Skip to content

GitLab

Commit dc686f86 authored by Andrew J. Burns (Cont's avatar Andrew J. Burns (Cont
Browse files
Options

Finished converting documentation to tag-based version; adjusted line length where possible

parent a5f74bf5
Expand all Hide whitespace changes
Inline Side-by-side
Showing with 7756 additions and 3328 deletions
Xdmf.hpp
View file @ dc686f86
......@@ -66,6 +66,17 @@
* shared pointers can be created. These pointers are freed
* automatically by the shared pointer reference counting mechanism.
*
*
* Structure:
*
* Xdmf2 is structured in a tree format with an XdmfDomain serving
* as the base. The Domain contains multiple grid collections or
* grids; each with their own geometries, topologies, attributes,
* and/or sets. With the inclusion of shared pointers in Xdmf2
* a topology could be shared across multiple grids or a grid
* could be included in multiple grid collections and/or the domain.
*
*
* C++ Examples:
*
* \subpage cppwrite "C++ Example of Xdmf Creation"
......
XdmfAttribute.hpp
View file @ dc686f86
......@@ -62,7 +62,7 @@ public:
* @skipline #//initialization
* @until #//initialization
*
* @return constructed XdmfAttribute.
* @return constructed XdmfAttribute.
*/
static shared_ptr<XdmfAttribute> New();
......@@ -96,7 +96,7 @@ public:
* @skipline #//getCenter
* @until #//getCenter
*
* @return XdmfAttributeCenter of the attribute.
* @return XdmfAttributeCenter of the attribute.
*/
shared_ptr<const XdmfAttributeCenter> getCenter() const;
......@@ -129,7 +129,7 @@ public:
* @skipline #//getName
* @until #//getName
*
* @return a string containing the name of the attribute.
* @return a string containing the name of the attribute.
*/
std::string getName() const;
......@@ -158,7 +158,7 @@ public:
* @skipline #//getType
* @until #//getType
*
* @return XdmfAttributeType of the attribute.
* @return XdmfAttributeType of the attribute.
*/
shared_ptr<const XdmfAttributeType> getType() const;
......@@ -183,7 +183,7 @@ public:
* @skipline #//setCenter
* @until #//setCenter
*
* @param center the XdmfAttributeCenter to set.
* @param center the XdmfAttributeCenter to set.
*/
void setCenter(const shared_ptr<const XdmfAttributeCenter> center);
......@@ -208,7 +208,7 @@ public:
* @skipline #//setName
* @until #//setName
*
* @param name a string containing the name to set.
* @param name a string containing the name to set.
*/
void setName(const std::string & name);
......@@ -233,7 +233,7 @@ public:
* @skipline #//setType
* @until #//setType
*
* @param type XdmfAttributeType to set.
* @param type XdmfAttributeType to set.
*/
void setType(const shared_ptr<const XdmfAttributeType> type);
......
XdmfCurvilinearGrid.cpp
View file @ dc686f86
......@@ -182,7 +182,13 @@ public:
private:
XdmfTopologyTypeCurvilinear(const XdmfCurvilinearGrid * const curvilinearGrid) :
XdmfTopologyType(0, 0, std::vector<shared_ptr<const XdmfTopologyType> >(), 0, "foo", XdmfTopologyType::Structured, 0x1110),
XdmfTopologyType(0,
0,
std::vector<shared_ptr<const XdmfTopologyType> >(),
0,
"foo",
XdmfTopologyType::Structured,
0x1110),
mCurvilinearGrid(curvilinearGrid)
{
}
......
XdmfCurvilinearGrid.hpp
View file @ dc686f86
......@@ -65,10 +65,10 @@ public:
* @skipline #//constructor2
* @until #//constructor2
*
* @param xNumPoints the number of points in the x direction.
* @param yNumPoints the number of points in the y direction.
* @param xNumPoints the number of points in the x direction.
