The default values changed in the commit (ba1065c) breaks example such

as
https://github.com/BhallaLab/moose-examples/blob/09ca09e68f163a0920653a9400214aff10b6ba16/snippets/rxdFuncDiffusion.py
. The sparse matrix has upper limit of number of rows and columns to
20,000. In the example linked, new values makes it impossible to run the
example as is.

To overcome this, we notify the user whenever this limit is reached and
ask them to set `diffLength` before setting up the `x1`.

On top of this, we can also revert default values to original larger
values. Not sure why these values were changed to the scale of 1e-6?
Unless the reason is known, I am not going to change current values. The
above linked example  now works with this commit.

Author: Dilawar Singh

mesh/CylMesh.cpp

@@ -291,17 +291,23 @@ void CylMesh::setX1( const Eref& e, double v )
 
     size_t numVoxels = (v - x0_) / diffLength_;
     x1_ = v;
-    if( numVoxels > SM_MAX_COLUMNS )
+    if( numVoxels >= SM_MAX_COLUMNS )
     {
-        MOOSE_WARN( "Warn: Too many voxels (" << numVoxels << ") would be created  "
-                << " with current diffusion-length of " << diffLength_ 
-                << "(maximum voxels allowed=" <<  SM_MAX_COLUMNS << "). "
-                << " Rescaling length of compartment." );
-        x1_ = diffLength_ * SM_MAX_COLUMNS;
+        x1_ = diffLength_ * (SM_MAX_COLUMNS-1);
+        MOOSE_WARN("setX1: Too many voxels (" << numVoxels << ") would be created  "
+                << "with current diffLength of " << diffLength_ 
+                << "m (maximum voxels allowed=" <<  SM_MAX_COLUMNS << "). "
+                << " Changing length of the compartment: " 
+                << "x0=" << x0_ << ", x1=" << x1_
+                << ". You should change `diffLength` before setting `x1`."
+                );
+    }
+    if(numVoxels > 0) 
+    {
+        vector< double > childConcs;
+        getChildConcs( e, childConcs );
+        updateCoords( e, childConcs );
     }
-    vector< double > childConcs;
-    getChildConcs( e, childConcs );
-    updateCoords( e, childConcs );
 }
 
 double CylMesh::getX1( const Eref& e ) const
@@ -403,15 +409,21 @@ void CylMesh::setDiffLength( const Eref& e, double v )
     size_t numVoxels = (size_t) ((x1_-x0_)/diffLength_);
     if( numVoxels >= SM_MAX_COLUMNS )
     {
+        stringstream ss;
+        ss << "setDiffLength: Too many voxels (" << numVoxels << ") would be created "
+                << "for current value of x1=" << x1_ << "m, and x0=" << x0_ 
+                << "m (max " <<  SM_MAX_COLUMNS << " allowed). ";
         x1_ = x0_ + diffLength_ * (SM_MAX_COLUMNS - 1);
-        MOOSE_WARN( "Too many voxels (" << numVoxels << ") would be created  "
-                << "for diffLength of " << diffLength_ 
-                << " (maximum " <<  SM_MAX_COLUMNS << " allowed). "
-                << " Changing compartment length to " << (x1_ - x0_) << ".");
+        ss << " Changing the length of the compartment: " 
+            << "x0= " << x0_ << ", x1= " << x1_;
+        MOOSE_WARN(ss.str());
+    }
+    if(numVoxels > 0) 
+    {
+        vector< double > childConcs;
+        getChildConcs( e, childConcs );
+        updateCoords( e, childConcs );
     }
-    vector< double > childConcs;
-    getChildConcs( e, childConcs );
-    updateCoords( e, childConcs );
 }
 
 double CylMesh::getDiffLength( const Eref& e ) const

utility/print_function.hpp

@@ -70,7 +70,7 @@ using namespace std;
 #endif
 
 #define MOOSE_WARN( a ) { \
-    stringstream ss; ss << a; \
+    stringstream ss; ss << __func__ << ": " << a; \
     moose::showWarn( ss.str() ); \
     }