added online documentation (github.io, readthedocs), lots of fixes, L…

…ie group methods extended, fixes for openAI interface, CoordinateSpringDamperExt, OpenVR, MacOS fixes, see Issues and Bugs in theDoc.pdf

README.rst

@@ -1,4 +1,5 @@
-|Documentation GithubIO| |PyPI version exudyn| |PyPI pyversions| |PyPI download month|
+|RTD documentation| |PyPI version exudyn| |PyPI pyversions| |PyPI download month| |Github release date| 
+|Github issues| |Github stars| |Github commits| |Github last commit|
 
 .. |PyPI version exudyn| image:: https://badge.fury.io/py/exudyn.svg
    :target: https://pypi.python.org/pypi/exudyn/
@@ -9,9 +10,22 @@
 .. |PyPI download month| image:: https://img.shields.io/pypi/dm/exudyn.svg
    :target: https://pypi.python.org/pypi/exudyn/
 
+.. |RTD documentation| image:: https://readthedocs.org/projects/exudyn/badge/?version=latest
+   :target: https://exudyn.readthedocs.io/en/latest/?badge=latest
 
+.. |Github issues| image:: https://img.shields.io/github/issues-raw/jgerstmayr/exudyn
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github stars| image:: https://img.shields.io/github/stars/jgerstmayr/exudyn?style=plastic
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github release date| image:: https://img.shields.io/github/release-date/jgerstmayr/exudyn?label=release
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github commits| image:: https://img.shields.io/github/commits-since/jgerstmayr/exudyn/v1.0.6
+   :target: https://jgerstmayr.github.io/EXUDYN/
 
-.. |Documentation GithubIO| image:: https://img.shields.io/website-up-down-green-red/https/jgerstmayr.github.io/EXUDYN.svg
+.. |Github last commit| image:: https://img.shields.io/github/last-commit/jgerstmayr/exudyn
    :target: https://jgerstmayr.github.io/EXUDYN/
 
 
@@ -23,12 +37,10 @@ Exudyn
 
 **A flexible multibody dynamics systems simulation code with Python and C++**
 
-Exudyn version = 1.5.118.dev1 (Fitzgerald)
+Exudyn version = 1.6.0 (Gillespie)
 
 +  **University of Innsbruck**, Department of Mechatronics, Innsbruck, Austria
 
-Exudyn 1.5 is out! It includes now Python 3.7/8 - 3.10 wheels for MacOS (since 1.5.11.dev1 also showing tkinter dialogs!), linux and windows. See theDoc.pdf chapter **Issues and Bugs** for changes!
-
 If you like using Exudyn, please add a *star* on github and follow us on 
 `Twitter @RExudyn <https://twitter.com/RExudyn>`_ !
 
@@ -59,9 +71,7 @@ If you like using Exudyn, please add a *star* on github and follow us on
 
 A paper on Exudyn has been presented at the `6th Joint International Conference on Multibody System Dynamics <http://imsdacmd2020.iitd.ac.in>`_ and submitted to the proceedings: J. Gerstmayr, Exudyn - A C++ based Python package for flexible multibody systems, Proceedings of The 6th Joint International Conference on Multibody System Dynamics and the 10th Asian Conference on Multibody System Dynamics 2020, New Delhi, India, 2022. `PDF <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/publications/GerstmayrIMSD2022.pdf>`_
 
-This README document is a small part of the complete documentation found as PDF document in docs/theDoc/theDoc.pdf.
-It is auto-generated from .tex files (sorry for some conversion errors!). 
-Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_ !
+Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_! There may also be some conversion errors in the auto-generated html pages.
 
