diff --git a/doc/Makefile b/doc/Makefile
index eceae88da6..a3c4906cec 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -31,7 +31,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 SOURCES=$(filter-out $(wildcard $(TXTDIR)/lammps_commands*.txt) $(TXTDIR)/lammps_support.txt $(TXTDIR)/lammps_tutorials.txt,$(wildcard $(TXTDIR)/*.txt))
 OBJECTS=$(SOURCES:$(TXTDIR)/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi rst html pdf venv spelling anchor_check style_check
 
 # ------------------------------------------
 
@@ -46,6 +46,7 @@ help:
 	@echo "  clean      remove all intermediate RST files"
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
@@ -69,6 +70,7 @@ html: $(OBJECTS) $(ANCHORCHECK)
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -122,24 +124,27 @@ pdf: $(OBJECTS) $(ANCHORCHECK)
 		cd ../../; \
 	)
 	@(\
-                . $(VENV)/bin/activate ;\
-                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-                echo "############################################" ;\
-                rst_anchor_check src/*.rst ;\
-                echo "############################################" ;\
-                deactivate ;\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		echo "############################################" ;\
+		deactivate ;\
 	)
 	@cd latex && \
-          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
-	  mv temp Makefile && \
-	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
-	  mv tmp.tex LAMMPS.tex && \
-	  make && \
-	  make && \
-	  mv LAMMPS.pdf ../Manual.pdf && \
-	  cd ../;
+		sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+		mv temp Makefile && \
+		sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+		mv tmp.tex LAMMPS.tex && \
+		make && \
+		make && \
+		make && \
+		mv LAMMPS.pdf ../Manual.pdf && \
+		cd ../;
 	@rm -rf latex/_sources
 	@rm -rf latex/PDF
 	@rm -rf latex/USER
@@ -166,6 +171,13 @@ anchor_check : $(ANCHORCHECK)
 		deactivate ;\
 	)
 
+style_check :
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		deactivate ;\
+	)
+
 # ------------------------------------------
 
 $(RSTDIR)/%.rst : $(TXTDIR)/%.txt $(TXT2RST)
diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst
index c02b24641e..2cba59bde0 100644
--- a/doc/src/Build_extras.rst
+++ b/doc/src/Build_extras.rst
@@ -203,7 +203,7 @@ inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
-For using KIM web queries.
+For using OpenKIM web queries in LAMMPS.
 
 If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
 libcurl calls within the KIM web query display a lot of information about
diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst
index d47c3299d0..5ad8fff44c 100644
--- a/doc/src/Commands_all.rst
+++ b/doc/src/Commands_all.rst
@@ -25,26 +25,26 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
    * :doc:`bond_coeff <bond_coeff>`
-   * :doc:`bond\_style <bond_style>`
-   * :doc:`bond\_write <bond_write>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
    * :doc:`box <box>`
-   * :doc:`change\_box <change_box>`
+   * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
-   * :doc:`comm\_modify <comm_modify>`
-   * :doc:`comm\_style <comm_style>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
    * :doc:`compute <compute>`
-   * :doc:`compute\_modify <compute_modify>`
-   * :doc:`create\_atoms <create_atoms>`
-   * :doc:`create\_bonds <create_bonds>`
-   * :doc:`create\_box <create_box>`
-   * :doc:`delete\_atoms <delete_atoms>`
-   * :doc:`delete\_bonds <delete_bonds>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
    * :doc:`dielectric <dielectric>`
-   * :doc:`dihedral\_coeff <dihedral_coeff>`
-   * :doc:`dihedral\_style <dihedral_style>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
    * :doc:`dimension <dimension>`
-   * :doc:`displace\_atoms <displace_atoms>`
+   * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
    * :doc:`dump adios <dump_adios>`
    * :doc:`dump image <dump_image>`
@@ -52,75 +52,77 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`dump netcdf <dump_netcdf>`
    * :doc:`dump netcdf/mpiio <dump_netcdf>`
    * :doc:`dump vtk <dump_vtk>`
-   * :doc:`dump\_modify <dump_modify>`
-   * :doc:`dynamical\_matrix <dynamical_matrix>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
-   * :doc:`fix\_modify <fix_modify>`
+   * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`if <if>`
-   * :doc:`improper\_coeff <improper_coeff>`
-   * :doc:`improper\_style <improper_style>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
+   * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim\_init <kim_commands>`
-   * :doc:`kim\_interactions <kim_commands>`
-   * :doc:`kim\_query <kim_commands>`
-   * :doc:`kspace\_modify <kspace_modify>`
-   * :doc:`kspace\_style <kspace_style>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
-   * :doc:`min\_modify <min_modify>`
-   * :doc:`min\_style <min_style>`
-   * :doc:`min\_style spin <min_spin>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
    * :doc:`molecule <molecule>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`
    * :doc:`neb/spin <neb_spin>`
-   * :doc:`neigh\_modify <neigh_modify>`
+   * :doc:`neigh_modify <neigh_modify>`
    * :doc:`neighbor <neighbor>`
    * :doc:`newton <newton>`
    * :doc:`next <next>`
    * :doc:`package <package>`
-   * :doc:`pair\_coeff <pair_coeff>`
-   * :doc:`pair\_modify <pair_modify>`
-   * :doc:`pair\_write <pair_write>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`
    * :doc:`python <python>`
    * :doc:`quit <quit>`
-   * :doc:`read\_data <read_data>`
-   * :doc:`read\_dump <read_dump>`
-   * :doc:`read\_restart <read_restart>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset\_ids <reset_ids>`
-   * :doc:`reset\_timestep <reset_timestep>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
-   * :doc:`run\_style <run_style>`
+   * :doc:`run_style <run_style>`
    * :doc:`server <server>`
    * :doc:`set <set>`
    * :doc:`shell <shell>`
-   * :doc:`special\_bonds <special_bonds>`
+   * :doc:`special_bonds <special_bonds>`
    * :doc:`suffix <suffix>`
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
    * :doc:`temper/grem <temper_grem>`
    * :doc:`temper/npt <temper_npt>`
    * :doc:`thermo <thermo>`
-   * :doc:`thermo\_modify <thermo_modify>`
-   * :doc:`thermo\_style <thermo_style>`
-   * :doc:`third\_order <third_order>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -129,7 +131,11 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`units <units>`
    * :doc:`variable <variable>`
    * :doc:`velocity <velocity>`
-   * :doc:`write\_coeff <write_coeff>`
-   * :doc:`write\_data <write_data>`
-   * :doc:`write\_dump <write_dump>`
-   * :doc:`write\_restart <write_restart>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`
+   *
+   *
+   *
+   *
diff --git a/doc/src/Commands_bond.rst b/doc/src/Commands_bond.rst
index dbf7344394..27ff2d19da 100644
--- a/doc/src/Commands_bond.rst
+++ b/doc/src/Commands_bond.rst
@@ -13,7 +13,7 @@
 
 .. _bond:
 
-bond_style potentials
+Bond_style potentials
 =====================
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
@@ -44,16 +44,14 @@ OPT.
    * :doc:`nonlinear (o) <bond_nonlinear>`
    * :doc:`oxdna/fene <bond_oxdna>`
    * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
    * :doc:`table (o) <bond_table>`
    *
-   *
-
----
 
 .. _angle:
 
-angle_style potentials
+Angle_style potentials
 ======================
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
@@ -93,11 +91,9 @@ OPT.
    * :doc:`table (o) <angle_table>`
    *
 
----
-
 .. _dihedral:
 
-dihedral_style potentials
+Dihedral_style potentials
 =========================
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
@@ -136,7 +132,7 @@ OPT.
 
