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Merge pull request #1775 from rbberger/doc_updates

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Update bond docs
This commit is contained in:
Axel Kohlmeyer
2019-11-18 11:32:07 -05:00
committed by GitHub
parent 2e6b19ea5f 19b265f845
commit fbf280f6a3
69 changed files with 327 additions and 2755 deletions
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23
cmake/Modules/Documentation.cmake
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@ -9,9 +9,7 @@ if(BUILD_DOC)
set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.txt)
file(GLOB PDF_EXTRA_SOURCES ${LAMMPS_DOC_DIR}/src/lammps_commands*.txt ${LAMMPS_DOC_DIR}/src/lammps_support.txt ${LAMMPS_DOC_DIR}/src/lammps_tutorials.txt)
list(REMOVE_ITEM DOC_SOURCES ${PDF_EXTRA_SOURCES})
file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
add_custom_command(
OUTPUT docenv
@ -28,25 +26,10 @@ if(BUILD_DOC)
COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
)
set(RST_FILES "")
set(RST_DIR ${CMAKE_BINARY_DIR}/rst)
file(MAKE_DIRECTORY ${RST_DIR})
foreach(TXT_FILE ${DOC_SOURCES})
get_filename_component(FILENAME ${TXT_FILE} NAME_WE)
set(RST_FILE ${RST_DIR}/${FILENAME}.rst)
list(APPEND RST_FILES ${RST_FILE})
add_custom_command(
OUTPUT ${RST_FILE}
DEPENDS requirements.txt docenv ${TXT_FILE}
COMMAND ${DOCENV_BINARY_DIR}/txt2rst -o ${RST_DIR} ${TXT_FILE}
)
endforeach()
add_custom_command(
OUTPUT html
DEPENDS ${RST_FILES}
COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src ${RST_DIR}
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${RST_DIR} html
DEPENDS ${DOC_SOURCES} docenv requirements.txt
COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
)
add_custom_target(

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doc/src/Eqs/bond_class2.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
$$
\end{document}

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doc/src/Eqs/bond_fene.tex
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@ -1,11 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

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doc/src/Eqs/bond_fene_expand.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = -0.5 K R_0^2
\ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] +
4 \epsilon \left[ \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r -
\Delta\right)}\right)^6 \right] + \epsilon
$$
\end{document}

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doc/src/Eqs/bond_gromos.tex
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@ -1,10 +0,0 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = K (r^2 - r_0^2)^2
$$
\end{document}

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doc/src/Eqs/bond_harmonic.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - r_0)^2
$$
\end{document}

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doc/src/Eqs/bond_harmonic_shift.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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doc/src/Eqs/bond_harmonic_shift_cut.tex
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@ -1,9 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{Umin}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
$$
\end{document}

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doc/src/Eqs/bond_mm3.tex
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@ -1,9 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
\thispagestyle{empty}
$$
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
$$
\end{document}

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doc/src/Eqs/bond_morse.tex
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@ -1,10 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
$$
\end{document}

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doc/src/Eqs/bond_nonlinear.tex
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\documentclass[12pt]{article}
\begin{document}
$$
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
$$
\end{document}

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doc/src/Eqs/bond_oxdna_fene.tex
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@ -1,10 +0,0 @@
\documentclass[12pt]{article}
\pagestyle{empty}
\begin{document}
$$
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
$$
\end{document}

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doc/src/Eqs/bond_quartic.tex
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@ -1,11 +0,0 @@
\documentclass[12pt]{article}
\begin{document}
$$
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 +
4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
$$
\end{document}

15
doc/src/atom_modify.rst
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@ -1,13 +1,13 @@
.. index:: atom\_modify
.. index:: atom_modify
atom\_modify command
====================
atom_modify command
===================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_modify keyword values ...
@ -29,7 +29,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_modify map yes
atom_modify map hash sort 10000 2.0
@ -188,8 +188,3 @@ defined, sorting will be turned off.
**(Meloni)** Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

15
doc/src/atom_style.rst
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@ -1,13 +1,13 @@
.. index:: atom\_style
.. index:: atom_style
atom\_style command
===================
atom_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_style style args
@ -33,7 +33,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
atom_style atomic
atom_style bond
@ -371,8 +371,3 @@ atom\_style atomic
**(Grime)** Grime and Voth, to appear in J Chem Theory & Computation
(2014).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

39
doc/src/bond_class2.rst
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@ -1,19 +1,19 @@
.. index:: bond\_style class2
.. index:: bond_style class2
bond\_style class2 command
==========================
bond_style class2 command
=========================
bond\_style class2/omp command
==============================
bond\_style class2/kk command
bond_style class2/omp command
=============================
bond_style class2/kk command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style class2
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0
@ -31,10 +31,12 @@ Description
The *class2* bond style uses the potential
.. image:: Eqs/bond_class2.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance.
E = K_2 (r - r_0)^2 + K_3 (r - r_0)^3 + K_4 (r - r_0)^4
where :math:`r_0` is the equilibrium bond distance.
See :ref:`(Sun) <bond-Sun>` for a description of the COMPASS class2 force field.
@ -43,10 +45,10 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* R0 (distance)
* K2 (energy/distance\^2)
* K3 (energy/distance\^3)
* K4 (energy/distance\^4)
* :math:`r_0` (distance)
* :math:`K_2` (energy/distance\^2)
* :math:`K_3` (energy/distance\^3)
* :math:`K_4` (energy/distance\^4)
----------
@ -98,8 +100,3 @@ Related commands
**(Sun)** Sun, J Phys Chem B 102, 7338-7364 (1998).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

23
doc/src/bond_coeff.rst
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@ -1,13 +1,13 @@
.. index:: bond\_coeff
.. index:: bond_coeff
bond\_coeff command
===================
bond_coeff command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff N args
@ -18,11 +18,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff 5 80.0 1.2
bond_coeff \* 30.0 1.5 1.0 1.0
bond_coeff 1\*4 30.0 1.5 1.0 1.0
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0
Description
@ -47,9 +47,9 @@ for the same bond type. For example, these commands set the coeffs
for all bond types, then overwrite the coeffs for just bond type 2:
.. parsed-literal::
.. code-block:: LAMMPS
bond_coeff \* 100.0 1.2
bond_coeff * 100.0 1.2
bond_coeff 2 200.0 1.2
A line in a data file that specifies bond coefficients uses the exact
@ -97,8 +97,3 @@ Related commands
:doc:`bond\_style <bond_style>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

45
doc/src/bond_fene.rst
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@ -1,22 +1,22 @@
.. index:: bond\_style fene
.. index:: bond_style fene
bond\_style fene command
========================
bond_style fene command
=======================
bond\_style fene/intel command
==============================
bond_style fene/intel command
=============================
bond\_style fene/kk command
bond_style fene/kk command
==========================
bond_style fene/omp command
===========================
bond\_style fene/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0
@ -34,24 +34,26 @@ Description
The *fene* bond style uses the potential
.. image:: Eqs/bond_fene.jpg
:align: center
.. math::
E = -0.5 K R_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
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 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2\^(1/6) sigma, the minimum of the LJ potential.
first term extends to :math:`R_0`, the maximum extent of the bond. The 2nd
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:
* K (energy/distance\^2)
* R0 (distance)
* epsilon (energy)
* sigma (distance)
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
----------
@ -107,8 +109,3 @@ Related commands
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

40
doc/src/bond_fene_expand.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style fene/expand
.. index:: bond_style fene/expand
bond\_style fene/expand command
===============================
bond_style fene/expand command
==============================
bond\_style fene/expand/omp command
===================================
bond_style fene/expand/omp command
==================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene/expand
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5
@ -28,29 +28,30 @@ Description
The *fene/expand* bond style uses the potential
.. image:: Eqs/bond_fene_expand.jpg
:align: center
.. math::
E = -0.5 K R_0^2 \ln \left[1 -\left( \frac{\left(r - \Delta\right)}{R_0}\right)^2 \right] + 4 \epsilon \left[ \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^{12} - \left(\frac{\sigma}{\left(r - \Delta\right)}\right)^6 \right] + \epsilon
to define a finite extensible nonlinear elastic (FENE) potential
:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The *fene/expand* bond style is similar to *fene* except that an extra
shift factor of delta (positive or negative) is added to *r* to
shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2\^(1/6) sigma
+ delta.
now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
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:
* K (energy/distance\^2)
* R0 (distance)
* epsilon (energy)
* sigma (distance)
* delta (distance)
* :math:`K` (energy/distance\^2)
* :math:`R_0` (distance)
* :math:`\epsilon` (energy)
* :math:`\sigma` (distance)
* :math:`\Delta` (distance)
----------
@ -106,8 +107,3 @@ Related commands
**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

