Merge pull request #1307 from akohlmey/next-patch-release

Patch release 1 February 2019

cmake/CMakeLists.txt

@@ -178,7 +178,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
   USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
   USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM)
+  USER-QUIP USER-QMMM USER-YAFF)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -559,10 +559,15 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
-      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
+      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
       BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                                --enable-modules=all
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+    )
     ExternalProject_get_property(plumed_build INSTALL_DIR)
     set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
     list(APPEND LAMMPS_DEPS plumed_build)
@@ -614,8 +619,8 @@ if(PKG_USER-SMD)
     message(STATUS "Eigen3 download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(Eigen3_build
-      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
-      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
       CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     )
     ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@@ -756,7 +761,7 @@ endif()
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
 include(CheckIncludeFileCXX)
-foreach(HEADER math.h)
+foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")

doc/github-development-workflow.md

@@ -50,8 +50,8 @@ This is indicated by who the pull request is assigned to. LAMMPS core
 developers can self-assign or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine what this might be needed or not, and may either implement the
-required changes or ask the submitter of the pull request to implement
+determine whether this might be needed or not, and may either implement
+the required changes or ask the submitter of the pull request to implement
 them.  Even though, all LAMMPS developers may have write access to pull
 requests (if enabled by the submitter, which is the default), only the
 submitter or the assignee of a pull request may do so.  During this
@@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways:
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least one review from a LAMMPS developer with write access is required
-before merging in addition to the automated compilation tests.  The
-feature, that reviews from code owners are "hard" reviews (i.e. they
-must all be approved before merging is allowed), is currently disabled
-and it is in the discretion of the merge maintainer to assess when
-a sufficient degree of approval has been reached.  Reviews may be
+least two approvals from LAMMPS developers with write access are required
+before merging in addition to the automated compilation tests.
+Merging counts as implicit approval, so does submission of a pull request
+(by a LAMMPS developer). So the person doing the merge may not also submit
+an approving review. The feature, that reviews from code owners are "hard"
+reviews (i.e. they must all be approved before merging is allowed), is
+currently disabled and it is in the discretion of the merge maintainer to
+assess when a sufficient degree of approval, especially from external
+contributors, has been reached in these cases.  Reviews may be
 (automatically) dismissed, when the reviewed code has been changed,
 and then approval is required a second time.
 

doc/src/Build_extras.txt

@@ -95,6 +95,7 @@ which GPU hardware to build for.
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
+sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
 sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
 sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
 sm_50 or sm_52 for Maxwell (supported since CUDA 6)
@@ -135,7 +136,7 @@ specified by the "-m" switch.  For your convenience, machine makefiles
 for "mpi" and "serial" are provided, which have the same settings as
 the corresponding machine makefiles in the main LAMMPS source
 folder. In addition you can alter 4 important settings in the
-Makefile.machine you start from via the corresponding -h, -a, -p, -e
+Makefile.machine you start from via the corresponding -c, -a, -p, -e
 switches (as in the examples above), and also save a copy of the new
 Makefile if desired:
 

doc/src/Build_link.txt

@@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style
 interface.
 
 See the sample codes in examples/COUPLE/simple for examples of C++ and
-C and Fortran codes that invoke LAMMPS thru its library interface.
+C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the "Howto couple"_Howto_couple.html doc page.
 

doc/src/Commands_bond.txt

@@ -37,6 +37,7 @@ OPT.
 "harmonic (iko)"_bond_harmonic.html,
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"mm3"_bond_mm3.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
 "oxdna/fene"_bond_oxdna.html,
@@ -67,10 +68,12 @@ OPT.
 "cosine/shift (o)"_angle_cosine_shift.html,
 "cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
 "cosine/squared (o)"_angle_cosine_squared.html,
+"cross"_angle_cross.html,
 "dipole (o)"_angle_dipole.html,
 "fourier (o)"_angle_fourier.html,
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
+"mm3"_angle_mm3.html,
 "quartic (o)"_angle_quartic.html,
 "sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
@@ -120,8 +123,10 @@ OPT.
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,
 "distance"_improper_distance.html,
+"distharm"_improper_distharm.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
 "inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.html,
+"sqdistharm"_improper_sqdistharm.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_pair.txt

@@ -63,13 +63,13 @@ OPT.
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
 "coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/dsf (gko)"_pair_coul.html,
 "coul/long (gko)"_pair_coul.html,
 "coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/long/soft (o)"_pair_fep_soft.html,
 "coul/msm (o)"_pair_coul.html,
 "coul/shield"_pair_coul_shield.html,
 "coul/streitz"_pair_coul.html,
@@ -114,32 +114,35 @@ OPT.
 "lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/charmm/coul/msm (o)"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/cut/soft"_pair_fep_soft.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/class2/coul/long/soft"_pair_fep_soft.html,
+"lj/class2/soft"_pair_fep_soft.html,
 "lj/cubic (go)"_pair_lj_cubic.html,
 "lj/cut (gikot)"_pair_lj.html,
 "lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/debye (gko)"_pair_lj.html,
 "lj/cut/coul/dsf (gko)"_pair_lj.html,
 "lj/cut/coul/long (gikot)"_pair_lj.html,
 "lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/msm (go)"_pair_lj.html,
 "lj/cut/coul/wolf (o)"_pair_lj.html,
 "lj/cut/dipole/cut (go)"_pair_dipole.html,
 "lj/cut/dipole/long (g)"_pair_dipole.html,
 "lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/thole/long (o)"_pair_thole.html,
 "lj/cut/tip4p/cut (o)"_pair_lj.html,
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/expand/coul/long (g)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
@@ -154,6 +157,7 @@ OPT.
 "lj/sf/dipole/sf (go)"_pair_dipole.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
 "lj96/cut (go)"_pair_lj96.html,
 "lubricate (o)"_pair_lubricate.html,
 "lubricate/poly (o)"_pair_lubricate.html,
@@ -169,7 +173,7 @@ OPT.
 "momb"_pair_momb.html,
 "morse (gkot)"_pair_morse.html,
 "morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_morse.html,
+"morse/soft"_pair_fep_soft.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
 "nb3b/harmonic"_pair_nb3b_harmonic.html,
@@ -229,7 +233,7 @@ OPT.
 "thole"_pair_thole.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tip4p/long/soft (o)"_pair_fep_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
 "vashishta (gko)"_pair_vashishta.html,

doc/src/Eqs/angle_cross.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
+$$
+
+\end{document}

doc/src/Eqs/angle_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
+$$
+
+\end{document}

doc/src/Eqs/bond_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+$$
+
+\end{document}

doc/src/Eqs/improper_distharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d - d_0)^2
+$$
+
+\end{document}

doc/src/Eqs/improper_sqdistharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d^2 - d_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/pair_coulgauss.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_lj_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+
+\begin{eqnarray*}
+  E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
+% \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_mm3_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+  r_{v,ij} &=& r_{v,i} + r_{v,j} \\ 
+  \epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_switch3.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+\begin{eqnarray*}
+ S_3(r) = \left\lbrace \begin{array}{ll}
+                     1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
+                     3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
+                     0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
+                 \end{array} \right.
+\end{eqnarray*}
+
+\end{document}

doc/src/Errors_messages.txt

@@ -6917,7 +6917,7 @@ types. :dd
 
 {Invalid use of library file() function} :dt
 
-This function is called thru the library interface.  This
+This function is called through the library interface.  This
 error should not occur.  Contact the developers if it does. :dd
 
 {Invalid value in set command} :dt

doc/src/Howto_client_server.txt

@@ -82,7 +82,7 @@ Monte Carlo client code as the driver.
 
 The lammps_vasp dir shows how to couple LAMMPS as a client code
 running MD timestepping to VASP acting as a server providing quantum
-DFT forces, thru a Python wrapper script on VASP.
+DFT forces, through a Python wrapper script on VASP.
 
 Here is how to launch a client and server code together for any of the
 4 modes of message exchange that the "message"_message.html command

doc/src/Howto_couple.txt

@@ -50,7 +50,7 @@ In this scenario, the other code can be called as a library, as in
 (1), or it could be a stand-alone code, invoked by a system() call
 made by the command (assuming your parallel machine allows one or more
 processors to start up another program).  In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
+stand-alone code could communicate with LAMMPS through files that the
 command writes and reads.
 
