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https://github.com/pydy/pydy-tutorial-human-standing

PyDy tutorial materials for MASB 2014, PYCON 2014, and SciPy 2014/2015.
https://github.com/pydy/pydy-tutorial-human-standing

biomechanics dynamics engineering multibody-dynamics python simulation

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PyDy tutorial materials for MASB 2014, PYCON 2014, and SciPy 2014/2015.

Lists

README 

        
Introduction

============



This is the material for a tutorial on analyzing `multibody dynamics`_ with

scientific Python tools. It was first given as "Simulation and Control of

Biomechanical Systems with Python" at the `Midwest American Society of

Biomechanics Regional meeting

`_ on March 4th, 2014 in Akron,

Ohio. Modified versions have subsequently been given at PYCON2014, SCIPY2014,

SCIPY2015, and SCIPY 2016.



.. _multibody dynamics: http://en.wikipedia.org/wiki/Multibody_system



The tutorial covers these main topics:



- Symbolic derivation of equations of motion for multibody systems.

- Numerical simulation of the resulting system.

- 3D visualization of the motion of the system.

- Optimal feedback control for stabilization.



The attendees will be exposed to various functionality of these Python tools:



- Python_

- The SciPy Stack: SymPy_, NumPy_, SciPy_, matplotlib_, IPython_

- PyDy_



.. _Python: http://www.python.org

.. _SymPy: http://www.sympy.org

.. _NumPy: http://numpy.scipy.org

.. _SciPy: http://www.scipy.org/scipylib/index.html

.. _matplotlib: http://matplotlib.org

.. _IPython: http://www.ipython.org

.. _PyDy: http://www.pydy.org



The tutorial can be run locally or through the Binder service:



.. image:: https://mybinder.org/badge_logo.svg

   :target: https://mybinder.org/v2/gh/pydy/pydy-tutorial-human-standing/master



Videos

======



- PYCON 2014: https://youtu.be/IoMR-ESzqw8

- SCIPY 2014: https://youtu.be/lWbeuDwYVto, https://youtu.be/1-KqRvNX0po

- SCIPY 2015: https://youtu.be/mdo2NYtA-xY

- SCIPY 2016: https://youtu.be/r4piIKV4sDw



License

=======



All materials herein are licensed under `Create Commons Attribution 4.0`_.



.. _Create Commons Attribution 4.0: http://creativecommons.org/licenses/by/4.0/



Versions

========



A new version of the tutorial is typically created each time the tutorial is

given to incorporate feedback from the attendees and for software updates.

These versions can be downloaded from:



https://github.com/pydy/pydy-tutorial-human-standing/releases



Example Problem

===============



The tutorial will go through the PyDy workflow in small steps. At the end the

students should have a working 3-link 2D inverted pendulum model of a human

that can be used for balancing studies. The free body diagram of the model is

shown below:



.. image:: notebooks/figures/human_balance_diagram.png



Installation

============



Python Packages

---------------



To run these notebooks the `SciPy Stack`_ is required. To obtain the needed

packages, we are recommending users install the `Anaconda Scientific Python

Distribution`_ which contains most of the necessary software and eases cross

platform installation. You should install Anaconda to your home directory. The

installation directory can simply be deleted when the tutorial is over if you

no longer want the files.



.. _SciPy Stack: http://www.scipy.org/stackspec.html

.. _Anaconda Scientific Python Distribution: https://store.continuum.io/cshop/anaconda/



First, `download and install Anaconda `_ for

your operating system. After Anaconda is installed, update various packages to

the latest versions by issuing this command in a terminal::



   $ conda update numpy scipy sympy matplotlib notebook ipywidgets



Now install the latest PyDy with::



   $ conda install -c conda-forge pydy



MathJax

-------



**This is only required if you want to run the tutorial without internet

access.**



These notebooks make use of the MathJax_ javascript library to render and

display mathematics. By default IPython loads MathJax from the internet (i.e.

from a CDN), however, because of potentially questionable internet access at

the conference we recommend you install MathJax locally. To do so, type the

following in a terminal::



   $ conda install mathjax



.. _MathJax: http://www.mathjax.org/



Web Browser

-----------



If you want to see the 3D visualizations you must use a WebGL compliant

browser. Visit http://get.webgl.org/ to see if your current browser supports

WebGL. If not, you will need to upgrade or install another browser. Visit

http://caniuse.com/webgl to choose a suitable browser. We've only confirmed the

following:



**Linux**



Latest versions of Firefox and Chrome work.



**Mac OSX**



Latest version Firefox works.



**Windows**



Latest version of Chrome works and IE 11 works.



We know that some OS browser combinations do not work. See

https://github.com/pydy/pydy/issues/36 for more details.



Download the tutorial

=====================



Either download the latest zipped tutorial materials from:



https://github.com/pydy/pydy-tutorial-human-standing/archive/master.zip



Or download the specific release for your conference from:



https://github.com/pydy/pydy-tutorial-human-standing/releases



and then extract the zip file.



Use

===



From the terminal, navigate to the extracted tutorial directory, for example::



   $ cd /home/username/pydy-tutorial-human-standing



Check the environment

---------------------



To make sure your software environment is correctly setup, run the

`check_env.py` script in a terminal with::



   $ python check_env.py



If no errors are returned, then you've correctly installed the software and can

run the tutorial. If errors appear, then install or upgrade the software as

needed.



Open a terminal window in the ``notebooks`` directory and type::



   $ cd notebooks

   $ ipython notebook



Your web browser should open and you see a list of all the notebooks and can

click to open them and execute.



Notebooks

=========



These are the notebooks for the tutorial.



- [15 min] n00_python_intro.ipynb_

- [14 min] n01_dynamics_overview.ipynb_

- [ 4 min] n02_problem_introduction.ipynb_

- [39 min] n03_kinematics.ipynb_

- [18 min] n04_inertia.ipynb_

- [25 min] n05_kinetics.ipynb_

- [25 min] n06_equations_of_motion.ipynb_

- [32 min] n07_simulation.ipynb_

- [25 min] n08_visualization.ipynb_

- [28 min] n09_control.ipynb_



.. _n00_python_intro.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n00_python_intro.ipynb

.. _n01_dynamics_overview.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n01_dynamics_overview.ipynb

.. _n02_problem_introduction.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n02_problem_introduction.ipynb

.. _n03_kinematics.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n03_kinematics.ipynb

.. _n04_inertia.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n04_inertia.ipynb

.. _n05_kinetics.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n05_kinetics.ipynb

.. _n06_equations_of_motion.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n06_equations_of_motion.ipynb

.. _n07_simulation.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n07_simulation.ipynb

.. _n08_visualization.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n08_visualization.ipynb

.. _n09_control.ipynb: http://nbviewer.ipython.org/github/pydy/pydy-tutorial-human-standing/blob/master/notebooks/n09_control.ipynb