110 lines
3.2 KiB
ReStructuredText
110 lines
3.2 KiB
ReStructuredText
.. index:: bond_style fene/expand
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bond_style fene/expand command
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==============================
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bond_style fene/expand/omp command
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==================================
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Syntax
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""""""
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.. code-block:: LAMMPS
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bond_style fene/expand
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Examples
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""""""""
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.. code-block:: LAMMPS
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bond_style fene/expand
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bond_coeff 1 30.0 1.5 1.0 1.0 0.5
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Description
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"""""""""""
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The *fene/expand* bond style uses the potential
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.. math::
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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
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to define a finite extensible nonlinear elastic (FENE) potential
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:ref:`(Kremer) <feneexpand-Kremer>`, used for bead-spring polymer models. The first
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term is attractive, the 2nd Lennard-Jones term is repulsive.
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The *fene/expand* bond style is similar to *fene* except that an extra
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shift factor of :math:`\Delta` (positive or negative) is added to :math:`r` to
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effectively change the bead size of the bonded atoms. The first term
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now extends to :math:`R_0 + \Delta` and the 2nd term is cutoff at :math:`2^\frac{1}{6} \sigma + \Delta`.
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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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* :math:`K` (energy/distance\^2)
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* :math:`R_0` (distance)
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* :math:`\epsilon` (energy)
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* :math:`\sigma` (distance)
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* :math:`\Delta` (distance)
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----------
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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 :doc:`Speed packages <Speed_packages>` 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 :doc:`Build package <Build_package>` 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 :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
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:doc:`suffix <suffix>` command in your input script.
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See the :doc:`Speed packages <Speed_packages>` doc page for more
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instructions on how to use the accelerated styles effectively.
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----------
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Restrictions
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""""""""""""
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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 :doc:`Build package <Build_package>` doc page for more
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info.
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You typically should specify :doc:`special_bonds fene <special_bonds>`
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or :doc:`special_bonds lj/coul 0 1 1 <special_bonds>` to use this bond
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style. LAMMPS will issue a warning it that's not the case.
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Related commands
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""""""""""""""""
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:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
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**Default:** none
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----------
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.. _feneexpand-Kremer:
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**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
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