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clarify docs for bond style fene/nm/split and rename to fene/nm

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This commit is contained in:
Axel Kohlmeyer
2021-12-06 16:20:39 -05:00
parent 021a59965e
commit 6314290558
6 changed files with 47 additions and 36 deletions
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2
doc/src/Commands_bond.rst
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@ -35,7 +35,7 @@ OPT.
* :doc:`class2 (ko) <bond_class2>`
* :doc:`fene (iko) <bond_fene>`
* :doc:`fene/expand (o) <bond_fene_expand>`
* :doc:`fene/nm/split <bond_fene>`
* :doc:`fene/nm <bond_fene>`
* :doc:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`

39
doc/src/bond_fene.rst
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@ -1,5 +1,5 @@
.. index:: bond_style fene
.. index:: bond_style fene/nm/split
.. index:: bond_style fene/nm
.. index:: bond_style fene/intel
.. index:: bond_style fene/kk
.. index:: bond_style fene/omp
@ -9,8 +9,8 @@ bond_style fene command
Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
bond_style fene/nm/split command
================================
bond_style fene/nm command
==========================
Syntax
""""""
@ -18,7 +18,7 @@ Syntax
.. code-block:: LAMMPS
bond_style fene
bond_style fene/nm/split
bond_style fene/nm
Examples
""""""""
@ -28,7 +28,7 @@ Examples
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_style fene/nm/split
bond_style fene/nm
bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
Description
@ -46,23 +46,33 @@ term is attractive, the second Lennard-Jones term is repulsive. The
first term extends to :math:`R_0`, the maximum extent of the bond. The second
term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
The *fene/nm/split* bond style substitutes the standard LJ potential with the generalized LJ potential. The bond energy is then given by
The *fene/nm* bond style substitutes the standard LJ potential with the generalized LJ potential
in the same form as in pair style :doc:`nm/cut <pair_nm>`. The bond energy is then given by
.. math::
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{\epsilon}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
E = -0.5 K r_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
The following coefficients must be defined for each bond type via the
:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
the data file or restart files read by the :doc:`read_data <read_data>`
or :doc:`read_restart <read_restart>` commands:
Similar to the *fene* style, the generalized Lennard-Jones is cut off at
the potential minimum, :math:`r_0`, to be repulsive only. The following
coefficients must be defined for each bond type via the :doc:`bond_coeff
<bond_coeff>` command as in the example above, or in the data file or
restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands:
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
For the *fene/nm/split* style, the following additional coefficients are needed. Note, the standard LJ potential is recovered for (n=12 m=6).
For the *fene/nm* style, the following coefficients are used. Please
note, that the standard LJ potential and thus the regular FENE potential
is recovered for (n=12 m=6) and :math:`r_0 = 2^\frac{1}{6} \sigma`.
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`E_0` (energy)
* :math:`r_0` (distance)
* :math:`n` (unitless)
* :math:`m` (unitless)
@ -76,7 +86,7 @@ Restrictions
""""""""""""
The *fene* bond style can only be used if LAMMPS was built with the MOLECULE
package; the *fene/nm/split* bond style can only be used if LAMMPS was built
package; the *fene/nm* bond style can only be used if LAMMPS was built
with the EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
page for more info.
@ -87,7 +97,8 @@ style. LAMMPS will issue a warning it that's not the case.
Related commands
""""""""""""""""
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`,
:doc:`pair style lj/cut <pair_lj>`, :doc:`pair style nm/cut <pair_nm>`.
Default
"""""""

2
doc/src/bond_style.rst
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@ -87,7 +87,7 @@ accelerated styles exist.
* :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
* :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
* :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
* :doc:`fene/nm/split <bond_fene>` - FENE bonds with a generalized Lennard-Jones potential
* :doc:`fene/nm <bond_fene>` - FENE bonds with a generalized Lennard-Jones potential
* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond

2
doc/src/pair_nm.rst
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@ -180,7 +180,7 @@ LAMMPS was built with that package. See the
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair style lj/cut <pair_lj>`, :doc:`bond style fene/nm <bond_fene>`
Default
"""""""