From 875ba17dd8447e199f33be1967d0b77106f68ad3 Mon Sep 17 00:00:00 2001 From: Trung Nguyen Date: Thu, 15 Aug 2024 09:38:58 -0500 Subject: [PATCH] Edits/corrections to doc pages 2315-2589 --- doc/src/pair_cosine_squared.rst | 10 +++++----- doc/src/pair_coul_diel.rst | 8 ++++---- doc/src/pair_coul_slater.rst | 2 +- doc/src/pair_dipole.rst | 2 +- doc/src/pair_dpd.rst | 2 +- doc/src/pair_eff.rst | 15 +-------------- doc/src/pair_extep.rst | 2 +- doc/src/pair_gran.rst | 6 +++--- doc/src/pair_granular.rst | 4 ++-- doc/src/pair_lj_cut_coul.rst | 2 +- doc/src/pair_pedone.rst | 10 +++++----- 11 files changed, 25 insertions(+), 38 deletions(-) diff --git a/doc/src/pair_cosine_squared.rst b/doc/src/pair_cosine_squared.rst index f68df419a4..405c92f854 100644 --- a/doc/src/pair_cosine_squared.rst +++ b/doc/src/pair_cosine_squared.rst @@ -14,12 +14,12 @@ Syntax .. code-block:: LAMMPS - pair_coeff i j eps sigma - pair_coeff i j eps sigma cutoff - pair_coeff i j eps sigma wca - pair_coeff i j eps sigma cutoff wca + pair_coeff I J eps sigma + pair_coeff I J eps sigma cutoff + pair_coeff I J eps sigma wca + pair_coeff I J eps sigma cutoff wca -* i,j = a particle type +* I, J = a particle type * eps = interaction strength, i.e. the depth of the potential minimum (energy units) * sigma = distance of the potential minimum from 0 * cutoff = the cutoff distance for this pair type, if different from global (distance units) diff --git a/doc/src/pair_coul_diel.rst b/doc/src/pair_coul_diel.rst index 7dc245f449..77c00c633a 100644 --- a/doc/src/pair_coul_diel.rst +++ b/doc/src/pair_coul_diel.rst @@ -28,7 +28,7 @@ Description Style *coul/diel* computes a Coulomb correction for implicit solvent ion interactions in which the dielectric permittivity is distance dependent. -The dielectric permittivity epsilon_D(r) connects to limiting regimes: +The dielectric permittivity :math:`\epsilon_D(r)` connects to limiting regimes: One limit is defined by a small dielectric permittivity (close to vacuum) at or close to contact separation between the ions. At larger separations the dielectric permittivity reaches a bulk value used in the regular Coulomb @@ -45,7 +45,7 @@ where :math:`r_{me}` is the inflection point of :math:`\epsilon_D(r)` and :math: defining length scale. C is the same Coulomb conversion factor as in the pair_styles coul/cut, coul/long, and coul/debye. In this way the Coulomb interaction between ions is corrected at small distances r. The lower -limit of epsilon_D(r->0)=5.2 due to dielectric saturation :ref:`(Stiles) ` +limit of :math:`\epsilon_D(r \to 0) = 5.2` due to dielectric saturation :ref:`(Stiles) ` while the Coulomb interaction reaches its bulk limit by setting :math:`\epsilon_D(r \to \infty) = \epsilon`, the bulk value of the solvent which is 78 for water at 298K. @@ -113,12 +113,12 @@ none .. _Stiles: -**(Stiles)** Stiles , Hubbard, and Kayser, J Chem Phys, 77, +**(Stiles)** Stiles, Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982). .. _Lenart1: -**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, +**(Lenart)** Lenart, Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007). .. _Jusufi1: diff --git a/doc/src/pair_coul_slater.rst b/doc/src/pair_coul_slater.rst index bde14276db..7abc1f8b07 100644 --- a/doc/src/pair_coul_slater.rst +++ b/doc/src/pair_coul_slater.rst @@ -43,7 +43,7 @@ Examples Description """"""""""" -Styles *coul/slater* compute electrostatic interactions in mesoscopic models +Styles *coul/slater/** compute electrostatic interactions in mesoscopic models which employ potentials without explicit excluded-volume interactions. The goal is to prevent artificial ionic pair formation by including a charge distribution in the Coulomb potential, following the formulation of diff --git a/doc/src/pair_dipole.rst b/doc/src/pair_dipole.rst index