diff --git a/doc/src/pair_ylz.rst b/doc/src/pair_ylz.rst index 744a868cb6..cb59385579 100644 --- a/doc/src/pair_ylz.rst +++ b/doc/src/pair_ylz.rst @@ -27,47 +27,58 @@ Description .. versionadded:: TBD -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 +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 :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 by: .. 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}`, -nanoparticle endocytosis :ref:`(Huang) `, modeling of red blood cell membranes :ref:`(Fu) `, -:ref:`(Appshaw) `, and modeling of cell elasticity :ref:`(Becton) `. +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) `. -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. +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: +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) @@ -112,16 +123,17 @@ 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. 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 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 particles, the shape parameters ought +to be non-spherical, like [1 0.99 0.99]. Unlike the :doc:`resquared +` 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 influences the rotational dynamics of individual +particles. This pair style requires that **all** atoms are ellipsoids as defined by the :doc:`atom_style ellipsoid ` command. @@ -144,7 +156,7 @@ none .. _Yuan: -**(Yuan2010a)** 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). @@ -154,12 +166,12 @@ none .. _Fu: -**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017). +**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017). .. _Appshaw: -**(Appshaw)** Appshaw, Seddonb, Hannaa, Soft. Matter,18, 1747(2022). +**(Appshaw)** Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022). .. _Becton: -**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiol, 18, 425-433(2019). +**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019). diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index cc46fd01fe..61c1d45ba7 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -182,6 +182,7 @@ Avalos avalue aveforce Avendano +Averett avi AVX awpmd @@ -272,6 +273,7 @@ bilayers binsize binstyle binutils +Biomech biomolecular biomolecule Biomolecules @@ -926,6 +928,7 @@ Emmrich emol eN endian +endocytosis energetics energyCorr eng @@ -1157,6 +1160,7 @@ ftm ftol fuer fugacity +Fu Fumi func funcs @@ -1308,6 +1312,7 @@ Hamaker Hamel Hammerschmidt Hanley +Hanna haptic Haque Hara @@ -1659,6 +1664,7 @@ kepler keV Keyes keyfile +Kfoury Khersonskii Khrapak Khvostov @@ -2025,6 +2031,7 @@ MEAM meamf meanDist mech +Mechanobiology Mecke mediumaquamarine mediumblue @@ -3146,6 +3153,7 @@ seagreen Secor sectoring sed +Seddon segmental Seifert Seleson