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- ParMA: parma.h Source File

int Parma Run apf Mesh mesh apf MeshTag weight const double maxImb 00022 00037 int Parma RunPtnImprovement apf Mesh mesh int priority 4 00038 const double maxImb 1 05 const int verbosity 0 const int maxItr 20 00039 00051 int Parma RunGhostPtnImprovement apf Mesh mesh apf MeshTag weight 00052 const double maxImb const int numlayers const int bridgeDim 00053 const int verbosity 0 00054 00059 int Parma RunWeightedPtnImprovement apf Mesh mesh apf MeshTag weight 00060 int priority 4 const double maxImb 1 05 const int dbgLvl 0 00061 const int maxItr 20 00062 00072 int Parma RunSelp apf Mesh mesh apf MeshTag weight const int factor 00073 const int verbosity 0 00074 00080 void Parma GetEntImbalance apf Mesh mesh double entImb 4 00081 00088 void Parma GetWeightedEntImbalance apf Mesh mesh apf MeshTag weight 00089 double entImb 4 00090 00101 void Parma GetNeighborStats apf Mesh m int max double avg int loc 00102 00108 long Parma GetNumBdryVtx apf Mesh m 00109 00118 void Parma GetDisconnectedStats apf Mesh m int max double avg int loc 00119 00128 void Parma PrintPtnStats apf Mesh m std string key 00129 00134 void Parma ProcessDisconnectedParts apf Mesh m 00135 00142 apf Balancer Parma MakeCentroidDiffuser apf Mesh

Original URL path: http://www.scorec.rpi.edu/parma/doxygen/parma_8h_source.html (2015-07-15)

Open archived version from archive - SCOREC core: Todo List

get used much maybe remove it Member apf Matrix3x3 toArray double array 3 const this could be templated Member apf NaiveOrder Numbering num name should be lower case Member apf SetNumberingOffset Numbering num int off name should be lower case Member apf Vector3 fromArray const double abc this could be templated Member apf Vector3 toArray double abc const this could be templated Member apf Vector3 Vector3 double const abc this

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/todo.html (2015-07-15)

Open archived version from archive - SCOREC core: Class Members

i l m n p q r s t u v w z Here is a list of all documented namespace members with links to the namespaces they belong to a accumulate apf adapt ma ADAPT REPART apf adaptMatching ma

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/namespacemembers.html (2015-07-15)

