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Merge branch 'doc-pdf' of https://github.com/ndtrung81/lammps into collected-small-fixes

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Axel Kohlmeyer
2024-08-15 13:37:11 -04:00
parent 68b808d3b5 875ba17dd8
commit db603a380e
11 changed files with 25 additions and 38 deletions
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10
doc/src/pair_cosine_squared.rst
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@ -14,12 +14,12 @@ Syntax
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_coeff i j eps sigma pair_coeff I J eps sigma
pair_coeff i j eps sigma cutoff pair_coeff I J eps sigma cutoff
pair_coeff i j eps sigma wca pair_coeff I J eps sigma wca
pair_coeff i j eps sigma cutoff 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) * eps = interaction strength, i.e. the depth of the potential minimum (energy units)
* sigma = distance of the potential minimum from 0 * sigma = distance of the potential minimum from 0
* cutoff = the cutoff distance for this pair type, if different from global (distance units) * cutoff = the cutoff distance for this pair type, if different from global (distance units)

8
doc/src/pair_coul_diel.rst
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@ -28,7 +28,7 @@ Description
Style *coul/diel* computes a Coulomb correction for implicit solvent Style *coul/diel* computes a Coulomb correction for implicit solvent
ion interactions in which the dielectric permittivity is distance dependent. 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) One limit is defined by a small dielectric permittivity (close to vacuum)
at or close to contact separation between the ions. At larger separations at or close to contact separation between the ions. At larger separations
the dielectric permittivity reaches a bulk value used in the regular Coulomb 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 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 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 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) <Stiles>` limit of :math:`\epsilon_D(r \to 0) = 5.2` due to dielectric saturation :ref:`(Stiles) <Stiles>`
while the Coulomb interaction reaches its bulk limit by setting 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 :math:`\epsilon_D(r \to \infty) = \epsilon`, the bulk value of the solvent which is 78
for water at 298K. for water at 298K.
@ -113,12 +113,12 @@ none
.. _Stiles: .. _Stiles:
**(Stiles)** Stiles , Hubbard, and Kayser, J Chem Phys, 77, **(Stiles)** Stiles, Hubbard, and Kayser, J Chem Phys, 77,
6189 (1982). 6189 (1982).
.. _Lenart1: .. _Lenart1:
**(Lenart)** Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, **(Lenart)** Lenart, Jusufi, and Panagiotopoulos, J Chem Phys, 126,
044509 (2007). 044509 (2007).
.. _Jusufi1: .. _Jusufi1:

2
doc/src/pair_coul_slater.rst
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@ -43,7 +43,7 @@ Examples
Description 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. which employ potentials without explicit excluded-volume interactions.
The goal is to prevent artificial ionic pair formation by including a charge The goal is to prevent artificial ionic pair formation by including a charge
distribution in the Coulomb potential, following the formulation of distribution in the Coulomb potential, following the formulation of

2
doc/src/pair_dipole.rst
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@ -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 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 :math:`C/\epsilon` prefactor, the same as the Coulombic term in the
LJ + Coulombic pair styles discussed :doc:`here <pair_lj>`. C is an LJ + Coulombic pair styles discussed :doc:`here <pair_lj>`. 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 <dielectric>` command. The which can be set by the :doc:`dielectric <dielectric>` command. The
same is true of the equations that follow for other dipole pair same is true of the equations that follow for other dipole pair
styles. styles.

2
doc/src/pair_dpd.rst
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@ -118,7 +118,7 @@ atoms types via the :doc:`pair_coeff <pair_coeff>` command are:
The cutoff coefficient is optional. 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) <Afshar>` and :ref:`(Phillips) <Phillips>`. the work of :ref:`(Afshar) <Afshar>` and :ref:`(Phillips) <Phillips>`.
.. note:: .. note::

