more documentation tweaks and corrections. make consistent across package styles
This commit is contained in:
Axel Kohlmeyer
@ -20,30 +20,31 @@ Examples
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angle_style lepton
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angle_coeff 1 120.0 "k*theta^2; k=250.0"
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angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
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angle_coeff 3 109.45 "k*theta^2; k=350.0"
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angle_coeff 1 120.0 "k*theta^2; k=250.0"
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angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
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angle_coeff 3 109.47 "k*theta^2; k=350.0"
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Description
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"""""""""""
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.. versionadded:: TBD
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Angle style *lepton* computes angular interactions between three atoms
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based on evaluating strings. The potential function must be provided as an
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expression string using "theta" as the angle variable relative to the
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reference angle :math:`\theta_0` which is provided as an angle coefficient.
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For example `"200.0*(theta)^2"` represents a harmonic potential with a
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force constant *K* of 200.0 energy units:
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Angle style *lepton* computes angular interactions between three atoms,
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between which an angle has been defined, based on evaluating strings.
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The potential function must be provided as an expression string using
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"theta" as the angle variable relative to the reference angle
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:math:`\theta_0` which is provided as an angle coefficient. For example
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`"200.0*theta^2"` represents a harmonic potential with a force constant
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*K* of 200.0 energy units:
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.. math::
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U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad theta = \theta_i - \theta_0
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U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the
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*lepton* angle style interfaces with, evaluates this expression string at
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run time to compute the pairwise energy. It also creates an analytical
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representation of the differentiation of this expression with respect to
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representation of the first derivative of this expression with respect to
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"r" and then uses that to compute the force between the pairs atoms forming
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angles as defined by the topology data.
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@ -59,10 +60,10 @@ The Lepton expression must be either enclosed in quotes or must not
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contain any whitespace so that LAMMPS recognizes it as a single keyword.
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More on valid Lepton expressions below. The :math:`\theta_0`
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coefficient is the "equilibrium angle". It is entered in degrees, but
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internally converted to radians. Thus the expression must assume "theta"
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is in radians. The potential energy function in the Lepton expression
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is shifted in such a way, that the potential energy is 0 for a angle
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:math:`\theta_i == \theta_0`.
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internally converted to radians. Thus the expression must assume
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"theta" is in radians. The potential energy function in the Lepton
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expression is shifted in such a way, that the potential energy is 0 for
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a angle :math:`\theta_i == \theta_0`.
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----------
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@ -77,14 +78,15 @@ is shifted in such a way, that the potential energy is 0 for a angle
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Restrictions
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""""""""""""
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This angle style can only be used if LAMMPS was built with the LEPTON
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package. See the :doc:`Build package <Build_package>` page for more
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info.
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This angle style is part of the LEPTON package and only enabled if LAMMPS
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was built with this package. See the :doc:`Build package
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<Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`angle_coeff <angle_coeff>`
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:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style table <angle_table>`,
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:doc:`bond_style lepton <bond_lepton>`
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Default
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"""""""
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@ -20,21 +20,22 @@ Examples
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bond_style lepton
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1 1.5 "k*r^2; k=250.0"
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2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
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3 1.3 "k*r^2; k=350.0"
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bond_coeff 1 1.5 "k*r^2; k=250.0"
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bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
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bond_coeff 3 1.3 "k*r^2; k=350.0"
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Description
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"""""""""""
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.. versionadded:: TBD
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Bond style *lepton* computes bonded interactions between two atom based
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on evaluating strings. The potential function must be provided as an
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expression string using "r" as the distance variable relative to the
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reference distance :math:`r_0` which is provided as a bond coefficient.
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For example `"200.0*(r)^2"` represents a harmonic potential with a force
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constant *K* of 200.0 energy units:
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Bond style *lepton* computes bonded interactions between two atoms,
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between which a bond has been defined, based on evaluating strings. The
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potential function must be provided as an expression string using "r" as
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the distance variable relative to the reference distance :math:`r_0`
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which is provided as a bond coefficient. For example `"200.0*r^2"`
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represents a harmonic potential with a force constant *K* of 200.0
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energy units:
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.. math::
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@ -43,12 +44,12 @@ constant *K* of 200.0 energy units:
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the
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*lepton* bond style interfaces with, evaluates this expression string at
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run time to compute the pairwise energy. It also creates an analytical
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representation of the differentiation of this expression with respect to
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representation of the first derivative of this expression with respect to
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"r" and then uses that to compute the force between the pairs atoms forming
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bonds as defined by the topology data.
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The following coefficients must be defined for each bond type via the
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:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
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:doc:`bond_coeff <bond_coeff>` command as in the examples above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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or :doc:`read_restart <read_restart>` commands:
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@ -57,7 +58,7 @@ or :doc:`read_restart <read_restart>` commands:
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The Lepton expression must be either enclosed in quotes or must not
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contain any whitespace so that LAMMPS recognizes it as a single keyword.
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More on valid Lepton expressions below. The :math:`r_0` it the
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More on valid Lepton expressions below. The :math:`r_0` is the
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"equilibrium distance". The potential energy function in the Lepton
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expression is shifted in such a way, that the potential energy is 0 for
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a bond length :math:`r_i == r_0`.
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@ -75,14 +76,15 @@ a bond length :math:`r_i == r_0`.
