Merge pull request #1172 from akohlmey/next-patch-release

Patch release 24 October 2018

.github/CODEOWNERS

@@ -30,6 +30,7 @@ src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
 src/USER-PHONON/*     @lingtikong
+src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey
 src/USER-QMMM/*       @akohlmey
 src/USER-REAXC/*      @hasanmetin

cmake/CMakeLists.txt

@@ -69,6 +69,8 @@ get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
+include(PreventInSourceBuilds)
+
 if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
   #release comes with -O3 by default
   set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
@@ -164,12 +166,13 @@ set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK SPIN SNAP
-  SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD USER-BOCS
-  USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE
-  USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD USER-MEAMC USER-MGPT USER-MISC
-  USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-QTB USER-REAXC USER-SCAFACOS 
-  USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
+  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+  SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
+  USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
+  USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
+  USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
+  USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SCAFACOS USER-SMD USER-SMTBQ
+  USER-SPH USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})

cmake/Modules/PreventInSourceBuilds.cmake

@@ -0,0 +1,23 @@
+# - Prevent in-source builds.
+# https://stackoverflow.com/questions/1208681/with-cmake-how-would-you-disable-in-source-builds/
+
+function(prevent_in_source_builds)
+  # make sure the user doesn't play dirty with symlinks
+  get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
+  get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH)
+  get_filename_component(srcdir3 "${CMAKE_SOURCE_DIR}/../src" REALPATH)
+  get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
+
+  # disallow in-source builds
+  if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
+    message(FATAL_ERROR "\
+
+CMake must not to be run in the source directory. \
+Rather create a dedicated build directory and run CMake there. \
+To clean up after this aborted in-place compilation:
+  rm -r CMakeCache.txt CMakeFiles
+")
+  endif()
+endfunction()
+
+prevent_in_source_builds()

doc/Makefile

@@ -38,7 +38,7 @@ OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
-	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
+	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
 	@echo "  old        create old-style HTML doc pages in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
@@ -95,9 +95,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	@echo "Spell check finished."
 
 epub: $(OBJECTS)
-	@mkdir -p epub
+	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
+	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
@@ -116,17 +117,17 @@ mobi: epub
 pdf: utils/txt2html/txt2html.exe
 	@(\
 		set -e; \
-		cd src; \
-		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q $$s lammps.book || \
-			echo doc file $$s missing in src/lammps.book; done; \
-		rm *.html; \
-		cd Developer; \
+		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
+		cd ..; \
+		../utils/txt2html/txt2html.exe -b *.txt; \
+		htmldoc --batch lammps.book;          \
+		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q ^$$s lammps.book || \
+			echo WARNING: doc file $$s missing in src/lammps.book; done; \
+		rm *.html; \
 	)
 
 old: utils/txt2html/txt2html.exe

doc/src/Build_extras.txt

@@ -563,9 +563,9 @@ file.
 VORONOI package :h4,link(voronoi)
 
 To build with this package, you must download and build the "Voro++
-library"_voro_home.
+library"_voro-home.
 
-:link(voro_home,http://math.lbl.gov/voro++)
+:link(voro-home,http://math.lbl.gov/voro++)
 
 [CMake build]:
 
@@ -932,9 +932,9 @@ successfully build on your system.
 USER-SCAFACOS package :h4,link(user-scafacos)
 
 To build with this package, you must download and build the "ScaFaCoS
-Coulomb solver library"_scafacos_home
+Coulomb solver library"_scafacos-home
 
-:link(scafacos_home,http://www.scafacos.de)
+:link(scafacos-home,http://www.scafacos.de)
 
 [CMake build]:
 

doc/src/Commands_bond.txt

@@ -34,7 +34,7 @@ OPT.
 "fene (iko)"_bond_fene.html,
 "fene/expand (o)"_bond_fene_expand.html,
 "gromos (o)"_bond_gromos.html,
-"harmonic (ko)"_bond_harmonic.html,
+"harmonic (iko)"_bond_harmonic.html,
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
 "morse (o)"_bond_morse.html,
@@ -57,9 +57,11 @@ OPT.
 "zero"_angle_zero.html,
 "hybrid"_angle_hybrid.html :tb(c=3,ea=c)
 
-"charmm (ko)"_angle_charmm.html,
+"charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
+"class2/p6"_angle_class2.html,
 "cosine (o)"_angle_cosine.html,
+"cosine/buck6d"_angle_cosine_buck6d.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
 "cosine/shift (o)"_angle_cosine_shift.html,
@@ -70,7 +72,7 @@ OPT.
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
 "quartic (o)"_angle_quartic.html,
-"sdk"_angle_sdk.html,
+"sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
 
 :line
@@ -97,7 +99,7 @@ OPT.
 "nharmonic (o)"_dihedral_nharmonic.html,
 "opls (iko)"_dihedral_opls.html,
 "quadratic (o)"_dihedral_quadratic.html,
-"spherical (o)"_dihedral_spherical.html,
+"spherical"_dihedral_spherical.html,
 "table (o)"_dihedral_table.html,
 "table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
 
@@ -112,7 +114,7 @@ OPT.
 
 "none"_improper_none.html,
 "zero"_improper_zero.html,
-"hybrid"_improper_hybrid.html  :tb(c=3,ea=c)
+"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
 
 "class2 (ko)"_improper_class2.html,
 "cossq (o)"_improper_cossq.html,
@@ -120,5 +122,6 @@ OPT.
 "distance"_improper_distance.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
+"inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_compute.txt

@@ -25,6 +25,7 @@ additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
 KOKKOS, o = USER-OMP, t = OPT.
 
 "ackland/atom"_compute_ackland_atom.html,
+"adf"_compute_adf.html,
 "aggregate/atom"_compute_cluster_atom.html,
 "angle"_compute_angle.html,
 "angle/local"_compute_angle_local.html,
@@ -92,10 +93,12 @@ KOKKOS, o = USER-OMP, t = OPT.
 "pe/tally"_compute_tally.html,
 "plasticity/atom"_compute_plasticity_atom.html,
 "pressure"_compute_pressure.html,
+"pressure/cylinder"_compute_pressure_cylinder.html,
 "pressure/uef"_compute_pressure_uef.html,
 "property/atom"_compute_property_atom.html,
 "property/chunk"_compute_property_chunk.html,
 "property/local"_compute_property_local.html,
+"ptm/atom"_compute_ptm_atom.html,
 "rdf"_compute_rdf.html,
 "reduce"_compute_reduce.html,
 "reduce/chunk"_compute_reduce_chunk.html,
@@ -117,7 +120,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "smd/tlsph/strain"_compute_smd_tlsph_strain.html,
 "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
 "smd/tlsph/stress"_compute_smd_tlsph_stress.html,
-"smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
 "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
 "smd/ulsph/strain"_compute_smd_ulsph_strain.html,
 "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
@@ -128,6 +131,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "snav/atom"_compute_sna_atom.html,
 "spin"_compute_spin.html,
 "stress/atom"_compute_stress_atom.html,
+"stress/mop"_compute_stress_mop.html,
+"stress/mop/profile"_compute_stress_mop.html,
 "stress/tally"_compute_tally.html,
 "tdpd/cc/atom"_compute_tdpd_cc_atom.html,
 "temp (k)"_compute_temp.html,
@@ -135,6 +140,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "temp/body"_compute_temp_body.html,
 "temp/chunk"_compute_temp_chunk.html,
 "temp/com"_compute_temp_com.html,
+"temp/cs"_compute_temp_cs.html,
 "temp/deform"_compute_temp_deform.html,
 "temp/deform/eff"_compute_temp_deform_eff.html,
 "temp/drude"_compute_temp_drude.html,

doc/src/Commands_fix.txt

@@ -40,11 +40,13 @@ OPT.
 "ave/time"_fix_ave_time.html,
 "aveforce"_fix_aveforce.html,
 "balance"_fix_balance.html,
+"bocs"_fix_bocs.html,
 "bond/break"_fix_bond_break.html,
 "bond/create"_fix_bond_create.html,
 "bond/react"_fix_bond_react.html,
 "bond/swap"_fix_bond_swap.html,
 "box/relax"_fix_box_relax.html,
+"client/md"_fix_client_md.html,
 "cmap"_fix_cmap.html,
 "colvars"_fix_colvars.html,
 "controller"_fix_controller.html,
@@ -54,7 +56,7 @@ OPT.
 "drag"_fix_drag.html,
 "drude"_fix_drude.html,
 "drude/transform/direct"_fix_drude_transform.html,
-"drude/transform/reverse"_fix_drude_transform.html,
+"drude/transform/inverse"_fix_drude_transform.html,
 "dt/reset"_fix_dt_reset.html,
 "edpd/source"_fix_dpd_source.html,
 "efield"_fix_efield.html,
@@ -65,13 +67,14 @@ OPT.
 "eos/table/rx (k)"_fix_eos_table_rx.html,
 "evaporate"_fix_evaporate.html,
 "external"_fix_external.html,
+"ffl"_fix_ffl.html,
 "filter/corotate"_fix_filter_corotate.html,
 "flow/gauss"_fix_flow_gauss.html,
-"freeze"_fix_freeze.html,
+"freeze (k)"_fix_freeze.html,
 "gcmc"_fix_gcmc.html,
 "gld"_fix_gld.html,
 "gle"_fix_gle.html,
-"gravity (o)"_fix_gravity.html,
+"gravity (ko)"_fix_gravity.html,
 "grem"_fix_grem.html,
 "halt"_fix_halt.html,
 "heat"_fix_heat.html,
@@ -104,17 +107,18 @@ OPT.
 "nph/asphere (o)"_fix_nph_asphere.html,
 "nph/body"_fix_nph_body.html,
 "nph/eff"_fix_nh_eff.html,
-"nph/sphere (o)"_fix_nph_sphere.html,
+"nph/sphere (ko)"_fix_nph_sphere.html,
 "nphug (o)"_fix_nphug.html,
-"npt (kio)"_fix_nh.html,
+"npt (iko)"_fix_nh.html,
 "npt/asphere (o)"_fix_npt_asphere.html,
 "npt/body"_fix_npt_body.html,
 "npt/eff"_fix_nh_eff.html,
 "npt/sphere (o)"_fix_npt_sphere.html,
 "npt/uef"_fix_nh_uef.html,
-"nve (kio)"_fix_nve.html,
+"nve (iko)"_fix_nve.html,
 "nve/asphere (i)"_fix_nve_asphere.html,
 "nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/awpmd"_fix_nve_awpmd.html,
 "nve/body"_fix_nve_body.html,
 "nve/dot"_fix_nve_dot.html,
 "nve/dotc/langevin"_fix_nve_dotc_langevin.html,
@@ -169,26 +173,26 @@ OPT.
 "rhok"_fix_rhok.html,
 "rigid (o)"_fix_rigid.html,
 "rigid/nph (o)"_fix_rigid.html,
+"rigid/nph/small"_fix_rigid.html,
 "rigid/npt (o)"_fix_rigid.html,
+"rigid/npt/small"_fix_rigid.html,
 "rigid/nve (o)"_fix_rigid.html,
+"rigid/nve/small"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
+"rigid/nvt/small"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph"_fix_rigid.html,
-"rigid/small/npt"_fix_rigid.html,
-"rigid/small/nve"_fix_rigid.html,
-"rigid/small/nvt"_fix_rigid.html,
 "rx (k)"_fix_rx.html,
 "saed/vtk"_fix_saed_vtk.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "shardlow (k)"_fix_shardlow.html,
 "smd"_fix_smd.html,
-"smd/adjust/dt"_fix_smd_adjust_dt.html,
-"smd/integrate/tlsph"_fix_smd_integrate_tlsph.html,
-"smd/integrate/ulsph"_fix_smd_integrate_ulsph.html,
-"smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html,
+"smd/adjust_dt"_fix_smd_adjust_dt.html,
+"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
 "smd/setvel"_fix_smd_setvel.html,
-"smd/wall/surface"_fix_smd_wall_surface.html,
+"smd/wall_surface"_fix_smd_wall_surface.html,
 "spring"_fix_spring.html,
 "spring/chunk"_fix_spring_chunk.html,
 "spring/rg"_fix_spring_rg.html,
@@ -216,7 +220,7 @@ OPT.
 "wall/body/polyhedron"_fix_wall_body_polyhedron.html,
 "wall/colloid"_fix_wall.html,
 "wall/ees"_fix_wall_ees.html,
-"wall/gran"_fix_wall_gran.html,
+"wall/gran (o)"_fix_wall_gran.html,
 "wall/gran/region"_fix_wall_gran_region.html,
 "wall/harmonic"_fix_wall.html,
 "wall/lj1043"_fix_wall.html,

doc/src/Commands_pair.txt

@@ -26,13 +26,13 @@ OPT.
 
 "none"_pair_none.html,
 "zero"_pair_zero.html,
-"hybrid"_pair_hybrid.html,
+"hybrid (k)"_pair_hybrid.html,
 "hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
 
 "adp (o)"_pair_adp.html,
 "agni (o)"_pair_agni.html,
-"airebo (oi)"_pair_airebo.html,
-"airebo/morse (oi)"_pair_airebo.html,
+"airebo (io)"_pair_airebo.html,
+"airebo/morse (io)"_pair_airebo.html,
 "atm"_pair_atm.html,
 "awpmd/cut"_pair_awpmd.html,
 "beck (go)"_pair_beck.html,
@@ -42,21 +42,23 @@ OPT.
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
 "born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
+"born/coul/dsf/cs"_pair_cs.html,
 "born/coul/long (go)"_pair_born.html,
-"born/coul/long/cs"_pair_born.html,
+"born/coul/long/cs (g)"_pair_cs.html,
 "born/coul/msm (o)"_pair_born.html,
 "born/coul/wolf (go)"_pair_born.html,
-"born/coul/wolf/cs"_pair_born.html,
+"born/coul/wolf/cs (g)"_pair_cs.html,
 "brownian (o)"_pair_brownian.html,
 "brownian/poly (o)"_pair_brownian.html,
 "buck (giko)"_pair_buck.html,
 "buck/coul/cut (giko)"_pair_buck.html,
 "buck/coul/long (giko)"_pair_buck.html,
-"buck/coul/long/cs"_pair_buck.html,
+"buck/coul/long/cs"_pair_cs.html,
 "buck/coul/msm (o)"_pair_buck.html,
 "buck/long/coul/long (o)"_pair_buck_long.html,
 "buck/mdf"_pair_mdf.html,
+"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
+"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
 "colloid (go)"_pair_colloid.html,
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
@@ -66,13 +68,13 @@ OPT.
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/dsf (gko)"_pair_coul.html,
 "coul/long (gko)"_pair_coul.html,
-"coul/long/cs"_pair_coul.html,
+"coul/long/cs (g)"_pair_cs.html,
 "coul/long/soft (o)"_pair_lj_soft.html,
-"coul/msm"_pair_coul.html,
+"coul/msm (o)"_pair_coul.html,
 "coul/shield"_pair_coul_shield.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"coul/wolf/cs"_pair_coul.html,
+"coul/wolf/cs"_pair_cs.html,
 "dpd (gio)"_pair_dpd.html,
 "dpd/fdt"_pair_dpd_fdt.html,
 "dpd/fdt/energy (k)"_pair_dpd_fdt.html,
@@ -81,6 +83,7 @@ OPT.
 "eam (gikot)"_pair_eam.html,
 "eam/alloy (gikot)"_pair_eam.html,
 "eam/cd (o)"_pair_eam.html,
+"eam/cd/old (o)"_pair_eam.html,
 "eam/fs (gikot)"_pair_eam.html,
 "edip (o)"_pair_edip.html,
 "edip/multi"_pair_edip.html,
@@ -90,11 +93,11 @@ OPT.
 "exp6/rx (k)"_pair_exp6_rx.html,
 "extep"_pair_extep.html,
 "gauss (go)"_pair_gauss.html,
-"gauss/cut"_pair_gauss.html,
+"gauss/cut (o)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
 "gran/hertz/history (o)"_pair_gran.html,
 "gran/hooke (o)"_pair_gran.html,
-"gran/hooke/history (o)"_pair_gran.html,
+"gran/hooke/history (ko)"_pair_gran.html,
 "gw"_pair_gw.html,
 "gw/zbl"_pair_gw.html,
 "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
@@ -109,9 +112,9 @@ OPT.
 "list"_pair_list.html,
 "lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_charmm.html,
-"lj/charmm/coul/msm"_pair_charmm.html,
+"lj/charmm/coul/long (gikot)"_pair_charmm.html,
+"lj/charmm/coul/long/soft (o)"_pair_lj_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,
@@ -124,12 +127,12 @@ OPT.
 "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_lj.html,
+"lj/cut/coul/long/cs"_pair_cs.html,
 "lj/cut/coul/long/soft (o)"_pair_lj_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"_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/thole/long (o)"_pair_thole.html,
@@ -137,15 +140,17 @@ OPT.
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
 "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
 "lj/expand (gko)"_pair_lj_expand.html,
+"lj/expand/coul/long (g)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
 "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
-"lj/long/coul/long (io)"_pair_lj_long.html,
+"lj/long/coul/long (iot)"_pair_lj_long.html,
 "lj/long/dipole/long"_pair_dipole.html,
-"lj/long/tip4p/long"_pair_lj_long.html,
+"lj/long/tip4p/long (o)"_pair_lj_long.html,
 "lj/mdf"_pair_mdf.html,
 "lj/sdk (gko)"_pair_sdk.html,
 "lj/sdk/coul/long (go)"_pair_sdk.html,
 "lj/sdk/coul/msm (o)"_pair_sdk.html,
+"lj/sf/dipole/sf (go)"_pair_dipole.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
 "lj96/cut (go)"_pair_lj96.html,
@@ -160,14 +165,14 @@ OPT.
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.html,
-"mie/cut (o)"_pair_mie.html,
+"mie/cut (g)"_pair_mie.html,
 "momb"_pair_momb.html,
 "morse (gkot)"_pair_morse.html,
-"morse/smooth/linear"_pair_morse.html,
+"morse/smooth/linear (o)"_pair_morse.html,
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
-"nb3b/harmonic (o)"_pair_nb3b_harmonic.html,
+"nb3b/harmonic"_pair_nb3b_harmonic.html,
 "nm/cut (o)"_pair_nm.html,
 "nm/cut/coul/cut (o)"_pair_nm.html,
 "nm/cut/coul/long (o)"_pair_nm.html,
@@ -179,7 +184,9 @@ OPT.
 "oxdna2/coaxstk"_pair_oxdna2.html,
 "oxdna2/dh"_pair_oxdna2.html,
 "oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/hbond"_pair_oxdna2.html,
 "oxdna2/stk"_pair_oxdna2.html,
+"oxdna2/xstk"_pair_oxdna2.html,
 "peri/eps"_pair_peri.html,
 "peri/lps (o)"_pair_peri.html,
 "peri/pmb (o)"_pair_peri.html,
@@ -189,11 +196,11 @@ OPT.
 "quip"_pair_quip.html,
 "reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
-"rebo (oi)"_pair_airebo.html,
+"rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
-"smd/triangulated/surface"_pair_smd_triangulated_surface.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html,
 "smd/ulsph"_pair_smd_ulsph.html,
 "smtbq"_pair_smtbq.html,
 "snap (k)"_pair_snap.html,
@@ -225,8 +232,8 @@ OPT.
 "tip4p/long/soft (o)"_pair_lj_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
-"vashishta (ko)"_pair_vashishta.html,
+"vashishta (gko)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
-"yukawa (gok)"_pair_yukawa.html,
+"yukawa (gko)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
-"zbl (gok)"_pair_zbl.html :tb(c=4,ea=c)
+"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Developer/developer.tex

@@ -22,10 +22,10 @@ users.
 LAMMPS source files are in two directories of the distribution
 tarball.  The src directory has the majority of them, all of which are
 C++ files (*.cpp and *.h).  Many of these files are in the src
-directory itself.  There are also dozens of "packages", which can be
+directory itself.  There are also dozens of ``packages'', which can be
 included or excluded when LAMMPS is built.  See the
 doc/Section\_build.html section of the manual for more information
-about packages, or type "make" from within the src directory, which
+about packages, or type ``make'' from within the src directory, which
 lists package-related commands, such as ``make package-status''.  The
 source files for each package are in an all-uppercase sub-directory of
 src, like src/MOLECULE or src/USER-CUDA.  If the package is currently
@@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries,
 used by a few of the packages.  Each sub-directory, like meam or gpu,
 contains the source files, some of which are in different languages
 such as Fortran.  The files are compiled into libraries from within
-each sub-directory, e.g. performing a "make" in the lib/meam directory
+each sub-directory, e.g. performing a ``make'' in the lib/meam directory
 creates a libmeam.a file.  These libraries are linked to during a
 LAMMPS build, if the corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as run.cpp
 and run.h.  The pair of files defines a C++ class, the Run class in
-this case, which contains the code invoked by the "run" command in a
+this case, which contains the code invoked by the ``run'' command in a
 LAMMPS input script.  As this example illustrates, source file and
 class names often have a one-to-one correspondence with a command used
 in a LAMMPS input script.  Some source files and classes do not have a
-corresponding input script command, e.g. force.cpp and the Force
+corresponding input script command, e.g. ``force.cpp'' and the Force
 class.  They are discussed in the next section.
 
 \pagebreak
@@ -57,12 +57,12 @@ class.  They are discussed in the next section.
 Though LAMMPS has a lot of source files and classes, its class
 hierarchy is quite simple, as outlined in Fig \ref{fig:classes}.  Each
 boxed name refers to a class and has a pair of associated source files
-in lammps/src, e.g. memory.cpp and memory.h.  More details on the
+in lammps/src, e.g. ``memory.cpp'' and ``memory.h''.  More details on the
 class and its methods and data structures can be found by examining
 its *.h file.
 