 .. _improper:
 
-improper_style potentials
+Improper_style potentials
 =========================
 
 All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst
index 4cd9a4487c..9584cbf64f 100644
--- a/doc/src/Commands_fix.rst
+++ b/doc/src/Commands_fix.rst
@@ -105,13 +105,13 @@ OPT.
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
-   * :doc:`neb\_spin <fix_neb_spin>`
+   * :doc:`neb/spin <fix_neb_spin>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
-   * :doc:`nphug (o) <fix_nphug>`
+   * :doc:`nphug <fix_nphug>`
    * :doc:`npt (iko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
@@ -188,15 +188,16 @@ OPT.
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <fix_setforce>`
    * :doc:`shake <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
-   * :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
-   * :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
-   * :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
-   * :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
    * :doc:`smd/setvel <fix_smd_setvel>`
-   * :doc:`smd/wall\_surface <fix_smd_wall_surface>`
+   * :doc:`smd/wall_surface <fix_smd_wall_surface>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
@@ -237,4 +238,3 @@ OPT.
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
    *
-   *
diff --git a/doc/src/Commands_kspace.rst b/doc/src/Commands_kspace.rst
index fc2418ecf7..3a23520171 100644
--- a/doc/src/Commands_kspace.rst
+++ b/doc/src/Commands_kspace.rst
@@ -24,12 +24,16 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
-   * :doc:`pppm (gok) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
-   * :doc:`pppm/disp (i) <kspace_style>`
-   * :doc:`pppm/disp/tip4p <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst
index b4371420a7..06eda554a3 100644
--- a/doc/src/Commands_pair.rst
+++ b/doc/src/Commands_pair.rst
@@ -11,10 +11,10 @@
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
-Pair\_style potentials
+Pair_style potentials
 ======================
 
-All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have
+All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -146,7 +146,7 @@ OPT.
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
    * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
-   * :doc:`lj/cut/tip4p/long (ot) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
    * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@@ -162,7 +162,7 @@ OPT.
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (o) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
-   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
    * :doc:`local/density <pair_local_density>`
    * :doc:`lubricate (o) <pair_lubricate>`
@@ -176,6 +176,7 @@ OPT.
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -197,10 +198,17 @@ OPT.
    * :doc:`oxdna2/hbond <pair_oxdna2>`
    * :doc:`oxdna2/stk <pair_oxdna2>`
    * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
    * :doc:`peri/ves <pair_peri>`
+   * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`reax/c (ko) <pair_reaxc>`
@@ -209,7 +217,7 @@ OPT.
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smd/hertz <pair_smd_hertz>`
    * :doc:`smd/tlsph <pair_smd_tlsph>`
-   * :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
diff --git a/doc/src/Errors_warnings.rst b/doc/src/Errors_warnings.rst
index ad5323c6ad..4a944eeb18 100644
--- a/doc/src/Errors_warnings.rst
+++ b/doc/src/Errors_warnings.rst
@@ -195,6 +195,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Fix SRD walls overlap but fix srd overlap not set*
    You likely want to set this in your input script.
 
+* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
+   When using fix bond/create multiple times or in combination with
+   fix bond/break, the individual fix instances do not share information
+   about changes they made at the same time step and thus it may result
+   in unexpected behavior.
+
 *Fix bond/swap will ignore defined angles*
    See the doc page for fix bond/swap for more info on this
    restriction.
diff --git a/doc/src/Examples.rst b/doc/src/Examples.rst
index a223939d5a..993090baf1 100644
--- a/doc/src/Examples.rst
+++ b/doc/src/Examples.rst
@@ -133,6 +133,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | reax        | RDX and TATB models using the ReaxFF                             |
 +-------------+------------------------------------------------------------------+
+| rerun       | use of rerun and read\_dump commands                             |
++-------------+------------------------------------------------------------------+
 | rigid       | rigid bodies modeled as independent or coupled                   |
 +-------------+------------------------------------------------------------------+
 | shear       | sideways shear applied to 2d solid, with and without a void      |
diff --git a/doc/src/Howto_client_server.rst b/doc/src/Howto_client_server.rst
index 6e36369667..26f14e8e5b 100644
--- a/doc/src/Howto_client_server.rst
+++ b/doc/src/Howto_client_server.rst
@@ -24,9 +24,38 @@ atoms.  The quantum code computes energy and forces based on the
 coords.  It returns them as a message to LAMMPS, which completes the
 timestep.
 
