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Commit bac0308d authored by Tom Fischer's avatar Tom Fischer Committed by GitHub
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Merge pull request #1739 from TomFischer/Cleanup 

Cleanup: Clang format, fix spelling, remove debug code, ...
parents bdd2fa0a e38cb1b7
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with 172 additions and 206 deletions
Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.cpp
+ 11
− 33
View file @ bac0308d
......@@ -84,8 +84,8 @@ void NodeWiseMeshPartitioner::readMetisData(const std::string& file_name_base)
std::remove(fname_eparts.c_str());
}
void NodeWiseMeshPartitioner
::partitionByMETIS(const bool is_mixed_high_order_linear_elems)
void NodeWiseMeshPartitioner::partitionByMETIS(
const bool is_mixed_high_order_linear_elems)
{
std::vector<MeshLib::Node*> const& nodes = _mesh->getNodes();
for (std::size_t part_id = 0; part_id < _partitions.size(); part_id++)
......@@ -186,8 +186,8 @@ void NodeWiseMeshPartitioner
renumberNodeIndices(is_mixed_high_order_linear_elems);
}
void NodeWiseMeshPartitioner::renumberNodeIndices
(const bool is_mixed_high_order_linear_elems)
void NodeWiseMeshPartitioner::renumberNodeIndices(
const bool is_mixed_high_order_linear_elems)
{
std::size_t node_global_id_offset = 0;
// Renumber the global indices.
......@@ -252,7 +252,7 @@ NodeWiseMeshPartitioner::IntegerType
NodeWiseMeshPartitioner::getNumberOfIntegerVariablesOfElements(
const std::vector<const MeshLib::Element*>& elements) const
{
// Number of material ID, element type, and number of the nodes of
// Element ID, element type, and number of the nodes of
// an element of all elements in the current partition.
IntegerType nmb_element_idxs = 3 * elements.size();
for (const auto* elem : elements)
......@@ -262,9 +262,10 @@ NodeWiseMeshPartitioner::getNumberOfIntegerVariablesOfElements(
return nmb_element_idxs;
}
std::tuple< std::vector<NodeWiseMeshPartitioner::IntegerType>,
std::vector<NodeWiseMeshPartitioner::IntegerType>>
NodeWiseMeshPartitioner::writeConfigDataBinary(const std::string& file_name_base)
std::tuple<std::vector<NodeWiseMeshPartitioner::IntegerType>,
std::vector<NodeWiseMeshPartitioner::IntegerType>>
NodeWiseMeshPartitioner::writeConfigDataBinary(
const std::string& file_name_base)
{
const std::string fname = file_name_base + "_partitioned_msh_cfg"
+ std::to_string(_npartitions) + ".bin";
......@@ -305,10 +306,10 @@ NodeWiseMeshPartitioner::writeConfigDataBinary(const std::string& file_name_base
// Update offsets
num_elem_integers[loop_id] =
partition.regular_elements.size() + config_data[8];
// Offset the ending enrtry of the element integer variales of
// Offset the ending entry of the element integer variales of
// the non-ghost elements of this partition in the vector of elem_info.
config_data[11] += num_elem_integers[loop_id] * sizeof(IntegerType);
// Offset the ending enrtry of the element integer variales of
// Offset the ending entry of the element integer variales of
// the ghost elements of this partition in the vector of elem_info.
num_g_elem_integers[loop_id] =
partition.ghost_elements.size() + config_data[9];
......@@ -518,29 +519,6 @@ void NodeWiseMeshPartitioner::writeASCII(const std::string& file_name_base)
writeNodesASCII(file_name_base);
}
void NodeWiseMeshPartitioner::resetGlobalNodeIndices()
{
for (std::size_t i = 0; i < _mesh->_nodes.size(); i++)
{
_mesh->_nodes[i]->setID(_nodes_global_ids[i]);
}
// sort
std::sort(_mesh->_nodes.begin(), _mesh->_nodes.end(),
[](const MeshLib::Node* a, const MeshLib::Node* b) {
return a->getID() < b->getID();
});
}
void NodeWiseMeshPartitioner::writeGlobalMeshVTU(
const std::string& file_name_base)
{
resetGlobalNodeIndices();
MeshLib::IO::VtuInterface writer(_mesh.get());
const std::string npartitions_str = std::to_string(_npartitions);
writer.writeToFile(file_name_base + "_node_id_renumbered_partitions_" +
npartitions_str + ".vtu");
}
void NodeWiseMeshPartitioner::getElementIntegerVariables(
const MeshLib::Element& elem,
const std::vector<IntegerType>& local_node_ids,
......