 See the "Modify command"_Modify_command.html doc page for info on how

doc/src/Howto_library.txt

@@ -87,7 +87,7 @@ commands to LAMMPS to execute, the same as if they were coming from an
 input script.
 
 Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
+LAMMPS commands one or multiple at a time and pass it through the library
 interface to setup a problem and then run it in stages.  The caller
 can interleave the command function calls with operations it performs,
 calls to extract information from or set information within LAMMPS, or

doc/src/Install_git.txt

@@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above.
 between them at any time using "git checkout <branch name>".)
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_svn.txt

@@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on
 your machine.
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_windows.txt

@@ -42,7 +42,7 @@ environment manipulations.
 
 Note that to update to a newer version of LAMMPS, you should typically
 uninstall the version you currently have, download a new installer,
-and go thru the install procedure described above.  I.e. the same
+and go through the install procedure described above.  I.e. the same
 procedure for installing/updating most Windows programs.  You can
 install multiple versions of LAMMPS (in different directories), but
 only the executable for the last-installed package will be found

doc/src/Intro_features.txt

@@ -40,7 +40,7 @@ General features :h4,link(general)
   syntax for defining and using variables and formulas
   syntax for looping over runs and breaking out of loops
   run one or multiple simulations simultaneously (in parallel) from one script
-  build as library, invoke LAMMPS thru library interface or provided Python wrapper
+  build as library, invoke LAMMPS through library interface or provided Python wrapper
   couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
 
 Particle and model types :h4,link(particle)

doc/src/Intro_nonfeatures.txt

@@ -15,7 +15,7 @@ functionality for setting up simulations and analyzing their output.
 
 Specifically, LAMMPS was not conceived and designed for:
 
-being run thru a GUI
+being run through a GUI
 building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="4 Jan 2019 version">
+<META NAME="docnumber" CONTENT="1 Feb 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-4 Jan 2019 version :c,h2
+1 Feb 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -100,7 +100,8 @@ as contained in the file name.
 "USER-SPH"_#PKG-USER-SPH,
 "USER-TALLY"_#PKG-USER-TALLY,
 "USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+"USER-VTK"_#PKG-USER-VTK,
+"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
 
 :line
 
@@ -1305,7 +1306,7 @@ src/USER-FEP: filenames -> commands
 src/USER-FEP/README
 "fix adapt/fep"_fix_adapt_fep.html
 "compute fep"_compute_fep.html
-"pair_style */soft"_pair_lj_soft.html
+"pair_style */soft"_pair_fep_soft.html
 examples/USER/fep
 tools/fep/README
 tools/fep :ul
@@ -2067,3 +2068,39 @@ lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
 
 
+:line
+
+USER-YAFF package :link(PKG-USER-YAFF),h4
+
+[Contents:]
+
+Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
+The expressions and their use are discussed in the following papers
+
+Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
+Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
+
+which discuss the "QuickFF"_quickff methodology.
+
+
+:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
+:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
+:link(quickff,http://molmod.github.io/QuickFF)
+:link(yaff,https://github.com/molmod/yaff)
+
+
+[Author:] Steven Vandenbrande.
+
+[Supporting info:]
+
+src/USER-YAFF/README
+"angle_style cross"_angle_cross.html
+"angle_style mm3"_angle_mm3.html
+"bond_style mm3"_bond_mm3.html
+"improper_style distharm"_improper_distharm.html
+"improper_style sqdistharm"_improper_sqdistharm.html
+"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
+"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
+examples/USER/yaff :ul
+
+

doc/src/Packages_user.txt

@@ -75,7 +75,8 @@ Package, Description, Doc page, Example, Library
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
 "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
 "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext
+"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l)
 
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
 :link(PLUMED,http://www.plumed.org)

doc/src/Python_examples.txt

@@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS.  If you create your
 own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 
-trivial.py, read/run a LAMMPS input script thru Python,
+trivial.py, read/run a LAMMPS input script through Python,
 demo.py, invoke various LAMMPS library interface routines,
 simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
 split.py, same as simple.py but running in parallel on a subset of procs,

doc/src/Python_run.txt

@@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid
 development and debugging.  If you use it to mostly invoke costly
 operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
-LAMMPS thru Python will be negligible.
+LAMMPS through Python will be negligible.
 
 The Python wrapper for LAMMPS uses the "ctypes" package in Python,
 which auto-generates the interface code needed between Python and a

doc/src/Python_test.txt

@@ -32,7 +32,7 @@ first importing from the lammps.py file:
 >>> from ctypes import CDLL
 >>> CDLL("liblammps.so") :pre
 
-If an error occurs, carefully go thru the steps on the
+If an error occurs, carefully go through the steps on the
 "Build_basics"_Build_basics.html doc page about building a shared
 library and the "Python_install"_Python_install.html doc page about
 insuring Python can find the necessary two files it needs.

doc/src/Tools.txt

@@ -391,15 +391,16 @@ definition file.  This tool was used to create the system for the
 
 moltemplate tool :h4,link(moltemplate)
 
-The moltemplate sub-directory contains a Python-based tool for
-building molecular systems based on a text-file description, and
-creating LAMMPS data files that encode their molecular topology as
-lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
-more information.
+The moltemplate sub-directory contains instructions for installing
+moltemplate, a Python-based tool for building molecular systems based
+on a text-file description, and creating LAMMPS data files that encode
+their molecular topology as lists of bonds, angles, dihedrals, etc.
+See the README.txt file for more information.
 
 This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
 supports it.  It has its own WWW page at
 "http://moltemplate.org"_http://moltemplate.org.
+The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases
 
 :line
 

doc/src/angle_cross.txt

@@ -0,0 +1,62 @@
+"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
+
+angle_style cross command :h3
+
+[Syntax:]
+
+angle_style cross :pre
+
+[Examples:]
+
+angle_style cross
+angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
+
+[Description:]
+
+The {cross} angle style uses a potential that couples the bond stretches of
+a bend with the angle stretch of that bend:
+
+:c,image(Eqs/angle_cross.jpg)
+
+where r12,0 is the rest value of the bond length between atom 1 and 2,
+r32,0 is the rest value of the bond length between atom 2 and 2,
+and theta0 is the rest value of the angle. KSS is the force constant of
+the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
+of the bond stretch-angle stretch terms.
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_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:
+
+KSS (energy/distance^2)
+KBS0 (energy/distance/rad)
+KBS1 (energy/distance/rad)
+r12,0 (distance)
+r32,0 (distance)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+
+

doc/src/angle_mm3.txt

@@ -0,0 +1,55 @@
+"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
+
+angle_style mm3 command :h3
+
+[Syntax:]
+
+angle_style mm3 :pre
+
+[Examples:]
+
+angle_style mm3
+angle_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} angle style uses the potential that is anharmonic in the angle
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/angle_mm3.jpg)
+
+where theta0 is the equilibrium value of the angle, and K is a
+prefactor. The anharmonic prefactors have units deg^(-n), for example
+-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_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:
+
+K (energy/radian^2)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+

doc/src/angle_style.txt

@@ -81,10 +81,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
 "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
 "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
+"cross"_angle_cross.html - cross term coupling angle and bond lengths
 "dipole"_angle_dipole.html - angle that controls orientation of a point dipole
 "fourier"_angle_fourier.html - angle with multiple cosine terms
 "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
 "harmonic"_angle_harmonic.html - harmonic angle
+"mm3"_angle_mm3.html - anharmonic angle
 "quartic"_angle_quartic.html - angle with cubic and quartic terms
 "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
 "table"_angle_table.html - tabulated by angle :ul

doc/src/angles.txt

@@ -14,11 +14,13 @@ Angle Styles :h1
    angle_cosine_shift
    angle_cosine_shift_exp
    angle_cosine_squared
+   angle_cross
    angle_dipole
    angle_fourier
    angle_fourier_simple
    angle_harmonic
    angle_hybrid
+   angle_mm3
    angle_none
    angle_quartic
    angle_sdk

