Merge pull request #1453 from mjwen/pair_drip

add pair style drip

doc/src/Commands_pair.txt

@@ -80,6 +80,7 @@ OPT.
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
+"drip"_pair_drip.html,
 "eam (gikot)"_pair_eam.html,
 "eam/alloy (gikot)"_pair_eam.html,
 "eam/cd (o)"_pair_eam.html,

doc/src/Eqs/pair_drip.tex

@@ -0,0 +1,14 @@
+\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_{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/lammps.book

@@ -574,6 +574,7 @@ pair_dipole.html
 pair_dpd.html
 pair_dpd_fdt.html
 pair_dsmc.html
+pair_drip.html
 pair_eam.html
 pair_edip.html
 pair_eff.html

doc/src/pair_drip.txt

@@ -0,0 +1,141 @@
+"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)"_#Wen2018, which is based on the "(Kolmogorov)"_#Kolmogorov2005
+potential and provides an improved 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 potential parameters developed in "(Wen)"_#Wen2018 are provided with
+LAMMPS (see the "potentials" directory). Besides those in "Wen"_#Wen2018, an
+additional parameter "normal_cutoff", specific to the LAMMPS implementation, is
+used to find the three nearest neighbors of an atom to construct the normal.
+
+
+: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 custom
+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(Wen2018)
+[(Wen)] M. Wen, S. Carr, S. Fang, E. Kaxiras, and E. B. Tadmor, Phys. Rev. B,
+98, 235404 (2018)
+
+:link(Kolmogorov2005)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+

doc/src/pair_ilp_graphene_hbn.txt

@@ -50,11 +50,11 @@ calculating the normals.
 NOTE: This potential (ILP) is intended for interlayer interactions between two
 different layers of graphene, hexagonal boron nitride (h-BN) and their hetero-junction.
 To perform a realistic simulation, this potential must be used in combination with
-intra-layer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
-To keep the intra-layer properties unaffected, the interlayer interaction
+intralayer potential, such as "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
+To keep the intralayer properties unaffected, the interlayer interaction
 within the same layers should be avoided. Hence, each atom has to have a layer
 identifier such that atoms residing on the same layer interact via the
-appropriate intra-layer potential and atoms residing on different layers
+appropriate intralayer potential and atoms residing on different layers
 interact via the ILP. Here, the molecule id is chosen as the layer identifier,
 thus a data file with the "full" atom style is required to use this potential.
 
@@ -117,6 +117,7 @@ units, if your simulation does not use {metal} units.
 "pair_coeff"_pair_coeff.html,
 "pair_none"_pair_none.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style drip"_pair_drip.html,
 "pair_style pair_kolmogorov_crespi_z"_pair_kolmogorov_crespi_z.html,
 "pair_style pair_kolmogorov_crespi_full"_pair_kolmogorov_crespi_full.html,
 "pair_style pair_lebedeva_z"_pair_lebedeva_z.html,

doc/src/pair_kolmogorov_crespi_full.txt

@@ -44,12 +44,12 @@ can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 
 NOTE: This potential (ILP) is intended for interlayer interactions between two
 different layers of graphene. To perform a realistic simulation, this potential 
-must be used in combination with intra-layer potential, such as 
+must be used in combination with intralayer potential, such as 
 "AIREBO"_pair_airebo.html or "Tersoff"_pair_tersoff.html potential.
-To keep the intra-layer properties unaffected, the interlayer interaction
+To keep the intralayer properties unaffected, the interlayer interaction
 within the same layers should be avoided. Hence, each atom has to have a layer
 identifier such that atoms residing on the same layer interact via the
-appropriate intra-layer potential and atoms residing on different layers
+appropriate intralayer potential and atoms residing on different layers
 interact via the ILP. Here, the molecule id is chosen as the layer identifier,
 thus a data file with the "full" atom style is required to use this potential.
 
@@ -106,6 +106,7 @@ units.
 "pair_coeff"_pair_coeff.html,
 "pair_none"_pair_none.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style drip"_pair_drip.html,
 "pair_style pair_lebedeva_z"_pair_lebedeva_z.html,
 "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.

doc/src/pair_kolmogorov_crespi_z.txt

@@ -59,6 +59,7 @@ package"_Build_package.html doc page for more info.
 "pair_coeff"_pair_coeff.html,
 "pair_none"_pair_none.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style drip"_pair_drip.html,
 "pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 "pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
 "pair_style lebedeva/z"_pair_lebedeva_z.html

doc/src/pair_lebedeva_z.txt

@@ -53,6 +53,7 @@ package"_Build_package.html doc page for more info.
 "pair_coeff"_pair_coeff.html,
 "pair_style none"_pair_none.html,
 "pair_style hybrid/overlay"_pair_hybrid.html,
+"pair_style drip"_pair_drip.html,
 "pair_style ilp/graphene/hbd"_pair_ilp_graphene_hbn.html,
 "pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "pair_style kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html.

doc/src/pair_style.txt

@@ -147,6 +147,7 @@ accelerated styles exist.
 "dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
 "dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
 "dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
+"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
 "eam"_pair_eam.html - embedded atom method (EAM)
 "eam/alloy"_pair_eam.html - alloy EAM
 "eam/cd"_pair_eam.html - concentration-dependent EAM
@@ -174,7 +175,7 @@ accelerated styles exist.
 "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
 "lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
-"lebedeva/z"_pair_lebedeva_z.html - Lebedeva inter-layer potential for graphene with normals along z-axis
+"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
 "lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
 "line/lj"_pair_line_lj.html - LJ potential between line segments
 "list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file

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