33
doc/src/bond_gromos.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style gromos
.. index:: bond_style gromos
bond\_style gromos command
==========================
bond_style gromos command
=========================
bond\_style gromos/omp command
==============================
bond_style gromos/omp command
=============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style gromos
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style gromos
bond_coeff 5 80.0 1.2
@ -28,19 +28,21 @@ Description
The *gromos* bond style uses the potential
.. image:: Eqs/bond_gromos.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance. Note that the usual 1/4
factor is included in K.
E = K (r^2 - r_0^2)^2
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/4
factor is included in :math:`K`.
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:
* K (energy/distance\^4)
* r0 (distance)
* :math:`K` (energy/distance\^4)
* :math:`r_0` (distance)
----------
@ -82,8 +84,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

41
doc/src/bond_harmonic.rst
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@ -1,22 +1,22 @@
.. index:: bond\_style harmonic
.. index:: bond_style harmonic
bond\_style harmonic command
============================
bond_style harmonic command
===========================
bond\_style harmonic/intel command
==================================
bond_style harmonic/intel command
=================================
bond\_style harmonic/kk command
bond_style harmonic/kk command
==============================
bond_style harmonic/omp command
===============================
bond\_style harmonic/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
@ -24,7 +24,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
bond_coeff 5 80.0 1.2
@ -34,19 +34,21 @@ Description
The *harmonic* bond style uses the potential
.. image:: Eqs/bond_harmonic.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
E = K (r - r_0)^2
where :math:`r_0` is the equilibrium bond distance. Note that the usual 1/2
factor is included in :math:`K`.
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:
* K (energy/distance\^2)
* r0 (distance)
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
----------
@ -88,8 +90,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

37
doc/src/bond_harmonic_shift.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style harmonic/shift
.. index:: bond_style harmonic/shift
bond\_style harmonic/shift command
==================================
bond_style harmonic/shift command
=================================
bond\_style harmonic/shift/omp command
======================================
bond_style harmonic/shift/omp command
=====================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0
@ -29,23 +29,25 @@ Description
The *harmonic/shift* bond style is a shifted harmonic bond that uses
the potential
.. image:: Eqs/bond_harmonic_shift.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / [ 2 (r0-rc)\^2].
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and :math:`r_c` the critical distance.
The potential is :math:`-U_{\text{min}}` at :math:`r0` and zero at :math:`r_c`. The spring constant is
:math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
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:
* Umin (energy)
* :math:`U_{\text{min}}` (energy)
* r0 (distance)
* :math:`r_0` (distance)
* rc (distance)
* :math:`r_c` (distance)
----------
@ -88,8 +90,3 @@ Related commands
:doc:`bond\_harmonic <bond_harmonic>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

37
doc/src/bond_harmonic_shift_cut.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style harmonic/shift/cut
.. index:: bond_style harmonic/shift/cut
bond\_style harmonic/shift/cut command
======================================
bond_style harmonic/shift/cut command
=====================================
bond\_style harmonic/shift/cut/omp command
==========================================
bond_style harmonic/shift/cut/omp command
=========================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift/cut
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0
@ -29,21 +29,23 @@ Description
The *harmonic/shift/cut* bond style is a shifted harmonic bond that
uses the potential
.. image:: Eqs/bond_harmonic_shift_cut.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / [ 2 (r0-rc)\^2].
E = \frac{U_{\text{min}}}{(r_0-r_c)^2} \left[ (r-r_0)^2-(r_c-r_0)^2 \right]
where :math:`r_0` is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances :math:`r > r_c`. The potential is :math:`-U_{\text{min}}`
at :math:`r_0` and zero at :math:`r_c`. The spring constant is :math:`k = U_{\text{min}} / [ 2 (r_0-r_c)^2]`.
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:
* Umin (energy)
* r0 (distance)
* rc (distance)
* :math:`U_{\text{min}}` (energy)
* :math:`r_0` (distance)
* :math:`r_c` (distance)
----------
@ -87,8 +89,3 @@ Related commands
:doc:`bond\_harmonic\_shift <bond_harmonic_shift>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_hybrid.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style hybrid
.. index:: bond_style hybrid
bond\_style hybrid command
==========================
bond_style hybrid command
=========================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style hybrid style1 style2 ...
@ -17,11 +17,11 @@ Examples
""""""""
.. parsed-literal::
.. code-block: LAMMPS
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2\* fene 30.0 1.5 1.0 1.0
bond_coeff 2* fene 30.0 1.5 1.0 1.0
Description
"""""""""""
@ -31,19 +31,19 @@ simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
*fene* potential and bonds in the wall boundary (of bond type 2) could
be computed with a *harmonic* potential. The assignment of bond type
to style is made via the :doc:`bond\_coeff <bond_coeff>` command or in
to style is made via the :doc:`bond_coeff <bond_coeff>` command or in
the data file.
In the bond\_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond\_coeff
commands set bonds of bond type 1 to be computed with a *harmonic*
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
potential with coefficients 80.0, 1.2 for :math:`K`, :math:`r_0`. All other bond types
(2-N) are computed with a *fene* potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
1.5, 1.0, 1.0 for :math:`K`, :math:`R_0`, :math:`\epsilon`, :math:`\sigma`.
If bond coefficients are specified in the data file read via the
:doc:`read\_data <read_data>` command, then the same rule applies.
:doc:`read_data <read_data>` command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
@ -80,11 +80,6 @@ file, you need to re-specify bond\_coeff commands.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_mm3.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style mm3
.. index:: bond_style mm3
bond\_style mm3 command
=======================
bond_style mm3 command
======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style mm3
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style mm3
bond_coeff 1 100.0 107.0
@ -26,10 +26,12 @@ Description
The *mm3* bond style uses the potential that is anharmonic in the bond
as defined in :ref:`(Allinger) <mm3-allinger1989>`
.. image:: Eqs/bond_mm3.jpg
:align: center
.. math::
where r0 is the equilibrium value of the bond, and K is a
E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
prefactor. The anharmonic prefactors have units angstrom\^(-n):
-2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
care of the necessary unit conversion for these factors internally.
@ -41,8 +43,8 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^2)
* r0 (distance)
* :math:`K` (energy/distance\^2)
* :math:`r_0` (distance)
Restrictions
""""""""""""
@ -69,8 +71,3 @@ Related commands
**(Allinger)** Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
(1989),
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

35
doc/src/bond_morse.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style morse
.. index:: bond_style morse
bond\_style morse command
=========================
bond_style morse command
========================
bond\_style morse/omp command
=============================
bond_style morse/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style morse
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style morse
bond_coeff 5 1.0 2.0 1.2
@ -28,20 +28,22 @@ Description
The *morse* bond style uses the potential
.. image:: Eqs/bond_morse.jpg
:align: center
.. math::
where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness
parameter, and :math:`D` determines the depth of the potential well.
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:
* D (energy)
* alpha (inverse distance)
* r0 (distance)
* :math:`D` (energy)
* :math:`\alpha` (inverse distance)
* :math:`r_0` (distance)
----------
@ -83,8 +85,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
doc/src/bond_none.rst
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@ -1,13 +1,13 @@
.. index:: bond\_style none
.. index:: bond_style none
bond\_style none command
========================
bond_style none command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style none
@ -15,7 +15,7 @@ Examples
""""""""
.. parsed-literal::
.. code-blocK:: LAMMPS
bond_style none
@ -24,9 +24,9 @@ Description
Using a bond style of none means bond forces and energies are not
computed, even if pairs of bonded atoms were listed in the data file
read by the :doc:`read\_data <read_data>` command.
read by the :doc:`read_data <read_data>` command.
See the :doc:`bond\_style zero <bond_zero>` command for a way to
See the :doc:`bond_style zero <bond_zero>` command for a way to
calculate bond statistics, but compute no bond interactions.
Restrictions
@ -35,11 +35,6 @@ Restrictions
**Related commands:** none
:doc:`bond\_style zero <bond_zero>`
:doc:`bond_style zero <bond_zero>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

33
doc/src/bond_nonlinear.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style nonlinear
.. index:: bond_style nonlinear
bond\_style nonlinear command
=============================
bond_style nonlinear command
============================
bond\_style nonlinear/omp command
=================================
bond_style nonlinear/omp command
================================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style nonlinear
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4
@ -28,20 +28,22 @@ Description
The *nonlinear* bond style uses the potential
.. image:: Eqs/bond_nonlinear.jpg
:align: center
.. math::
E = \frac{\epsilon (r - r_0)^2}{ [ \lambda^2 - (r - r_0)^2 ]}
to define an anharmonic spring :ref:`(Rector) <Rector>` of equilibrium
length r0 and maximum extension lamda.
length :math:`r_0` and maximum extension lamda.
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:
* epsilon (energy)
* r0 (distance)
* lamda (distance)
* :math:`\epsilon` (energy)
* :math:`r_0` (distance)
* :math:`\lambda` (distance)
----------
@ -93,8 +95,3 @@ Related commands
**(Rector)** Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