+A more complex example is where LAMMPS is the client code and
+processes a series of data files, sending each configuration to a
+quantum code to compute energy and forces.  Or LAMMPS runs dynamics
+with an atomistic force field, but pauses every N steps to ask the
+quantum code to compute energy and forces.
+
 Alternate methods for code coupling with LAMMPS are described on
 the :doc:`Howto couple <Howto_couple>` doc page.
 
+The protocol for using LAMMPS as a client is to use these 3 commands
+in this order (other commands may come in between):
+
+* :doc:`message client <message>`  # initiate client/server interaction
+* :doc:`fix client/md <fix_client_md>`   # any client fix which makes specific requests to the server
+* :doc:`message quit <message>`    # terminate client/server interaction
+
+In between the two message commands, a client fix command and
+:doc:`unfix <unfix>` command can be used multiple times.  Similarly,
+this sequence of 3 commands can be repeated multiple times, assuming
+the server program operates in a similar fashion, to initiate and
+terminate client/server communication.
+
+The protocol for using LAMMPS as a server is to use these 2 commands
+in this order (other commands may come in between):
+
+* :doc:`message server <message>`  # initiate client/server interaction
+* :doc:`server md <server_md>`    # any server command which responds to specific requests from the client
+
+This sequence of 2 commands can be repeated multiple times, assuming
+the client program operates in a similar fashion, to initiate and
+terminate client/server communication.
+
 LAMMPS support for client/server coupling is in its :ref:`MESSAGE package <PKG-MESSAGE>` which implements several
 commands that enable LAMMPS to act as a client or server, as discussed
 below.  The MESSAGE package also wraps a client/server library called
@@ -39,8 +68,8 @@ programs.
 .. note::
 
    For client/server coupling to work between LAMMPS and another
-   code, the other code also has to use the CSlib.  This can sometimes be
-   done without any modifications to the other code by simply wrapping it
+   code, the other code also has to use the CSlib.  This can often be
+   done without any modification to the other code by simply wrapping it
    with a Python script that exchanges CSlib messages with LAMMPS and
    prepares input for or processes output from the other code.  The other
    code also has to implement a matching protocol for the format and
diff --git a/doc/src/Manual_build.rst b/doc/src/Manual_build.rst
index a8bc093812..c1cd1aabb9 100644
--- a/doc/src/Manual_build.rst
+++ b/doc/src/Manual_build.rst
@@ -55,9 +55,9 @@ the doc dir.
    make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
    make clean        # remove intermediate RST files created by HTML build
    make clean-all    # remove entire build folder and any cached data
-
-make anchor\_check # check for duplicate anchor labels
-make spelling     # spell-check the manual
+   make anchor_check # check for duplicate anchor labels
+   style_check       # check for complete and consistent style lists
+   make spelling     # spell-check the manual
 
 
 ----------
diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst
index a8274d5403..62615a8fb7 100644
--- a/doc/src/Packages_details.rst
+++ b/doc/src/Packages_details.rst
@@ -2438,8 +2438,8 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`bond\_style mm3 <bond_mm3>`
 * :doc:`improper\_style distharm <improper_distharm>`
 * :doc:`improper\_style sqdistharm <improper_sqdistharm>`
-* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss>`
-* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+* :doc:`pair\_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair\_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/USER/yaff
 
 
diff --git a/doc/src/bond_style.rst b/doc/src/bond_style.rst
index 3c5c97b96b..dd3acb6833 100644
--- a/doc/src/bond_style.rst
+++ b/doc/src/bond_style.rst
@@ -100,6 +100,7 @@ accelerated styles exist.
 * :doc:`nonlinear <bond_nonlinear>` - nonlinear bond
 * :doc:`oxdna/fene <bond_oxdna>` - modified FENE bond suitable for DNA modeling
 * :doc:`oxdna2/fene <bond_oxdna>` - same as oxdna but used with different pair styles
+* :doc:`oxrna2/fene <bond_oxdna>` - modified FENE bond suitable for RNA modeling
 * :doc:`quartic <bond_quartic>` - breakable quartic bond
 * :doc:`table <bond_table>` - tabulated by bond length
 
diff --git a/doc/src/fix.rst b/doc/src/fix.rst
index a9ec639b33..cc99940f81 100644
--- a/doc/src/fix.rst
+++ b/doc/src/fix.rst
@@ -64,16 +64,16 @@ with new settings).  This is the same as if an "unfix" command were
 first performed on the old fix, except that the new fix is kept in the
 same order relative to the existing fixes as the old one originally
 was.  Note that this operation also wipes out any additional changes
-made to the old fix via the :doc:`fix\_modify <fix_modify>` command.
+made to the old fix via the :doc:`fix_modify <fix_modify>` command.
 