15
doc/src/pair_eff.rst
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@ -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 the minimum image criterion, i.e. half of the minimum unit cell
length. 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 <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 <atom_style>` definitions, in order to handle the This potential is designed to be used with :doc:`atom_style electron <atom_style>` definitions, in order to handle the
description of systems with interacting nuclei and explicit electrons. 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 (as in some of the examples above), the default global value specified
in the pair_style command is used. 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 <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. The *limit/eradius* and *pressure/evirials* keywords are optional.
@ -190,7 +177,7 @@ representations, after the "ecp" keyword.
.. note:: .. 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 when defining this pair_style, one (default) that considers electrons
do not contribute radial virial components (i.e. electrons treated as do not contribute radial virial components (i.e. electrons treated as
incompressible 'rigid' spheres) and one that does. The radial incompressible 'rigid' spheres) and one that does. The radial

2
doc/src/pair_extep.rst
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@ -33,7 +33,7 @@ none
Related commands Related commands
"""""""""""""""" """"""""""""""""
`pair_tersoff <pair tersoff>` :doc:`pair_tersoff <pair_tersoff>`
Default Default
""""""" """""""

6
doc/src/pair_gran.rst
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@ -80,7 +80,7 @@ The two Hookean styles use this formula:
F_{hk} = (k_n \delta \mathbf{n}_{ij} - F_{hk} = (k_n \delta \mathbf{n}_{ij} -
m_{eff} \gamma_n\mathbf{ v}_n) - 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) m_{eff} \gamma_t \mathbf{v}_t)
The Hertzian style uses this formula: 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}} \sqrt{\delta} \sqrt{\frac{R_i R_j}{R_i + R_j}}
\Big[ (k_n \delta \mathbf{n}_{ij} - \Big[ (k_n \delta \mathbf{n}_{ij} -
m_{eff} \: \gamma_n \mathbf{ v}_n) - 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] m_{eff} \: \gamma_t \mathbf{v}_t) \Big]
In both equations the first parenthesized term is the normal force 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_n` = viscoelastic damping constant for normal contact
* :math:`\gamma_t` = viscoelastic damping constant for tangential 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:`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:`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_n =` normal component of the relative velocity of the 2 particles
* :math:`V_t =` tangential component of the relative velocity of the 2 particles * :math:`V_t =` tangential component of the relative velocity of the 2 particles

4
doc/src/pair_granular.rst
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@ -328,7 +328,7 @@ keyword also affects the tangential damping. The parameter
literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`, literature use :math:`x_{\gamma,t} = 1` (:ref:`Marshall <Marshall2009>`,
:ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`). The relative :ref:`Tsuji et al <Tsuji1992>`, :ref:`Silbert et al <Silbert2001>`). The relative
tangential velocity at the point of contact is given by 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` . :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}}\|` . 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} \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 <Wang2015>` and velocity, as given in :ref:`Wang et al <Wang2015>` and
:ref:`Luding <Luding2008>`. This differs from the expressions given by :ref:`Kuhn and Bagi <Kuhn2004>` and used in :ref:`Marshall <Marshall2009>`; see :ref:`Wang et al <Wang2015>` for details. The rolling displacement is given by: :ref:`Luding <Luding2008>`. This differs from the expressions given by :ref:`Kuhn and Bagi <Kuhn2004>` and used in :ref:`Marshall <Marshall2009>`; see :ref:`Wang et al <Wang2015>` for details. The rolling displacement is given by:

2
doc/src/pair_lj_cut_coul.rst
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@ -188,7 +188,7 @@ specified for this style means that pairwise interactions within this
distance are computed directly; interactions outside that distance are distance are computed directly; interactions outside that distance are
computed in reciprocal space. 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 <Wolf3>`, given by: summation method, described in :ref:`Wolf <Wolf3>`, given by:
.. math:: .. math::

10
doc/src/pair_pedone.rst
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@ -27,12 +27,12 @@ Examples
.. code-block:: LAMMPS .. code-block:: LAMMPS
pair_style hybrid/overlay pedone 15.0 coul/long 15.0 pair_style hybrid/overlay pedone 15.0 coul/long 15.0
kspace_style pppm 1.0e-5 kspace_style pppm 1.0e-5
pair_coeff * * coul/long pair_coeff * * coul/long
pair_coeff 1 2 pedone 0.030211 2.241334 2.923245 5.0 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 2 2 pedone 0.042395 1.379316 3.618701 22.0
Used in input scripts: Used in input scripts: