Table of contents

• Table of contents
• How to install
  • Anaconda (For Windows, Linux and Mac)
  • Download binaries (For MATLAB users on Windows, Linux and Mac)
  • Compiling (For Windows, Linux and Mac)
  • Dependencies
  • CMake
• How to use
  • The C++ API
  • Create an empty yet valid model
  • Read and write a bioMod file
  • Perform some analyses
  • MATLAB
  • Perform some analyses
  • Help
  • Python 3
  • Perform some analyses
• Model files
  • bioMod files
  • Header
    • version
    • gravity
    • variables / endvariables
  • Definition of the model
    • Segment
    • Marker
    • Imu
    • Loopconstraint
    • Actuators
  • Convert from OpenSim models
• How to contribute
• Graphical User Interface (GUI)
• Documentation
• Troubleshoots
  • Slow BIORBD
• Cite

BIORBD is a library to analyze biomechanical data. It provides several useful functions for the direct and inverse flow including rigid body (based on Feathestone equations implemented in RBDL) and muscle elements.

Biomechanical data are often analyzed using similar flow, that is inverse or direct. BIORBD implements these common analyses providing high-level and easy to use Python and MATLAB interfaces of an efficient C++ implementation.

So, without further ado, let's begin our investigation of BIORBD!

You can get the online version of the paper for BIORBD here:

Futhermore, anyone can play with bioptim with a working (but slightly limited in terms of graphics) MyBinder by clicking the following badge

How to install

There are two main ways to install BIORBD on your computer: installing the binaries from Anaconda (easiest, but limited to C++ and Python3) or compiling the source code yourself (more versatile and up to date; for C++, Python3 and MATLAB).

Anaconda (For Windows, Linux and Mac)

The easiest way to install BIORBD is to download the binaries from Anaconda (https://anaconda.org/) repositories (binaries are not available though for MATLAB). The project is hosted on the conda-forge channel (https://anaconda.org/conda-forge/biorbd).

After having installed properly an anaconda client [my suggestion would be Miniconda (https://conda.io/miniconda.html)] and loaded the desired environment to install BIORBD in, just type the following command: bash conda install -c conda-forge biorbd The binaries and includes of the core of BIORBD will be installed in bin and include folders of the environment respectively. Moreover, the Python3 binder will also be installed in the environment.

Please note that because of the way Ipopt is compiled on conda-forge, it was not possible to link it with biorbd. Therefore, the MODULE_STATIC_OPTIM was set to OFF for this particular OS.

The current building status for Anaconda release is as follow.

| License | Name | Downloads | Version | Platforms | | --- | --- | --- | --- | --- | | | | | | |

Download binaries (For MATLAB users on Windows, Linux and Mac)

The MATLAB users can download the binaries directly from the Release page of biorbd at this URL: https://github.com/pyomeca/biorbd/releases/latest.

Once the folder is download, you simply unzip it, add it to the MATLAB's path and enjoy biorbd!

Compiling (For Windows, Linux and Mac)

The main drawback with downloading the pre-compiled version from Anaconda is that this version may be out-of-date (even if I do my best to keep the release versions up-to-date). Moreover, since it is already compiled, it doesn't allow you to modify BIORBD if you need to. Therefore, a more versatile way to enjoy BIORBD is to compile it by yourself.

The building status for the current BIORBD branches is as follow

| Name | Status | | --- | --- | | master | | | Code coverage | | | DOI | |

Dependencies

BIORBD relies on several libraries (namely eigen ([http://eigen.tuxfamily.org]) or CasADi ([https://web.casadi.org/]), rbdl-casadi (https://github.com/pyomeca/rbdl-casadi), tinyxml2(https://github.com/leethomason/tinyxml2) and Ipopt (https://github.com/coin-or/Ipopt)) that one must install prior to compiling. Fortunately, all these dependencies are also hosted on the conda-forge channel of Anaconda or will automatically be compiled when building BIORBD. Therefore the following command will install everything you need to compile BIORBD: bash conda install -c conda-forge rbdl [ipopt] [pkgconfig] [cmake] [scipy] Please note: - tinyxml2 will be automatically downloaded and linked if the MODULE_VTP_FILES_READER is set to ON; - ipopt is optional, but is required for the Static optimization module; - pkgconfig and cmake are very useful tools that can prevents lot of headaches when compiling;

Additionnally, for the Python3 interface requires numpy (https://numpy.org/) and SWIG (http://www.swig.org/). Again, one can easily install these dependencies from Anaconda using the following command: bash conda install -c conda-forge numpy swig

Finally, the MATLAB interface (indeed) requires MATLAB to be installed.