 The :doc:`fix modify <fix_modify>` command allows settings for some
 fixes to be reset.  See the doc page for individual fixes for details.
 
 Some fixes store an internal "state" which is written to binary
 restart files via the :doc:`restart <restart>` or
-:doc:`write\_restart <write_restart>` commands.  This allows the fix to
+:doc:`write_restart <write_restart>` commands.  This allows the fix to
 continue on with its calculations in a restarted simulation.  See the
-:doc:`read\_restart <read_restart>` command for info on how to re-specify
+:doc:`read_restart <read_restart>` command for info on how to re-specify
 a fix in an input script that reads a restart file.  See the doc pages
 for individual fixes for info on which ones can be restarted.
 
@@ -133,7 +133,7 @@ various commands explain the details.
 
 In LAMMPS, the values generated by a fix can be used in several ways:
 
-* Global values can be output via the :doc:`thermo\_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
+* Global values can be output via the :doc:`thermo_style custom <thermo_style>` or :doc:`fix ave/time <fix_ave_time>` command.
   Or the values can be referenced in a :doc:`variable equal <variable>` or
   :doc:`variable atom <variable>` command.
 * Per-atom values can be output via the :doc:`dump custom <dump>` command.
@@ -257,6 +257,7 @@ accelerated styles exist.
 * :doc:`mvv/edpd <fix_mvv_dpd>` - constant energy DPD using the modified velocity-Verlet algorithm
 * :doc:`mvv/tdpd <fix_mvv_dpd>` - constant temperature DPD using the modified velocity-Verlet algorithm
 * :doc:`neb <fix_neb>` - nudged elastic band (NEB) spring forces
+* :doc:`neb/spin <fix_neb_spin>` - nudged elastic band (NEB) spring forces for spins
 * :doc:`nph <fix_nh>` - constant NPH time integration via Nose/Hoover
 * :doc:`nph/asphere <fix_nph_asphere>` - NPH for aspherical particles
 * :doc:`nph/body <fix_nph_body>` - NPH for body particles
@@ -339,15 +340,16 @@ accelerated styles exist.
 * :doc:`rx <fix_rx>` -
 * :doc:`saed/vtk <fix_saed_vtk>` -
 * :doc:`setforce <fix_setforce>` - set the force on each atom
+* :doc:`setforce/spin <fix_setforce>` - set magnetic precession vectors on each atom
 * :doc:`shake <fix_shake>` - SHAKE constraints on bonds and/or angles
 * :doc:`shardlow <fix_shardlow>` - integration of DPD equations of motion using the Shardlow splitting
 * :doc:`smd <fix_smd>` - applied a steered MD force to a group
-* :doc:`smd/adjust\_dt <fix_smd_adjust_dt>` -
-* :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>` -
-* :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>` -
-* :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>` -
+* :doc:`smd/adjust_dt <fix_smd_adjust_dt>` -
+* :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>` -
+* :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>` -
+* :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>` -
 * :doc:`smd/setvel <fix_smd_setvel>` -
-* :doc:`smd/wall\_surface <fix_smd_wall_surface>` -
+* :doc:`smd/wall_surface <fix_smd_wall_surface>` -
 * :doc:`spring <fix_spring>` - apply harmonic spring force to group of atoms
 * :doc:`spring/chunk <fix_spring_chunk>` - apply harmonic spring force to each chunk of atoms
 * :doc:`spring/rg <fix_spring_rg>` - spring on radius of gyration of group of atoms
@@ -399,7 +401,7 @@ individual fixes tell if it is part of a package.
 Related commands
 """"""""""""""""
 
-:doc:`unfix <unfix>`, :doc:`fix\_modify <fix_modify>`
+:doc:`unfix <unfix>`, :doc:`fix_modify <fix_modify>`
 
 **Default:** none
 
diff --git a/doc/src/fix_client_md.rst b/doc/src/fix_client_md.rst
index 853a09a9c4..d935144cc0 100644
--- a/doc/src/fix_client_md.rst
+++ b/doc/src/fix_client_md.rst
@@ -41,10 +41,10 @@ computes their interaction, and returns the energy, forces, and virial
 for the interacting particles to LAMMPS, so it can complete the
 timestep.
 