35
doc/src/bond_oxdna.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style oxdna/fene
.. index:: bond_style oxdna/fene
bond\_style oxdna/fene command
bond_style oxdna/fene command
=============================
bond_style oxdna2/fene command
==============================
bond\_style oxdna2/fene command
===============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style oxdna/fene
@ -20,21 +20,23 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style oxdna/fene
bond_coeff \* 2.0 0.25 0.7525
bond_coeff * 2.0 0.25 0.7525
bond_style oxdna2/fene
bond_coeff \* 2.0 0.25 0.7564
bond_coeff * 2.0 0.25 0.7564
Description
"""""""""""
The *oxdna/fene* and *oxdna2/fene* bond styles use the potential
.. image:: Eqs/bond_oxdna_fene.jpg
:align: center
.. math::
E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r_0}{\Delta}\right)^2\right]
to define a modified finite extensible nonlinear elastic (FENE)
potential :ref:`(Ouldridge) <oxdna_fene>` to model the connectivity of the
@ -47,9 +49,9 @@ in the data file or restart files read by the
:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
commands:
* epsilon (energy)
* Delta (distance)
* r0 (distance)
* :math:`\epsilon` (energy)
* :math:`\Delta` (distance)
* :math:`r_0` (distance)
.. note::
@ -121,8 +123,3 @@ J. Chem. Phys. 134, 085101 (2011).
**(Snodin)** B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

64
doc/src/bond_quartic.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style quartic
.. index:: bond_style quartic
bond\_style quartic command
===========================
bond_style quartic command
==========================
bond\_style quartic/omp command
===============================
bond_style quartic/omp command
==============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style quartic
@ -18,7 +18,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
@ -28,11 +28,12 @@ Description
The *quartic* bond style uses the potential
.. image:: Eqs/bond_quartic.jpg
:align: center
.. math::
E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
due to a polymer being stretched). The :math:`\sigma` and :math:`\epsilon` used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
The following coefficients must be defined for each bond type via the
@ -40,23 +41,31 @@ The following coefficients must be defined for each bond type via the
the data file or restart files read by the :doc:`read\_data <read_data>`
or :doc:`read\_restart <read_restart>` commands:
* K (energy/distance\^4)
* B1 (distance)
* B2 (distance)
* Rc (distance)
* U0 (energy)
* :math:`K` (energy/distance\^4)
* :math:`B_1` (distance)
* :math:`B_2` (distance)
* :math:`R_c` (distance)
* :math:`U_0` (energy)
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the :doc:`bond\_coeff <bond_coeff>` command, but
you will need to choose them carefully so they form a suitable bond
potential.
coarse-grained polymer chains. When monomers with :math:`\sigma = \epsilon = 1.0`
are used, the following choice of parameters gives a quartic potential that
looks nearly like the FENE potential:
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
.. math::
K &= 1200 \\
B_1 &= -0.55 \\
B_2 &= 0.25 \\
R_c &= 1.3 \\
U_0 &= 34.6878
Different parameters can be specified using the :doc:`bond_coeff <bond_coeff>`
command, but you will need to choose them carefully so they form a suitable
bond potential.
:math:`R_c` is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes :math:`> R_c`, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
@ -75,7 +84,7 @@ Note that when bonds are dumped to a file via the :doc:`dump local <dump>` comma
status of broken bonds or permanently delete them, e.g.:
.. parsed-literal::
.. code-block:: LAMMPS
delete_bonds all stats
delete_bonds all bond 0 remove
@ -124,8 +133,3 @@ Related commands
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

27
doc/src/bond_style.rst
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@ -1,29 +1,27 @@
.. index:: bond\_style
.. index:: bond_style
bond\_style command
===================
bond_style command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style style args
* style = *none* or *hybrid* or *class2* or *fene* or *fene/expand* or *harmonic* or *morse* or *nonlinear* or *quartic*
* args = none for any style except *hybrid*
.. parsed-literal::
args = none for any style except *hybrid*
*hybrid* args = list of one or more styles
* *hybrid* args = list of one or more styles
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style harmonic
bond_style fene
@ -74,11 +72,11 @@ between the 2 atoms in the bond.
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
specified by the associated :doc:`bond_coeff <bond_coeff>` command.
Click on the style to display the formula it computes, any additional
arguments specified in the bond\_style command, and coefficients
specified by the associated :doc:`bond\_coeff <bond_coeff>` command.
specified by the associated :doc:`bond_coeff <bond_coeff>` command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@ -128,9 +126,6 @@ Related commands
Default
"""""""
bond\_style none
.. code-block:: LAMMPS
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html
bond_style none

31
doc/src/bond_table.rst
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@ -1,16 +1,16 @@
.. index:: bond\_style table
.. index:: bond_style table
bond\_style table command
=========================
bond_style table command
========================
bond\_style table/omp command
=============================
bond_style table/omp command
============================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style table style N
@ -21,7 +21,7 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1
@ -31,14 +31,14 @@ Description
Style *table* creates interpolation tables of length *N* from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the :doc:`bond\_coeff <bond_coeff>`
length. The files are read by the :doc:`bond_coeff <bond_coeff>`
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of *N*
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: *linear* or *spline*\ .
of 2 styles: *linear* or *spline*.
For the *linear* style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
@ -50,7 +50,7 @@ used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the
:doc:`bond\_coeff <bond_coeff>` command as in the example above.
:doc:`bond_coeff <bond_coeff>` command as in the example above.
* filename
* keyword
@ -84,14 +84,14 @@ A section begins with a non-blank line whose 1st character is not a
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
:doc:`bond\_coeff <bond_coeff>` command. The next line lists (in any
:doc:`bond_coeff <bond_coeff>` command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the *N*
specified in the :doc:`bond\_style table <bond_style>` command. Let
Ntable = *N* in the bond\_style command, and Nfile = "N" in the
Ntable = *N* in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
@ -173,11 +173,6 @@ info.
Related commands
""""""""""""""""
:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

24
doc/src/bond_write.rst
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@ -1,13 +1,13 @@
.. index:: bond\_write
.. index:: bond_write
bond\_write command
===================
bond_write command
==================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_write btype N inner outer file keyword itype jtype
@ -17,13 +17,12 @@ Syntax
* file = name of file to write values to
* keyword = section name in file for this set of tabulated values
* itype,jtype = 2 atom types (optional)
*
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_write 1 500 0.5 3.5 table.txt Harmonic_1
bond_write 3 1000 0.1 6.0 table.txt Morse
@ -40,14 +39,14 @@ file.
The energy and force values are computed at distances from inner to
outer for 2 interacting atoms forming a bond of type btype, using the
appropriate :doc:`bond\_coeff <bond_coeff>` coefficients. N evenly spaced
appropriate :doc:`bond_coeff <bond_coeff>` coefficients. N evenly spaced
distances are used.
For example, for N = 7, inner = 1.0, and outer = 4.0,
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
The file is written in the format used as input for the
:doc:`bond\_style <bond_style>` *table* option with *keyword* as the
:doc:`bond_style <bond_style>` *table* option with *keyword* as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).
@ -65,12 +64,7 @@ be specified even if the potential has a finite value at r = 0.0.
Related commands
""""""""""""""""
:doc:`bond\_style table <bond_table>`,
:doc:`bond\_style <bond_style>`, :doc:`bond\_coeff <bond_coeff>`
:doc:`bond_style table <bond_table>`,
:doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

21
doc/src/bond_zero.rst
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@ -1,26 +1,26 @@
.. index:: bond\_style zero
.. index:: bond_style zero
bond\_style zero command
========================
bond_style zero command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style zero *nocoeff*
bond_style zero [nocoeff]
Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
bond_style zero
bond_style zero nocoeff
bond_coeff \*
bond_coeff \* 2.14
bond_coeff *
bond_coeff * 2.14
Description
"""""""""""
@ -53,8 +53,3 @@ Related commands
:doc:`bond\_style none <bond_none>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

54
doc/src/pair_list.rst
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@ -1,13 +1,13 @@
.. index:: pair\_style list
.. index:: pair_style list
pair\_style list command
========================
pair_style list command
=======================
Syntax
""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style list listfile cutoff keyword
@ -19,14 +19,14 @@ Examples
""""""""
.. parsed-literal::
.. code-block:: LAMMPS
pair_style list restraints.txt 200.0
pair_coeff \* \*
pair_coeff * *
pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
pair_coeff \* \* lj/cut 1.0 1.0
pair_coeff 3\* 3\* list
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 3* 3* list
Description
"""""""""""
@ -77,36 +77,41 @@ Here is an example file:
The style *lj126* computes pairwise interactions with the formula
.. image:: Eqs/pair_lj.jpg
:align: center
.. math::
E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad r < r_c
and the coefficients:
* epsilon (energy units)
* sigma (distance units)
* :math:`\epsilon` (energy units)
* :math:`\sigma` (distance units)
The style *morse* computes pairwise interactions with the formula
.. image:: Eqs/pair_morse.jpg
:align: center
.. math::
E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right] \qquad r < r_c
and the coefficients:
* D0 (energy units)
* alpha (1/distance units)
* r0 (distance units)
* :math:`D_0` (energy units)
* :math:`\alpha` (1/distance units)
* :math:`r_0` (distance units)
The style *harmonic* computes pairwise interactions with the formula
.. image:: Eqs/bond_harmonic.jpg
:align: center
.. math::
E = K (r - r_0)^2
and the coefficients:
* K (energy units)
* r0 (distance units)
* :math:`K` (energy units)
* :math:`r_0` (distance units)
Note that the usual 1/2 factor is included in K.
Note that the usual 1/2 factor is included in :math:`K`.
----------
@ -161,8 +166,3 @@ Related commands
:doc:`bond\_style harmonic <bond_harmonic>`
**Default:** none
.. _lws: http://lammps.sandia.gov
.. _ld: Manual.html
.. _lc: Commands_all.html