doc/src/bond_mm3.txt

@@ -0,0 +1,58 @@
+"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
+
+bond_style mm3 command :h3
+
+[Syntax:]
+
+bond_style mm3 :pre
+
+[Examples:]
+
+bond_style mm3
+bond_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} bond style uses the potential that is anharmonic in the bond
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/bond_mm3.jpg)
+
+where r0 is the equilibrium value of the bond, and K is a
+prefactor. The anharmonic prefactors have units angstrom^(-n):
+-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
+care of the necessary unit conversion for these factors internally.
+Note that the MM3 papers contains an error in Eq (1):
+(7/12)2.55 should be replaced with (7/12)2.55^2
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_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:
+
+K (energy/distance^2)
+r0 (distance) :ul
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html
+
+[Default:] none
+
+:line
+
+:link(mm3-allinger1989)
+[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
+(1989),

doc/src/bond_style.txt

@@ -86,6 +86,7 @@ accelerated styles exist.
 "harmonic"_bond_harmonic.html - harmonic bond
 "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
 "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
+"mm3"_bond_mm3.html - MM3 anharmonic bond
 "morse"_bond_morse.html - Morse bond
 "nonlinear"_bond_nonlinear.html - nonlinear bond
 "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling

doc/src/bonds.txt

@@ -13,6 +13,7 @@ Bond Styles :h1
    bond_harmonic_shift
    bond_harmonic_shift_cut
    bond_hybrid
+   bond_mm3
    bond_morse
    bond_none
    bond_nonlinear

doc/src/compute_angmom_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the angular momentum
 vector for each chunk, due to the velocity/momentum of the individual
 atoms in the chunk around the center-of-mass of the chunk.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_com.txt

@@ -22,7 +22,7 @@ compute 1 all com :pre
 [Description:]
 
 Define a computation that calculates the center-of-mass of the group
-of atoms, including all effects due to atoms passing thru periodic
+of atoms, including all effects due to atoms passing through periodic
 boundaries.
 
 A vector of three quantities is calculated by this compute, which

doc/src/compute_com_chunk.txt

@@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the center-of-mass
-for each chunk, which includes all effects due to atoms passing thru
+for each chunk, which includes all effects due to atoms passing through
 periodic boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_dipole_chunk.txt

@@ -38,7 +38,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the dipole vector
 and the total dipole moment for each chunk, which includes all effects
-due to atoms passing thru periodic boundaries. For chunks with a net
+due to atoms passing through periodic boundaries. For chunks with a net
 charge the resulting dipole is made position independent by subtracting
 the position vector of the center of mass or geometric center times the
 net charge from the computed dipole vector.

doc/src/compute_displace_atom.txt

@@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre
 
 Define a computation that calculates the current displacement of each
 atom in the group from its original (reference) coordinates, including
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.

doc/src/compute_fep.txt

@@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it.
 
 The {pstyle} argument is the name of the pair style. For example,
 {pstyle} could be specified as "lj/cut".  The {pparam} argument is the
-name of the parameter to change.  This is a (non-exclusive) list of
+name of the parameter to change.  This is a list of
 pair styles and parameters that can be used with this compute.  See
 the doc pages for individual pair styles and their energy formulas for
 the meaning of these parameters:
 
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
-"coul/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
 "born"_pair_born.html: a,b,c: type pairs:
-"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:)
+"buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
+"coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
+"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 Note that it is easy to add new potentials and their parameters to
 this list.  All it typically takes is adding an extract() method to
@@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info.
 [Related commands:]
 
 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_style lj/soft/coul/soft"_pair_lj_soft.html
+"pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/compute_gyration.txt

@@ -22,7 +22,7 @@ compute 1 molecule gyration :pre
 [Description:]
 
 Define a computation that calculates the radius of gyration Rg of the
-group of atoms, including all effects due to atoms passing thru
+group of atoms, including all effects due to atoms passing through
 periodic boundaries.
 
 Rg is a measure of the size of the group of atoms, and is computed as

doc/src/compute_gyration_chunk.txt

@@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the radius of gyration Rg for each chunk,
-which includes all effects due to atoms passing thru periodic
+which includes all effects due to atoms passing through periodic
 boundaries.
 
 Rg is a measure of the size of a chunk, and is computed by this

doc/src/compute_inertia_chunk.txt

@@ -36,7 +36,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the 6 components of the symmetric inertia
 tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd.txt

@@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) of the group of atoms, including all effects due to atoms
-passing thru periodic boundaries.  For computation of the non-Gaussian
+passing through periodic boundaries.  For computation of the non-Gaussian
 parameter of mean-squared displacement, see the "compute
 msd/nongauss"_compute_msd_nongauss.html command.
 

doc/src/compute_msd_chunk.txt

@@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
 center-of-mass.  The 4th component is the total squared displacement,
 i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These
-calculations include all effects due to atoms passing thru periodic
+calculations include all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd_nongauss.txt

@@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) and non-Gaussian parameter (NGP) of the group of atoms,
-including all effects due to atoms passing thru periodic boundaries.
+including all effects due to atoms passing through periodic boundaries.
 
 A vector of three quantities is calculated by this compute.  The first
 element of the vector is the total squared dx,dy,dz displacements

doc/src/compute_omega_chunk.txt

@@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity
 vector for each chunk, via the formula L = Iw where L is the angular
 momentum vector of the chunk, I is its moment of inertia tensor, and w
 is omega = angular velocity of the chunk.  The calculation includes
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/compute_rigid_local.txt

@@ -107,7 +107,7 @@ mass (COM) of the body.  The {x}, {y}, {z} attributes write the COM
 "unscaled", in the appropriate distance "units"_units.html (Angstroms,
 sigma, etc).  Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
-COM has passed thru a periodic boundary one or more times, the value
+COM has passed through a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been
 wrapped back into the periodic box.
 

doc/src/compute_sna_atom.txt

@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
   {diagonal} value = {0} or {1} or {2} or {3}
      {0} = all j1, j2, j <= twojmax, j2 <= j1
      {1} = subset satisfying j1 == j2

doc/src/compute_torque_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the torque vector for eqch
 chunk, due to the forces on the individual atoms in the chunk around
 the center-of-mass of the chunk.  The calculation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/displace_atoms.txt

@@ -83,7 +83,7 @@ used in such a way that the displacement of a particular atom is the
 same, regardless of how many processors are being used.
 
 The {rotate} style rotates each atom in the group by the angle {theta}
-around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
+around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} =
 (Px,Py,Pz).  The direction of rotation for the atoms around the
 rotation axis is consistent with the right-hand rule: if your
 right-hand thumb points along {R}, then your fingers wrap around the

doc/src/dump.txt

@@ -312,7 +312,7 @@ so that any machine which supports XDR should be able to read them.
 The number of atoms per snapshot cannot change with the {xtc} style.
 The {unwrap} option of the "dump_modify"_dump_modify.html command allows
 XTC coordinates to be written "unwrapped" by the image flags for each
-atom.  Unwrapped means that if the atom has passed thru a periodic
+atom.  Unwrapped means that if the atom has passed through a periodic
 boundary one or more times, the value is printed for what the
 coordinate would be if it had not been wrapped back into the periodic
 box.  Note that these coordinates may thus be far outside the box size
@@ -534,7 +534,7 @@ on the "Howto triclinic"_Howto_triclinic.html doc page.
 
 Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
 image flags for each atom.  Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
+passed through a periodic boundary one or more times, the value is
 printed for what the coordinate would be if it had not been wrapped
 back into the periodic box.  Note that using {xu}, {yu}, {zu} means
 that the coordinate values may be far outside the box bounds printed

doc/src/dump_modify.txt

@@ -344,7 +344,7 @@ The {image} keyword applies only to the dump {atom} style.  If the
 image value is {yes}, 3 flags are appended to each atom's coords which
 are the absolute box image of the atom in each dimension.  For
 example, an x image flag of -2 with a normalized coord of 0.5 means
-the atom is in the center of the box, but has passed thru the box
+the atom is in the center of the box, but has passed through the box
 boundary 2 times and is really 2 box lengths to the left of its
 current coordinate.  Note that for dump style {custom} these various
 values can be printed in the dump file by using the appropriate atom
@@ -622,7 +622,7 @@ threshold criterion is met.  Otherwise it is not met.
 
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
-flags for each atom.  Unwrapped means that if the atom has passed thru
+flags for each atom.  Unwrapped means that if the atom has passed through
 a periodic boundary one or more times, the value is printed for what
 the coordinate would be if it had not been wrapped back into the
 periodic box.  Note that these coordinates may thus be far outside the

doc/src/fix_adapt.txt

@@ -112,17 +112,43 @@ pages for individual pair styles and their energy formulas for the
 meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
+"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
 "coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
+"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:
+"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs:
 "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: A,B: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs:
 "lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs:
+"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:
+"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
 "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
 "lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
 "lubricate"_pair_lubricate.html: mu: global:
-"gauss"_pair_gauss.html: a: type pairs:
-"morse"_pair_morse.html: d0,r0,alpha: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs:
+"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:
+"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:
+"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:
+"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:
+"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:
+"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
+"table"_pair_table.html: table_cutoff: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
 "soft"_pair_soft.html: a: type pairs:
 "kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
 
@@ -217,6 +243,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are
 
+"gromos"_bond_gromos.html: k, r0: type bonds:
 "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
 
 :line

doc/src/fix_adapt_fep.txt

@@ -114,24 +114,37 @@ styles and their energy formulas for the meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
-"coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
-"lubricate"_pair_lubricate.html: mu: global:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
 "gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
 "soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 NOTE: It is easy to add new potentials and their parameters to this
 list.  All it typically takes is adding an extract() method to the
 pair_*.cpp file associated with the potential.
 
-Some parameters are global settings for the pair style, e.g. the
-viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
-Other parameters apply to atom type pairs within the pair style,
-e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
-
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
 potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
@@ -253,7 +266,7 @@ minimization"_minimize.html.
 [Related commands:]
 
 "compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute
-ti"_compute_ti.html
+ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/fix_ave_histo.txt

@@ -241,7 +241,7 @@ first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
 values > {hi} are counted in the last bin (Nbins+1).  Values between
-{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1.  The
+{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
 

doc/src/fix_bond_react.txt

@@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
   template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
   map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
   zero or more individual keyword/value pairs may be appended to each react argument :l
-  individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
+  individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
     {prob} values = fraction seed
       fraction = initiate reaction with this probability if otherwise eligible
       seed = random number seed (positive integer)
+    {max_rxn} value = N
+      N = maximum number of reactions allowed to occur
     {stabilize_steps} value = timesteps
       timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
     {update_edges} value = {none} or {charges} or {custom}
@@ -142,7 +144,7 @@ modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms I,J within the specified react-group-ID of type
-itype and jtype must separated by a distance between {Rmin} and
+itype and jtype must be separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
 identified: if the bonding atoms in the pre-reacted template are not
 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
@@ -211,9 +213,10 @@ mandatory keyword is 'equivalences' and the optional keywords are
 N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
 N {deleteIDs} = # of atoms N that are specified for deletion
-N {customIDs} = # of atoms N that are specified for a custom update :pre
+N {customIDs} = # of atoms N that are specified for a custom update
+N {constraints} = # of specified reaction constraints N :pre
 
-The body of the map file contains two mandatory sections and three
+The body of the map file contains two mandatory sections and four
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -230,7 +233,10 @@ Edges' and allows for forcing the update of a specific atom's atomic
 charge. The first column is the ID of an atom near the edge of the
 pre-reacted molecule template, and the value of the second column is
 either 'none' or 'charges.' Further details are provided in the
-discussion of the 'update_edges' keyword.
+discussion of the 'update_edges' keyword. The fourth optional section
+begins with the keyword 'Constraints' and lists additional criteria
+that must be satisfied in order for the reaction to occur. Currently,
+there is one type of constraint available, as discussed below.
 
 A sample map file is given below:
 
@@ -263,6 +269,18 @@ Equivalences :pre
 
 :line
 
+Any number of additional constraints may be specified in the
+Constraints section of the map file. Currently there is one type of
+additional constraint, of type 'distance', whose syntax is as follows:
+
+distance {ID1} {ID2} {rmin} {rmax} :pre
+
+where 'distance' is the required keyword, {ID1} and {ID2} are
+pre-reaction atom IDs, and these two atoms must be separated by a
+distance between {rmin} and {rmax} for the reaction to occur. This
+constraint can be used to enforce a certain orientation between
+reacting molecules.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -285,7 +303,8 @@ The {prob} keyword can affect whether an eligible reaction actually
 occurs. The fraction setting must be a value between 0.0 and 1.0. A
 uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
-fraction.
+fraction. Up to N reactions are permitted to occur, as optionally
+specified by the {max_rxn} keyword.
 
 The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the

doc/src/fix_meso_move.txt

@@ -56,7 +56,7 @@ by other fixes (e.g. "fix meso"_fix_meso.html, "fix
 meso/stationary"_fix_meso_stationary.html), since that will change their
 positions and velocities twice.
 
-NOTE: As particles move due to this fix, they will pass thru periodic
+NOTE: As particles move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 meso"_fix_meso.html command).  It is up to you to decide whether periodic
@@ -126,7 +126,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates particles around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 particles around the rotation axis is consistent with the right-hand
 rule: if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_move.txt

@@ -51,7 +51,7 @@ integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
 nvt"_fix_nh.html), since that will change their positions and
 velocities twice.
 
-NOTE: As atoms move due to this fix, they will pass thru periodic
+NOTE: As atoms move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 nve"_fix_nve.html command).  It is up to you to decide whether
@@ -121,7 +121,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates atoms around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 atoms around the rotation axis is consistent with the right-hand rule:
 if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_qeq.txt

@@ -22,7 +22,7 @@ Nevery = perform charge equilibration every this many steps :l
 cutoff = global cutoff for charge-charge interactions (distance unit) :l
 tolerance = precision to which charges will be equilibrated :l
 maxiter = maximum iterations to perform charge equilibration :l
-qfile = a filename with QEq parameters :l
+qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l
 
 zero or more keyword/value pairs may be appended :l
 keyword = {alpha} or {qdamp} or {qstep} :l
@@ -122,7 +122,9 @@ field"_#vanDuin paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
 as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
 reax/c"_pair_reaxc.html.  Only the {chi}, {eta}, and {gamma}
-parameters from the {qfile} file are used.  This style solves partial
+parameters from the {qfile} file are used. When using the string
+{reax/c} as filename, these parameters are extracted directly from
+an active {reax/c} pair style.  This style solves partial
 charges on atoms via the matrix inversion method.  A tolerance of
 1.0e-6 is usually a good number.
 
@@ -132,7 +134,9 @@ that the interaction between a pair of charged particles is the
 product of two Slater 1{s} orbitals.  The expression for the Slater
 1{s} orbital is given under equation (6) of the
 "Streitz-Mintmire"_#Streitz1 paper.  Only the {chi}, {eta}, {zeta}, and
-{qcore} parameters from the {qfile} file are used.  This style solves
+{qcore} parameters from the {qfile} file are used. When using the string
+{coul/streitz} as filename, these parameters are extracted directly from
+an active {coul/streitz} pair style.  This style solves
 partial charges on atoms via the matrix inversion method.  A tolerance
 of 1.0e-6 is usually a good number.  Keyword {alpha} can be used to
 change the Slater type orbital exponent.

doc/src/fix_srd.txt

@@ -117,7 +117,7 @@ Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
 SRD particles are bounded by Vmax, which is set so that an SRD
 particle will not advect further than Dmax = 4*lamda in dt_SRD.  This
 means that roughly speaking, Dmax should not be larger than a big
-particle diameter, else SRDs may pass thru big particles without
+particle diameter, else SRDs may pass through big particles without
 colliding.  A warning is generated if this is the case.
 
 Collisions between SRD particles and big particles or walls are

doc/src/fix_wall_reflect.txt

@@ -41,7 +41,7 @@ fix top all wall/reflect zhi v_pressdown :pre
 [Description:]
 
 Bound the simulation with one or more walls which reflect particles
-in the specified group when they attempt to move thru them.
+in the specified group when they attempt to move through them.
 