-The server code could be a quantum code, or another classical MD code
-which encodes a force field (pair\_style in LAMMPS lingo) which LAMMPS
-does not have.  In the quantum case, this fix is a mechanism for
-running *ab initio* MD with quantum forces.
+Note that the server code can be a quantum code, or another classical
+MD code which encodes a force field (pair\_style in LAMMPS lingo) which
+LAMMPS does not have.  In the quantum case, this fix is a mechanism
+for running *ab initio* MD with quantum forces.
 
 The group associated with this fix is ignored.
 
@@ -99,8 +99,8 @@ This fix is part of the MESSAGE package.  It is only enabled if LAMMPS
 was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
 
 A script that uses this command must also use the
-:doc:`message <message>` command to setup the messaging protocol with
-the other server code.
+:doc:`message <message>` command to setup and shut down the messaging
+protocol with the server code.
 
 Related commands
 """"""""""""""""
diff --git a/doc/src/fix_deposit.rst b/doc/src/fix_deposit.rst
index 45ae785f89..29b4381441 100644
--- a/doc/src/fix_deposit.rst
+++ b/doc/src/fix_deposit.rst
@@ -57,6 +57,8 @@ Syntax
          fix-ID = ID of :doc:`fix rigid/small <fix_rigid>` command
        *shake* value = fix-ID
          fix-ID = ID of :doc:`fix shake <fix_shake>` command
+       *orient* values = rx ry rz
+         rx,ry,rz = vector to randomly rotate an inserted molecule around
        *units* value = *lattice* or *box*
          lattice = the geometry is defined in lattice units
          box = the geometry is defined in simulation box units
@@ -236,6 +238,13 @@ sputtering process.  E.g. the target point can be far away, so that
 all incident particles strike the surface as if they are in an
 incident beam of particles at a prescribed angle.
 
+The *orient* keyword is only used when molecules are deposited.  By
+default, each molecule is inserted at a random orientation.  If this
+keyword is specified, then (rx,ry,rz) is used as an orientation
+vector, and each inserted molecule is rotated around that vector with
+a random value from zero to 2*PI.  For a 2d simulation, rx = ry = 0.0
+is required, since rotations can only be performed around the z axis.
+
 The *id* keyword determines how atom IDs and molecule IDs are assigned
 to newly deposited particles.  Molecule IDs are only assigned if
 molecules are being inserted.  For the *max* setting, the atom and
diff --git a/doc/src/kspace_style.rst b/doc/src/kspace_style.rst
index b5c649a885..32179f8be0 100644
--- a/doc/src/kspace_style.rst
+++ b/doc/src/kspace_style.rst
@@ -11,26 +11,30 @@ Syntax
 
    kspace_style style value
 
-* style = *none* or *ewald* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
-  
+* style = *none* or *ewald* or *ewald/dipole* or *ewald/dipole/spin* or *ewald/disp* or *ewald/omp* or *pppm* or *pppm/cg* or *pppm/disp* or *pppm/tip4p* or *pppm/stagger* or *pppm/disp/tip4p* or *pppm/gpu* or *pppm/intel* or *pppm/disp/intel* or *pppm/kk* or *pppm/omp* or *pppm/cg/omp* or *pppm/disp/tip4p/omp* or *pppm/tip4p/omp* or *msm* or *msm/cg* or *msm/omp* or *msm/cg/omp* or *scafacos*
+
   .. parsed-literal::
-  
+
        *none* value = none
        *ewald* value = accuracy
          accuracy = desired relative error in forces
-       *ewald/disp* value = accuracy
-         accuracy = desired relative error in forces
-       *ewald/omp* value = accuracy
-         accuracy = desired relative error in forces
        *ewald/dipole* value = accuracy
          accuracy = desired relative error in forces
        *ewald/dipole/spin* value = accuracy
          accuracy = desired relative error in forces
+       *ewald/disp* value = accuracy
+         accuracy = desired relative error in forces
+       *ewald/omp* value = accuracy
+         accuracy = desired relative error in forces
        *pppm* value = accuracy
          accuracy = desired relative error in forces
        *pppm/cg* values = accuracy (smallq)
          accuracy = desired relative error in forces
          smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/dipole* value = accuracy
+         accuracy = desired relative error in forces
+       *pppm/dipole/spin* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/disp* value = accuracy
          accuracy = desired relative error in forces
        *pppm/tip4p* value = accuracy
@@ -41,22 +45,23 @@ Syntax
          accuracy = desired relative error in forces
        *pppm/intel* value = accuracy
          accuracy = desired relative error in forces
+       *pppm/disp/intel* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/kk* value = accuracy
          accuracy = desired relative error in forces
        *pppm/omp* value = accuracy
          accuracy = desired relative error in forces
-       *pppm/cg/omp* value = accuracy
+       *pppm/cg/omp* values = accuracy (smallq)
          accuracy = desired relative error in forces
-       *pppm/disp/intel* value = accuracy
+         smallq = cutoff for charges to be considered (optional) (charge units)
+       *pppm/disp/omp* value = accuracy
          accuracy = desired relative error in forces
        *pppm/tip4p/omp* value = accuracy
          accuracy = desired relative error in forces
+       *pppm/disp/tip4p/omp* value = accuracy
+         accuracy = desired relative error in forces
        *pppm/stagger* value = accuracy
          accuracy = desired relative error in forces
-       *pppm/dipole* value = accuracy
-         accuracy = desired relative error in forces
-       *pppm/dipole/spin* value = accuracy
-         accuracy = desired relative error in forces
        *msm* value = accuracy
          accuracy = desired relative error in forces
        *msm/cg* value = accuracy (smallq)
diff --git a/doc/src/message.rst b/doc/src/message.rst
index f81b498152..6891512b85 100644
--- a/doc/src/message.rst
+++ b/doc/src/message.rst
@@ -11,7 +11,7 @@ Syntax
 
    message which protocol mode arg
 
-* which = *client* or *server*
+* which = *client* or *server* or *quit*
 * protocol = *md* or *mc*
 * mode = *file* or *zmq* or *mpi/one* or *mpi/two*
   
@@ -46,6 +46,8 @@ Examples
    message client md mpi/two tmp.couple
    message server md mpi/two tmp.couple
 
+   message quit
+
 Description
 """""""""""
 
@@ -64,6 +66,10 @@ enables the two codes to work in tandem to perform a simulation.
 
 The *which* argument defines LAMMPS to be the client or the server.
 
+As explained below the *quit* option should be used when LAMMPS is
+finished as a client.  It sends a message to the server to tell it to
+shut down.
+
 
 ----------
 
@@ -146,12 +152,12 @@ path/file in a common filesystem.
 ----------
 
 
-Normally, the message command should be used at the top of a LAMMPS
-input script.  It performs an initial handshake with the other code to
-setup messaging and to verify that both codes are using the same
-message protocol and mode.  Assuming both codes are launched at
-(nearly) the same time, the other code should perform the same kind of
-initialization.
+Normally, the message client or message server command should be used
+at the top of a LAMMPS input script.  It performs an initial handshake
+with the other code to setup messaging and to verify that both codes
+are using the same message protocol and mode.  Assuming both codes are
+launched at (nearly) the same time, the other code should perform the
+same kind of initialization.
 
 If LAMMPS is the client code, it will begin sending messages when a
 LAMMPS client command begins its operation.  E.g. for the :doc:`fix client/md <fix_client_md>` command, it is when a :doc:`run <run>`
@@ -160,16 +166,25 @@ command is executed.
 If LAMMPS is the server code, it will begin receiving messages when
 the :doc:`server <server>` command is invoked.
 