175
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS
Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
atom_modify command :h3
[Syntax:]
atom_modify keyword values ... :pre
one or more keyword/value pairs may be appended :ulb,l
keyword = {id} or {map} or {first} or {sort} :l
{id} value = {yes} or {no}
{map} value = {yes} or {array} or {hash}
{first} value = group-ID = group whose atoms will appear first in internal atom lists
{sort} values = Nfreq binsize
Nfreq = sort atoms spatially every this many time steps
binsize = bin size for spatial sorting (distance units) :pre
:ule
[Examples:]
atom_modify map yes
atom_modify map hash sort 10000 2.0
atom_modify first colloid :pre
[Description:]
Modify certain attributes of atoms defined and stored within LAMMPS,
in addition to what is specified by the "atom_style"_atom_style.html
command. The {id} and {map} keywords must be specified before a
simulation box is defined; other keywords can be specified any time.
The {id} keyword determines whether non-zero atom IDs can be assigned
to each atom. If the value is {yes}, which is the default, IDs are
assigned, whether you use the "create atoms"_create_atoms.html or
"read_data"_read_data.html or "read_restart"_read_restart.html
commands to initialize atoms. If the value is {no} the IDs for all
atoms are assumed to be 0.
If atom IDs are used, they must all be positive integers. They should
also be unique, though LAMMPS does not check for this. Typically they
should also be consecutively numbered (from 1 to Natoms), though this
is not required. Molecular "atom styles"_atom_style.html are those
that store bond topology information (styles bond, angle, molecular,
full). These styles require atom IDs since the IDs are used to encode
the topology. Some other LAMMPS commands also require the use of atom
IDs. E.g. some many-body pair styles use them to avoid double
computation of the I-J interaction between two atoms.
The only reason not to use atom IDs is if you are running an atomic
simulation so large that IDs cannot be uniquely assigned. For a
default LAMMPS build this limit is 2^31 or about 2 billion atoms.
However, even in this case, you can use 64-bit atom IDs, allowing 2^63
or about 9e18 atoms, if you build LAMMPS with the - DLAMMPS_BIGBIG
switch. This is described on the "Build_settings"_Build_settings.html
doc page. If atom IDs are not used, they must be specified as 0 for
all atoms, e.g. in a data or restart file.
The {map} keyword determines how atoms with specific IDs are found
when required. An example are the bond (angle, etc) methods which
need to find the local index of an atom with a specific global ID
which is a bond (angle, etc) partner. LAMMPS performs this operation
efficiently by creating a "map", which is either an {array} or {hash}
table, as described below.
When the {map} keyword is not specified in your input script, LAMMPS
only creates a map for "atom_styles"_atom_style.html for molecular
systems which have permanent bonds (angles, etc). No map is created
for atomic systems, since it is normally not needed. However some
LAMMPS commands require a map, even for atomic systems, and will
generate an error if one does not exist. The {map} keyword thus
allows you to force the creation of a map. The {yes} value will
create either an {array} or {hash} style map, as explained in the next
paragraph. The {array} and {hash} values create an atom-style or
hash-style map respectively.
For an {array}-style map, each processor stores a lookup table of
length N, where N is the largest atom ID in the system. This is a
fast, simple method for many simulations, but requires too much memory
for large simulations. For a {hash}-style map, a hash table is
created on each processor, which finds an atom ID in constant time
(independent of the global number of atom IDs). It can be slightly
slower than the {array} map, but its memory cost is proportional to
the number of atoms owned by a processor, i.e. N/P when N is the total
number of atoms in the system and P is the number of processors.
The {first} keyword allows a "group"_group.html to be specified whose
atoms will be maintained as the first atoms in each processor's list
of owned atoms. This in only useful when the specified group is a
small fraction of all the atoms, and there are other operations LAMMPS
is performing that will be sped-up significantly by being able to loop
over the smaller set of atoms. Otherwise the reordering required by
this option will be a net slow-down. The "neigh_modify
include"_neigh_modify.html and "comm_modify group"_comm_modify.html
commands are two examples of commands that require this setting to
work efficiently. Several "fixes"_fix.html, most notably time
integration fixes like "fix nve"_fix_nve.html, also take advantage of
this setting if the group they operate on is the group specified by
this command. Note that specifying "all" as the group-ID effectively
turns off the {first} option.
It is OK to use the {first} keyword with a group that has not yet been
defined, e.g. to use the atom_modify first command at the beginning of
your input script. LAMMPS does not use the group until a simulation
is run.
The {sort} keyword turns on a spatial sorting or reordering of atoms
within each processor's sub-domain every {Nfreq} timesteps. If
{Nfreq} is set to 0, then sorting is turned off. Sorting can improve
cache performance and thus speed-up a LAMMPS simulation, as discussed
in a paper by "(Meloni)"_#Meloni. Its efficacy depends on the problem
size (atoms/processor), how quickly the system becomes disordered, and
various other factors. As a general rule, sorting is typically more
effective at speeding up simulations of liquids as opposed to solids.
In tests we have done, the speed-up can range from zero to 3-4x.
Reordering is performed every {Nfreq} timesteps during a dynamics run
or iterations during a minimization. More precisely, reordering
occurs at the first reneighboring that occurs after the target
timestep. The reordering is performed locally by each processor,
using bins of the specified {binsize}. If {binsize} is set to 0.0,
then a binsize equal to half the "neighbor"_neighbor.html cutoff
distance (force cutoff plus skin distance) is used, which is a
reasonable value. After the atoms have been binned, they are
reordered so that atoms in the same bin are adjacent to each other in
the processor's 1d list of atoms.
The goal of this procedure is for atoms to put atoms close to each
other in the processor's one-dimensional list of atoms that are also
near to each other spatially. This can improve cache performance when
pairwise interactions and neighbor lists are computed. Note that if
bins are too small, there will be few atoms/bin. Likewise if bins are
too large, there will be many atoms/bin. In both cases, the goal of
cache locality will be undermined.
NOTE: Running a simulation with sorting on versus off should not
change the simulation results in a statistical sense. However, a
different ordering will induce round-off differences, which will lead
to diverging trajectories over time when comparing two simulations.
Various commands, particularly those which use random numbers
(e.g. "velocity create"_velocity.html, and "fix
langevin"_fix_langevin.html), may generate (statistically identical)
results which depend on the order in which atoms are processed. The
order of atoms in a "dump"_dump.html file will also typically change
if sorting is enabled.
[Restrictions:]
The {first} and {sort} options cannot be used together. Since sorting
is on by default, it will be turned off if the {first} keyword is
used with a group-ID that is not "all".
[Related commands:] none
[Default:]
By default, {id} is yes. By default, atomic systems (no bond topology
info) do not use a map. For molecular systems (with bond topology
info), a map is used. The default map style is array if no atom ID is
larger than 1 million, otherwise the default is hash. By default, a
"first" group is not defined. By default, sorting is enabled with a
frequency of 1000 and a binsize of 0.0, which means the neighbor
cutoff will be used to set the bin size. If no neighbor cutoff is
defined, sorting will be turned off.
:line
:link(Meloni)
[(Meloni)] Meloni, Rosati and Colombo, J Chem Phys, 126, 121102 (2007).