* @param yNumPoints the number of points in the y direction.
*
* @return constructed curvilinear grid.
* @return constructed curvilinear grid.
*/
static shared_ptr<XdmfCurvilinearGrid>
New(const unsigned int xNumPoints,
......@@ -93,11 +93,11 @@ public:
* @skipline #//constructor3
* @until #//constructor3
*
* @param xNumPoints the number of points in the x direction.
* @param yNumPoints the number of points in the y direction.
* @param zNumPoints the number of points in the z direction.
* @param xNumPoints the number of points in the x direction.
* @param yNumPoints the number of points in the y direction.
* @param zNumPoints the number of points in the z direction.
*
* @return constructed curvilinear grid.
* @return constructed curvilinear grid.
*/
static shared_ptr<XdmfCurvilinearGrid>
New(const unsigned int xNumPoints,
......@@ -123,9 +123,9 @@ public:
* @skipline #//constructorvector
* @until #//constructorvector
*
* @param numPoints the number of points in each direction.
* @param numPoints the number of points in each direction.
*
* @return constructed curvilinear grid.
* @return constructed curvilinear grid.
*/
static shared_ptr<XdmfCurvilinearGrid>
New(const shared_ptr<XdmfArray> numPoints);
......@@ -163,7 +163,7 @@ public:
* @skipline #//getDimensions
* @until #//getDimensions
*
* @return XdmfArray containing dimensions of this grid.
* @return XdmfArray containing dimensions of this grid.
*/
shared_ptr<XdmfArray> getDimensions();
......@@ -185,7 +185,7 @@ public:
*
* Python: Python doesn't have a constant version
*
* @return XdmfArray containing the dimensions of this grid.
* @return XdmfArray containing the dimensions of this grid.
*/
shared_ptr<const XdmfArray> getDimensions() const;
......@@ -216,7 +216,7 @@ public:
* @skipline #//getGeometry
* @until #//getGeometry
*
* @return the geometry associated with this grid.
* @return the geometry associated with this grid.
*/
shared_ptr<XdmfGeometry> getGeometry();
......@@ -244,7 +244,7 @@ public:
* @skipline #//setDimensions
* @until #//setDimensions
*
* @param dimensions the dimension of the grid.
* @param dimensions the dimension of the grid.
*/
void setDimensions(const shared_ptr<XdmfArray> dimensions);
......@@ -271,7 +271,7 @@ public:
* @skipline #//setGeometry
* @until #//setGeometry
*
* @param geometry an XdmfGeometry to associate with this grid.
* @param geometry an XdmfGeometry to associate with this grid.
*/
void setGeometry(const shared_ptr<XdmfGeometry> geometry);
......
XdmfFunction.cpp
View file @ dc686f86
......@@ -37,7 +37,11 @@ const std::string XdmfFunction::mValidDigitChars = "-1234567890.";
// List the priorities for the operations, based on the order of operations
// The index of the corresponding operation in validOperationChars
// is the same as the index of its priority in this array
std::map<char, int> XdmfFunction::mOperationPriority = boost::assign::map_list_of ('|', 2) ('#', 1) ('(', 0) (')', 0);
std::map<char, int> XdmfFunction::mOperationPriority =
boost::assign::map_list_of ('|', 2)
('#', 1)
('(', 0)
(')', 0);
// The higher the value, the earlier the operation is
// evaluated in the order of operations
// With the exception of parenthesis which are evaluated
......@@ -75,7 +79,7 @@ const std::string XdmfFunction::ItemTag = "Function";
int
XdmfFunction::addFunction(std::string name,
shared_ptr<XdmfArray>(*functionref)(std::vector<shared_ptr<XdmfArray> >))
shared_ptr<XdmfArray>(*functionref)(std::vector<shared_ptr<XdmfArray> >))
{
// Check to ensure that the name has valid characters
for (unsigned int i = 0; i < name.size(); ++i) {
......@@ -127,8 +131,11 @@ XdmfFunction::chunk(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2)
