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Axel Kohlmeyer
2023-01-06 08:43:44 -05:00
parent 523821d83e
commit 92df9f1c71
3 changed files with 49 additions and 19 deletions
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1
doc/src/Commands_pair.rst
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@ -135,6 +135,7 @@ OPT.
* :doc:`lebedeva/z <pair_lebedeva_z>` * :doc:`lebedeva/z <pair_lebedeva_z>`
* :doc:`lennard/mdf <pair_mdf>` * :doc:`lennard/mdf <pair_mdf>`
* :doc:`lepton (o) <pair_lepton>` * :doc:`lepton (o) <pair_lepton>`
* :doc:`lepton/coul (o) <pair_lepton>`
* :doc:`line/lj <pair_line_lj>` * :doc:`line/lj <pair_line_lj>`
* :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>` * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
* :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>` * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`

66
doc/src/pair_lepton.rst
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@ -1,10 +1,12 @@
.. index:: pair_style lepton .. index:: pair_style lepton
.. index:: pair_style lepton/omp .. index:: pair_style lepton/omp
.. index:: pair_style lepton/coul
.. index:: pair_style lepton/coul/omp
pair_style lepton command pair_style lepton command
========================= =========================
Accelerator Variants: *lepton/omp* Accelerator Variants: *lepton/omp*, *lepton/coul/comp*
Syntax Syntax
"""""" """"""
@ -13,13 +15,17 @@ Syntax
pair_style style args pair_style style args
* style = *lepton* * style = *lepton* or *lepton/coul*
* args = list of arguments for a particular style * args = list of arguments for a particular style
.. parsed-literal:: .. parsed-literal::
*lepton* args = cutoff *lepton* args = cutoff
cutoff = global cutoff for the interactions (distance units) cutoff = global cutoff for the interactions (distance units)
*lepton/coul* args = cutoff keyword
cutoff = global cutoff for the interactions (distance units)
zero or more keywords may be appended
keyword = *ewald* or *pppm* or *msm* or *dispersion* or *tip4p*
Examples Examples
"""""""" """"""""
@ -32,18 +38,26 @@ Examples
pair_coeff 1 2 "4.0*eps*((sig/r)^12 - (sig/r)^6);eps=1.0;sig=1.0" 1.12246204830937 pair_coeff 1 2 "4.0*eps*((sig/r)^12 - (sig/r)^6);eps=1.0;sig=1.0" 1.12246204830937
pair_coeff 2 2 "eps*(2.0*(sig/r)^9 - 3.0*(sig/r)^6);eps=1.0;sig=1.0" pair_coeff 2 2 "eps*(2.0*(sig/r)^9 - 3.0*(sig/r)^6);eps=1.0;sig=1.0"
pair_style lepton/coul 2.5
pair_coeff 1 1 "qi*qj/r" 4.0
pair_coeff 1 2 "lj+coul; lj=4.0*eps*((sig/r)^12 - (sig/r)^6); eps=1.0; sig=1.0; coul=qi*qj/r"
Description Description
""""""""""" """""""""""
.. versionadded:: TBD .. versionadded:: TBD
Pair style *lepton* computes pairwise interactions between particles Pair styles *lepton* and *lepton/coul* compute pairwise interactions
which depend solely on the distance and have a cutoff. The potential between particles which depend solely on the distance and have a cutoff.
function must be provided as an expression string using "r" as the The potential function must be provided as an expression string using
distance variable. Note that additional constants in the expression can "r" as the distance variable. With pair style *lepton/coul* one may
be defined in the same string as additional expressions separated by additionally reference the charges of the two atoms of the pair with
semi-colons as shown in the examples above. The expression "qi" and "qj", respectively. Note that further constants in the
`"200.0*(r-1.5)^2"`, for instance, represents a harmonic potential expression can be defined in the same string as additional expressions
separated by semi-colons as shown in the examples above.