338
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@ -1,338 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
atom_style command :h3
[Syntax:]
atom_style style args :pre
style = {angle} or {atomic} or {body} or {bond} or {charge} or {dipole} or \
{dpd} or {edpd} or {mdpd} or {tdpd} or {electron} or {ellipsoid} or \
{full} or {line} or {meso} or {molecular} or {peri} or {smd} or \
{sphere} or {spin} or {tri} or {template} or {hybrid} :ulb,l
args = none for any style except the following
{body} args = bstyle bstyle-args
bstyle = style of body particles
bstyle-args = additional arguments specific to the bstyle
see the "Howto body"_Howto_body.html doc page for details
{tdpd} arg = Nspecies
Nspecies = # of chemical species
{template} arg = template-ID
template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
{hybrid} args = list of one or more sub-styles, each with their args :pre
accelerated styles (with same args) = {angle/kk} or {atomic/kk} or {bond/kk} or {charge/kk} or {full/kk} or {molecular/kk} :l
:ule
[Examples:]
atom_style atomic
atom_style bond
atom_style full
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style spin
atom_style template myMols
atom_style tdpd 2 :pre
[Description:]
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a "read_data"_read_data.html,
"read_restart"_read_restart.html, or "create_box"_create_box.html
command.
NOTE: Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style {bond}, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the "read_data"_read_data.html command.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
"read_data"_read_data.html, "create_atoms"_create_atoms.html, and
"set"_set.html commands for info on how to set these various
quantities.
{angle} | bonds and angles | bead-spring polymers with stiffness |
{atomic} | only the default values | coarse-grain liquids, solids, metals |
{body} | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
{bond} | bonds | bead-spring polymers |
{charge} | charge | atomic system with charges |
{dipole} | charge and dipole moment | system with dipolar particles |
{dpd} | internal temperature and internal energies | DPD particles |
{edpd} | temperature and heat capacity | eDPD particles |
{mdpd} | density | mDPD particles |
{tdpd} | chemical concentration | tDPD particles |
{electron} | charge and spin and eradius | electronic force field |
{ellipsoid} | shape, quaternion, angular momentum | aspherical particles |
{full} | molecular + charge | bio-molecules |
{line} | end points, angular velocity | rigid bodies |
{meso} | rho, e, cv | SPH particles |
{molecular} | bonds, angles, dihedrals, impropers | uncharged molecules |
{peri} | mass, volume | mesoscopic Peridynamic models |
{smd} | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
{sphere} | diameter, mass, angular velocity | granular models |
{spin} | magnetic moment | system with magnetic particles |
{template} | template index, template atom | small molecules with fixed topology |
{tri} | corner points, angular momentum | rigid bodies |
{wavepacket} | charge, spin, eradius, etag, cs_re, cs_im | AWPMD :tb(c=3,s=|)
NOTE: It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the "fix
property/atom"_fix_property_atom.html command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the "fix
property/atom"_fix_property_atom.html doc page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
All of the above styles define point particles, except the {sphere},
{ellipsoid}, {electron}, {peri}, {wavepacket}, {line}, {tri}, and
{body} styles, which define finite-size particles. See the "Howto
spherical"_Howto_spherical.html doc page for an overview of using
finite-size particle models with LAMMPS.
All of the point-particle styles assign mass to particles on a
per-type basis, using the "mass"_mass.html command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
For the {sphere} style, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle. Note that by use of the {disc} keyword with the "fix
nve/sphere"_fix_nve_sphere.html, "fix nvt/sphere"_fix_nvt_sphere.html,
"fix nph/sphere"_fix_nph_sphere.html, "fix
npt/sphere"_fix_npt_sphere.html commands, spheres can be effectively
treated as 2d discs for a 2d simulation if desired. See also the "set
density/disc"_set.html command.
For the {ellipsoid} style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the {dipole} style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use atom_style hybrid sphere dipole, which will assign both a
diameter and dipole moment to each particle.
For the {electron} style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the {peri} style, the particles are spherical and each stores a
per-particle mass and volume.
The {dpd} style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the USER-DPD package, and is not for use with
the "pair_style dpd or dpd/stat"_pair_dpd.html commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).
The {edpd} style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity(edpd_cv).
The {mdpd} style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering
density-dependent many-body interactions.
The {tdpd} style is for transport dissipative particle dynamics (tDPD)
particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The {meso} style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (e), and heat capacity
(cv).
The {smd} style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetrating each other.
For the {spin} style, a magnetic spin is associated to each atom.
Those spins have a norm (their magnetic moment) and a direction.
The {wavepacket} style is similar to {electron}, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical {etag} values.
For the {line} style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the {tri} style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The {template} style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the "molecule"_molecule.html
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
{template} style instead of the {bond}, {angle}, {molecular} styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in "(Grime)"_#Grime, for examples of how this
can be advantageous for large-scale coarse-grained systems.
NOTE: When using the {template} style with a "molecule
template"_molecule.html that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the "read_data"_read_data.html command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.
For the {body} style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
the {bstyle} argument. Body particles can represent complex entities,
such as surface meshes of discrete points, collections of
sub-particles, deformable objects, etc.
The "Howto body"_Howto_body.html doc page describes the body styles
LAMMPS currently supports, and provides more details as to the kind of
body particles they represent. For all styles, each body particle
stores moments of inertia and a quaternion 4-vector, so that its
orientation and position can be time integrated due to forces and
torques.
Note that there may be additional arguments required along with the
{bstyle} specification, in the atom_style body command. These
arguments are described on the "Howto body"_Howto_body.html doc page.
:line
Typically, simulations require only a single (non-hybrid) atom style.
If some atoms in the simulation do not have all the properties defined
by a particular style, use the simplest style that defines all the
needed properties by any atom. For example, if some atoms in a
simulation are charged, but others are not, use the {charge} style.
If some atoms have bonds, but others do not, use the {bond} style.
The only scenario where the {hybrid} style is needed is if there is no
single style which defines all needed properties of all atoms. For
example, as mentioned above, if you want dipolar particles which will
rotate due to torque, you need to use "atom_style hybrid sphere
dipole". When a hybrid style is used, atoms store and communicate the
union of all quantities implied by the individual styles.
When using the {hybrid} style, you cannot combine the {template} style
with another molecular style that stores bond,angle,etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see the "Modify"_Modify.html doc page.
:line
Styles with a {kk} suffix are functionally the same as the
corresponding style without the suffix. They have been optimized to
run faster, depending on your available hardware, as discussed in on
the "Speed packages"_Speed_packages.html doc page. The accelerated
styles take the same arguments and should produce the same results,
except for round-off and precision issues.
Note that other acceleration packages in LAMMPS, specifically the GPU,
USER-INTEL, USER-OMP, and OPT packages do not use accelerated atom
styles.
The accelerated styles are part of the KOKKOS package. They are only
enabled if LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
[Restrictions:]
This command cannot be used after the simulation box is defined by a
"read_data"_read_data.html or "create_box"_create_box.html command.
Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the "Build
package"_Build_package.html doc page for more info.
The {angle}, {bond}, {full}, {molecular}, and {template} styles are
part of the MOLECULE package.
The {line} and {tri} styles are part of the ASPHERE package.
The {body} style is part of the BODY package.
The {dipole} style is part of the DIPOLE package.
The {peri} style is part of the PERI package for Peridynamics.
The {electron} style is part of the USER-EFF package for "electronic
force fields"_pair_eff.html.
The {dpd} style is part of the USER-DPD package for dissipative
particle dynamics (DPD).
The {edpd}, {mdpd}, and {tdpd} styles are part of the USER-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The {meso} style is part of the USER-SPH package for smoothed particle
hydrodynamics (SPH). See "this PDF
guide"_USER/sph/SPH_LAMMPS_userguide.pdf to using SPH in LAMMPS.
The {spin} style is part of the SPIN package.
The {wavepacket} style is part of the USER-AWPMD package for the
"antisymmetrized wave packet MD method"_pair_awpmd.html.
[Related commands:]
"read_data"_read_data.html, "pair_style"_pair_style.html
[Default:]
atom_style atomic
:line
:link(Grime)
[(Grime)] Grime and Voth, to appear in J Chem Theory & Computation
(2014).

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@ -1,81 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style class2 command :h3
bond_style class2/omp command :h3
bond_style class2/kk command :h3
[Syntax:]
bond_style class2 :pre
[Examples:]
bond_style class2
bond_coeff 1 1.0 100.0 80.0 80.0 :pre
[Description:]
The {class2} bond style uses the potential
:c,image(Eqs/bond_class2.jpg)
where r0 is the equilibrium bond distance.
See "(Sun)"_#bond-Sun for a description of the COMPASS class2 force field.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
R0 (distance)
K2 (energy/distance^2)
K3 (energy/distance^3)
K4 (energy/distance^4) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the CLASS2
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(bond-Sun)
[(Sun)] Sun, J Phys Chem B 102, 7338-7364 (1998).