 For license, see LICENSE.txt in the root github folder on github!
 

docs/RST/AdvancedTopics.rst

@@ -14,6 +14,17 @@ Camera following objects and interacting with model view
 --------------------------------------------------------
 
 For some models, it may be advantageous to track the translation and/or rotation of certain bodies, e.g., for cars, (wheeled) robots or bicycles. 
+Since Exudyn 1.4.18 you can attach view to a marker, using the visualization setting
+
+.. code-block:: python
+
+  SC.visualizationSettings.interactive.trackMarker = nMarker
+
+
+in which \ ``nMarker``\  represents the desired marker number to follow.
+See also related options in \ ``SC.visualizationSettings.interactive``\  in Section :ref:`sec-vsettingsinteractive`\ .
+
+The following paragraph represents a slower, slightly outdated approach, which may be interesting for advanced usage of object tracking.
 To do so, the current render state (\ ``SC.GetRenderState()``\ , \ ``SC.SetRenderState(...)``\ ) can be obtained and modified, in order to always follow a certain position.
 As this needs to be done during redraw of every frame, it is conveniently done in a graphicsUserFunction, e.g., within the ground body. This is shown in the following example, in which \ ``mbs.variables['nTrackNode']``\  is a node number to be tracked:
 
@@ -37,6 +48,7 @@ As this needs to be done during redraw of every frame, it is conveniently done i
   #.... further code for simulation here
 
 
+NOTE that this approach is slower and it may lead to a (usually silient) crash after closing the renderer, as the renderer thread is somehow coupled to Python which is prohibited from Python side.
 
 .. _sec-overview-advanced-contact:
 
@@ -177,7 +189,7 @@ To show the interoperability with julia, test the following example (similar to
   """
 
 
-We can access Python variables from julia via \ ``py"..."``\  to read out, e.g., \tetttmbs:
+We can access Python variables from julia via \ ``py"..."``\  to read out, e.g., \ ``mbs``\ :
 
 .. code-block:: 
 

docs/RST/Exudyn.rst

@@ -1,4 +1,5 @@
-|PyPI version exudyn| |PyPI pyversions| |PyPI download month|
+|RTD documentation| |PyPI version exudyn| |PyPI pyversions| |PyPI download month| |Github release date| 
+|Github issues| |Github stars| |Github commits| |Github last commit|
 
 .. |PyPI version exudyn| image:: https://badge.fury.io/py/exudyn.svg
    :target: https://pypi.python.org/pypi/exudyn/
@@ -9,6 +10,24 @@
 .. |PyPI download month| image:: https://img.shields.io/pypi/dm/exudyn.svg
    :target: https://pypi.python.org/pypi/exudyn/
 
+.. |RTD documentation| image:: https://readthedocs.org/projects/exudyn/badge/?version=latest
+   :target: https://exudyn.readthedocs.io/en/latest/?badge=latest
+
+.. |Github issues| image:: https://img.shields.io/github/issues-raw/jgerstmayr/exudyn
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github stars| image:: https://img.shields.io/github/stars/jgerstmayr/exudyn?style=plastic
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github release date| image:: https://img.shields.io/github/release-date/jgerstmayr/exudyn?label=release
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github commits| image:: https://img.shields.io/github/commits-since/jgerstmayr/exudyn/v1.0.6
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
+.. |Github last commit| image:: https://img.shields.io/github/last-commit/jgerstmayr/exudyn
+   :target: https://jgerstmayr.github.io/EXUDYN/
+
 
 
 ******
@@ -18,12 +37,10 @@ Exudyn
 
 **A flexible multibody dynamics systems simulation code with Python and C++**
 
-Exudyn version = 1.5.118.dev1 (Fitzgerald)
+Exudyn version = 1.6.0 (Gillespie)
 
 +  **University of Innsbruck**, Department of Mechatronics, Innsbruck, Austria
 
-Exudyn 1.5 is out! It includes now Python 3.7/8 - 3.10 wheels for MacOS (since 1.5.11.dev1 also showing tkinter dialogs!), linux and windows. See theDoc.pdf chapter **Issues and Bugs** for changes!
-
 If you like using Exudyn, please add a *star* on github and follow us on 
 `Twitter @RExudyn <https://twitter.com/RExudyn>`_ !
 
