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CHANGELOG.md

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This document lists the changes to opensim-core that are introduced with each new version, starting with version 4.0. When possible, we provide the GitHub issues or pull requests that are related to the items below. If there is no issue or pull request related to the change, then we may provide the commit.

This is not a comprehensive list of changes but rather a hand-curated collection of the more notable ones. For a comprehensive history, see the OpenSim Core GitHub repo.

Note: This document is currently under construction.

v4.0 (in development)

Converting from v3.x to v4.0

  • The Actuator class has been renamed to ScalarActuator (and Actuator_ has been renamed to Actuator) (PR #126). If you have subclassed from Actuator, you must now subclass from ScalarActuator.

  • Methods like Actuator::getForce are renamed to use "Actuator" instead (e.g., Actuator::getActuator) (PR #209).

  • Markers are now ModelComponents (PR #188). Code is included for conversion on serialization/de-serialization.

  • Body::getMassCenter now returns a Vec3 instead of taking a Vec3 reference as an argument (commit cb0697d98).

  • The following virtual methods in ModelComponent have been moved:

    • connectToModel -> extendConnectToModel
    • addToSystem -> extendAddToSystem
    • initStateFromProperties -> extendInitStateFromProperties
    • setPropertiesFromState -> extendSetPropertiesFromState

    The original methods (without extend) still exist, but they are now non-virtual. To invoke connectToModel on an entire Model, you still call Model::connectToModel. This change has been made to make a distinction between the user interface and the Component developer (extension) interface. IMPORTANT The calls to Super::addToSystem, etc. in the implementation of these methods must now also use the extend variants. Otherwise, you will enter into an infinite recursion.

  • OpenSim now makes substantial use of C++11 features; if you compile OpenSim, your compiler must support C++11. Also, any C++ project in which you use OpenSim must also be compiled with C++11.

  • The following components have been upgraded to use Sockets to connect to other components they depend on (instead of string properties):

    • ContactGeometry (ContactSphere, ContactHalfSpace, ContactMesh)

  • Many of the methods in ScaleTool have now been marked const.

  • We created a new unified command line interface that will replace the single-tool command line executables (scale, ik, id, rra, cmc, etc.).

    • scale -S setup.xml -> opensim run-tool setup.xml.
    • scale -PS -> opensim print-xml scale
    • scale -PropertyInfo ... -> opensim info ...
    • versionUpdate ... -> opensim update-file ...

  • The CoordinateSet property in Joint has been replaced with a coordinates list property and enumerations have been added for accessing the Coordinates owned by a Joint. Code like myPlanarJoint.getCoordinateSet()[0] now becomes myPlanarJoint.getCoordinate(PlanarJoint::Coord::RotationZ) (PRs #1116, #1210, and #1222).

  • The reverse property in Joint can no longer be set by the user; Model uses SimTK::MultibodyGraphMaker to determine whether joints should be reversed when building the multibody system. The joint's transform and coordinates maintain a parent->child sense even if the joint has been reversed. For backwards compatibility, a joint's parent and child PhysicalFrames are swapped when opening a Model if the reverse element is set to true.

  • The Manager::integrate(SimTK::State&) call is deprecated and replaced by Manager::integrate(SimTK::State&, double). Here is a before-after example (see the documentation in the Manager class for more details):

    • Before:
      • manager.setInitialTime(0.0);
      • manager.setFinalTime(1.0);
      • manager.integrate(state);
    • After:
      • state.setTime(0.0);
      • manager.integrate(state, 1.0);

  • Muscle::equilibrate(SimTK::State&) has been removed from the Muscle interface in order to reduce the number and variety of muscle equilibrium methods. Actuator::computeEquilibrium(SimTK::State&) is overridden by Muscle and invokes pure virtual Muscle::computeInitialFiberEquilibrium(SimTK::State&).

  • Millard2012EquilibriumMuscle::computeFiberEquilibriumAtZeroVelocity(SimTK::State&) and computeInitialFiberEquilibrium(SimTK::State&) were combined into a single method: Millard2012EquilibriumMuscle::computeFiberEquilibrium(SimTK::State&, bool useZeroVelocity) where fiber-velocity can be estimated from the state or assumed to be zero if the flag is true.

  • Millard2012EquilibriumMuscle::computeInitialFiberEquilibrium(SimTK::State&) invokes computeFiberEquilibrium() with useZeroVelocity = true to maintain its previous behavior.

Composing a Component from other components

Component now maintains a list property of components which it owns. You add a (sub) Component to a parent Component by calling addComponent and passing a heap allocated (new Component) to the parent which you want to take ownership of the new subcomponent. Ownership determines how the subcomponent is serialized (appears within the parent) and the order in which of Component interface methods (above) are propagated to the subcomponent. Access to contained components is provided through getComponent<C>(path) or getComponentList<C> where C is any Component type (default is Component to get all subcomponents). These methods always traverse down into a Component's list of components. All subcomponents that are properties of (and thus owned by) a parent Component are accessible this way. The Model's typed %Sets and add####() methods are no longer necessary to compose a Model, since any Component can now be composed of components. Model still supports addd####() methods and de/serialization of Sets, but components added via addComponent are NOT included in the Sets but contained in the Component's components property list. Details in PR#1014.

