forked from lijiext/lammps
122 lines
4.1 KiB
Plaintext
122 lines
4.1 KiB
Plaintext
"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,Section_commands.html#comm)
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:line
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angle_style dipole command :h3
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angle_style dipole/omp command :h3
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[Syntax:]
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angle_style dipole :pre
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[Examples:]
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angle_style dipole
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angle_coeff 6 2.1 180.0 :pre
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[Description:]
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The {dipole} angle style is used to control the orientation of a dipolar
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atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle
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style restrains the orientation of a point dipole mu_j (embedded in atom
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'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i'
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is another atom of the same molecule (typically, 'i' and 'j' are also
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covalently bonded).
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It is convenient to define an angle gamma between the 'free' vector mu_j
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and the reference (bond) vector r_ij:
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:c,image(Eqs/angle_dipole_gamma.jpg)
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The {dipole} angle style uses the potential:
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:c,image(Eqs/angle_dipole_potential.jpg)
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where K is a rigidity constant and gamma0 is an equilibrium (reference)
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angle.
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The torque on the dipole can be obtained by differentiating the
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potential using the 'chain rule' as in appendix C.3 of
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"(Allen)"_#Allen:
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:c,image(Eqs/angle_dipole_torque.jpg)
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Example: if gamma0 is set to 0 degrees, the torque generated by
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the potential will tend to align the dipole along the reference
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direction defined by the (bond) vector r_ij (in other words, mu_j is
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restrained to point towards atom 'i').
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Note that the angle dipole potential does not give rise to any force,
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because it does not depend on the distance between i and j (it only
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depends on the angle between mu_j and r_ij).
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The following coefficients must be defined for each angle type via the
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"angle_coeff"_angle_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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K (energy)
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gamma0 (degrees) :ul
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:line
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Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
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the same as the corresponding style without the suffix. They have
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been optimized to run faster, depending on your available hardware, as
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discussed in "Section_accelerate"_Section_accelerate.html of the
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manual. 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 USER-CUDA, GPU, USER-OMP and OPT
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packages, respectively. They are only enabled if LAMMPS was built with
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those packages. See the "Making LAMMPS"_Section_start.html#start_3
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section 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"_Section_start.html#start_6 when you invoke LAMMPS, or you can
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use the "suffix"_suffix.html command in your input script.
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See "Section_accelerate"_Section_accelerate.html of the manual for
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more instructions on how to use the accelerated styles effectively.
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[Restrictions:]
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This angle style can only be used if LAMMPS was built with the
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USER-MISC package. See the "Making LAMMPS"_Section_start.html#2_3
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section for more info on packages.
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IMPORTANT NOTE: In the "Angles" section of the data file, the atom ID
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'j' corresponding to the dipole to restrain must come before the atom
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ID of the reference atom 'i'. A third atom ID 'k' must also be
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provided, although 'k' is just a 'dummy' atom which can be any atom;
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it may be useful to choose a convention (e.g., 'k'='i') and adhere to
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it. For example, if ID=1 for the dipolar atom to restrain, and ID=2
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for the reference atom, the corresponding line in the "Angles" section
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of the data file would read: X X 1 2 2
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The "newton" command for intramolecular interactions must be "on"
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(which is the default).
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This angle style should not be used with SHAKE.
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[Related commands:]
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"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html
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[Default:] none
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:line
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:link(Orsi)
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[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of
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lipid membranes, PloS ONE 6(12): e28637, 2011.
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:link(Allen)
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[(Allen)] Allen & Tildesley, Computer Simulation of Liquids,
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Clarendon Press, Oxford, 1987.
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