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18 #ifndef __WEIPA_ESCRIPTDATASET_H__
19 #define __WEIPA_ESCRIPTDATASET_H__
21 #include <weipa/weipa.h>
89 const std::string units =
"");
101 bool loadNetCDF(
const std::string domainFilePattern,
121 void setMeshLabels(
const std::string x,
const std::string y,
const std::string z=
"");
125 void setMeshUnits(
const std::string x,
const std::string y,
const std::string z=
"");
130 const std::string metadata)
131 { mdSchema=schema; mdString=metadata; }
137 bool saveSilo(
const std::string fileName,
bool useMultiMesh=
true);
140 void saveVTK(
const std::string fileName);
159 bool loadDomain(
const std::string filePattern,
int nChunks);
161 bool loadData(
const std::string filePattern,
const std::string name,
162 const std::string units);
164 void convertMeshVariables();
165 void updateSampleDistribution(
VarInfo& vi);
166 void putSiloMultiMesh(DBfile* dbfile,
const std::string& meshName);
167 void putSiloMultiTensor(DBfile* dbfile,
const VarInfo& vi);
168 void putSiloMultiVar(DBfile* dbfile,
const VarInfo& vi,
169 bool useMeshFile =
false);
170 void saveVTKsingle(
const std::string& fileName,
171 const std::string& meshName,
const VarVector& vars);
172 void writeVarToVTK(
const VarInfo& varInfo, std::ostream& os);
191 #endif // __WEIPA_ESCRIPTDATASET_H__
Data ComplexVector(double value, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:145
IntVec sampleDistribution
Definition: EscriptDataset.h:42
Data interpolateFromTable3DP(boost::python::object table, DataTypes::real_t Amin, DataTypes::real_t Astep, Data &B, DataTypes::real_t Bmin, DataTypes::real_t Bstep, Data &C, DataTypes::real_t Cmin, DataTypes::real_t Cstep, DataTypes::real_t undef, bool check_boundaries)
Definition: Data.cpp:4737
void setAcceptanceConvergenceFailure(bool acceptance)
Definition: SolverOptions.cpp:755
@ SO_INTERPOLATION_CLASSIC_WITH_FF_COUPLING
Definition: SolverOptions.h:161
DataTypes::dim_t getReferenceIDFromDataPointNo(DataTypes::dim_t dataPointNo) const
Returns the reference number associated with the given data-point number.
Definition: FunctionSpace.cpp:179
double getDropTolerance() const
Definition: SolverOptions.cpp:609
bool isReady() const
Return true if this data is ready.
Definition: Data.cpp:1153
BOOST_PYTHON_MODULE(escriptcpp)
Definition: escriptcpp.cpp:117
@ SO_REORDERING_NONE
Definition: SolverOptions.h:167
virtual void saveMM(const std::string &filename) const
writes the matrix to a file using the Matrix Market file format
Definition: AbstractSystemMatrix.cpp:134
std::string mdSchema
Definition: EscriptDataset.h:176
bool isComplex() const
True if components of this data are stored as complex.
Definition: Data.cpp:1160
void MPIBarrierWorld()
performs a barrier synchronization across all processors.
Definition: Utils.cpp:377
escript::Data getSize() const
Returns the sample size (e.g. the diameter of elements, radius of particles).
Definition: FunctionSpace.cpp:295
Data erf() const
Return the error function erf of each data point of this Data object.
Definition: Data.cpp:2111
Domain_ptr getDomainPython() const
Return the function space domain. Internal use only! This gets around some python difficulties by cas...
Definition: FunctionSpace.cpp:109
int getSvnVersion()
some functions
Definition: Utils.cpp:43
Data sign() const
Return the sign of each data point of this Data object. -1 for negative values, zero for zero values,...
Definition: Data.cpp:2157
void saveDataCSV(const std::string &filename, bp::dict arg, const std::string &sep, const std::string &csep, bool refid, bool append)
Definition: Utils.cpp:388
Reducer_ptr makeDataReducer(std::string type)
Definition: MPIDataReducer.cpp:47
virtual int getTransportTypeId(int solver, int preconditioner, int package, bool symmetry) const
return the identifier of the matrix type to be used for the global stiffness matrix when a particular...
Definition: AbstractContinuousDomain.cpp:142
FinleyDomain implements the AbstractContinuousDomain interface for the Finley library.
Definition: finley/src/FinleyDomain.h:143
void setInnerToleranceAdaptionOff()
Definition: SolverOptions.cpp:727
std::string mdString
Definition: EscriptDataset.h:176
void getNumpy(bp::dict arg)
Definition: Utils.cpp:920
void setDropStorage(double drop)
Definition: SolverOptions.cpp:614
DataTypes::real_t getScalarVariable(const std::string &name)
Definition: SplitWorld.cpp:30
Data atanh() const
Return the atanh of each data point of this Data object.
Definition: Data.cpp:2136
Reducer_ptr makeScalarReducer(std::string type)
Definition: MPIScalarReducer.cpp:32
double getMaxFloat()
Definition: Utils.cpp:372
Data atan() const
Return the atan of each data point of this Data object.
Definition: Data.cpp:2082
#define REGISTER_ESCRIPT_EXCEPTION_TRANSLATORS
Definition: ExceptionTranslators.h:26
@ SO_METHOD_GMRES
Definition: SolverOptions.h:133
Data rtruedivO(const boost::python::object &left)
Newer style division operator for python.
Definition: Data.h:2205
FunctionSpace reducedFunctionOnBoundary(const AbstractDomain &domain)
Return a function on boundary FunctionSpace with reduced integration order.
Definition: FunctionSpaceFactory.cpp:75
Data antihermitian() const
Return the anti-hermitian part of a matrix which is half the matrix minus its hermitian.
Definition: Data.cpp:2808
FunctionSpace reducedContinuousFunction(const AbstractDomain &domain)
Return a continuous with reduced order FunctionSpace (overlapped node values on reduced element order...
Definition: FunctionSpaceFactory.cpp:51
void setToZero()
set all values to zero
Definition: Data.cpp:815
Data cos() const
Return the cos of each data point of this Data object.
