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Quaternion formalism comments and docs #3392

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11 changes: 11 additions & 0 deletions doc/doxygen/bibliography.bib
Original file line number Diff line number Diff line change
Expand Up @@ -394,6 +394,17 @@ @Article{sonnenschein85a
doi = {10.1016/0021-9991(85)90151-2},
}

@book{allen2017,
title={Computer simulation of liquids},
author={Allen, Michael P and Tildesley, Dominic J},
year={2017},
publisher={Oxford university press},
url={https://global.oup.com/academic/product/computer-simulation-of-liquids-9780198803201},
doi={10.1093/oso/9780198803195.001.0001},
isbn={9780198803195},
edition={2nd},
}

@Article{swope92a,
author = {Swope, William C. and Ferguson, David M.},
title = {{Alternative expressions for energies and forces due to angle bending and torsional energy}},
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2 changes: 1 addition & 1 deletion doc/sphinx/running.rst
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Expand Up @@ -184,7 +184,7 @@ Rotational degrees of freedom and particle anisotropy
When the feature ``ROTATION`` is compiled in, particles not only have a position, but also an orientation that changes with an angular velocity. A torque on a particle leads to a change in angular velocity depending on the particles rotational inertia. The property :attr:`espressomd.particle_data.ParticleHandle.rinertia` has to be specified as the three eigenvalues of the particles rotational inertia tensor.

The rotational degrees of freedom are also integrated using a velocity Verlet scheme.
The implementation is based on a quaternion representation of the particle orientation and described in :cite:`omelyan98`.
The implementation is based on a quaternion representation of the particle orientation and described in :cite:`omelyan98` with quaternion components indexing made according to the formalism :math:`q = a + b\mathbf{i} + c\mathbf{j} + d\mathbf{k}` :cite:`allen2017`.

When the Langevin thermostat is enabled, the rotational degrees of freedom are also thermalized.

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11 changes: 11 additions & 0 deletions doc/sphinx/zrefs.bib
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Expand Up @@ -688,6 +688,17 @@ @article{omelyan98
URL = {https://aip.scitation.org/doi/abs/10.1063/1.168642}
}

@book{allen2017,
title={Computer simulation of liquids},
author={Allen, Michael P and Tildesley, Dominic J},
year={2017},
publisher={Oxford university press},
url={https://global.oup.com/academic/product/computer-simulation-of-liquids-9780198803201},
doi={10.1093/oso/9780198803195.001.0001},
isbn={9780198803195},
edition={2nd},
}

@ARTICLE{pasichnyk04a,
author = {Igor Pasichnyk and Burkhard D{\"u}nweg},
title = {Coulomb interactions via local dynamics: {A} molecular-dynamics algorithm},
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5 changes: 3 additions & 2 deletions src/core/rotation.cpp
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Expand Up @@ -23,8 +23,9 @@
*
* A velocity Verlet <a
* HREF="http://ciks.cbt.nist.gov/~garbocz/dpd1/dpd.html">algorithm</a>
* using quaternions is implemented to tackle rotational motion. A random
* torque and a friction
* using quaternions is implemented to tackle rotational motion.
* See @cite allen2017 for the quaternion components indexing used here.
* A random torque and a friction
* term are added to provide the constant NVT conditions. Due to this feature
* all particles are
* treated as 3D objects with 3 translational and 3 rotational degrees of
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