 LAMMPS (lammps.cpp/h) is the top-level class for the entire code.  It
-holds an "instance" of LAMMPS and can be instantiated one or more
+holds an ``instance'' of LAMMPS and can be instantiated one or more
 times by a calling code.  For example, the file src/main.cpp simply
 instantiates one instance of LAMMPS and passes it the input script.
 
@@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see
 src/pointers.h) which every class inherits from.
 
 There are a handful of virtual parent classes in LAMMPS that define
-what LAMMPS calls "styles".  They are shaded red in Fig
+what LAMMPS calls ``styles''.  They are shaded red in Fig
 \ref{fig:classes}.  Each of these are parents of a number of child
 classes that implement the interface defined by the parent class.  For
 example, the fix style has around 100 child classes.  They are the
@@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input
 script, e.g. fix nve, fix shake, fix ave/time, etc.  The corresponding
 classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
 etc.  The source files for these classes are easy to identify in the
-src directory, since they begin with the word "fix", e,g,
+src directory, since they begin with the word ``fix'', e,g,
 fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
 
-The one exception is child class files for the "command" style.  These
+The one exception is child class files for the ``command'' style.  These
 implement specific commands in the input script that can be invoked
 before/after/between runs or which launch a simulation.  Examples are
 the create\_box, minimize, run, and velocity commands which encode the
 CreateBox, Minimize, Run, and Velocity classes.  The corresponding
 files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
-The list of command style files can be found by typing "grep
-COMMAND\_CLASS *.h" from within the src directory, since that word in
+The list of command style files can be found by typing ``grep
+COMMAND\_CLASS *.h'' from within the src directory, since that word in
 the header file identifies the class as an input script command.
 Similar words can be grepped to list files for the other LAMMPS
 styles.  E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
@@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine)
   \end{verbatim}
  \end{center}
 
-Where "your/fix/name" is a name of your fix in the script and FixMine
+Where ``your/fix/name'' is a name of your fix in the script and FixMine
 is the name of the class. This code allows LAMMPS to find your fix
 when it parses input script. In addition, your fix header must be
-included in the file "style\_fix.h". In case if you use LAMMPS make,
+included in the file ``style\_fix.h''. In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
 fix\_ are included, so call your header the same way. Otherwise, don't
-forget to add your include into "style\_fix.h".
+forget to add your include into ``style\_fix.h''.
 
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
@@ -567,11 +567,11 @@ void FixPrintVel::end_of_step()
 \end{center}
 
 In the code above, we use MathExtra routines defined in
-"math\_extra.h".  There are bunch of math functions to work with
+``math\_extra.h''.  There are bunch of math functions to work with
 arrays of doubles as with math vectors.
 
 In this code we use an instance of Atom class. This object is stored
-in the Pointers class (see "pointers.h"). This object contains all
+in the Pointers class (see ``pointers.h''). This object contains all
 global information about the simulation system. Data from Pointers
 class available to all classes inherited from it using protected
 inheritance. Hence when you write you own class, which is going to use
@@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf)
 
 Now, a little bit about memory allocation. We used Memory class which
 is just a bunch of template functions for allocating 1D and 2D
-arrays. So you need to add include "memory.h" to have access to them.
+arrays. So you need to add include ``memory.h'' to have access to them.
 
 Finally, if you need to write/read some global information used in
 your fix to the restart file, you might do it by setting flag

doc/src/Eqs/ptm_rmsd.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
+
+\begin{document}
+
+\begin{equation*}
+\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+\norm{
+s[\vec{u_i} - \mean{\set{u}}]
+-
+\set{Q} \vec{v_i}
+}^2}
+\end{equation*}
+
+\end{document}

doc/src/Errors_messages.txt

@@ -1092,11 +1092,6 @@ correct. :dd
 The specified file cannot be opened.  Check that the path and name are
 correct. :dd
 
-{Cannot open fix ave/spatial file %s} :dt
-
-The specified file cannot be opened.  Check that the path and name are
-correct. :dd
-
 {Cannot open fix ave/time file %s} :dt
 
 The specified file cannot be opened.  Check that the path and name are
@@ -1677,10 +1672,6 @@ provided by an atom map.  An atom map does not exist (by default) for
 non-molecular problems.  Using the atom_modify map command will force
 an atom map to be created. :dd
 
-{Cannot use fix ave/spatial z for 2 dimensional model} :dt
-
-Self-explanatory. :dd
-
 {Cannot use fix bond/break with non-molecular systems} :dt
 
 Only systems with bonds that can be changed can be used.  Atom_style
@@ -2425,10 +2416,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Compute ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Compute ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -4074,10 +4061,6 @@ Self-explanatory. :dd
 
 Self-explanatory. :dd
 
-{Fix ID for fix ave/spatial does not exist} :dt
-
-Self-explanatory. :dd
-
 {Fix ID for fix ave/time does not exist} :dt
 
 Self-explanatory. :dd
@@ -4379,51 +4362,6 @@ same style. :dd
 
 Self-explanatory. :dd
 
-{Fix ave/spatial compute does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial compute does not calculate a per-atom vector} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute does not calculate per-atom values} :dt
-
-A compute used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial compute vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom array} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial fix does not calculate a per-atom vector} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix does not calculate per-atom values} :dt
-
-A fix used by fix ave/spatial must generate per-atom values. :dd
-
-{Fix ave/spatial fix vector is accessed out-of-range} :dt
-
-The index for the vector is out of bounds. :dd
-
-{Fix ave/spatial for triclinic boxes requires units reduced} :dt
-
-Self-explanatory. :dd
-
-{Fix ave/spatial settings invalid with changing box size} :dt
-
-If the box size changes, only the units reduced option can be
-used. :dd
-
-{Fix ave/spatial variable is not atom-style variable} :dt
-
-A variable used by fix ave/spatial must generate per-atom values. :dd
-
 {Fix ave/time cannot set output array intensive/extensive from these inputs} :dt
 
 One of more of the vector inputs has individual elements which are

doc/src/Errors_warnings.txt

@@ -291,24 +291,6 @@ This may cause accuracy problems. :dd
 
 This may cause accuracy problems. :dd
 
-{Fix thermal/conductivity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that fix
-thermal/conductivity comes first.  If you are using fix ave/spatial to
-measure the temperature profile induced by fix viscosity, then this
-may cause a glitch in the profile since you are averaging immediately
-after swaps have occurred.  Flipping the order of the 2 fixes
-typically helps. :dd
-
-{Fix viscosity comes before fix ave/spatial} :dt
-
-The order of these 2 fixes in your input script is such that
-fix viscosity comes first.  If you are using fix ave/spatial
-to measure the velocity profile induced by fix viscosity, then
-this may cause a glitch in the profile since you are averaging
-immediately after swaps have occurred.  Flipping the order
-of the 2 fixes typically helps. :dd
-
 {Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
 
 This is current restriction with Kokkos. :dd

doc/src/Install_linux.txt

@@ -9,39 +9,16 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
 
 Download an executable for Linux :h3
 
-Binaries are available for many different versions of Linux:
+Binaries are available for different versions of Linux:
 
-"Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE"_#rpm
 "Pre-built Ubuntu Linux executables"_#ubuntu
+"Pre-built Fedora Linux executables"_#fedora
+"Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
+"Pre-built OpenSuse Linux executables"_#opensuse
 "Pre-built Gentoo Linux executable"_#gentoo :all(b)
 
 :line
 
-Pre-built binary RPMs for Fedora/RedHat/CentOS/openSUSE :h4,link(rpm)
-
-Pre-built LAMMPS executables for various Linux distributions
-can be downloaded as binary RPM files from this site:
-
-"http://rpm.lammps.org"_http://rpm.lammps.org
-
-There are multiple package variants supporting serial, parallel and
-Python wrapper versions.  The LAMMPS binaries contain all optional
-packages included in the source distribution except: GPU, KIM, REAX,
-and USER-INTEL.
-
-Installation instructions for the various versions are here:
-
-"http://rpm.lammps.org/install.html"_http://rpm.lammps.org/install.html
-
-The instructions show how to enable the repository in the respective
-system's package management system.  Installing and updating are then
-straightforward and automatic.  
-
-Thanks to Axel Kohlmeyer (Temple U, akohlmey at gmail.com) for setting
-up this RPM capability.
-
-:line
-
 Pre-built Ubuntu Linux executables :h4,link(ubuntu)
 
 A pre-built LAMMPS executable suitable for running on the latest
@@ -60,10 +37,10 @@ To install LAMMPS do the following once:
 
 sudo apt-get install lammps-daily :pre
 
-This downloads an executable named "lammps-daily" to your box, which
+This downloads an executable named "lmp_daily" to your box, which
 can then be used in the usual way to run input scripts:
 
-lammps-daily < in.lj :pre
+lmp_daily -in in.lj :pre
 
 To update LAMMPS to the most current version, do the following:
 
@@ -99,6 +76,80 @@ Ubuntu package capability.
 
 :line
 
+Pre-built Fedora Linux executables :h4,link(fedora)
+
+Pre-built LAMMPS packages for stable releases are available
+in the Fedora Linux distribution as of version 28. The packages
+can be installed via the dnf package manager. There are 3 basic
+varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+lammps-openmpi = OpenMPI MPI library) and for each support for
+linking to the C library interface (lammps-devel, lammps-mpich-devel,
+lammps-openmpi-devel), the header for compiling programs using
+the C library interface (lammps-headers), and the LAMMPS python
+module for Python 3. All packages can be installed at the same
+time and the name of the LAMMPS executable is {lmp} in all 3 cases.
+By default, {lmp} will refer to the serial executable, unless
+one of the MPI environment modules is loaded 
+("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
+Then the corresponding parallel LAMMPS executable is used.
+The same mechanism applies when loading the LAMMPS python module.
+
+To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
+
+dnf install lammps-openmpi
+module load mpi/openmpi-x86_64
+mpirun -np 2 lmp -in in.lj :pre
+
+The "dnf install" command is needed only once. In case of a new LAMMPS
+stable release, "dnf update" will automatically update to the newer
+version as soon at the RPM files are built and uploaded to the download
+mirrors. The "module load" command is needed once per (shell) session
+or shell terminal instance, unless it is automatically loaded from the
+shell profile.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in Fedora.
+
+:line
+
+Pre-built EPEL Linux executable :h4,link(epel)
+
+Pre-built LAMMPS packages for stable releases are available
+in the "Extra Packages for Enterprise Linux (EPEL) repository"_https://fedoraproject.org/wiki/EPEL
+for use with Red Hat Enterprise Linux (RHEL) or CentOS version 7.x
+and compatible Linux distributions. Names of packages, executable,
+and content are the same as described above for Fedora Linux.
+But RHEL/CentOS 7.x uses the "yum" package manager instead of "dnf"
+in Fedora 28.
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in EPEL.
+
+:line
+
+Pre-built OpenSuse Linux executable :h4,link(opensuse)
+
+A pre-built LAMMPS package for stable releases is available
+in OpenSuse as of Leap 15.0. You can install the package with:
+
+zypper install lammps :pre
+
+This includes support for OpenMPI. The name of the LAMMPS executable
+is {lmp}. Thus to run an input in parallel on 2 CPUs you would do:
+
+mpirun -np 2 lmp -in in.lj :pre
+
+Please use "lmp -help" to see which compilation options, packages,
+and styles are included in the binary.
+
+Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
+
+:line
+
 Pre-built Gentoo Linux executable :h4,link(gentoo)
 
 LAMMPS is part of Gentoo's main package tree and can be installed by

doc/src/Install_mac.txt

@@ -49,7 +49,8 @@ Lennard-Jones benchmark file:
 % brew test lammps -v :pre
 
 If you have problems with the installation you can post issues to
-"this link"_https://github.com/Homebrew/homebrew-science/issues.
+"this link"_homebrew.
 
 Thanks to Derek Thomas (derekt at cello.t.u-tokyo.ac.jp) for setting
 up the Homebrew capability.
+:link(homebrew,https://github.com/Homebrew/homebrew-science/issues)

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="18 Sep 2018 version">
+<META NAME="docnumber" CONTENT="24 Oct 2018 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
-18 Sep 2018 version :c,h2
+24 Oct 2018 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 

doc/src/Packages_details.txt

@@ -89,6 +89,7 @@ as contained in the file name.
 "USER-NETCDF"_#PKG-USER-NETCDF,
 "USER-OMP"_#PKG-USER-OMP,
 "USER-PHONON"_#PKG-USER-PHONON,
+"USER-PTM"_#PKG-USER-PTM,
 "USER-QMMM"_#PKG-USER-QMMM,
 "USER-QTB"_#PKG-USER-QTB,
 "USER-QUIP"_#PKG-USER-QUIP,
@@ -461,10 +462,10 @@ dynamics can be run with LAMMPS using density-functional tight-binding
 quantum forces calculated by LATTE.
 
 More information on LATTE can be found at this web site:
-"https://github.com/lanl/LATTE"_latte_home.  A brief technical
+"https://github.com/lanl/LATTE"_latte-home.  A brief technical
 description is given with the "fix latte"_fix_latte.html command.
 
-:link(latte_home,https://github.com/lanl/LATTE)
+:link(latte-home,https://github.com/lanl/LATTE)
 
 [Authors:] Christian Negre (LANL) and Steve Plimpton (Sandia).  LATTE
 itself is developed at Los Alamos National Laboratory by Marc
@@ -667,9 +668,9 @@ MSCG package :link(PKG-mscg),h4
 
 A "fix mscg"_fix_mscg.html command which can parameterize a
 Multi-Scale Coarse-Graining (MSCG) model using the open-source "MS-CG
-library"_mscg_home.
+library"_mscg-home.
 
-:link(mscg_home,https://github.com/uchicago-voth/MSCG-release)
+:link(mscg-home,https://github.com/uchicago-voth/MSCG-release)
 
 To use this package you must have the MS-CG library available on your
 system.
@@ -1007,11 +1008,11 @@ VORONOI package :link(PKG-VORONOI),h4
 [Contents:]
 
 A compute command which calculates the Voronoi tesselation of a
-collection of atoms by wrapping the "Voro++ library"_voro_home.  This
+collection of atoms by wrapping the "Voro++ library"_voro-home.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-:link(voro_home,http://math.lbl.gov/voro++)
+:link(voro-home,http://math.lbl.gov/voro++)
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -1519,7 +1520,7 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
 [Contents:]
 
 A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_MEAM package
+translated from the Fortran version in the "MEAM"_#PKG-MEAM package
 to plain C++. In contrast to the MEAM package, no library
 needs to be compiled and the pair style can be instantiated
 multiple times.
@@ -1600,7 +1601,7 @@ USER-MOLFILE package :link(PKG-USER-MOLFILE),h4
 [Contents:]
 
 A "dump molfile"_dump_molfile.html command which uses molfile plugins
-that are bundled with the "VMD"_vmd_home
+that are bundled with the "VMD"_vmd-home
 molecular visualization and analysis program, to enable LAMMPS to dump
 snapshots in formats compatible with various molecular simulation
 tools.
@@ -1652,11 +1653,11 @@ Note that NetCDF files can be directly visualized with the following
 tools:
 
 "Ovito"_ovito (Ovito supports the AMBER convention and the extensions mentioned above)
-"VMD"_vmd_home
+"VMD"_vmd-home
 "AtomEye"_atomeye (the libAtoms version of AtomEye contains a NetCDF reader not present in the standard distribution) :ul
 
 :link(ovito,http://www.ovito.org)
-:link(vmd_home,https://www.ks.uiuc.edu/Research/vmd/)
+:link(vmd-home,https://www.ks.uiuc.edu/Research/vmd/)
 :link(atomeye,http://www.libatoms.org)
 
 [Author:] Lars Pastewka (Karlsruhe Institute of Technology).
@@ -1744,6 +1745,25 @@ examples/USER/phonon :ul
 
 :line
 
+USER-PTM package :link(PKG-USER-PTM),h4
+
+[Contents:]
+
+A "compute ptm/atom"_compute_ptm_atom.html command that calculates
+local structure characterization using the Polyhedral Template
+Matching methodology.
+
+[Author:] Peter Mahler Larsen (MIT).
+
+[Supporting info:]
+
+src/USER-PTM: filenames not starting with ptm_ -> commands
+src/USER-PTM: filenames starting with ptm_ -> supporting code
+src/USER-PTM/LICENSE
+"compute ptm/atom"_compute_ptm_atom.html :ul
+
+:line
+
 USER-QMMM package :link(PKG-USER-QMMM),h4
 
 [Contents:]

doc/src/Packages_user.txt

@@ -62,6 +62,7 @@ Package, Description, Doc page, Example, Library
 "USER-NETCDF"_Packages_details.html#PKG-USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, n/a, ext
 "USER-OMP"_Packages_details.html#PKG-USER-OMP, OpenMP-enabled styles,"Speed omp"_Speed_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-PHONON"_Packages_details.html#PKG-USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, no
+"USER-PTM"_Packages_details.html#PKG-USER-PTM, Polyhedral Template Matching,"compute ptm/atom"_compute_ptm_atom.html, n/a, no
 "USER-QMMM"_Packages_details.html#PKG-USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_Packages_details.html#PKG-USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, no
 "USER-QUIP"_Packages_details.html#PKG-USER-QUIP, QUIP/libatoms interface,"pair_style quip"_pair_quip.html, USER/quip, ext
@@ -73,3 +74,4 @@ Package, Description, Doc page, Example, Library
 "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)
+:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)

doc/src/Run_options.txt

@@ -24,8 +24,9 @@ letter abbreviation can be used:
 "-p or -partition"_#partition
 "-pl or -plog"_#plog
 "-ps or -pscreen"_#pscreen
-"-r or -restart"_#restart
 "-ro or -reorder"_#reorder
+"-r2data or -restart2data"_#restart2data
+"-r2dump or -restart2dump"_#restart2dump
 "-sc or -screen"_#screen
 "-sf or -suffix"_#suffix
 "-v or -var"_#var :ul
@@ -280,34 +281,6 @@ specified by the -screen command-line option.
 
 :line
 
-[-restart restartfile {remap} datafile keyword value ...] :link(restart)
-
-Convert the restart file into a data file and immediately exit.  This
-is the same operation as if the following 2-line input script were
-run:
-
-read_restart restartfile {remap}
-write_data datafile keyword value ... :pre
-
-Note that the specified restartfile and datafile can have wild-card
-characters ("*",%") as described by the
-"read_restart"_read_restart.html and "write_data"_write_data.html
-commands.  But a filename such as file.* will need to be enclosed in
-quotes to avoid shell expansion of the "*" character.
-
-Note that following restartfile, the optional flag {remap} can be
-used.  This has the same effect as adding it to the
-"read_restart"_read_restart.html command, as explained on its doc
-page.  This is only useful if the reading of the restart file triggers
-an error that atoms have been lost.  In that case, use of the remap
-flag should allow the data file to still be produced.
-
-Also note that following datafile, the same optional keyword/value
-pairs can be listed as used by the "write_data"_write_data.html
-command.
-
-:line
-
 [-reorder] :link(reorder)
 
 This option has 2 forms:
@@ -381,6 +354,77 @@ the LAMMPS simulation domain.
 
 :line
 
+[-restart2data restartfile (remap) datafile keyword value ...] :link(restart2data)
+
+Convert the restart file into a data file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+read_restart restartfile (remap)
+write_data datafile keyword value ... :pre
+
+Note that the specified restartfile and/or datafile can have the
+wild-card character "*".  The restartfile can also have the wild-card
+character "%".  The meaning of these characters is explained on the
+"read_restart"_read_restart.html and "write_data"_write_data.html doc
+pages.  The use of "%" means that a parallel restart file can be read.
+Note that a filename such as file.* will need to be enclosed in quotes
+to avoid shell expansion of the "*" character.
+
+Note that following restartfile, the optional word "remap" can be
+used.  This has the effect of adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page.  This is useful if reading the restart file triggers an error
+that atoms have been lost.  In that case, use of the remap flag should
+allow the data file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+datafile keyword value ... :pre
+
+is identical to the arguments of the "write_data"_write_data.html
+command.  See its doc page for details.  This includes its
+optional keyword/value settings.
+
+:line
+
+[-restart2dump restartfile {remap} group-ID dumpstyle dumpfile arg1 arg2 ...] :link(restart2dump)
+
+Convert the restart file into a dump file and immediately exit.  This
+is the same operation as if the following 2-line input script were
+run:
+
+read_restart restartfile (remap)
+write_dump group-ID dumpstyle dumpfile arg1 arg2 ... :pre
+
+Note that the specified restartfile and dumpfile can have wild-card
+characters ("*","%") as explained on the
+"read_restart"_read_restart.html and "write_dump"_write_dump.html doc
+pages.  The use of "%" means that a parallel restart file and/or
+parallel dump file can be read and/or written.  Note that a filename
+such as file.* will need to be enclosed in quotes to avoid shell
+expansion of the "*" character.
+
+Note that following restartfile, the optional word "remap" can be
+used.  This has the effect as adding it to the
+"read_restart"_read_restart.html command, as explained on its doc
+page.  This is useful if reading the restart file triggers an error
+that atoms have been lost.  In that case, use of the remap flag should
+allow the dump file to still be produced.
+
+The syntax following restartfile (or remap), namely
+
+group-ID dumpstyle dumpfile arg1 arg2 ... :pre
+
+is identical to the arguments of the "write_dump"_write_dump.html
+command.  See its doc page for details.  This includes what per-atom
+fields are written to the dump file and optional dump_modify settings,
+including ones that affect how parallel dump files are written, e.g.
+the {nfile} and {fileper} keywords.  See the
+"dump_modify"_dump_modify.html doc page for details.
+
+:line
+
 [-screen file] :link(screen)
 
 Specify a file for LAMMPS to write its screen information to.  In

doc/src/Speed_intel.txt

@@ -499,7 +499,7 @@ MPI task.
 When offloading to a coprocessor, "hybrid"_pair_hybrid.html styles
 that require skip lists for neighbor builds cannot be offloaded.
 Using "hybrid/overlay"_pair_hybrid.html is allowed.  Only one intel
-accelerated style may be used with hybrid styles.
+accelerated style may be used with hybrid styles when offloading.
 "Special_bonds"_special_bonds.html exclusion lists are not currently
 supported with offload, however, the same effect can often be
 accomplished by setting cutoffs for excluded atom types to 0.  None of

doc/src/angle_class2.txt

@@ -7,8 +7,8 @@
 :line
 
 angle_style class2 command :h3
-angle_style class2/omp command :h3
 angle_style class2/kk command :h3
+angle_style class2/omp command :h3
 angle_style class2/p6 command :h3
 
 [Syntax:]

doc/src/angle_cosine_buck6d.txt

@@ -38,10 +38,10 @@ Theta0 (degrees) :ul
 Theta0 is specified in degrees, but LAMMPS converts it to radians 
 internally.
 
-Additional to the cosine term the {cosine/buck6d} angle style computes 
-the short range (vdW) interaction belonging to the 
-"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of 
-the angle.  For this reason this angle style only works in combination
+Additional to the cosine term the {cosine/buck6d} angle style computes
+the short range (vdW) interaction belonging to the
+"pair_buck6d"_pair_buck6d_coul_gauss.html between the end atoms of the
+angle.  For this reason this angle style only works in combination
 with the "pair_buck6d"_pair_buck6d_coul_gauss.html styles and needs
 the "special_bonds"_special_bonds.html 1-3 interactions to be weighted
 0.0 to prevent double counting.

doc/src/angle_sdk.txt

@@ -7,6 +7,7 @@
 :line
 
 angle_style sdk command :h3
+angle_style sdk/omp command :h3
 
 [Syntax:]
 
@@ -43,6 +44,30 @@ internally; hence the units of K are in energy/radian^2.
 The also required {lj/sdk} parameters will be extracted automatically
 from the pair_style.
 
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restrictions:]
 
 This angle style can only be used if LAMMPS was built with the

doc/src/angle_style.txt

@@ -62,18 +62,27 @@ which are included in the LAMMPS distribution.  The full list of all
 angle styles are is on the "Commands bond"_Commands_bond.html#angle
 doc page.
 
-"angle_style none"_angle_none.html - turn off angle interactions
-"angle_style zero"_angle_zero.html - topology but no interactions
-"angle_style hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
+"none"_angle_none.html - turn off angle interactions
+"zero"_angle_zero.html - topology but no interactions
+"hybrid"_angle_hybrid.html - define multiple styles of angle interactions :ul
 
-"angle_style charmm"_angle_charmm.html - CHARMM angle
-"angle_style class2"_angle_class2.html - COMPASS (class 2) angle
-"angle_style cosine"_angle_cosine.html - cosine angle potential
-"angle_style cosine/delta"_angle_cosine_delta.html - difference of cosines angle potential
-"angle_style cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
-"angle_style cosine/squared"_angle_cosine_squared.html - cosine squared angle potential
-"angle_style harmonic"_angle_harmonic.html - harmonic angle
-"angle_style table"_angle_table.html - tabulated by angle :ul
+"charmm"_angle_charmm.html - CHARMM angle
+"class2"_angle_class2.html - COMPASS (class 2) angle
+"class2/p6"_angle_class2.html - COMPASS (class 2) angle expanded to 6th order
+"cosine"_angle_cosine.html - angle with cosine term
+"cosine/buck6d"_angle_cosine_buck6d.html - same as cosine with Buckingham term between 1-3 atoms
+"cosine/delta"_angle_cosine_delta.html - angle with difference of cosines
+"cosine/periodic"_angle_cosine_periodic.html - DREIDING angle
+"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
+"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
+"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
 
 :line
 

doc/src/balance.txt

@@ -516,3 +516,4 @@ appear in {dimstr} for the {shift} style.
 "fix balance"_fix_balance.html
 
 [Default:] none
+:link(pizza,http://pizza.sandia.gov)

doc/src/bond_oxdna.txt

@@ -28,34 +28,44 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
 
 :c,image(Eqs/bond_oxdna_fene.jpg)
 
-to define a modified finite extensible nonlinear elastic (FENE) potential
-"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
-in the oxDNA force field for coarse-grained modelling of DNA.
+to define a modified finite extensible nonlinear elastic (FENE)
+potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the
+phosphate backbone in the oxDNA force field for coarse-grained
+modelling of DNA.
 
 The following coefficients must be defined for the bond type via the
-"bond_coeff"_bond_coeff.html command as given in the above example, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
+"bond_coeff"_bond_coeff.html command as given in the above example, 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)
 Delta (distance)
 r0 (distance) :ul
 
-NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
-for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
-"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
-style {oxdna2/dh} have to be defined.
-The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+NOTE: The oxDNA bond style has to be used together with the
+corresponding oxDNA pair styles for excluded volume interaction
+{oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and
+coaxial stacking interaction {oxdna/coaxstk} as well as
+hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
+"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2
+"(Snodin)"_#oxdna2 bond style the analogous pair styles and an
+additional Debye-Hueckel pair style {oxdna2/dh} have to be defined.
+The coefficients in the above example have to be kept fixed and cannot
+be changed without reparametrizing the entire model.
 
-Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
-A simple python setup tool which creates single straight or helical DNA strands,
-DNA duplexes or arrays of DNA duplexes can be found in examples/USER/cgdna/util/.
+Example input and data files for DNA duplexes can be found in
+examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.  A simple python
+setup tool which creates single straight or helical DNA strands, DNA
+duplexes or arrays of DNA duplexes can be found in
+examples/USER/cgdna/util/.
 
-Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in any publication that uses this implementation. 
-The article contains more information on the model, the structure of the input file, the setup tool
-and the performance of the LAMMPS-implementation of oxDNA.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
+Please cite "(Henrich)"_#Henrich2 and the relevant oxDNA articles in
+any publication that uses this implementation.  The article contains
+more information on the model, the structure of the input file, the
+setup tool and the performance of the LAMMPS-implementation of oxDNA.
+The preprint version of the article can be found
+"here"_PDF/USER-CGDNA.pdf.
 
 :line
 
@@ -65,20 +75,25 @@ This bond style can only be used if LAMMPS was built with the
 USER-CGDNA package and the MOLECULE and ASPHERE package.  See the
 "Build package"_Build_package.html doc page for more info.
 
-
 [Related commands:]
 
-"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
+"pair_style oxdna/excv"_pair_oxdna.html, "pair_style
+oxdna2/excv"_pair_oxdna2.html, "fix
+nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"bond_coeff"_bond_coeff.html
 
 [Default:] none
 
 :line
 
 :link(Henrich2)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
+[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk,
+T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
 :link(oxdna_fene)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
+[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye,
+J. Chem. Phys. 134, 085101 (2011).
 
 :link(oxdna2)
-[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
+[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al.,
+J. Chem. Phys. 142, 234901 (2015).

doc/src/bond_style.txt

@@ -69,18 +69,23 @@ Note that there are also additional bond styles submitted by users
 which are included in the LAMMPS distribution.  The full list of all
 bond styles is on the "Commands bond"_Commands_bond.html doc page.
 
-"bond_style none"_bond_none.html - turn off bonded interactions
-"bond_style zero"_bond_zero.html - topology but no interactions
-"bond_style hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
+"none"_bond_none.html - turn off bonded interactions
+"zero"_bond_zero.html - topology but no interactions
+"hybrid"_bond_hybrid.html - define multiple styles of bond interactions :ul
 
-"bond_style class2"_bond_class2.html - COMPASS (class 2) bond
-"bond_style fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
-"bond_style fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
-"bond_style harmonic"_bond_harmonic.html - harmonic bond
-"bond_style morse"_bond_morse.html - Morse bond
-"bond_style nonlinear"_bond_nonlinear.html - nonlinear bond
-"bond_style quartic"_bond_quartic.html - breakable quartic bond
-"bond_style table"_bond_table.html - tabulated by bond length :ul
+"class2"_bond_class2.html - COMPASS (class 2) bond
+"fene"_bond_fene.html - FENE (finite-extensible non-linear elastic) bond
+"fene/expand"_bond_fene_expand.html - FENE bonds with variable size particles
+"gromos"_bond_gromos.html - GROMOS force field bond
+"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
+"morse"_bond_morse.html - Morse bond
+"nonlinear"_bond_nonlinear.html - nonlinear bond
+"oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling
+"oxdna2/fene"_bond_oxdna.html - same as oxdna but used with different pair styles 
+"quartic"_bond_quartic.html - breakable quartic bond
+"table"_bond_table.html - tabulated by bond length :ul
 
 :line
 

doc/src/compute.txt

@@ -175,9 +175,13 @@ The individual style names on the "Commands
 compute"_Commands_compute.html doc page are followed by one or more of
 (g,i,k,o,t) to indicate which accelerated styles exist.
 
+"ackland/atom"_compute_ackland_atom.html - 
 "aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
+"angle"_compute_angle.html - 
+"angle/local"_compute_angle_local.html - 
 "angle/local"_compute_bond_local.html - theta and energy of each angle
 "angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
+"basal/atom"_compute_basal_atom.html - 
 "body/local"_compute_body_local.html - attributes of body sub-particles
 "bond"_compute_bond.html - values computed by a bond style
 "bond/local"_compute_bond_local.html - distance and energy of each bond
@@ -186,30 +190,48 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
 "cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
 "cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
+"cnp/atom"_compute_cnp_atom.html - 
 "com"_compute_com.html - center-of-mass of group of atoms
 "com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
 "contact/atom"_compute_contact_atom.html - contact count for each spherical particle
 "coord/atom"_compute_coord_atom.html - coordination number for each atom
 "damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
+"dihedral"_compute_dihedral.html - 
 "dihedral/local"_compute_dihedral_local.html - angle of each dihedral
 "dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
+"dipole/chunk"_compute_dipole_chunk.html - 
 "displace/atom"_compute_displace_atom.html - displacement of each atom
+"dpd"_compute_dpd.html - 
+"dpd/atom"_compute_dpd_atom.html - 
+"edpd/temp/atom"_compute_edpd_temp_atom.html - 
+"entropy/atom"_compute_entropy_atom.html - 
 "erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
 "erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
 "erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
 "erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html - 
 "event/displace"_compute_event_displace.html - detect event on atom displacement
+"fep"_compute_fep.html - 
+"force/tally"_compute_tally.html - 
 "fragment/atom"_compute_cluster_atom.html - fragment ID for each atom
+"global/atom"_compute_global_atom.html - 
 "group/group"_compute_group_group.html - energy/force between two groups of atoms
 "gyration"_compute_gyration.html - radius of gyration of group of atoms
 "gyration/chunk"_compute_gyration_chunk.html - radius of gyration for each chunk
 "heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
+"heat/flux/tally"_compute_tally.html - 
 "hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
+"improper"_compute_improper.html - 
 "improper/local"_compute_improper_local.html - angle of each improper
 "inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
 "ke"_compute_ke.html - translational kinetic energy
 "ke/atom"_compute_ke_atom.html - kinetic energy for each atom
+"ke/atom/eff"_compute_ke_atom_eff.html - 
+"ke/eff"_compute_ke_eff.html - 
 "ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
+"meso/e/atom"_compute_meso_e_atom.html - 
+"meso/rho/atom"_compute_meso_rho_atom.html - 
+"meso/t/atom"_compute_meso_t_atom.html - 
 "msd"_compute_msd.html - mean-squared displacement of group of atoms
 "msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
 "msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
@@ -219,37 +241,77 @@ compute"_Commands_compute.html doc page are followed by one or more of
 "pair/local"_compute_pair_local.html - distance/energy/force of each pairwise interaction
 "pe"_compute_pe.html - potential energy
 "pe/atom"_compute_pe_atom.html - potential energy for each atom
+"pe/mol/tally"_compute_tally.html - 
+"pe/tally"_compute_tally.html - 
 "plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
 "pressure"_compute_pressure.html - total pressure and pressure tensor
+"pressure/cylinder"_compute_pressure_cylinder.html - 
+"pressure/uef"_compute_pressure_uef.html - 
 "property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
-"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
 "property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
+"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
+"ptm/atom"_compute_ptm_atom.html - 
 "rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
 "reduce"_compute_reduce.html - combine per-atom quantities into a single global value
 "reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
 "reduce/region"_compute_reduce.html - same as compute reduce, within a region
 "rigid/local"_compute_rigid_local.html - extract rigid body attributes
+"saed"_compute_saed.html - 
 "slice"_compute_slice.html - extract values from global vector or array
+"smd/contact/radius"_compute_smd_contact_radius.html - 
+"smd/damage"_compute_smd_damage.html - 
+"smd/hourglass/error"_compute_smd_hourglass_error.html - 
+"smd/internal/energy"_compute_smd_internal_energy.html - 
+"smd/plastic/strain"_compute_smd_plastic_strain.html - 
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - 
+"smd/rho"_compute_smd_rho.html - 
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - 
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html - 
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html - 
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html - 
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html - 
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html - 
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html - 
+"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
+"smd/triangle/vertices"_compute_smd_triangle_vertices.html - 
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html - 
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html - 
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html - 
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html - 
+"smd/vol"_compute_smd_vol.html - 
 "sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
 "snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
 "snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
+"spin"_compute_spin.html - 
 "stress/atom"_compute_stress_atom.html - stress tensor for each atom
+"stress/mop"_compute_stress_mop.html - 
+"stress/mop/profile"_compute_stress_mop.html - 
+"stress/tally"_compute_tally.html - 
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html - 
 "temp"_compute_temp.html - temperature of group of atoms
 "temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
 "temp/body"_compute_temp_body.html - temperature of body particles
 "temp/chunk"_compute_temp_chunk.html - temperature of each chunk
 "temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
+"temp/cs"_compute_temp_cs.html - 
 "temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
+"temp/deform/eff"_compute_temp_deform_eff.html - 
+"temp/drude"_compute_temp_drude.html - 
+"temp/eff"_compute_temp_eff.html - 
 "temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
 "temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
 "temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
 "temp/region"_compute_temp_region.html - temperature of a region of atoms
+"temp/region/eff"_compute_temp_region_eff.html - 
+"temp/rotate"_compute_temp_rotate.html - 
 "temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
+"temp/uef"_compute_temp_uef.html - 
 "ti"_compute_ti.html - thermodynamic integration free energy values
 "torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
 "vacf"_compute_vacf.html - velocity-autocorrelation function of group of atoms
 "vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
-"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom :ul
+"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
+"xrd"_compute_xrd.html - :ul
 
 [Restrictions:] none
 

doc/src/compute_adf.txt

@@ -0,0 +1,213 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute adf command :h3
+
+[Syntax:]
+
+compute ID group-ID adf Nbin itype1 jtype1 ktype1 Rjinner1 Rjouter1 Rkinner1 Rkouter1 ... :pre
+
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+adf = style name of this compute command :l
+Nbin = number of ADF bins :l
+itypeN = central atom type for Nth ADF histogram (see asterisk form below) :l
+jtypeN = J atom type for Nth ADF histogram (see asterisk form below) :l
+ktypeN = K atom type for Nth ADF histogram (see asterisk form below) :l
+RjinnerN =  inner radius of J atom shell for Nth ADF histogram (distance units) :l
+RjouterN =  outer radius of J atom shell for Nth ADF histogram (distance units) :l
+RkinnerN = inner radius of K atom shell for Nth ADF histogram (distance units) :l
+RkouterN =  outer radius of K atom shell for Nth ADF histogram (distance units) :l
+
+zero or one keyword/value pairs may be appended :l
+keyword = {ordinate} :l
+  {ordinate} value = {degree} or {radian} or {cosine}
+    Choose the ordinate parameter for the histogram :pre
+:ule
+
+[Examples:]
+
+compute 1 fluid adf 32 1 1 1 0.0 1.2 0.0 1.2 &
+                       1 1 2 0.0 1.2 0.0 1.5 &
+                       1 2 2 0.0 1.5 0.0 1.5 & 
+                       2 1 1 0.0 1.2 0.0 1.2 &
+                       2 1 2 0.0 1.5 2.0 3.5 &
+                       2 2 2 2.0 3.5 2.0 3.5  
+compute 1 fluid adf 32 1*2 1*2 1*2 0.5 3.5
+compute 1 fluid adf 32 :pre
+
+[Description:]
+
+Define a computation that calculates one or more angular distribution functions
+(ADF) for a group of particles.  Each ADF is calculated in histogram form 
+by measuring the angle formed by a central atom and two neighbor atoms and
+binning these angles into {Nbin} bins.
+Only neighbors for which {Rinner} < {R} < {Router} are counted, where
+{Rinner} and {Router} are specified separately for the first and second
+neighbor atom in each requested ADF. 
+
+NOTE: If you have a bonded system, then the settings of
+"special_bonds"_special_bonds.html command can remove pairwise
+interactions between atoms in the same bond, angle, or dihedral.  This
+is the default setting for the "special_bonds"_special_bonds.html
+command, and means those pairwise interactions do not appear in the
+neighbor list.  Because this fix uses a neighbor list, it also means
+those pairs will not be included in the ADF. This does not apply when
+using long-range coulomb interactions ({coul/long}, {coul/msm},
+{coul/wolf} or similar.  One way to get around this would be to set
+special_bond scaling factors to very tiny numbers that are not exactly
+zero (e.g. 1.0e-50). Another workaround is to write a dump file, and
+use the "rerun"_rerun.html command to compute the ADF for snapshots in
+the dump file.  The rerun script can use a
+"special_bonds"_special_bonds.html command that includes all pairs in
+the neighbor list.
+
+NOTE: If you request any outer cutoff {Router} > force cutoff, or if no 
+pair style is defined,  e.g. the "rerun"_rerun.html command is being used to
+post-process a dump file of snapshots you must insure ghost atom information 
+out to the largest value of {Router} + {skin} is communicated, via the 
+"comm_modify cutoff"_comm_modify.html command, else the ADF computation 
+cannot be performed, and LAMMPS will give an error message.  The {skin} value 
+is what is specified with the "neighbor"_neighbor.html command.  
+
+The {itypeN},{jtypeN},{ktypeN} settings can be specified in one of two
+ways.  An explicit numeric value can be used, as in the 1st example
+above.  Or a wild-card asterisk can be used to specify a range of atom
+types as in the 2nd example above.  
+This takes the form "*" or "*n" or "n*" or "m*n".  If N = the
+number of atom types, then an asterisk with no numeric values means
+all types from 1 to N.  A leading asterisk means all types from 1 to n
+(inclusive).  A trailing asterisk means all types from n to N
+(inclusive).  A middle asterisk means all types from m to n
+(inclusive).
+
+If {itypeN}, {jtypeN}, and {ktypeN} are single values, as in the 1st example
+above, this means that the ADF is computed where atoms of type {itypeN}
+are the central atom, and neighbor atoms of type {jtypeN} and {ktypeN}
+are forming the angle.  If any of {itypeN}, {jtypeN}, or {ktypeN} 
+represent a range of values via
+the wild-card asterisk, as in the 2nd example above, this means that the
+ADF is computed where atoms of any of the range of types represented
+by {itypeN} are the central atom, and the angle is formed by two neighbors,
+one neighbor in the range of types represented by {jtypeN} and another neighbor 
+in the range of types represented by {ktypeN}. 
+
+If no {itypeN}, {jtypeN}, {ktypeN} settings are specified, then
+LAMMPS will generate a single ADF for all atoms in the group.
+The inner cutoff is set to zero and the outer cutoff is set
+to the force cutoff. If no pair_style is specified, there is no
+force cutoff and LAMMPS will give an error message. Note that
+in most cases, generating an ADF for all atoms is not a good thing.
+Such an ADF is both uninformative and
+extremely expensive to compute.  For example, with liquid water
+with a 10 A force cutoff, there are 80,000 angles per atom.
+In addition, most of the interesting angular structure occurs for
+neighbors that are the closest to the central atom, involving 
+just a few dozen angles.
+
+Angles for each ADF are generated by double-looping over the list of 
+neighbors of each central atom I, 
+just as they would be in the force calculation for 
+a threebody potential such as "Stillinger-Weber"_pair_sw.html.  
+The angle formed by central atom I and neighbor atoms J and K is included in an
+ADF if the following criteria are met:
+
+atoms I,J,K are all in the specified compute group
+the distance between atoms I,J is between Rjinner and Rjouter
+the distance between atoms I,K is between Rkinner and Rkouter
+the type of the I atom matches itypeN (one or a range of types)
+atoms I,J,K are distinct
+the type of the J atom matches jtypeN (one or a range of types) 
+the type of the K atom matches ktypeN (one or a range of types) :ul
+
+Each unique angle satisfying the above criteria is counted only once, regardless
+of whether either or both of the neighbor atoms making up the
+angle appear in both the J and K lists. 
+It is OK if a particular angle is included in more than
+one individual histogram, due to the way the {itypeN}, {jtypeN}, {ktypeN}
+arguments are specified.
+
+The first ADF value for a bin is calculated from the histogram count by
+dividing by the total number of triples satisfying the criteria,
+so that the integral of the ADF w.r.t. angle is 1, i.e. the ADF
+is a probability density function.
+
+The second ADF value is reported as a cumulative sum of
+all bins up to the current bins, averaged
+over atoms of type {itypeN}. It represents the
+number of angles per central atom with angle less
+than or equal to the angle of the current bin,
+analogous to the coordination
+number radial distribution function.
+
+The {ordinate} optional keyword determines
+whether the bins are of uniform angular size from zero
+to 180 ({degree}), zero to Pi ({radian}), or the 
+cosine of the angle uniform in the range \[-1,1\] ({cosine}).
+{cosine} has the advantage of eliminating the {acos()} function
+call, which speeds up the compute by 2-3x, and it is also preferred
+on physical grounds, because the for uniformly distributed particles 
+in 3D, the angular probability density w.r.t dtheta is
+sin(theta)/2, while for d(cos(theta)), it is 1/2,  
+Regardless of which ordinate is chosen, the first column of ADF 
+values is normalized w.r.t. the range of that ordinate, so that 
+the integral is 1.
+
+The simplest way to output the results of the compute adf calculation
+to a file is to use the "fix ave/time"_fix_ave_time.html command, for
+example:
+
+compute myADF all adf 32 2 2 2 0.5 3.5 0.5 3.5
+fix 1 all ave/time 100 1 100 c_myADF\[*\] file tmp.adf mode vector :pre
+
+[Output info:]
+
+This compute calculates a global array with the number of rows =
+{Nbins}, and the number of columns = 1 + 2*Ntriples, where Ntriples is the
+number of I,J,K triples specified.  The first column has the bin
+coordinate (angle-related ordinate at midpoint of bin). Each subsequent column has
+the two ADF values for a specific set of ({itypeN},{jtypeN},{ktypeN}) 
+interactions, as described above.  These values can be used
+by any command that uses a global values from a compute as input.  See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
+
+The array values calculated by this compute are all "intensive".
+
+The first column of array values is the angle-related ordinate, either
+the angle in degrees or radians, or the cosine of the angle.  Each
+subsequent pair of columns gives the first and second kinds of ADF
+for a specific set of ({itypeN},{jtypeN},{ktypeN}). The values 
+in the first ADF column are normalized numbers >= 0.0,
+whose integral w.r.t. the ordinate is 1,
+i.e. the first ADF is a normalized probability distribution. 
+The values in the second ADF column are also numbers >= 0.0.
+They are the cumulative density distribution of angles per atom.
+By definition, this ADF is monotonically increasing from zero to
+a maximum value equal to the average total number of
+angles per atom satisfying the ADF criteria. 
+
+[Restrictions:]
+
+The ADF is not computed for neighbors outside the force cutoff,
+since processors (in parallel) don't know about atom coordinates for
+atoms further away than that distance.  If you want an ADF for larger
+distances, you can use the "rerun"_rerun.html command to post-process
+a dump file and set the cutoff for the potential to be longer in the
+rerun script.  Note that in the rerun context, the force cutoff is
+arbitrary, since you aren't running dynamics and thus are not changing
+your model.  
+
+[Related commands:]
+
+"compute rdf"_compute_rdf.html, "fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
+
+[Default:]
+
+The keyword default is ordinate = degree.
+
+

doc/src/compute_msd_chunk.txt

@@ -90,12 +90,12 @@ This is so that the fix this compute creates to store per-chunk
 quantities will also have the same ID, and thus be initialized
 correctly with chunk reference positions from the restart file.
 
-The simplest way to output the results of the compute com/msd
+The simplest way to output the results of the compute msd/chunk
 calculation to a file is to use the "fix ave/time"_fix_ave_time.html
 command, for example:
 
 compute cc1 all chunk/atom molecule
-compute myChunk all com/msd cc1
+compute myChunk all msd/chunk cc1
 fix 1 all ave/time 100 1 100 c_myChunk\[*\] file tmp.out mode vector :pre
 
 [Output info:]

doc/src/compute_pair.txt

@@ -10,17 +10,20 @@ compute pair command :h3
 
 [Syntax:]
 
-compute ID group-ID pair pstyle evalue :pre
+compute ID group-ID pair pstyle \[nstyle\] \[evalue\]  :pre
 
-ID, group-ID are documented in "compute"_compute.html command
-pair = style name of this compute command
-pstyle = style name of a pair style that calculates additional values
-evalue = {epair} or {evdwl} or {ecoul} or blank (optional setting) :ul
+ID, group-ID are documented in "compute"_compute.html command :ulb,l
+pair = style name of this compute command :l
+pstyle = style name of a pair style that calculates additional values :l
+nsub = {n}-instance of a substyle, if a pair style is used multiple times in a hybrid style :l
+{evalue} = {epair} or {evdwl} or {ecoul} or blank (optional) :l
+:ule
 
 [Examples:]
 
 compute 1 all pair gauss
 compute 1 all pair lj/cut/coul/cut ecoul
+compute 1 all pair tersoff 2 epair
 compute 1 all pair reax :pre
 
 [Description:]
@@ -33,15 +36,19 @@ NOTE: The group specified for this command is [ignored].
 
 The specified {pstyle} must be a pair style used in your simulation
 either by itself or as a sub-style in a "pair_style hybrid or
-hybrid/overlay"_pair_hybrid.html command.
+hybrid/overlay"_pair_hybrid.html command. If the sub-style is
+used more than once, an additional number {nsub} has to be specified
+in order to choose which instance of the sub-style will be used by
+the compute. Not specifying the number in this case will cause the
+compute to fail.
 
-The {evalue} setting is optional; it may be left off the command.  All
+The {evalue} setting is optional.  All
 pair styles tally a potential energy {epair} which may be broken into
 two parts: {evdwl} and {ecoul} such that {epair} = {evdwl} + {ecoul}.
 If the pair style calculates Coulombic interactions, their energy will
 be tallied in {ecoul}.  Everything else (whether it is a Lennard-Jones
 style van der Waals interaction or not) is tallied in {evdwl}.  If
-{evalue} is specified as {epair} or left out, then {epair} is stored
+{evalue} is blank or specified as {epair}, then {epair} is stored
 as a global scalar by this compute.  This is useful when using
 "pair_style hybrid"_pair_hybrid.html if you want to know the portion
 of the total energy contributed by one sub-style.  If {evalue} is
@@ -82,4 +89,4 @@ the doc page for the pair style for details.
 
 [Default:]
 
-The default for {evalue} is {epair}.
+The keyword defaults are {evalue} = {epair}, nsub = 0.

doc/src/compute_pressure_cylinder.txt

@@ -0,0 +1,81 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute pressure/cylinder command :h3
+
+[Syntax:]
+
+compute ID group-ID pressure/cylinder zlo zhi Rmax bin_width :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+pressure/cylinder = style name of this compute command
+zlo = minimum z-boundary for cylinder
+zhi = maximum z-boundary for cylinder
+Rmax = maximum radius to perform calculation to
+bin_width = width of radial bins to use for calculation :ul
+
+[Examples:]
+
+compute 1 all pressure/cylinder -10.0 10.0 15.0 0.25 :pre
+
+[Description:]
+
+Define a computation that calculates the pressure tensor of a system in
+cylindrical coordinates, as discussed in "(Addington)"_#Addington1.
+This is useful for systems with a single axis of rotational symmetry,
+such as cylindrical micelles or carbon nanotubes. The compute splits the
+system into radial, cylindrical-shell-type bins of width bin_width,
+centered at x=0,y=0, and calculates the radial (P_rhorho), azimuthal
+(P_phiphi), and axial (P_zz) components of the configurational pressure
+tensor. The local density is also calculated for each bin, so that the
+true pressure can be recovered as P_kin+P_conf=density*k*T+P_conf.  The
+output is a global array with 5 columns; one each for bin radius, local
+number density, P_rhorho, P_phiphi, and P_zz. The number of rows is
+governed by the values of Rmax and bin_width. Pressure tensor values are
+output in pressure units.
+
+[Output info:]
+
+This compute calculates a global array with 5 columns and Rmax/bin_width
+rows. The output columns are: R (distance units), number density (inverse 
+volume units), configurational radial pressure (pressure units), 
+configurational azimuthal pressure (pressure units), and configurational
+axial pressure (pressure units).
+
+The values calculated by this compute are
+"intensive".  The pressure values will be in pressure
+"units"_units.html. The number density values will be in 
+inverse volume "units"_units.html.
+
+[Restrictions:]
+
+This compute currently calculates the pressure tensor contributions
+for pair styles only (i.e. no bond, angle, dihedral, etc. contributions
+and in the presence of bonded interactions, the result will be incorrect
+due to exclusions for special bonds)  and requires pair-wise force
+calculations not available for most manybody pair styles. K-space
+calculations are also excluded. Note that this pressure compute outputs
+the configurational terms only; the kinetic contribution is not included
+and may be calculated from the number density output by P_kin=density*k*T.
+
+This compute is part of the USER-MISC package.  It is only enabled
+if LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute temp"_compute_temp.html, "compute
+stress/atom"_compute_stress_atom.html,
+"thermo_style"_thermo_style.html,
+
+[Default:] none
+
+:line
+
+:link(Addington1)
+[(Addington)] Addington, Long, Gubbins, J Chem Phys, 149, 084109 (2018).

doc/src/compute_ptm_atom.txt

@@ -0,0 +1,121 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute ptm/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID ptm/atom structures threshold :pre
+
+ID, group-ID are documented in "compute"_compute.html command
+ptm/atom = style name of this compute command
+structures = structure types to search for
+threshold = lattice distortion threshold (RMSD) :ul
+
+[Examples:]
+
+compute 1 all ptm/atom default 0.1
+compute 1 all ptm/atom fcc-hcp-dcub-dhex 0.15
+compute 1 all ptm/atom all 0 :pre
+
+[Description:]
+
+Define a computation that determines the local lattice structure
+around an atom using the PTM (Polyhedral Template Matching) method.
+The PTM method is described in "(Larsen)"_#Larsen.
+
+Currently, there are seven lattice structures PTM recognizes:
+
+fcc = 1
+hcp = 2
+bcc = 3
+ico (icosahedral) = 4
+sc (simple cubic) = 5
+dcub (diamond cubic) = 6
+dhex (diamond hexagonal) = 7
+other = 8 :ul
+
+The value of the PTM structure will be 0 for atoms not in the specified
+compute group.  The choice of structures to search for can be specified using the "structures"
+argument, which is a hyphen-separated list of structure keywords.
+Two convenient pre-set options are provided:
+
+default: fcc-hcp-bcc-ico
+all: fcc-hcp-bcc-ico-sc-dcub-dhex :ul
+
+The 'default' setting detects the same structures as the Common Neighbor Analysis method.
+The 'all' setting searches for all structure types.  A small performance penalty is
+incurred for the diamond structures, so it is not recommended to use this option if
+it is known that the simulation does not contain diamond structures.
+
+
+PTM identifies structures using two steps.  First, a graph isomorphism test is used
+to identify potential structure matches.  Next, the deviation is computed between the
+local structure (in the simulation) and a template of the ideal lattice structure.
+The deviation is calculated as:
+
+:c,image(Eqs/ptm_rmsd.jpg)
+
+Here, u and v contain the coordinates of the local and ideal structures respectively,
+s is a scale factor, and Q is a rotation.  The best match is identified by the
+lowest RMSD value, using the optimal scaling, rotation, and correspondence between the
+points.
+
+The 'threshold' keyword sets an upper limit on the maximum permitted deviation before
+a local structure is identified as disordered.  Typical values are in the range 0.1-0.15,
+but larger values may be desirable at higher temperatures.
+A value of 0 is equivalent to infinity and can be used if no threshold is desired.
+
+
+The neighbor list needed to compute this quantity is constructed each
+time the calculation is performed (e.g. each time a snapshot of atoms
+is dumped).  Thus it can be inefficient to compute/dump this quantity
+too frequently or to have multiple compute/dump commands, each with a
+{ptm/atom} style.
+
+[Output info:]
+
+This compute calculates a per-atom arry, which can be accessed by
+any command that uses per-atom values from a compute as input.  See
+the "Howto output"_Howto_output.html doc page for an overview of
+LAMMPS output options.
+
+Results are stored in the per-atom array in the following order:
+
+type
+rmsd
+interatomic distance
+qw
+qx
+qy
+qw :ul
+
+The type is a number from 0 to 8.  The rmsd is a positive real number.
+The interatomic distance is computed from the scale factor in the RMSD equation.
+The (qw,qx,qy,qz) parameters represent the orientation of the local structure
+in quaternion form.  The reference coordinates for each template (from which the
+orientation is determined) can be found in the {ptm_constants.h} file in the PTM source directory.
+
+[Restrictions:]
+
+This fix is part of the USER-PTM package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"compute centro/atom"_compute_centro_atom.html
+"compute cna/atom"_compute_cna_atom.html
+
+[Default:] none
+
+:line
+
+:link(Larsen)
+[(Larsen)] Larsen, Schmidt, Schiøtz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
+

doc/src/compute_rdf.txt

@@ -191,7 +191,8 @@ via "compute_modify dynamic yes"_compute_modify.html
 
 [Related commands:]
 
-"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html
+"fix ave/time"_fix_ave_time.html, "compute_modify"_compute_modify.html,
+"compute adf"_compute_adf.html
 
 [Default:]
 

doc/src/compute_smd_triangle_vertices.txt

@@ -6,14 +6,14 @@
 
 :line
 
-compute smd/triangle/mesh/vertices :h3
+compute smd/triangle/vertices command :h3
 
 [Syntax:]
 
-compute ID group-ID smd/triangle/mesh/vertices :pre
+compute ID group-ID smd/triangle/vertices :pre
 
 ID, group-ID are documented in "compute"_compute.html command
-smd/triangle/mesh/vertices = style name of this compute command :ul
+smd/triangle/vertices = style name of this compute command :ul
 
 [Examples:]
 

doc/src/compute_spin.txt

@@ -10,14 +10,14 @@ compute spin command :h3
 
 [Syntax:]
 
-compute ID group-ID compute/spin :pre
+compute ID group-ID spin :pre
 
 ID, group-ID are documented in "compute"_compute.html command
-compute/spin = style name of this compute command :ul
+spin = style name of this compute command :ul
 
 [Examples:]
 
-compute out_mag all compute/spin :pre
+compute out_mag all spin :pre
 
 [Description:]
 
@@ -26,7 +26,8 @@ of atoms having spins.
 
 This compute calculates 6 magnetic quantities.
 
-The three first quantities are the x,y and z coordinates of the total magnetization.
+The three first quantities are the x,y and z coordinates of the total
+magnetization.
 
 The fourth quantity is the norm of the total magnetization.
 
@@ -39,7 +40,7 @@ The simplest way to output the results of the compute spin calculation
 is to define some of the quantities as variables, and to use the thermo and
 thermo_style commands, for example:
 
-compute out_mag		all compute/spin :pre
+compute out_mag		all spin :pre
 
 variable mag_z      	equal c_out_mag\[3\]
 variable mag_norm	equal c_out_mag\[4\]
@@ -53,7 +54,6 @@ the total magnetization, and the magnetic temperature. Three variables are
 assigned to those quantities. The thermo and thermo_style commands print them 
 every 10 timesteps.
 
-
 [Output info:]
 
 The array values are "intensive".  The array values will be in
@@ -68,7 +68,6 @@ has to be "spin" for this compute to be valid.
 
 [Related commands:] none
 
-
 [Default:] none
 
 :line

doc/src/computes.txt

@@ -6,6 +6,7 @@ Computes :h1
    :maxdepth: 1
 
    compute_ackland_atom
+   compute_adf
    compute_angle
    compute_angle_local
    compute_angmom_chunk
@@ -67,10 +68,12 @@ Computes :h1
    compute_pe_atom
    compute_plasticity_atom
    compute_pressure
+   compute_pressure_cylinder
    compute_pressure_uef
    compute_property_atom
    compute_property_chunk
    compute_property_local
+   compute_ptm_atom
    compute_rdf
    compute_reduce
    compute_reduce_chunk
@@ -91,7 +94,7 @@ Computes :h1
    compute_smd_tlsph_strain
    compute_smd_tlsph_strain_rate
    compute_smd_tlsph_stress
-   compute_smd_triangle_mesh_vertices
+   compute_smd_triangle_vertices
    compute_smd_ulsph_num_neighs
    compute_smd_ulsph_strain
    compute_smd_ulsph_strain_rate

doc/src/dihedral_nharmonic.txt

@@ -16,7 +16,7 @@ dihedral_style nharmonic :pre
 [Examples:]
 
 dihedral_style nharmonic
-dihedral_coeff 3 10.0 20.0 30.0 :pre
+dihedral_coeff * 3 10.0 20.0 30.0 :pre
 
 [Description:]
 

doc/src/dihedral_style.txt

@@ -85,16 +85,24 @@ which are included in the LAMMPS distribution.  The full list of all
 dihedral styles is on the "Commands bond"_Commands_bond.html#dihedral
 doc page.
 
-"dihedral_style none"_dihedral_none.html - turn off dihedral interactions
-"dihedral_style zero"_dihedral_zero.html - topology but no interactions
-"dihedral_style hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
+"none"_dihedral_none.html - turn off dihedral interactions
+"zero"_dihedral_zero.html - topology but no interactions
+"hybrid"_dihedral_hybrid.html - define multiple styles of dihedral interactions :ul
 
-"dihedral_style charmm"_dihedral_charmm.html - CHARMM dihedral
-"dihedral_style class2"_dihedral_class2.html - COMPASS (class 2) dihedral
-"dihedral_style harmonic"_dihedral_harmonic.html - harmonic dihedral
-"dihedral_style helix"_dihedral_helix.html - helix dihedral
-"dihedral_style multi/harmonic"_dihedral_multi_harmonic.html - multi-harmonic dihedral
-"dihedral_style opls"_dihedral_opls.html - OPLS dihedral :ul
+"charmm"_dihedral_charmm.html - CHARMM dihedral
+"charmmfsw"_dihedral_charmm.html - CHARMM dihedral with force switching
+"class2"_dihedral_class2.html - COMPASS (class 2) dihedral
+"cosine/shift/exp"_dihedral_cosine_shift_exp.html - dihedral with exponential in spring constant
+"fourier"_dihedral_fourier.html - dihedral with multiple cosine terms
+"harmonic"_dihedral_harmonic.html - harmonic dihedral
+"helix"_dihedral_helix.html - helix dihedral
+"multi/harmonic"_dihedral_multi_harmonic.html - dihedral with 5 harmonic terms
+"nharmonic"_dihedral_nharmonic.html - same as multi-harmonic with N terms
+"opls"_dihedral_opls.html - OPLS dihedral
+"quadratic"_dihedral_quadratic.html - dihedral with quadratic term in angle
+"spherical"_dihedral_spherical.html - dihedral which includes angle terms to avoid singularities
+"table"_dihedral_table.html - tabulated dihedral
+"table/cut"_dihedral_table_cut.html - tabulated dihedral with analytic cutoff :ul
 
 :line
 

doc/src/dump_h5md.txt

@@ -50,7 +50,7 @@ dump h5md1 all h5md 100 dump_h5md.h5 velocity author "John Doe" :pre
 [Description:]
 
 Dump a snapshot of atom coordinates every N timesteps in the
-"HDF5"_HDF5_ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
+"HDF5"_HDF5-ws based "H5MD"_h5md file format "(de Buyl)"_#h5md_cpc.
 HDF5 files are binary, portable and self-describing.  This dump style
 will write only one file, on the root node.
 
@@ -102,11 +102,11 @@ enabled if LAMMPS was built with that package. See the "Build
 package"_Build_package.html doc page for more info. It also requires
 (i) building the ch5md library provided with LAMMPS (See the "Build
 package"_Build_package.html doc page for more info.) and (ii) having
-the "HDF5"_HDF5_ws library installed (C bindings are sufficient) on
+the "HDF5"_HDF5-ws library installed (C bindings are sufficient) on
 your system.  The library ch5md is compiled with the h5cc wrapper
 provided by the HDF5 library.
 
-:link(HDF5_ws,http://www.hdfgroup.org/HDF5/)
+:link(HDF5-ws,http://www.hdfgroup.org/HDF5/)
 
 :line
 

doc/src/dump_image.txt

@@ -384,12 +384,7 @@ change this via the "dump_modify"_dump_modify.html command.
 :line
 
 The {fix} keyword can be used with a "fix"_fix.html that produces
-objects to be drawn.  An example is the "fix
-surface/global"_fix_surface_global.html command which can draw lines
-or triangles for 2d/3d simulations.
-
-NOTE: Aug 2016 - The fix surface/global command is not yet added to
-LAMMPS.
+objects to be drawn.
 
 The {fflag1} and {fflag2} settings are numerical values which are
 passed to the fix to affect how the drawing of its objects is done.

doc/src/fix.txt

@@ -167,136 +167,211 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 "adapt"_fix_adapt.html - change a simulation parameter over time
+"adapt/fep"_fix_adapt_fep.html - 
 "addforce"_fix_addforce.html - add a force to each atom
+"addtorque"_fix_addtorque.html - 
 "append/atoms"_fix_append_atoms.html - append atoms to a running simulation
+"atc"_fix_atc.html - 
 "atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
-"aveforce"_fix_aveforce.html - add an averaged force to each atom
 "ave/atom"_fix_ave_atom.html - compute per-atom time-averaged quantities
 "ave/chunk"_fix_ave_chunk.html - compute per-chunk time-averaged quantities
 "ave/correlate"_fix_ave_correlate.html - compute/output time correlations
+"ave/correlate/long"_fix_ave_correlate_long.html - 
 "ave/histo"_fix_ave_histo.html - compute/output time-averaged histograms
+"ave/histo/weight"_fix_ave_histo.html - 
 "ave/time"_fix_ave_time.html - compute/output global time-averaged quantities
+"aveforce"_fix_aveforce.html - add an averaged force to each atom
 "balance"_fix_balance.html - perform dynamic load-balancing
+"bocs"_fix_bocs.html - 
 "bond/break"_fix_bond_break.html - break bonds on the fly
 "bond/create"_fix_bond_create.html - create bonds on the fly
+"bond/react"_fix_bond_react.html - 
 "bond/swap"_fix_bond_swap.html - Monte Carlo bond swapping
 "box/relax"_fix_box_relax.html - relax box size during energy minimization
+"client/md"_fix_client_md.html - 
+"cmap"_fix_cmap.html - 
+"colvars"_fix_colvars.html - 
+"controller"_fix_controller.html - 
 "deform"_fix_deform.html - change the simulation box size/shape
 "deposit"_fix_deposit.html - add new atoms above a surface
+"dpd/energy"_fix_dpd_energy.html - 
 "drag"_fix_drag.html - drag atoms towards a defined coordinate
+"drude"_fix_drude.html - 
+"drude/transform/direct"_fix_drude_transform.html - 
+"drude/transform/inverse"_fix_drude_transform.html - 
 "dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
+"edpd/source"_fix_dpd_source.html - 
 "efield"_fix_efield.html - impose electric field on system
 "ehex"_fix_ehex.html - ehanced heat exchange algorithm
 "enforce2d"_fix_enforce2d.html - zero out z-dimension velocity and force
+"eos/cv"_fix_eos_cv.html - 
+"eos/table"_fix_eos_table.html - 
+"eos/table/rx"_fix_eos_table_rx.html - 
 "evaporate"_fix_evaporate.html - remove atoms from simulation periodically
 "external"_fix_external.html - callback to an external driver program
+"ffl"_fix_ffl.html - 
+"filter/corotate"_fix_filter_corotate.html - 
+"flow/gauss"_fix_flow_gauss.html - 
 "freeze"_fix_freeze.html - freeze atoms in a granular simulation
 "gcmc"_fix_gcmc.html - grand canonical insertions/deletions
 "gld"_fix_gcmc.html - generalized Langevin dynamics integrator
+"gld"_fix_gld.html - 
+"gle"_fix_gle.html - 
 "gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
+"grem"_fix_grem.html - 
 "halt"_fix_halt.html - terminate a dynamics run or minimization
 "heat"_fix_heat.html - add/subtract momentum-conserving heat
+"imd"_fix_imd.html - 
 "indent"_fix_indent.html - impose force due to an indenter
-"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
+"ipi"_fix_ipi.html - 
 "langevin"_fix_langevin.html - Langevin temperature control
+"langevin/drude"_fix_langevin_drude.html - 
+"langevin/eff"_fix_langevin_eff.html - 
+"langevin/spin"_fix_langevin_spin.html - 
+"latte"_fix_latte.html - wrapper on LATTE density-functional tight-binding code
+"lb/fluid"_fix_lb_fluid.html - 
+"lb/momentum"_fix_lb_momentum.html - 
+"lb/pc"_fix_lb_pc.html - 
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html - 
+"lb/viscous"_fix_lb_viscous.html - 
 "lineforce"_fix_lineforce.html - constrain atoms to move in a line
+"manifoldforce"_fix_manifoldforce.html - 
+"meso"_fix_meso.html - 
+"meso/stationary"_fix_meso_stationary.html - 
 "momentum"_fix_momentum.html - zero the linear and/or angular momentum of a group of atoms
 "move"_fix_move.html - move atoms in a prescribed fashion
+"mscg"_fix_mscg.html - 
 "msst"_fix_msst.html - multi-scale shock technique (MSST) integration
+"mvv/dpd"_fix_mvv_dpd.html - 
+"mvv/edpd"_fix_mvv_dpd.html - 
+"mvv/tdpd"_fix_mvv_dpd.html - 
 "neb"_fix_neb.html - nudged elastic band (NEB) spring forces
 "nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
-"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
 "nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
+"nph/body"_fix_nph_body.html - 
 "nph/body"_fix_nve_body.html - NPH for body particles
+"nph/eff"_fix_nh_eff.html - 
 "nph/sphere"_fix_nph_sphere.html - NPH for spherical particles
+"nphug"_fix_nphug.html - constant-stress Hugoniostat integration
 "npt"_fix_nh.html - constant NPT time integration via Nose/Hoover
 "npt/asphere"_fix_npt_asphere.html - NPT for aspherical particles
+"npt/body"_fix_npt_body.html - 
 "npt/body"_fix_nve_body.html - NPT for body particles
+"npt/eff"_fix_nh_eff.html - 
 "npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
+"npt/uef"_fix_nh_uef.html - 
 "nve"_fix_nve.html - constant NVE time integration
 "nve/asphere"_fix_nve_asphere.html - NVE for aspherical particles
 "nve/asphere/noforce"_fix_nve_asphere_noforce.html - NVE for aspherical particles without forces"
+"nve/awpmd"_fix_nve_awpmd.html - 
 "nve/body"_fix_nve_body.html - NVE for body particles
+"nve/dot"_fix_nve_dot.html - 
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html - 
+"nve/eff"_fix_nve_eff.html - 
 "nve/limit"_fix_nve_limit.html - NVE with limited step length
 "nve/line"_fix_nve_line.html - NVE for line segments
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html - 
 "nve/noforce"_fix_nve_noforce.html - NVE without forces (v only)
 "nve/sphere"_fix_nve_sphere.html - NVE for spherical particles
+"nve/spin"_fix_nve_spin.html - 
 "nve/tri"_fix_nve_tri.html - NVE for triangles
+"nvk"_fix_nvk.html - 
 "nvt"_fix_nh.html - constant NVT time integration via Nose/Hoover
 "nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
 "nvt/body"_fix_nve_body.html - NVT for body particles
+"nvt/body"_fix_nvt_body.html - 
+"nvt/eff"_fix_nh_eff.html - 
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html - 
 "nvt/sllod"_fix_nvt_sllod.html - NVT for NEMD with SLLOD equations
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html - 
 "nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
+"nvt/uef"_fix_nh_uef.html - 
 "oneway"_fix_oneway.html - constrain particles on move in one direction
 "orient/bcc"_fix_orient.html - add grain boundary migration force for BCC
 "orient/fcc"_fix_orient.html - add grain boundary migration force for FCC
+"phonon"_fix_phonon.html - 
+"pimd"_fix_pimd.html - 
 "planeforce"_fix_planeforce.html - constrain atoms to move in a plane
-"poems"_fix_poems.html - constrain clusters of atoms to move \
-  as coupled rigid bodies
+"poems"_fix_poems.html - constrain clusters of atoms to move as coupled rigid bodies
 "pour"_fix_pour.html - pour new atoms/molecules into a granular simulation domain
-"press/berendsen"_fix_press_berendsen.html - pressure control by \
-     Berendsen barostat
+"precession/spin"_fix_precession_spin.html - 
+"press/berendsen"_fix_press_berendsen.html - pressure control by Berendsen barostat
 "print"_fix_print.html - print text and variables during a simulation
 "property/atom"_fix_property_atom.html - add customized per-atom values
-"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential \
-"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method \
-"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer \
-"qeq/point"_fix_qeq.html - charge equilibration via point method \
-"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method \
-"qeq/slater"_fix_qeq.html - charge equilibration via Slater method \
+"python/invoke"_fix_python_invoke.html - 
+"python/move"_fix_python_move.html - 
+"qbmsst"_fix_qbmsst.html - 
+"qeq/comb"_fix_qeq_comb.html - charge equilibration for COMB potential
+"qeq/dynamic"_fix_qeq.html - charge equilibration via dynamic method
+"qeq/fire"_fix_qeq.html - charge equilibration via FIRE minimizer
+"qeq/point"_fix_qeq.html - charge equilibration via point method
+"qeq/reax"_fix_qeq_reax.html - 
+"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
+"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
+"qmmm"_fix_qmmm.html - 
+"qtb"_fix_qtb.html - 
 "rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information \
-"recenter"_fix_recenter.html - constrain the center-of-mass position \
-  of a group of atoms
+"reax/bonds"_fix_reax_bonds.html - write out ReaxFF bond information
+"reax/c/bonds"_fix_reax_bonds.html - 
+"reax/c/species"_fix_reaxc_species.html - 
+"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
 "restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rigid"_fix_rigid.html - constrain one or more clusters of atoms to \
-     move as a rigid body with NVE integration
-"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to \
-     move as a rigid body with NPH integration
-"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to \
-     move as a rigid body with NPT integration
-"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to \
-     move as a rigid body with alternate NVE integration
-"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to \
-     move as a rigid body with NVT integration
-"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to \
-     move as a rigid body with NVE integration
-"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to \
-     move as a rigid body with NPH integration
-"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to \
-     move as a rigid body with NPT integration
-"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to \
-     move as a rigid body with alternate NVE integration
-"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to \
-     move as a rigid body with NVT integration
+"rhok"_fix_rhok.html - 
+"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
+"rigid/nph"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPH integration
+"rigid/nph/small"_fix_rigid.html - 
+"rigid/npt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NPT integration
+"rigid/npt/small"_fix_rigid.html - 
+"rigid/nve"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with alternate NVE integration
+"rigid/nve/small"_fix_rigid.html - 
+"rigid/nvt"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVT integration
+"rigid/nvt/small"_fix_rigid.html - 
+"rigid/small"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVE integration
+"rigid/small/nph"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPH integration
+"rigid/small/npt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NPT integration
+"rigid/small/nve"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with alternate NVE integration
+"rigid/small/nvt"_fix_rigid.html - constrain many small clusters of atoms to move as a rigid body with NVT integration
+"rx"_fix_rx.html - 
+"saed/vtk"_fix_saed_vtk.html - 
 "setforce"_fix_setforce.html - set the force on each atom
 "shake"_fix_shake.html - SHAKE constraints on bonds and/or angles
+"shardlow"_fix_shardlow.html - 
+"smd"_fix_smd.html - 
+"smd/adjust_dt"_fix_smd_adjust_dt.html - 
+"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html - 
+"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html - 
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html - 
+"smd/setvel"_fix_smd_setvel.html - 
+"smd/wall_surface"_fix_smd_wall_surface.html - 
 "spring"_fix_spring.html - apply harmonic spring force to group of atoms
 "spring/chunk"_fix_spring_chunk.html - apply harmonic spring force to each chunk of atoms
-"spring/rg"_fix_spring_rg.html - spring on radius of gyration of \
-     group of atoms
+"spring/rg"_fix_spring_rg.html - spring on radius of gyration of group of atoms
 "spring/self"_fix_spring_self.html - spring from each atom to its origin
 "srd"_fix_srd.html - stochastic rotation dynamics (SRD)
 "store/force"_fix_store_force.html - store force on each atom
 "store/state"_fix_store_state.html - store attributes for each atom
-"temp/berendsen"_fix_temp_berendsen.html - temperature control by \
-     Berendsen thermostat
+"tdpd/source"_fix_dpd_source.html - 
+"temp/berendsen"_fix_temp_berendsen.html - temperature control by Berendsen thermostat
 "temp/csld"_fix_temp_csvr.html - canonical sampling thermostat with Langevin dynamics
 "temp/csvr"_fix_temp_csvr.html - canonical sampling thermostat with Hamiltonian dynamics
-"temp/rescale"_fix_temp_rescale.html - temperature control by \
-     velocity rescaling
+"temp/rescale"_fix_temp_rescale.html - temperature control by velocity rescaling
+"temp/rescale/eff"_fix_temp_rescale_eff.html - 
 "tfmc"_fix_tfmc.html - perform force-bias Monte Carlo with time-stamped method
-"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for \
-     thermal conductivity calculation
+"thermal/conductivity"_fix_thermal_conductivity.html - Muller-Plathe kinetic energy exchange for thermal conductivity calculation
+"ti/spring"_fix_ti_spring.html - 
 "tmd"_fix_tmd.html - guide a group of atoms to a new configuration
 "ttm"_fix_ttm.html - two-temperature model for electronic/atomic coupling
+"ttm/mod"_fix_ttm.html - 
 "tune/kspace"_fix_tune_kspace.html - auto-tune KSpace parameters
 "vector"_fix_vector.html - accumulate a global vector every N timesteps
-"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for \
-     viscosity calculation
+"viscosity"_fix_viscosity.html - Muller-Plathe momentum exchange for viscosity calculation
 "viscous"_fix_viscous.html - viscous damping for granular simulations
+"wall/body/polygon"_fix_wall_body_polygon.html - 
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html - 
 "wall/colloid"_fix_wall.html - Lennard-Jones wall interacting with finite-size particles
+"wall/ees"_fix_wall_ees.html - 
 "wall/gran"_fix_wall_gran.html - frictional wall(s) for granular simulations
+"wall/gran/region"_fix_wall_gran_region.html - 
 "wall/harmonic"_fix_wall.html - harmonic spring wall
 "wall/lj1043"_fix_wall.html - Lennard-Jones 10-4-3 wall
 "wall/lj126"_fix_wall.html - Lennard-Jones 12-6 wall
@@ -304,6 +379,7 @@ accelerated styles exist.
 "wall/piston"_fix_wall_piston.html - moving reflective piston wall
 "wall/reflect"_fix_wall_reflect.html - reflecting wall(s)
 "wall/region"_fix_wall_region.html - use region surface as wall
+"wall/region/ees"_fix_wall_ees.html - 
 "wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
 
 [Restrictions:]

doc/src/fix_balance.txt

@@ -376,3 +376,4 @@ appear in {dimstr} for the {shift} style.
 "group"_group.html, "processors"_processors.html, "balance"_balance.html
 
 [Default:] none
+:link(pizza,http://pizza.sandia.gov)

doc/src/fix_ffl.txt

@@ -0,0 +1,124 @@
+<script type="text/javascript"
+  src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+</script>
+<script type="text/x-mathjax-config">
+  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
+</script>
+
+"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
+
+fix ffl command :h3
+
+[Syntax:]
+
+fix ID id-group ffl tau Tstart Tstop seed \[flip-type\]  :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+ffl = style name of this fix command :l
+tau = thermostat parameter (positive real) :l
+Tstart, Tstop = temperature ramp during the run :l
+seed = random number seed to use for generating noise (positive integer) :l
+one more value may be appended :l
+    flip-type  = determines the flipping type, can be chosen between rescale - no_flip - hard - soft, if no flip type is given, rescale will be chosen by default :pre
+:ule
+
+[Examples:]
+
+fix 3 boundary ffl 10 300 300 31415
+fix 1 all ffl 100 500 500 9265 soft :pre
+
+[Description:]
+
+Apply a Fast-Forward Langevin Equation (FFL) thermostat as described
+in "(Hijazi)"_#Hijazi. Contrary to
+"fix langevin"_fix_langevin.html, this fix performs both
+thermostatting and evolution of the Hamiltonian equations of motion, so it
+should not be used together with "fix nve"_fix_nve.html -- at least not
+on the same atom groups.
+
+The time-evolution of a single particle undergoing Langevin dynamics is described
+by the equations
+
+\begin\{equation\} \frac \{dq\}\{dt\} = \frac\{p\}\{m\}, \end\{equation\}
+
+\begin\{equation\} \frac \{dp\}\{dt\} = -\gamma p + W + F, \end\{equation\}
+
+where \(F\) is the physical force, \(\gamma\) is the friction coefficient, and \(W\) is a
+Gaussian random force.
+
+The friction coefficient is the inverse of the thermostat parameter : \(\gamma = 1/\tau\), with \(\tau\) the thermostat parameter {tau}.
+The thermostat parameter is given in the time units, \(\gamma\) is in inverse time units.
+
+Equilibrium sampling a temperature T is obtained by specifying the
+target value as the {Tstart} and {Tstop} arguments, so that the internal
+constants depending on the temperature are computed automatically.
+
+The random number {seed} must be a positive integer.  A Marsaglia random
+number generator is used.  Each processor uses the input seed to
+generate its own unique seed and its own stream of random numbers.
+Thus the dynamics of the system will not be identical on two runs on
+different numbers of processors.
+
+The flipping type {flip-type} can be chosen between 4 types described in
+"(Hijazi)"_#Hijazi. The flipping operation occurs during the thermostatting
+step and it flips the momenta of the atoms. If no_flip is chosen, no flip
+will be executed and the integration will be the same as a standard
+Langevin thermostat "(Bussi)"_#Bussi3. The other flipping types are : rescale - hard - soft.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+The instantaneous values of the extended variables are written to
+"binary restart files"_restart.html.  Because the state of the random
+number generator is not saved in restart files, this means you cannot
+do "exact" restarts with this fix, where the simulation continues on
+the same as if no restart had taken place. However, in a statistical
+sense, a restarted simulation should produce the same behavior.
+Note however that you should use a different seed each time you
+restart, otherwise the same sequence of random numbers will be used
+each time, which might lead to stochastic synchronization and
+subtle artefacts in the sampling.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+The "fix_modify"_fix_modify.html {energy} option is supported by this
+fix to add the energy change induced by Langevin thermostatting to the
+system's potential energy as part of "thermodynamic
+output"_thermo_style.html.
+
+This fix computes a global scalar which can be accessed by various
+"output commands"_Howto_output.html.  The scalar is the cumulative
+energy change due to this fix.  The scalar value calculated by this
+fix is "extensive".
+
+[Restrictions:]
+
+In order to perform constant-pressure simulations please use
+"fix press/berendsen"_fix_press_berendsen.html, rather than
+"fix npt"_fix_nh.html, to avoid duplicate integration of the
+equations of motion.
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix nvt"_fix_nh.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
+viscous"_fix_viscous.html, "fix nvt"_fix_nh.html, "pair_style
+dpd/tstat"_pair_dpd.html, "fix gld"_fix_gld.html, "fix gle"_fix_gle.html
+
+:line
+
+:link(Hijazi)
+[(Hijazi)] M. Hijazi, D. M. Wilkins, M. Ceriotti, J. Chem. Phys. 148, 184109 (2018)
+:link(Bussi3)
+[(Bussi)] G. Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
+

doc/src/fix_freeze.txt

@@ -7,6 +7,7 @@
 :line
 
 fix freeze command :h3
+fix freeze/kk command :h3
 
 [Syntax:]
 

doc/src/fix_gravity.txt

@@ -8,6 +8,7 @@
 
 fix gravity command :h3
 fix gravity/omp command :h3
+fix gravity/kk command :h3
 
 [Syntax:]
 

doc/src/fix_halt.txt

@@ -135,8 +135,7 @@ files"_restart.html.  None of the "fix_modify"_fix_modify.html options
 are relevant to this fix.  No global or per-atom quantities are stored
 by this fix for access by various "output commands"_Howto_output.html.
 No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.  This fix is not invoked during "energy
-minimization"_minimize.html.
+the "run"_run.html command.
 
 [Restrictions:] none
 

doc/src/fix_msst.txt

@@ -6,7 +6,7 @@
 
 :line
 
- fix msst command :h3
+fix msst command :h3
 
 [Syntax:]
 

doc/src/fix_neb.txt

@@ -35,7 +35,7 @@ keyword = {parallel} or {perp} or {end} :l
 fix 1 active neb 10.0
 fix 2 all neb 1.0 perp 1.0 end last
 fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0
-fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre
+fix 1 all neb 1.0 parallel ideal end last/efirst 1 :pre
 
 [Description:]
 
@@ -212,7 +212,7 @@ page for more info.
 
 [Default:]
 
-The option defaults are nudge = neigh, perp = 0.0, ends is not
+The option defaults are parallel = neigh, perp = 0.0, ends is not
 specified (no inter-replica force on the end replicas).
 
 :line

doc/src/fix_nve_awpmd.txt

@@ -0,0 +1,56 @@
+"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
+
+fix nve/awpmd command :h3
+
+[Syntax:]
+
+fix ID group-ID nve/awpmd :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+nve/awpmd = style name of this fix command :ul
+
+[Examples:]
+
+fix 1 all nve/awpmd :pre
+
+[Description:]
+
+Perform constant NVE integration to update position and velocity for
+nuclei and electrons in the group for the "Antisymmetrized Wave Packet
+Molecular Dynamics"_pair_awpmd.html model.  V is volume; E is energy.
+This creates a system trajectory consistent with the microcanonical
+ensemble.
+
+The operation of this fix is exactly like that described by the "fix
+nve"_fix_nve.html command, except that the width and width-velocity of
+the electron wavefunctions are also updated.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.  None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.  No global or per-atom quantities are stored
+by this fix for access by various "output commands"_Howto_output.html.
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command.  This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:]
+
+This fix is part of the USER-AWPMD package.  It is only enabled if
+LAMMPS was built with that package.  See the "Build
+package"_Build_package.html doc page for more info.
+
+[Related commands:]
+
+"fix nve"_fix_nve.html
+
+[Default:] none

doc/src/fix_nve_sphere.txt

@@ -8,6 +8,7 @@
 
 fix nve/sphere command :h3
 fix nve/sphere/omp command :h3
+fix nve/sphere/kk command :h3
 
 [Syntax:]
 

doc/src/fix_poems.txt

@@ -6,7 +6,7 @@
 
 :line
 
-fix poems :h3
+fix poems command :h3
 
 Syntax:
 

doc/src/fix_property_atom.txt

@@ -7,6 +7,7 @@
 :line
 
 fix property/atom command :h3
+fix property/atom/kk command :h3
 
 [Syntax:]
 
@@ -201,6 +202,7 @@ added classes.
 :line
 
 :link(isotopes)
+
 Example for using per-atom masses with TIP4P water to
 study isotope effects. When setting up simulations with the "TIP4P
 pair styles"_Howto_tip4p.html for water, you have to provide exactly
@@ -238,6 +240,28 @@ set group hwat mass 2.0141018 :pre
 
 :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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the per-atom values it stores to "binary restart

doc/src/fix_smd_move_triangulated_surface.txt

@@ -73,7 +73,7 @@ package"_Build_package.html doc page for more info.
 
 [Related commands:]
 
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
 "smd/wall_surface"_fix_smd_wall_surface.html
 
 [Default:] none

doc/src/fix_smd_wall_surface.txt

@@ -64,7 +64,7 @@ multiple objects in one file.
 
 [Related commands:]
 
-"smd/triangle_mesh_vertices"_compute_smd_triangle_mesh_vertices.html,
+"smd/triangle_mesh_vertices"_compute_smd_triangle_vertices.html,
 "smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
 "smd/tri_surface"_pair_smd_triangulated_surface.html
 

doc/src/fix_surface_global.txt

@@ -1,19 +0,0 @@
-"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
-
-fix wall/surface/global command :h3
-
-[Description:]
-
-This feature is not yet implemented.
-
-[Related commands:]
-
-"dump image"_dump_image.html
-
-

doc/src/fix_wall_gran.txt

@@ -7,6 +7,7 @@
 :line
 
 fix wall/gran command :h3
+fix wall/gran/omp command :h3
 
 [Syntax:]
 
@@ -136,6 +137,28 @@ the clockwise direction for {vshear} > 0 or counter-clockwise for
 {vshear} < 0.  In this case, {vshear} is the tangential velocity of
 the wall at whatever {radius} has been defined.
 
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the shear friction state of atoms interacting with the

doc/src/fixes.txt

@@ -46,6 +46,7 @@ Fixes :h1
    fix_eos_table_rx
    fix_evaporate
    fix_external
+   fix_ffl
    fix_filter_corotate
    fix_flow_gauss
    fix_freeze
@@ -92,6 +93,7 @@ Fixes :h1
    fix_nve
    fix_nve_asphere
    fix_nve_asphere_noforce
+   fix_nve_awpmd
    fix_nve_body
    fix_nve_dot
    fix_nve_dotc_langevin
@@ -154,7 +156,6 @@ Fixes :h1
    fix_srd
    fix_store_force
    fix_store_state
-   fix_surface_global
    fix_temp_berendsen
    fix_temp_csvr
    fix_temp_rescale

doc/src/improper_style.txt

@@ -64,14 +64,19 @@ which are included in the LAMMPS distribution.  The full list of all
 improper styles is on the "Commands bond"_Commands_bond.html#improper
 doc page.
 
-"improper_style none"_improper_none.html - turn off improper interactions
-"improper_style zero"_improper_zero.html - topology but no interactions
-"improper_style hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
+"none"_improper_none.html - turn off improper interactions
+"zero"_improper_zero.html - topology but no interactions
+"hybrid"_improper_hybrid.html - define multiple styles of improper interactions :ul
 
-"improper_style class2"_improper_class2.html - COMPASS (class 2) improper
-"improper_style cvff"_improper_cvff.html - CVFF improper
-"improper_style harmonic"_improper_harmonic.html - harmonic improper
-"improper_style umbrella"_improper_umbrella.html - DREIDING improper :ul
+"class2"_improper_class2.html - COMPASS (class 2) improper
+"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
+"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
 
 :line
 

doc/src/lammps.book

@@ -266,6 +266,7 @@ fix_eos_table.html
 fix_eos_table_rx.html
 fix_evaporate.html
 fix_external.html
+fix_ffl.html
 fix_filter_corotate.html
 fix_flow_gauss.html
 fix_freeze.html
@@ -311,6 +312,7 @@ fix_npt_sphere.html
 fix_nve.html
 fix_nve_asphere.html
 fix_nve_asphere_noforce.html
+fix_nve_awpmd.html
 fix_nve_body.html
 fix_nve_dot.html
 fix_nve_dotc_langevin.html
@@ -374,7 +376,6 @@ fix_spring_self.html
 fix_srd.html
 fix_store_force.html
 fix_store_state.html
-fix_surface_global.html
 fix_temp_berendsen.html
 fix_temp_csvr.html
 fix_temp_rescale.html
@@ -403,6 +404,7 @@ lammps_commands_compute.html
 compute.html
 compute_modify.html
 compute_ackland_atom.html
+compute_adf.html
 compute_angle.html
 compute_angle_local.html
 compute_angmom_chunk.html
@@ -464,10 +466,12 @@ compute_pe.html
 compute_pe_atom.html
 compute_plasticity_atom.html
 compute_pressure.html
+compute_pressure_cylinder.html
 compute_pressure_uef.html
 compute_property_atom.html
 compute_property_chunk.html
 compute_property_local.html
+compute_ptm_atom.html
 compute_rdf.html
 compute_reduce.html
 compute_reduce_chunk.html
@@ -488,7 +492,7 @@ compute_smd_tlsph_shape.html
 compute_smd_tlsph_strain.html
 compute_smd_tlsph_strain_rate.html
 compute_smd_tlsph_stress.html
-compute_smd_triangle_mesh_vertices.html
+compute_smd_triangle_vertices.html
 compute_smd_ulsph_num_neighs.html
 compute_smd_ulsph_strain.html
 compute_smd_ulsph_strain_rate.html

doc/src/message.txt

@@ -137,8 +137,8 @@ If LAMMPS is the server code, it will begin receiving messages when
 the "server"_server.html command is invoked.
 
 A fix client command will terminate its messaging with the server when
-LAMMPS ends, or the fix is deleted via the "unfix"_unfix command.  The
-server command will terminate its messaging with the client when the
+LAMMPS ends, or the fix is deleted via the "unfix"_unfix.html command.
+The server command will terminate its messaging with the client when the
 client signals it.  Then the remainder of the LAMMPS input script will
 be processed.
 

doc/src/pair_body_nparticle.txt

@@ -6,7 +6,7 @@
 
 :line
 
-pair_style body command :h3
+pair_style body/nparticle command :h3
 
 [Syntax:]
 

doc/src/pair_born.txt

@@ -11,39 +11,34 @@ pair_style born command :h3
 pair_style born/omp command :h3
 pair_style born/gpu command :h3
 pair_style born/coul/long command :h3
-pair_style born/coul/long/cs command :h3
-pair_style born/coul/long/cs/gpu command :h3
 pair_style born/coul/long/gpu command :h3
 pair_style born/coul/long/omp command :h3
 pair_style born/coul/msm command :h3
 pair_style born/coul/msm/omp command :h3
 pair_style born/coul/wolf command :h3
-pair_style born/coul/wolf/cs command :h3
-pair_style born/coul/wolf/cs/gpu command :h3
 pair_style born/coul/wolf/gpu command :h3
 pair_style born/coul/wolf/omp command :h3
 pair_style born/coul/dsf command :h3
-pair_style born/coul/dsf/cs command :h3
 
 [Syntax:]
 
 pair_style style args :pre
 
-style = {born} or {born/coul/long} or {born/coul/long/cs} or {born/coul/msm} or {born/coul/wolf}
+style = {born} or {born/coul/long} or {born/coul/msm} or {born/coul/wolf}
 args = list of arguments for a particular style :ul
   {born} args = cutoff
     cutoff = global cutoff for non-Coulombic interactions (distance units)
-  {born/coul/long} or {born/coul/long/cs} args = cutoff (cutoff2)
+  {born/coul/long} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {born/coul/msm} args = cutoff (cutoff2)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {born/coul/wolf} or {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
+  {born/coul/wolf} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
+  {born/coul/dsf} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (distance units) :pre
@@ -55,9 +50,7 @@ pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/long 10.0
-pair_style born/coul/long/cs 10.0
-pair_style born/coul/long 10.0 8.0
-pair_style born/coul/long/cs 10.0 8.0
+pair_style born/coul/long 10.0 8.
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -68,7 +61,6 @@ pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
 pair_style born/coul/wolf 0.25 10.0
 pair_style born/coul/wolf 0.25 10.0 9.0
-pair_style born/coul/wolf/cs 0.25 10.0 9.0
 pair_coeff * * 6.08 0.317 2.340 24.18 11.51
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
@@ -107,13 +99,6 @@ Wolf potential in the "coul/wolf"_pair_coul.html pair style.
 The {born/coul/dsf} style computes the Coulomb contribution with the
 damped shifted force model as in the "coul/dsf"_pair_coul.html style.
 
-Style {born/coul/long/cs} is identical to {born/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-The same correction is introduced for the {born/coul/dsf/cs} style
-which is identical to {born/coul/dsf}.  And likewise for
-{born/coul/wolf/cs} style which is identical to {born/coul/wolf}.
-
 Note that these potentials are related to the "Buckingham
 potential"_pair_buck.html.
 
@@ -174,7 +159,7 @@ for the energy of the exp(), 1/r^6, and 1/r^8 portion of the pair
 interaction.
 
 The {born/coul/long} pair style supports the
-"pair_modify"_pair_modify.html table option ti tabulate the
+"pair_modify"_pair_modify.html table option to tabulate the
 short-range portion of the long-range Coulombic interaction.
 
 These styles support the pair_modify tail option for adding long-range

doc/src/pair_buck.txt

@@ -17,7 +17,6 @@ pair_style buck/coul/cut/intel command :h3
 pair_style buck/coul/cut/kk command :h3
 pair_style buck/coul/cut/omp command :h3
 pair_style buck/coul/long command :h3
-pair_style buck/coul/long/cs command :h3
 pair_style buck/coul/long/gpu command :h3
 pair_style buck/coul/long/intel command :h3
 pair_style buck/coul/long/kk command :h3
@@ -29,14 +28,14 @@ pair_style buck/coul/msm/omp command :h3
 
 pair_style style args :pre
 
-style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/long/cs} or {buck/coul/msm}
+style = {buck} or {buck/coul/cut} or {buck/coul/long} or {buck/coul/msm}
 args = list of arguments for a particular style :ul
   {buck} args = cutoff
     cutoff = global cutoff for Buckingham interactions (distance units)
   {buck/coul/cut} args = cutoff (cutoff2)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {buck/coul/long} or {buck/coul/long/cs} args = cutoff (cutoff2)
+  {buck/coul/long} args = cutoff (cutoff2)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {buck/coul/msm} args = cutoff (cutoff2)
@@ -56,9 +55,7 @@ pair_coeff 1 1 100.0 1.5 200.0 9.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 8.0 :pre
 
 pair_style buck/coul/long 10.0
-pair_style buck/coul/long/cs 10.0
 pair_style buck/coul/long 10.0 8.0
-pair_style buck/coul/long/cs 10.0 8.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
 
@@ -92,10 +89,6 @@ A,C and Coulombic terms.  If two cutoffs are specified, the first is
 used as the cutoff for the A,C terms, and the second is the cutoff for
 the Coulombic term.
 
-Style {buck/coul/long/cs} is identical to {buck/coul/long} except that
-a term is added for the "core/shell model"_Howto_coreshell.html to
-allow charges on core and shell particles to be separated by r = 0.0.
-
 Note that these potentials are related to the "Born-Mayer-Huggins
 potential"_pair_born.html.
 
@@ -184,8 +177,7 @@ respa"_run_style.html command.  They do not support the {inner},
 
 [Restrictions:]
 
-The {buck/coul/long} style is part of the KSPACE package.  The
-{buck/coul/long/cs} style is part of the CORESHELL package.  They are
+The {buck/coul/long} style is 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.
 

doc/src/pair_buck6d_coul_gauss.txt

@@ -6,8 +6,8 @@
 
 :line
 
-pair_style buck6d/coul/gauss/dsf :h3
-pair_style buck6d/coul/gauss/long :h3
+pair_style buck6d/coul/gauss/dsf command :h3
+pair_style buck6d/coul/gauss/long command :h3
 
 [Syntax:]
 

doc/src/pair_charmm.txt

@@ -8,12 +8,15 @@
 
 pair_style lj/charmm/coul/charmm command :h3
 pair_style lj/charmm/coul/charmm/intel command :h3
+pair_style lj/charmm/coul/charmm/kk command :h3
 pair_style lj/charmm/coul/charmm/omp command :h3
 pair_style lj/charmm/coul/charmm/implicit command :h3
+pair_style lj/charmm/coul/charmm/implicit/kk command :h3
 pair_style lj/charmm/coul/charmm/implicit/omp command :h3
 pair_style lj/charmm/coul/long command :h3
 pair_style lj/charmm/coul/long/gpu command :h3
 pair_style lj/charmm/coul/long/intel command :h3
+pair_style lj/charmm/coul/long/kk command :h3
 pair_style lj/charmm/coul/long/opt command :h3
 pair_style lj/charmm/coul/long/omp command :h3
 pair_style lj/charmm/coul/msm command :h3

doc/src/pair_coul.txt

@@ -19,8 +19,6 @@ pair_style coul/dsf/gpu command :h3
 pair_style coul/dsf/kk command :h3
 pair_style coul/dsf/omp command :h3
 pair_style coul/long command :h3
-pair_style coul/long/cs command :h3
-pair_style coul/long/cs/gpu command :h3
 pair_style coul/long/omp command :h3
 pair_style coul/long/gpu command :h3
 pair_style coul/long/kk command :h3
@@ -30,7 +28,6 @@ pair_style coul/streitz command :h3
 pair_style coul/wolf command :h3
 pair_style coul/wolf/kk command :h3
 pair_style coul/wolf/omp command :h3
-pair_style coul/wolf/cs command :h3
 pair_style tip4p/cut command :h3
 pair_style tip4p/long command :h3
 pair_style tip4p/cut/omp command :h3
@@ -42,10 +39,8 @@ pair_style coul/cut cutoff
 pair_style coul/debye kappa cutoff
 pair_style coul/dsf alpha cutoff
 pair_style coul/long cutoff
-pair_style coul/long/cs cutoff
 pair_style coul/long/gpu cutoff
 pair_style coul/wolf alpha cutoff
-pair_style coul/wolf/cs alpha cutoff
 pair_style coul/streitz cutoff keyword alpha
 pair_style tip4p/cut otype htype btype atype qdist cutoff
 pair_style tip4p/long otype htype btype atype qdist cutoff :pre
@@ -68,14 +63,12 @@ pair_style coul/dsf 0.05 10.0
 pair_coeff * * :pre
 
 pair_style coul/long 10.0
-pair_style coul/long/cs 10.0
 pair_coeff * * :pre
 
 pair_style coul/msm 10.0
 pair_coeff * * :pre
 
 pair_style coul/wolf 0.2 9.0
-pair_style coul/wolf/cs 0.2 9.0
 pair_coeff * * :pre
 
 pair_style coul/streitz 12.0 ewald
@@ -204,12 +197,6 @@ option.  The Coulombic cutoff specified for this style means that
 pairwise interactions within this distance are computed directly;
 interactions outside that distance are computed in reciprocal space.
 
-Style {coul/long/cs} is identical to {coul/long} except that a term is
-added for the "core/shell model"_Howto_coreshell.html to allow charges
-on core and shell particles to be separated by r = 0.0.  The same
-correction is introduced for the {coul/wolf/cs} style which is
-identical to {coul/wolf}.
-
 Styles {tip4p/cut} and {tip4p/long} implement the coulomb part of
 the TIP4P water model of "(Jorgensen)"_#Jorgensen3, which introduces
 a massless site located a short distance away from the oxygen atom
@@ -317,9 +304,9 @@ This pair style can only be used via the {pair} keyword of the
 [Restrictions:]
 
 The {coul/long}, {coul/msm} and {tip4p/long} styles are part of the
-KSPACE package.  The {coul/long/cs} style is part of the CORESHELL
-package.  They are only enabled if LAMMPS was built with that package.
-See the "Build package"_Build_package.html doc page for more info.
+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.
 
 [Related commands:]
 

doc/src/pair_coul_shield.txt

@@ -38,7 +38,8 @@ charge and molecule ID information is included.
 
 Where Tap(r_ij) is the taper function which provides a continuous cutoff
 (up to third derivative) for inter-atomic separations larger than r_c
-"(Maaravi)"_#Maaravi1. Here {lambda} is the shielding parameter that
+"(Leven1)"_#Leven3, "(Leven2)"_#Leven4 and "(Maaravi)"_#Maaravi1.
+Here {lambda} is the shielding parameter that
 eliminates the short-range singularity of the classical mono-polar
 electrostatic interaction expression "(Maaravi)"_#Maaravi1.
 
@@ -82,5 +83,11 @@ package"_Build_package.html doc page for more info.
 
 :line
 
+:link(Leven3)
+[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+:link(Leven4)
+[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
+
 :link(Maaravi1)
 [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).

doc/src/pair_cs.txt

@@ -6,49 +6,74 @@
 
 :line
 
-pair_style born/coul/long/cs command :h3
-pair_style buck/coul/long/cs command :h3
 pair_style born/coul/dsf/cs command :h3
+pair_style born/coul/long/cs command :h3
+pair_style born/coul/long/cs/gpu command :h3
 pair_style born/coul/wolf/cs command :h3
+pair_style born/coul/wolf/cs/gpu command :h3
+pair_style buck/coul/long/cs command :h3
+pair_style coul/long/cs command :h3
+pair_style coul/long/cs/gpu command :h3
+pair_style coul/wolf/cs command :h3
+pair_style lj/cut/coul/long/cs command :h3
 
 [Syntax:]
 
 pair_style style args :pre
 
-style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/cs}
+style = {born/coul/dsf/cs} or {born/coul/long/cs} or {born/coul/wolf/cs} or {buck/coul/long/cs} or {coul/long/cs} or {coul/wolf/cs} or {lj/cut/coul/long/cs}
 args = list of arguments for a particular style :ul
-  {born/coul/long/cs} args = cutoff (cutoff2)
-    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-  {buck/coul/long/cs} args = cutoff (cutoff2)
-    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (distance units) :pre
+    cutoff2 = global cutoff for Coulombic (distance units)
+  {born/coul/long/cs} args = cutoff (cutoff2)
+    cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
   {born/coul/wolf/cs} args = alpha cutoff (cutoff2)
     alpha = damping parameter (inverse distance units)
     cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
     cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {buck/coul/long/cs} args = cutoff (cutoff2)
+    cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units)
+  {coul/long} args = cutoff
+    cutoff = global cutoff for Coulombic (distance units)
+  {coul/wolf} args = alpha cutoff
+    alpha = damping parameter (inverse distance units)
+    cutoff = global cutoff for Coulombic (distance units)
+  {lj/cut/coul/long/cs} args = cutoff (cutoff2)
+    cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
+    cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
 
 [Examples:]
 
+pair_style born/coul/dsf/cs 0.1 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 pair_style born/coul/long/cs 10.0 8.0
 pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre
 
+pair_style born/coul/wolf/cs 0.25 10.0 12.0
+pair_coeff * *   0.0 1.00 0.00 0.00 0.00
+pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+
 pair_style buck/coul/long/cs 10.0
 pair_style buck/coul/long/cs 10.0 8.0
 pair_coeff * * 100.0 1.5 200.0
 pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre
 
-pair_style born/coul/dsf/cs 0.1 10.0 12.0
-pair_coeff * *   0.0 1.00 0.00 0.00 0.00
-pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+pair_style coul/long/cs 10.0
+pair_coeff * * :pre
 
-pair_style born/coul/wolf/cs 0.25 10.0 12.0
-pair_coeff * *   0.0 1.00 0.00 0.00 0.00
-pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre
+pair_style coul/wolf/cs 0.2 9.0
+pair_coeff * * :pre
+
+pair_style lj/cut/coul/long/cs 10.0
+pair_style lj/cut/coul/long/cs 10.0 8.0
+pair_coeff * * 100.0 3.0
+pair_coeff 1 1 100.0 3.5 9.0 :pre
 
 [Description:]
 
@@ -57,16 +82,28 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham2.  See
 the "Howto coreshell"_Howto_coreshell.html doc page for an overview of
 the model as implemented in LAMMPS.
 
-The styles with a {coul/long} term are identical to the "pair_style
-born/coul/long"_pair_born.html and "pair_style
-buck/coul/long"_pair_buck.html styles, except they correctly treat the
-special case where the distance between two charged core and shell
-atoms in the same core/shell pair approach r = 0.0.  This needs
-special treatment when a long-range solver for Coulombic interactions
-is also used, i.e. via the "kspace_style"_kspace_style.html command.
+All the styles are identical to the corresponding pair style without
+the "/cs" in the name:
 
-More specifically, the short-range Coulomb interaction between a core
-and its shell should be turned off using the
+"pair_style born/coul/dsf"_pair_born.html
+"pair_style born/coul/long"_pair_born.html
+"pair_style born/coul/wolf"_pair_born.html
+"pair_style buck/coul/long"_pair_buck.html
+"pair_style coul/long"_pair_coul.html
+"pair_style coul/wolf"_pair_coul.html
+"pair_style lj/cut/coul/long"_pair_lj.html :ul
+
+except that they correctly treat the special case where the distance
+between two charged core and shell atoms in the same core/shell pair
+approach r = 0.0.  
+
+Styles with a "/long" in the name are used with a long-range solver
+for Coulombic interactions via the "kspace_style"_kspace_style.html
+command.  They require special treatment of the short-range Coulombic
+interactions within the cor/shell model.
+
+Specifically, the short-range Coulomb interaction between a core and
+its shell should be turned off using the
 "special_bonds"_special_bonds.html command by setting the 1-2 weight
 to 0.0, which works because the core and shell atoms are bonded to
 each other.  This induces a long-range correction approximation which
@@ -81,21 +118,42 @@ where C is an energy-conversion constant, Qi and Qj are the charges on
 the core and shell, epsilon is the dielectric constant and r_min is the
 minimal distance.
 
-The pair style {born/coul/dsf/cs} is identical to the
-"pair_style born/coul/dsf"_pair_born.html style, which uses
-the damped shifted force model as in "coul/dsf"_pair_coul.html
-to compute the Coulomb contribution. This approach does not require
-a long-range solver, thus the only correction is the addition of a
-minimal distance to avoid the possible r = 0.0 case for a
-core/shell pair.
+For styles that are not used with a long-range solver, i.e. those with
+"/dsf" or "/wolf" in the name, the only correction is the addition of
+a minimal distance to avoid the possible r = 0.0 case for a core/shell
+pair.
 
-The pair style {born/coul/wolf/cs} is identical to the
-"pair_style born/coul/wolf"_pair_born.html style, which uses
-the Wolf summation as in "coul/wolf"_pair_coul.html to compute
-the Coulomb contribution. This approach does not require
-a long-range solver, thus the only correction is the addition of a
-minimal distance to avoid the possible r = 0.0 case for a
-core/shell pair.
+: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
+hardware, as discussed on the "Speed packages"_Speed_packages.html doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
+USER-OMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the "Build
+package"_Build_package.html doc page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the "-suffix command-line
+switch"_Run_options.html when you invoke LAMMPS, or you can use the
+"suffix"_suffix.html command in your input script.
+
+See the "Speed packages"_Speed_packages.html doc page for more
+instructions on how to use the accelerated styles effectively.
+
+:line
+
+[Mixing, shift, table, tail correction, restart, rRESPA info]:
+
+See the corresponding doc pages for pair styles without the "cs"
+suffix to see how mixing, shifting, tabulation, tail correction,
+restarting, and rRESPA are handled by theses pair styles.
+
+:line
 
 [Restrictions:]
 

doc/src/pair_dipole.txt

@@ -13,6 +13,7 @@ pair_style lj/sf/dipole/sf command :h3
 pair_style lj/sf/dipole/sf/gpu command :h3
 pair_style lj/sf/dipole/sf/omp command :h3
 pair_style lj/cut/dipole/long command :h3
+pair_style lj/cut/dipole/long/gpu command :h3
 pair_style lj/long/dipole/long command :h3
 
 [Syntax:]

doc/src/pair_eam.txt

@@ -20,6 +20,8 @@ pair_style eam/alloy/omp command :h3
 pair_style eam/alloy/opt command :h3
 pair_style eam/cd command :h3
 pair_style eam/cd/omp command :h3
+pair_style eam/cd/old command :h3
+pair_style eam/cd/old/omp command :h3
 pair_style eam/fs command :h3
 pair_style eam/fs/gpu command :h3
 pair_style eam/fs/intel command :h3
@@ -31,7 +33,7 @@ pair_style eam/fs/opt command :h3
 
 pair_style style :pre
 
-style = {eam} or {eam/alloy} or {eam/cd} or {eam/fs} :ul
+style = {eam} or {eam/alloy} or {eam/cd} or {eam/cd/old} or {eam/fs} :ul
 
 [Examples:]
 
@@ -268,7 +270,8 @@ Style {eam/cd} is similar to the {eam/alloy} style, except that it
 computes alloy pairwise interactions using the concentration-dependent
 embedded-atom method (CD-EAM).  This model can reproduce the enthalpy
 of mixing of alloys over the full composition range, as described in
-"(Stukowski)"_#Stukowski.
+"(Stukowski)"_#Stukowski. Style {eam/cd/old} is an older, slightly
+different and slower two-site formulation of the model "(Caro)"_#Caro.
 
 The pair_coeff command is specified the same as for the {eam/alloy}
 style.  However the DYNAMO {setfl} file must has two
@@ -442,3 +445,6 @@ Daw, Baskes, Phys Rev B, 29, 6443 (1984).
 :link(Stukowski)
 [(Stukowski)] Stukowski, Sadigh, Erhart, Caro; Modeling Simulation
 Materials Science & Engineering, 7, 075005 (2009).
+
+:link(Caro)
+[(Caro)] A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)

doc/src/pair_edip.txt

@@ -7,6 +7,7 @@
 :line
 
 pair_style edip command :h3
+pair_style edip/omp command :h3
 pair_style edip/multi command :h3
 
 [Syntax:]

doc/src/pair_gran.txt

@@ -7,9 +7,10 @@
 :line
 
 pair_style gran/hooke command :h3
-pair_style gran/omp command :h3
+pair_style gran/hooke/omp command :h3
 pair_style gran/hooke/history command :h3
 pair_style gran/hooke/history/omp command :h3
+pair_style gran/hooke/history/kk command :h3
 pair_style gran/hertz/history command :h3
 pair_style gran/hertz/history/omp command :h3
 

doc/src/pair_gromacs.txt

@@ -8,8 +8,10 @@
 
 pair_style lj/gromacs command :h3
 pair_style lj/gromacs/gpu command :h3
+pair_style lj/gromacs/kk command :h3
 pair_style lj/gromacs/omp command :h3
 pair_style lj/gromacs/coul/gromacs command :h3
+pair_style lj/gromacs/coul/gromacs/kk command :h3
 pair_style lj/gromacs/coul/gromacs/omp command :h3
 
 [Syntax:]

doc/src/pair_hybrid.txt

@@ -7,9 +7,8 @@
 :line
 
 pair_style hybrid command :h3
-pair_style hybrid/omp command :h3
+pair_style hybrid/kk command :h3
 pair_style hybrid/overlay command :h3
-pair_style hybrid/overlay/omp command :h3
 pair_style hybrid/overlay/kk command :h3
 
 [Syntax:]

doc/src/pair_ilp_graphene_hbn.txt

@@ -25,22 +25,24 @@ pair_coeff  * * rebo                 CH.airebo   NULL NULL C
 pair_coeff  * * tersoff              BNC.tersoff B    N    NULL
 pair_coeff  * * ilp/graphene/hbn     BNCH.ILP    B    N    C
 pair_coeff  1 1 coul/shield 0.70
-pair_coeff  1 2 coul/shield 0.69498201415576216335
+pair_coeff  1 2 coul/shield 0.695
 pair_coeff  2 2 coul/shield 0.69 :pre
 
 [Description:]
 
 The {ilp/graphene/hbn} style computes the registry-dependent interlayer
-potential (ILP) potential as described in "(Leven)"_#Leven and
-"(Maaravi)"_#Maaravi2. The normals are calculated in the way as described
+potential (ILP) potential as described in "(Leven1)"_#Leven1,
+"(Leven2)"_#Leven2 and "(Maaravi)"_#Maaravi2.
+The normals are calculated in the way as described
 in "(Kolmogorov)"_#Kolmogorov2.
 
 :c,image(Eqs/pair_ilp_graphene_hbn.jpg)
 
 Where Tap(r_ij) is the taper function which provides a continuous
 cutoff (up to third derivative) for interatomic separations larger than
-r_c "(Maaravi)"_#Maaravi2. The definitions of each parameter in the above
-equation can be found in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2.
+r_c "(Maaravi)"_#Maaravi2. The definitons of each parameter in the above
+equation can be found in "(Leven1)"_#Leven1 and "(Maaravi)"_#Maaravi2.
+
 
 It is important to include all the pairs to build the neighbor list for
 calculating the normals.
@@ -61,13 +63,15 @@ NOTE: The parameters presented in the parameter file (e.g. BNCH.ILP),
 are fitted with taper function by setting the cutoff equal to 16.0
 Angstrom.  Using different cutoff or taper function should be careful.
 
-NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal Materials
-are presented in "(Ouyang)"_#Ouyang1. These parameters provide a good description
-in both short- and long-range interaction regime, while the old ILP parameters
-published in "(Leven)"_#Leven and "(Maaravi)"_#Maaravi2 are only suitable for
-long-range interaction regime. This feature is essential for simulations in
-high-pressure regime (i.e., the interlayer distance smaller than the equilibrium distance).
-The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
+NOTE: Two new sets of parameters of ILP for two-dimensional hexagonal
+Materials are presented in "(Ouyang)"_#Ouyang.  These parameters provide
+a good description in both short- and long-range interaction regimes.
+While the old ILP parameters published in "(Leven2)"_#Leven2 and
+"(Maaravi)"_#Maaravi2 are only suitable for long-range interaction
+regime. This feature is essential for simulations in high pressure
+regime (i.e., the interlayer distance is smaller than the equilibrium
+distance).  The benchmark tests and comparison of these parameters can
+be found in "(Ouyang)"_#Ouyang.
 
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
@@ -112,14 +116,17 @@ units, if your simulation does not use {metal} units.
 
 :line
 
-:link(Leven)
-[(Leven)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016)
+:link(Leven1)
+[(Leven1)] I. Leven, I. Azuri, L. Kronik and O. Hod, J. Chem. Phys. 140, 104106 (2014).
+
+:link(Leven2)
+[(Leven2)] I. Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
 
 :link(Maaravi2)
 [(Maaravi)] T. Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
 
 :link(Kolmogorov2)
-[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
+[(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005).
 
-:link(Ouyang1)
-[(Ouyang)] W. Ouyang, D. Mandelli,  M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
+:link(Ouyang)
+[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

doc/src/pair_kolmogorov_crespi_full.txt

@@ -19,11 +19,11 @@ tap_flag = 0/1 to turn off/on the taper function
 
 pair_style hybrid/overlay kolmogorov/crespi/full 20.0 0
 pair_coeff * * none
-pair_coeff * * kolmogorov/crespi/full  CC.KC   C C :pre
+pair_coeff * * kolmogorov/crespi/full  CH.KC   C C :pre
 
-pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0
-pair_coeff * * rebo                    CH.airebo  C C
-pair_coeff * * kolmogorov/crespi/full  CC.KC      C C :pre
+pair_style hybrid/overlay rebo kolmogorov/crespi/full 16.0 1
+pair_coeff * * rebo                    CH.airebo    C H
+pair_coeff * * kolmogorov/crespi/full  CH_taper.KC  C H :pre
 
 [Description:]
 
@@ -38,27 +38,32 @@ forces and to include all the pairs to build the neighbor list for
 calculating the normals.  Energies are shifted so that they go
 continuously to zero at the cutoff assuming that the exponential part of
 {Vij} (first term) decays sufficiently fast.  This shift is achieved by
-the last term in the equation for {Vij} above.
+the last term in the equation for {Vij} above. This is essential only
+when the tapper function is turned off. The formula of taper function
+can be found in pair style "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html.
 
 NOTE: This potential is intended for interactions between two different
 graphene layers. Therefore, to avoid interaction within the same layers,
 each layer should have a separate molecule id and is recommended to use
 "full" atom style in the data file.
 
-The parameter file (e.g. CC.KC), is intended for use with {metal}
+The parameter file (e.g. CH.KC), is intended for use with {metal}
 "units"_units.html, with energies in meV. Two additional parameters, {S},
 and {rcut} are included in the parameter file. {S} is designed to
 facilitate scaling of energies. {rcut} is designed to build the neighbor
 list for calculating the normals for each atom pair.
 
-NOTE: A new set of parameters of KC potential for hydrocarbons (CH.KC)
-is presented in "(Ouyang)"_#Ouyang2. The parameters in CH.KC provides
-a good description in both short- and long-range interaction regime,
-while the original parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1
-are only suitable for long-range interaction regime. 
-This feature is essential for simulations in high-pressure regime
-(i.e., the interlayer distance smaller than the equilibrium distance).
-The benchmark tests and comparison of these parameters can be found in "(Ouyang)"_#Ouyang2.
+NOTE: Two new sets of parameters of KC potential for hydrocarbons, CH.KC
+(without the taper function) and CH_taper.KC (with the taper function)
+are presented in "(Ouyang)"_#Ouyang1.  The energy for the KC potential
+with the taper function goes continuously to zero at the cutoff.  The
+parameters in both CH.KC and CH_taper.KC provide a good description in
+both short- and long-range interaction regimes. While the original
+parameters (CC.KC) published in "(Kolmogorov)"_#Kolmogorov1 are only
+suitable for long-range interaction regime.  This feature is essential
+for simulations in high pressure regime (i.e., the interlayer distance
+is smaller than the equilibrium distance).  The benchmark tests and
+comparison of these parameters can be found in "(Ouyang)"_#Ouyang1.
 
 This potential must be used in combination with hybrid/overlay.
 Other interactions can be set to zero using pair_style {none}.
@@ -84,7 +89,7 @@ package"_Build_package.html doc page for more info.
 This pair potential requires the newton setting to be {on} for pair
 interactions.
 
-The CC.KC potential file provided with LAMMPS (see the potentials
+The CH.KC potential file provided with LAMMPS (see the potentials
 folder) are parameterized for metal units.  You can use this potential
 with any LAMMPS units, but you would need to create your own custom
 CC.KC potential file with all coefficients converted to the appropriate
@@ -105,5 +110,5 @@ units.
 :link(Kolmogorov1)
 [(Kolmogorov)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
 
-:link(Ouyang2)
-[(Ouyang)] W. Ouyang, D. Mandelli,  M. Urbakh, O. Hod, arXiv:1806.09555 (2018).
+:link(Ouyang1)
+[(Ouyang)] W. Ouyang, D. Mandelli, M. Urbakh and O. Hod, Nano Lett. 18, 6009-6016 (2018).

doc/src/pair_lj.txt

@@ -14,6 +14,7 @@ pair_style lj/cut/opt command :h3
 pair_style lj/cut/omp command :h3
 pair_style lj/cut/coul/cut command :h3
 pair_style lj/cut/coul/cut/gpu command :h3
+pair_style lj/cut/coul/cut/kk command :h3
 pair_style lj/cut/coul/cut/omp command :h3
 pair_style lj/cut/coul/debye command :h3
 pair_style lj/cut/coul/debye/gpu command :h3
@@ -24,8 +25,8 @@ pair_style lj/cut/coul/dsf/gpu command :h3
 pair_style lj/cut/coul/dsf/kk command :h3
 pair_style lj/cut/coul/dsf/omp command :h3
 pair_style lj/cut/coul/long command :h3
-pair_style lj/cut/coul/long/cs command :h3
 pair_style lj/cut/coul/long/gpu command :h3
+pair_style lj/cut/coul/long/kk command :h3
 pair_style lj/cut/coul/long/intel command :h3
 pair_style lj/cut/coul/long/opt command :h3
 pair_style lj/cut/coul/long/omp command :h3
@@ -44,7 +45,7 @@ pair_style lj/cut/tip4p/long/opt command :h3
 
 pair_style style args :pre
 
-style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} or {lj/cut/coul/long/cs} or {lj/cut/coul/msm} or {lj/cut/tip4p/long}
+style = {lj/cut} or {lj/cut/coul/cut} or {lj/cut/coul/debye} or {lj/cut/coul/dsf} or {lj/cut/coul/long} {lj/cut/coul/msm} or {lj/cut/tip4p/long}
 args = list of arguments for a particular style :ul
   {lj/cut} args = cutoff
     cutoff = global cutoff for Lennard Jones interactions (distance units)
@@ -105,9 +106,7 @@ pair_coeff * * 1.0 1.0
 pair_coeff 1 1 1.0 1.0 2.5 :pre
 
 pair_style lj/cut/coul/long 10.0
-pair_style lj/cut/coul/long/cs 10.0
 pair_style lj/cut/coul/long 10.0 8.0
-pair_style lj/cut/coul/long/cs 10.0 8.0
 pair_coeff * * 100.0 3.0
 pair_coeff 1 1 100.0 3.5 9.0 :pre
 
@@ -184,11 +183,6 @@ specified for this style means that pairwise interactions within this
 distance are computed directly; interactions outside that distance are
 computed in reciprocal space.
 
-Style {lj/cut/coul/long/cs} is identical to {lj/cut/coul/long} except
-that a term is added for the "core/shell model"_Howto_coreshell.html
-to allow charges on core and shell particles to be separated by r =
-0.0.
-
 Style {coul/wolf} adds a Coulombic pairwise interaction via the Wolf
 summation method, described in "Wolf"_#Wolf1, given by:
 

doc/src/pair_lj_expand.txt

@@ -8,7 +8,10 @@
 
 pair_style lj/expand command :h3
 pair_style lj/expand/gpu command :h3
+pair_style lj/expand/kk command :h3
 pair_style lj/expand/omp command :h3
+pair_style lj/expand/coul/long command :h3
+pair_style lj/expand/coul/long/gpu command :h3
 
 [Syntax:]
 
@@ -22,6 +25,11 @@ pair_style lj/expand 2.5
 pair_coeff * * 1.0 1.0 0.5
 pair_coeff 1 1 1.0 1.0 -0.2 2.0 :pre
 
+pair_style lj/expand/coul/long 2.5
+pair_style lj/expand/coul/long 2.5 4.0
+pair_coeff * * 1.0 1.0 0.5
+pair_coeff 1 1 1.0 1.0 -0.2 3.0 :pre
+
 [Description:]
 
 Style {lj/expand} computes a LJ interaction with a distance shifted by
@@ -34,11 +42,12 @@ formula:
 Rc is the cutoff which does not include the delta distance.  I.e. the
 actual force cutoff is the sum of cutoff + delta.
 
-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 all of the {lj/expand} 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:
 
 epsilon (energy units)
 sigma (distance units)
@@ -48,6 +57,11 @@ cutoff (distance units) :ul
 The delta values can be positive or negative.  The last coefficient is
 optional.  If not specified, the global LJ cutoff is used.
 
+For {lj/expand/coul/long} only the LJ cutoff can be specified since a
+Coulombic cutoff cannot be specified for an individual I,J type pair.
+All type pairs use the same global Coulombic cutoff specified in the
+pair_style command.
+
 :line
 
 Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are

doc/src/pair_lj_long.txt

@@ -11,6 +11,7 @@ pair_style lj/long/coul/long/intel command :h3
 pair_style lj/long/coul/long/omp command :h3
 pair_style lj/long/coul/long/opt command :h3
 pair_style lj/long/tip4p/long command :h3
+pair_style lj/long/tip4p/long/omp command :h3
 
 [Syntax:]
 

doc/src/pair_meam_spline.txt

@@ -6,8 +6,8 @@
 
 :line
 
-pair_style meam/spline :h3
-pair_style meam/spline/omp :h3
+pair_style meam/spline command :h3
+pair_style meam/spline/omp command :h3
 
 [Syntax:]
 

doc/src/pair_meam_sw_spline.txt

@@ -6,8 +6,7 @@
 
 :line
 
-pair_style meam/sw/spline :h3
-pair_style meam/sw/spline/omp :h3
+pair_style meam/sw/spline command :h3
 
 [Syntax:]
 

doc/src/pair_nb3b_harmonic.txt

@@ -7,7 +7,6 @@
 :line
 
 pair_style nb3b/harmonic command :h3
-pair_style nb3b/harmonic/omp command :h3
 
 [Syntax:]
 
@@ -89,28 +88,6 @@ a particular simulation; LAMMPS ignores those entries.
 
 :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
-hardware, as discussed on the "Speed packages"_Speed_packages.html doc
-page.  The accelerated styles take the same arguments and should
-produce the same results, except for round-off and precision issues.
-
-These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
-USER-OMP and OPT packages, respectively.  They are only enabled if
-LAMMPS was built with those packages.  See the "Build
-package"_Build_package.html doc page for more info.
-
-You can specify the accelerated styles explicitly in your input script
-by including their suffix, or you can use the "-suffix command-line
-switch"_Run_options.html when you invoke LAMMPS, or you can use the
-"suffix"_suffix.html command in your input script.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
 [Restrictions:]
 
 This pair style can only be used if LAMMPS was built with the MANYBODY

doc/src/pair_sdk.txt

@@ -13,6 +13,8 @@ pair_style lj/sdk/omp command :h3
 pair_style lj/sdk/coul/long command :h3
 pair_style lj/sdk/coul/long/gpu command :h3
 pair_style lj/sdk/coul/long/omp command :h3
+pair_style lj/sdk/coul/msm command :h3
+pair_style lj/sdk/coul/msm/omp command :h3
 
 [Syntax:]
 
@@ -35,6 +37,10 @@ pair_style lj/sdk/coul/long 10.0
 pair_style lj/sdk/coul/long 10.0 12.0
 pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
 
+pair_style lj/sdk/coul/msm 10.0
+pair_style lj/sdk/coul/msm 10.0 12.0
+pair_coeff 1 1 lj9_6 100.0 3.5 12.0 :pre
+
 [Description:]
 
 The {lj/sdk} styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
@@ -75,10 +81,10 @@ and Coulombic interactions for this type pair.  If both coefficients
 are specified, they are used as the LJ and Coulombic cutoffs for this
 type pair.
 
-For {lj/sdk/coul/long} only the LJ cutoff can be specified since a
-Coulombic cutoff cannot be specified for an individual I,J type pair.
-All type pairs use the same global Coulombic cutoff specified in the
-pair_style command.
+For {lj/sdk/coul/long} and {lj/sdk/coul/msm} only the LJ cutoff can be
+specified since a Coulombic cutoff cannot be specified for an
+individual I,J type pair.  All type pairs use the same global
+Coulombic cutoff specified in the pair_style command.
 
 :line
 

doc/src/pair_spin_magelec.txt

@@ -6,11 +6,11 @@
 
 :line
 
-pair_style spin/me command :h3
+pair_style spin/magelec command :h3
 
 [Syntax:]
 
-pair_style spin/me cutoff :pre
+pair_style spin/magelec cutoff :pre
 
 cutoff = global cutoff pair (distance in metal units) :ulb,l
 
@@ -18,8 +18,8 @@ cutoff = global cutoff pair (distance in metal units) :ulb,l
 
 [Examples:]
 
-pair_style spin/me 4.5
-pair_coeff * * me 4.5 0.00109 1.0 1.0 1.0 :pre
+pair_style spin/magelec 4.5
+pair_coeff * * magelec 4.5 0.00109 1.0 1.0 1.0 :pre
 
 [Description:]
 

doc/src/pair_spin_neel.txt

@@ -29,34 +29,36 @@ between pairs of magnetic spins:
 
 :c,image(Eqs/pair_spin_neel_interaction.jpg)
 
-where si and sj are two neighboring magnetic spins of two particles, 
+where si and sj are two neighboring magnetic spins of two particles,
 rij = ri - rj is the inter-atomic distance between the two particles,
-eij = (ri - rj)/|ri-rj| is their normalized separation vector 
-and g1, q1 and q2 are three functions defining the intensity of the
-dipolar and quadrupolar contributions, with:
+eij = (ri - rj)/|ri-rj| is their normalized separation vector and g1,
+q1 and q2 are three functions defining the intensity of the dipolar
+and quadrupolar contributions, with:
 
 :c,image(Eqs/pair_spin_neel_functions.jpg)
 
-With the functions g(rij) and q(rij) defined and fitted according to the same
-Bethe-Slater function used to fit the exchange interaction: 
+With the functions g(rij) and q(rij) defined and fitted according to
+the same Bethe-Slater function used to fit the exchange interaction:
 
 :c,image(Eqs/pair_spin_exchange_function.jpg)
 
-where a, b and d are the three constant coefficients defined in the associated 
-"pair_coeff" command.   
+where a, b and d are the three constant coefficients defined in the
+associated "pair_coeff" command.
 
-The coefficients a, b, and d need to be fitted so that the function above matches with 
-the values of the magneto-elastic constant of the materials at stake. 
+The coefficients a, b, and d need to be fitted so that the function
+above matches with the values of the magneto-elastic constant of the
+materials at stake.
 
-Examples and more explanations about this function and its parametrization are reported 
-in "(Tranchida)"_#Tranchida6. More examples of parametrization will be provided in 
-future work.
+Examples and more explanations about this function and its
+parametrization are reported in "(Tranchida)"_#Tranchida6. More
+examples of parametrization will be provided in future work.
 
-From this DM interaction, each spin i will be submitted to a magnetic torque
-omega and its associated atom to a force F (for spin-lattice calculations only). 
+From this DM interaction, each spin i will be submitted to a magnetic
+torque omega and its associated atom to a force F (for spin-lattice
+calculations only).
 
-More details about the derivation of these torques/forces are reported in
-"(Tranchida)"_#Tranchida6.
+More details about the derivation of these torques/forces are reported
+in "(Tranchida)"_#Tranchida6.
 
 :line
 

doc/src/pair_style.txt

@@ -95,120 +95,217 @@ GPUs, and KNLs.  The individual style names on the "Commands
 pair"_Commands_pair.html doc page are followed by one or more of
 (g,i,k,o,t) to indicate which accelerated styles exist.
 
-"pair_style none"_pair_none.html - turn off pairwise interactions
-"pair_style hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
-"pair_style hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
-"pair_style zero"_pair_zero.html - neighbor list but no interactions :ul
+"none"_pair_none.html - turn off pairwise interactions
+"hybrid"_pair_hybrid.html - multiple styles of pairwise interactions
+"hybrid/overlay"_pair_hybrid.html - multiple styles of superposed pairwise interactions
+"zero"_pair_zero.html - neighbor list but no interactions :ul
 
-"pair_style adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
-"pair_style airebo"_pair_airebo.html - AIREBO potential of Stuart
-"pair_style airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
-"pair_style atm"_pair_atm.html - Axilrod-Teller-Muto potential
-"pair_style beck"_pair_beck.html - Beck potential
-"pair_style body/nparticle"_pair_body_nparticle.html - interactions between body particles
-"pair_style bop"_pair_bop.html - BOP potential of Pettifor
-"pair_style born"_pair_born.html - Born-Mayer-Huggins potential
-"pair_style born/coul/long"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics
-"pair_style born/coul/long/cs"_pair_born.html - Born-Mayer-Huggins with long-range Coulombics and core/shell
-"pair_style born/coul/msm"_pair_born.html - Born-Mayer-Huggins with long-range MSM Coulombics
-"pair_style born/coul/wolf"_pair_born.html - Born-Mayer-Huggins with Coulombics via Wolf potential
-"pair_style brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
-"pair_style brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
-"pair_style buck"_pair_buck.html - Buckingham potential
-"pair_style buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
-"pair_style buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
-"pair_style buck/coul/long/cs"_pair_buck.html - Buckingham with long-range Coulombics and core/shell
-"pair_style buck/coul/msm"_pair_buck.html - Buckingham long-range MSM Coulombics
-"pair_style buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics
-"pair_style colloid"_pair_colloid.html - integrated colloidal potential
-"pair_style comb"_pair_comb.html - charge-optimized many-body (COMB) potential
-"pair_style comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
-"pair_style coul/cut"_pair_coul.html - cutoff Coulombic potential
-"pair_style coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
-"pair_style coul/dsf"_pair_coul.html - Coulombics via damped shifted forces
-"pair_style coul/long"_pair_coul.html - long-range Coulombic potential
-"pair_style coul/long/cs"_pair_coul.html - long-range Coulombic potential and core/shell
-"pair_style coul/msm"_pair_coul.html - long-range MSM Coulombics
-"pair_style coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
-"pair_style coul/wolf"_pair_coul.html - Coulombics via Wolf potential
-"pair_style dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
-"pair_style dpd/tstat"_pair_dpd.html - DPD thermostatting
-"pair_style dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
-"pair_style eam"_pair_eam.html - embedded atom method (EAM)
-"pair_style eam/alloy"_pair_eam.html - alloy EAM
-"pair_style eam/fs"_pair_eam.html - Finnis-Sinclair EAM
-"pair_style eim"_pair_eim.html - embedded ion method (EIM)
-"pair_style gauss"_pair_gauss.html - Gaussian potential
-"pair_style gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
-"pair_style gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
-"pair_style gran/hooke"_pair_gran.html - granular potential with history effects
-"pair_style gran/hooke/history"_pair_gran.html - granular potential without history effects
-"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
-"pair_style hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
-"pair_style kim"_pair_kim.html - interface to potentials provided by KIM project
-"pair_style lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
-"pair_style line/lj"_pair_line_lj.html - LJ potential between line segments
-"pair_style lj/charmm/coul/charmm"_pair_charmm.html - CHARMM potential with cutoff Coulomb
-"pair_style lj/charmm/coul/charmm/implicit"_pair_charmm.html - CHARMM for implicit solvent
-"pair_style lj/charmm/coul/long"_pair_charmm.html - CHARMM with long-range Coulomb
-"pair_style lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
-"pair_style lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
-"pair_style lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
-"pair_style lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
-"pair_style lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
-"pair_style lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"pair_style lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"pair_style lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
-"pair_style lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
-"pair_style lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
-"pair_style lj/cut/coul/long/cs"_pair_lj.html - LJ with long-range Coulombics and core/shell
-"pair_style lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
-"pair_style lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
-"pair_style lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"pair_style lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
-"pair_style lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"pair_style lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
-"pair_style lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
-"pair_style lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
-"pair_style lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
-"pair_style lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles
-"pair_style lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulomb for TIP4P water
-"pair_style lj/smooth"_pair_lj_smooth.html - smoothed Lennard-Jones potential
-"pair_style lj/smooth/linear"_pair_lj_smooth_linear.html - linear smoothed Lennard-Jones potential
-"pair_style lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
-"pair_style lubricate"_pair_lubricate.html - hydrodynamic lubrication forces
-"pair_style lubricate/poly"_pair_lubricate.html - hydrodynamic lubrication forces with polydispersity
-"pair_style lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
-"pair_style lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
-"pair_style meam"_pair_meam.html - modified embedded atom method (MEAM)
-"pair_style mie/cut"_pair_mie.html - Mie potential
-"pair_style morse"_pair_morse.html - Morse potential
-"pair_style nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential
-"pair_style nm/cut"_pair_nm.html - N-M potential
-"pair_style nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
-"pair_style nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
-"pair_style peri/eps"_pair_peri.html - peridynamic EPS potential
-"pair_style peri/lps"_pair_peri.html - peridynamic LPS potential
-"pair_style peri/pmb"_pair_peri.html - peridynamic PMB potential
-"pair_style peri/ves"_pair_peri.html - peridynamic VES potential
-"pair_style polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
-"pair_style reax"_pair_reax.html - ReaxFF potential
-"pair_style rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
-"pair_style resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
-"pair_style snap"_pair_snap.html - SNAP quantum-accurate potential
-"pair_style soft"_pair_soft.html - Soft (cosine) potential
-"pair_style sw"_pair_sw.html - Stillinger-Weber 3-body potential
-"pair_style table"_pair_table.html - tabulated pair potential
-"pair_style tersoff"_pair_tersoff.html - Tersoff 3-body potential
-"pair_style tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
-"pair_style tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
-"pair_style tip4p/cut"_pair_coul.html - Coulomb for TIP4P water w/out LJ
-"pair_style tip4p/long"_pair_coul.html - long-range Coulombics for TIP4P water w/out LJ
-"pair_style tri/lj"_pair_tri_lj.html - LJ potential between triangles
-"pair_style vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
-"pair_style yukawa"_pair_yukawa.html - Yukawa potential
-"pair_style yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
-"pair_style zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
+"adp"_pair_adp.html - angular dependent potential (ADP) of Mishin
+"agni"_pair_agni.html - machine learned potential mapping atomic environment to forces
+"airebo"_pair_airebo.html - AIREBO potential of Stuart
+"airebo/morse"_pair_airebo.html - AIREBO with Morse instead of LJ
+"atm"_pair_atm.html - Axilrod-Teller-Muto potential
+"awpmd/cut"_pair_awpmd.html - Antisymmetrized Wave Packet MD potential for atoms and electrons
+"beck"_pair_beck.html - Beck potential
+"body/nparticle"_pair_body_nparticle.html - interactions between body particles
+"body/rounded/polygon"_pair_body_rounded_polygon.html - granular-style 2d polygon potential
+"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html - granular-style 3d polyhedron potential
+"bop"_pair_bop.html - BOP potential of Pettifor
+"born"_pair_born.html - Born-Mayer-Huggins potential
+"born/coul/dsf"_pair_born.html - Born with damped-shifted-force model
+"born/coul/dsf/cs"_pair_cs.html - Born with damped-shifted-force and core/shell model
+"born/coul/long"_pair_born.html - Born with long-range Coulombics
+"born/coul/long/cs"_pair_cs.html - Born with long-range Coulombics and core/shell
+"born/coul/msm"_pair_born.html - Born with long-range MSM Coulombics
+"born/coul/wolf"_pair_born.html - Born with Wolf potential for Coulombics
+"born/coul/wolf/cs"_pair_cs.html - Born with Wolf potential for Coulombics and core/shell model
+"brownian"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics
+"brownian/poly"_pair_brownian.html - Brownian potential for Fast Lubrication Dynamics with polydispersity
+"buck"_pair_buck.html - Buckingham potential
+"buck/coul/cut"_pair_buck.html - Buckingham with cutoff Coulomb
+"buck/coul/long"_pair_buck.html - Buckingham with long-range Coulombics
+"buck/coul/long/cs"_pair_cs.html - Buckingham with long-range Coulombics and core/shell
+"buck/coul/msm"_pair_buck.html - Buckingham with long-range MSM Coulombics
+"buck/long/coul/long"_pair_buck_long.html - long-range Buckingham with long-range Coulombics
+"buck/mdf"_pair_mdf.html - Buckingham with a taper function
+"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with damped-shift-force model
+"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html - dispersion-damped Buckingham with long-range Coulombics
+"colloid"_pair_colloid.html - integrated colloidal potential
+"comb"_pair_comb.html - charge-optimized many-body (COMB) potential
+"comb3"_pair_comb.html - charge-optimized many-body (COMB3) potential
+"coul/cut"_pair_coul.html - cutoff Coulombic potential
+"coul/cut/soft"_pair_lj_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/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
+"coul/wolf"_pair_coul.html - Coulombics via Wolf potential
+"coul/wolf/cs"_pair_cs.html - ditto with core/shell adjustments
+"dpd"_pair_dpd.html - dissipative particle dynamics (DPD)
+"dpd/fdt"_pair_dpd_fdt.html - DPD for constant temperature and pressure
+"dpd/fdt/energy"_pair_dpd_fdt.html - DPD for constant energy and enthalpy
+"dpd/tstat"_pair_dpd.html - pair-wise DPD thermostatting
+"dsmc"_pair_dsmc.html - Direct Simulation Monte Carlo (DSMC)
+"eam"_pair_eam.html - embedded atom method (EAM)
+"eam/alloy"_pair_eam.html - alloy EAM
+"eam/cd"_pair_eam.html - concentration-dependent EAM
+"eam/cd/old"_pair_eam.html - older two-site model for concentration-dependent EAM
+"eam/fs"_pair_eam.html - Finnis-Sinclair EAM
+"edip"_pair_edip.html - three-body EDIP potential
+"edip/multi"_pair_edip.html - multi-element EDIP potential
+"edpd"_pair_meso.html - eDPD particle interactions
+"eff/cut"_pair_eff.html - electron force field with a cutoff
+"eim"_pair_eim.html - embedded ion method (EIM)
+"exp6/rx"_pair_exp6_rx.html - reactive DPD potential
+"extep"_pair_extep.html - extended Tersoff potential
+"gauss"_pair_gauss.html - Gaussian potential
+"gauss/cut"_pair_gauss.html - generalized Gaussian potential
+"gayberne"_pair_gayberne.html - Gay-Berne ellipsoidal potential
+"gran/hertz/history"_pair_gran.html - granular potential with Hertzian interactions
+"gran/hooke"_pair_gran.html - granular potential with history effects
+"gran/hooke/history"_pair_gran.html - granular potential without history effects
+"gw"_pair_gw.html - Gao-Weber potential
+"gw/zbl"_pair_gw.html - Gao-Weber potential with a repulsive ZBL core
+"hbond/dreiding/lj"_pair_hbond_dreiding.html - DREIDING hydrogen bonding LJ potential
+"hbond/dreiding/morse"_pair_hbond_dreiding.html - DREIDING hydrogen bonding Morse potential
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html - registry-dependent interlayer potential (ILP)
+"kim"_pair_kim.html - interface to potentials provided by KIM project
+"kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html - Kolmogorov-Crespi (KC) potential with no simplifications
+"kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html - Kolmogorov-Crespi (KC) potential with normals along z-axis
+"lcbop"_pair_lcbop.html - long-range bond-order potential (LCBOP)
+"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
+"line/lj"_pair_line_lj.html - LJ potential between line segments
+"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
+"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/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/long"_pair_class2.html - COMPASS with long-range Coulomb
+"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/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/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/thole/long"_pair_thole.html - LJ with Coulomibics 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/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
+"lj/gromacs/coul/gromacs"_pair_gromacs.html - GROMACS-style LJ and Coulombic potential
+"lj/long/coul/long"_pair_lj_long.html - long-range LJ and long-range Coulombics
+"lj/long/dipole/long"_pair_dipole.html - long-range LJ and long-range point dipoles
+"lj/long/tip4p/long"_pair_lj_long.html - long-range LJ and long-range Coulombics for TIP4P water
+"lj/mdf"_pair_mdf.html - LJ potential with a taper function
+"lj/sdk"_pair_sdk.html - LJ for SDK coarse-graining
+"lj/sdk/coul/long"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics
+"lj/sdk/coul/msm"_pair_sdk.html - LJ for SDK coarse-graining with long-range Coulombics via MSM
+"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
+"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
+"lubricateU"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication Dynamics
+"lubricateU/poly"_pair_lubricateU.html - hydrodynamic lubrication forces for Fast Lubrication with polydispersity
+"mdpd"_pair_meso.html - mDPD particle interactions
+"mdpd/rhosum"_pair_meso.html - mDPD particle interactions for mass density
+"meam"_pair_meam.html - modified embedded atom method (MEAM) in Fortran
+"meam/c"_pair_meam.html - modified embedded atom method (MEAM) in C
+"meam/spline"_pair_meam_spline.html - splined version of MEAM
+"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
+"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
+"morse/soft"_pair_morse.html - Morse potential with a soft core
+"multi/lucy"_pair_multi_lucy.html - DPD potential with density-dependent force
+"multi/lucy/rx"_pair_multi_lucy_rx.html - reactive DPD potential with density-dependent force
+"nb3b/harmonic"_pair_nb3b_harmonic.html - nonbonded 3-body harmonic potential
+"nm/cut"_pair_nm.html - N-M potential
+"nm/cut/coul/cut"_pair_nm.html - N-M potential with cutoff Coulomb
+"nm/cut/coul/long"_pair_nm.html - N-M potential with long-range Coulombics
+"oxdna/coaxstk"_pair_oxdna.html - 
+"oxdna/excv"_pair_oxdna.html - 
+"oxdna/hbond"_pair_oxdna.html - 
+"oxdna/stk"_pair_oxdna.html - 
+"oxdna/xstk"_pair_oxdna.html - 
+"oxdna2/coaxstk"_pair_oxdna2.html - 
+"oxdna2/dh"_pair_oxdna2.html - 
+"oxdna2/excv"_pair_oxdna2.html - 
+"oxdna2/hbond"_pair_oxdna2.html - 
+"oxdna2/stk"_pair_oxdna2.html - 
+"oxdna2/xstk"_pair_oxdna2.html - 
+"peri/eps"_pair_peri.html - peridynamic EPS potential
+"peri/lps"_pair_peri.html - peridynamic LPS potential
+"peri/pmb"_pair_peri.html - peridynamic PMB potential
+"peri/ves"_pair_peri.html - peridynamic VES potential
+"polymorphic"_pair_polymorphic.html - polymorphic 3-body potential
+"python"_pair_python.html - 
+"quip"_pair_quip.html - 
+"reax"_pair_reax.html - ReaxFF potential in Fortran
+"reax/c"_pair_reaxc.html - ReaxFF potential in C
+"rebo"_pair_airebo.html - 2nd generation REBO potential of Brenner
+"resquared"_pair_resquared.html - Everaers RE-Squared ellipsoidal potential
+"smd/hertz"_pair_smd_hertz.html - 
+"smd/tlsph"_pair_smd_tlsph.html - 
+"smd/tri_surface"_pair_smd_triangulated_surface.html - 
+"smd/ulsph"_pair_smd_ulsph.html - 
+"smtbq"_pair_smtbq.html - 
+"snap"_pair_snap.html - SNAP quantum-accurate potential
+"soft"_pair_soft.html - Soft (cosine) potential
+"sph/heatconduction"_pair_sph_heatconduction.html - 
+"sph/idealgas"_pair_sph_idealgas.html - 
+"sph/lj"_pair_sph_lj.html - 
+"sph/rhosum"_pair_sph_rhosum.html - 
+"sph/taitwater"_pair_sph_taitwater.html - 
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html - 
+"spin/dmi"_pair_spin_dmi.html - 
+"spin/exchange"_pair_spin_exchange.html - 
+"spin/magelec"_pair_spin_magelec.html - 
+"spin/neel"_pair_spin_neel.html - 
+"srp"_pair_srp.html - 
+"sw"_pair_sw.html - Stillinger-Weber 3-body potential
+"table"_pair_table.html - tabulated pair potential
+"table/rx"_pair_table_rx.html - 
+"tdpd"_pair_meso.html - tDPD particle interactions
+"tersoff"_pair_tersoff.html - Tersoff 3-body potential
+"tersoff/mod"_pair_tersoff_mod.html - modified Tersoff 3-body potential
+"tersoff/mod/c"_pair_tersoff_mod.html - 
+"tersoff/table"_pair_tersoff.html - 
+"tersoff/zbl"_pair_tersoff_zbl.html - Tersoff/ZBL 3-body potential
+"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 - 
+"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
+"vashishta/table"_pair_vashishta.html - 
+"yukawa"_pair_yukawa.html - Yukawa potential
+"yukawa/colloid"_pair_yukawa_colloid.html - screened Yukawa potential for finite-size particles
+"zbl"_pair_zbl.html - Ziegler-Biersack-Littmark potential :ul
 
 :line
 

doc/src/pair_tersoff.txt

@@ -8,10 +8,10 @@
 
 pair_style tersoff command :h3
 pair_style tersoff/table command :h3
-pair_style tersoff/gpu :h3
-pair_style tersoff/intel :h3
-pair_style tersoff/kk :h3
-pair_style tersoff/omp :h3
+pair_style tersoff/gpu command :h3
+pair_style tersoff/intel command :h3
+pair_style tersoff/kk command :h3
+pair_style tersoff/omp command :h3
 pair_style tersoff/table/omp command :h3
 
 [Syntax:]

doc/src/special_bonds.txt

@@ -13,7 +13,7 @@ special_bonds command :h3
 special_bonds keyword values ... :pre
 
 one or more keyword/value pairs may be appended :ulb,l
-keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
+keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} :l
   {amber} values = none
   {charmm} values = none
   {dreiding} values = none
@@ -219,7 +219,7 @@ each time the command is issued.
 [Default:]
 
 All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
-angle = no, dihedral = no, and extra = 0.
+angle = no, dihedral = no.
 
 :line
 

examples/SPIN/bfo/in.spin.bfo

@@ -36,7 +36,7 @@ fix 		3 all nve/spin lattice no
 
 timestep	0.0002
 
-compute 	out_mag	 all compute/spin
+compute 	out_mag	 all spin
 compute 	out_pe	 all pe
 compute 	out_ke	 all ke
 compute 	out_temp all temp

examples/SPIN/cobalt_fcc/in.spin.cobalt_fcc

@@ -40,7 +40,7 @@ timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/cobalt_hcp/in.spin.cobalt_hcp

@@ -40,7 +40,7 @@ fix 		3 all nve/spin lattice yes
 timestep	0.0001
 
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/iron/in.spin.iron

@@ -37,7 +37,7 @@ timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/nickel/in.spin.nickel

@@ -38,7 +38,7 @@ timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/read_restart/in.spin.read_data

@@ -25,7 +25,7 @@ timestep	0.0001
 
 # define outputs and computes
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/read_restart/in.spin.restart

@@ -29,7 +29,7 @@ timestep	0.0001
 
 # define outputs
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/SPIN/read_restart/in.spin.write_restart

@@ -34,7 +34,7 @@ timestep	0.0001
 
 # compute and output options
 
-compute 	out_mag    all compute/spin
+compute 	out_mag    all spin
 compute 	out_pe     all pe
 compute 	out_ke     all ke
 compute 	out_temp   all temp

examples/USER/scafacos/in.scafacos

@@ -1,7 +1,7 @@
 # Point dipoles in a 2d box
 
 units		lj
-atom_style  full	
+atom_style  charge	
 
 read_data data.NaCl
 
@@ -29,7 +29,7 @@ pair_coeff	* *
 #fix		2 all scafacos p3m tolerance field 0.001
 
 kspace_style    scafacos p3m 0.001
-kspace_style    scafacos tolerance field 
+#kspace_style    scafacos tolerance field 
 
 timestep	0.005
 thermo          10

examples/USER/smd/fluid_structure_interaction/fluid_structure_interaction.lmp

@@ -129,7 +129,7 @@ compute         contact_radius all smd/contact/radius
 compute         S solids smd/tlsph/stress
 compute         nn water smd/ulsph/num/neighs
 compute         epl solids smd/plastic/strain
-compute         vol all smd/volume
+compute         vol all smd/vol
 compute         rho all smd/rho
 
 dump            dump_id all custom 100 dump.LAMMPS id type x y &