113 lines
3.2 KiB
ReStructuredText
113 lines
3.2 KiB
ReStructuredText
.. index:: bond_style fene
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.. index:: bond_style fene/nm
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.. index:: bond_style fene/intel
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.. index:: bond_style fene/kk
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.. index:: bond_style fene/omp
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bond_style fene command
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=======================
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Accelerator Variants: *fene/intel*, *fene/kk*, *fene/omp*
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bond_style fene/nm 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
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bond_style fene/nm
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Examples
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""""""""
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.. code-block:: LAMMPS
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bond_style fene
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bond_coeff 1 30.0 1.5 1.0 1.0
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bond_style fene/nm
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bond_coeff 1 2.25344 1.5 1.0 1.12246 2 6
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Description
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"""""""""""
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The *fene* 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{r}{R_0}\right)^2\right] + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
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to define a finite extensible nonlinear elastic (FENE) potential
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:ref:`(Kremer) <fene-Kremer>`, used for bead-spring polymer models. The first
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term is attractive, the second Lennard-Jones term is repulsive. The
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first term extends to :math:`R_0`, the maximum extent of the bond. The second
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term is cutoff at :math:`2^\frac{1}{6} \sigma`, the minimum of the LJ potential.
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The *fene/nm* bond style substitutes the standard LJ potential with the generalized LJ potential
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in the same form as in pair style :doc:`nm/cut <pair_nm>`. The bond energy is then given by
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.. math::
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E = -0.5 K r_0^2 \ln \left[ 1 - \left(\frac{r}{R_0}\right)^2\right] + \frac{E_0}{(n-m)} \left[ m \left(\frac{r_0}{r}\right)^n - n \left(\frac{r_0}{r}\right)^m \right]
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Similar to the *fene* style, the generalized Lennard-Jones is cut off at
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the potential minimum, :math:`r_0`, to be repulsive only. The following
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coefficients must be defined for each bond type via the :doc:`bond_coeff
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<bond_coeff>` command as in the example above, or in the data file or
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restart files read by the :doc:`read_data <read_data>` or
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: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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For the *fene/nm* style, the following coefficients are used. Please
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note, that the standard LJ potential and thus the regular FENE potential
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is recovered for (n=12 m=6) and :math:`r_0 = 2^\frac{1}{6} \sigma`.
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* :math:`K` (energy/distance\^2)
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* :math:`R_0` (distance)
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* :math:`E_0` (energy)
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* :math:`r_0` (distance)
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* :math:`n` (unitless)
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* :math:`m` (unitless)
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----------
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.. include:: accel_styles.rst
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----------
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Restrictions
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""""""""""""
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The *fene* bond style can only be used if LAMMPS was built with the MOLECULE
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package; the *fene/nm* bond style can only be used if LAMMPS was built
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with the EXTRA-MOLECULE package. See the :doc:`Build package <Build_package>`
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page for more 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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:doc:`pair style lj/cut <pair_lj>`, :doc:`pair style nm/cut <pair_nm>`.
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Default
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"""""""
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none
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----------
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.. _fene-Kremer:
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**(Kremer)** Kremer, Grest, J Chem Phys, 92, 5057 (1990).
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