 Reflection means that if an atom moves outside the wall on a timestep
 by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is

doc/src/if.txt

@@ -107,7 +107,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/improper_distharm.txt

@@ -0,0 +1,53 @@
+"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
+
+improper_style distharm command :h3
+
+[Syntax:]
+
+improper_style distharm
+
+[Examples:]
+
+improper_style distharm
+improper_coeff 1 25.0 0.5 :pre
+
+[Description:]
+
+The {distharm} improper style uses the potential
+
+:c,image(Eqs/improper_distharm.jpg)
+
+where d is the oriented distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance. The distance d is oriented and can take
+on negative values. This may lead to unwanted behavior if d0 is not equal to zero.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^2)
+d0 (distance) :ul
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none

doc/src/improper_sqdistharm.txt

@@ -0,0 +1,54 @@
+"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
+
+improper_style sqdistharm command :h3
+
+[Syntax:]
+
+improper_style sqdistharm
+
+[Examples:]
+
+improper_style sqdistharm
+improper_coeff 1 50.0 0.1 :pre
+
+[Description:]
+
+The {sqdistharm} improper style uses the potential
+
+:c,image(Eqs/improper_sqdistharm.jpg)
+
+where d is the distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^4)
+d0^2 (distance^2) :ul
+
+Note that d0^2 (in units distance^2) has be provided and not d0.
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none

doc/src/improper_style.txt

@@ -78,11 +78,13 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
 "cossq"_improper_cossq.html - improper with a cosine squared term
 "cvff"_improper_cvff.html - CVFF improper
 "distance"_improper_distance.html - improper based on distance between atom planes
+"distharm"_improper_distharm.html - improper that is harmonic in the out-of-plane distance
 "fourier"_improper_fourier.html - improper with multiple cosine terms
 "harmonic"_improper_harmonic.html - harmonic improper
 "inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition
 "ring"_improper_ring.html - improper which prevents planar conformations
 "umbrella"_improper_umbrella.html - DREIDING improper :ul
+"sqdistharm"_improper_sqdistharm.html - improper that is harmonic in the square of the out-of-plane distance
 
 :line
 

doc/src/impropers.txt

@@ -9,6 +9,7 @@ Improper Styles :h1
    improper_cossq
    improper_cvff
    improper_distance
+   improper_distharm
    improper_fourier
    improper_harmonic
    improper_hybrid
@@ -16,6 +17,7 @@ Improper Styles :h1
    improper_none
    improper_ring
    improper_umbrella
+   improper_sqdistharm
    improper_zero
 
 END_RST -->

doc/src/jump.txt

@@ -100,7 +100,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/kspace_style.txt

@@ -370,8 +370,7 @@ of these styles.
 
 All of the kspace styles are part of the KSPACE package.  They are
 only enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
 
 For MSM, a simulation must be 3d and one can use any combination of
 periodic, non-periodic, or shrink-wrapped boundaries (specified using

doc/src/lammps.book

@@ -595,7 +595,8 @@ pair_lj_expand.html
 pair_lj_long.html
 pair_lj_smooth.html
 pair_lj_smooth_linear.html
-pair_lj_soft.html
+pair_fep_soft.html
+pair_lj_switch3_coulgauss.html
 pair_lubricate.html
 pair_lubricateU.html
 pair_mdf.html
@@ -605,6 +606,7 @@ pair_meam_sw_spline.html
 pair_meso.html
 pair_mgpt.html
 pair_mie.html
+pair_mm3_switch3_coulgauss.html
 pair_momb.html
 pair_morse.html
 pair_multi_lucy.html
@@ -668,6 +670,7 @@ bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
 bond_hybrid.html
 bond_morse.html
+bond_mm3.html
 bond_none.html
 bond_nonlinear.html
 bond_oxdna.html
@@ -687,11 +690,13 @@ angle_cosine_periodic.html
 angle_cosine_shift.html
 angle_cosine_shift_exp.html
 angle_cosine_squared.html
+angle_cross.html
 angle_dipole.html
 angle_fourier.html
 angle_fourier_simple.html
 angle_harmonic.html
 angle_hybrid.html
+angle_mm3.html
 angle_none.html
 angle_quartic.html
 angle_sdk.html
@@ -725,6 +730,7 @@ improper_class2.html
 improper_cossq.html
 improper_cvff.html
 improper_distance.html
+improper_distharm.html
 improper_fourier.html
 improper_harmonic.html
 improper_hybrid.html
@@ -732,6 +738,7 @@ improper_inversion_harmonic.html
 improper_none.html
 improper_ring.html
 improper_umbrella.html
+improper_sqdistharm.html
 improper_zero.html
 
 lammps_commands_kspace.html

doc/src/minimize.txt

@@ -82,12 +82,12 @@ coordinates:
 
 where the first term is the sum of all non-bonded "pairwise
 interactions"_pair_style.html including "long-range Coulombic
-interactions"_kspace_style.html, the 2nd thru 5th terms are
+interactions"_kspace_style.html, the 2nd through 5th terms are
 "bond"_bond_style.html, "angle"_angle_style.html,
 "dihedral"_dihedral_style.html, and "improper"_improper_style.html
 interactions respectively, and the last term is energy due to
 "fixes"_fix.html which can act as constraints or apply force to atoms,
-such as thru interaction with a wall.  See the discussion below about
+such as through interaction with a wall.  See the discussion below about
 how fix commands affect minimization.
 
 The starting point for the minimization is the current configuration

doc/src/next.txt

@@ -79,7 +79,7 @@ and after such a LAMMPS run.
 Here is an example of running a series of simulations using the next
 command with an {index}-style variable.  If this input script is named
 in.polymer, 8 simulations would be run using data files from
-directories run1 thru run8.
+directories run1 through run8.
 
 variable d index run1 run2 run3 run4 run5 run6 run7 run8
 shell cd $d
@@ -114,7 +114,7 @@ jump in.script :pre
 
 Here is an example of a double loop which uses the "if"_if.html and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/pair_buck_long.txt

@@ -154,8 +154,7 @@ details.
 
 This style is part of the KSPACE package.  It is only enabled if
 LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
 
 [Related commands:]
 

doc/src/pair_charmm.txt

@@ -249,8 +249,7 @@ All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
 of the MOLECULE package.  All the styles with {coul/long} style are
 part of the KSPACE package.  They are only enabled if LAMMPS was built
 with those packages.  See the "Build package"_Build_package.html doc
-page for more info.  Note that the MOLECULE and KSPACE packages are
-installed by default.
+page for more info.
 
 [Related commands:]
 

doc/src/pair_class2.txt

@@ -99,6 +99,14 @@ cutoff distance.
 
 :line
 
+A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
+only available if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+:line
+
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
@@ -159,7 +167,7 @@ package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html
 
 [Default:] none
 

doc/src/pair_fep_soft.txt

@@ -16,18 +16,21 @@ pair_style lj/cut/tip4p/long/soft command :h3
 pair_style lj/cut/tip4p/long/soft/omp command :h3
 pair_style lj/charmm/coul/long/soft command :h3
 pair_style lj/charmm/coul/long/soft/omp command :h3
-pair_style coul/cut/soft command :h3
+pair_style lj/class2/soft command :h3
+pair_style lj/class2/coul/cut/soft command :h3
+pair_style lj/class2/coul/long/soft command :h3
+ pair_style coul/cut/soft command :h3
 pair_style coul/cut/soft/omp command :h3
 pair_style coul/long/soft command :h3
 pair_style coul/long/soft/omp command :h3
 pair_style tip4p/long/soft command :h3
 pair_style tip4p/long/soft/omp command :h3
-
+pair_style morse/soft command :h3
 [Syntax:]
 
 pair_style style args :pre
 
-style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft}
+style = {lj/cut/soft} or {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} or {lj/cut/tip4p/long/soft} or {lj/charmm/coul/long/soft} or {lj/class2/soft} or {lj/class2/coul/cut/soft} or {lj/class2/coul/long/soft} or {coul/cut/soft} or {coul/long/soft} or {tip4p/long/soft} or {morse/soft}
 args = list of arguments for a particular style :ul
   {lj/cut/soft} args = n alpha_lj cutoff
     n, alpha_LJ = parameters of soft-core potential
@@ -51,6 +54,17 @@ args = list of arguments for a particular style :ul
     n, alpha_LJ, alpha_C = parameters of the soft-core potential
     inner, outer = global switching cutoffs for LJ (and Coulombic if only 5 args)
     cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 5 args)
+  {lj/class2/soft} args = n alpha_lj cutoff
+    n, alpha_LJ = parameters of soft-core potential
+    cutoff = global cutoff for Lennard-Jones interactions (distance units)
+  {lj/class2/coul/cut/soft} args = n alpha_LJ alpha_C cutoff (cutoff2)
+    n, alpha_LJ, alpha_C = parameters of soft-core potential
+    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {lj/class2/coul/long/soft} args = n alpha_LJ alpha_C cutoff (cutoff2)
+    n, alpha_LJ, alpha_C = parameters of soft-core potential
+    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {coul/cut/soft} args = n alpha_C cutoff
     n, alpha_C = parameters of the soft-core potential
     cutoff = global cutoff for Coulomb interactions (distance units)
@@ -63,6 +77,10 @@ args = list of arguments for a particular style :ul
     qdist = distance from O atom to massless charge (distance units)
     n, alpha_C = parameters of the soft-core potential
     cutoff = global cutoff for Coulomb interactions (distance units)
+  {morse/soft} args = n lf cutoff
+    n = soft-core parameter
+    lf = transformation range is lf < lambda < 1
+    cutoff = global cutoff for Morse interactions (distance units)
 :pre
 
 [Examples:]
@@ -93,6 +111,12 @@ pair_style lj/charmm/coul/long 2.0 0.5 10.0 8.0 10.0 9.0
 pair_coeff * * 0.28 3.1 1.0
 pair_coeff 1 1 0.28 3.1 1.0 0.14 3.1 :pre
 
+pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5
+pair_style lj/class2/coul/long/soft 2.0 0.5 10.0 9.5 9.5
+pair_coeff * * 0.28 3.1 1.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0
+pair_coeff 1 1 0.28 3.1 0.0 10.0 9.5 :pre
+
 pair_style coul/long/soft 1.0 10.0 9.5
 pair_coeff * * 1.0
 pair_coeff 1 1 1.0 9.5 :pre
@@ -101,17 +125,31 @@ pair_style tip4p/long/soft 1 2 7 8 0.15 2.0 0.5 10.0 9.8
 pair_coeff * * 1.0
 pair_coeff 1 1 1.0 9.5 :pre
 
+pair_style morse/soft 4 0.9 10.0
+pair_coeff * * 100.0 2.0 1.5 1.0
+pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre
+
 [Description:]
 
-The {lj/cut/soft} style and sub-styles compute the 12/6 Lennard-Jones
-and Coulomb potential modified by a soft core, in order to avoid
-singularities during free energy calculations when sites are created
-or annihilated "(Beutler)"_#Beutler,
+These pair styles have a soft repulsive core, tunable by a parameter lambda,
+in order to avoid singularities during free energy calculations when sites are
+created or annihilated "(Beutler)"_#Beutler.  When lambda tends to 0 the pair
+interaction vanishes with a soft repulsive core.  When lambda tends to 1, the pair
+interaction approaches the normal, non-soft potential. These pair styles
+are suited for "alchemical" free energy calculations using the "fix
+adapt/fep"_fix_adapt_fep.html and "compute fep"_compute_fep.html commands.
+
+The {lj/cut/soft} style and related sub-styles compute the 12-6 Lennard-Jones
+and Coulomb potentials modified by a soft core, with the functional form
 
 :c,image(Eqs/pair_lj_soft.jpg)
 
-Coulomb interactions are also damped with a soft core at short
-distance,
+The {lj/class2/soft} style is a 9-6 potential with the exponent of the
+denominator of the first term in brackets taking the value 1.5 instead of 2
+(other details differ, see the form of the potential in
+"pair_class2"_pair_class2.html).
+
+Coulomb interactions can also be damped with a soft core at short distance,
 
 :c,image(Eqs/pair_coul_soft.jpg)
 
@@ -119,34 +157,32 @@ In the Coulomb part C is an energy-conversion constant, q_i and q_j
 are the charges on the 2 atoms, and epsilon is the dielectric constant
 which can be set by the "dielectric"_dielectric.html command.
 
-The coefficient lambda is an activation parameter. When lambda = 1 the
-pair potential is identical to a Lennard-Jones term or a Coulomb term
-or a combination of both. When lambda = 0 the interactions are
-deactivated. The transition between these two extrema is smoothed by a
-soft repulsive core in order to avoid singularities in potential
-energy and forces when sites are created or annihilated and can overlap
-"(Beutler)"_#Beutler.
+The coefficient lambda is an activation parameter. When lambda = 1 the pair
+potential is identical to a Lennard-Jones term or a Coulomb term or a
+combination of both. When lambda = 0 the interactions are deactivated. The
+transition between these two extrema is smoothed by a soft repulsive core in
+order to avoid singularities in potential energy and forces when sites are
+created or annihilated and can overlap "(Beutler)"_#Beutler.
 
 The parameters n, alpha_LJ and alpha_C are set in the
-"pair_style"_pair_style.html command, before the cutoffs.  Usual
-choices for the exponent are n = 2 or n = 1. For the remaining
-coefficients alpha_LJ = 0.5 and alpha_C = 10 Angstrom^2 are
-appropriate choices. Plots of the LJ and Coulomb terms are shown
-below, for lambda ranging from 1 to 0 every 0.1.
+"pair_style"_pair_style.html command, before the cutoffs.  Usual choices for the
+exponent are n = 2 or n = 1. For the remaining coefficients alpha_LJ = 0.5 and
+alpha_C = 10 Angstrom^2 are appropriate choices. Plots of the 12/6 LJ and
+Coulomb terms are shown below, for lambda ranging from 1 to 0 every 0.1.
 
 :image(JPG/lj_soft.jpg),image(JPG/coul_soft.jpg)
 :c
 
-For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles,
-the following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands, or by mixing as described below:
+For the {lj/cut/coul/cut/soft} or {lj/cut/coul/long/soft} pair styles, as well
+as for the equivalent {class2} versions, the following coefficients must be
+defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html
+command as in the examples above, or in the data file or restart files read by
+the "read_data"_read_data.html or "read_restart"_read_restart.html commands, or
+by mixing as described below:
 
 epsilon (energy units)
 sigma (distance units)
-lambda (activation parameter between 0 and 1)
+lambda (activation parameter, between 0 and 1)
 cutoff1 (distance units)
 cutoff2 (distance units) :ul
 
@@ -160,24 +196,29 @@ since it has no Coulombic terms. For the {coul/cut/soft} and
 {coul/long/soft} only lambda and the optional cutoff2 are to be
 specified.
 
-Style {lj/cut/tip4p/long/soft} implements a soft-core version of the
-TIP4P water model. The usage of this pair style is documented in the
-"pair_lj"_pair_lj.html styles. The soft-core version introduces the
-lambda parameter to the list of arguments, after epsilon and sigma in
-the "pair_coeff"_pair_coeff.html command. The parameters n, alpha_LJ
-and alpha_C are set in the "pair_style"_pair_style.html command,
-before the cutoffs.
+Style {lj/cut/tip4p/long/soft} implements a soft-core version of the TIP4P water
+model. The usage of the TIP4P pair style is documented in the
+"pair_lj"_pair_lj.html styles. In the soft version the parameters n, alpha_LJ
+and alpha_C are set in the "pair_style"_pair_style.html command, after the
+specific parameters of the TIP4P water model and before the cutoffs. The
+activation parameter lambda is supplied as an argument of the the
+"pair_coeff"_pair_coeff.html command, after epsilon and sigma and before the
+optional cutoffs.
 
-Style {lj/charmm/coul/long/soft} implements a soft-core version of the
-CHARMM version of LJ interactions with an additional switching
-function S(r) that ramps the energy and force smoothly to zero between
-an inner and outer cutoff. The usage of this pair style is documented
-in the "pair_charmm"_pair_charmm.html styles. The soft-core version
-introduces the lambda parameter to the list of arguments, after
-epsilon and sigma in the "pair_coeff"_pair_coeff.html command (and
-before the optional eps14 and sigma14). The parameters n,
-alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html
-command, before the cutoffs.
+Style {lj/charmm/coul/long/soft} implements a soft-core version of the modified
+12-6 LJ potential used in CHARMM and documented in the
+"pair_lj_charmm"_pair_charmm.html style. In the soft version the parameters n,
+alpha_LJ and alpha_C are set in the "pair_style"_pair_style.html command, before
+the global cutoffs. The activation parameter lambda is introduced as an argument
+of the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and
+before the optional eps14 and sigma14.
+
+Style {lj/class2/soft} implements a soft-core version of the 9-6 potential in
+"pair_class2"_pair_class2.html. In the soft version the parameters n, alpha_LJ
+and alpha_C are set in the "pair_style"_pair_style.html command, before the
+global cutoffs. The activation parameter lambda is introduced as an argument of
+the the "pair_coeff"_pair_coeff.html command, after epsilon and sigma and before
+the optional cutoffs.
 