Applications/Utils/ModelPreparation/PartitionMesh/NodeWiseMeshPartitioner.h
+ 2
− 9
View file @ bac0308d
......@@ -64,8 +64,6 @@ public:
/// interpolation
void partitionByMETIS(const bool is_mixed_high_order_linear_elems);
void resetGlobalNodeIndices();
/// Read metis data
/// \param file_name_base The prefix of the file name.
void readMetisData(const std::string& file_name_base);
......@@ -82,10 +80,6 @@ public:
/// \param file_name_base The prefix of the file name.
void writeBinary(const std::string& file_name_base);
/// Write the global mesh into a VTU file
/// \param file_name_base The prefix of the file name.
void writeGlobalMeshVTU(const std::string& file_name_base);
private:
/// Number of partitions.
IntegerType _npartitions;
......@@ -113,12 +107,11 @@ private:
/*!
Calculate the total number of integer variables of an element
vector.
Each element has three integer variables for material ID,
vector. Each element has three integer variables for element ID,
element type, number of nodes of the element. Therefore
the total number of the integers in an element vector is
3 * vector size + sum (number of nodes of each element)
*/
*/
IntegerType getNumberOfIntegerVariablesOfElements(
const std::vector<const MeshLib::Element*>& elements) const;
......
Applications/Utils/ModelPreparation/PartitionMesh/PartitionMesh.cpp
+ 0
− 3
View file @ bac0308d
......@@ -134,9 +134,6 @@ int main(int argc, char* argv[])
INFO("Write the data of partitions into binary files ...");
mesh_partitioner.writeBinary(file_name_base);
}
INFO("Write the mesh with renumbered node indices into VTU ...");
mesh_partitioner.writeGlobalMeshVTU(file_name_base);
}
INFO("Total runtime: %g s.", run_timer.elapsed());
......
MeshLib/IO/MPI_IO/NodePartitionedMeshReader.h
+ 18
− 11
View file @ bac0308d
......@@ -76,17 +76,24 @@ private:
/// A collection of integers that configure the partitioned mesh data.
struct PartitionedMeshInfo
{
unsigned long nodes; ///< 0: Number of all nodes of a partition,
unsigned long base_nodes; ///< 1: Number of nodes for linear elements of a parition,
unsigned long regular_elements; ///< 2: Number of non-ghost elements of a partition,
unsigned long ghost_elements; ///< 3: Number of ghost element of a partition,
unsigned long active_base_nodes; ///< 4: Number of active nodes for linear element of a parition,
unsigned long active_nodes; ///< 5: Number of all active nodes a parition,
unsigned long global_base_nodes; ///< 6: Number of nodes for linear element of global mesh,
unsigned long global_nodes; ///< 7: Number of all nodes of global mesh,
unsigned long offset[5]; ///< 8~12: Offsets of positions of partitions in the data arrays
/// (only 8 and 9 are used for ascii input)
unsigned long extra_flag; ///< 13: Reserved for extra flag.
unsigned long nodes; ///< 0: Number of all nodes of a partition,
unsigned long base_nodes; ///< 1: Number of nodes for linear
///elements of a parition,
unsigned long regular_elements; ///< 2: Number of non-ghost elements
///of a partition,
unsigned long
ghost_elements; ///< 3: Number of ghost element of a partition,
unsigned long active_base_nodes; ///< 4: Number of active nodes for
/// linear element of a parition,
unsigned long
active_nodes; ///< 5: Number of all active nodes a parition,
unsigned long global_base_nodes; ///< 6: Number of nodes for linear
/// element of global mesh,
unsigned long global_nodes; ///< 7: Number of all nodes of global mesh,
unsigned long offset[5]; ///< 8~12: Offsets of positions of partitions
/// in the data arrays (only 8 and 9 are used
/// for ascii input)
unsigned long extra_flag; ///< 13: Reserved for extra flag.
std::size_t size() const { return 14; }
unsigned long* data() { return &nodes; }
......