@@ -54,9 +71,7 @@ If you like using Exudyn, please add a *star* on github and follow us on
 
 A paper on Exudyn has been presented at the `6th Joint International Conference on Multibody System Dynamics <http://imsdacmd2020.iitd.ac.in>`_ and submitted to the proceedings: J. Gerstmayr, Exudyn - A C++ based Python package for flexible multibody systems, Proceedings of The 6th Joint International Conference on Multibody System Dynamics and the 10th Asian Conference on Multibody System Dynamics 2020, New Delhi, India, 2022. `PDF <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/publications/GerstmayrIMSD2022.pdf>`_
 
-This README document is a small part of the complete documentation found as PDF document in docs/theDoc/theDoc.pdf.
-It is auto-generated from .tex files (sorry for some conversion errors!). 
-Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_ !
+Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_! There may also be some conversion errors in the auto-generated html pages.
 
 For license, see LICENSE.txt in the root github folder on github!
 

docs/RST/InstallationAndGettingStarted.rst

@@ -8,7 +8,12 @@ Installation and Getting Started
 
 Exudyn is hosted on `GitHub <https://github.com>`_ :
 
-+  web: `https://github.com/jgerstmayr/EXUDYN <https://github.com/jgerstmayr/EXUDYN>`_
++  `https://github.com/jgerstmayr/EXUDYN <https://github.com/jgerstmayr/EXUDYN>`_
+
+Online documentation is available at:
+
++  `https://jgerstmayr.github.io/EXUDYN <https://jgerstmayr.github.io/EXUDYN>`_
++  `https://exudyn.readthedocs.io <https://exudyn.readthedocs.io>`_
 
 For any comments, requests, issues, bug reports, send an email to: 
 

docs/RST/items/MarkerSuperElementRigid.rst

@@ -26,6 +26,8 @@ The item \ **MarkerSuperElementRigid**\  with type = 'SuperElementRigid' has the
   | a list of \ :math:`n_m`\  weighting factors per node to compute the final local position and orientation; these factors could be based on surface integrals of the constrained mesh faces
 * | **useAlternativeApproach** [type = Bool, default = True]:
   | this flag switches between two versions for the computation of the rotation and angular velocity of the marker; alternative approach uses skew symmetric matrix of reference position; follows the inertia concept
+* | **rotationsExponentialMap** [type = Index, default = 2]:
+  | Experimental flag (2 is the correct value and will be used in future, removing this flag): This value switches different behavior for computation of rotations and angular velocities: 0 uses linearized rotations and angular velocities, 1 uses the exponential map for rotations but linear angular velocities, 2 uses the exponential map for rotations and the according tangent map for angular velocities
 * | **visualization** [type = VMarkerSuperElementRigid]:
   | parameters for visualization of item
 

docs/RST/pythonUtilities/processing.rst

@@ -86,7 +86,7 @@ Function: ParameterVariation
 
 Relevant Examples (Ex) and TestModels (TM) with weblink to github:
 
-    \ `dispyParameterVariationExample.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/Examples/dispyParameterVariationExample.py>`_\  (Ex), \ `dispyParameterVariationExampleAlt.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/Examples/dispyParameterVariationExampleAlt.py>`_\  (Ex), \ `parameterVariationExample.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/Examples/parameterVariationExample.py>`_\  (Ex), \ `geneticOptimizationTest.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/TestModels/geneticOptimizationTest.py>`_\  (TM)
+    \ `dispyParameterVariationExample.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/Examples/dispyParameterVariationExample.py>`_\  (Ex), \ `parameterVariationExample.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/Examples/parameterVariationExample.py>`_\  (Ex), \ `geneticOptimizationTest.py <https://github.com/jgerstmayr/EXUDYN/blob/master/main/pythonDev/TestModels/geneticOptimizationTest.py>`_\  (TM)
 
 
 ----

docs/theDoc/bibliographyDoc.bib

@@ -1,7 +1,8 @@
-@manual{EXUDYNgit,
-annote = {$\backslash$url{\{}https://github.com/jgerstmayr/EXUDYN{\}}},
+@misc{EXUDYNgit,
 author = {Gerstmayr, Johannes},
-title = {{Exudyn github repository}}
+howpublished = {\url{https://github.com/jgerstmayr/EXUDYN} (accessed on March 8, 2023)},
+title = {{Exudyn github repository}},
+year = {2023},
 }
 