Definition: Data.cpp:2053
void saveVTKsingle(const std::string &fileName, const std::string &meshName, const VarVector &vars)
Definition: EscriptDataset.cpp:583
DataTypes::real_t Lsup()
Return the maximum absolute value of this Data object.
Definition: Data.cpp:2215
Data grad() const
Definition: Data.cpp:1350
bool hasConverged() const
Definition: SolverOptions.cpp:326
double getDiagnostics(const std::string name) const
Definition: SolverOptions.cpp:306
bool useLocalPreconditioner() const
Definition: SolverOptions.cpp:763
@ SO_METHOD_DIRECT_TRILINOS
Definition: SolverOptions.h:132
virtual int getTag(const std::string &name) const =0
Return the tag key for tag name.
Represents a full Speckley domain including nodes and elements.
Definition: weipa/src/SpeckleyDomain.h:50
@ SO_METHOD_HRZ_LUMPING
Definition: SolverOptions.h:134
bool loadDomain(const std::string filePattern, int nChunks)
Definition: EscriptDataset.cpp:838
Data Tensor4FromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:377
void removeVariable(std::string name)
Definition: SplitWorld.cpp:300
void setValueOfDataPoint(int dataPointNo, const DataTypes::real_t)
sets the values of a data-point on this process
Definition: Data.cpp:1655
int getDim()
Definition: SolverOptions.cpp:837
bool isEmpty() const
returns true if the matrix is empty
Definition: AbstractSystemMatrix.h:100
boost::python::object getVarPyInfo()
Definition: SplitWorld.cpp:332
void setTruncation(int truncation)
Definition: SolverOptions.cpp:518
@ SO_METHOD_LSQR
Definition: SolverOptions.h:136
virtual ASM_ptr newSystemMatrix(const int row_blocksize, const escript::FunctionSpace &row_functionspace, const int column_blocksize, const escript::FunctionSpace &column_functionspace, const int type) const
creates a SystemMatrixAdapter stiffness matrix and initializes it with zeros:
Definition: AbstractContinuousDomain.cpp:178
void setVerbosityOff()
Definition: SolverOptions.cpp:704
double getTolerance() const
Definition: SolverOptions.cpp:573
Data whereNonNegative() const
Return a Data with a 1 for +ive or 0 values and a 0 for -ive values.
Definition: Data.cpp:1275
@ SO_METHOD_DIRECT_SUPERLU
Definition: SolverOptions.h:131
bool loadConfigured()
returns true if the load funtion is configured.
Definition: DataFactory.cpp:932
virtual void saveHB(const std::string &filename) const
writes the matrix to a file using the Harwell-Boeing file format
Definition: AbstractSystemMatrix.cpp:139
Data tan() const
Return the tan of each data point of this Data object.
Definition: Data.cpp:2060
int getCycle() const
Returns the cycle number.
Definition: EscriptDataset.h:114
@ SO_METHOD_DIRECT
Definition: SolverOptions.h:128
std::string getSummary() const
Definition: SolverOptions.cpp:75
void tag()
If possible convert this Data to DataTagged. This will only allow Constant data to be converted to ta...
Definition: Data.cpp:1204
boost::python::object integrateToTuple()
Calculate the integral over the function space domain as a python tuple.
Definition: Data.cpp:1784
double getAbsoluteTolerance() const
Definition: SolverOptions.cpp:585
int getSubWorldCount()
Definition: SplitWorld.cpp:428
@ SO_ODESOLVER_BACKWARD_EULER
Definition: SolverOptions.h:155
void setAcceptanceConvergenceFailureOn()
Definition: SolverOptions.cpp:745
virtual bool isValidTagName(const std::string &name) const
Returns True if name is a defined tag name.
Definition: AbstractDomain.cpp:67
int getTruncation() const
Definition: SolverOptions.cpp:525
Data sinh() const
Return the sinh of each data point of this Data object.
Definition: Data.cpp:2089
Data abs() const
Return the absolute value of each data point of this Data object.
Definition: Data.cpp:2165
DomainChunks getConvertedDomain()
Returns the dataset's converted domain so it can be reused.
Definition: EscriptDataset.h:143
WeipaException exception class.
Definition: WeipaException.h:42
virtual DataTypes::dim_t getNumDataPointsGlobal() const
Return the number of data points summed across all MPI processes.
Definition: AbstractContinuousDomain.cpp:198
void setTaggedValueByName(std::string name, const boost::python::object &value)
Assign the given value to the tag assocciated with name. Implicitly converts this object to type Data...
Definition: Data.cpp:3577
Data ComplexTensorFromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:244
Data ComplexVectorFromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:171
Data getItem(const boost::python::object &key) const
Returns a slice from this Data object.
Definition: Data.cpp:3468
@ SO_PRECONDITIONER_ILU0
Definition: SolverOptions.h:147
Data swapaxes(const int axis0, const int axis1) const
swaps the components axis0 and axis1
Definition: Data.cpp:2665
SolverOptions getPackage() const
Definition: SolverOptions.cpp:472
void resetDiagnostics(bool all=false)
Definition: SolverOptions.cpp:181
VarVector meshVariables
Definition: EscriptDataset.h:180
FunctionSpace continuousFunction(const AbstractDomain &domain)
Create function space objects.
Definition: FunctionSpaceFactory.cpp:45
bool saveSilo(const std::string fileName, bool useMultiMesh=true)
Saves the dataset in the Silo file format.
Definition: EscriptDataset.cpp:309
int getNumSweeps() const
Definition: SolverOptions.cpp:561
void setReordering(int ordering)
Definition: SolverOptions.cpp:477
void resolveGroup(bp::object obj)
Definition: Utils.cpp:986
int getEscriptParamInt(const std::string &name, int sentinel=0)
get the value of a named parameter. See listEscriptParams() for available parameters.
Definition: EscriptParams.h:92
virtual void addPDEToSystem(AbstractSystemMatrix &mat, escript::Data &rhs, const escript::Data &A, const escript::Data &B, const escript::Data &C, const escript::Data &D, const escript::Data &X, const escript::Data &Y, const escript::Data &d, const escript::Data &y, const escript::Data &d_contact, const escript::Data &y_contact, const escript::Data &d_dirac, const escript::Data &y_dirac) const
adds a PDE onto the stiffness matrix mat and a rhs
Definition: AbstractContinuousDomain.cpp:147
Data interpolate(const FunctionSpace &functionspace) const
Interpolates this onto the given functionspace and returns the result as a Data object.
Definition: Data.cpp:1311
Data exp() const
Return the exponential function of each data point of this Data object.
Definition: Data.cpp:2191
boost::python::object __mul__(const boost::python::object &right)
wrapper for python multiply operation
Definition: Data.cpp:5985
void setSymmetryOn()
Definition: SolverOptions.cpp:653
Definition: FileWriter.h:43
Data interpolateFromTable2DP(boost::python::object table, DataTypes::real_t Amin, DataTypes::real_t Astep, Data &B, DataTypes::real_t Bmin, DataTypes::real_t Bstep, DataTypes::real_t undef, bool check_boundaries)
Definition: Data.cpp:4747
SolverOptions getSolverMethod() const
Definition: SolverOptions.cpp:409
bool isTagged() const
Return true if this Data is tagged.
Definition: Data.cpp:1125
Data ScalarFromObj(boost::python::object o, const FunctionSpace &what, bool expanded)
Python interface for the Scalar factory.
Definition: DataFactory.cpp:96
Data besselSecondKind(int order)
Return the Bessel function of the second kind for each data point of this Data object.
Definition: Data.cpp:1864
#define MPI_SUM
Definition: EsysMPI.h:52
virtual bool isCellOriented(int functionSpaceCode) const =0
returns true if data on this domain and a function space of type functionSpaceCode has to considered ...
boost::python::object raw_addJob(boost::python::tuple t, boost::python::dict kwargs)
Definition: SplitWorld.cpp:473
Data TensorFromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:219
void writeVarToVTK(const VarInfo &varInfo, std::ostream &os)
Definition: EscriptDataset.cpp:810
bool loadNetCDF(const std::string domainFilePattern, const StringVec &varFiles, const StringVec &varNames, int nChunks)
Loads domain and variables from escript NetCDF files.
Definition: EscriptDataset.cpp:255
int getNumRefinements() const
Definition: SolverOptions.cpp:793
Data gradOn(const FunctionSpace &functionspace) const
Calculates the gradient of the data at the data points of functionspace. If functionspace is not pres...
Definition: Data.cpp:1323
StringVec meshUnits
Definition: EscriptDataset.h:177
virtual escript::Data getX() const =0
Returns locations in the domain. The function space is chosen appropriately.
void setRestart(int restart)
Definition: SolverOptions.cpp:497
std::string units
Definition: EscriptDataset.h:40
Data vectorMultiply(const Data &right) const
returns the matrix-vector product this*right
Definition: AbstractSystemMatrix.cpp:79
@ SO_ODESOLVER_LINEAR_CRANK_NICOLSON
Definition: SolverOptions.h:157
std::vector< DomainChunk_ptr > DomainChunks
Definition: EscriptDataset.h:36
Data phase() const
Return the phase/arg/angular-part of complex values.
Definition: Data.cpp:2023
DataTypes::real_t sup()
Return the maximum value of this Data object.
Definition: Data.cpp:2264
void setSymmetryOff()
Definition: SolverOptions.cpp:658
@ SO_PRECONDITIONER_REC_ILU
Definition: SolverOptions.h:151
bool isConstant() const
Return true if this Data is constant.
Definition: Data.cpp:1139
@ SO_REORDERING_MINIMUM_FILL_IN
Definition: SolverOptions.h:165
void putSiloMultiTensor(DBfile *dbfile, const VarInfo &vi)
Definition: EscriptDataset.cpp:1179
int getMPISizeWorld()
returns the total number of available MPI processes for MPI_COMM_WORLD
Definition: Utils.cpp:94
@ SO_PRECONDITIONER_ILUT
Definition: SolverOptions.h:148
bool addData(escript::Data &data, const std::string name, const std::string units="")
Adds an escript data instance to this dataset. You must ensure that the data is defined on the domain...
Definition: EscriptDataset.cpp:219
bool isHermitian() const
Definition: SolverOptions.cpp:671
boost::python::object __add__(const boost::python::object &right)
wrapper for python add operation
Definition: Data.cpp:5912
boost::python::list listFeatures()
returns a list of features escript was compiled with.
Definition: EscriptParams.h:119
bool isComplex() const
Definition: SolverOptions.cpp:638
void setHermitianOn()
Definition: SolverOptions.cpp:676
Data interpolateFromTable1DP(boost::python::object table, DataTypes::real_t Amin, DataTypes::real_t Astep, DataTypes::real_t undef, bool check_boundaries)
Definition: Data.cpp:4756
Definition: FunctionSpace.h:49
Data truedivO(const boost::python::object &right)
Newer style division operator for python.
Definition: Data.h:2192
Domain_ptr getDomainPython() const
Return the domain. TODO: For internal use only. This should be removed.
Definition: Data.h:501
void updateDiagnosticsPy(const std::string &key, const boost::python::object &value)
Definition: SolverOptions.cpp:247
Data tanh() const
Return the tanh of each data point of this Data object.
Definition: Data.cpp:2103
@ SO_METHOD_NONLINEAR_GMRES
Definition: SolverOptions.h:138
@ SO_INTERPOLATION_DIRECT
Definition: SolverOptions.h:162
const FunctionSpace & getFunctionSpace() const
Return the function space.
Definition: Data.h:463
void complicate()
Definition: Data.cpp:6057
void setIterMax(int iter_max)
Definition: SolverOptions.cpp:542
void setNumSweeps(int sweeps)
Definition: SolverOptions.cpp:554
boost::shared_ptr< DataVar > DataVar_ptr
Definition: weipa.h:65
Definition: DataVar.cpp:51
VarVector variables
Definition: EscriptDataset.h:180
void insertConstraint(Data &source, Data &q, Data &r)
inserts constraint u_{,t}=r where q>0 into the problem
Definition: AbstractTransportProblem.cpp:87
#define MPI_INT
Definition: EsysMPI.h:46
void setNumRefinements(int refinements)
Definition: SolverOptions.cpp:786
void copyVariable(const std::string &src, const std::string &dest)
Definition: SplitWorld.cpp:438
Data ComplexTensor4(double value, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:355
Data whereZero(DataTypes::real_t tol=0.0) const
Return a Data with a 1 for 0 values and a 0 for +ive or -ive values.
Definition: Data.cpp:1297
Represents a full Ripley domain including nodes and elements.
Definition: weipa/src/RipleyDomain.h:50
#define MPI_MAX
Definition: EsysMPI.h:54
Data C_GeneralTensorProduct(Data &arg_0, Data &arg_1, int axis_offset=0, int transpose=0)
Compute a tensor product of two Data objects.
Definition: Data.cpp:3690
void setMeshLabels(const std::string x, const std::string y, const std::string z="")
Sets labels for the mesh axes.
Definition: EscriptDataset.cpp:559
void setDim(int dim)
Definition: SolverOptions.cpp:830
void setAbsoluteTolerance(double atol)
Definition: SolverOptions.cpp:578
void setLocalPreconditioner(bool local)
Definition: SolverOptions.cpp:778
virtual StatusType getStatus() const
Returns a status indicator of the domain. The status identifier should be unique over the live time i...
Definition: AbstractDomain.cpp:62
FunctionSpace reducedSolution(const AbstractDomain &domain)
Return a FunctionSpace with reduced integration order.
Definition: FunctionSpaceFactory.cpp:111
std::vector< DataVar_ptr > DataChunks
Definition: EscriptDataset.h:35
virtual void resetValues(bool preserveSolverData=false)
resets the matrix entries
Definition: AbstractSystemMatrix.cpp:144
boost::python::list listEscriptParams()
describe available parameters.
Definition: EscriptParams.h:101
bool isVerbose() const
Definition: SolverOptions.cpp:694
const VarVector & getMeshVariables() const
Returns a vector with the mesh variables.
Definition: EscriptDataset.h:149
@ SO_PACKAGE_PASO
Definition: SolverOptions.h:118
Reducer_ptr makeNonReducedVariable()
Definition: NonReducedVariable.cpp:123
virtual void addPDEToRHS(escript::Data &rhs, const escript::Data &X, const escript::Data &Y, const escript::Data &y, const escript::Data &y_contact, const escript::Data &y_dirac) const
adds a PDE onto the stiffness matrix mat and a rhs
Definition: AbstractContinuousDomain.cpp:158
int getNumberOfThreads()
returns the number of threads
Definition: Utils.cpp:85
virtual void nullifyRowsAndCols(Data &row_q, Data &col_q, double mdv)
sets matrix entries to zero in specified rows and columns. The rows and columns are marked by positiv...
Definition: AbstractSystemMatrix.cpp:127
escript::Data getNormal() const
Returns the surface normal field.
Definition: FunctionSpace.cpp:286
Data powD(const Data &right) const
Return the given power of each data point of this Data object.
Definition: Data.cpp:3337
FunctionSpace functionOnContactZero(const AbstractDomain &domain)
Return a FunctionSpace on left side of contact.
Definition: FunctionSpaceFactory.cpp:81
void setRelaxationFactor(double factor)
Definition: SolverOptions.cpp:626
char NcFType(const std::string &name)
Definition: NCHelper.cpp:42
virtual bool onMasterProcessor() const =0
Return true if on MPI master, else false.
Data represents a collection of datapoints.
Definition: Data.h:64
std::string toString() const
Write the data as a string. For large amounts of data, a summary is printed.
Definition: Data.cpp:4643
RipleyDomain extends the AbstractContinuousDomain interface for the Ripley library and is the base cl...
Definition: ripley/src/RipleyDomain.h:116
DomainChunks domainChunks
Definition: EscriptDataset.h:179
FunctionSpace reducedFunctionOnContactZero(const AbstractDomain &domain)
Return a FunctionSpace on left side of contact with reduced integration order.
Definition: FunctionSpaceFactory.cpp:87
Data whereNonPositive() const
Return a Data with a 1 for -ive or 0 values and a 0 for +ive values.
Definition: Data.cpp:1286
bool valid
Definition: EscriptDataset.h:43
DataChunks dataChunks
Definition: EscriptDataset.h:41
void resolve()
If this data is lazy, then convert it to ready data. What type of ready data depends on the expressio...
Definition: Data.cpp:1230
escript::Data getX() const
Returns the spatial locations of the data points.
Definition: FunctionSpace.cpp:229
Data powO(const boost::python::object &right) const
Return the given power of each data point of this boost python object.
Definition: Data.cpp:3330
const boost::python::tuple getShapeTuple() const
Return the data point shape as a tuple of integers.
Definition: Data.cpp:724
bool externalDomain
Definition: EscriptDataset.h:178
int runMPIProgram(bp::list args)
Definition: Utils.cpp:312
@ SO_REORDERING_DEFAULT
Definition: SolverOptions.h:164
void putSiloMultiMesh(DBfile *dbfile, const std::string &meshName)
Definition: EscriptDataset.cpp:1055
Data symmetric() const
Return the symmetric part of a matrix which is half the matrix plus its transpose.
Definition: Data.cpp:2722
int cycle
Definition: EscriptDataset.h:174
bool acceptConvergenceFailure() const
Definition: SolverOptions.cpp:740
void setComplex(bool complex)
Definition: SolverOptions.cpp:643
virtual double getUnlimitedTimeStepSize() const
Definition: AbstractTransportProblem.cpp:132
void setTags(const int newTag, const escript::Data &mask) const
Assigns new tag newTag to all samples with a positive value of mask for any of its sample points.
Definition: FunctionSpace.cpp:304
const boost::python::object toListOfTuples(bool scalarastuple=true)
returns the values of the object as a list of tuples (one for each datapoint).
Definition: Data.cpp:1378
FunctionSpace diracDeltaFunctions(const AbstractDomain &domain)
Return a FunctionSpace.
Definition: FunctionSpaceFactory.cpp:117
virtual std::string getDescription() const
Return a description for this domain.
