142 lines
5.6 KiB
ReStructuredText
142 lines
5.6 KiB
ReStructuredText
.. index:: dihedral_style
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dihedral_style 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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dihedral_style style
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* style = *none* or *zero* or *hybrid* or *charmm* or *charmmfsw* or *class2* or *cosine/shift/exp* or *cosine/squared/restricted* or *fourier* or *harmonic* or *helix* or *lepton* or *multi/harmonic* or *nharmonic* or *opls* or *spherical* or *table* or *table/cut*
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Examples
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""""""""
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.. code-block:: LAMMPS
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dihedral_style harmonic
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dihedral_style multi/harmonic
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dihedral_style hybrid harmonic charmm
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Description
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"""""""""""
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Set the formula(s) LAMMPS uses to compute dihedral interactions
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between quadruplets of atoms, which remain in force for the duration
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of the simulation. The list of dihedral quadruplets is read in by a
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` command
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from a data or restart file.
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Hybrid models where dihedrals are computed using different dihedral
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potentials can be setup using the *hybrid* dihedral style.
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The coefficients associated with a dihedral style can be specified in
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a data or restart file or via the :doc:`dihedral_coeff <dihedral_coeff>`
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command.
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All dihedral potentials store their coefficient data in binary restart
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files which means dihedral_style and
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:doc:`dihedral_coeff <dihedral_coeff>` commands do not need to be
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re-specified in an input script that restarts a simulation. See the
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:doc:`read_restart <read_restart>` command for details on how to do
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this. The one exception is that dihedral_style *hybrid* only stores
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the list of sub-styles in the restart file; dihedral coefficients need
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to be re-specified.
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.. note::
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When both a dihedral and pair style is defined, the
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:doc:`special_bonds <special_bonds>` command often needs to be used to
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turn off (or weight) the pairwise interaction that would otherwise
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exist between four bonded atoms.
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In the formulas listed for each dihedral style, *phi* is the torsional
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angle defined by the quadruplet of atoms. This angle has a sign
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convention as shown in this diagram:
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.. image:: JPG/dihedral_sign.jpg
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:align: center
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where the :math:`I,J,K,L` ordering of the four atoms that define the dihedral
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is from left to right.
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This sign convention effects several of the dihedral styles listed
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below (e.g., charmm, helix) in the sense that the energy formula
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depends on the sign of phi, which may be reflected in the value of the
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coefficients you specify.
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.. note::
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When comparing the formulas and coefficients for various LAMMPS
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dihedral styles with dihedral equations defined by other force fields,
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note that some force field implementations divide/multiply the energy
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prefactor *K* by the multiple number of torsions that contain the
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*J*\ --\ *K* bond in an *I*\ --\ *J*\ --\ *K*\ --\ *L* torsion. LAMMPS does
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not do this (i.e., the listed dihedral equation applies to each individual
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dihedral). Thus, you need to define *K* appropriately via the
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:doc:`dihedral_coeff <dihedral_coeff>` command to account for this
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difference if necessary.
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----------
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Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
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the style to display the formula it computes and coefficients
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specified by the associated :doc:`dihedral_coeff <dihedral_coeff>` command.
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Click on the style to display the formula it computes, any additional
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arguments specified in the dihedral_style command, and coefficients
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specified by the associated :doc:`dihedral_coeff <dihedral_coeff>`
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command.
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There are also additional accelerated pair styles included in the
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LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
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The individual style names on the :ref:`Commands dihedral <dihedral>` page are
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followed by one or more of (g,i,k,o,t) to indicate which accelerated styles
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exist.
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* :doc:`none <dihedral_none>` - turn off dihedral interactions
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* :doc:`zero <dihedral_zero>` - topology but no interactions
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* :doc:`hybrid <dihedral_hybrid>` - define multiple styles of dihedral interactions
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* :doc:`charmm <dihedral_charmm>` - CHARMM dihedral
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* :doc:`charmmfsw <dihedral_charmm>` - CHARMM dihedral with force switching
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* :doc:`class2 <dihedral_class2>` - COMPASS (class 2) dihedral
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* :doc:`cosine/shift/exp <dihedral_cosine_shift_exp>` - dihedral with exponential in spring constant
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* :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>` - squared cosine dihedral with restricted term
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* :doc:`fourier <dihedral_fourier>` - dihedral with multiple cosine terms
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* :doc:`harmonic <dihedral_harmonic>` - harmonic dihedral
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* :doc:`helix <dihedral_helix>` - helix dihedral
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* :doc:`lepton <dihedral_lepton>` - dihedral potential from evaluating a string
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* :doc:`multi/harmonic <dihedral_multi_harmonic>` - dihedral with 5 harmonic terms
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* :doc:`nharmonic <dihedral_nharmonic>` - same as multi-harmonic with N terms
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* :doc:`opls <dihedral_opls>` - OPLS dihedral
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* :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
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* :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
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* :doc:`table <dihedral_table>` - tabulated dihedral
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* :doc:`table/cut <dihedral_table>` - tabulated dihedral with analytic cutoff
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----------
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Restrictions
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""""""""""""
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Dihedral styles can only be set for atom styles that allow dihedrals
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to be defined.
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Most dihedral styles are part of the MOLECULE package. They are only
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enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info. The doc pages for
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individual dihedral potentials tell if it is part of a package.
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Related commands
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""""""""""""""""
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:doc:`dihedral_coeff <dihedral_coeff>`
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Default
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"""""""
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dihedral_style none
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