 @article{Newmark1959,
@@ -586,7 +587,6 @@ @article{Holzinger2021
 volume = {53},
 number = {4},
 year = {2021},
-pages={(online)}
 }
 
 @article{ZwoelferGerstmayr2021,
@@ -610,19 +610,19 @@ @inproceedings{ManzlGerstmayr2021
 @misc{2022_Gerstmayr_theDoc,
   author = {Gerstmayr, Johannes},
   title = {{Exudyn -- Flexible Multibody Dynamics Systems with Python and C++}},
-  year = {2022},
+  year = {2023},
   publisher = {GitHub},
   journal = {GitHub repository},
-  howpublished = {\url{https://github.com/jgerstmayr/EXUDYN} (accessed on April 29, 2022)},
+  howpublished = {\url{https://github.com/jgerstmayr/EXUDYN} (accessed on March 8, 2023)},
 }
 
 
 @misc{2022_ExudynYoutube,
   author = {Gerstmayr, Johannes},
   title = {{Exudyn -- Youtube channel}},
-  year = {2022},
+  year = {2023},
   publisher = {Youtube},
-  howpublished = {\url{https://www.youtube.com/playlist?list=PLZduTa9mdcmOh5KVUqatD9GzVg_jtl6fx} (accessed on April 29, 2022)},
+  howpublished = {\url{https://www.youtube.com/playlist?list=PLZduTa9mdcmOh5KVUqatD9GzVg_jtl6fx} (accessed on March 8, 2023)},
 }
 
 @inproceedings{GerstmayrExudyn2022,

docs/theDoc/buildDate.tex

@@ -1 +1 @@
-build date and time=2023-02-28  16:38
+build date and time=2023-03-08  16:59

docs/theDoc/gettingStarted.tex

@@ -2,8 +2,6 @@
 \onlyRST{
 +  **University of Innsbruck**, Department of Mechatronics, Innsbruck, Austria
 
-Exudyn 1.5 is out! It includes now Python 3.7/8 - 3.10 wheels for MacOS (since 1.5.11.dev1 also showing tkinter dialogs!), linux and windows. See theDoc.pdf chapter **Issues and Bugs** for changes!
-
 If you like using Exudyn, please add a *star* on github and follow us on 
 `Twitter @RExudyn <https://twitter.com/RExudyn>`_ !
 
@@ -34,9 +32,7 @@
 
 A paper on Exudyn has been presented at the `6th Joint International Conference on Multibody System Dynamics <http://imsdacmd2020.iitd.ac.in>`_ and submitted to the proceedings: J. Gerstmayr, Exudyn - A C++ based Python package for flexible multibody systems, Proceedings of The 6th Joint International Conference on Multibody System Dynamics and the 10th Asian Conference on Multibody System Dynamics 2020, New Delhi, India, 2022. `PDF <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/publications/GerstmayrIMSD2022.pdf>`_
 
-This README document is a small part of the complete documentation found as PDF document in docs/theDoc/theDoc.pdf.
-It is auto-generated from .tex files (sorry for some conversion errors!). 
-Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_ !
+Due to limitations for complex formulas and tables in .rst files, details of the reference manual and many other parts of the documentation are only available in theDoc.pdf, see the `github page of Exudyn <https://github.com/jgerstmayr/EXUDYN/blob/master/docs/theDoc/theDoc.pdf>`_! There may also be some conversion errors in the auto-generated html pages.
 
 For license, see LICENSE.txt in the root github folder on github!
 
