+Syntax: +
+angle_style dipole ++
Examples: +
+angle_style dipole +angle_coeff 6 2.1 180.0 ++
Description: +
+The dipole angle style is used to control the orientation of a dipolar +atom within a molecule (Orsi). Specifically, the dipole angle +style restrains the orientation of a point dipole mu_j (embedded in atom +'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' +is another atom of the same molecule (typically, 'i' and 'j' are also +covalently bonded). +
+It is convenient to define an angle gamma between the 'free' vector mu_j +and the reference (bond) vector r_ij: +
+
+The dipole angle style uses the potential: +
+
+where K is a rigidity constant and gamma0 is an equilibrium (reference) +angle. +
+The torque on the dipole can be obtained by differentiating the +potential using the 'chain rule' as in appendix C.3 of +(Allen): +
+
+Example: if gamma0 is set to 0 degrees, the torque generated by +the potential will tend to align the dipole along the reference +direction defined by the (bond) vector r_ij (in other words, mu_j is +restrained to point towards atom 'i'). +
+Note that the angle dipole potential does not give rise to any force, +because it does not depend on the distance between i and j (it only +depends on the angle between mu_j and r_ij). +
+The following coefficients must be defined for each angle type via the +angle_coeff command as in the example above, or in +the data file or restart files read by the read_data +or read_restart commands: +
+Restrictions: +
+This angle style can only be used if LAMMPS was built with the +"user-misc" package. See the Making LAMMPS +section for more info on packages. +
+IMPORTANT: In the "Angles" section of the data file, the atom id 'j' +corresponding to the dipole to restrain must come before the atom id +of the reference atom 'i'. A third atom id 'k' must also be provided, +although 'k' is just a 'dummy' atom which can be any atom; it may be +useful to choose a convention (e.g., 'k'='i') and adhere to it. For +example, if id=1 for the dipolar atom to restrain, and id=2 for the +reference atom, the corresponding line in the "Angles" section of the +data file would read: X X 1 2 2 +
+The "newton" command for intramolecular interactions must be "on" +(which is the default). +
+This angle style should not be used with SHAKE. +
+Related commands: +
+ +Default: none +
+(Orsi) Orsi & Essex, The ELBA force field for coarse-grain modeling of +lipid membranes, PloS ONE 6(12): e28637, 2011. +
+ + +(Allen) Allen & Tildesley, Computer Simulation of Liquids, +Clarendon Press, Oxford, 1987. +
+ diff --git a/doc/angle_dipole.txt b/doc/angle_dipole.txt new file mode 100644 index 0000000000..7ead336f8a --- /dev/null +++ b/doc/angle_dipole.txt @@ -0,0 +1,98 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +angle_style dipole command :h3 + +[Syntax:] + +angle_style dipole :pre + +[Examples:] + +angle_style dipole +angle_coeff 6 2.1 180.0 :pre + +[Description:] + +The {dipole} angle style is used to control the orientation of a dipolar +atom within a molecule "(Orsi)"_#Orsi. Specifically, the {dipole} angle +style restrains the orientation of a point dipole mu_j (embedded in atom +'j') with respect to a reference (bond) vector r_ij = r_i - r_j, where 'i' +is another atom of the same molecule (typically, 'i' and 'j' are also +covalently bonded). + +It is convenient to define an angle gamma between the 'free' vector mu_j +and the reference (bond) vector r_ij: + +:c,image(Eqs/angle_dipole_gamma.jpg) + +The {dipole} angle style uses the potential: + +:c,image(Eqs/angle_dipole_potential.jpg) + +where K is a rigidity constant and gamma0 is an equilibrium (reference) +angle. + +The torque on the dipole can be obtained by differentiating the +potential using the 'chain rule' as in appendix C.3 of +"(Allen)"_#Allen: + +:c,image(Eqs/angle_dipole_torque.jpg) + +Example: if gamma0 is set to 0 degrees, the torque generated by +the potential will tend to align the dipole along the reference +direction defined by the (bond) vector r_ij (in other words, mu_j is +restrained to point towards atom 'i'). + +Note that the angle dipole potential does not give rise to any force, +because it does not depend on the distance between i and j (it only +depends on the angle between mu_j and r_ij). + +The following coefficients must be defined for each angle type via the +"angle_coeff"_angle_coeff.html command as in the example above, or in +the data file or restart files read by the "read_data"_read_data.html +or "read_restart"_read_restart.html commands: + +K (energy) +gamma0 (degrees) :ul + +[Restrictions:] + +This angle style can only be used if LAMMPS was built with the +"user-misc" package. See the "Making LAMMPS"_Section_start.html#2_3 +section for more info on packages. + +IMPORTANT: In the "Angles" section of the data file, the atom id 'j' +corresponding to the dipole to restrain must come before the atom id +of the reference atom 'i'. A third atom id 'k' must also be provided, +although 'k' is just a 'dummy' atom which can be any atom; it may be +useful to choose a convention (e.g., 'k'='i') and adhere to it. For +example, if id=1 for the dipolar atom to restrain, and id=2 for the +reference atom, the corresponding line in the "Angles" section of the +data file would read: X X 1 2 2 + +The "newton" command for intramolecular interactions must be "on" +(which is the default). + +This angle style should not be used with SHAKE. + +[Related commands:] + +"angle_coeff"_angle_coeff.html, "angle_hybrid"_angle_hybrid.html + +[Default:] none + +:line + +:link(Orsi) +[(Orsi)] Orsi & Essex, The ELBA force field for coarse-grain modeling of +lipid membranes, PloS ONE 6(12): e28637, 2011. + +:link(Allen) +[(Allen)] Allen & Tildesley, Computer Simulation of Liquids, +Clarendon Press, Oxford, 1987.