 The {coul/cut/soft}, {coul/long/soft} and {tip4p/long/soft} sub-styles
 are designed to be combined with other pair potentials via the
@@ -189,7 +230,7 @@ occur.  These sub-styles are suitable to represent charges embedded in
 the Lennard-Jones radius of another site (for example hydrogen atoms
 in several water models).
 
-NOTES: When using the soft-core Coulomb potentials with long-range
+NOTE: When using the soft-core Coulomb potentials with long-range
 solvers ({coul/long/soft}, {lj/cut/coul/long/soft}, etc.)  in a free
 energy calculation in which sites holding electrostatic charges are
 being created or annihilated (using "fix adapt/fep"_fix_adapt_fep.html
@@ -202,6 +243,31 @@ Waals site is present during the free-energy route, thus avoiding
 overlap of the charges. Examples are provided in the LAMMPS source
 directory tree, under examples/USER/fep.
 
+NOTE: To avoid division by zero do not set sigma = 0 in the {lj/cut/soft} and
+related styles; use the lambda parameter instead to activate/deactivate
+interactions, or use epsilon = 0 and sigma = 1. Alternatively, when sites do not
+interact though the Lennard-Jones term the {coul/long/soft} or similar sub-style
+can be used via the "pair_style hybrid/overlay"_pair_hybrid.html command.
+
+:line
+
+The {morse/soft} variant modifies the "pair_morse"_pair_morse.html style at
+short range to have a soft core. The functional form differs from that of the
+{lj/soft} styles, and is instead given by:
+
+:c,image(Eqs/pair_morse_soft.jpg)
+
+The {morse/soft} style requires the following pair coefficients:
+
+D0 (energy units)
+alpha (1/distance units)
+r0 (distance units)
+lambda (unitless, between 0.0 and 1.0)
+cutoff (distance units) :ul
+
+The last coefficient is optional. If not specified, the global morse cutoff is
+used.
+
 :line
 
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
@@ -228,40 +294,57 @@ instructions on how to use the accelerated styles effectively.
 
 [Mixing, shift, tail correction, restart info]:
 
-For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for this pair style can be mixed.
-The default mix value is {geometric}.  See the "pair_modify" command
-for details.
+The different versions of the {lj/cut/soft} pair styles support mixing.  For atom
+type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff
+distance for these pair style can be mixed.  The default mix value is
+{geometric} for 12-6 styles.
 
-These pair styles support the "pair_modify"_pair_modify.html shift
-option for the energy of the Lennard-Jones portion of the pair
+The mixing rule for epsilon and sigma for {lj/class2/soft} 9-6 potentials is to use the
+{sixthpower} formulas. The "pair_modify mix"_pair_modify.html setting is thus
+ignored for class2 potentials for epsilon and sigma. However it is still
+followed for mixing the cutoff distance. See the "pair_modify"_pair_modify.html
+command for details.
+
+The {morse/soft} pair style does not support mixing. Thus, coefficients for all
+LJ pairs must be specified explicitly.
+
+All of the pair styles with soft core support the "pair_modify"_pair_modify.html
+shift option for the energy of the Lennard-Jones portion of the pair
 interaction.
 
-These pair styles support the "pair_modify"_pair_modify.html tail
-option for adding a long-range tail correction to the energy and
-pressure for the Lennard-Jones portion of the pair interaction.
+The different versions of the {lj/cut/soft} pair styles support the
+"pair_modify"_pair_modify.html tail option for adding a long-range tail
+correction to the energy and pressure for the Lennard-Jones portion of the pair
+interaction.
 
-These pair styles write 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.
+NOTE: The analytical form of the tail corrections for energy and pressure used
+in the {lj/cut/soft} potentials are approximate, being identical to that of the
+corresponding non-soft potentials scaled by a factor lambda^n. The errors due to
+this approximation should be negligible. For example, for a cutoff of 2.5 sigma
+this approximation leads to maximum relative errors in tail corrections of the
+order of 1e-4 for energy and virial (alpha_LJ = 0.5, n = 2). The error vanishes
+when lambda approaches 0 or 1. Note that these are the errors affecting the
+long-range tail (itself a correction to the interaction energy) which includes
+other approximations, namely that the system is homogeneous (local density equal
+the average density) beyond the cutoff.
+
+The {morse/soft} pair style does not support the "pair_modify"_pair_modify.html
+tail option for adding long-range tail corrections to energy and pressure.
+
+All of these pair styles write 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.
 
 :line
 
 [Restrictions:]
 
-To avoid division by zero do not set sigma = 0; use the lambda
-parameter instead to activate/deactivate interactions, or use
-epsilon = 0 and sigma = 1. Alternatively, when sites do not
-interact though the Lennard-Jones term the {coul/long/soft} or
-similar sub-style can be used via the
-"pair_style hybrid/overlay"_pair_hybrid.html command.
-
-:line
-
-All of the plain {soft} pair styles are part of the USER-FEP package.
-The {long} styles also requires the KSPACE package to be installed.
-They are only enabled if LAMMPS was built with those packages.  See
-the "Build package"_Build_package.html doc page for more info.
+The pair styles with soft core are only enabled if LAMMPS was built with the
+USER-FEP package. The {long} versions also require the KSPACE package to be
+installed. The soft {tip4p} versions also require the MOLECULE package to be
+installed. These styles are only enabled if LAMMPS was built with those
+packages.  See the "Build package"_Build_package.html doc page for more
+info.
 
 [Related commands:]
 

doc/src/pair_lj.txt

@@ -260,6 +260,14 @@ pair_style command.
 
 :line
 
+A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
+only available if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+:line
+
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
@@ -321,8 +329,7 @@ The {lj/cut/coul/long} and {lj/cut/tip4p/long} styles are part of the
 KSPACE package. The {lj/cut/tip4p/cut} style is part of the MOLECULE
 package. These styles are only enabled if LAMMPS was built with those
 packages.  See the "Build package"_Build_package.html doc page for
-more info.  Note that the KSPACE and MOLECULE packages are installed
-by default.
+more info.
 
 [Related commands:]
 

doc/src/pair_lj_long.txt

@@ -154,6 +154,14 @@ specified in the pair_style command.
 
 :line
 
+A version of these styles with a soft core, {lj/cut/soft}, suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is
+only available if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
+
+:line
+
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
@@ -211,8 +219,7 @@ different levels of the rRESPA hierarchy.  See the
 
 These styles are part of the KSPACE package.  They are only enabled if
 LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
 
 [Related commands:]
 

doc/src/pair_lj_switch3_coulgauss.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,Commands_all.html)
+
+:line
+
+pair_style lj/switch3/coulgauss/long command :h3
+
+[Syntax:]
+
+pair_style style args :pre
+
+style = {lj/switch3/coulgauss/long}
+args = list of arguments for a particular style :ul
+  {lj/switch3/coulgauss/long} args = cutoff (cutoff2) width
+    cutoff  = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+    width  = width parameter of the smoothing function (distance units) :pre
+
+[Examples:]
+
+pair_style lj/switch3/coulgauss/long    12.0 3.0
+pair_coeff 1  0.2 2.5 1.2 :pre
+
+pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
+pair_coeff 1  0.2 2.5 1.2 :pre
+
+[Description:]
+
+The {lj/switch3/coulgauss} style evaluates the LJ
+vdW potential
+
+:c,image(Eqs/pair_lj_switch3.jpg)
+
+, which goes smoothly to zero at the cutoff r_c as defined
+by the switching function
+
+:c,image(Eqs/pair_switch3.jpg)
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+:c,image(Eqs/pair_coulgauss.jpg)
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+epsilon (energy)
+sigma (distance)
+gamma (distance) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+
+[Restrictions:]
+
+These styles are part of the USER-YAFF package.  They are only
+enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+