// Join chunk (add the new array to the end of the first one)
// Joins into new array and returns it
shared_ptr<XdmfArray> returnArray = XdmfArray::New();
// Determining what type to class it as in order to not lose data, and to still have the smallest data type of the two
shared_ptr<const XdmfArrayType> resultType = XdmfArrayType::comparePrecision(val1->getArrayType(), val2->getArrayType());
// Determining what type to class it as in order to not lose data
// and to still have the smallest data type of the two
shared_ptr<const XdmfArrayType> resultType =
XdmfArrayType::comparePrecision(val1->getArrayType(),
val2->getArrayType());
if (resultType == XdmfArrayType::Int8()) {
char sampleValue = 0;
......@@ -233,7 +240,8 @@ XdmfFunction::evaluateExpression(std::string expression,
}
}
else {
std::string currentFunction = expression.substr(valueStart, i + 1 - valueStart);
std::string currentFunction =
expression.substr(valueStart, i + 1 - valueStart);
// Check if next character is an open parenthesis
if (i+1 >= expression.size()) {
if (expression[i+1] != '(') {
......@@ -278,7 +286,9 @@ XdmfFunction::evaluateExpression(std::string expression,
parameterVector.push_back(evaluateExpression(functionParameters, variables));
}
else {
parameterVector.push_back(evaluateExpression(functionParameters.substr(0, parameterSplit), variables));
parameterVector.push_back(
evaluateExpression(functionParameters.substr(0, parameterSplit),
variables));
functionParameters = functionParameters.substr(parameterSplit+1);
}
}
......@@ -573,8 +583,10 @@ XdmfFunction::interlace(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2)
// Builds a new array
shared_ptr<XdmfArray> returnArray = XdmfArray::New();
// Resize to the combined size of both arrays
// Determining what type to class it as in order to not lose data, and to still have the smallest data type of the two
shared_ptr<const XdmfArrayType> resultType = XdmfArrayType::comparePrecision(val1->getArrayType(), val2->getArrayType());
// Determining what type to class it as in order to not lose data
// and to still have the smallest data type of the two
shared_ptr<const XdmfArrayType> resultType =
XdmfArrayType::comparePrecision(val1->getArrayType(), val2->getArrayType());
if (resultType == XdmfArrayType::Int8()) {
char sampleValue = 0;
......@@ -635,7 +647,8 @@ XdmfFunction::interlace(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2)
int arrayExcess1 = 0;
int arrayExcess2 = 0;
for (int i = 0; i < stride; ++i) {
// Add the values of each array, using strides to interlace and starting index to offset
// Add the values of each array
// using strides to interlace and starting index to offset
// first array gets the first value of the new array
if (i<arrayRatio1) {
int amountWritten = val1->getSize()/arrayRatio1;
......@@ -662,10 +675,20 @@ XdmfFunction::interlace(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2)
}
}
if (arrayExcess1 > 0) {
returnArray->insert(val1->getSize()+val2->getSize()-arrayExcess1, val1, 0, arrayExcess1, 1, 1);
returnArray->insert(val1->getSize()+val2->getSize()-arrayExcess1,
val1,
0,
arrayExcess1,
1,
1);
}
else if (arrayExcess2 > 0) {
returnArray->insert(val1->getSize()+val2->getSize()-arrayExcess2, val2, 0, arrayExcess2, 1, 1);
returnArray->insert(val1->getSize()+val2->getSize()-arrayExcess2,
val2,
0,
arrayExcess2,
1,
1);
}
// After all inserts are done, add the excess values to the end of the array
return returnArray;
......
XdmfFunction.hpp
View file @ dc686f86
......@@ -29,9 +29,9 @@
#include "XdmfArray.hpp"
/**
* @brief
* @brief Manipulates arrays based on expressions.
