Merge pull request #839 from oywg11/master

New registry dependent interlayer potential in LAMMPS

doc/src/Eqs/pair_coul_shield.tex

@@ -0,0 +1,33 @@
+\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
+\pdfoutput=1
+\bibliographystyle{apsrev4}
+\usepackage{color}
+\usepackage{dcolumn} %Align table columns on decimal point
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{amsthm}
+\usepackage{graphicx}
+\usepackage[pdftex]{hyperref}
+\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
+\usepackage[all]{hypcap}
+\newcommand{\red}{\color{red}}
+\newcommand{\blue}{\color{blue}}
+\definecolor{green}{rgb}{0,0.5,0}
+\newcommand{\green}{\color{green}}
+\newcommand{\white}{\color{white}}
+%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
+\thickmuskip=0.5\thickmuskip %shorter spaces in math
+
+\begin{document}
+\begingroup
+\Large
+\begin{eqnarray*}
+  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
+  V_{ij} & = & {\rm Tap}(r_{ij})\frac{\kappa q_i q_j}{\sqrt[3]{r_{ij}^3+(1/\lambda_{ij})^3}}\\[15pt]
+  {\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+                          70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
+                          84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
+                          35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
+\end{eqnarray*}
+\endgroup
+\end{document}

doc/src/Eqs/pair_ilp_graphene_hbn.tex

@@ -0,0 +1,42 @@
+\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
+\pdfoutput=1
+\bibliographystyle{apsrev4}
+\usepackage{color}
+\usepackage{dcolumn} %Align table columns on decimal point
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{amsthm}
+\usepackage{graphicx}
+\usepackage[pdftex]{hyperref}
+\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
+\usepackage[all]{hypcap}
+\newcommand{\red}{\color{red}}
+\newcommand{\blue}{\color{blue}}
+\definecolor{green}{rgb}{0,0.5,0}
+\newcommand{\green}{\color{green}}
+\newcommand{\white}{\color{white}}
+%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
+\thickmuskip=0.5\thickmuskip %shorter spaces in math
+%
+\begin{document}
+%
+\begingroup
+\Large
+\begin{eqnarray*}
+  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
+  V_{ij} & = & {\rm Tap}(r_{ij})\left \{ e^{-\alpha (r_{ij}/\beta -1)} 
+               \left [ \epsilon + f(\rho_{ij}) + f(\rho_{ji})\right ] - 
+                \frac{1}{1+e^{-d\left [ \left ( r_{ij}/\left (s_R \cdot r^{eff} \right ) \right )-1 \right ]}}
+                \cdot \frac{C_6}{r^6_{ij}} \right \}\\[15pt]
+  \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_i)^2 \\[15pt]
+  \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij} \cdot {\bf n}_j)^2 \\[15pt]
+  f(\rho) & = &  C e^{ -( \rho / \delta )^2 }\\[15pt]
+  {\rm Tap}(r_{ij}) & = & 20\left ( \frac{r_{ij}}{R_{cut}} \right )^7 -
+                          70\left ( \frac{r_{ij}}{R_{cut}} \right )^6 +
+                          84\left ( \frac{r_{ij}}{R_{cut}} \right )^5 -
+                          35\left ( \frac{r_{ij}}{R_{cut}} \right )^4 + 1
+\end{eqnarray*}
+\endgroup
+%
+\end{document}
+%