Definition: AbstractContinuousDomain.cpp:39
int getApproximationOrder() const
Returns the approximation order used for this function space.
Definition: FunctionSpace.cpp:359
virtual void dump(const std::string &filename) const =0
dumps the domain to an external file filename.
Data real() const
Definition: Data.cpp:1984
virtual void setTagMap(const std::string &name, int tag)=0
sets a map from a clear tag name to a tag key
Data sin() const
Return the sin of each data point of this Data object.
Definition: Data.cpp:2046
Data maxval() const
Return the maximum value of each data point of this Data object.
Definition: Data.cpp:2647
double getRelaxationFactor() const
Definition: SolverOptions.cpp:633
Data solve(const Data &in, boost::python::object &options) const
returns the solution u of the linear system this*u=in
Definition: AbstractSystemMatrix.cpp:103
boost::shared_ptr< ElementData > ElementData_ptr
Definition: weipa.h:67
Data besselFirstKind(int order)
Return the Bessel function of the first kind for each data point of this Data object.
Definition: Data.cpp:1857
void * mpiComm
Definition: EscriptDataset.h:185
int getInnerIterMax() const
Definition: SolverOptions.cpp:537
int mpiRank
Definition: EscriptDataset.h:181
virtual void resetTransport(bool preserveSolverData) const
resets the transport operator typically as they have been updated.
Definition: AbstractTransportProblem.cpp:124
Data acosh() const
Return the acosh of each data point of this Data object.
Definition: Data.cpp:2129
void setSaveMeshData(bool flag)
Enables/Disables saving of mesh-related data.
Definition: EscriptDataset.h:134
int getMPIWorldSum(int val)
returns sum of an integer over all processors with MPI_COMM_WORLD
Definition: Utils.cpp:124
double getInnerTolerance() const
Definition: SolverOptions.cpp:597
void setTolerance(double rtol)
Definition: SolverOptions.cpp:566
virtual bool supportsContactElements() const =0
Data cosh() const
Return the cosh of each data point of this Data object.
Definition: Data.cpp:2096
virtual escript::Data getNormal() const =0
Return boundary normals. The function space is chosen appropriately.
@ SO_ODESOLVER_CRANK_NICOLSON
Definition: SolverOptions.h:156
boost::python::list getListOfTags() const
Returns a list of the tags used in this function space.
Definition: FunctionSpace.cpp:343
const boost::python::tuple eigenvalues_and_eigenvectors(const DataTypes::real_t tol=1.e-12) const
Return the eigenvalues and corresponding eigenvcetors of the symmetric part at each data point of thi...
Definition: Data.cpp:2954
Data trace(int axis_offset) const
Return the trace of a matrix.
Definition: Data.cpp:2848
SpeckleyDomain extends the AbstractContinuousDomain interface for the Speckley library and is the bas...
Definition: speckley/src/SpeckleyDomain.h:99
void setTaggedValue(int tagKey, const boost::python::object &value)
Assign the given value to the tag. Implicitly converts this object to type DataTagged if it is consta...
Definition: Data.cpp:3594
const char * getName(int key) const
Definition: SolverOptions.cpp:119
@ SO_METHOD_CGS
Definition: SolverOptions.h:125
const boost::python::tuple minGlobalDataPoint() const
Definition: Data.cpp:2980
FunctionSpace reducedFunction(const AbstractDomain &domain)
Return a function FunctionSpace with reduced integration order.
Definition: FunctionSpaceFactory.cpp:63
Data copySelf() const
Return a pointer to a deep copy of this object.
Definition: Data.cpp:770
@ SO_METHOD_CGLS
Definition: SolverOptions.h:124
bool isEmpty() const
Definition: Data.cpp:1132
void replaceInfPython(boost::python::object obj)
Definition: Data.cpp:2465
Data ComplexData(boost::python::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:428
int getNumDataPoints() const
Return the number of data points.
Definition: Data.h:523
EscriptDataset()
Default constructor.
Definition: EscriptDataset.cpp:76
void runJobs()
Definition: SplitWorld.cpp:124
bool setExternalDomain(const DomainChunks &domain)
Definition: EscriptDataset.cpp:911
Definition: EscriptDataset.h:38
void dump(const std::string fileName) const
dumps the object into a netCDF file
Definition: Data.cpp:5417
void setPackage(int package)
Definition: SolverOptions.cpp:414
const VarVector & getVariables() const
Returns a vector with the dataset's variables.
Definition: EscriptDataset.h:146
virtual int getDim() const =0
Returns the spatial dimension of the domain.
const boost::python::object getValueOfGlobalDataPointAsTuple(int procNo, int dataPointNo)
Return a data point across all processors as a python tuple.
Definition: Data.cpp:1699
int getIterMax() const
Definition: SolverOptions.cpp:549
@ SO_METHOD_ROWSUM_LUMPING
Definition: SolverOptions.h:141
@ SO_PRECONDITIONER_AMG
Definition: SolverOptions.h:145
FunctionSpace functionOnContactOne(const AbstractDomain &domain)
Return a FunctionSpace on right side of contact.
Definition: FunctionSpaceFactory.cpp:93
void setItemD(const boost::python::object &key, const Data &value)
Copies slice from value into this Data object.
Definition: Data.cpp:3498
@ SO_METHOD_ITERATIVE
Definition: SolverOptions.h:135
void setInnerToleranceAdaption(bool adaption)
Definition: SolverOptions.cpp:732
const boost::python::tuple maxGlobalDataPoint() const
Definition: Data.cpp:3083
virtual void setNewX(const escript::Data &arg)
assigns new location to the domain
Definition: AbstractContinuousDomain.cpp:210
Data Tensor3(double value, const FunctionSpace &what, bool expanded)
Return a Data object containing tensor3 datapoints. ie: rank 3 data-points.
Definition: DataFactory.cpp:270
void copyWithMask(const Data &other, const Data &mask)
Copy other Data object into this Data object where mask is positive.
Definition: Data.cpp:851
virtual int getSystemMatrixTypeId(const boost::python::object &options) const
return the identifier of the matrix type to be used for the global stiffness matrix when particular s...