bea80bfc45..3e236a275b 100644 --- a/doc/src/pair_dipole.rst +++ b/doc/src/pair_dipole.rst @@ -129,7 +129,7 @@ torques do not act symmetrically. These formulas are discussed in Also note, that in the code, all of these terms (except Elj) have a :math:`C/\epsilon` prefactor, the same as the Coulombic term in the LJ + Coulombic pair styles discussed :doc:`here `. C is an -energy-conversion constant and epsilon is the dielectric constant +energy-conversion constant and :math:`\epsilon` is the dielectric constant which can be set by the :doc:`dielectric ` command. The same is true of the equations that follow for other dipole pair styles. diff --git a/doc/src/pair_dpd.rst b/doc/src/pair_dpd.rst index 4c8deab152..74766d4d15 100644 --- a/doc/src/pair_dpd.rst +++ b/doc/src/pair_dpd.rst @@ -118,7 +118,7 @@ atoms types via the :doc:`pair_coeff ` command are: The cutoff coefficient is optional. -The GPU-accelerated versions of these styles are implemented based on +Styles with a *gpu* suffix are implemented based on the work of :ref:`(Afshar) ` and :ref:`(Phillips) `. .. note:: diff --git a/doc/src/pair_eff.rst b/doc/src/pair_eff.rst index b104b01b40..93f4c3ae9c 100644 --- a/doc/src/pair_eff.rst +++ b/doc/src/pair_eff.rst @@ -122,14 +122,6 @@ distance. The recommended cutoff for this pair style should follow the minimum image criterion, i.e. half of the minimum unit cell length. -Style *eff/long* (not yet available) computes the same interactions as -style *eff/cut* except that an additional damping factor is applied so -it can be used in conjunction with the -:doc:`kspace_style ` command and its *ewald* or *pppm* -option. The Coulombic cutoff specified for this style means that -pairwise interactions within this distance are computed directly; -interactions outside that distance are computed in reciprocal space. - This potential is designed to be used with :doc:`atom_style electron ` definitions, in order to handle the description of systems with interacting nuclei and explicit electrons. @@ -145,11 +137,6 @@ For *eff/cut*, the cutoff coefficient is optional. If it is not used (as in some of the examples above), the default global value specified in the pair_style command is used. -For *eff/long* (not yet available) no cutoff will be specified for an -individual I,J type pair via the :doc:`pair_coeff ` command. -All type pairs use the same global cutoff specified in the pair_style -command. - ---------- The *limit/eradius* and *pressure/evirials* keywords are optional. @@ -190,7 +177,7 @@ representations, after the "ecp" keyword. .. note:: - there are two different pressures that can be reported for eFF + There are two different pressures that can be reported for eFF when defining this pair_style, one (default) that considers electrons do not contribute radial virial components (i.e. electrons treated as incompressible 'rigid' spheres) and one that does. The radial diff --git a/doc/src/pair_extep.rst b/doc/src/pair_extep.rst index 53ffdf5d8c..94705e9567 100644 --- a/doc/src/pair_extep.rst +++ b/doc/src/pair_extep.rst @@ -33,7 +33,7 @@ none Related commands """""""""""""""" -`pair_tersoff ` +:doc:`pair_tersoff ` Default """"""" diff --git a/doc/src/pair_gran.rst b/doc/src/pair_gran.rst index 3249bae866..14f996f7c0 100644 --- a/doc/src/pair_gran.rst +++ b/doc/src/pair_gran.rst @@ -80,7 +80,7 @@ The two Hookean styles use this formula: F_{hk} = (k_n \delta \mathbf{n}_{ij} - m_{eff} \gamma_n\mathbf{ v}_n) - - (k_t \mathbf{ \Delta s}_t + + (k_t \boldsymbol{\Delta} \mathbf{s}_t + m_{eff} \gamma_t \mathbf{v}_t) The Hertzian style uses this formula: @@ -91,7 +91,7 @@ The Hertzian style uses this formula: \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}} \Big[ (k_n \delta \mathbf{n}_{ij} - m_{eff} \: \gamma_n \mathbf{ v}_n) - - (k_t \mathbf{ \Delta s}_t + + (k_t \boldsymbol{\Delta} \mathbf{s}_t + m_{eff} \: \gamma_t \mathbf{v}_t) \Big] In both equations the first parenthesized term is the normal force @@ -114,7 +114,7 @@ The other quantities in the equations are as follows: * :math:`\gamma_n` = viscoelastic damping constant for normal contact * :math:`\gamma_t` = viscoelastic damping constant for tangential contact * :math:`m_{eff} = M_i M_j / (M_i + M_j) =` effective mass of 2 particles of mass M_i and M_j -* :math:`\mathbf{\Delta s}_t =` tangential displacement vector between 2 particles which is truncated to satisfy a frictional yield criterion +* :math:`\boldsymbol{\Delta} \mathbf{s}_t =` tangential displacement vector between 2 particles which is truncated to satisfy a frictional yield criterion * :math:`n_{ij} =` unit vector along the line connecting the centers of the 2 particles * :math:`V_n =` normal component of the relative velocity of the 2 particles * :math:`V_t =` tangential component of the relative velocity of the 2 particles diff --git a/doc/src/pair_granular.rst b/doc/src/pair_granular.rst index dca85d8be1..f061331497 100644 --- a/doc/src/pair_granular.rst +++ b/doc/src/pair_granular.rst @@ -328,7 +328,7 @@ keyword also affects the tangential damping. The parameter literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall `, :ref:`Tsuji et al `, :ref:`Silbert et al `). The relative tangential velocity at the point of contact is given by -:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\mathbf{\Omega}_i + R_j\mathbf{\Omega}_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}\ \mathbf{n}`, +:math:`\mathbf{v}_{t, rel} = \mathbf{v}_{t} - (R_i\boldsymbol{\Omega}_i + R_j\boldsymbol{\Omega}_j) \times \mathbf{n}`, where :math:`\mathbf{v}_{t} = \mathbf{v}_r - \mathbf{v}_r\cdot\mathbf{n}\ \mathbf{n}`, :math:`\mathbf{v}_r = \mathbf{v}_j - \mathbf{v}_i` . The direction of the applied force is :math:`\mathbf{t} = \mathbf{v_{t,rel}}/\|\mathbf{v_{t,rel}}\|` . @@ -548,7 +548,7 @@ the tangential force: \mathbf{F}_{roll,0} = k_{roll} \mathbf{\xi}_{roll} - \gamma_{roll} \mathbf{v}_{roll} -Here, :math:`\mathbf{v}_{roll} = -R(\mathbf{\Omega}_i - \mathbf{\Omega}_j) \times \mathbf{n}` is the relative rolling +Here, :math:`\mathbf{v}_{roll} = -R(\boldsymbol{\Omega}_i - \boldsymbol{\Omega}_j) \times \mathbf{n}` is the relative rolling velocity, as given in :ref:`Wang et al ` and :ref:`Luding `. This differs from the expressions given by :ref:`Kuhn and Bagi ` and used in :ref:`Marshall `; see :ref:`Wang et al ` for details. The rolling displacement is given by: diff --git a/doc/src/pair_lj_cut_coul.rst b/doc/src/pair_lj_cut_coul.rst index e04da852dd..d1d80aa7e8 100644 --- a/doc/src/pair_lj_cut_coul.rst +++ b/doc/src/pair_lj_cut_coul.rst @@ -188,7 +188,7 @@ specified for this style means that pairwise interactions within this distance are computed directly; interactions outside that distance are computed in reciprocal space. -Style *coul/wolf* adds a Coulombic pairwise interaction via the Wolf +Style *lj/cut/coul/wolf* adds a Coulombic pairwise interaction via the Wolf summation method, described in :ref:`Wolf `, given by: .. math:: diff --git a/doc/src/pair_pedone.rst b/doc/src/pair_pedone.rst index 10fcb63e2e..6230ee19bd 100644 --- a/doc/src/pair_pedone.rst +++ b/doc/src/pair_pedone.rst @@ -27,12 +27,12 @@ Examples .. code-block:: LAMMPS -pair_style hybrid/overlay pedone 15.0 coul/long 15.0 -kspace_style pppm 1.0e-5 + pair_style hybrid/overlay pedone 15.0 coul/long 15.0 + kspace_style pppm 1.0e-5 -pair_coeff * * coul/long -pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 -pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 + pair_coeff * * coul/long + pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 + pair_coeff 2 2 pedone 0.042395 1.379316 3.618701 22.0 Used in input scripts: