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Merge pull request #2958 from jddietz/nm_split_styles

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nm split styles
This commit is contained in:
Axel Kohlmeyer
2021-12-10 13:42:31 -05:00
committed by GitHub
parent e1e46b5322 ac57c44552
commit fa8e2ccee8
14 changed files with 837 additions and 12 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 <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>`

46
doc/src/bond_fene.rst
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@ -1,4 +1,5 @@
.. index:: bond_style fene
.. index:: bond_style fene/nm
.. index:: bond_style fene/intel
.. index:: bond_style fene/kk
.. index:: bond_style fene/omp
@ -8,12 +9,16 @@ bond_style fene command
Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
bond_style fene/nm command
==========================
Syntax
""""""
.. code-block:: LAMMPS
bond_style fene
bond_style fene/nm
Examples
""""""""
@ -23,6 +28,9 @@ Examples
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
bond_style fene/nm
bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
Description
"""""""""""
@ -38,16 +46,36 @@ 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 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:
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{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
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* 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)
----------
.. include:: accel_styles.rst
@ -57,9 +85,10 @@ or :doc:`read_restart <read_restart>` commands:
Restrictions
""""""""""""
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the :doc:`Build package <Build_package>` page for more
info.
The *fene* bond style can only be used if LAMMPS was built with the MOLECULE
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.
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
@ -68,7 +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
"""""""

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 <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

30
doc/src/pair_nm.rst
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@ -1,4 +1,5 @@
.. index:: pair_style nm/cut
.. index:: pair_style nm/cut/split
.. index:: pair_style nm/cut/coul/cut
.. index:: pair_style nm/cut/coul/long
.. index:: pair_style nm/cut/omp
@ -10,6 +11,9 @@ pair_style nm/cut command
Accelerator Variants: *nm/cut/omp*
pair_style nm/cut/split command
===============================
pair_style nm/cut/coul/cut command
==================================
@ -27,13 +31,15 @@ Syntax
pair_style style args
* style = *nm/cut* or *nm/cut/coul/cut* or *nm/cut/coul/long*
* style = *nm/cut* or *nm/cut/split* or *nm/cut/coul/cut* or *nm/cut/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*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)
*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)
@ -50,6 +56,10 @@ Examples
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
pair_style nm/cut/split 1.12246
pair_coeff 1 1 1.0 1.1246 12 6
pair_coeff * * 1.0 1.1246 11 6
pair_style nm/cut/coul/cut 12.0 15.0
pair_coeff * * 0.01 5.4 8.0 7.0
pair_coeff 1 1 0.01 4.4 7.0 6.0
@ -71,7 +81,15 @@ interaction has the following form:
E = \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n
\left(\frac{r_0}{r}\right)^m \right] \qquad r < r_c
where :math:`r_c` is the cutoff.
where :math:`r_c` is the cutoff and :math:`r_0` is the minimum of the
potential. Please note that this differs from the convention used for
other Lennard-Jones potentials in LAMMPS where :math:`\sigma` represents
the location where the energy is zero.
Style *nm/cut/split* applies the standard LJ (12-6) potential above
:math:`r_0 = 2^\frac{1}{6}\sigma`. Style *nm/cut/split* is employed in
polymer equilibration protocols that combine core-softening approaches
with topology-changing moves :ref:`Dietz <Dietz>`.
Style *nm/cut/coul/cut* adds a Coulombic pairwise interaction given by
@ -155,7 +173,6 @@ the :doc:`run_style respa <run_style>` command. They do not support the
Restrictions
""""""""""""
These pair styles are part of the EXTRA-PAIR package. They are only enabled if
LAMMPS was built with that package. See the
:doc:`Build package <Build_package>` page for more info.
@ -163,7 +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
"""""""
@ -175,3 +192,8 @@ none
.. _Clarke:
**(Clarke)** Clarke and Smith, J Chem Phys, 84, 2290 (1986).
.. _Dietz:
**(Dietz)** J.D. Dietz, R.S. Hoy, "Facile equilibration of well-entangled
semi-flexible bead-spring polymer melts" arXiv:2109.11001

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>` -

2
doc/utils/sphinx-config/false_positives.txt
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@ -692,6 +692,7 @@ diblock
dichalcogenide
Dickel
diel
Dietz
differentiable
diffusively
diffusivity
@ -1311,6 +1312,7 @@ hotpink
Houlle
howto
Howto
Hoy
Hoyt
Hs
hstyle