MeshLib/Node.h
+ 1
− 1
View file @ bac0308d
......@@ -73,7 +73,7 @@ public:
return Node(_x[0]-v[0], _x[1]-v[1], _x[2]-v[2]);
}
protected:
private:
/// Update coordinates of a node.
/// This method automatically also updates the areas/volumes of all connected elements.
void updateCoordinates(double x, double y, double z);
......
MeshLib/NodePartitionedMesh.h
+ 133
− 140
View file @ bac0308d
......@@ -27,150 +27,143 @@ namespace MeshLib
/// A subdomain mesh.
class NodePartitionedMesh : public Mesh
{
public:
// Copy a global mesh for the case of the thread number is one,
// i.e the gobal mesh is not partitioned.
// \param mesh The gobal mesh
explicit NodePartitionedMesh(const Mesh& mesh)
: Mesh(mesh), _global_node_ids(mesh.getNumberOfNodes()),
_n_global_base_nodes(mesh.getNumberOfBaseNodes()),
_n_global_nodes(mesh.getNumberOfNodes()),
_n_active_base_nodes(mesh.getNumberOfBaseNodes()),
_n_active_nodes(mesh.getNumberOfNodes())
public:
// Copy a global mesh for the case of the thread number is one,
// i.e the gobal mesh is not partitioned.
// \param mesh The gobal mesh
explicit NodePartitionedMesh(const Mesh& mesh)
: Mesh(mesh),
_global_node_ids(mesh.getNumberOfNodes()),
_n_global_base_nodes(mesh.getNumberOfBaseNodes()),
_n_global_nodes(mesh.getNumberOfNodes()),
_n_active_base_nodes(mesh.getNumberOfBaseNodes()),
_n_active_nodes(mesh.getNumberOfNodes())
{
const auto& mesh_nodes = mesh.getNodes();
for (std::size_t i = 0; i < _nodes.size(); i++)
{
const auto& mesh_nodes = mesh.getNodes();
for (std::size_t i = 0; i < _nodes.size(); i++)
_global_node_ids[i] = _nodes[i]->getID();
// TODO To add copying of the connected nodes (and elements)
// in the copy constructor of class Node in order to
// drop the following lines.
auto node = _nodes[i];
// Copy constructor of Mesh does not copy the connected
// nodes to node.
if (node->_connected_nodes.size() == 0)
{
_global_node_ids[i] = _nodes[i]->getID();
// TODO To add copying of the connected nodes (and elements)
// in the copy constructor of class Node in order to
// drop the following lines.
auto node = _nodes[i];
// Copy constructor of Mesh does not copy the connected
// nodes to node.
if (node->_connected_nodes.size() == 0)
{
std::copy(mesh_nodes[i]->_connected_nodes.begin(),
mesh_nodes[i]->_connected_nodes.end(),
std::back_inserter(node->_connected_nodes));
}
std::copy(mesh_nodes[i]->_connected_nodes.begin(),
mesh_nodes[i]->_connected_nodes.end(),
std::back_inserter(node->_connected_nodes));
}
}
/*!
\brief Constructor
\param name Name assigned to the mesh.
\param nodes Vector for nodes, which storage looks like:
||--active base nodes--|--ghost base nodes--|
--active extra nodes--|--ghost extra nodes--||
(extra nodes: nodes for high order interpolations)
\param glb_node_ids Global IDs of nodes of a partition.
\param elements Vector for elements. Ghost elements are stored
after regular (non-ghost) elements.
\param properties Mesh property.
\param n_global_base_nodes Number of the base nodes of the global mesh.
\param n_global_nodes Number of all nodes of the global mesh.
\param n_base_nodes Number of the base nodes.
\param n_active_base_nodes Number of the active base nodes.
\param n_active_nodes Number of all active nodes.