doc/src/Eqs/pair_kolmogorov_crespi_full.tex

@@ -0,0 +1,33 @@
+\documentclass[aps,pr,onecolumn,superscriptaddress,noshowpacs,a4paper,15pt]{revtex4}
+\pdfoutput=1
+\bibliographystyle{apsrev4}
+\usepackage{color}
+\usepackage{dcolumn} %Align table columns on decimal point
+\usepackage{amssymb}
+\usepackage{amsmath}
+\usepackage{amsthm}
+\usepackage{graphicx}
+\usepackage[pdftex]{hyperref}
+\hypersetup{colorlinks=true,citecolor=blue,linkcolor=red,urlcolor=blue}
+\usepackage[all]{hypcap}
+\newcommand{\red}{\color{red}}
+\newcommand{\blue}{\color{blue}}
+\definecolor{green}{rgb}{0,0.5,0}
+\newcommand{\green}{\color{green}}
+\newcommand{\white}{\color{white}}
+%\newcommand{\cite}[1]{\hspace{-1 ex} % \nocite{#1}\citenum{#1}}
+\thickmuskip=0.5\thickmuskip %shorter spaces in math
+
+\begin{document}
+
+\begingroup
+\Large
+\begin{eqnarray*}
+  E & = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij} \\[15pt]
+  V_{ij} & = & e^{-\lambda (r_{ij} -z_0)} \left [ C + f(\rho_{ij}) + f(\rho_{ji}) - A \left ( \frac{r_{ij}}{z_0}\right )^{-6} \right ] \\
+  \rho_{ij}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot {\bf n}_{i})^2 \\[15pt]
+  \rho_{ji}^2 & = & r_{ij}^2 - ({\bf r}_{ij}\cdot  {\bf n}_{j})^2 \\[15pt]
+  f(\rho) & = &  e^{-(\rho/\delta)^2} \sum_{n=0}^2 C_{2n} { \rho/\delta }^{2n}
+\end{eqnarray*}
+\endgroup
+\end{document}

doc/src/Section_commands.txt

@@ -1040,6 +1040,7 @@ package"_Section_start.html#start_3.
 "coul/cut/soft (o)"_pair_lj_soft.html,
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/long/soft (o)"_pair_lj_soft.html,
+"coul/shield"_pair_coul_shield.html,
 "dpd/fdt"_pair_dpd_fdt.html,
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
 "eam/cd (o)"_pair_eam.html,
@@ -1050,6 +1051,8 @@ package"_Section_start.html#start_3.
 "exp6/rx (k)"_pair_exp6_rx.html,
 "extep"_pair_extep.html,
 "gauss/cut"_pair_gauss.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lennard/mdf"_pair_mdf.html,
 "list"_pair_list.html,

doc/src/lammps.book

@@ -437,6 +437,7 @@ pair_colloid.html
 pair_comb.html
 pair_coul.html
 pair_coul_diel.html
+pair_coul_shield.html
 pair_cs.html
 pair_dipole.html
 pair_dpd.html
@@ -453,9 +454,11 @@ pair_gayberne.html
 pair_gran.html
 pair_gromacs.html
 pair_gw.html
+pair_ilp_graphene_hbn.html
 pair_hbond_dreiding.html
 pair_hybrid.html
 pair_kim.html
+pair_kolmogorov_crespi_full.html
 pair_kolmogorov_crespi_z.html
 pair_lcbop.html
 pair_line_lj.html

doc/src/pair_coul_shield.txt

@@ -0,0 +1,86 @@
+"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 coul/shield command :h3
+
+[Syntax:]
+
+pair_style coul/shield cutoff tap_flag :pre
+
+cutoff = global cutoff (distance units)
+tap_flag = 0/1 to turn off/on the taper function
+
+[Examples:]
+
+pair_style coul/shield 16.0 1
+pair_coeff 1 2 0.70 :pre
+
+
+[Description:]
+
+Style {coul/shield} computes a Coulomb interaction for boron and
+nitrogen atoms located in different layers of hexagonal boron
+nitride. This potential is designed be used in combination with
+the pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
+
+NOTE: This potential is intended for electrostatic interactions between
+two different layers of hexagonal boron nitride. Therefore, to avoid
+interaction within the same layers, each layer should have a separate
+molecule id and is recommended to use the "full" atom style, so that
+charge and molecule ID information is included.
+
+:c,image(Eqs/pair_coul_shield.jpg)
+
+Where Tap(r_ij) is the taper function which provides a continuous cutoff
+(up to third derivative) for inter-atomic separations larger than r_c
+"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
+eliminates the short-range singularity of the classical mono-polar
+electrostatic interaction expression "(Maaravi)"_#Maaravi1.
+
+The shielding parameter {lambda} (1/distance units) must be defined for
+each pair of atom types via the "pair_coeff"_pair_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:
+
+The global cutoff (r_c) specified in the pair_style command is used.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+This pair style does not support parameter mixing. Coefficients must
+be given explicitly for each type of particle pairs.
+
+The "pair_modify"_pair_modify.html {table} option is not relevant
+for this pair style.
+
+This pair style does not support the "pair_modify"_pair_modify.html
+{tail} option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  It does not support the
+{inner}, {middle}, {outer} keywords.
+
+[Restrictions:]
+
+This style is part of the USER-MISC package.  It is only enabled
+if LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_2_3 section for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
+
+[Default:] tap_flag = 1
+
+:line
+
+:link(Maaravi1)
+[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

