lammps · akohlmey · Aug 20, 2019 · Feb 21, 2019 · Feb 21, 2019 · Mar 3, 2019
diff --git a/doc/src/Commands_pair.txt b/doc/src/Commands_pair.txt
@@ -65,6 +65,7 @@ OPT.
 "colloid (go)"_pair_colloid.html,
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
+"cosine/squared"_pair_cosine_squared.html,
 "coul/cut (gko)"_pair_coul.html,
 "coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,

diff --git a/doc/src/Eqs/pair_cosine_squared.jpg b/doc/src/Eqs/pair_cosine_squared.jpg
diff --git a/doc/src/Eqs/pair_cosine_squared.tex b/doc/src/Eqs/pair_cosine_squared.tex
@@ -0,0 +1,16 @@
+\documentclass[12pt]{article}
+
+\usepackage{amsmath}
+
+\begin{document}
+
+\begin{align*}
+E = 
+\begin{cases}
+-\epsilon& \quad r < \sigma \\
+-\epsilon\cos\left(\frac{\pi\left(r - \sigma\right)}{2\left(r_c - \sigma\right)}\right)&\quad \sigma \leq r < r_c \\
+0& \quad r \geq r_c
+\end{cases}
+\end{align*}
+
+\end{document}
diff --git a/doc/src/Eqs/pair_cosine_squared_wca.jpg b/doc/src/Eqs/pair_cosine_squared_wca.jpg
diff --git a/doc/src/Eqs/pair_cosine_squared_wca.tex b/doc/src/Eqs/pair_cosine_squared_wca.tex
@@ -0,0 +1,11 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+$$
+ E = \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - 
+                       2\left(\frac{\sigma}{r}\right)^6 + 1\right]
+                       , \quad r < \sigma
+$$
+
+\end{document}
diff --git a/doc/src/JPG/pair_cosine_squared_graphs.jpg b/doc/src/JPG/pair_cosine_squared_graphs.jpg
diff --git a/doc/src/fix.txt b/doc/src/fix.txt
@@ -244,7 +244,7 @@ accelerated styles exist.
 "mscg"_fix_mscg.html - apply MSCG method for force-matching to generate coarse grain models
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
 "mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
-"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algrithm
+"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
 "mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover

diff --git a/doc/src/lammps.book b/doc/src/lammps.book
@@ -569,6 +569,7 @@ pair_charmm.html
 pair_class2.html
 pair_colloid.html
 pair_comb.html
+pair_cosine_squared.html
 pair_coul.html
 pair_coul_diel.html
 pair_coul_shield.html

diff --git a/doc/src/pair_cosine_squared.txt b/doc/src/pair_cosine_squared.txt
@@ -0,0 +1,108 @@
+"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 cosine/squared command :h3
+
+[Syntax:]
+
+pair_style cosine/squared cutoff :pre
+
+cutoff = global cutoff for cosine-squared interactions (distance units) :ul
+
+pair_coeff i j eps sigma
+pair_coeff i j eps sigma cutoff
+pair_coeff i j eps sigma wca
+pair_coeff i j eps sigma cutoff wca :pre
+
+i,j = a particle type
+eps = interaction strength, i.e. the depth of the potential minimum (energy units)
+sigma = distance of the potential minimum from 0
+cutoff = the cutoff distance for this pair type, if different from global (distance units)
+wca = if specified a Weeks-Chandler-Andersen potential (with eps strength and minimum at sigma) is added, otherwise not :ul
+
+[Examples:]
+
+pair_style cosine/squared 3.0
+pair_coeff * * 1.0 1.3
+pair_coeff 1 3 1.0 1.3 2.0
+pair_coeff 1 3 1.0 1.3 wca
+pair_coeff 1 3 1.0 1.3 2.0 wca :pre
+
+[Description:]
+
+Style {cosine/squared} computes a potential of the form
+
+:c,image(Eqs/pair_cosine_squared.jpg)
+
+between two point particles, where (sigma, -epsilon) is the location of
+the (rightmost) minimum of the potential, as explained in the syntax
+section above.
+
+This potential was first used in (Cooke)_#CKD for a coarse-grained lipid
+membrane model.  It is generally very useful as a non-specific
+interaction potential because it is fully adjustable in depth and width
+while joining the minimum at (sigma, -epsilon) and zero at (cutoff, 0)
+smoothly, requiring no shifting and causing no related artifacts, tail
+energy calculations etc. This evidently requires {cutoff} to be larger
+than {sigma}.
+
+If the {wca} option is used then a Weeks-Chandler-Andersen potential
+(Weeks)_#WCA is added to the above specified cosine-squared potential,
+specifically the following:
+
+:c,image(Eqs/pair_cosine_squared_wca.jpg)
+
+In this case, and this case only, the {sigma} parameter can be equal to
+{cutoff} (sigma = cutoff) which will result in ONLY the WCA potential
+being used (and print a warning), so the minimum will be attained at
+(sigma, 0). This is a convenience feature that enables a purely
+repulsive potential to be used without a need to define an additional
+pair style and use the hybrid styles.
+
+The energy and force of this pair style for parameters epsilon = 1.0,
+sigma = 1.0, cutoff = 2.5, with and without the WCA potential, are shown
+in the graphs below:
+
+:c,image(JPG/pair_cosine_squared_graphs.jpg)
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing is not supported for this style.
+
+The {shift}, {table} and {tail} options are not relevant for this style.
+
+This pair style writes its information to "binary restart
+files"_restart.html, so pair_style and pair_coeff commands do not need
+to be specified in an input script that reads a restart file.
+
+These pair styles can only be used via the {pair} keyword of the
+"run_style respa"_run_style.html command.  They do not support the
+{inner}, {middle}, {outer} keywords.
+
+:line
+
+[Restrictions:]
+
+The {cosine/squared} style is part of the "USER-MISC" package. It is only
+enabled if LAMMPS is build with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html,
+"pair_style lj/cut"_pair_lj.html
+
+[Default:] none
+
+:link(CKD)
+[(Cooke)] "Cooke, Kremer and Deserno, Phys. Rev. E, 72, 011506 (2005)"
+
+:link(WCA)
+[(Weeks)] "Weeks, Chandler and Andersen, J. Chem. Phys., 54, 5237 (1971)"
diff --git a/doc/src/pair_style.txt b/doc/src/pair_style.txt
@@ -129,6 +129,7 @@ accelerated styles exist.
 "colloid"_pair_colloid.html - integrated colloidal potential
 "comb"_pair_comb.html - charge-optimized many-body (COMB) potential
 "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
+"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
 "coul/cut"_pair_coul.html - cutoff Coulombic potential
 "coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
 "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening

diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt
@@ -24,6 +24,7 @@ Pair Styles :h1
    pair_class2
    pair_colloid
    pair_comb
+   pair_cosine_squared
    pair_coul
    pair_coul_diel
    pair_coul_shield

diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
@@ -356,6 +356,7 @@ Cii
 Cij
 cis
 civ
+CKD
 Clang
 clearstore
 Cleary
@@ -421,6 +422,7 @@ coreshell
 cornflowerblue
 cornsilk
 corotate
+corotation
 corotational
 correlator
 cosineshifted
@@ -2991,6 +2993,7 @@ Waltham
 wavepacket
 wB
 Wbody
+wca
 webpage
 Weckner
 WeinanE

diff --git a/src/.gitignore b/src/.gitignore
@@ -801,6 +801,8 @@
 /pair_comb3.h
 /pair_colloid.cpp
 /pair_colloid.h
+/pair_cosine_squared.cpp
+/pair_cosine_squared.h
 /pair_coul_diel.cpp
 /pair_coul_diel.h
 /pair_coul_long.cpp

diff --git a/src/USER-MISC/README b/src/USER-MISC/README
@@ -69,6 +69,7 @@ improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12
 improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
 pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16
 pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15
+pair_style cosine/squared, Eugen Rozic, eugen.rozic.17 at ucl.ac.uk, 9 Aug 19
 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