*
*
* The function class provides a way to manipulate XdmfArrays via predefined functions.
*/
class XDMF_EXPORT XdmfFunction : public XdmfItem {
......@@ -80,11 +80,13 @@ public:
* @skipline #//addOperation
* @until #//addOperation
*
* @param newoperator the character to be associated with the provided binary operation
* @param functionref a pointer to the function to be associated with the provided operator
* @param priority used to determine order of operations the higher the value the earlier it is evaluated
* @param newoperator the character to be associated with the provided binary operation
* @param functionref a pointer to the function to be associated with the provided operator
* @param priority used to determine order of operations the higher the value the earlier it is evaluated
*/
static int addOperation(char newoperator, shared_ptr<XdmfArray>(*functionref)(shared_ptr<XdmfArray>, shared_ptr<XdmfArray>), int priority);
static int addOperation(char newoperator,
shared_ptr<XdmfArray>(*functionref)(shared_ptr<XdmfArray>, shared_ptr<XdmfArray>),
int priority);
/*
* adds a specified function to the list of functions used while evaluating strings
......@@ -113,11 +115,12 @@ public:
* @skipline #//addFunction
* @until #//addFunction
*
* @param name A string to be associated with the provided function during string evaluation
* @param functionref A pointer to the function to be associated with the given string
* @return The total number of functions currently associated
* @param name A string to be associated with the provided function during string evaluation
* @param functionref A pointer to the function to be associated with the given string
* @return The total number of functions currently associated
*/
static int addFunction(std::string name, shared_ptr<XdmfArray>(*functionref)(std::vector<shared_ptr<XdmfArray> >));
static int addFunction(std::string name,
shared_ptr<XdmfArray>(*functionref)(std::vector<shared_ptr<XdmfArray> >));
/**
* Averages the values contained in all the provided arrays.
......@@ -138,8 +141,8 @@ public:
* @skipline #//average
* @until #//average
*
* @param values a vector containing the arrays to be used
* @return an XdmfArray containing one value which is the average of all values contained within the provided arrays
* @param values a vector containing the arrays to be used
* @return an XdmfArray containing one value which is the average of all values contained within the provided arrays
*/
static shared_ptr<XdmfArray> average(std::vector<shared_ptr<XdmfArray> > values);
......@@ -164,11 +167,12 @@ public:
* @skipline #//chunk
* @until #//chunk
*
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @return the arrays joined end to end
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @return the arrays joined end to end
*/
static shared_ptr<XdmfArray> chunk(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2);
static shared_ptr<XdmfArray> chunk(shared_ptr<XdmfArray> val1,
shared_ptr<XdmfArray> val2);
/**
* Evaluates an expression based on the list of variables provided.
......@@ -219,11 +223,12 @@ public:
* @skipline #//evaluateExpression
* @until #//evaluateExpression
*
* @param expression a string containing the expresion to be evaluated
* @param variables a map of strings to their XdmfArray equivalent
* @return a shared pointer to the XdmfArray resulting from the expression
* @param expression a string containing the expresion to be evaluated
* @param variables a map of strings to their XdmfArray equivalent
* @return a shared pointer to the XdmfArray resulting from the expression
*/
static shared_ptr<XdmfArray> evaluateExpression(std::string expression, std::map<std::string, shared_ptr<XdmfArray> > variables);
static shared_ptr<XdmfArray> evaluateExpression(std::string expression,
std::map<std::string, shared_ptr<XdmfArray> > variables);
/**
* Evaluates the operation specified using the two shared pointers to XdmfArrays provided.
......@@ -264,12 +269,14 @@ public:
* @skipline #//evaluateOperation
* @until #//evaluateOperation
*
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @param operation a character specifying the operation performed
* @return a shared pointer to the Xdmf Array that results from the calculation
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @param operation a character specifying the operation performed
* @return a shared pointer to the Xdmf Array that results from the calculation
*/
static shared_ptr<XdmfArray> evaluateOperation(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2, char operation);
static shared_ptr<XdmfArray> evaluateOperation(shared_ptr<XdmfArray> val1,
shared_ptr<XdmfArray> val2,
char operation);
/**
* Evaluates the function specified using the vector of XdmfArrays provided.