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@ -1,82 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_coeff command :h3
[Syntax:]
bond_coeff N args :pre
N = bond type (see asterisk form below)
args = coefficients for one or more bond types :ul
[Examples:]
bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0 :pre
[Description:]
Specify the bond force field coefficients for one or more bond types.
The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the
"read_data"_read_data.html command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can
be used, as in the 1st example above. Or a wild-card asterisk can be
used to set the coefficients for multiple bond types. This takes the
form "*" or "*n" or "n*" or "m*n". If N = the number of bond types,
then an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs
for all bond types, then overwrite the coeffs for just bond type 2:
bond_coeff * 100.0 1.2
bond_coeff 2 200.0 1.2 :pre
A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example,
under the "Bond Coeffs" section of a data file, the line that
corresponds to the 1st example above would be listed as
5 80.0 1.2 :pre
:line
The list of all bond styles defined in LAMMPS is given on the
"bond_style"_bond_style.html doc page. They are also listed in more
compact form on the "Commands bond"_Commands_bond.html doc page.
On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated
bond_coeff command.
:line
[Restrictions:]
This command must come after the simulation box is defined by a
"read_data"_read_data.html, "read_restart"_read_restart.html, or
"create_box"_create_box.html command.
A bond style must be defined before any bond coefficients are set,
either in the input script or in a data file.
[Related commands:]
"bond_style"_bond_style.html
[Default:] none

88
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style fene command :h3
bond_style fene/intel command :h3
bond_style fene/kk command :h3
bond_style fene/omp command :h3
[Syntax:]
bond_style fene :pre
[Examples:]
bond_style fene
bond_coeff 1 30.0 1.5 1.0 1.0 :pre
[Description:]
The {fene} bond style uses the potential
:c,image(Eqs/bond_fene.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#fene-Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive. The
first term extends to R0, the maximum extent of the bond. The 2nd
term is cutoff at 2^(1/6) sigma, the minimum of the LJ potential.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(fene-Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style fene/expand command :h3
bond_style fene/expand/omp command :h3
[Syntax:]
bond_style fene/expand :pre
[Examples:]
bond_style fene/expand
bond_coeff 1 30.0 1.5 1.0 1.0 0.5 :pre
[Description:]
The {fene/expand} bond style uses the potential
:c,image(Eqs/bond_fene_expand.jpg)
to define a finite extensible nonlinear elastic (FENE) potential
"(Kremer)"_#feneexpand-Kremer, used for bead-spring polymer models. The first
term is attractive, the 2nd Lennard-Jones term is repulsive.
The {fene/expand} bond style is similar to {fene} except that an extra
shift factor of delta (positive or negative) is added to {r} to
effectively change the bead size of the bonded atoms. The first term
now extends to R0 + delta and the 2nd term is cutoff at 2^(1/6) sigma
+ delta.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
R0 (distance)
epsilon (energy)
sigma (distance)
delta (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
You typically should specify "special_bonds fene"_special_bonds.html
or "special_bonds lj/coul 0 1 1"_special_bonds.html to use this bond
style. LAMMPS will issue a warning it that's not the case.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(feneexpand-Kremer)
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style gromos command :h3
bond_style gromos/omp command :h3
[Syntax:]
bond_style gromos :pre
[Examples:]
bond_style gromos
bond_coeff 5 80.0 1.2 :pre
[Description:]
The {gromos} bond style uses the potential
:c,image(Eqs/bond_gromos.jpg)
where r0 is the equilibrium bond distance. Note that the usual 1/4
factor is included in K.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^4)
r0 (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

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@ -1,74 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style harmonic command :h3
bond_style harmonic/intel command :h3
bond_style harmonic/kk command :h3
bond_style harmonic/omp command :h3
[Syntax:]
bond_style harmonic :pre
[Examples:]
bond_style harmonic
bond_coeff 5 80.0 1.2 :pre
[Description:]
The {harmonic} bond style uses the potential
:c,image(Eqs/bond_harmonic.jpg)
where r0 is the equilibrium bond distance. Note that the usual 1/2
factor is included in K.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

76
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style harmonic/shift command :h3
bond_style harmonic/shift/omp command :h3
[Syntax:]
bond_style harmonic/shift :pre
[Examples:]
bond_style harmonic/shift
bond_coeff 5 10.0 0.5 1.0 :pre
[Description:]
The {harmonic/shift} bond style is a shifted harmonic bond that uses
the potential
:c,image(Eqs/bond_harmonic_shift.jpg)
where r0 is the equilibrium bond distance, and rc the critical distance.
The potential is -Umin at r0 and zero at rc. The spring constant is
k = Umin / \[ 2 (r0-rc)^2\].
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
Umin (energy) :ul
r0 (distance) :ul
rc (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
"bond_harmonic"_bond_harmonic.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style harmonic/shift/cut command :h3
bond_style harmonic/shift/cut/omp command :h3
[Syntax:]
bond_style harmonic/shift/cut :pre
[Examples:]
bond_style harmonic/shift/cut
bond_coeff 5 10.0 0.5 1.0 :pre
[Description:]
The {harmonic/shift/cut} bond style is a shifted harmonic bond that
uses the potential
:c,image(Eqs/bond_harmonic_shift_cut.jpg)
where r0 is the equilibrium bond distance, and rc the critical distance.
The bond potential is zero for distances r > rc. The potential is -Umin
at r0 and zero at rc. The spring constant is k = Umin / \[ 2 (r0-rc)^2\].
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
Umin (energy)
r0 (distance)
rc (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
USER-MISC package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html,
"bond_harmonic"_bond_harmonic.html,
"bond_harmonic_shift"_bond_harmonic_shift.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style hybrid command :h3
[Syntax:]
bond_style hybrid style1 style2 ... :pre
style1,style2 = list of one or more bond styles :ul
[Examples:]
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2* fene 30.0 1.5 1.0 1.0 :pre
[Description:]
The {hybrid} style enables the use of multiple bond styles in one
simulation. A bond style is assigned to each bond type. For example,
bonds in a polymer flow (of bond type 1) could be computed with a
{fene} potential and bonds in the wall boundary (of bond type 2) could
be computed with a {harmonic} potential. The assignment of bond type
to style is made via the "bond_coeff"_bond_coeff.html command or in
the data file.
In the bond_coeff commands, the name of a bond style must be added
after the bond type, with the remaining coefficients being those
appropriate to that style. In the example above, the 2 bond_coeff
commands set bonds of bond type 1 to be computed with a {harmonic}
potential with coefficients 80.0, 1.2 for K, r0. All other bond types
(2-N) are computed with a {fene} potential with coefficients 30.0,
1.5, 1.0, 1.0 for K, R0, epsilon, sigma.
If bond coefficients are specified in the data file read via the
"read_data"_read_data.html command, then the same rule applies.
E.g. "harmonic" or "fene" must be added after the bond type, for each
line in the "Bond Coeffs" section, e.g.
Bond Coeffs :pre
1 harmonic 80.0 1.2
2 fene 30.0 1.5 1.0 1.0
... :pre
A bond style of {none} with no additional coefficients can be used in
place of a bond style, either in a input script bond_coeff command or
in the data file, if you desire to turn off interactions for specific
bond types.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
Unlike other bond styles, the hybrid bond style does not store bond
coefficient info for individual sub-styles in a "binary restart
files"_restart.html. Thus when restarting a simulation from a restart
file, you need to re-specify bond_coeff commands.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

58
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@ -1,58 +0,0 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style mm3 command :h3
[Syntax:]
bond_style mm3 :pre
[Examples:]
bond_style mm3
bond_coeff 1 100.0 107.0 :pre
[Description:]
The {mm3} bond style uses the potential that is anharmonic in the bond
as defined in "(Allinger)"_#mm3-allinger1989
:c,image(Eqs/bond_mm3.jpg)
where r0 is the equilibrium value of the bond, and K is a
prefactor. The anharmonic prefactors have units angstrom^(-n):
-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
care of the necessary unit conversion for these factors internally.
Note that the MM3 papers contains an error in Eq (1):
(7/12)2.55 should be replaced with (7/12)2.55^2
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^2)
r0 (distance) :ul
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
USER_YAFF package. See the "Build package"_Build_package.html doc
page for more info.
[Related commands:]
"bond_coeff"_bond_coeff.html
[Default:] none
:line
:link(mm3-allinger1989)
[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
(1989),

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style morse command :h3
bond_style morse/omp command :h3
[Syntax:]
bond_style morse :pre
[Examples:]
bond_style morse
bond_coeff 5 1.0 2.0 1.2 :pre
[Description:]
The {morse} bond style uses the potential
:c,image(Eqs/bond_morse.jpg)
where r0 is the equilibrium bond distance, alpha is a stiffness
parameter, and D determines the depth of the potential well.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
D (energy)
alpha (inverse distance)
r0 (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style none command :h3
[Syntax:]
bond_style none :pre
[Examples:]
bond_style none :pre
[Description:]
Using a bond style of none means bond forces and energies are not
computed, even if pairs of bonded atoms were listed in the data file
read by the "read_data"_read_data.html command.
See the "bond_style zero"_bond_zero.html command for a way to
calculate bond statistics, but compute no bond interactions.
[Restrictions:] none
[Related commands:] none
"bond_style zero"_bond_zero.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style nonlinear command :h3
bond_style nonlinear/omp command :h3
[Syntax:]
bond_style nonlinear :pre
[Examples:]
bond_style nonlinear
bond_coeff 2 100.0 1.1 1.4 :pre
[Description:]
The {nonlinear} bond style uses the potential
:c,image(Eqs/bond_nonlinear.jpg)
to define an anharmonic spring "(Rector)"_#Rector of equilibrium
length r0 and maximum extension lamda.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
epsilon (energy)
r0 (distance)
lamda (distance) :ul
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none
:line
:link(Rector)
[(Rector)] Rector, Van Swol, Henderson, Molecular Physics, 82, 1009 (1994).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style oxdna/fene command :h3
bond_style oxdna2/fene command :h3
[Syntax:]
bond_style oxdna/fene :pre
bond_style oxdna2/fene :pre
[Examples:]
bond_style oxdna/fene
bond_coeff * 2.0 0.25 0.7525 :pre
bond_style oxdna2/fene
bond_coeff * 2.0 0.25 0.7564 :pre
[Description:]
The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
:c,image(Eqs/bond_oxdna_fene.jpg)
to define a modified finite extensible nonlinear elastic (FENE)
potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
phosphate backbone in the oxDNA force field for coarse-grained
modelling of DNA.
The following coefficients must be defined for the bond type via the
"bond_coeff"_bond_coeff.html command as given in the above example, or
in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands:
epsilon (energy)
Delta (distance)
r0 (distance) :ul
NOTE: The oxDNA bond style has to be used together with the
corresponding oxDNA pair styles for excluded volume interaction
{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
coaxial stacking interaction {oxdna/coaxstk} as well as
hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
The coefficients in the above example have to be kept fixed and cannot
be changed without reparameterizing the entire model.
Example input and data files for DNA duplexes can be found in
examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. A simple python
setup tool which creates single straight or helical DNA strands, DNA
duplexes or arrays of DNA duplexes can be found in
examples/USER/cgdna/util/.
Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
any publication that uses this implementation. The article contains
more information on the model, the structure of the input file, the
setup tool and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found
"here"_PDF/USER-CGDNA.pdf.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the
USER-CGDNA package and the MOLECULE and ASPHERE package. See the
"Build package"_Build_package.html doc page for more info.
[Related commands:]
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
oxdna2/excv"_pair_oxdna2.html, "fix
nve/dotc/langevin"_fix_nve_dotc_langevin.html,
"bond_coeff"_bond_coeff.html
[Default:] none
:line
:link(Henrich2)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
J. Chem. Phys. 134, 085101 (2011).
:link(oxdna2)
[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
J. Chem. Phys. 142, 234901 (2015).