Open archived version from archive - SCOREC core: apf Namespace Reference

N M transpose Matrix M N const m transpose a matrix template std size t M std size t N Matrix M N tensorProduct Vector M const a Vector N const b tensor product of two vectors template std size t M std size t N Matrix M 1 N 1 getMinor Matrix M N const A std size t i std size t j get the minor matrix associated with entry i j of matrix A template std size t M std size t N double getCofactor Matrix M N const A std size t i std size t j get the cofactor associated with entry i j of matrix A template std size t M std size t N double getDeterminant Matrix M N const A get the determinant of a matrix A Matrix 3 3 cofactor Matrix 3 3 const m get the matrix of cofactors for a given matrix Matrix 2 2 invert Matrix 2 2 const m invert a 2 by 2 matrix Matrix 3 3 invert Matrix 3 3 const m invert a 3 by 3 matrix template std size t M std size t N double getInnerProduct Matrix M N const a Matrix M N const b get the component wise inner product of two matrices Matrix3x3 cross Vector3 const u get the skew symmetric cross product matrix of a vector Matrix3x3 rotate Vector3 const u double a get the rotation matrix around an axis Matrix3x3 getFrame Vector3 const v derive an orthogonal frame whose x axis is the given vector int eigen Matrix3x3 const A Vector 3 eigenVectors double eigenValues get the eigenvectors and eigenvalues of a 3 by 3 matrix template std size t N DynamicVector fromVector Vector N other convert an apf Matrix into an apf DynamicMatrix void multiply DynamicMatrix const a DynamicVector const b DynamicVector r multiply a DynamicMatrix by a DynamicVector void multiply DynamicVector const b DynamicMatrix const a DynamicVector r multiply a DynamicVector by a DynamicMatrix void multiply DynamicMatrix const a DynamicMatrix const b DynamicMatrix r multiply two DynamicMatrix objects void transpose DynamicMatrix const a DynamicMatrix r get the transpose of a DynamicMatrix template std size t N std size t M DynamicMatrix fromMatrix Matrix N M other convert an apf Matrix into an apf DynamicMatrix void remapPartition apf Mesh2 m Remap remap remap all part ids in the mesh structure Mesh2 makeEmptyMdsMesh gmi model model int dim bool isMatched create an empty MDS part Mesh2 loadMdsMesh gmi model model const char meshfile load an MDS mesh from files Mesh2 loadMdsMesh const char modelfile const char meshfile load an MDS mesh and model from file Mesh2 createMdsMesh gmi model model Mesh from create an MDS mesh from an existing mesh void reorderMdsMesh Mesh2 mesh apply adjacency based reordering void splitMdsMesh Mesh2 m Migration plan int n void runAfter Mesh2 split an MDS mesh into multiple parts per process using threads bool alignMdsMatches Mesh2 in align the downward adjacencies of matched entities bool alignMdsRemotes Mesh2 in align the downward adjacencies of remote copies void deriveMdsModel Mesh2 in build a null model such that apf verify accepts the mesh void changeMdsDimension Mesh2 in int d change the dimension of an MDS mesh int getMdsIndex Mesh2 in MeshEntity e returns the dimension unique index for this entity MeshEntity getMdsEntity Mesh2 in int dimension int index retrieve an entity by dimension and index Mesh2 loadMdsFromANSYS const char nodefile const char elemfile load an MDS mesh from ANSYS node and elem files Splitter makeZoltanSplitter Mesh mesh int method int approach bool debug true bool sync true Make a Zoltan Splitter object Splitter makeZoltanGlobalSplitter Mesh mesh int method int approach bool debug true Make a Zoltan Splitter object Balancer makeZoltanBalancer Mesh mesh int method int approach bool debug true Make a Zoltan Balancer object MeshTag tagOpposites GlobalNumbering gn const char name Tag global ids of opposite elements to boundary faces int getElementToElement apf Mesh m Get an element to element connectivity array Variables int const tri edge verts 3 2 map from triangle edge order to triangle vertex order int const quad edge verts 4 2 map from quad edge order to quad vertex order int const tet edge verts 6 2 map from tet edge order to tet vertex order int const prism edge verts 9 2 map from prism edge order to prism vertex order int const pyramid edge verts 8 2 map from pyramid edge order to pyramid vertex order int const tet tri verts 4 3 map from tet triangle order to tet vertex order int const hex quad verts 6 4 map from hex quad order to hex vertex order int const prism tri verts 2 3 map from prism triangle order to prism vertex order int const prism quad verts 3 4 map from prism quad order to prism vertex order int const pyramid tri verts 4 3 map from pyramid triangle order to pyramid vertex order double const pi The mathematical constant pi Detailed Description All APF symbols are contained in this namespace Wrapping a namespace over everything gives reasonable insurance against future symbol conflicts with other packages while very common names are being used like Mesh or VECTOR Users will be able to use the simple names directly with a using statement likewise all APF code is written without apf Typedef Documentation typedef DynamicArray MeshEntity apf Adjacent Set of adjacent mesh entities see also apf Downward and apf Up typedef std map int MeshEntity apf Copies Remote copy container the key is the part id the value is the on part pointer to the remote copy typedef MeshEntity apf Downward 12 a static array type downward adjacency queries using statically sized arrays saves time by avoiding dynamic allocation and downward adjacencies have a guaranteed bound Enumeration Type Documentation enum apf ValueType The type of value the field stores The near future may bring more complex tensors Enumerator SCALAR a single scalar value VECTOR a 3D vector value MATRIX a 3x3 matrix PACKED a user defined set of components VALUE TYPES placeholder used to set array sizes enum apf ZoltanApproach