diff --git a/doc/src/pair_ylz.rst b/doc/src/pair_ylz.rst index baa97bfe3a..744a868cb6 100644 --- a/doc/src/pair_ylz.rst +++ b/doc/src/pair_ylz.rst @@ -27,31 +27,47 @@ Description .. versionadded:: TBD -The *ylz* (Yuan-Li-Zhang) :ref:`(Yuan) ` style computes -anisotropic interactions between pairs of particles considering the -relative particle orientations via the formulas +The *ylz* (Yuan-Li-Zhang) style computes an anisotropic interaction between pairs of +coarse-grained particles considering the relative particle orientations. This potential +was originally developed as a particle-based solvent-free model for biological membranes +:ref:`(Yuan2010a) `. Unlike the :doc:`pair_style gayberne ` whose +orientation dependence is strictly derived from the closest distance between two +ellipsoidal rigid bodies, the orientation-dependence of this pair style is mathematically +defined such that the particles can self-assemble into one-particle-thick +fluid membranes. The potential of this pair style is described via the formulas .. math:: U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} {u}_R(r)+\left [ 1-\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<{r}_{min} \\ {u}_A(r)\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~ {r}_{min}`) in order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid ` should be used since it defines the rotational state of each particle. +This pair style is suited for solvent-free coarse-grained simulations of biological systems +involving lipid bilayer membranes, such as vesicle shape transformations :ref:`(Yuan2010b) `, +nanoparticle endocytosis :ref:`(Huang) `, modeling of red blood cell membranes :ref:`(Fu) `, +:ref:`(Appshaw) `, and modeling of cell elasticity :ref:`(Becton) `. -The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff ` command as in the examples above, or in the data file or restart files read by the :doc:`read_data ` or :doc:`read_restart ` commands, or by mixing as described below: +Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension +(e.g. :doc:`fix nve/asphere `) in order to integrate particle rotation. +Additionally, :doc:`atom_style ellipsoid ` should be used since it defines +the rotational state of each particle. + +The following coefficients must be defined for each pair of atoms types via the +:doc:`pair_coeff ` command as in the examples above, or in the data file +or restart files read by the :doc:`read_data ` or +:doc:`read_restart ` commands, or by mixing as described below: * :math:`\epsilon` = well depth (energy units) * :math:`\sigma` = minimum effective particle radii (distance units) @@ -96,10 +112,16 @@ The *ylz* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` page for more info. -This pair style requires that atoms store torque and a quaternion to -represent their orientation, as defined by the :doc:`atom_style -`. It also requires they store a per-atom :doc:`shape -`. The particles cannot store a per-particle diameter. +This pair style requires that atoms store torque and a quaternion to represent +their orientation, as defined by the :doc:`atom_style `. It also +requires they store a per-atom :doc:`shape `. The particles cannot store +a per-particle diameter. To avoid being mistakenly considered as point masses, +the shape parameters ought to be non-spherical, like [1 0.99 0.99]. Unlike +the :doc:`pair_style gayberne ` pair style for which the shape +directly determines the mathematical expressions of the potential, the shape +parameters for this pair style is only involved in the computation of the +moment of inertia and thus only play a role to the rotational dynamics of +individual particles. This pair style requires that **all** atoms are ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. @@ -111,7 +133,7 @@ Related commands :doc:`pair_coeff `, :doc:`fix nve/asphere :doc:`, `compute temp/asphere `, :doc::doc:`pair_style resquared `, :doc:`pair_style -:doc:gayberne ` +:doc:gayberne ` Default """"""" @@ -122,4 +144,22 @@ none .. _Yuan: -**(Yuan)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010). +**(Yuan2010a)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010). + +**(Yuan2010b)** Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010). + +.. _Huang: + +**(Huang)** Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013). + +.. _Fu: + +**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017). + +.. _Appshaw: + +**(Appshaw)** Appshaw, Seddonb, Hannaa, Soft. Matter,18, 1747(2022). + +.. _Becton: + +**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiol, 18, 425-433(2019). diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 880124a04d..cc46fd01fe 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -123,6 +123,7 @@ Antonelli api Apoorva Appl +Appshaw apptainer Apu arallel @@ -237,6 +238,7 @@ bcolor bdiam bdw Beckman +Becton Belak Bellott bem