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style quartic command :h3
bond_style quartic/omp command :h3
[Syntax:]
bond_style quartic :pre
[Examples:]
bond_style quartic
bond_coeff 2 1200 -0.55 0.25 1.3 34.6878 :pre
[Description:]
The {quartic} bond style uses the potential
:c,image(Eqs/bond_quartic.jpg)
to define a bond that can be broken as the simulation proceeds (e.g.
due to a polymer being stretched). The sigma and epsilon used in the
LJ portion of the formula are both set equal to 1.0 by LAMMPS.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above, or in
the data file or restart files read by the "read_data"_read_data.html
or "read_restart"_read_restart.html commands:
K (energy/distance^4)
B1 (distance)
B2 (distance)
Rc (distance)
U0 (energy) :ul
This potential was constructed to mimic the FENE bond potential for
coarse-grained polymer chains. When monomers with sigma = epsilon =
1.0 are used, the following choice of parameters gives a quartic
potential that looks nearly like the FENE potential: K = 1200, B1 =
-0.55, B2 = 0.25, Rc = 1.3, and U0 = 34.6878. Different parameters
can be specified using the "bond_coeff"_bond_coeff.html command, but
you will need to choose them carefully so they form a suitable bond
potential.
Rc is the cutoff length at which the bond potential goes smoothly to a
local maximum. If a bond length ever becomes > Rc, LAMMPS "breaks"
the bond, which means two things. First, the bond potential is turned
off by setting its type to 0, and is no longer computed. Second, a
pairwise interaction between the two atoms is turned on, since they
are no longer bonded.
LAMMPS does the second task via a computational sleight-of-hand. It
subtracts the pairwise interaction as part of the bond computation.
When the bond breaks, the subtraction stops. For this to work, the
pairwise interaction must always be computed by the
"pair_style"_pair_style.html command, whether the bond is broken or
not. This means that "special_bonds"_special_bonds.html must be set
to 1,1,1, as indicated as a restriction below.
Note that when bonds are dumped to a file via the "dump
local"_dump.html command, bonds with type 0 are not included. The
"delete_bonds"_delete_bonds.html command can also be used to query the
status of broken bonds or permanently delete them, e.g.:
delete_bonds all stats
delete_bonds all bond 0 remove :pre
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
The {quartic} style requires that "special_bonds"_special_bonds.html
parameters be set to 1,1,1. Three- and four-body interactions (angle,
dihedral, etc) cannot be used with {quartic} bonds.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style command :h3
[Syntax:]
bond_style style args :pre
style = {none} or {hybrid} or {class2} or {fene} or {fene/expand} or \
{harmonic} or {morse} or {nonlinear} or {quartic} :ul
args = none for any style except {hybrid}
{hybrid} args = list of one or more styles :pre
[Examples:]
bond_style harmonic
bond_style fene
bond_style hybrid harmonic fene :pre
[Description:]
Set the formula(s) LAMMPS uses to compute bond interactions between
pairs of atoms. In LAMMPS, a bond differs from a pairwise
interaction, which are set via the "pair_style"_pair_style.html
command. Bonds are defined between specified pairs of atoms and
remain in force for the duration of the simulation (unless the bond
breaks which is possible in some bond potentials). The list of bonded
atoms is read in by a "read_data"_read_data.html or
"read_restart"_read_restart.html command from a data or restart file.
By contrast, pair potentials are typically defined between all pairs
of atoms within a cutoff distance and the set of active interactions
changes over time.
Hybrid models where bonds are computed using different bond potentials
can be setup using the {hybrid} bond style.
The coefficients associated with a bond style can be specified in a
data or restart file or via the "bond_coeff"_bond_coeff.html command.
All bond potentials store their coefficient data in binary restart
files which means bond_style and "bond_coeff"_bond_coeff.html commands
do not need to be re-specified in an input script that restarts a
simulation. See the "read_restart"_read_restart.html command for
details on how to do this. The one exception is that bond_style
{hybrid} only stores the list of sub-styles in the restart file; bond
coefficients need to be re-specified.
NOTE: When both a bond and pair style is defined, the
"special_bonds"_special_bonds.html command often needs to be used to
turn off (or weight) the pairwise interaction that would otherwise
exist between 2 bonded atoms.
In the formulas listed for each bond style, {r} is the distance
between the 2 atoms in the bond.
:line
Here is an alphabetic list of bond styles defined in LAMMPS. Click on
the style to display the formula it computes and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
Click on the style to display the formula it computes, any additional
arguments specified in the bond_style command, and coefficients
specified by the associated "bond_coeff"_bond_coeff.html command.
There are also additional accelerated pair styles included in the
LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
The individual style names on the "Commands bond"_Commands_bond.html
doc page are followed by one or more of (g,i,k,o,t) to indicate which
accelerated styles exist.
"none"_bond_none.html - turn off bonded interactions
"zero"_bond_zero.html - topology but no interactions
"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
"class2"_bond_class2.html - COMPASS (class 2) bond
"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
"gromos"_bond_gromos.html - GROMOS force field bond
"harmonic"_bond_harmonic.html - harmonic bond
"harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
"harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
"mm3"_bond_mm3.html - MM3 anharmonic bond
"morse"_bond_morse.html - Morse bond
"nonlinear"_bond_nonlinear.html - nonlinear bond
"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles
"quartic"_bond_quartic.html - breakable quartic bond
"table"_bond_table.html - tabulated by bond length :ul
:line
[Restrictions:]
Bond styles can only be set for atom styles that allow bonds to be
defined.
Most bond styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the "Build
package"_Build_package.html doc page for more info. The doc pages for
individual bond potentials tell if it is part of a package.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:]
bond_style none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style table command :h3
bond_style table/omp command :h3
[Syntax:]
bond_style table style N :pre
style = {linear} or {spline} = method of interpolation
N = use N values in table :ul
[Examples:]
bond_style table linear 1000
bond_coeff 1 file.table ENTRY1 :pre
[Description:]
Style {table} creates interpolation tables of length {N} from bond
potential and force values listed in a file(s) as a function of bond
length. The files are read by the "bond_coeff"_bond_coeff.html
command.
The interpolation tables are created by fitting cubic splines to the
file values and interpolating energy and force values at each of {N}
distances. During a simulation, these tables are used to interpolate
energy and force values as needed. The interpolation is done in one
of 2 styles: {linear} or {spline}.
For the {linear} style, the bond length is used to find 2 surrounding
table values from which an energy or force is computed by linear
interpolation.
For the {spline} style, a cubic spline coefficients are computed and
stored at each of the {N} values in the table. The bond length is
used to find the appropriate set of coefficients which are used to
evaluate a cubic polynomial which computes the energy or force.
The following coefficients must be defined for each bond type via the
"bond_coeff"_bond_coeff.html command as in the example above.
filename
keyword :ul
The filename specifies a file containing tabulated energy and force
values. The keyword specifies a section of the file. The format of
this file is described below.
:line
The format of a tabulated file is as follows (without the
parenthesized comments):
# Bond potential for harmonic (one or more comment or blank lines) :pre
HAM (keyword is the first text on line)
N 101 FP 0 0 EQ 0.5 (N, FP, EQ parameters)
(blank line)
1 0.00 338.0000 1352.0000 (index, bond-length, energy, force)
2 0.01 324.6152 1324.9600
...
101 1.00 338.0000 -1352.0000 :pre
A section begins with a non-blank line whose 1st character is not a
"#"; blank lines or lines starting with "#" can be used as comments
between sections. The first line begins with a keyword which
identifies the section. The line can contain additional text, but the
initial text must match the argument specified in the
"bond_coeff"_bond_coeff.html command. The next line lists (in any
order) one or more parameters for the table. Each parameter is a
keyword followed by one or more numeric values.
The parameter "N" is required and its value is the number of table
entries that follow. Note that this may be different than the {N}
specified in the "bond_style table"_bond_style.html command. Let
Ntable = {N} in the bond_style command, and Nfile = "N" in the
tabulated file. What LAMMPS does is a preliminary interpolation by
creating splines using the Nfile tabulated values as nodal points. It
uses these to interpolate as needed to generate energy and force
values at Ntable different points. The resulting tables of length
Ntable are then used as described above, when computing energy and
force for individual bond lengths. This means that if you want the
interpolation tables of length Ntable to match exactly what is in the
tabulated file (with effectively no preliminary interpolation), you
should set Ntable = Nfile.
The "FP" parameter is optional. If used, it is followed by two values
fplo and fphi, which are the derivatives of the force at the innermost
and outermost bond lengths. These values are needed by the spline
construction routines. If not specified by the "FP" parameter, they
are estimated (less accurately) by the first two and last two force
values in the table.
The "EQ" parameter is also optional. If used, it is followed by a the
equilibrium bond length, which is used, for example, by the "fix
shake"_fix_shake.html command. If not used, the equilibrium bond
length is to the distance in the table with the lowest potential energy.
Following a blank line, the next N lines list the tabulated values.
On each line, the 1st value is the index from 1 to N, the 2nd value is
the bond length r (in distance units), the 3rd value is the energy (in
energy units), and the 4th is the force (in force units). The bond
lengths must range from a LO value to a HI value, and increase from
one line to the next. If the actual bond length is ever smaller than
the LO value or larger than the HI value, then the bond energy and
force is evaluated as if the bond were the LO or HI length.
Note that one file can contain many sections, each with a tabulated
potential. LAMMPS reads the file section by section until it finds
one that matches the specified keyword.
:line
Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed on the "Speed packages"_Speed_packages.html doc
page. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
USER-OMP and OPT packages, respectively. They are only enabled if
LAMMPS was built with those packages. See the "Build
package"_Build_package.html doc page for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Run_options.html when you invoke LAMMPS, or you can use the
"suffix"_suffix.html command in your input script.
See the "Speed packages"_Speed_packages.html doc page for more
instructions on how to use the accelerated styles effectively.
:line
[Restart info:]
This bond style writes the settings for the "bond_style table"
command to "binary restart files"_restart.html, so a bond_style
command does not need to specified in an input script that reads a
restart file. However, the coefficient information is not stored in
the restart file, since it is tabulated in the potential files. Thus,
bond_coeff commands do need to be specified in the restart input
script.
[Restrictions:]
This bond style can only be used if LAMMPS was built with the MOLECULE
package. See the "Build package"_Build_package.html doc page for more
info.
[Related commands:]
"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_write command :h3
[Syntax:]
bond_write btype N inner outer file keyword itype jtype :pre
btype = bond types
N = # of values
inner,outer = inner and outer bond length (distance units)
file = name of file to write values to
keyword = section name in file for this set of tabulated values
itype,jtype = 2 atom types (optional)
:ul
[Examples:]
bond_write 1 500 0.5 3.5 table.txt Harmonic_1
bond_write 3 1000 0.1 6.0 table.txt Morse :pre
[Description:]
Write energy and force values to a file as a function of distance for
the currently defined bond potential. This is useful for plotting the
potential function or otherwise debugging its values. If the file
already exists, the table of values is appended to the end of the file
to allow multiple tables of energy and force to be included in one
file.
The energy and force values are computed at distances from inner to
outer for 2 interacting atoms forming a bond of type btype, using the
appropriate "bond_coeff"_bond_coeff.html coefficients. N evenly spaced
distances are used.
For example, for N = 7, inner = 1.0, and outer = 4.0,
values are computed at r = 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0.
The file is written in the format used as input for the
"bond_style"_bond_style.html {table} option with {keyword} as the
section name. Each line written to the file lists an index number
(1-N), a distance (in distance units), an energy (in energy units),
and a force (in force units).
[Restrictions:]
All force field coefficients for bond and other kinds of interactions
must be set before this command can be invoked.
Due to how the bond force is computed, an inner value > 0.0 must
be specified even if the potential has a finite value at r = 0.0.
[Related commands:]
"bond_style table"_bond_table.html,
"bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
bond_style zero command :h3
[Syntax:]
bond_style zero {nocoeff} :pre
[Examples:]
bond_style zero
bond_style zero nocoeff
bond_coeff *
bond_coeff * 2.14 :pre
[Description:]
Using an bond style of zero means bond forces and energies are not
computed, but the geometry of bond pairs is still accessible to other
commands.
As an example, the "compute bond/local"_compute_bond_local.html
command can be used to compute distances for the list of pairs of bond
atoms listed in the data file read by the "read_data"_read_data.html
command. If no bond style is defined, this command cannot be used.
The optional {nocoeff} flag allows to read data files with a BondCoeff
section for any bond style. Similarly, any bond_coeff commands
will only be checked for the bond type number and the rest ignored.
Note that the "bond_coeff"_bond_coeff.html command must be used for
all bond types. If specified, there can be only one value, which is
going to be used to assign an equilibrium distance, e.g. for use with
"fix shake"_fix_shake.html.
[Restrictions:] none
[Related commands:]
"bond_style none"_bond_none.html
[Default:] none