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Restrictions
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""""""""""""
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This bond style can only be used if LAMMPS was built with the LEPTON
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package. See the :doc:`Build package <Build_package>` page for more
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info.
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This bond style is part of the LEPTON package and only enabled if LAMMPS
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was built with this package. See the :doc:`Build package
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<Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
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:doc:`bond_coeff <bond_coeff>`, :doc:`bond_style table <bond_table>`,
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:doc:`bond_write <bond_write>`, :doc:`angle_style lepton <angle_lepton>`
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Default
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"""""""
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@ -84,7 +84,7 @@ variables. If necessary, a custom scalar variable needs to be defined
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that can access the desired (single) item from a non-scalar variable.
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As an example, the following lines will instruct LAMMPS to ramp
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the force constant for a harmonic bond from 100.0 to 200.0 during the
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next run;
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next run:
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.. code-block:: LAMMPS
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@ -113,5 +113,10 @@ definition. For efficiency reasons, the expression string is parsed,
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optimized, and then stored in an internal, pre-parsed representation for
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evaluation.
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Evaluating Lepton expressions is typically between 2.5 and 5 times
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slower than the corresponding compiled and optimized C++ code.
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Evaluating a Lepton expression is typically between 2.5 and 5 times
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slower than the corresponding compiled and optimized C++ code. If
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additional speed or GPU acceleration (via GPU or KOKKOS) is required,
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the interaction can be represented as a table. Suitable table files
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can be created either internally using the :doc:`pair_write <pair_write>`
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or :doc:`bond_write <bond_write>` command or through the Python scripts
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in the :ref:`tools/tabulate <tabulate>` folder.
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@ -27,9 +27,10 @@ Examples
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.. code-block:: LAMMPS
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pair_style lepton 2.5
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pair_coeff * * "k*((r-r0)^2*step(r0-r)); k=200; r0=1.5" 2.0
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pair_coeff 1 2 "4.0*eps*((sig/r)^12 - (sig/r)^6);eps=1.0;sig=1.0" 1.12246204830937
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pair_coeff 2 2 "eps*(2.0*(sig/r)^9 - 3.0*(sig/r)^6);eps=1.0;sig=1.0"
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pair_coeff * * "k*((r-r0)^2*step(r0-r)); k=200; r0=1.5" 2.0
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pair_coeff 1 2 "4.0*eps*((sig/r)^12 - (sig/r)^6);eps=1.0;sig=1.0" 1.12246204830937
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pair_coeff 2 2 "eps*(2.0*(sig/r)^9 - 3.0*(sig/r)^6);eps=1.0;sig=1.0"
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Description
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"""""""""""
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@ -37,11 +38,11 @@ Description
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.. versionadded:: TBD
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Pair style *lepton* computes spherical pairwise interactions based on
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evaluating strings. The potential function must be provided as an
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expression string using "r" as the distance variable, for example
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`"200.0*(r-1.5)^2"` represents a harmonic potential with equilibrium
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distance :math:`r_0` of 1.5 distance units and a force constant *K* of
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200.0 energy units:
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evaluating strings between neighboring atoms within the given cutoff.
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The potential function must be provided as an expression string using
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"r" as the distance variable. For example `"200.0*(r-1.5)^2"` represents
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a harmonic potential around the distance :math:`r_0` of 1.5 distance
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units and a force constant *K* of 200.0 energy units:
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.. math::
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@ -50,7 +51,7 @@ distance :math:`r_0` of 1.5 distance units and a force constant *K* of
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The `Lepton library <https://simtk.org/projects/lepton>`_, that the
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*lepton* pair style interfaces with, evaluates this expression string at
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run time to compute the pairwise energy. It also creates an
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analytical representation of the differentiation of this expression with
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analytical representation of the first derivative of this expression with
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respect to "r" and then uses that to compute the force between the pairs
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of particles within the given cutoff.
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@ -81,18 +82,19 @@ different value than the global cutoff.
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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Pair style *lepton* does **not** support mixing. Thus, expressions for
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all I,J pairs must be specified explicitly.
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Pair style *lepton* does not support mixing. Thus, expressions for
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*all* I,J pairs must be specified explicitly.
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This pair style supports the :doc:`pair_modify <pair_modify>`
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shift option for the energy of the pair interaction.
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This pair style does supports the :doc:`pair_modify shift <pair_modify>`
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option for shifting the energy of the pair interaction so that it is
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0 at the cutoff.
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The :doc:`pair_modify <pair_modify>` table options are not relevant for
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The :doc:`pair_modify table <pair_modify>` options are not relevant for
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the this pair style.
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This pair style does not support the :doc:`pair_modify <pair_modify>`
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tail option for adding long-range tail corrections to energy and
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pressure.
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This pair style does not support the :doc:`pair_modify tail
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<pair_modify>` option for adding long-range tail corrections to energy
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and pressure.
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This pair style writes its information to :doc:`binary restart files
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<restart>`, so pair_style and pair_coeff commands do not need to be
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@ -107,7 +109,7 @@ This pair style can only be used via the *pair* keyword of the
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Restrictions
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""""""""""""
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The *lepton* pair style is part of the LEPTON package and only enabled if
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This pair style is part of the LEPTON package and only enabled if
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LAMMPS was built with this package. See the :doc:`Build package
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<Build_package>` page for more info.
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