Zoltan partitioning approach Enumerator PARTITION Hyper Graph does not consider the initial distribution REPARTITION Hyper Graph considers the initial distribution REFINE HYPER Graph targets partitions needing only small changes PART KWAY Graph multilevel PART GEOM Graph space filling curves PART GEOM KWAY Graph hybrid method combining PART KWAY and PART GEOM ADAPT REPART Graph targets graphs generated from adaptively refined meshes REFINE KWAY Graph targets partitions needing only small changes enum apf ZoltanMethod Zoltan partitioning method Enumerator RCB Recursive Coordinate Bisection RIB Recursive Inertial Bisection HYPERGRAPH Hyper graph partitioning PARMETIS Use ParMetis GRAPH General graph partitionig Function Documentation void apf accumulate Field f Sharing shr 0 Add field values along partition boundary Using the copies described by an apf Sharing object add up the field values of all copies of an entity and assign the sum as the value for all copies int apf AdjReorder Numbering num like apf reorder but numbers all free nodal components Todo name should be lower case MeshEntity apf buildElement Mesh2 m ModelEntity c int type MeshEntity verts BuildCallback cb 0 build an entity from its vertices any missing intermediate entities will also be built and all will be classified to c If a non zero BuildCallback pointer is given it will be called for each entity created including intermediate ones MeshEntity apf buildOneElement Mesh2 m ModelEntity c int type Vector3 const points build a one element mesh this is mostly useful for debugging Todo this doesn t get used much maybe remove it void apf changeMdsDimension Mesh2 in int d change the dimension of an MDS mesh this should be called before adding entities of dimension higher than the previous mesh dimension when building a higher dimensional mesh from a lower one or after removing all entities of higher dimension when reducing a high dimensional mesh to a lower one Field apf cloneField Field f Mesh onto Declare a copy of a field on another apf Mesh This will just make a Field object with the same properties but not fill in any data void apf construct Mesh2 m const int conn int nelem int etype GlobalToVert globalToVert construct a mesh from just a connectivity array this function is here to interface with very simple mesh formats Given a set of elements described only in terms of the ordered global ids of their vertices this function builds a reasonable apf Mesh2 structure and as a side effect returns a map from global ids to local vertices This is a fully scalable parallel mesh construction algorithm no processor incurs memory or runtime costs proportional to the global mesh size Note that all vertices will have zero coordinates so it is often good to use apf setCoords after this void apf convert Mesh in Mesh2 out convert one mesh data structure to another this function will fill in a structure that fully implements apf Mesh2 by using information from an implementation of apf Mesh This is a fully scalable parallel mesh conversion tool int apf countElementNodes FieldShape s int type count the number of nodes affecting an element type Parameters type select from apf Mesh Type int apf countIntPoints MeshElement e int order Get the number of integration points for an element Parameters order the polynomial order of accuracy desired for the integration not to be confused with the polynomial order of shape functions int apf countNodes Element e Returns the number of element nodes This is the number of nodes affecting an element as opposed to the nodes tagged to an entity Element apf createElement Field f MeshEntity e Create a Field Element without a parent Mesh Element Warning most users should call the version which takes a MeshElement as input Only call this function if you know the other one isn t right for you Element apf createElement Field f MeshElement e Create a Field Element from a Mesh Element A Field Element object caches elemental data for use in evaluation mapping and integration use destroyElement to free this data Parameters f The field which the Element will represent e An existing MeshElement for the desired entity Returns The new field Element GlobalNumbering apf createGlobalNumbering Mesh mesh const char name FieldShape shape create global numbering see apf createNumbering so far global numberings have one component Field apf createHierarchicField Mesh m const char name int valueType Create a quadratic apf Field using hierarchic shape functions Parameters m the mesh over which the field is defined name a unique name for this field valueType the type of field data only quadratic hierarchic fields are supported Field apf createIPField Mesh m const char name int valueType int order Create an apf Field of integration point data Parameters m the mesh over which the field is defined name a unique name for this field valueType the type of field data order polynomial order of accuracy Field apf createLagrangeField Mesh m const char name int valueType int order Create an apf Field using a Lagrange distribution Parameters m the mesh over which the field is defined name a unique name for this field valueType the type of field data order the polynomial order of the shape functions so far 1 or 2 Mesh2 apf createMdsMesh gmi model model Mesh from create an MDS mesh from an existing mesh Parameters from the mesh to copy this function uses apf convert to copy any apf Mesh MeshElement apf createMeshElement Mesh m MeshEntity e Creates a Mesh Element over an entity A Mesh Element allows queries to the coordinate field including mapping differential and total volume as well as gauss integration point data A Mesh Element is also required to build a Field Element Numbering apf createNumbering Mesh mesh const char name FieldShape shape int components Create a generally defined Numbering This numbering will be available via mesh