Definition: AbstractContinuousDomain.cpp:137
SolverOptions getReordering() const
Definition: SolverOptions.cpp:492
FunctionSpace reducedFunctionOnContactOne(const AbstractDomain &domain)
Return a FunctionSpace on right side of contact with reduced integration order.
Definition: FunctionSpaceFactory.cpp:99
bool isSymmetric() const
Definition: SolverOptions.cpp:648
boost::python::object __rsub__(const boost::python::object &right)
wrapper for python reverse subtract operation
Definition: Data.cpp:5960
Data transpose(int axis_offset) const
Transpose each data point of this Data object around the given axis.
Definition: Data.cpp:2903
Data delay()
produce a delayed evaluation version of this Data.
Definition: Data.cpp:786
@ SO_REORDERING_NESTED_DISSECTION
Definition: SolverOptions.h:166
void setEscriptParamInt(const std::string &name, int value)
Set the value of a named parameter. See listEscriptParams() for available parameters.
Definition: EscriptParams.h:83
@ SO_METHOD_BICGSTAB
Definition: SolverOptions.h:123
FunctionSpace getTestDomainFunctionSpace(int dpps, DataTypes::dim_t samples, int dpsize)
Definition: TestDomain.cpp:352
SolverOptions getPreconditioner() const
Definition: SolverOptions.cpp:353
void releaseUnusedMemory()
releases unused memory in the memory manager.
Definition: DataVectorTaipan.cpp:41
virtual escript::Data getSize() const =0
Returns the local size of samples. The function space is chosen appropriately.
Data hermitian() const
Return the hermitian part of a matrix which is half the matrix plus its adjoint.
Definition: Data.cpp:2781
virtual MPI_Comm getMPIComm() const =0
get the communicator for this domain. Returns an integer on non-MPI builds Routine must be implemente...
Data load(const std::string fileName, const AbstractDomain &domain)
reads Data on domain from file in netCDF format
Definition: DataFactory.cpp:722
Data solve(Data &u0, Data &source, const double dt, boost::python::object &options)
returns the solution u for a time step dt>0 with initial value u0 at time t=0
Definition: AbstractTransportProblem.cpp:64
Data whereNegative() const
Return a Data with a 1 for -ive values and a 0 for +ive or 0 values.
Definition: Data.cpp:1264
Data minval() const
Return the minimum value of each data point of this Data object.
Definition: Data.cpp:2656
int getSubWorldID()
Definition: SplitWorld.cpp:433
void setHermitianOff()
Definition: SolverOptions.cpp:681
virtual double getSafeTimeStepSize() const
Definition: AbstractTransportProblem.cpp:128
const boost::python::object getValueOfDataPointAsTuple(int dataPointNo)
Return the value of a data point as a python tuple.
Definition: Data.cpp:1520
void setInnerIterMax(int iter_max)
Definition: SolverOptions.cpp:530
void setInnerToleranceAdaptionOn()
Definition: SolverOptions.cpp:722
@ SO_METHOD_MINRES
Definition: SolverOptions.h:137
escript::Data getXFromFunctionSpace() const
Returns the spatial locations of the data points.
Definition: Data.h:474
Data log() const
Return the natural log of each data point of this Data object.
Definition: Data.cpp:2150
Data truedivD(const Data &right)
Newer style division operator for python.
Definition: Data.h:2180
void printParallelThreadCnt()
print a message about how many MPI CPUs and OpenMP threads we're using
Definition: Utils.cpp:136
Data rpowO(const boost::python::object &left) const
Return the given power of each data point of this boost python object.
Definition: Data.cpp:3323
boost::python::object __div__(const boost::python::object &right)
wrapper for python divide operation
Definition: Data.cpp:6009
void updateSampleDistribution(VarInfo &vi)
Definition: EscriptDataset.cpp:1031
void setVerbosityOn()
Definition: SolverOptions.cpp:699
@ SO_METHOD_DIRECT_PARDISO
Definition: SolverOptions.h:130
void setSolverMethod(int method)
Definition: SolverOptions.cpp:358
bool canInterpolate(FunctionSpace src, FunctionSpace dest)
Definition: FunctionSpace.cpp:34
#define WEIPA_DLL_API
Definition: weipa.h:38
Definition: AbstractContinuousDomain.cpp:23
Data matrixInverse() const
return inverse of matricies.
Definition: Data.cpp:3295
DataTypes::real_t inf()
Return the minimum value of this Data object.
Definition: Data.cpp:2303
StringVec meshLabels
Definition: EscriptDataset.h:177
Data wherePositive() const
Return a Data with a 1 for +ive values and a 0 for 0 or -ive values.
Definition: Data.cpp:1253
double time
Definition: EscriptDataset.h:175
bool isExpanded() const
Return true if this Data is expanded.
Definition: Data.cpp:1111
@ SO_METHOD_CR
Definition: SolverOptions.h:127
void setPreconditioner(int preconditioner)
Definition: SolverOptions.cpp:331
@ SO_METHOD_DIRECT_MUMPS
Definition: SolverOptions.h:129
Data ComplexTensor3(double value, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:276
bool hasInf()
Definition: Data.cpp:2434
void setSymmetry(bool symmetry)
Definition: SolverOptions.cpp:663
Data Tensor(double value, const FunctionSpace &what, bool expanded)
Return a Data object containing tensor datapoints. ie: rank 2 data-points.
Definition: DataFactory.cpp:190
Data nonuniformslope(boost::python::object in, boost::python::object out, bool check_boundaries)
Definition: Data.cpp:5308
int getTagNumber(int dpno)
Return the tag number associated with the given data-point.
Definition: Data.cpp:3673
boost::python::object __sub__(const boost::python::object &right)
wrapper for python subtract operation
Definition: Data.cpp:5936
Data antisymmetric() const
Return the antisymmetric part of a matrix which is half the matrix minus its transpose.
Definition: Data.cpp:2745
void saveVTK(const std::string fileName)
Saves the dataset in the VTK XML file format.