The expression `"200.0*(r-1.5)^2"` represents a harmonic potential
around the pairwise distance :math:`r_0` of 1.5 distance units and a around the pairwise distance :math:`r_0` of 1.5 distance units and a
force constant *K* of 200.0 energy units: force constant *K* of 200.0 energy units:
@ -51,6 +65,12 @@ force constant *K* of 200.0 energy units:
U_{ij} = K (r-r_0)^2 U_{ij} = K (r-r_0)^2
The expression `"qi*qj/r"` represents a regular Coulombic potential with cutoff:
.. math::
U_{ij} = \frac{C q_i q_j}{\epsilon r} \qquad r < r_c
The `Lepton library <https://simtk.org/projects/lepton>`_, that the The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* pair style interfaces with, evaluates this expression string at *lepton* pair style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical run time to compute the pairwise energy. It also creates an analytical
@ -72,6 +92,14 @@ More on valid Lepton expressions below. The last coefficient is
optional; it allows to set the cutoff for a pair of atom types to a optional; it allows to set the cutoff for a pair of atom types to a
different value than the global cutoff. different value than the global cutoff.
For pair style *lepton* only the "lj" value of the :doc:`special_bonds <special_bonds>`
settings apply in case the interacting pair is also connected with a bond.
The potential energy will *only* be added to the "evdwl" property.
For pair style *lepton/coul* only the "coul" value of the :doc:`special_bonds <special_bonds>`
settings apply in case the interacting pair is also connected with a bond.
The potential energy will *only* be added to the "ecoul" property.
---------- ----------
.. include:: lepton_expression.rst .. include:: lepton_expression.rst
@ -85,26 +113,26 @@ different value than the global cutoff.
Mixing, shift, table, tail correction, restart, rRESPA info Mixing, shift, table, tail correction, restart, rRESPA info
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
Pair style *lepton* does not support mixing. Thus, expressions for Pair styles *lepton* and *lepton/coul* do not support mixing. Thus,
*all* I,J pairs must be specified explicitly. expressions for *all* I,J pairs must be specified explicitly.
This pair style does supports the :doc:`pair_modify shift <pair_modify>` Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
option for shifting the energy of the pair interaction so that it is option for shifting the energy of the pair interaction so that it is
0 at the cutoff. 0 at the cutoff, pair style *lepton/coul* does *not*.
The :doc:`pair_modify table <pair_modify>` options are not relevant for The :doc:`pair_modify table <pair_modify>` options are not relevant for
the this pair style. the these pair styles.
This pair style does not support the :doc:`pair_modify tail These pair styles do not support the :doc:`pair_modify tail
<pair_modify>` option for adding long-range tail corrections to energy <pair_modify>` option for adding long-range tail corrections to energy
and pressure. and pressure.
This pair style writes its information to :doc:`binary restart files These pair styles write its information to :doc:`binary restart files
<restart>`, so pair_style and pair_coeff commands do not need to be <restart>`, so pair_style and pair_coeff commands do not need to be
specified in an input script that reads a restart file. specified in an input script that reads a restart file.
This pair style can only be used via the *pair* keyword of the These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the :doc:`run_style respa <run_style>` command. They do not support the
*inner*, *middle*, *outer* keywords. *inner*, *middle*, *outer* keywords.
---------- ----------
@ -112,7 +140,7 @@ This pair style can only be used via the *pair* keyword of the
Restrictions Restrictions
"""""""""""" """"""""""""
This pair style is part of the LEPTON package and only enabled if These pair styles are part of the LEPTON package and only enabled if
LAMMPS was built with this package. See the :doc:`Build package LAMMPS was built with this package. See the :doc:`Build package
<Build_package>` page for more info. <Build_package>` page for more info.

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doc/src/pair_style.rst
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@ -213,6 +213,7 @@ accelerated styles exist.
* :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis * :doc:`lebedeva/z <pair_lebedeva_z>` - Lebedeva interlayer potential for graphene with normals along z-axis
* :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function * :doc:`lennard/mdf <pair_mdf>` - LJ potential in A/B form with a taper function
* :doc:`lepton <pair_lepton>` - pair potential from evaluating a string * :doc:`lepton <pair_lepton>` - pair potential from evaluating a string
* :doc:`lepton/coul <pair_lepton>` - pair potential from evaluating a string with support for charges
* :doc:`line/lj <pair_line_lj>` - LJ potential between line segments * :doc:`line/lj <pair_line_lj>` - LJ potential between line segments
* :doc:`list <pair_list>` - potential between pairs of atoms explicitly listed in an input file * :doc:`list <pair_list>` - potential between pairs of atoms explicitly listed in an input file
* :doc:`lj/charmm/coul/charmm <pair_charmm>` - CHARMM potential with cutoff Coulomb * :doc:`lj/charmm/coul/charmm <pair_charmm>` - CHARMM potential with cutoff Coulomb