findNumbering etc The shape determines where the nodes are and the component count determines how many integers there are per node Field apf createPackedField Mesh m const char name int components Create a field of N components without a tensor type Packed fields are used to interface with applications whose fields are not easily categorized as tensors of order 0 1 2 They contain enough information to interpolate values in an element and such but some higher level functionality is left out Field apf createStepField Mesh m const char name int valueType Create an apf Field using a step distribution A step wise distribution is a C 1 continuous field defined by one node at each element with the field value being constant over the element and discontinuous at element boundaries Parameters m the mesh over which the field is defined name a unique name for this field valueType the type of field data Field apf createUserField Mesh m const char name int valueType FieldShape s Function f Create a Field from a user s analytic function This field will use no memory has values on all nodes and calls the user Function for all value queries Writing to this field does nothing void apf deriveMdsModel Mesh2 in build a null model such that apf verify accepts the mesh given an MDS mesh that is wrongly classified on a null model this algorithm will classify all interior entities onto a model region and all boundary entities onto a boundary model entity as defined by mesh upward adjacencies void apf destroyField Field f Destroy an apf Field This function will also remove any field data that this field attached to its Mesh domain void apf destroyMesh Mesh m Destroys an apf Mesh This only destroys the apf Mesh object the underlying mesh database is unaffected Mesh objects are wrappers over mesh databases and are created by functions provided outside the APF core void apf destroyMeshElement MeshElement e Destroys a Mesh Element This only destroys the apf MeshElement object the underlying mesh entity and field data are unaffected void apf destruct Mesh2 m int conn int nelem int etype convert an apf Mesh2 object into a connectivity array this is useful for debugging the apf convert function void apf displaceMesh Mesh2 m Field d double factor 1 0 add a field times a factor to the mesh coordinates this is useful in mechanical deformation problems to transform the mesh from reference space to deformed space Setting the factor to 1 will undo the deformation void apf extractCoords Mesh2 m double coords int nverts get a contiguous set of global vertex coordinates this is used for debugging apf setCoords void apf fail const char why Declare failure of code inside APF This function prints the string as an APF failure to stderr and then calls abort It can be called from code that is part of the apf namespace but not outside of that int apf findIn MeshEntity a int n MeshEntity e find pointer e in array a of length n Returns 1 if not found otherwise i such that a i e void apf findTriDown Mesh m MeshEntity verts MeshEntity down given the vertices of a triangle find its edges Parameters down the resulting array of edges MeshEntity apf findUpward Mesh m int type MeshEntity down find an entity from one level downward adjacencies this function ignores the ordering of adjacent entities void apf fix Numbering n MeshEntity e int node int component bool fixed Set the fixed free status of a degree of freedom must be called prior to making any isFixed calls on the same node component Parameters n the numbering object e the mesh entity with which the node is associated node the node number withing the mesh entity component the component number within the nodal tensor void apf getAlignment Mesh m MeshEntity elem MeshEntity boundary int which bool flip int rotate boundary entity alignment to an element Parameters m the mesh elem the element boundary an entity on the boundary of elem which index of boundary in getDownward elem flip true iff orientation of boundary is opposite canonical rotate position of canonical vertex 0 in boundary vertices or in boundary vertices reversed if flip true double apf getArrayData Field f Return the contiguous array storing this field This function is only defined for fields which are using array storage for which apf isFrozen returns true template std size t M std size t N double apf getCofactor Matrix M N const A std size t i std size t j get the cofactor associated with entry i j of matrix A this is only instantiated for square matrices up to 4 by 4 void apf getComponents Field f MeshEntity e int node double components Copy the nodal value into an array of component values the output array must already be allocated apf countComponents can help with this FieldShape apf getConstant int dimension Get the Constant shape function over some dimension this pseudo shape function places a node on every element of the given dimension Dimensions up to 3 are available void apf getCurl Element e Vector3 const param Vector3 curl Evaluate the curl of a vector field at a point Parameters param The local coordinates in the element curl The curl vector at that point template std size t M std size t N double apf getDeterminant Matrix M N const A get the determinant of a matrix A this is only instantiated for square matrices up to 4 by 4 double apf getDiv Element e Vector3 const param Evaluate the divergence of a vector field at a point Parameters param The local coordinates in the element Returns The divergence at that point double apf getDV MeshElement e Vector3 const param Get the differential volume at a point This function is meant to provide the differential measure of an element at a point based on the Jacobian determinant in the case of regions and equivalent terms for lower dimensions Returns The differential volume void apf getElementNumbers Numbering n MeshEntity e NewArray int numbers returns the node numbers

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/namespaceapf.html (2015-07-15)

Open archived version from archive - SCOREC core: ma Namespace Reference

entity support Input configure Mesh m AnisotropicFunction f SolutionTransfer s 0 generate a configuration based on an anisotropic function Input configure Mesh m IsotropicFunction f SolutionTransfer s 0 generate a configuration based on an isotropic function Input configure Mesh m apf Field sizes apf Field frames SolutionTransfer s 0 generate a configuration based on anisotropic fields Input configure Mesh m apf Field size SolutionTransfer s 0 generate a configuration based on an isotropic field Input configureUniformRefine Mesh m int n 1 SolutionTransfer s 0 generate a uniform refinement configuration Input configureMatching Mesh m int n 1 SolutionTransfer s 0 generate a matched uniform refinement configuration Input configureIdentity Mesh m SizeField f 0 SolutionTransfer s 0 generate a no op configuration void validateInput Input in used internally but users can call this if they want Vector getPosition Mesh m Entity vertex get vertex spatial coordinates Entity rebuildElement Mesh m Entity original Entity oldVert Entity newVert apf BuildCallback cb rebuild an element with one vertex being different double getInsphere Mesh m Entity e Computes the insphere radius of an element SolutionTransfer createFieldTransfer apf Field f Creates a default solution transfer object for a field Detailed Description All MeshAdapt symbols Function Documentation void ma adapt Mesh m IsotropicFunction f SolutionTransfer s 0 adapt based on an isotropic function see maSize h for how to define a function void ma adapt Input in adapt with custom configuration see maInput h for details note that this function will delete the Input object void ma adaptMatching Mesh m int n 1 SolutionTransfer s 0 run uniform refinement with matched entity support currently this supports snapping but not shape correction Input ma configure Mesh m apf Field sizes apf Field frames SolutionTransfer s 0 generate a configuration based on anisotropic fields Parameters sizes a vector field of

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/namespacema.html (2015-07-15)

Open archived version from archive - SCOREC core: spr Namespace Reference

the QR factorization of A void solveFromQR apf DynamicMatrix V apf DynamicMatrix R apf DynamicVector b apf DynamicVector x solves A x b given A s QR factorization Detailed Description All SPR error estimator functions Function Documentation bool spr decompQR apf DynamicMatrix A apf DynamicMatrix V apf DynamicMatrix R finds the QR factorization of A Parameters A the input matrix rows cols V the output representation of Q as the Householder vectors V k R the output R matrix Returns true iff the matrix A is full rank apf Field spr getGradIPField apf Field f const char name int order compute the gradient of a vector or scalar field at integration points Parameters f In scalar or vector nodal field name In name of integration point field order In integration order of accuracy apf Field spr getSPRSizeField apf Field f double adapt ratio run the SPR ZZ error estimator Parameters f the integration point input field adapt ratio the fraction of allowable error scales the output size field Returns a nodal scalar size field with the same distribution as the mesh coordinate field apf Field spr recoverField apf Field ip field recover a nodal field using patch recovery Parameters ip

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/namespacespr.html (2015-07-15)

Open archived version from archive - SCOREC core: Alphabetical List

Multiply apf SolutionTransfer ma Array apf DynamicVector apf Input ma N SolutionTransfers ma AutoSolutionTransfer ma E Integrator apf NewArray apf Splitter apf B EntityShape apf IsotropicFunction ma Node apf U Balancer apf F M P Unmodulo apf BuildCallback apf FieldShape apf Matrix apf Parma GroupCode Up apf C Function apf Matrix3x3 apf R V CavityOp apf G Mesh apf Remap apf Vector apf Copy apf gmi model Mesh2 apf Round

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/classes.html (2015-07-15)

Open archived version from archive - SCOREC core: Hierarchical Index

apf Vector3 apf Array Vector N M apf Matrix M N apf Matrix 3 3 apf Matrix3x3 apf Balancer apf BuildCallback apf CavityOp apf Copy apf DynamicArray T apf DynamicArray double apf DynamicVector apf DynamicMatrix apf EntityShape apf FieldShape apf Function gmi model gmi model ops gmi set ma Input apf Integrator ma IsotropicFunction apf Mesh apf Mesh2 apf Migration apf NewArray T apf NewArray double apf Node Parma GroupCode

Original URL path: http://www.scorec.rpi.edu/~dibanez/core/hierarchy.html (2015-07-15)

Open archived version from archive