replace geosx with geos in varios variable names and comments

Author: rrsettgast

src/coreComponents/common/DataTypes.hpp

@@ -65,7 +65,7 @@
 #include <vector>
 
 /*
- * top level geosx namespace contains all code that is specific to GEOSX
+ * top level geos namespace contains all code that is specific to GEOSX
  */
 namespace geos
 {

src/coreComponents/common/LifoStorageCuda.hpp

@@ -78,7 +78,7 @@ class LifoStorageCuda : public LifoStorageCommon< T, INDEX_TYPE >
 
     if( baseLifo::m_maxNumberOfBuffers - id > (int)m_deviceDeque.capacity() )
     {
-      LIFO_MARK_SCOPE( geosx::lifoStorage::pushAddTasks );
+      LIFO_MARK_SCOPE( geos::lifoStorage::pushAddTasks );
       // This buffer will go to host memory, and maybe on disk
       std::packaged_task< void() > task( std::bind( &LifoStorageCuda< T, INDEX_TYPE >::deviceToHost, this, baseLifo::m_bufferToHostCount++ ) );
       {
@@ -112,7 +112,7 @@ class LifoStorageCuda : public LifoStorageCommon< T, INDEX_TYPE >
 
     if( baseLifo::m_bufferToHostCount > 0 )
     {
-      LIFO_MARK_SCOPE( geosx::LifoStorageCuda::popAddTasks );
+      LIFO_MARK_SCOPE( geos::LifoStorageCuda::popAddTasks );
       // Trigger pull one buffer from host, and maybe from disk
       std::packaged_task< void() > task( std::bind( &LifoStorageCuda< T, INDEX_TYPE >::hostToDevice, this, --baseLifo::m_bufferToHostCount, id ) );
       {

src/coreComponents/common/LifoStorageHost.hpp

@@ -74,7 +74,7 @@ class LifoStorageHost : public LifoStorageCommon< T, INDEX_TYPE >
 
       if( baseLifo::m_maxNumberOfBuffers - pushId > (int)baseLifo::m_hostDeque.capacity() )
       {
-        LIFO_MARK_SCOPE( geosx::lifoStorage::pushAddTasks );
+        LIFO_MARK_SCOPE( geos::lifoStorage::pushAddTasks );
         // This buffer will go to host memory, and maybe on disk
         std::packaged_task< void() > t2( std::bind( &LifoStorageHost< T, INDEX_TYPE >::hostToDisk, this, baseLifo::m_bufferToDiskCount++ ) );
         {
@@ -117,7 +117,7 @@ class LifoStorageHost : public LifoStorageCommon< T, INDEX_TYPE >
 
       if( baseLifo::m_bufferToDiskCount > 0 )
       {
-        LIFO_MARK_SCOPE( geosx::LifoStorageHost::popAddTasks );
+        LIFO_MARK_SCOPE( geos::LifoStorageHost::popAddTasks );
         // Trigger pull one buffer from host, and maybe from disk
         std::packaged_task< void() > task2( std::bind( &LifoStorageHost< T, INDEX_TYPE >::diskToHost, this, --baseLifo::m_bufferToDiskCount ) );
         {

src/coreComponents/common/Stopwatch.hpp

@@ -89,6 +89,6 @@ class Stopwatch
   real64 * m_result{};
 };
 
-} // end geosx
+} // end geos
 
 #endif

src/coreComponents/constitutive/solid/DamageSpectralUtilities.hpp

@@ -413,6 +413,6 @@ void getTestStress( real64 (& strain)[6], real64 (& stress)[6] )
   LvArray::tensorOps::scaledAdd< 6 >( stress, positiveStress, damageFactor );
 }
 
-} //namespacegeosx
+} //namespacegeos
 
 #endif /* GEOS_CONSTITUTIVE_SOLID_DAMAGESPECTRALUTILITIES_HPP_ */

src/coreComponents/denseLinearAlgebra/interfaces/blaslapack/BlasLapackLA.cpp

@@ -24,7 +24,7 @@
 
 #include <random>
 
-// Put everything under the geosx namespace.
+// Put everything under the geos namespace.
 namespace geos
 {
 
@@ -1115,4 +1115,4 @@ void BlasLapackLA::matrixLeastSquaresSolutionSolve( arraySlice2d< real64 const,
   detail::matrixLeastSquaresSolutionSolve( ACOPY.toSlice(), BCOPY.toSlice(), X );
 }
 
-} // end geosx namespace
+} // end geos namespace

src/coreComponents/fileIO/Outputs/ChomboIO.cpp

@@ -40,7 +40,7 @@ ChomboIO::ChomboIO( string const & name, Group * const parent ):
 {
   registerWrapper( viewKeyStruct::outputPathString(), &m_outputPath ).
     setInputFlag( InputFlags::REQUIRED ).
-    setDescription( "Path at which the geosx to chombo file will be written." );
+    setDescription( "Path at which the geos to chombo file will be written." );
 
   registerWrapper( viewKeyStruct::beginCycleString(), &m_beginCycle ).
     setInputFlag( InputFlags::REQUIRED ).
@@ -49,17 +49,17 @@ ChomboIO::ChomboIO( string const & name, Group * const parent ):
   registerWrapper( viewKeyStruct::inputPathString(), &m_inputPath ).
     setInputFlag( InputFlags::OPTIONAL ).
     setDefaultValue( "/INVALID_INPUT_PATH" ).
-    setDescription( "Path at which the chombo to geosx file will be written." );
+    setDescription( "Path at which the chombo to geos file will be written." );
 
   registerWrapper( viewKeyStruct::waitForInputString(), &m_waitForInput ).
     setInputFlag( InputFlags::REQUIRED ).
     setDefaultValue( 0 ).
-    setDescription( "True iff geosx should wait for chombo to write out a file. When true the inputPath must be set." );
+    setDescription( "True iff geos should wait for chombo to write out a file. When true the inputPath must be set." );
 
   registerWrapper( viewKeyStruct::useChomboPressuresString(), &m_useChomboPressures ).
     setInputFlag( InputFlags::OPTIONAL ).
     setDefaultValue( 0 ).
-    setDescription( "True iff geosx should use the pressures chombo writes out." );
+    setDescription( "True iff geos should use the pressures chombo writes out." );
 }
 
 ChomboIO::~ChomboIO()

src/coreComponents/fileIO/vtk/VTKPolyDataWriterInterface.cpp

@@ -122,11 +122,11 @@ getVtkToGeosxNodeOrdering( ParticleType const particleType )
 /**
  * @brief Provide the local list of nodes or face streams for the corresponding VTK element
  *
- * @param elementType geosx element type
+ * @param elementType geos element type
  * @return list of nodes or face streams
  *
- * For geosx element with existing standard VTK element the corresponding list of nodes is provided.
- * For Prism7+, the geosx element is converted to VTK_POLYHEDRON. The vtkUnstructuredGrid
+ * For geos element with existing standard VTK element the corresponding list of nodes is provided.
+ * For Prism7+, the geos element is converted to VTK_POLYHEDRON. The vtkUnstructuredGrid
  * stores polyhedron cells as face streams of the following format:
  * [numberOfCellFaces,
  * (numberOfPointsOfFace0, pointId0, pointId1, ... ),
@@ -358,8 +358,8 @@ getSurface( FaceElementSubRegion const & subRegion,
   std::vector< int > cellTypes;
   cellTypes.reserve( subRegion.size() );
 
-  std::unordered_map< localIndex, localIndex > geosx2VTKIndexing;
-  geosx2VTKIndexing.reserve( subRegion.size() * subRegion.numNodesPerElement() );
+  std::unordered_map< localIndex, localIndex > geos2VTKIndexing;
+  geos2VTKIndexing.reserve( subRegion.size() * subRegion.numNodesPerElement() );
   localIndex nodeIndexInVTK = 0;
   // FaceElementSubRegion being heterogeneous, the size of the connectivity vector may vary for each element.
   // In order not to allocate a new vector every time, we combine the usage of `clear` and `push_back`.
@@ -386,15 +386,15 @@ getSurface( FaceElementSubRegion const & subRegion,
     connectivity.clear();
     for( int const & ordering : vtkOrdering )
     {
-      auto const & VTKIndexPos = geosx2VTKIndexing.find( nodes[ordering] );
-      if( VTKIndexPos == geosx2VTKIndexing.end() )
+      auto const & VTKIndexPos = geos2VTKIndexing.find( nodes[ordering] );
+      if( VTKIndexPos == geos2VTKIndexing.end() )
       {
-        /// If the node is not found in the geosx2VTKIndexing map:
-        /// 1. we assign the current value of nodeIndexInVTK to this node in the map (geosx2VTKIndexing[nodes[ordering]] =
+        /// If the node is not found in the geos2VTKIndexing map:
+        /// 1. we assign the current value of nodeIndexInVTK to this node in the map (geos2VTKIndexing[nodes[ordering]] =
         /// nodeIndexInVTK++).
         /// 2. we increment nodeIndexInVTK to ensure the next new node gets a unique index.
         /// 3. we add this new VTK node index to the connectivity vector (connectivity.push_back).
-        connectivity.push_back( geosx2VTKIndexing[nodes[ordering]] = nodeIndexInVTK++ );
+        connectivity.push_back( geos2VTKIndexing[nodes[ordering]] = nodeIndexInVTK++ );
       }
       else
       {
@@ -407,10 +407,10 @@ getSurface( FaceElementSubRegion const & subRegion,
   }
 
   auto points = vtkSmartPointer< vtkPoints >::New();
-  points->SetNumberOfPoints( geosx2VTKIndexing.size() );
+  points->SetNumberOfPoints( geos2VTKIndexing.size() );
   arrayView2d< real64 const, nodes::REFERENCE_POSITION_USD > const referencePosition = nodeManager.referencePosition();
 
-  for( auto nodeIndex: geosx2VTKIndexing )
+  for( auto nodeIndex: geos2VTKIndexing )
   {
     auto point = referencePosition[nodeIndex.first];
     points->SetPoint( nodeIndex.second, point[0], point[1], point[2] );
@@ -547,7 +547,7 @@ getVtkCells( CellElementRegion const & region,
     std::vector< int > const vtkOrdering = getVtkConnectivity( subRegion.getElementType(), subRegionNumNodes );
     localIndex const numVtkData = vtkOrdering.size();
 
-    // For all geosx element, the corresponding VTK data are copied in "connectivity".
+    // For all geos element, the corresponding VTK data are copied in "connectivity".
     // Local nodes are mapped to global indices. Any negative value in "vtkOrdering"
     // corresponds to the number of faces or the number of nodes per faces, and they
     // are copied as positive values.

src/coreComponents/linearAlgebra/interfaces/hypre/HypreSolver.cpp

@@ -297,4 +297,4 @@ void HypreSolver::clear()
   m_solver.reset();
 }
 
-} // end geosx namespace
+} // end geos namespace

src/coreComponents/linearAlgebra/interfaces/hypre/HypreSolver.hpp

@@ -99,6 +99,6 @@ class HypreSolver final : public LinearSolverBase< HypreInterface >
   real64 m_computeAuuTime;
 };
 
-} // end geosx namespace
+} // end geos namespace
 
 #endif /* HYPRESOLVER_HPP_ */