "totalInitialParticles was %u. If actual is < requested, it means some particles were not "
- "identified by any processor as inside their domain. If actual > requested, it means that "
- "some particles were identified by _multiple_ processors as belonging to their domain. Both "
- "these states are erroneous.\n",
+ "actual global count of particles initialised was %u, whereas the user requested global total "
+ "totalInitialParticles was %u.\n"
+ "If actual is < requested, it means some particles were not identified by any processor as "
+ "inside their domain.\n"
+ "This is usually caused because some particles are outside the mesh domain.\n"
+ "If actual > requested, it means that some particles were identified by _multiple_ processors "
+ "as belonging to their domain.\n"
+ "Both these states are erroneous.\n",
__func__, self->name, self->type, globalParticlesInitialisedCount, self->totalInitialParticles );
Stream_UnIndentBranch( Swarm_Debug );
diff -r 5579dd441349 -r b045449155c4 Utils/src/MeshShapeVC.c
--- a/Utils/src/MeshShapeVC.c Mon Mar 22 16:37:46 2010 -0700
+++ b/Utils/src/MeshShapeVC.c Tue Mar 23 08:16:05 2010 -0700
@@ -281,7 +281,7 @@ void _MeshShapeVC_Build( void* variable
/****************** VariableCondition Virtual Functions ******************/
void _MeshShapeVC_BuildSelf( void* variableCondition, void* data /* for build phase */ ) {
MeshShapeVC* self = (MeshShapeVC*)variableCondition;
- AbstractContext* context = (AbstractContext*) data;
+ AbstractContext* context = (AbstractContext*) self->context;
assert( context && Stg_Class_IsInstance( context, AbstractContext_Type ) );
assert( self->shapeName );
diff -r 5579dd441349 -r b045449155c4 libStgDomain/src/Init.c
--- a/libStgDomain/src/Init.c Mon Mar 22 16:37:46 2010 -0700
+++ b/libStgDomain/src/Init.c Tue Mar 23 08:16:05 2010 -0700
@@ -62,7 +62,6 @@ Bool StgDomain_Init( int* argc, char** a
StgDomainUtils_Init( argc, argv );
StgDomainSwarm_Init( argc, argv );
- ToolboxesManager_SetInitialised( stgToolboxesManager, "StgDomain" );
return True;
}
return False;
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