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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Commands_all.html)
:line
pair_style list command :h3
[Syntax:]
pair_style list listfile cutoff keyword :pre
listfile = name of file with list of pairwise interactions
cutoff = global cutoff (distance units)
keyword = optional flag {nocheck} or {check} (default is {check}) :ul
[Examples:]
pair_style list restraints.txt 200.0
pair_coeff * * :pre
pair_style hybrid/overlay lj/cut 1.1225 list pair_list.txt 300.0
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 3* 3* list :pre
[Description:]
Style {list} computes interactions between explicitly listed pairs of
atoms with the option to select functional form and parameters for
each individual pair. Because the parameters are set in the list
file, the pair_coeff command has no parameters (but still needs to be
provided). The {check} and {nocheck} keywords enable/disable a test
that checks whether all listed bonds were present and computed.
This pair style can be thought of as a hybrid between bonded,
non-bonded, and restraint interactions. It will typically be used as
an additional interaction within the {hybrid/overlay} pair style. It
currently supports three interaction styles: a 12-6 Lennard-Jones, a
Morse and a harmonic potential.
The format of the list file is as follows:
one line per pair of atoms :ulb,l
empty lines will be ignored :l
comment text starts with a '#' character :l
line syntax: {ID1 ID2 style coeffs cutoff} :l
ID1 = atom ID of first atom
ID2 = atom ID of second atom
style = style of interaction
coeffs = list of coeffs
cutoff = cutoff for interaction (optional) :pre
:ule
The cutoff parameter is optional. If not specified, the global cutoff
is used.
Here is an example file:
# this is a comment :pre
15 259 lj126 1.0 1.0 50.0
15 603 morse 10.0 1.2 2.0 10.0 # and another comment
18 470 harmonic 50.0 1.2 5.0 :pre
The style {lj126} computes pairwise interactions with the formula
:c,image(Eqs/pair_lj.jpg)
and the coefficients:
epsilon (energy units)
sigma (distance units) :ul
The style {morse} computes pairwise interactions with the formula
:c,image(Eqs/pair_morse.jpg)
and the coefficients:
D0 (energy units)
alpha (1/distance units)
r0 (distance units) :ul
The style {harmonic} computes pairwise interactions with the formula
:c,image(Eqs/bond_harmonic.jpg)
and the coefficients:
K (energy units)
r0 (distance units) :ul
Note that the usual 1/2 factor is included in K.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
This pair style does not support mixing since all parameters are
explicit for each pair.
The "pair_modify"_pair_modify.html shift option is supported by this
pair style.
The "pair_modify"_pair_modify.html table and tail options are not
relevant for this pair style.
This pair style does not write its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This pair style does not use a neighbor list and instead identifies
atoms by their IDs. This has two consequences: 1) The cutoff has to be
chosen sufficiently large, so that the second atom of a pair has to be
a ghost atom on the same node on which the first atom is local;
otherwise the interaction will be skipped. You can use the {check}
option to detect, if interactions are missing. 2) Unlike other pair
styles in LAMMPS, an atom I will not interact with multiple images of
atom J (assuming the images are within the cutoff distance), but only
with the nearest image.
This style is part of the USER-MISC package. It is only enabled if
LAMMPS is build with that package. See the "Build
package"_Build_package.html doc page on for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html,
"pair_style hybrid/overlay"_pair_hybrid.html,
"pair_style lj/cut"_pair_lj.html,
"pair_style morse"_pair_morse.html,
"bond_style harmonic"_bond_harmonic.html
[Default:] none