doc/src/pair_ilp_graphene_hbn.txt

@@ -0,0 +1,125 @@
+"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 ilp/graphene/hbn command :h3
+
+[Syntax:]
+
+pair_style hybrid/overlay ilp/graphene/hbn cutoff tap_flag :pre
+
+cutoff = global cutoff (distance units)
+tap_flag = 0/1 to turn off/on the taper function 
+
+[Examples:]
+
+pair_style hybrid/overlay ilp/graphene/hbn 16.0 1
+pair_coeff * * ilp/graphene/hbn  BNCH.ILP B N C :pre
+
+pair_style  hybrid/overlay rebo tersoff ilp/graphene/hbn 16.0 coul/shield 16.0
+pair_coeff  * * rebo                 CH.airebo   NULL NULL C
+pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
+pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C :pre
+pair_coeff  1 1 coul/shield 0.70
+pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  2 2 coul/shield 0.69
+
+[Description:]
+
+The {ilp/graphene/hbn} style computes the registry-dependent interlayer
+potential (RDILP) potential as described in "(Leven)"_#Leven and
+"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
+in "(Kolmogorov)"_#Kolmogorov2.
+
+:c,image(Eqs/pair_ilp_graphene_hbn.jpg)
+
+Where Tap(r_ij) is the taper function which provides a continuous
+cutoff (up to third derivative) for interatomic separations larger than
+r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
+equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
+
+It is important to include all the pairs to build the neighbor list for
+calculating the normals.
+
+NOTE: This potential is intended for interactions between two different
+layers of graphene or hexagonal boron nitride. Therefore, to avoid
+interaction within the same layers, each layer should have a separate
+molecule id and is recommended to use "full" atom style in the data
+file.
+
+The parameter file (e.g. BNCH.ILP), is intended for use with {metal}
+"units"_units.html, with energies in meV. Two additional parameters,
+{S}, and {rcut} are included in the parameter file. {S} is designed to
+facilitate scaling of energies. {rcut} is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
+are fitted with taper function by setting the cutoff equal to 16.0
+Angstrom.  Using different cutoff or taper function should be careful.
+
+NOTE: Two parameter files (BNCH.ILP and BNCH-old.ILP) are presented,
+BNCH-old.ILP contains the parameters published in "(Leven)"_#Leven and
+"(Maaravi)"_#Maaravi2, which is only suitable for long-range
+interaction. The parameters in BNCH.ILP provides a good description both
+for short- and long-range interaction. This is useful for simulations in
+the high pressure (small interlayer distances) regime. The comparison of
+two sets of parameters can be found in "(Ouyang)"_#Ouyang.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style {none}.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA 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 fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This pair potential requires the newton setting to be {on} for pair
+interactions.
+
+The BNCH.ILP potential file provided with LAMMPS (see the potentials
+directory) are parameterized for {metal} units.  You can use this
+potential with any LAMMPS units, but you would need to create your
+BNCH.ILP potential file with coefficients listed in the appropriate
+units, if your simulation does not use {metal} units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair_none"_pair_none.html
+"pair_style hybrid/overlay"_pair_hybrid.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_coul_shield"_pair_coul_shield.html
+
+[Default:] tap_flag = 1
+
+:line
+
+:link(Leven)
+[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
+
+:link(Maaravi2)
+[(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
+
+:link(Kolmogorov2)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+
+:link(Ouyang)
+[(Ouyang)] W. Ouyang, D. Mandelli, O. Hod, M. Urbakh, In preparation.

