diff --git a/doc/doxygen/bibliography.bib b/doc/doxygen/bibliography.bib index 3a215288175..e30b3f9fd6b 100644 --- a/doc/doxygen/bibliography.bib +++ b/doc/doxygen/bibliography.bib @@ -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}}, diff --git a/doc/sphinx/running.rst b/doc/sphinx/running.rst index 7532d01770a..47992b71184 100644 --- a/doc/sphinx/running.rst +++ b/doc/sphinx/running.rst @@ -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. diff --git a/doc/sphinx/zrefs.bib b/doc/sphinx/zrefs.bib index 5750d701fb5..c5beac32854 100644 --- a/doc/sphinx/zrefs.bib +++ b/doc/sphinx/zrefs.bib @@ -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}, diff --git a/src/core/rotation.cpp b/src/core/rotation.cpp index 46ea60a879c..f0b044f339f 100644 --- a/src/core/rotation.cpp +++ b/src/core/rotation.cpp @@ -23,8 +23,9 @@ * * A velocity Verlet algorithm - * 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