*/
NodePartitionedMesh(const std::string &name,
const std::vector<Node*> &nodes,
const std::vector<std::size_t> &glb_node_ids,
const std::vector<Element*> &elements,
Properties properties,
const std::size_t n_global_base_nodes,
const std::size_t n_global_nodes,
const std::size_t n_base_nodes,
const std::size_t n_active_base_nodes,
const std::size_t n_active_nodes)
: Mesh(name, nodes, elements, properties, n_base_nodes),
_global_node_ids(glb_node_ids),
_n_global_base_nodes(n_global_base_nodes),
_n_global_nodes(n_global_nodes),
_n_active_base_nodes(n_active_base_nodes),
_n_active_nodes(n_active_nodes)
{
}
/// Get the number of nodes of the global mesh for linear elements.
std::size_t getNumberOfGlobalBaseNodes() const
{
return _n_global_base_nodes;
}
/// Get the number of all nodes of the global mesh.
std::size_t getNumberOfGlobalNodes() const
{
return _n_global_nodes;
}
/// Get the global node ID of a node with its local ID.
std::size_t getGlobalNodeID(const std::size_t node_id) const
{
return _global_node_ids[node_id];
}
/// Get the number of the active nodes of the partition for linear elements.
std::size_t getNumberOfActiveBaseNodes() const
{
return _n_active_base_nodes;
}
/// Get the number of all active nodes of the partition.
std::size_t getNumberOfActiveNodes() const
{
return _n_active_nodes;
}
/// Check whether a node with ID of node_id is a ghost node
bool isGhostNode(const std::size_t node_id) const
{
if(node_id < _n_active_base_nodes)
return false;
else if(node_id >= _n_base_nodes && node_id < getLargestActiveNodeID() )
return false;
else
return true;
}
/// Get the largest ID of active nodes for higher order elements in a partition.
std::size_t getLargestActiveNodeID() const
{
return _n_base_nodes + _n_active_nodes - _n_active_base_nodes;
}
// TODO I guess that is a simplified version of computeSparsityPattern()
/// Get the maximum number of connected nodes to node.
std::size_t getMaximumNConnectedNodesToNode() const
{
std::vector<Node *>::const_iterator it_max_ncn = std::max_element(
_nodes.cbegin(), _nodes.cend(),
[](Node const *const node_a, Node const *const node_b)
{
return (node_a->getConnectedNodes().size() <
node_b->getConnectedNodes().size());
});
// Return the number of connected nodes +1 for the node itself.
return (*it_max_ncn)->getConnectedNodes().size() + 1;
}
private:
/// Global IDs of nodes of a partition
std::vector<std::size_t> _global_node_ids;
/// Number of the nodes of the global mesh linear interpolations.
std::size_t _n_global_base_nodes;
/// Number of all nodes of the global mesh.
std::size_t _n_global_nodes;
/// Number of the active nodes for linear interpolations
std::size_t _n_active_base_nodes;
/// Number of the all active nodes.
std::size_t _n_active_nodes;
}
/*!
\brief Constructor
\param name Name assigned to the mesh.
\param nodes Vector for nodes, which storage looks like:
||--active base nodes--|--ghost base nodes--|
--active extra nodes--|--ghost extra nodes--||
(extra nodes: nodes for high order interpolations)
\param glb_node_ids Global IDs of nodes of a partition.
\param elements Vector for elements. Ghost elements are stored
after regular (non-ghost) elements.
\param properties Mesh property.
\param n_global_base_nodes Number of the base nodes of the global mesh.
\param n_global_nodes Number of all nodes of the global mesh.
\param n_base_nodes Number of the base nodes.
\param n_active_base_nodes Number of the active base nodes.
\param n_active_nodes Number of all active nodes.
*/
NodePartitionedMesh(const std::string& name,
const std::vector<Node*>& nodes,
const std::vector<std::size_t>& glb_node_ids,
const std::vector<Element*>& elements,
Properties properties,
const std::size_t n_global_base_nodes,
const std::size_t n_global_nodes,
const std::size_t n_base_nodes,
const std::size_t n_active_base_nodes,
const std::size_t n_active_nodes)
: Mesh(name, nodes, elements, properties, n_base_nodes),
_global_node_ids(glb_node_ids),
_n_global_base_nodes(n_global_base_nodes),
_n_global_nodes(n_global_nodes),
_n_active_base_nodes(n_active_base_nodes),
_n_active_nodes(n_active_nodes)
{
}
/// Get the number of nodes of the global mesh for linear elements.
std::size_t getNumberOfGlobalBaseNodes() const
{
return _n_global_base_nodes;
}
/// Get the number of all nodes of the global mesh.
std::size_t getNumberOfGlobalNodes() const { return _n_global_nodes; }
/// Get the global node ID of a node with its local ID.