doc/src/pair_kolmogorov_crespi_full.txt

@@ -0,0 +1,97 @@
+"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 kolmogorov/crespi/full command :h3
+
+[Syntax:]
+
+pair_style hybrid/overlay kolmogorov/crespi/full cutoff tap_flag :pre
+
+cutoff = global cutoff (distance units)
+tap_flag = 0/1 to turn off/on the taper function 
+
+[Examples:]
+
+pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
+pair_coeff * * none
+pair_coeff * * kolmogorov/crespi/full  CC.KC   C C :pre
+
+pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
+pair_coeff * * rebo                    CH.airebo  C C
+pair_coeff * * kolmogorov/crespi/full  CC.KC      C C :pre
+
+[Description:]
+
+The {kolmogorov/crespi/full} style computes the Kolmogorov-Crespi
+interaction potential as described in "(Kolmogorov)"_#Kolmogorov1.
+No simplification is made,
+
+:c,image(Eqs/pair_kolmogorov_crespi_full.jpg)
+
+It is important to have a sufficiently large cutoff to ensure smooth
+forces and to include all the pairs to build the neighbor list for
+calculating the normals.  Energies are shifted so that they go
+continuously to zero at the cutoff assuming that the exponential part of
+{Vij} (first term) decays sufficiently fast.  This shift is achieved by
+the last term in the equation for {Vij} above.
+
+NOTE: This potential is intended for interactions between two different
+graphene layers. Therefore, to avoid interaction within the same layers,
+each layer should have a separate molecule id and is recommended to use
+"full" atom style in the data file.
+
+The parameter file (e.g. CC.KC), is intended for use with {metal}
+"units"_units.html, with energies in meV. Two additional parameters, {S},
+and {rcut} are included in the parameter file. {S} is designed to
+facilitate scaling of energies. {rcut} is designed to build the neighbor
+list for calculating the normals for each atom pair.
+
+This potential must be used in combination with hybrid/overlay.
+Other interactions can be set to zero using pair_style {none}.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA 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 fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+This pair potential requires the newton setting to be {on} for pair
+interactions.
+
+The CC.KC potential file provided with LAMMPS (see the potentials
+folder) are parameterized for metal units.  You can use this potential
+with any LAMMPS units, but you would need to create your own custom
+CC.KC potential file with all coefficients converted to the appropriate
+units.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+"pair_none"_pair_none.html
+"pair_style hybrid/overlay"_pair_hybrid.html
+"pair_style kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html
+"pair_style ilp/graphene/hbn"_pair_ilp_graphene_hbn.html
+
+[Default:] tap_flag = 0
+
+:line
+
+:link(Kolmogorov1)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)

doc/src/pair_kolmogorov_crespi_z.txt

@@ -25,7 +25,7 @@ pair_coeff 1 2 kolmogorov/crespi/z  CC.KC      C C :pre
 [Description:]
 
 The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
-potential as described in "(KC05)"_#KC05. An important simplification is made,
+potential as described in "(Kolmogorov)"_#KC05. An important simplification is made,
 which is to take all normals along the z-axis.
 
 :c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
@@ -65,7 +65,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 :line
 
 :link(KC05)
-[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
 
 :link(vanWijk)
 [(vanWijk)] M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino,

doc/src/pairs.txt

@@ -24,6 +24,7 @@ Pair Styles :h1
    pair_comb
    pair_coul
    pair_coul_diel
+   pair_coul_shield
    pair_cs
    pair_dipole
    pair_dpd
@@ -42,7 +43,9 @@ Pair Styles :h1
    pair_gw
    pair_hbond_dreiding
    pair_hybrid
+   pair_ilp_graphene_hbn
    pair_kim
+   pair_kolmogorov_crespi_full
    pair_kolmogorov_crespi_z
    pair_lcbop
    pair_line_lj