Syntax: +
+pair_style thole damp cutoff ++
Examples: +
+pair_style hybrid/overlay ... thole 2.6 12.0 +pair_coeff 1 1 thole 1.0 +pair_coeff 1 2 thole 1.0 2.6 10.0 +pair_coeff * 2 thole 1.0 2.6 ++
Description: +
+The thole pair style is meant to be used with force fields that +include explicit polarization through Drude dipoles. This link +describes how to use the thermalized Drude oscillator +model in LAMMPS and polarizable models in LAMMPS +are discussed in this Section. +
+The thole pair style should be used as a sub-style within in the +pair_hybrid/overlay command, in conjunction with a +main pair style including Coulomb interactions, i.e. any pair style +containing coul/cut or coul/long in its style name. +
+The thole pair style computes the Coulomb interaction damped at +short distances by a function +
+\begin{equation} T_{ij}(r_{ij}) = 1 - \left( 1 + +\frac{s_{ij} r_{ij} }{2} \right) +\exp \left( - s_{ij} r_{ij} \right) \end{equation} +
+This function results from an adaptation to point charges +(Noskov) of the dipole screening scheme originally proposed +by Thole. The scaling coefficient \(s_{ij} \) is determined +by the polarizability of the atoms, \( \alpha_i \), and by a Thole +damping parameter \( a \). This Thole damping parameter usually takes +a value of 2.6, but in certain force fields the value can depend upon +the atom types. The mixing rule for Thole damping parameters is the +arithmetic average, and for polarizabilities the geometric average +between the atom-specific values. +
+\begin{equation} s_{ij} = \frac{ a_{ij} }{ +(\alpha_{ij})^{1/3} } = \frac{ (a_i + a_j)/2 }{ +[(\alpha_i\alpha_j)^{1/2}]^{1/3} } \end{equation} +
+The damping function is only applied to the interactions between the +point charges representing the induced dipoles on polarizable sites, +that is, charges on Drude particles, \( q_{D,i} \), and opposite +charges, \( -q_{D,i} \), located on the respective core particles +(to which each Drude particle is bonded). Therefore, Thole screening +is not applied to the full charge of the core particle \( q_i \), but +only to the \( -q_{D,i} \) part of it. +
+The interactions between core charges are subject to the weighting +factors set by the special_bonds command. The +interactions between Drude particles and core charges or +non-polarizable atoms are also subject to these weighting factors. The +Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from +their respective cores. +
+The following coefficients must be defined for each pair of atoms +types via the pair_coeff command as in the example +above. +
+The last two coefficients are optional. If not specified the global +Thole damping parameter or global cutoff specified in the pair_style +command are used. In order to specify a cutoff (third argument) a damp +parameter (second argument) must also be specified. +
+Mixing: +
+The thole pair style does not support mixing. Thus, coefficients +for all I,J pairs must be specified explicitly. +
+Restrictions: +
+These pair styles are part of the USER-DRUDE package. They are only +enabled if LAMMPS was built with that package. See the Making +LAMMPS section for more info. +
+This pair_style should currently not be used with the charmm dihedral +style if the latter non-zero 1-4 weighting +factors. This is because the thole pair style does not know which +pairs are 1-4 partners of which dihedrals. +
+Related commands: +
+fix drude, fix +langevin/drude, fix +drude/transform, compute +temp/drude +
+Default: none +
+(Noskov) Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). +
+ + +(Thole) Chem Phys, 59, 341 (1981). +
+ diff --git a/doc/pair_thole.txt b/doc/pair_thole.txt new file mode 100644 index 0000000000..a0eb451e8b --- /dev/null +++ b/doc/pair_thole.txt @@ -0,0 +1,126 @@ + + + +"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 + +pair_style thole command :h3 + +[Syntax:] + +pair_style thole damp cutoff :pre + +thole = style name +damp = global damping parameter +cutoff = global cutoff :ul + +[Examples:] + +pair_style hybrid/overlay ... thole 2.6 12.0 +pair_coeff 1 1 thole 1.0 +pair_coeff 1 2 thole 1.0 2.6 10.0 +pair_coeff * 2 thole 1.0 2.6 :pre + +[Description:] + +The {thole} pair style is meant to be used with force fields that +include explicit polarization through Drude dipoles. This link +describes how to use the "thermalized Drude oscillator +model"_tutorial_drude.html in LAMMPS and polarizable models in LAMMPS +are discussed in "this Section"_Section_howto.html#howto_25. + +The {thole} pair style should be used as a sub-style within in the +"pair_hybrid/overlay"_pair_hybrid.html command, in conjunction with a +main pair style including Coulomb interactions, i.e. any pair style +containing {coul/cut} or {coul/long} in its style name. + +The {thole} pair style computes the Coulomb interaction damped at +short distances by a function + +\begin\{equation\} T_\{ij\}(r_\{ij\}) = 1 - \left( 1 + +\frac\{s_\{ij\} r_\{ij\} \}\{2\} \right) +\exp \left( - s_\{ij\} r_\{ij\} \right) \end\{equation\} + +This function results from an adaptation to point charges +"(Noskov)"_#Noskov of the dipole screening scheme originally proposed +by "Thole"_#Thole. The scaling coefficient \(s_\{ij\} \) is determined +by the polarizability of the atoms, \( \alpha_i \), and by a Thole +damping parameter \( a \). This Thole damping parameter usually takes +a value of 2.6, but in certain force fields the value can depend upon +the atom types. The mixing rule for Thole damping parameters is the +arithmetic average, and for polarizabilities the geometric average +between the atom-specific values. + +\begin\{equation\} s_\{ij\} = \frac\{ a_\{ij\} \}\{ +(\alpha_\{ij\})^\{1/3\} \} = \frac\{ (a_i + a_j)/2 \}\{ +\[(\alpha_i\alpha_j)^\{1/2\}\]^\{1/3\} \} \end\{equation\} + +The damping function is only applied to the interactions between the +point charges representing the induced dipoles on polarizable sites, +that is, charges on Drude particles, \( q_\{D,i\} \), and opposite +charges, \( -q_\{D,i\} \), located on the respective core particles +(to which each Drude particle is bonded). Therefore, Thole screening +is not applied to the full charge of the core particle \( q_i \), but +only to the \( -q_\{D,i\} \) part of it. + +The interactions between core charges are subject to the weighting +factors set by the "special_bonds"_special_bonds.html command. The +interactions between Drude particles and core charges or +non-polarizable atoms are also subject to these weighting factors. The +Drude particles inherit the 1-2, 1-3 and 1-4 neighbor relations from +their respective cores. + +The following coefficients must be defined for each pair of atoms +types via the "pair_coeff"_pair_coeff.html command as in the example +above. + +alpha (distance units^3) +damp +cutoff (distance units) :ul + +The last two coefficients are optional. If not specified the global +Thole damping parameter or global cutoff specified in the pair_style +command are used. In order to specify a cutoff (third argument) a damp +parameter (second argument) must also be specified. + +[Mixing]: + +The {thole} pair style does not support mixing. Thus, coefficients +for all I,J pairs must be specified explicitly. + +[Restrictions:] + +These pair styles are part of the USER-DRUDE package. They are only +enabled if LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +This pair_style should currently not be used with the "charmm dihedral +style"_dihedral_charmm.html if the latter non-zero 1-4 weighting +factors. This is because the {thole} pair style does not know which +pairs are 1-4 partners of which dihedrals. + +[Related commands:] + +"fix drude"_fix_drude.html, "fix +langevin/drude"_fix_langevin_drude.html, "fix +drude/transform"_fix_drude_transform.html, "compute +temp/drude"_compute_temp_drude.html + +[Default:] none + +:line + +:link(Noskov) +[(Noskov)] Noskov, Lamoureux and Roux, J Phys Chem B, 109, 6705 (2005). + +:link(Thole) +[(Thole)] Chem Phys, 59, 341 (1981).