Bug Fixes

  • Fixed a typo in one of the method names for AbstractTool verifyUniqueComulnLabels -> verifyUniqueColumnLabels (PR #130)
  • Fixed bug where Body VisibleObject was not serialized when writing a model to XML (PR #139)
  • Fixed memory leaks in AssemblySolver and using Simtk::XML (PR #176)
  • Fixed model mass scaling. When 'preserve mass distribution' is unchecked (GUI) the input mass was previously not respected and the resulting scaled model mass does not equal the input mass. The modelscaler() now alters the body masses and inertias to match the input mass. (PR #230)
  • Fixed a bug in the equilibrium solution of Millard and Thelen muscles, where the initial activation and fiber-length values (for solving for equilibrium) were always coming from the default values. This was unnecessary, because unless specified otherwise, the state automatically contains the default values. This fixes an issue where initial states activations from a file were not respected by the Forward Tool and instead, the initial activations would revert to the model defaults. (PR #272)
  • Fixed a bug where MuscleAnalysis was producing empty moment arm files. We now avoid creating empty Moment and MomentArm storage files when _computeMoments is False. (PR #324)
  • Fixed bug causing the muscle equilibrium solve routine in both Thelen2003Muscle and Millard2012EquilibriumMuscle to fail to converge and erroneously return the minimum fiber length. The fix added a proper reduction in step-size when errors increase and limiting the fiber-length to its minimum. (PR #1728)

New Classes

  • Added a BodyActuator component, which applies a spatial force on a specified Point of a Body (PR #126)
  • Created Frame, PhysicalFrame, OffsetFrame, PhysicalOffsetFrame, Station and Marker ModelComponents (PR #188, PR #325, PR #339). Marker did not previously comply with the Model Component interface.
  • A Body is a PhysicalFrame
  • Connections to Bodies upgraded to PhysicalFrames and locations on these frames are now represented by PhysicalOffsetFrame (PR #370)
  • Joints were refactored so that the base Joint manages the parent and child frame connections, including the definition of local PhysicalOffsetFrames to handle offsets defined as separate location and orientation properties. (PR #589)
  • The WeldConstraint and BushingForces (BushingForce, CoupledBushingForce, FunctionBasedBushingForce, and ExpressionBasedBushingForce) were similarly unified (like Joints) to handle the two Frames that these classes require to operate. A LinkTwoFrames intermediate class was introduced to house the common operations. Convenience constructors for WeldConstraint and BushingFrames were affected and now require the name of the Component as the first argument. (PR #649)
  • The new StatesTrajectory class allows users to load an exact representation of previously-computed states from a file. (PR #730)
  • Added Point as a new base class for all points, which include: Station, Marker, and PathPoints

Removed Classes

The following classes are no longer supported in OpenSim and are removed in OpenSim 4.0.

  • Muscle class ContDerivMuscle_Depredated.

MATLAB and Python interfaces

  • The SimbodyMatterSubsystem class--which provides operators related to the mass matrix, Jacobians, inverse dynamics, etc.--is now accessible in MATLAB and Python (PR #930).

MATLAB interface

  • The configureOpenSim.m function should no longer require administrator privileges for most users, and gives more verbose output to assist with troubleshooting.

Python interface

  • Improved error handling. Now, OpenSim's error messages show up as exceptions in Python.

Other Changes

  • There is now a formal CMake mechanism for using OpenSim in your own C++ project. See cmake/SampleCMakeLists.txt. (PR #187)
  • Substantial cleanup of the internal CMake scripts.
  • Lepton was upgraded to the latest version (PR #349)
  • Made Object::print a const member function (PR #191)
  • Improved the testOptimization/OptimizationExample to reduce the runtime (PR #416)
  • InverseKinematics tool outputs marker error .sto file if report error flag is true.
  • Marker location file output name in IK changed to reflect trial name for batch processing.
  • Created a method ScaleTool::run(), making it easier to run the Scale Tool programmatically in MATLAB or python.
  • Thelen2003Muscle, Millard2012EquilibriumMuscle, and Millard2012AccelerationMuscle now throw an exception if the force equilibrium calculation fails to converge (PR #1201).
  • Thelen2003Muscle and Millard2012EquilibriumMuscle no longer clamp excitations (i.e. controls) internally. If controls are out of bounds an Exception is thrown. Also, the min_control property now defaults to the minimum_activation. It is the responsibility of the controller (or solver) to provide controls that are within the valid ranges defined by the Actuators and that includes the specific bounds of Muscle models. (PR #1548)
  • The buildinfo.txt file, which contains the name of the compiler used to compile OpenSim and related information, is now named OpenSim_buildinfo.txt and may be installed in a different location.
  • macOS and Linux users should no longer need to set LD_LIBRARY_PATH or DYLD_LIBRARY_PATH to use OpenSim libraries.

Documentation

  • Improved Doxygen layout and fixed several bugs and warnings (various)
  • All mentions of SimTK/Simbody classes in OpenSim's Doxygen now provide links directly to SimTK/Simbody's doxygen.
  • Added a detailed README.md wtith build instructions, as well as guides to contributing and developing (CONTRIBUTING.md).
  • Included GIFs in Doxygen for several commonly used Joint types

STILL NEED TO ADD:

  • Additional changes to Model Component Interface, Iterator (any PRs labeled "New MCI")
  • PR #364
  • PR #370
  • PR #378