Definition: EscriptDataset.cpp:488
void setTagsByString(const std::string &name, const escript::Data &mask) const
Definition: FunctionSpace.cpp:314
@ SO_PRECONDITIONER_GAUSS_SEIDEL
Definition: SolverOptions.h:146
@ SO_DEFAULT
Definition: SolverOptions.h:110
int getMPIWorldMax(int val)
returns the maximum value of an integer over all processors within MPI_COMM_WORLD
Definition: Utils.cpp:112
int mpiSize
Definition: EscriptDataset.h:181
bool hasFeature(const std::string &name)
returns true if escript was compiled with the feature name, false otherwise.
Definition: EscriptParams.h:110
@ SO_PRECONDITIONER_NONE
Definition: SolverOptions.h:150
std::vector< std::string > StringVec
Definition: weipa.h:61
int getTypeCode() const
Returns the function space type code.
Definition: FunctionSpace.cpp:95
Data asinh() const
Return the asinh of each data point of this Data object.
Definition: Data.cpp:2122
void setDropTolerance(double drop_tol)
Definition: SolverOptions.cpp:602
boost::python::object getVarPyList()
Definition: SplitWorld.cpp:317
int getDim() const
Return the number of spatial dimensions of the underlying domain.
Definition: FunctionSpace.h:197
DudleyDomain implements the AbstractContinuousDomain interface for the Dudley library.
Definition: DudleyDomain.h:125
std::string toString() const
Returns a text description of the function space.
Definition: FunctionSpace.cpp:118
virtual void MPIBarrier() const =0
If compiled for MPI then execute an MPI_Barrier, else do nothing.
bool isLazy() const
Return true if this Data is lazy.
Definition: Data.cpp:1146
int isEmpty() const
Definition: AbstractTransportProblem.cpp:58
FunctionSpace function(const AbstractDomain &domain)
Return a function FunctionSpace.
Definition: FunctionSpaceFactory.cpp:57
Data Vector(double value, const FunctionSpace &what, bool expanded)
Return a Data object containing vector data-points. ie: rank 1 data-points.
Definition: DataFactory.cpp:139
Data whereNonZero(DataTypes::real_t tol=0.0) const
Return a Data with a 0 for 0 values and a 1 for +ive or -ive values.
Definition: Data.cpp:1304
std::vector< VarInfo > VarVector
Definition: EscriptDataset.h:46
Data ComplexTensor3FromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:323
void setTupleForGlobalDataPoint(int id, int proc, boost::python::object)
Set the value of a global data point.
Definition: Data.cpp:1567
void setVerbosity(bool verbose)
Definition: SolverOptions.cpp:709
virtual int getMPISize() const =0
return the number of processors used for this domain
Represents an escript dataset including a domain and data variables for one timestep.
Definition: EscriptDataset.h:63
double getTime() const
Returns the time value.
Definition: EscriptDataset.h:117
void setValueOfDataPointToArray(int dataPointNo, const boost::python::object &)
sets the values of a data-point from a array-like object on this process
Definition: Data.cpp:1612
void setCycleAndTime(int c, double t)
Sets the cycle number and time value for this dataset.
Definition: EscriptDataset.h:111
FunctionSpace functionOnBoundary(const AbstractDomain &domain)
Return a function on boundary FunctionSpace.
Definition: FunctionSpaceFactory.cpp:69
void setItemO(const boost::python::object &key, const boost::python::object &value)
Definition: Data.cpp:3490
Data condEval(escript::Data &mask, escript::Data &trueval, escript::Data &falseval)
Definition: Data.cpp:5648
void setODESolver(int solver)
Definition: SolverOptions.cpp:798
int MPI_Comm
Definition: EsysMPI.h:42
Data log10() const
Return the log to base 10 of each data point of this Data object.
Definition: Data.cpp:2143
Data pos() const
Return the identity of each data point of this Data object. Simply returns this object unmodified.
Definition: Data.cpp:2179
Data ComplexScalarFromObj(boost::python::object o, const FunctionSpace &what, bool expanded)
Python interface for the Complex Scalar factory.
Definition: DataFactory.cpp:118
boost::python::object __rdiv__(const boost::python::object &right)
wrapper for python reverse divide operation
Definition: Data.cpp:6033
void setHermitian(bool hermitian)
Definition: SolverOptions.cpp:686
void replaceNaNPython(boost::python::object obj)
replaces all NaN values with value
Definition: Data.cpp:2420
Data VectorFromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:153
Data imag() const
Definition: Data.cpp:2003
bool hasNaN()
returns return true if data contains NaN.
Definition: Data.cpp:2389
void setAcceptanceConvergenceFailureOff()
Definition: SolverOptions.cpp:750
virtual std::pair< int, DataTypes::dim_t > getDataShape(int functionSpaceCode) const
Return the number of data points per sample, and the number of samples as a pair.
Definition: AbstractContinuousDomain.cpp:204
void setInnerTolerance(double rtol)
Definition: SolverOptions.cpp:590
std::string varName
Definition: EscriptDataset.h:39
Base class for all escript domains.
Definition: AbstractDomain.h:64
Data Tensor3FromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:298
virtual ATP_ptr newTransportProblem(const int blocksize, const escript::FunctionSpace &functionspace, const int type) const
creates a TransportProblemAdapter
Definition: AbstractContinuousDomain.cpp:189
bool setDomain(const escript::AbstractDomain *domain)
Sets the escript domain for this dataset. This method can only be called once and should be the first...
Definition: EscriptDataset.cpp:112
const char * MESH_VARS
Definition: EscriptDataset.cpp:71
void copy(const Data &other)
Make this object a deep copy of "other".
Definition: Data.cpp:777
int getMPIRankWorld()
returns the MPI processor number within MPI_COMM_WORLD
Definition: Utils.cpp:103
virtual std::string showTagNames() const =0
Returns all tag names in a single string sperated by commas.
boost::python::object raw_addJobPerWorld(boost::python::tuple t, boost::python::dict kwargs)
Definition: SplitWorld.cpp:492
bool loadData(const std::string filePattern, const std::string name, const std::string units)
Definition: EscriptDataset.cpp:947
void convertToNumpy(escript::Data data)
Definition: Utils.cpp:981
boost::python::object raw_addVariable(boost::python::tuple t, boost::python::dict kwargs)
Definition: SplitWorld.cpp:513
boost::python::object getLocalObjectVariable(const std::string &name)
Definition: SplitWorld.cpp:36
Data neg() const
Return the negation of each data point of this Data object.