doc/src/pair_mm3_switch3_coulgauss.txt

@@ -0,0 +1,88 @@
+"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 mm3/switch3/coulgauss/long command :h3
+
+[Syntax:]
+
+pair_style style args :pre
+
+style = {mm3/switch3/coulgauss/long}
+args = list of arguments for a particular style :ul
+  {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width
+    cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+    width  = width parameter of the smoothing function (distance units) :pre
+
+[Examples:]
+
+pair_style mm3/switch3/coulgauss/long    12.0 3.0
+pair_coeff 1  0.2 2.5 1.2 :pre
+
+pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
+pair_coeff 1  0.2 2.5 1.2 :pre
+
+[Description:]
+
+The {mm3/switch3/coulgauss} style evaluates the MM3
+vdW potential "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/pair_mm3_switch3.jpg)
+
+, which goes smoothly to zero at the cutoff r_c as defined
+by the switching function
+
+:c,image(Eqs/pair_switch3.jpg)
+
+where w is the width defined in the arguments. This potential
+is combined with Coulomb interaction between Gaussian charge densities:
+
+:c,image(Eqs/pair_coulgauss.jpg)
+
+where qi and qj are the
+charges on the 2 atoms, epsilon is the dielectric constant which
+can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
+are the widths of the Gaussian charge distribution and erf() is the error-function.
+This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
+
+If one cutoff is specified it is used for both the vdW and Coulomb
+terms.  If two cutoffs are specified, the first is used as the cutoff
+for the vdW terms, and the second is the cutoff for the Coulombic term.
+
+The following coefficients must be defined for each pair of atoms
+types via the "pair_coeff"_pair_coeff.html command as in the examples
+above, or in the data file or restart files read by the
+"read_data"_read_data.html or "read_restart"_read_restart.html
+commands:
+
+epsilon (energy)
+r_v (distance)
+gamma (distance) :ul
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+Mixing rules are fixed for this style as defined above. 
+
+Shifting the potential energy is not necessary because the switching
+function ensures that the potential is zero at the cut-off.
+
+
+[Restrictions:]
+
+These styles are part of the USER-YAFF package.  They are only
+enabled if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"pair_coeff"_pair_coeff.html
+
+[Default:] none
+

doc/src/pair_morse.txt

@@ -12,7 +12,6 @@ pair_style morse/omp command :h3
 pair_style morse/opt command :h3
 pair_style morse/smooth/linear command :h3
 pair_style morse/smooth/linear/omp command :h3
-pair_style morse/soft command :h3
 pair_style morse/kk command :h3
 
 [Syntax:]
@@ -25,10 +24,6 @@ args = list of arguments for a particular style :ul
    cutoff = global cutoff for Morse interactions (distance units)
  {morse/smooth/linear} args = cutoff
    cutoff = global cutoff for Morse interactions (distance units)
- {morse/soft} args = n lf cutoff
-   n       = soft-core parameter
-   lf      = transformation range is lf < lambda < 1
-   cutoff  = global cutoff for Morse interactions (distance units)
 :pre
 
 [Examples:]
@@ -38,10 +33,6 @@ pair_style morse/smooth/linear 2.5
 pair_coeff * * 100.0 2.0 1.5
 pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre
 
-pair_style morse/soft 4 0.9 10.0
-pair_coeff * * 100.0 2.0 1.5 1.0
-pair_coeff 1 1 100.0 2.0 1.5 1.0 3.0 :pre
-
 [Description:]
 
 Style {morse} computes pairwise interactions with the formula
@@ -77,24 +68,11 @@ the {morse} and {morse/smooth/linear} styles.
 
 :line
 
-The {morse/soft} variant is similar to the {lj/cut/soft} pair style
-in that it modifies the potential at short range to have a soft core.
-This helps to avoid singularities during free energy calculation in
-which sites are created or annihilated. The formula differs from that
-of {lj/cut/soft}, and is instead given by:
-
-:c,image(Eqs/pair_morse_soft.jpg)
-
-The {morse/soft} style requires the following pair coefficients:
-
-D0 (energy units)
-alpha (1/distance units)
-r0 (distance units)
-lamda (unitless, between 0.0 and 1.0)
-cutoff (distance units) :ul
-
-The last coefficient is optional.  If not specified, the global morse
-cutoff is used.
+A version of the {morse} style with a soft core, {morse/soft}, suitable for use in
+free energy calculations, is part of the USER-FEP package and is documented with
+the "pair_fep_soft"_pair_fep_soft.html styles. The version with soft core is only
+available if LAMMPS was built with that package. See the "Build
+package"_Build_package.html doc page for more info.
 
 :line
 
@@ -151,12 +129,8 @@ The {morse/smooth/linear} pair style is only enabled if LAMMPS was
 built with the USER-MISC package.  See the "Build
 package"_Build_package.html doc page for more info.
 
-The {morse/soft} pair style is only enabled if LAMMPS was built with
-the USER-FEP package.  See the "Build package"_Build_package.html doc
-page for more info.
-
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html
+"pair_coeff"_pair_coeff.html, "pair_fep_soft"_pair_fep_soft.html
 
 [Default:] none

doc/src/pair_style.txt

@@ -130,13 +130,13 @@ accelerated styles exist.
 "comb"_pair_comb.html - charge-optimized many-body (COMB) potential
 "comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
 "coul/cut"_pair_coul.html - cutoff Coulombic potential
-"coul/cut/soft"_pair_lj_soft.html - Coulombic potential with a soft core
+"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
 "coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
 "coul/diel"_pair_coul_diel.html - Coulomb potential with dielectric permittivity
 "coul/dsf"_pair_coul.html - Coulombics with damped-shifted-force model
 "coul/long"_pair_coul.html - long-range Coulombic potential
 "coul/long/cs"_pair_cs.html - long-range Coulombic potential and core/shell
-"coul/long/soft"_pair_lj_soft.html - long-range Coulombic potential with a soft core
+"coul/long/soft"_pair_fep_soft.html - long-range Coulombic potential with a soft core
 "coul/msm"_pair_coul.html - long-range MSM Coulombics
 "coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
 "coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
@@ -181,31 +181,34 @@ accelerated styles exist.
 "lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
 "lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
 "lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"lj/charmm/coul/long/soft"_pair_lj_soft.html - CHARMM with long-range Coulomb and a soft core
+"lj/charmm/coul/long/soft"_pair_fep_soft.html - CHARMM with long-range Coulomb and a soft core
 "lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
 "lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
 "lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
 "lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
+"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
 "lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
+"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
+"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
 "lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
 "lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
 "lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"lj/cut/coul/cut/soft"_pair_lj_soft.html - LJ with cutoff Coulomb with a soft core
+"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
 "lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
 "lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
 "lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
 "lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
-"lj/cut/coul/long/soft"_pair_lj_soft.html - LJ with long-range Coulombics with a soft core
+"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
 "lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
 "lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
 "lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
 "lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"lj/cut/soft"_pair_lj_soft.html - LJ with a soft core
+"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
 "lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
 "lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
 "lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"lj/cut/tip4p/long/soft"_pair_lj_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
 "lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
 "lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
 "lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
@@ -220,6 +223,7 @@ accelerated styles exist.
 "lj/sf/dipole/sf"_pair_dipole.html - LJ with dipole interaction with shifted forces
 "lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
 "lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed LJ potential
+"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
 "lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
 "lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
 "lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
@@ -232,6 +236,7 @@ accelerated styles exist.
 "meam/sw/spline"_pair_meam_sw_spline.html - splined version of MEAM with a Stillinger-Weber term
 "mgpt"_pair_mgpt.html - simplified model generalized pseudopotential theory (MGPT) potential
 "mie/cut"_pair_mie.html - Mie potential
+"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
 "momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
 "morse"_pair_morse.html - Morse potential
 "morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
@@ -294,7 +299,7 @@ accelerated styles exist.
 "thole"_pair_thole.html - Coulomb interactions with thole damping
 "tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
 "tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
-"tip4p/long/soft"_pair_lj_soft.html -
+"tip4p/long/soft"_pair_fep_soft.html -
 "tri/lj"_pair_tri_lj.html - LJ potential between triangles
 "ufm"_pair_ufm.html -
 "vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential

doc/src/pairs.txt

@@ -38,6 +38,7 @@ Pair Styles :h1
    pair_eim
    pair_exp6_rx
    pair_extep
+   pair_fep_soft
    pair_gauss
    pair_gayberne
    pair_gran
@@ -60,7 +61,7 @@ Pair Styles :h1
    pair_lj_long
    pair_lj_smooth
    pair_lj_smooth_linear
-   pair_lj_soft
+   pair_lj_switch3_coulgauss
    pair_lubricate
    pair_lubricateU
    pair_mdf
@@ -70,6 +71,7 @@ Pair Styles :h1
    pair_meso
    pair_mgpt
    pair_mie
+   pair_mm3_switch3_coulgauss
    pair_momb
    pair_morse
    pair_multi_lucy