std::size_t getGlobalNodeID(const std::size_t node_id) const
{
return _global_node_ids[node_id];
}
/// Get the number of the active nodes of the partition for linear elements.
std::size_t getNumberOfActiveBaseNodes() const
{
return _n_active_base_nodes;
}
/// Get the number of all active nodes of the partition.
std::size_t getNumberOfActiveNodes() const { return _n_active_nodes; }
/// Check whether a node with ID of node_id is a ghost node
bool isGhostNode(const std::size_t node_id) const
{
if (node_id < _n_active_base_nodes)
return false;
else if (node_id >= _n_base_nodes && node_id < getLargestActiveNodeID())
return false;
else
return true;
}
/// Get the largest ID of active nodes for higher order elements in a
/// partition.
std::size_t getLargestActiveNodeID() const
{
return _n_base_nodes + _n_active_nodes - _n_active_base_nodes;
}
// TODO I guess that is a simplified version of computeSparsityPattern()
/// Get the maximum number of connected nodes to node.
std::size_t getMaximumNConnectedNodesToNode() const
{
std::vector<Node*>::const_iterator it_max_ncn = std::max_element(
_nodes.cbegin(), _nodes.cend(),
[](Node const* const node_a, Node const* const node_b) {
return (node_a->getConnectedNodes().size() <
node_b->getConnectedNodes().size());
});
// Return the number of connected nodes +1 for the node itself.
return (*it_max_ncn)->getConnectedNodes().size() + 1;
}
private:
/// Global IDs of nodes of a partition
std::vector<std::size_t> _global_node_ids;
/// Number of the nodes of the global mesh linear interpolations.
std::size_t _n_global_base_nodes;
/// Number of all nodes of the global mesh.
std::size_t _n_global_nodes;
/// Number of the active nodes for linear interpolations
std::size_t _n_active_base_nodes;
/// Number of the all active nodes.
std::size_t _n_active_nodes;
};
} // namespace MeshLib
MeshLib/PropertyVector.h
+ 7
− 8
View file @ bac0308d
......@@ -22,9 +22,6 @@
namespace MeshLib
{
//template <typename T> class PropertyVector;
class PropertyVectorBase
{
public:
......@@ -86,10 +83,11 @@ public:
component);
}
PropertyVectorBase* clone(std::vector<std::size_t> const& exclude_positions) const
PropertyVectorBase* clone(
std::vector<std::size_t> const& exclude_positions) const
{
PropertyVector<PROP_VAL_TYPE> *t(new PropertyVector<PROP_VAL_TYPE>(_property_name,
_mesh_item_type, _n_components));
PropertyVector<PROP_VAL_TYPE>* t(new PropertyVector<PROP_VAL_TYPE>(
_property_name, _mesh_item_type, _n_components));
BaseLib::excludeObjectCopy(*this, exclude_positions, *t);
return t;
}
......@@ -220,7 +218,7 @@ public:
assert(component < _n_components);
assert(tuple_index < getNumberOfTuples());
const double* p = this->operator[](tuple_index);
if (p==nullptr)
if (p == nullptr)
OGS_FATAL("No data found in the property vector %s "
"for the tuple index %d and component %d",
getPropertyName().c_str(), tuple_index, component);
......@@ -235,7 +233,8 @@ public:
std::copy(this->cbegin(), this->cend(),
std::ostream_iterator<std::size_t>(os, " "));
os << "\n\tvalues (" << _values.size() << "):\n";
for (std::size_t k(0); k<_values.size(); k++) {
for (std::size_t k(0); k < _values.size(); k++)
{
os << "val: " << *(_values[k]) << ", address: " << _values[k] << "\n";
}
return os;
......
ProcessLib/LiquidFlow/LiquidFlowMaterialProperties.cpp
+ 0
− 1
View file @ bac0308d
......@@ -24,7 +24,6 @@
#include "MaterialLib/Fluid/FluidProperty.h"
#include "MaterialLib/PorousMedium/Porosity/Porosity.h"
#include "MaterialLib/PorousMedium/Storage/Storage.h"
#include "MaterialLib/Fluid/FluidProperties/CreateFluidProperties.h"
#include "MaterialLib/Fluid/FluidPropertyHeaders.h"
#include "MaterialLib/PorousMedium/PorousPropertyHeaders.h"
......
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