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make documentation consistent and properly integrate it

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This commit is contained in:
Axel Kohlmeyer
2021-10-08 16:24:57 -04:00
parent fc42992cdf
commit 3313d3bfa3
6 changed files with 19 additions and 17 deletions
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1
doc/src/Commands_bond.rst
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@ -35,6 +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:`gaussian <bond_gaussian>`
* :doc:`gromos (o) <bond_gromos>`
* :doc:`harmonic (iko) <bond_harmonic>`

1
doc/src/Commands_pair.rst
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@ -210,6 +210,7 @@ OPT.
* :doc:`nm/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/cut (o) <pair_nm>`
* :doc:`nm/cut/coul/long (o) <pair_nm>`
* :doc:`nm/cut/split <pair_nm>`
* :doc:`oxdna/coaxstk <pair_oxdna>`
* :doc:`oxdna/excv <pair_oxdna>`
* :doc:`oxdna/hbond <pair_oxdna>`

24
doc/src/bond_fene.rst
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@ -1,5 +1,5 @@
.. index:: bond_style fene
.. index:: bond_style fene/nm/cut
.. index:: bond_style fene/nm/split
.. index:: bond_style fene/intel
.. index:: bond_style fene/kk
.. index:: bond_style fene/omp
@ -9,9 +9,8 @@ bond_style fene command
Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
bond_style fene/nm/cut command
==============================
bond_style fene/nm/split command
================================
Syntax
""""""
@ -19,7 +18,7 @@ Syntax
.. code-block:: LAMMPS
bond_style fene
bond_style fene/nm/cut
bond_style fene/nm/split
Examples
""""""""
@ -29,7 +28,7 @@ Examples
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_style fene/nm/cut
bond_style fene/nm/split
bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
Description
@ -43,11 +42,11 @@ The *fene* bond style uses the potential
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the second Lennard-Jones (LJ) term is repulsive. The
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/cut* bond style substitutes the standard LJ potential with the generalized LJ potential. The bond energy is then given by
The *fene/nm/split* bond style substitutes the standard LJ potential with the generalized LJ potential. 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]
@ -62,7 +61,7 @@ or :doc:`read_restart <read_restart>` commands:
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
For the *fene/nm/cut* style, the following additional coefficients are needed. Note, the standard LJ potential is recovered for (n=12 m=6).
For the *fene/nm/split* style, the following additional coefficients are needed. Note, the standard LJ potential is recovered for (n=12 m=6).
* :math:`n` (unitless)
* :math:`m` (unitless)
@ -76,9 +75,10 @@ For the *fene/nm/cut* style, the following additional coefficients are needed. N
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the :doc:`Build package <Build_package>` doc page for more
info.
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
with the EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
page for more info.
You typically should specify :doc:`special_bonds fene <special_bonds>`
or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond

1
doc/src/bond_style.rst
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@ -87,6 +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:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
* :doc:`gromos <bond_gromos>` - GROMOS force field bond
* :doc:`harmonic <bond_harmonic>` - harmonic bond

8
doc/src/pair_nm.rst
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@ -14,8 +14,6 @@ Accelerator Variants: *nm/cut/omp*
pair_style nm/cut/split command
===============================
Accelerator Variants:*nm/cut/split/omp*
pair_style nm/cut/coul/cut command
==================================
@ -41,7 +39,7 @@ Syntax
*nm/cut* args = cutoff
cutoff = global cutoff for Pair interactions (distance units)
*nm/cut/split* args = cutoff
cutoff = global cutoff for Pair interactions (distance units)
cutoff = global cutoff for Pair interactions (distance units)
*nm/cut/coul/cut* args = cutoff (cutoff2)
cutoff = global cutoff for Pair (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -128,7 +126,7 @@ N-M and Coulombic cutoffs specified in the pair_style command are used.
If only one cutoff is specified, it is used as the cutoff for both N-M
and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the N-M and Coulombic cutoffs for this
type pair. You cannot specify 2 cutoffs for style *nm*\ , since it
type pair. You cannot specify 2 cutoffs for style *nm*, since it
has no Coulombic terms.
For *nm/cut/coul/long* only the N-M cutoff can be specified since a
@ -161,7 +159,7 @@ to be specified in an input script that reads a restart file.
All of the *nm* pair styles can only be used via the *pair* keyword of
the :doc:`run_style respa <run_style>` command. They do not support the
*inner* , *middle* , *outer* keywords.
*inner*, *middle*, *outer* keywords.
----------

1
doc/src/pair_style.rst
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@ -274,6 +274,7 @@ accelerated styles exist.
* :doc:`nm/cut <pair_nm>` - N-M potential
* :doc:`nm/cut/coul/cut <pair_nm>` - N-M potential with cutoff Coulomb
* :doc:`nm/cut/coul/long <pair_nm>` - N-M potential with long-range Coulomb
* :doc:`nm/cut/split <pair_nm>` - Split 12-6 Lennard-Jones and N-M potential
* :doc:`oxdna/coaxstk <pair_oxdna>` -
* :doc:`oxdna/excv <pair_oxdna>` -
* :doc:`oxdna/hbond <pair_oxdna>` -