If ones is interested in developping BIORBD, the googletest suite is required to test your modifications. Fortunately, the CMake should download and compile the test suite for you!

CMake

BIORBD comes with a CMake (https://cmake.org/) project. If you don't know how to use CMake, you will find many examples on Internet. The main variables to set are:

CMAKE_INSTALL_PREFIX Which is the path/to/install BIORBD in. If you compile the Python3 binder, a valid installation of Python with Numpy should be installed relatived to this path.

BUILD_SHARED_LIBS If you wan to build BIORBD in a shared TRUE or static FALSE library manner. Default is TRUE. Please note that due to the dependencies, on Windows BIORBD must be statically built.

CMAKE_BUILD_TYPE Which type of build you want. Options are Debug, RelWithDebInfo, MinSizeRel or Release. This is relevant only for the build done using the make command. Please note that you will experience a slow BIORBD library if you compile it without any optimization (i.e. Debug), especially for all functions that requires linear algebra.

MATH_LIBRARY_BACKEND Choose between the two linear algebra backends, either Eigen3 or Casadi. Default is Eigen3.

BUILD_EXAMPLE If you want (TRUE) or not (FALSE) to build the C++ example. Default is TRUE.

BUILD_TESTS If you want (ON) or not (OFF) to build the tests of the project. Please note that this will automatically download gtest (https://github.com/google/googletest). Default is OFF.

BUILD_DOC If you want (ON) or not (OFF) to build the documentation of the project. Default is OFF.

BINDER_C If you want (ON) or not (OFF) to build the low level C binder. Default is OFF. Please note that this binder is very light and will not contain most of BIORBD features.

BINDER_PYTHON3 If you want (ON) or not (OFF) to build the Python binder. Default is OFF.

SWIG_EXECUTABLE If BINDER_PYTHON3 is set to ON then this variable should point to the SWIG executable. This variable should be found automatically.

BINDER_MATLAB If you want (ON) or not (OFF) to build the MATLAB binder. Default is OFF. Pleaes note that BINDER_MATLAB can't be set to ON alonside to CasADi backend.

Matlab_ROOT_DIR If BINDER_MATLAB is set to ON then this variable should point to the root path of MATLAB directory. Please note that the MATLAB binder is based on MATLAB R2018a API and won't compile on earlier versions. This variable should be found automatically, except on Mac where the value should manually be set to the MATLAB in the App folder.

Matlab_biorbd_INSTALL_DIR If BINDER_MATLAB is set to ON then this variable should point to the path where you want to install BIORBD. Typically, this is {MY DOCUMENTS}/MATLAB. The default value is the toolbox folder of MATLAB. Please note that if you leave the default value, you will probably need to grant administrator rights to the installer. In all cases, after the installation, you will have to add the path to the MATLAB search path by typing the following command in the MATLAB's prompt (or to add it to the startup.m) addpath(genpath($Matlab_biorbd_INSTALL_DIR)), and replacing Matlab_biorbd_INSTALL_DIR by your own path.

MODULE_ACTUATORS If you want (ON) or not (OFF) to build with the actuators module. Default is ON. This allows to use exotic joint torques.

MODULE_KALMAN If you want (ON) or not (OFF) to build the Kalman filter module. Default is ON. The main reason to skip Kalman is that in Debug mode Eigen3 will perform this very slowly and CasADi will always perform this slowly.

MODULE_MUSCLES If you want (ON) or not (OFF) to build with the muscle module. Default is ON. This allows to read and interact with models that include muscles.

