Add documentation

doc/src/Eqs/pair_drip.tex

@@ -0,0 +1,15 @@
+\documentclass[12pt]{article}
+\usepackage{amsmath}
+\usepackage{bm}
+
+\begin{document}
+
+\begin{eqnarray*}
+E &=& \frac{1}{2} \sum_{i} \sum_{j\notin\text{layer}\,i} (\phi_{ij} + \phi_{ji}) \\
+\phi_{ij} &=& f_\text{c}(x_r) \left[ e^{-\lambda(r_{ij} - z_0 )} \left[C+f(\rho_{ij})+  g(\rho_{ij}, \{\alpha_{ij}^{(m)}\}) \right]- A\left (\frac{z_0}{r_{ij}} \right)^6 \right] \\
+\end{eqnarray*}  
+
+
+
+                        
+\end{document}

doc/src/pair_drip.txt

@@ -0,0 +1,139 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+pair_style drip command :h3
+
+[Syntax:]
+
+pair_style hybrid/overlay drip \[styles ...\] :pre
+
+styles = other styles to be overlayed with drip (optional) :ul
+
+[Examples:]
+
+pair_style hybrid/overlay drip
+pair_coeff * * none
+pair_coeff * * drip  C.drip  C :pre
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C
+pair_coeff * * rebo  CH.airebo  C :pre
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C NULL
+pair_coeff * * rebo  CH.airebo  C H :pre
+
+
+[Description:]
+
+Style {drip} computes the interlayer interactions of layered materials using
+the dihedral-angle-corrected registry-dependent (DRIP) potential as described
+in "(Wen)"_#Wen1, which is based on the "(Kolmogorov)"_#Kolmogorov1 potential
+and provides an improvded prediction for forces.
+The total potential energy of a system is
+
+:c,image(Eqs/pair_drip.jpg)
+
+where the {r^-6} term models the attractive London dispersion,
+the exponential term is designed to capture the registry effect due to
+overlapping {pi} bonds, and {fc} is a cutoff function.
+
+
+This potential (DRIP) only provides the interlayer interactions between
+graphene layers. So, to perform a realistic simulation, it should be used in
+combination with an intralayer potential such as "REBO"_pair_airebo.html and
+"Tersoff"_pair_tersoff.html.
+To keep the intralayer interactions unaffected, we should avoid applying DRIP
+to contribute energy to intralayer interactions. This can be achieved by
+assigning different molecular IDs to atoms in different layers, and DRIP is
+implemented such that only atoms with different molecular ID can interact with
+each other. For this purpose, "atom style"_atom_style.html "molecular" or
+"full" has to be used.
+
+On the other way around, "REBO"_pair_airebo.html ("Tersoff"_pair_tersoff.html
+or any other potential used to provide the intralayer interactions) should not
+interfere with the interlayer interactions described by DRIP. This is typically
+automatically achieved using the commands provided in the {Examples} section
+above, since the cutoff distance for carbon-carbon interaction in the intralayer
+potentials (e.g. 2 Angstrom for "REBO"_pair_airebo.html) is much smaller than
+the equilibrium layer distance of graphene layers (about 3.4 Angstrom).
+If you want, you can enforce this by assigning different atom types to atoms in
+different layers, and apply an intralayer potential to one atom type.
+See "pair_hybrid"_pair_hybrid.html for details.
+
+:line
+
+The "pair_coeff"_pair_coeff.html command for DRIP takes {4+N} arguments, where
+{N} is the number of LAMMPS atom types. The fist three arguments must be fixed
+to be {* * drip}, the fourth argument is the path to the DRIP parameter file,
+and the remaining N arguments specifying the mapping between element in the
+parameter file and atom types. For example, if your LAMMPS simulation has 3 atom
+types and you want all of them to be C, you would use the following pair_coeff
+command:
+
+pair_coeff * * drip  C.drip  C C C :pre
+
+If a mapping value is specified as NULL, the mapping is not performed. This
+could be useful when DRIP is used to model part of the system where other
+element exists. Suppose you have a hydrocarbon system, with C of atom type 1
+and H of atom type 2, you can use the following command to inform DRIP not to
+model H atoms:
+
+pair_style hybrid/overlay drip rebo
+pair_coeff * * drip  C.drip     C NULL
+pair_coeff * * rebo  CH.airebo  C H :pre
+
+NOTE: The parameter file developed in "(Wen)"_#Wen1 is provided with LAMMPS (see
+the "potentials" directory).
+
+
+
+:line
+
+[Mixing, shift, table, tail correction, and restart info]:
+
+This pair style does not support the pair_modify mix, shift, table,
+and tail options.
+
+This pair style does not write their information to binary restart files, since
+it is stored in potential files. Thus, you need to re-specify the pair_style and
+pair_coeff commands in an input script that reads a restart file.
+
+[Restrictions:]
+
+This pair style is part of the USER-MISC package. It is only enabled if LAMMPS
+was built with that package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+This pair potential requires the "newton"_newton.html setting to be "on" for
+pair interactions.
+
+
+The {C.drip} parameter file provided with LAMMPS (see the "potentials"
+directory) is parameterized for metal "units"_units.html. You can use the DRIP
+potential with any LAMMPS units, but you would need to create your own cutstom
+parameter file with coefficients listed in the appropriate units, if your
+simulation doesn't use "metal" units.
+
+
+[Related commands:]
+
+"pair_style lebedeva_z"_pair_lebedeva_z.html,
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
+"pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
+
+
+:line
+
+:link(Wen1)
+[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B, 98, 235404 (2018)
+
+:link(Kolmogorov1)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+

doc/src/pairs.txt

@@ -31,6 +31,7 @@ Pair Styles :h1
    pair_dipole
    pair_dpd
    pair_dpd_fdt
+   pair_drip
    pair_dsmc
    pair_eam
    pair_edip

src/USER-MISC/README

@@ -70,6 +70,7 @@ pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11
 pair_style coul/shield, Wengen Ouyang (Tel Aviv University), w.g.ouyang at gmail dot com, 30 Mar 18
 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11
+pair_style drip, Mingjian Wen, University of Minnesota, wenxx151 at umn.edu, 17 Apr 19
 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11
 pair_style extep, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Nov 17
 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11