Definition: Data.cpp:2172
@ SO_PRECONDITIONER_RILU
Definition: SolverOptions.h:152
Data nonuniforminterp(boost::python::object in, boost::python::object out, bool check_boundaries)
Definition: Data.cpp:5232
@ SO_PACKAGE_TRILINOS
Definition: SolverOptions.h:119
void setTrilinosParameter(const std::string &name, const boost::python::object &value)
Definition: SolverOptions.cpp:817
boost::shared_ptr< DomainChunk > DomainChunk_ptr
Definition: weipa.h:66
bool adaptInnerTolerance() const
Definition: SolverOptions.cpp:717
void setValueOfDataPointToPyObject(int dataPointNo, const boost::python::object &py_object)
sets the values of a data-point from a python object on this process
Definition: Data.cpp:1559
Data acos() const
Return the acos of each data point of this Data object.
Definition: Data.cpp:2074
virtual void Print_Mesh_Info(const bool full=false) const
Definition: AbstractContinuousDomain.cpp:216
@ SO_PACKAGE_MKL
Definition: SolverOptions.h:117
Data ComplexTensor4FromObj(bp::object o, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:402
@ SO_PRECONDITIONER_JACOBI
Definition: SolverOptions.h:149
void expand()
Whatever the current Data type make this into a DataExpanded.
Definition: Data.cpp:1180
std::vector< int > IntVec
Definition: weipa.h:60
void setLocalPreconditionerOn()
Definition: SolverOptions.cpp:768
@ SO_METHOD_PRES20
Definition: SolverOptions.h:140
~EscriptDataset()
Destructor.
Definition: EscriptDataset.cpp:105
bool wantsMeshVars
Definition: EscriptDataset.h:178
double getDropStorage() const
Definition: SolverOptions.cpp:621
@ SO_PACKAGE_UMFPACK
Definition: SolverOptions.h:120
void setNumberOfThreads(int num_threads)
set the number of threads
Definition: Utils.cpp:78
void setLocalPreconditionerOff()
Definition: SolverOptions.cpp:773
Data randomData(const boost::python::tuple &shape, const FunctionSpace &what, long seed, const boost::python::tuple &filter)
Create a new Expanded Data object filled with pseudo-random data.
Definition: Data.cpp:5872
Data conjugate() const
For complex values return the conjugate values. For non-complex data return a copy.
Definition: Data.cpp:1964
@ SO_METHOD_TFQMR
Definition: SolverOptions.h:142
@ SO_METHOD_PCG
Definition: SolverOptions.h:139
A class that provides functionality to read an escript data object from a dump file or an escript::Da...
Definition: DataVar.h:36
void setProtection()
switches on update protection
Definition: Data.cpp:1166
Data Tensor4(double value, const FunctionSpace &what, bool expanded)
Return a Data object containing tensor4 datapoints. ie: rank 4 data-points.
Definition: DataFactory.cpp:349
Data asin() const
Return the asin of each data point of this Data object.
Definition: Data.cpp:2067
void setMetadataSchemaString(const std::string schema, const std::string metadata)
Sets a metadata schema and content.
Definition: EscriptDataset.h:129
boost::python::dict getTrilinosParameters() const
Definition: SolverOptions.cpp:825
Data sqrt() const
Return the square root of each data point of this Data object.
Definition: Data.cpp:2198
boost::python::object raw_buildDomains(boost::python::tuple t, boost::python::dict kwargs)
Definition: SplitWorld.cpp:456
Data ComplexTensor(double value, const FunctionSpace &what, bool expanded)
Definition: DataFactory.cpp:196
void setMeshUnits(const std::string x, const std::string y, const std::string z="")
Sets units for the mesh axes.
Definition: EscriptDataset.cpp:571
bool isProtected() const
Returns true, if the data object is protected against update.
Definition: Data.cpp:1172
SolverOptions getODESolver() const
Definition: SolverOptions.cpp:812
void clearVariable(std::string name)
Definition: SplitWorld.cpp:306
virtual int getMPIRank() const =0
return the number MPI rank of this processor
double getMachinePrecision()
returns the machine precision
Definition: Utils.cpp:367
Data eigenvalues() const
Return the eigenvalues of the symmetric part at each data point of this Data object in increasing val...
Definition: Data.cpp:2927
int getTagFromDataPointNo(DataTypes::dim_t dataPointNo) const
Returns the tag associated with the given data-point number.
Definition: FunctionSpace.cpp:150
void convertMeshVariables()
Definition: EscriptDataset.cpp:1004
@ SO_METHOD_CHOLEVSKY
Definition: SolverOptions.h:126
int getRestart() const
Definition: SolverOptions.cpp:505
void * getMPIComm()
Definition: EscriptDataset.h:156
FunctionSpace solution(const AbstractDomain &domain)
Return a FunctionSpace.
Definition: FunctionSpaceFactory.cpp:105
virtual void addPDEToTransportProblem(AbstractTransportProblem &tp, escript::Data &source, const escript::Data &M, const escript::Data &A, const escript::Data &B, const escript::Data &C, const escript::Data &D, const escript::Data &X, const escript::Data &Y, const escript::Data &d, const escript::Data &y, const escript::Data &d_contact, const escript::Data &y_contact, const escript::Data &d_dirac, const escript::Data &y_dirac) const
adds a PDE onto a transport problem
Definition: AbstractContinuousDomain.cpp:166
void putSiloMultiVar(DBfile *dbfile, const VarInfo &vi, bool useMeshFile=false)
Definition: EscriptDataset.cpp:1123
Represents a full Finley or Dudley domain including nodes and elements.
Definition: weipa/src/FinleyDomain.h:42
@ SO_INTERPOLATION_CLASSIC
Definition: SolverOptions.h:160
unsigned int getDataPointRank() const
Return the rank of the point data.
Definition: Data.h:512