mwlc angle documentation

doc/src/Commands_bond.rst

@@ -90,6 +90,7 @@ OPT.
    * :doc:`lepton (o) <angle_lepton>`
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
+   * :doc:`mwlc <angle_mwlc>`
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`spica (ko) <angle_spica>`
    * :doc:`table (o) <angle_table>`

doc/src/angle_mwlc.rst

@@ -0,0 +1,81 @@
+.. index:: angle_style mwlc
+
+angle_style mwlc command
+==========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mwlc
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mwlc
+   angle_coeff * 25.0 1.0 10.0
+
+Description
+"""""""""""
+
+The *mwlc* angle style models a meltable wormlike chain, using a potential that is a canonical-ensemble superposition of
+a non-melted and a melted state :ref:`(Farrell) <Farrell>`,
+
+.. math::
+
+    \beta E = -\log [q + q^{m}],
+
+where
+
+.. math::
+    q = \exp [-l_{p}(1-\cos{\theta})/\sigma], \\
+    q^{m} = \exp [-\beta\mu-l_{p}^{m}(1-\cos{\theta})/\sigma],
+
+:math:`l_{p}` is the persistence length of the non-melted state,
+:math:`l_{p}^{m}` is the persistence length of the melted state,
+and :math:`\mu` is the melting energy.
+
+This potential is a continuous version of the two-state potential
+introduced by :ref:`(Yan) <Yan>`.
+
+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
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* :math:`l_{p}` (distance)
+* :math:`l_{p}^{m}` (distance)
+* :math:`\mu` (energy)
+
+----------
+
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
+for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Farrell:
+
+**(Farrell)** Farrell, Dobnikar, Podgornik, Curk, Phys Rev Lett, in production.
+
+.. _Yan:
+
+**(Yan)** Yan, Marko, Phys Rev Lett, 93, 108108 (2004).

doc/src/angle_style.rst

@@ -94,6 +94,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`lepton <angle_lepton>` - angle potential from evaluating a string
 * :doc:`mesocnt <angle_mesocnt>` - piecewise harmonic and linear angle for bending-buckling of nanotubes
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
+* :doc:`mwlc <angle_mwlc>` - meltable wormlike chain
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
 * :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
 * :doc:`table <angle_table>` - tabulated by angle

doc/utils/sphinx-config/false_positives.txt

@@ -711,6 +711,7 @@ Dasgupta
 dashpot
 dat
 datafile
+dataset
 datatype
 datums
 Davidchack
@@ -2109,6 +2110,7 @@ Marchi
 Mariella
 Marinica
 Markland
+Marko
 Marrink
 Marroquin
 Marsaglia
@@ -2191,6 +2193,7 @@ Meissner
 Melchor
 Meloni
 Melrose
+meltable
 mem
 Mem
 memalign
@@ -2399,6 +2402,7 @@ mV
 Mvapich
 mvh
 mvv
+mwlc
 MxN
 myCompute
 myIndex
@@ -2919,6 +2923,7 @@ Pmoltrans
 pN
 png
 podd
+Podgornik
 Podhorszki
 Poiseuille
 poisson
@@ -4100,6 +4105,7 @@ workflow
 workflows
 Workum
 Worley
+wormlike
 Wriggers
 writedata
 Wuppertal
@@ -4168,6 +4174,7 @@ yaff
 YAFF
 Yamada
 yaml
+Yan
 Yanxon
 Yaser
 Yazdani