MODULE_STATIC_OPTIM If you want (ON) or not (OFF) to build the Static optimization module. Default is ON (if ipopt is found).

MODULE_VTP_FILES_READER If you want (ON) or not (OFF) to build with the vtp files reader module. Default is ON (if tinyxml2 is found). This allows to read mesh files produced by OpenSim.

SKIP_ASSERT If you want (ON) or not (OFF) to skip the asserts in the functions (e.g. checks for sizes). Default is OFF. Putting this to OFF reduces the risks of Segmentation Faults, it will however slow down the code when using Eigen3 backend.

SKIP_LONG_TESTS If you want (ON) or not (OFF) to skip the tests that are long to perform. Default is OFF. This is useful when debugging.

How to use

BIORBD provides as much as possible explicit names for the filter so one can intuitively find what he wants from the library. Still, this is a C++ library and it can be sometimes hard to find what you need. Due to the varity of functions implemented in the library, minimal examples are shown here. One is encourage to have a look at the example and test folders to get a better overview of the possibility of the API. For an in-depth detail of the API, the Doxygen documentation (to come) is the way to go.

The C++ API

The core code is written in C++, meaning that you can fully use BIORBD from C++. Moreover, the linear algebra is using the Eigen library which makes it fairly easy to perform further computation and analyses. The informations that follows is a basic guide that should allow you to perform everything you want to do.

Create an empty yet valid model

To create a new valid yet empty model, just call the biorbd::Model class without parameter. ```C++

include "biorbd.h"

int main() { biorbd::Model myModel; } ``` This model can thereafter be populated using the biorbd add methods. Even if this is not the prefered way of loading a model, one can have a look at the src/ModelReader.cpp in order to know what functions that must be called to populate the model manually.

Read and write a bioMod file

The prefered method to load a model is to read the in-house .bioMod format file. To do so, one must simply call the biorbd::Model constructur with a valid path to the model. Afterward, one can modify manually the model and write it back to a new file. ```C++

include "biorbd.h"

int main() { biorbd::Model myModel myModel("path/to/mymodel.bioMod"); // Do some changes... biorbd::Writer::writeModel(myModel, "path/to/newFile.bioMod"); return 0; } `` Please note that on Windows, the path must be/or\separated (and not only`), for obvious reasons.

Perform some analyses

BIORBD is made to work with the RBDL functions (the doc can be found here https://rbdl.bitbucket.io/). Therefore, every functions available in RBDL is also available on BIORBD. Additionnal are of course also made available, for example the whole muscle module.

The most obvious and probably the most used function is the forward kinematics, where one knows the configuration of the body and is interested in the resulting position of skin markers. The following code performs that task. ```C++

include "biorbd.h"

int main() { // Load the model biorbd::Model model("path/to/model.bioMod");

// Prepare the model
biorbd::rigidbody::GeneralizedCoordinates Q(model); 
Q.setOnes()/10; // Set the model position

// Perform forward kinematics
std::vector<biorbd::rigidbody::NodeBone> markers(model.markers(Q));

// Print the results
for (auto marker : markers)
    std::cout << marker.name() << " is at the coordinates: " << marker.transpose() << std::endl;
return 0;

} ```

Another common analysis to perform is to compute the effect of the muscles on the acceleration of the model. Assuming that the model that is loaded has muscles, the following code perform this task. ```C++

include "biorbd.h"

int main() { // Load the model biorbd::Model model("path/to/model.bioMod");

// Prepare the model
biorbd::rigidbody::GeneralizedCoordinates Q(model), Qdot(model); // position, velocity
Q.setOnes()/10; // Set the model position
Qdot.setOnes()/10; // Set the model velocity
// Muscles activations
std::vector<std::shared_ptr<biorbd::muscles::StateDynamics>> states(model.nbMuscleTotal());
for (auto& state : states){
    state = std::make_shared<biorbd::muscles::StateDynamics>();
    state->setActivation(0.5); // Set the muscle activation
}

// Compute the joint torques based on muscle
biorbd::rigidbody::GeneralizedTorque muscleTorque(
            model.muscularJointTorque(states, true, &Q, &Qdot));

// Compute the acceleration of the model due to these torques
biorbd::rigidbody::GeneralizedCoordinates Qddot(model);
RigidBodyDynamics::ForwardDynamics(model, Q, Qdot, muscleTorque, Qddot);

// Print the results
std::cout << " The joints accelerations are: " << Qddot.transpose() << std::endl;
return 0;

} ```

There are many other analyses and filters that are available. Please refer to the BIORBD and RBDL Docs to see what is available.

MATLAB

MATLAB (https://www.mathworks.com/) is a prototyping langage largely used in industry and fairly used by the biomechanical scientific community. Despite the existence of Octave as an open-source and very similar language or the growing popularity of Python as a free and open-source alternative, MATLAB remains an important player as a programming languages. Therefore BIORBD comes with a binder for MATLAB (that can theoretically used with Octave as well with some minor changes to the CMakeLists.txt file).

Most of the functions available in C++ are also available in MATLAB. Still, they were manually binded, therefore it may happen that some important one (for you) are not there. If so, do not hesitate to open an issue on GitHub to required the add of that particular function. The philosophy behind the MATLAB binder is that you open a particular model and a reference to that model is gave back to you. Thereafter, the functions can be called, assuming the pass back that model reference. That implies, however, that ones must himself deallocate the memory of the model when it is no more needed. Failing to do so results in an certain memory leak.

Perform some analyses

Please find here the same tasks previously described for the C++ interface done in the MATLAB interface. Notice that the MATLAB interface takes advantage of the matrix nature of MATLAB and therefore can usually perform the analyses on multiple frames at once.

Forward kinematics can be performed as follow ```MATLAB nFrames = 10; % Set the number of frames to simulate

% Load the model model = biorbd('new', 'path/to/model.bioMod');

% Prepare the model Q = ones(biorbd('nQ', model), nFrames)/10; % Set the model position

% Perform the forward kinematics markers = biorbd('markers', model, Q);

% Print the results disp(markers);

% Deallocate the model biorbd('delete', model); ```

The joint accelerations from muscle activations can be performed as follow ```MATLAB nFrames = 10; % Set the number of frames to simulate

% Load the model model = biorbd('new', 'path/to/model.bioMod');

% Prepare the model Q = ones(biorbd('nQ', model), nFrames)/10; % Set the model position Qdot = ones(biorbd('nQdot', model), nFrames)/10; % Set the model velocity activations = ones(biorbd('nMuscles', model), nFrames)/2; % Set muscles activations

% Compute the joint torques based on muscle jointTorque = biorbd('jointTorqueFromActivation', model, activations, Q, Qdot);

% Compute the acceleration of the model due to these torques Qddot = biorbd('forwardDynamics', model, Q, Qdot, jointTorque);

% Print the results disp(Qddot);

% Deallocate the model biorbd('delete', model); ```

Help

One can print all the available functions by type the help command MATLAB biorbd('help') Please note that it seems that on Windows, the command returns nothing. One must therefore look in the source code (biorbd/binding/matlab/Matlab_help.h) what should the command have returned.

Python 3

Python (https://www.python.org/) is a scripting language that has taken more and more importance over the past years. So much that now it is one of the preferred language of the scientific community. Its simplicity yet its large power to perform a large variety of tasks makes it a certainty that its popularity won't decrease for the next years.

To interface the C++ code with Python, SWIG is a great tool. It creates very rapidly an interface in the target language with minimal code to write. However, the resulting code in the target language can be far from being easy to use. In effect, it gives a mixed-API not far from the original C++ language, which may not comply to best practices of the target language. When this is useful to rapidly create an interface, it sometime lacks of user-friendliness and expose the user to the possibility of the C++ such as segmentation fault (unlike the MATLAB API which won't suffer from this devil problem).

BIORBD interfaces the C++ code using SWIG. While it has some inherent limit as discussed previously, it has the great advantage of providing almost for free the complete API. Because of that, much more of the C++ API is interfaced in Python than the MATLAB one. Again, if for some reason, part of the code which is not accessible yet is important for you, don't hesitate to open an issue asking for that particular feature!

Perform some analyses

Please find here the same tasks previously described for the C++ interface done in the Python3 interface. Please note that the interface usually takes advantage of the numpy arrays in order to interact with the user while a vector is needed.

Forward kinematics can be performed as follow ```Python import numpy as np import biorbd

Load the model

model = biorbd.Model('path/to/model.bioMod')

Prepare the model

Q = np.ones(model.nbQ())/10 # Set the model position

Perform the forward kinematics

markers = model.markers(Q)

Print the results

for marker in markers: print(marker.to_array())

```

The joint accelerations from muscle activations can be performed as follow ```Python import numpy as np import biorbd

Load the model

model = biorbd.Model('path/to/model.bioMod')

Prepare the model

Q = np.ones(model.nbQ())/10 # Set the model position Qdot = np.ones(model.nbQ())/10 # Set the model velocity states = model.stateSet() for state in states: state.setActivation(0.5) # Set muscles activations

Compute the joint torques based on muscle

joint_torque = model.muscularJointTorque(states, Q, Qdot)

Compute the acceleration of the model due to these torques

Qddot = model.ForwardDynamics(Q, Qdot, joint_torque)

Print the results

print(Qddot.to_array())

```

Model files

bioMod files

The preferred method to load a model is by using a .bioMod file. This type of file is an in-house language that describes the segments of the model, their interactions and additionnal elements attached to them. The following section describe the structure of the file and all the tags that exists so far.

Comments can be added to the file in a C-style way, meaning that everything a on line following a // will be considered as a comment and everything between /* and */ will also be ignored.

Please note that the bioMod is not case dependent, so Versionand version are for instance fully equivalent. The bioMod reader also ignore the tabulation, which is therefore only aesthetic.

When a tag waits for multiple values, they must be separate by a space, a tabulation or a return of line. Also, anytime a tag waits for a value, it is possible to use simple equations (assuming no spaces are used) and/or variables. For example, the following snippet is a valid way to set the gravity parameter to $(0, 0, -9.81)$. c variables $my_useless_variable 0 endvariables gravity 2*(1-1) -2*$my_useless_variable -9.81

Header

version

The very first tag that must appear at the first line in file is the version of the file. The current version of the .bioMod files is $4$. Please note that most of the version are backward compatible, unless specified. This tag waits for $1$ value. c version 4 From that point, the order of the tags is not important, header can even be at the end of the file. For simplicity though we suggest to put everything related to the header at the top of the file.

gravity

The gravity tag is used to reorient and/or change the magnitude of the gravity. The default value is $(0, 0, -9.81)$. This tag waits for $3$ values. c // Restate the default value gravity 0 0 -9.81

variables / endvariables

The variables / endvariables tag pair allows to declare variables that can be used within the file. This allows for example to template the bioMod file by only changing the values in the variables. Please note that contrary to the rest of the file, the actual variables are case dependent.

The \$ sign is mandatory and later in the file, everything with that sign followed by the same name will be converted to the values specified in the tag. c // Restate the default value variables $my_first_variable_is_an_int 10 $my_second_variable_is_a_double 10.1 $myThirdVariableIsCamelCase 1 $myLastVariableIsPi pi endvariables As you may have noticed, the constant PI is defined as $3.141592653589793$.

Definition of the model

A BIORBD model consists of a chain of segment, linked by joints with up to six DoF (3 translations, 3 rotations). It is imperative when attaching something to a segment of the model that particular segment must have been previously defined. For instance, if the thorax is attached to the pelvis, then the latter must be defined before the former in the file.

Segment

The segment xxx / endsegmenttag pair is the core of a bioMod file. It describes a segment of the model with the name xxx, that is most of the time a bone of the skeleton. For internal reasons, the name cannot be root. The xxx must be present and consists of $1$ string. The segment is composed of multiple subtags, described here.

```c segment default_segment parent ROOT rtinmatrix 0 rt 0 0 0 xyz 0 0 0 translation xyz rotations xyz com 0 0 0 inertia 1 0 0 0 1 0 0 0 1 endsegment

segment secondsegment parent defaultsegment endsegment ```

parent <!-- omit from toc -->

The parent tag is the name of the segment that particular segment is attached to. If no segment parent is provided, it is considered to be attached to the environment. The parent must be defined earlier in the file and is case dependent. This tag is waits for $1$ string.

rt <!-- omit from toc -->

The homogeneous matrix of transformation (rototranslation) of the current segment relative to its parent. If rtinmatrix is defined to 1, rt waits for a 4 by 4 matrix (the 3 x 3 matrix of rotation and the 4th column being the translation and the last row being 0 0 0 1); if it is defined to 0 it waits for the 3 rotations, the rotation sequence and the translation. The default value is the identity matrix.

rtinmatrix <!-- omit from toc -->

The tag that defines if the rt is in matrix or not. If the version of the file is higher or equal than $3$, the default value is false ($0$), otherwise, it true ($1$).

translations <!-- omit from toc -->

The translations tag specifies the number of degrees-of-freedom in translation and their order. The possible values are x, y and/or z combined whatever fits the model. Please note that the vector of generalized coordinate will comply the the order wrote in this tag. If no translations are provided, then the segment has no translation relative to its parent. This tag waits for $1$ string.

rotations <!-- omit from toc -->

The rotations tag specifies the number of degrees-of-freedom in rotation and their order. The possible values are x, y and/or z combined whatever fits the model. Please note that the vector of generalized coordinate will comply the the order wrote in this tag. If no rotations are provided, then the segment has no rotation relative to its parent. This tag waits for $1$ string.

mass <!-- omit from toc -->

The mass tag specifies the mass of the segment in kilogram. This tag waits for $1$ value. The default value is $0.00001$. Please note that a pure $0$ can create a singularity.

com <!-- omit from toc -->

The $3$ values position of the center of mass relative to the local reference of the segment. The default values are 0 0 0.

inertia <!-- omit from toc -->

The inertia tag allows to specify the matrix of inertia of the segment ( computed with respect to the center of mass of the segment ). It waits for $9$ values. The default values are the identity matrix

foreceplate or externalforceindex <!-- omit from toc -->

This tag is deprecated and should therefore not be used.

meshfile or ply <!-- omit from toc -->

The path of the meshing .bioBone, .ply, .stl file respectively. It can be relative to the current running folder or absolute (relative being preferred) and UNIX or Windows formatted (/ vs \\, UNIX being preferred).

mesh <!-- omit from toc -->

If the mesh is not written in a file, it can be written directly in the segment. If so, the mesh tag stands for the vertex. Therefore, there are as many mesh tags as vertex. It waits for $3$ values being the position relative to reference of the segment.

meshcolor <!-- omit from toc -->

The color of the segment mesh given in RGV values [0, 1]. Default is 0.89, 0.855, 0.788, that is bone color-ish.

meshscale <!-- omit from toc -->

The scaling to apply to the provided mesh, given in X Y Z values. Default is 1 1 1.

meshrt <!-- omit from toc -->

The RT to apply to the provided mesh, given in RX RY RZ seq TX TY TZ as for RT. The default value is 0 0 0 xyz 0 0 0.

patch <!-- omit from toc -->

The patches to define the orientation of the patches of the mesh. It waits for $3$ values being the $0-based$ of the index of the vertex defined by the mesh.

Marker

The marker with a unique name attached to a body segment.

c marker my_marker parent segment_name position 0 0 0 technical 1 anatomical 0 endmarker

parent <!-- omit from toc -->

The parent tag is the name of the segment that particular segment is attached to. The parent must be defined earlier in the file and is case dependent. This tag is waits for $1$ string.

position <!-- omit from toc -->

The position of the marker in the local reference frame of the segment.

technical <!-- omit from toc -->

If the marker will be taged as technical (will be returned when asking technical markers). Default value is true ($1$).

anatomical <!-- omit from toc -->

If the marker will be taged as anatomical (will be returned when asking anatomical markers). Default value is false ($0$).

axestoremove <!-- omit from toc -->

It is possible to project the marker onto some axes, if so, write the name of the axes to project onto here. Waits for the axes in a string.

Imu

Same as a marker, but for inertial measurement unit. c imu my_imu parent segment_parent rtinmatrix 0 rt 0 0 0 xyz 0 0 0 technical 1 anatomical 0 endimu

parent <!-- omit from toc -->

The parent tag is the name of the segment that particular segment is attached to. The parent must be defined earlier in the file and is case dependent. This tag is waits for $1$ string.

rt <!-- omit from toc -->

The homogeneous matrix of transformation (rototranslation) of the current segment relative to its parent. If rtinmatrix is defined to 1, rt waits for a 4 by 4 matrix (the 3 x 3 matrix of rotation and the 4th column being the translation and the last row being 0 0 0 1); if it is defined to 0 it waits for the 3 rotations, the rotation sequence and the translation. The default value is the identity matrix.

rtinmatrix <!-- omit from toc -->

The tag that defines if the rt is in matrix or not. If the version of the file is higher or equal than $3$, the default value is false ($0$), otherwise, it true ($1$).

technical <!-- omit from toc -->

If the marker will be taged as technical (will be returned when asking technical markers). Default value is true ($1$).

anatomical <!-- omit from toc -->

If the marker will be taged as anatomical (will be returned when asking anatomical markers). Default value is false ($0$).

Contact <!-- omit from toc -->

The position of a non acceleration point while computing the forward dynamics. c contact my_contact parent parent_segment position 0 0 0 axis xyz endcontact

parent <!-- omit from toc -->

The parent tag is the name of the segment that particular segment is attached to. The parent must be defined earlier in the file and is case dependent. This tag is waits for $1$ string.

position <!-- omit from toc -->

The position of the marker in the local reference frame of the segment.

axis <!-- omit from toc -->

The name of the axis that the contact acts on. If the version of the file is $1$, this tag has no effect.

normal <!-- omit from toc -->

The normal that the contact acts on. This tags waits for $3$ values with a norm $1$. If the version of the file is not $1$, this tag has no effect. To get the x, y and z axes, one must therefore define three separate contacts.

acceleration <!-- omit from toc -->

The constant acceleration of the contact point. The default values are 0, 0, 0.

Loopconstraint

Actuators

The Actuators specifies the different parameters used to express the torque generated by a particular movement at a joint. These different parameters were described by M. Jackson (The mechanics of the table contact phase of gymnastics vaulting, 2019).

type <!-- omit from toc -->

Different types of actuator can be defined with the type tag : Constant, Linear, Gauss3p, Gauss6p, Sigmoidgauss3p. In function of the type of actuator the parameters are different.