......@@ -307,11 +314,12 @@ public:
* @skipline #//evaluateFunction
* @until #//evaluateFunction
*
* @param valueVector a vector containing the arrays to be used
* @param functionName the string associated with the function being called
* @return the result of the function being called, a scalar will be returned as an XdmfArray with one value
* @param valueVector a vector containing the arrays to be used
* @param functionName the string associated with the function being called
* @return the result of the function being called, a scalar will be returned as an XdmfArray with one value
*/
static shared_ptr<XdmfArray> evaluateFunction(std::vector<shared_ptr<XdmfArray> > valueVector, std::string functionName);
static shared_ptr<XdmfArray> evaluateFunction(std::vector<shared_ptr<XdmfArray> > valueVector,
std::string functionName);
std::map<std::string, std::string> getItemProperties() const;
......@@ -335,8 +343,8 @@ public:
* @skipline #//getOperationPriority
* @until #//getOperationPriority
*
* @param operation the character associated with the operation to be checked
* @return the priority of the operation
* @param operation the character associated with the operation to be checked
* @return the priority of the operation
*/
static int getOperationPriority(char operation);
......@@ -358,7 +366,7 @@ public:
* @skipline #//getSupportedOperations
* @until #//getSupportedOperations
*
* @return a string containing the characters for all supported operations
* @return a string containing the characters for all supported operations
*/
static const std::string getSupportedOperations();
......@@ -380,7 +388,7 @@ public:
* @skipline #//getSupportedFunctions
* @until #//getSupportedFunctions
*
* @return a vector containing the strings associated with all valid functions
* @return a vector containing the strings associated with all valid functions
*/
static const std::vector<std::string> getSupportedFunctions();
......@@ -402,7 +410,7 @@ public:
* @skipline #//getValidDigitChars
* @until #//getValidDigitChars
*
* @return a string containing all valid variable characters
* @return a string containing all valid variable characters
*/
static const std::string getValidDigitChars();
......@@ -424,7 +432,7 @@ public:
* @skipline #//getValidVariableChars
* @until #//getValidVariableChars
*
* @return a string containing all valid variable characters
* @return a string containing all valid variable characters
*/
static const std::string getValidVariableChars();
......@@ -448,11 +456,12 @@ public:
* @skipline #//interlace
* @until #//interlace
*
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @return the interlaced arrays
* @param val1 the first array being evaluated
* @param val2 the second array being evaluated
* @return the interlaced arrays
*/
static shared_ptr<XdmfArray> interlace(shared_ptr<XdmfArray> val1, shared_ptr<XdmfArray> val2);
static shared_ptr<XdmfArray> interlace(shared_ptr<XdmfArray> val1,
shared_ptr<XdmfArray> val2);
/**
* Adds together all the values contained in the provided arrays.
......@@ -473,8 +482,8 @@ public:
* @skipline #//sum
* @until #//sum
*
* @param values a vector containing the arrays to be used
* @return an XdmfArray containing one value which is the total of all the values contained within the provided arrays
* @param values a vector containing the arrays to be used
* @return an XdmfArray containing one value which is the total of all the values contained within the provided arrays
*/
static shared_ptr<XdmfArray> sum(std::vector<shared_ptr<XdmfArray> > values);
......
XdmfGeometry.hpp
View file @ dc686f86
......@@ -60,7 +60,7 @@ public:
* @skipline #//initialization
* @until #//initialization
*
* @return constructed XdmfGeometry.
* @return constructed XdmfGeometry.
