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make lepton package docs more consistent

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This commit is contained in:
Axel Kohlmeyer
2022-12-26 16:45:49 -05:00
parent 5a99cf0dd5
commit a5742a9147
2 changed files with 21 additions and 21 deletions
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24
doc/src/angle_lepton.rst
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@ -29,12 +29,12 @@ Description
.. versionadded:: TBD
Angle style *lepton* computes angular interactions between three atoms,
between which an angle has been defined, based on evaluating strings.
The potential function must be provided as an expression string using
"theta" as the angle variable relative to the reference angle
:math:`\theta_0` which is provided as an angle coefficient. For example
`"200.0*theta^2"` represents a harmonic potential with a force constant
Angle style *lepton* computes angular interactions between three atoms
with a custom potential function. The potential function must be
provided as an expression string using "theta" as the angle variable
relative to the reference angle :math:`\theta_0` which is provided as an
angle coefficient. For example `"200.0*theta^2"` represents a
:doc:`harmonic angle <angle_harmonic>` potential with a force constant
*K* of 200.0 energy units:
.. math::
@ -42,11 +42,11 @@ The potential function must be provided as an expression string using
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical
representation of the first derivative of this expression with respect to
"r" and then uses that to compute the force between the pairs atoms forming
angles as defined by the topology data.
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an
analytical representation of the first derivative of this expression
with respect to "theta" and then uses that to compute the force between
the angle atoms as defined by the topology data.
The following coefficients must be defined for each angle type via the
:doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@ -86,7 +86,7 @@ Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style table <angle_table>`,
:doc:`bond_style lepton <bond_lepton>`
:doc:`bond_style lepton <bond_lepton>`,:doc:`dihedral_style lepton <dihedral_lepton>`
Default
"""""""

18
doc/src/bond_lepton.rst
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@ -29,13 +29,12 @@ Description
.. versionadded:: TBD
Bond style *lepton* computes bonded interactions between two atoms,
between which a bond has been defined, based on evaluating strings. The
potential function must be provided as an expression string using "r" as
the distance variable relative to the reference distance :math:`r_0`
which is provided as a bond coefficient. For example `"200.0*r^2"`
represents a harmonic potential with a force constant *K* of 200.0
energy units:
Bond style *lepton* computes bonded interactions between two atoms with
a custom function. The potential function must be provided as an
expression string using "r" as the distance variable relative to the
reference distance :math:`r_0` which is provided as a bond coefficient.
For example `"200.0*r^2"` represents a harmonic potential with a force
constant *K* of 200.0 energy units:
.. math::
@ -45,7 +44,7 @@ The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical
representation of the first derivative of this expression with respect to
"r" and then uses that to compute the force between the pairs atoms forming
"r" and then uses that to compute the force between the atom pairs forming
bonds as defined by the topology data.
The following coefficients must be defined for each bond type via the
@ -84,7 +83,8 @@ Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`bond_style table <bond_table>`,
:doc:`bond_write <bond_write>`, :doc:`angle_style lepton <angle_lepton>`
:doc:`bond_write <bond_write>`, :doc:`angle_style lepton <angle_lepton>`,
:doc:`dihedral_style lepton <dihedral_lepton>`
Default
"""""""