@@ -66,7 +62,12 @@
 %
 \noindent \codeName\ is hosted on \exuUrl{https://github.com}{GitHub} \cite{EXUDYNgit}:
 \bi
-  \item web: \exuUrl{https://github.com/jgerstmayr/EXUDYN}{https://github.com/jgerstmayr/EXUDYN}
+  \item \exuUrl{https://github.com/jgerstmayr/EXUDYN}{https://github.com/jgerstmayr/EXUDYN}
+\ei
+\noindent Online documentation is available at:
+\bi
+  \item \exuUrl{https://jgerstmayr.github.io/EXUDYN}{https://jgerstmayr.github.io/EXUDYN}
+  \item \exuUrl{https://exudyn.readthedocs.io}{https://exudyn.readthedocs.io}
 \ei
 %
 For any comments, requests, issues, bug reports, send an email to: 

docs/theDoc/introduction.tex

@@ -828,6 +828,14 @@
 \mysubsubsectionlabel{Camera following objects and interacting with model view}{sec:overview:advanced:camerafollowing}
 %
 For some models, it may be advantageous to track the translation and/or rotation of certain bodies, e.g., for cars, (wheeled) robots or bicycles. 
+Since \codeName\ 1.4.18 you can attach view to a marker, using the visualization setting
+\pythonstyle\begin{lstlisting}
+  SC.visualizationSettings.interactive.trackMarker = nMarker
+\end{lstlisting}
+in which \texttt{nMarker} represents the desired marker number to follow.
+See also related options in \texttt{SC.visualizationSettings.interactive} in \refSection{sec:VSettingsInteractive}.
+
+The following paragraph represents a slower, slightly outdated approach, which may be interesting for advanced usage of object tracking.
 To do so, the current render state (\texttt{SC.GetRenderState()}, \texttt{SC.SetRenderState(...)}) can be obtained and modified, in order to always follow a certain position.
 As this needs to be done during redraw of every frame, it is conveniently done in a graphicsUserFunction, e.g., within the ground body. This is shown in the following example, in which \texttt{mbs.variables['nTrackNode']} is a node number to be tracked:
 %
@@ -849,6 +857,7 @@
                  VObjectGround(graphicsDataUserFunction=UFgraphics)))
   #.... further code for simulation here
 \end{lstlisting}
+NOTE that this approach is slower and it may lead to a (usually silient) crash after closing the renderer, as the renderer thread is somehow coupled to Python which is prohibited from Python side.
 %
 %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 %+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
@@ -987,7 +996,7 @@
   print('results can be found in local directory: solution/demo1.txt')
   """
 \end{lstlisting}
-We can access Python variables from julia via \texttt{py"..."} to read out, e.g., \tettt{mbs}:
+We can access Python variables from julia via \texttt{py"..."} to read out, e.g., \texttt{mbs}:
   \begin{lstlisting}
   py"mbs".systemData.Info()
 \end{lstlisting}

docs/theDoc/itemDefinition.tex

@@ -10696,6 +10696,7 @@
     meshNodeNumbers &     ArrayIndex &      &     [] &     a list of $n_m$ mesh node numbers of superelement (=interface nodes) which are used to compute the body-fixed marker position and orientation; the related nodes must provide 3D position information, such as NodePoint, NodePoint2D, NodeRigidBody[..]; in order to retrieve the global node number, the generic body needs to convert local into global node numbers\\ \hline
     weightingFactors &     Vector &      &     [] &     a list of $n_m$ weighting factors per node to compute the final local position and orientation; these factors could be based on surface integrals of the constrained mesh faces\\ \hline
     useAlternativeApproach &     Bool &      &     True &     this flag switches between two versions for the computation of the rotation and angular velocity of the marker; alternative approach uses skew symmetric matrix of reference position; follows the inertia concept\\ \hline
+    rotationsExponentialMap &     Index &      &     2 &     Experimental flag (2 is the correct value and will be used in future, removing this flag): This value switches different behavior for computation of rotations and angular velocities: 0 uses linearized rotations and angular velocities, 1 uses the exponential map for rotations but linear angular velocities, 2 uses the exponential map for rotations and the according tangent map for angular velocities\\ \hline
     visualization &     VMarkerSuperElementRigid &      &      &     parameters for visualization of item\\ \hline
 \end{longtable}
 \end{center}