*/
static shared_ptr<XdmfGeometry> New();
......@@ -117,7 +117,7 @@ public:
* @skipline #//getType
* @until #//getType
*
* @return XdmfGeometryType of this geometry.
* @return XdmfGeometryType of this geometry.
*/
shared_ptr<const XdmfGeometryType> getType() const;
......@@ -142,7 +142,7 @@ public:
* @skipline #//setType
* @until #//setType
*
* @param type the XdmfGeometryType to set.
* @param type the XdmfGeometryType to set.
*/
void setType(const shared_ptr<const XdmfGeometryType> type);
......
XdmfGeometryType.hpp
View file @ dc686f86
......@@ -88,7 +88,7 @@ public:
* @skipline #//getDimensions
* @until #//getDimensions
*
* @return an int containing number of dimensions.
* @return an int containing number of dimensions.
*/
virtual unsigned int getDimensions() const;
......@@ -109,7 +109,7 @@ public:
* @skipline #//getName
* @until #//getName
*
* @return the name of this geometry type.
* @return the name of this geometry type.
*/
std::string getName() const;
......
XdmfGraph.hpp
View file @ dc686f86
......@@ -60,7 +60,7 @@ public:
*
* @param numberNodes number of nodes in graph.
*
* @return constructed XdmfGraph.
* @return constructed XdmfGraph.
*/
static shared_ptr<XdmfGraph> New(const unsigned int numberNodes);
......
XdmfGrid.hpp
View file @ dc686f86
......@@ -84,7 +84,7 @@ public:
* @skipline #//getGeometry
* @until #//getGeometry
*
* @return the geometry associated with this grid.
* @return the geometry associated with this grid.
*/
shared_ptr<const XdmfGeometry> getGeometry() const;
......@@ -117,7 +117,7 @@ public:
* @skipline #//getName
* @until #//getName
*
* @return the name of the grid.
* @return the name of the grid.
*/
std::string getName() const;
......@@ -146,8 +146,8 @@ public:
* @skipline #//getTime
* @until #//getTime
*
* @return pointer to the XdmfTime attached to this grid. If no
* XdmfTime is attached, return a NULL pointer.
* @return pointer to the XdmfTime attached to this grid. If no
* XdmfTime is attached, return a NULL pointer.
*/
shared_ptr<XdmfTime> getTime();
......@@ -168,8 +168,8 @@ public:
*
* Python: Python doesn't have a constant version
*
* @return pointer to the XdmfTime attached to this grid. If no
* XdmfTime is attached, return a NULL pointer.
* @return pointer to the XdmfTime attached to this grid. If no
* XdmfTime is attached, return a NULL pointer.
*/
shared_ptr<const XdmfTime> getTime() const;
......@@ -194,7 +194,7 @@ public:
* @skipline #//getTopology
* @until #//getTopology
*
* @return the topology associated with this grid.
* @return the topology associated with this grid.
*/
shared_ptr<const XdmfTopology> getTopology() const;
......@@ -221,7 +221,7 @@ public:
* @skipline #//setName
* @until #//setName
*
* @param name of the grid to set.
* @param name name of the grid to set.
*/
void setName(const std::string & name);
......@@ -246,7 +246,7 @@ public:
* @skipline #//setTime
* @until #//setTime
*
* @param time an XdmfTime to associate with this grid.
* @param time an XdmfTime to associate with this grid.
*/
void setTime(const shared_ptr<XdmfTime> time);
......
XdmfGridCollection.hpp
View file @ dc686f86
......@@ -65,7 +65,7 @@ public:
* @skipline #//initalization
* @until #//initalization
*
* @return constructed XdmfGridCollection.
* @return constructed XdmfGridCollection.
*/
static shared_ptr<XdmfGridCollection> New();
......@@ -99,7 +99,7 @@ public:
* @skipline #//getType
* @until #//getType
*
* @return XdmfGridCollectionType of this collection.
* @return XdmfGridCollectionType of this collection.