File List

Here is a list of all files with brief descriptions:
AnalyticGeometry.h [code]This is the client-side interface to analytic geometry suitable for using to generate mass properties, collisions, etc
Array.h [code]
AtomicInteger.h [code]
basics.h [code]Includes internal headers providing declarations for the basic SimTK Core classes
BigMatrix.h [code]This file defines the client side of the SimTK::Matrix classes, which hold large, variable-sized matrices whose elements are packed SimTK "Composite Numerical Types" (CNTs)
Biotype.h [code]
Body.h [code]This defines the Body class, which represents a reference frame which can be used to describe mass properties and geometry
bondGeometry.h [code]
Clonable.h [code]
CollisionDetectionAlgorithm.h [code]
simtkcommon/trunk/include/SimTKcommon/internal/common.h [code]Mandatory first inclusion for any SimTK source or header file
simmath/trunk/include/simmath/internal/common.h [code]This is the header file that user code should include to pick up the SimTK Simmath numerical differentiation tools
simbody/trunk/include/simbody/internal/common.h [code]Every Simbody header and source file should include this header before any other Simbody header
molmodel/trunk/include/molmodel/internal/common.h [code]Every Molmodel header and source file should include this header before any other Molmodel header
CompositeNumericalTypes.h [code]The purpose of the CNT<T> class is to hide the differences between built-in numerical types and composite ones like Vec<3>
Compound.h [code]
CompoundSystem.h [code]
Concretize.h [code]
conf-explorer.2008.07.23.cpp
configall_system.h [code]
configall_system_msc.h [code]
conjugate.h [code]This file defines the conjugate<R> template class, where R is one of the three built-in real types
Constants.h [code]This header is the common gathering place for numerical, *machine-independent* constants in SimTK
ConstrainedNumericalDiffOptimization.cpp
ConstrainedOptimization.cpp
Constraint.h [code]This defines the Constraint class, which is used to specify limitations on the mobility of the MobilizedBodies in a MatterSubsystem
Contact.h [code]
ContactGeometry.h [code]
ContactGeometryImpl.h [code]
ContactImpl.h [code]
CoordinateAxis.h [code]
cpodes.h [code]
cpodes_band.h [code]
cpodes_bandpre.h [code]
cpodes_bbdpre.h [code]
cpodes_dense.h [code]
cpodes_direct.h [code]
cpodes_lapack.h [code]
cpodes_lapack_exports.h [code]
cpodes_spbcgs.h [code]
cpodes_spgmr.h [code]
cpodes_spils.h [code]
cpodes_sptfqmr.h [code]
CPodesIntegrator.h [code]
cpsadamsx.c
cpsAdvDiff_bnd.c
cpsAdvDiff_bndL.c
cpsAdvDiff_non.c
cpsbanx.c
cpsbanx_lap.c
cpsdenx.c
cpsdenx_lap.c
cpsNewtCrd_dns.c
cpsPend_dns.c
cpsPend_dnsL.c
cpsRoberts_dns.c
cpsRoberts_dnsL.c
cpsVanDPol_non.c
cvbanx.c
cvbanx_lap.c
cvdenx.c
cvdenx_lap.c
cvdenx_uw.c
cvdirectdem.c
cvkrydem_lin.c
cvkrydem_pre.c
cvkryx.c
cvkryx_bbd_p.c
cvkryx_bp.c
cvkryx_p.c
cvnonx_p.c
cvode.h [code]
cvode_band.h [code]
cvode_bandpre.h [code]
cvode_bbdpre.h [code]
cvode_dense.h [code]
cvode_diag.h [code]
cvode_direct.h [code]
cvode_lapack.h [code]
cvode_spbcgs.h [code]
cvode_spgmr.h [code]
cvode_spils.h [code]
cvode_sptfqmr.h [code]
cvodes.h [code]
cvodes_band.h [code]
cvodes_bandpre.h [code]
cvodes_bbdpre.h [code]
cvodes_dense.h [code]
cvodes_diag.h [code]
cvodes_direct.h [code]
cvodes_lapack.h [code]
cvodes_spbcgs.h [code]
cvodes_spgmr.h [code]
cvodes_spils.h [code]
cvodes_sptfqmr.h [code]
cvsadjbanx.c
cvsadjdenx.c
cvsadjkryx_int.c
cvsadjkryx_p.c
cvsadjkryx_pnt.c
cvsadjnonx_p.c
cvsbanx.c
cvsbanx_lap.c
cvsdenx.c
cvsdenx_lap.c
cvsdenx_uw.c
cvsdirectdem.c
cvsfwddenx.c
cvsfwdkryx.c
cvsfwdkryx_p.c
cvsfwdnonx.c
cvsfwdnonx_p.c
cvskrydem_lin.c
cvskrydem_pre.c
cvskryx.c
cvskryx_bbd_p.c
cvskryx_bp.c
cvskryx_p.c
cvsnonx_p.c
DecorationSubsystem.h [code]Define the public interface to DecorationSubsystem, a "do nothing" subsystem providing a place for a MultibodySystem Modeler to toss in some visuals which may optionally be displayed by an application which uses that System
DecorativeGeometry.h [code]This is the client-side interface to an implementation-independent representation of "Decorations" suitable for visualization, annotation, logging, or debugging but which cannot have any effect on the behavior of a System or the evolution of a Study
Differentiator.cppThis is a test program which uses the Differentiator class in various ways
Differentiator.h [code]This is the header file that user code should include to pick up the SimTK Simmath numerical differentiation tools
DuMMForceFieldSubsystem.h [code]Define the public interface to DuMMForceFieldSubsystem, a subsystem which provides some minimal molecular mechanics-like capability in a multi-rigid body framework
ElasticFoundationForce.h [code]
Element.h [code]
Enumeration.h [code]
EventHandler.h [code]
EventReporter.h [code]
ExampleAdenylateMobilitiesVMD.cpp
ExampleAdenylateMobilitiesVTK.cpp
ExampleCreatePropane.cpp
ExampleLoadPdb.cpp
ExampleLoadPdb2.cpp
ExampleLoadRNA.cpp
ExampleMeasureActualStepSize.cpp
ExamplePuckerRibose.cpp
ExampleRigidProtein.cpp
ExampleSimpleProtein.cpp
ExampleSimpleRNA.cpp
ExampleSodiumChloride.cpp
ExampleTwoArgonAtoms.cpp
ExampleTwoEthanes.cpp
Exception.h [code]
ExceptionMacros.h [code]This file contains macros which are convenient to use for sprinkling error checking around liberally in SimTK programs, a practice which is highly encouraged
ExplicitEulerIntegrator.h [code]
fcvbanx.f
fcvdenx.f
fcvdenx_lap.f
fcvkryx.f
fcvkryx_bbd_p.f
fcvkryx_bp.f
fcvkryx_p.f
fcvnonx_p.f
fidadenx.f
fidakryx_bbd_p.f
fkinkryx.f
fkinkryx_p.f
Force.h [code]
ForceSubsystem.h [code]
ForceSubsystemGuts.h [code]Define the extendible library-side implementation of the ForceSubsystem
Fortran.h [code]This header defines a set of macros which are useful for making calls to Fortran routines from C++ programs
Function.h [code]
GCVSPLUtil.h [code]
GeneralContactSubsystem.h [code]
GeneralForceSubsystem.h [code]
GrinPointer.h [code]
HuntCrossleyContact.h [code]Define the public interface to HuntCrossleyContact, a subsystem which provides some minimal contact behavior
HuntCrossleyForce.h [code]
ida.h [code]
ida_band.h [code]
ida_bbdpre.h [code]
ida_dense.h [code]
ida_direct.h [code]
ida_lapack.h [code]
ida_spbcgs.h [code]
ida_spgmr.h [code]
ida_spils.h [code]
ida_sptfqmr.h [code]
idabanx1.c
idabanx2.c
idadenx.c
idakrydem_lin.c
idakryx.c
idakryx1_bbd_p.c
idakryx1_p.c
idakryx2_bbd_p.c
idakryx2_p.c
imd.h [code]
initroot1.c
Integrator.h [code]This is the header file that user code should include to pick up the SimTK Simmath numerical integration tools
Ions.h [code]
IpAdaptiveMuUpdate.cpp
IpAdaptiveMuUpdate.hpp [code]
IpAlgBuilder.cpp
IpAlgBuilder.hpp [code]
IpAlgorithmRegOp.cpp
IpAlgorithmRegOp.hpp [code]
IpAlgStrategy.hpp [code]
IpAlgTypes.hpp [code]
IpAugRestoSystemSolver.cpp
IpAugRestoSystemSolver.hpp [code]
IpAugSystemSolver.hpp [code]
IpBacktrackingLineSearch.cpp
IpBacktrackingLineSearch.hpp [code]
IpBacktrackingLSAcceptor.hpp [code]
IpBlas.cpp
IpBlas.hpp [code]
IpCachedResults.hpp [code]
IpCompoundMatrix.cpp
IpCompoundMatrix.hpp [code]
IpCompoundSymMatrix.cpp
IpCompoundSymMatrix.hpp [code]
IpCompoundVector.cpp
IpCompoundVector.hpp [code]
IpConvCheck.hpp [code]
IpDebug.cpp
IpDebug.hpp [code]
IpDefaultIterateInitializer.cpp
IpDefaultIterateInitializer.hpp [code]
IpDenseGenMatrix.cpp
IpDenseGenMatrix.hpp [code]
IpDenseSymMatrix.cpp
IpDenseSymMatrix.hpp [code]
IpDenseVector.cpp
IpDenseVector.hpp [code]
IpDiagMatrix.cpp
IpDiagMatrix.hpp [code]
IpEqMultCalculator.hpp [code]
IpExactHessianUpdater.cpp
IpExactHessianUpdater.hpp [code]
IpException.hpp [code]
IpExpansionMatrix.cpp
IpExpansionMatrix.hpp [code]
IpFilter.cpp
IpFilter.hpp [code]
IpFilterLSAcceptor.cpp
IpFilterLSAcceptor.hpp [code]
IpGenTMatrix.cpp
IpGenTMatrix.hpp [code]
IpGradientScaling.cpp
IpGradientScaling.hpp [code]
IpHessianUpdater.hpp [code]
IpIdentityMatrix.cpp
IpIdentityMatrix.hpp [code]
IpInterfacesRegOp.cpp
IpInterfacesRegOp.hpp [code]
IpIpoptAlg.cpp
IpIpoptAlg.hpp [code]
IpIpoptApplication.cpp
IpIpoptApplication.hpp [code]
IpIpoptCalculatedQuantities.cpp
IpIpoptCalculatedQuantities.hpp [code]
IpIpoptData.cpp
IpIpoptData.hpp [code]
IpIpoptNLP.hpp [code]
IpIterateInitializer.hpp [code]
IpIteratesVector.cpp
IpIteratesVector.hpp [code]
IpIterationOutput.hpp [code]
IpJournalist.cpp
IpJournalist.hpp [code]
IpLapack.cpp
IpLapack.hpp [code]
IpLapackSolverInterface.cpp
IpLapackSolverInterface.hpp [code]
IpLeastSquareMults.cpp
IpLeastSquareMults.hpp [code]
IpLimMemQuasiNewtonUpdater.cpp
IpLimMemQuasiNewtonUpdater.hpp [code]
IpLinearSolversRegOp.cpp
IpLinearSolversRegOp.hpp [code]
IpLineSearch.hpp [code]
IpLoqoMuOracle.cpp
IpLoqoMuOracle.hpp [code]
IpLowRankAugSystemSolver.cpp
IpLowRankAugSystemSolver.hpp [code]
IpLowRankUpdateSymMatrix.cpp
IpLowRankUpdateSymMatrix.hpp [code]
IpMatrix.cpp
IpMatrix.hpp [code]
IpMonotoneMuUpdate.cpp
IpMonotoneMuUpdate.hpp [code]
IpMultiVectorMatrix.cpp
IpMultiVectorMatrix.hpp [code]
IpMuOracle.hpp [code]
IpMuUpdate.hpp [code]
IpNLP.hpp [code]
IpNLPScaling.cpp
IpNLPScaling.hpp [code]
IpObserver.cpp
IpObserver.hpp [code]
IpoptConfig.h [code]
IpOptErrorConvCheck.cpp
IpOptErrorConvCheck.hpp [code]
IpOptionsList.cpp
IpOptionsList.hpp [code]
IpOrigIpoptNLP.cpp
IpOrigIpoptNLP.hpp [code]
IpOrigIterationOutput.cpp
IpOrigIterationOutput.hpp [code]
IpPDFullSpaceSolver.cpp
IpPDFullSpaceSolver.hpp [code]
IpPDPerturbationHandler.cpp
IpPDPerturbationHandler.hpp [code]
IpPDSystemSolver.hpp [code]
IpProbingMuOracle.cpp
IpProbingMuOracle.hpp [code]
IpQualityFunctionMuOracle.cpp
IpQualityFunctionMuOracle.hpp [code]
IpReferenced.hpp [code]
IpRegOptions.cpp
IpRegOptions.hpp [code]
IpRestoFilterConvCheck.cpp
IpRestoFilterConvCheck.hpp [code]
IpRestoIpoptNLP.cpp
IpRestoIpoptNLP.hpp [code]
IpRestoIterateInitializer.cpp
IpRestoIterateInitializer.hpp [code]
IpRestoIterationOutput.cpp
IpRestoIterationOutput.hpp [code]
IpRestoMinC_1Nrm.cpp
IpRestoMinC_1Nrm.hpp [code]
IpRestoPhase.hpp [code]
IpRestoRestoPhase.cpp
IpRestoRestoPhase.hpp [code]
IpReturnCodes.h [code]
IpReturnCodes.hpp [code]
IpReturnCodes.inc
IpReturnCodes_inc.h [code]
IpScaledMatrix.cpp
IpScaledMatrix.hpp [code]
IpSmartPtr.hpp [code]
IpSolveStatistics.cpp
IpSolveStatistics.hpp [code]
IpSparseSymLinearSolverInterface.hpp [code]
IpStdAugSystemSolver.cpp
IpStdAugSystemSolver.hpp [code]
IpStdCInterface.cpp
IpStdCInterface.h [code]
IpStdFInterface.c
IpStdInterfaceTNLP.cpp
IpStdInterfaceTNLP.hpp [code]
IpSumMatrix.cpp
IpSumMatrix.hpp [code]
IpSumSymMatrix.cpp
IpSumSymMatrix.hpp [code]
IpSymLinearSolver.hpp [code]
IpSymMatrix.cpp
IpSymMatrix.hpp [code]
IpSymScaledMatrix.cpp
IpSymScaledMatrix.hpp [code]
IpSymTMatrix.cpp
IpSymTMatrix.hpp [code]
IpTaggedObject.cpp
IpTaggedObject.hpp [code]
IpTimedTask.hpp [code]
IpTimingStatistics.cpp
IpTimingStatistics.hpp [code]
IpTNLP.hpp [code]
IpTNLPAdapter.cpp
IpTNLPAdapter.hpp [code]
IpTripletHelper.cpp
IpTripletHelper.hpp [code]
IpTripletToCSRConverter.cpp
IpTripletToCSRConverter.hpp [code]
IpTripletToDenseConverter.cpp
IpTripletToDenseConverter.hpp [code]
IpTSymLinearSolver.cpp
IpTSymLinearSolver.hpp [code]
IpTSymScalingMethod.hpp [code]
IpTypes.hpp [code]
IpUserScaling.cpp
IpUserScaling.hpp [code]
IpUtils.cpp
IpUtils.hpp [code]
IpVector.cpp
IpVector.hpp [code]
IpWarmStartIterateInitializer.cpp
IpWarmStartIterateInitializer.hpp [code]
IpZeroMatrix.cpp
IpZeroMatrix.hpp [code]
kinbanx.c
kindenx1.c
kindenx2.c
kinkrydem_lin.c
kinkryx.c
kinkryx_bbd_p.c
kinkryx_p.c
kinsol.h [code]
kinsol_band.h [code]
kinsol_bbdpre.h [code]
kinsol_dense.h [code]
kinsol_direct.h [code]
kinsol_lapack.h [code]
kinsol_spbcgs.h [code]
kinsol_spgmr.h [code]
kinsol_spils.h [code]
kinsol_sptfqmr.h [code]
LigandDroplet.h [code]
Ligands.h [code]
LinearAlgebra.h [code]This is the header file that user code should include to pick up the SimTK Simmath linear algebra tools
List.h [code]
LocalEnergyMinimizer.h [code]
MassProperties.h [code]These are utility classes for dealing with mass properties, particularly those messy inertias
Mat.h [code]This file declares class Mat<NROWS, NCOLS, ELEMENT_TYPE, COL_SPACING, ROW_SPACING>
MatrixHelper.h [code]Here we define class MatrixHelper<S>, the scalar-type templatized helper class for the more general, composite numerical type-templatized class MatrixBase<ELT>
Mechanics.h [code]This header collects all the Mechanics header files in one place
MobilizedBody.h [code]This defines the MobilizedBody class, which associates a body (the "outboard" body) with a mobilizer and a reference frame (the parent or "inboard" body), already present in a MatterSubsystem
MolecularMechanicsSystem.h [code]
MultibodySystem.h [code]
negator.h [code]This file defines the negator<N> template which is an adaptor for the numeric types N (Real, Complex, conjugate)
newton.c
NTraits.h [code]This file contains classes and typedefs needed to provide uniform handling of floating point numeric values
NumericalMethods.h [code]
nvector_parallel.h [code]
nvector_serial.h [code]
nvector_SimTK.h [code]This header defines a Sundials N_Vector implementation which uses SimTK's Vector class internally
ObservedPointFitter.h [code]
Optimizer.h [code]
Orientation.h [code]These are numerical utility classes for dealing with the relative orientations of geometric objects
OrientedBoundingBox.h [code]
Parallel2DExecutor.h [code]
ParallelExecutor.h [code]
ParameterConstrainedOptimization.cpp
Pdb.h [code]
PDBReader.h [code]
pend.c
pend_test.c
pendEs.c
pendLr.c
PeriodicPdbWriter.h [code]
PeriodicVmdReporter.h [code]
PolygonalMesh.h [code]
PolynomialRootFinder.h [code]
PrivateImplementation.h [code]This header provides declarations of the user-visible portion of the PIMPLHandle template classes that are used in the SimTK Core to implement the PIMPL (private implementation) design pattern
PrivateImplementation_Defs.h [code]This header provides the definitions of the PIMPLHandle template methods as declared in PrivateImplementation.h, and also the declaration and definition of the template classes used for creating well- behaved implementation classes
Protein.h [code]
Quaternion.h [code]
Random.h [code]
RiboseMobilizer.h [code]
RNA.h [code]
Rotation.h [code]
Row.h [code]This file declares class Row<NCOLS, ELEMENT_TYPE, STRIDE>
RungeKuttaFeldbergIntegrator.h [code]
RungeKuttaMersonIntegrator.h [code]
Scalar.h [code]This is a user-includable header which includes everything needed to make use of SimMatrix Scalar code
SimbodyMatterSubsystem.h [code]
SimbodyMatterSubtree.h [code]
Simmatrix.h [code]This is the header which should be included in user programs that would like to make use of all the Simmatrix facilities, but none of the other parts of SimTKcommon
SimpleDifferentiator.cppThis is a test program which uses the Differentiator class in various ways
SimTKcommon.h [code]Includes internal headers providing declarations for the basic SimTK Core classes, including Simmatrix
SimTKcpodes.h [code]This is the header file that user code should include to pick up the SimTK C++ interface to the Sundials CPODES coordinate-projection integrator
SimTKmath.h [code]
SimTKmolmodel.h [code]This is the header file that user code should include to pick up all Molmodel capabilities
SimTKsimbody.h [code]This is the header file that user code should include to pick up all Simbody capabilities
SimTKsimbody_aux.h [code]This is the header file that user code should include to pick up all Simbody capabilities
SmallDefsThatNeedBig.h [code]This file defines leftover SmallMatrix implementations which need to know about Lapack
SmallMatrix.h [code]This file is the user-includeable header to be included in user programs to provide fixed-length Vec & Mat classes
SmallMatrixMixed.h [code]This file defines globals which use a mix of Vec, Row, and Mat types and hence need to wait until everything is defined
SpatialAlgebra.h [code]These are declarations for special matrices and vectors of use in implementing Rodriguez and Jain's Spatial Operator Algebra
Spline.h [code]
SplineFitter.h [code]
StableArray.h [code]
Stage.h [code]
State.h [code]
String.h [code]
Study.h [code]
StudyGuts.h [code]
Subsystem.h [code]
SubsystemGuts.h [code]
sundials_band.h [code]
sundials_config.h [code]
sundials_dense.h [code]
sundials_direct.h [code]
sundials_fnvector.h [code]
sundials_iterative.h [code]
sundials_lapack.h [code]
sundials_math.h [code]
sundials_nvector.h [code]
sundials_spbcgs.h [code]
sundials_spgmr.h [code]
sundials_sptfqmr.h [code]
sundials_types.h [code]
Superpose.h [code]Kabsch superposition algorithm implementation
SymMat.h [code]This file declares class SymMat<M, ELEMENT_TYPE, ROW_SPACING>
System.h [code]
SystemGuts.h [code]
TemplatizedLapack.h [code]These is a templatized, C++ callable interface to LAPACK and BLAS
TextDataEventReporter.h [code]
ThreadLocal.h [code]
TimeStepper.h [code]
TinkerDuMMForceFieldSubsystem.h [code]
Transform.h [code]
UnconstrainedNumericalDiffOptimization.cpp
UnconstrainedOptimization.cpp
units.h [code]
UnitVec.h [code]
UserFunction.h [code]
UserGuide.cpp
UserGuideLimits.cpp
Value.h [code]
VanderWallSphere.h [code]
Vec.h [code]Declaration of class Vec<NROWS, ELEMENT_TYPE, STRIDE>
VectorMath.h [code]
VelocityRescalingThermostat.h [code]
VerletIntegrator.h [code]
VmdConnection.h [code]
vmdsock.h [code]
VoxelHash.h [code]
VTKEventReporter.h [code]
VTKVisualizer.h [code]This is the user-visible handle class for the VTK Reporter which provides a 3d animation window for viewing MultibodySystem simulations
Water.h [code]
WaterDroplet.h [code]

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