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Update docs: bond_morse
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Richard Berger
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\documentclass[12pt]{article}
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\begin{document}
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$$
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% E = D \left[ 1 - \exp \left( -\alpha (r - r_0) \right) \right]^2
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E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
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$$
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\end{document}
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@ -1,16 +1,16 @@
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.. index:: bond\_style morse
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.. index:: bond_style morse
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bond\_style morse command
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=========================
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bond_style morse command
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========================
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bond\_style morse/omp command
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=============================
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bond_style morse/omp command
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============================
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Syntax
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""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style morse
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@ -18,7 +18,7 @@ Examples
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""""""""
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.. parsed-literal::
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.. code-block:: LAMMPS
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bond_style morse
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bond_coeff 5 1.0 2.0 1.2
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@ -28,20 +28,22 @@ Description
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The *morse* bond style uses the potential
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.. image:: Eqs/bond_morse.jpg
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:align: center
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.. math::
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where r0 is the equilibrium bond distance, alpha is a stiffness
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parameter, and D determines the depth of the potential well.
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E = D \left[ 1 - e^{-\alpha (r - r_0)} \right]^2
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where :math:`r_0` is the equilibrium bond distance, :math:`\alpha` is a stiffness
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parameter, and :math:`D` determines the depth of the potential well.
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The following coefficients must be defined for each bond type via the
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:doc:`bond\_coeff <bond_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read\_data <read_data>`
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or :doc:`read\_restart <read_restart>` commands:
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* D (energy)
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* alpha (inverse distance)
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* r0 (distance)
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* :math:`D` (energy)
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* :math:`\alpha` (inverse distance)
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* :math:`r_0` (distance)
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----------
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@ -83,8 +85,3 @@ Related commands
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:doc:`bond\_coeff <bond_coeff>`, :doc:`delete\_bonds <delete_bonds>`
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**Default:** none
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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@ -1,73 +0,0 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Commands_all.html)
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:line
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bond_style morse command :h3
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bond_style morse/omp command :h3
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[Syntax:]
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bond_style morse :pre
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[Examples:]
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bond_style morse
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bond_coeff 5 1.0 2.0 1.2 :pre
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[Description:]
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The {morse} bond style uses the potential
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:c,image(Eqs/bond_morse.jpg)
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where r0 is the equilibrium bond distance, alpha is a stiffness
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parameter, and D determines the depth of the potential well.
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The following coefficients must be defined for each bond type via the
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"bond_coeff"_bond_coeff.html command as in the example above, or in
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the data file or restart files read by the "read_data"_read_data.html
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or "read_restart"_read_restart.html commands:
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D (energy)
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alpha (inverse distance)
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r0 (distance) :ul
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:line
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Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed on the "Speed packages"_Speed_packages.html doc
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page. The accelerated styles take the same arguments and should
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produce the same results, except for round-off and precision issues.
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These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
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USER-OMP and OPT packages, respectively. They are only enabled if
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LAMMPS was built with those packages. See the "Build
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package"_Build_package.html doc page for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the "-suffix command-line
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switch"_Run_options.html when you invoke LAMMPS, or you can use the
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"suffix"_suffix.html command in your input script.
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See the "Speed packages"_Speed_packages.html doc page for more
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instructions on how to use the accelerated styles effectively.
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:line
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[Restrictions:]
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This bond style can only be used if LAMMPS was built with the MOLECULE
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package. See the "Build package"_Build_package.html doc page for more
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info.
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[Related commands:]
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"bond_coeff"_bond_coeff.html, "delete_bonds"_delete_bonds.html
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[Default:] none
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