```c actuator default_segment type Gauss3p dof RotX direction positive Tmax 220.3831 T0 157.4165 wmax 475.0000 wc 190.0000 amin 0.9900 wr 40.0000 w1 -90.0000 r 56.4021 qopt 25.6939 endactuator

```

dof (Constant, Linear, Gauss3p, Gauss6p, Sigmoidgauss3p) <!-- omit from toc -->

The dof tag defines the degree of fredoom of the segment. It can be a rotation (Rot) or a translation (Trans) on one of the 3 axis (x, y, z). This argument is not required.

direction (Constant, Linear, Gauss3p, Gauss6p, Sigmoidgauss3p) <!-- omit from toc -->

The direction of the torque can be positive or negative. This argument is not required.

Tmax (Constant, Gauss3p, Gauss6p) <!-- omit from toc -->

Tmax is the maximum eccentric torque.

T0 (Linear, Gauss3p, Gauss6p) <!-- omit from toc -->

The tag T0 defines the maximum concentric torque.

wmax (Gauss3p, Gauss6p) <!-- omit from toc -->

The values of wmax is the maximum angular velocity above which torque cannot be produced.

wc (Gauss3p, Gauss6p) <!-- omit from toc -->

The wc tag specifies the angular velocity of the vertical asymptote of the concentric hyperbola based of the relation between tetanic torque and contractile component angular velocity.

amin (Gauss3p, Gauss6p) <!-- omit from toc -->

The amin tag allows to specify the plateau low activation level (values between 0.5 and 0.99) based of the differential activation-velocity relationship.

wr (Gauss3p, Gauss6p) <!-- omit from toc -->

The tag wr is the angular velocity range over which the ramp occurs based of the differential activation-velocity relationship.

w1 (Gauss3p, Gauss6p) <!-- omit from toc -->

w1 represents the angular velocity of the midpoint between the maximum and the low plateau activation level based of the differential activation-velocity relationship.

qopt (Gauss3p, Gauss6p, Sigmoidguass3p) <!-- omit from toc -->

The qopt tag allows to specify the optimum angle for torque production. This argument is required, the default value is 0.

r (Gauss3p, Gauss6p, Sigmoidguass3p) <!-- omit from toc -->

The tag r represented the width of the curve based of the torque-angle relationship. This argument is required, the default value is 0.

facteur (Gauss6p) <!-- omit from toc -->

...

r2 (Gauss6p) <!-- omit from toc -->

...

qopt2 (Gauss6p) <!-- omit from toc -->

...

theta (Sigmoidgauss3p) <!-- omit from toc -->

...

lambda(Sigmoidgauss3p) <!-- omit from toc -->

...

offset (Sigmoidgauss3p) <!-- omit from toc -->

...

Convert from OpenSim models

For users who have well-established models in OpenSim and wish to convert them to a .bioMod, there's a handy tool called Osimtobiomod. This package facilitates the conversion process, ensuring that OpenSim models can be seamlessly integrated into our ecosystem.

To get started with the Osimtobiomod package, please refer to its documentation and source code available at Osimtobiomod GitHub Repository.

Let us know if you'd like any further modifications!

How to contribute

You are very welcome to contribute to the project! There are to main ways to contribute.

The first way is to actually code new features for BIORBD. The easiest way to do so is to fork the project, make the modifications and then open a pull request to the main project. Don't forget to add your name to the contributor in the documentation of the page if you do so!

The second way is to open issues to report bugs or to ask for new features. I am trying to be as reactive as possible, so don't hesitate to do so!

Graphical User Interface (GUI)

For now, there is no GUI for the C++ interface and the MATLAB one is so poor I decided not to release it. However, there is a Python interface that worths to have a look at. Installation procedure and documentation can be found at the GitHub repository (https://github.com/pyomeca/biorbd-viz).

Documentation

The documentation is automatically generated using Doxygen (http://www.doxygen.org/). You can compile it yourself if you want (by setting BUILD_DOC to ON). Otherwise, you can access a copy of it that I try to keep up-to-date in the Documentation project of pyomeca (https://pyomeca.github.io/Documentation/) by selecting biorbd.

Troubleshoots

Despite my efforts to make a bug-free library, BIORBD may fails sometimes. If it does, please refer to the section below to know what to do. I will fill this section with the issue over time.

Slow BIORBD

If you experience a slow BIORBD, you are probably using a non optimized version, that is compiled with debug level. Please use at least RelWithDebInfo level of optimization while compiling BIORBD.

If you actually are using a released level of optimization, you may actually experiencing a bug. You are therefore welcomed to provide me with a minimal example of your slow code and I'll see how to improve the speed!

Cite

If you use BIORBD, we would be grateful if you could cite it as follows:

```

@article{michaudBiorbd2021, title = {Biorbd: {{A C}}++, {{Python}} and {{MATLAB}} Library to Analyze and Simulate the Human Body Biomechanics}, shorttitle = {Biorbd}, author = {Michaud, Benjamin and Begon, Mickaël}, date = {2021-01-19}, journaltitle = {Journal of Open Source Software}, volume = {6}, pages = {2562}, issn = {2475-9066}, doi = {10.21105/joss.02562}, url = {https://joss.theoj.org/papers/10.21105/joss.02562}, urldate = {2021-01-19}, abstract = {Michaud et al., (2021). biorbd: A C++, Python and MATLAB library to analyze and simulate the human body biomechanics. Journal of Open Source Software, 6(57), 2562, https://doi.org/10.21105/joss.02562}, langid = {english}, number = {57} } ```