-A fix client command will terminate its messaging with the server when
-LAMMPS ends, or the fix is deleted via the :doc:`unfix <unfix>` 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.
+If LAMMPS is being used as a client, the message quit command will
+terminate its messaging with the server.  If you do not use this
+command and just allow LAMMPS to exit, then the server will continue
+to wait for further messages.  This may not be a problem, but if both
+the client and server programs were launched in the same batch script,
+then if the server runs indefinitely, it may consume the full allocation
+of computer time, even if the calculation finishes sooner.
 
-If both codes do something similar, this means a new round of
-client/server messaging can be initiated after termination by re-using
-a 2nd message command in your LAMMPS input script, followed by a new
-fix client or server command.
+Note that if LAMMPS is the client or server, it will continue
+processing the rest of its input script after client/server
+communication terminates.
+
+If both codes cooperate in this manner, a new round of client/server
+messaging can be initiated after termination by re-using a 2nd message
+command in your LAMMPS input script, followed by a new fix client or
+server command, followed by another message quit command (if LAMMPS is
+the client).  As an example, this can be performed in a loop to use a
+quantum code as a server to compute quantum forces for multiple LAMMPS
+data files or periodic snapshots while running dynamics.
 
 
 ----------
diff --git a/doc/src/pair_lj.rst b/doc/src/pair_lj.rst
index 54140a9faf..7a46f0a0db 100644
--- a/doc/src/pair_lj.rst
+++ b/doc/src/pair_lj.rst
@@ -90,6 +90,9 @@ pair\_style lj/cut/coul/wolf/omp command
 pair\_style lj/cut/tip4p/cut command
 ====================================
 
+pair\_style lj/cut/tip4p/cut/gpu command
+========================================
+
 pair\_style lj/cut/tip4p/cut/omp command
 ========================================
 
@@ -102,9 +105,6 @@ pair\_style lj/cut/tip4p/long/omp command
 pair\_style lj/cut/tip4p/long/opt command
 =========================================
 
-pair\_style lj/cut/tip4p/long/gpu command
-=====================================
-
 Syntax
 """"""
 
diff --git a/doc/src/pair_lj_switch3_coulgauss.rst b/doc/src/pair_lj_switch3_coulgauss_long.rst
similarity index 100%
rename from doc/src/pair_lj_switch3_coulgauss.rst
rename to doc/src/pair_lj_switch3_coulgauss_long.rst
diff --git a/doc/src/pair_mm3_switch3_coulgauss.rst b/doc/src/pair_mm3_switch3_coulgauss_long.rst
similarity index 98%
rename from doc/src/pair_mm3_switch3_coulgauss.rst
rename to doc/src/pair_mm3_switch3_coulgauss_long.rst
index c124b9b9b8..3f3a7cbc72 100644
--- a/doc/src/pair_mm3_switch3_coulgauss.rst
+++ b/doc/src/pair_mm3_switch3_coulgauss_long.rst
@@ -37,7 +37,7 @@ Examples
 Description
 """""""""""
 
-The *mm3/switch3/coulgauss* style evaluates the MM3
+The *mm3/switch3/coulgauss/long* style evaluates the MM3
 vdW potential :ref:`(Allinger) <mm3-allinger1989>`
 
 .. image:: Eqs/pair_mm3_switch3.jpg
diff --git a/doc/src/pair_modify.rst b/doc/src/pair_modify.rst
index 664937ef61..b45a50573a 100644
--- a/doc/src/pair_modify.rst
+++ b/doc/src/pair_modify.rst
@@ -247,7 +247,9 @@ or *lj/coul* to change both to the same set of 3 values.  The wt1,wt2,wt3
 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
 1-3, and 1-4 bond topology neighbors, respectively. The *special*
 keyword can only be used in conjunction with the *pair* keyword
-and has to directly follow it.
+and has to directly follow it.  This option is not compatible with
+pair styles from the GPU or the USER-INTEL package and attempting
+it will cause an error.
 
 .. note::
 
@@ -278,10 +280,11 @@ and allows to selectively disable or enable processing of the various
 
 Restrictions
 """"""""""""
- none
 
 You cannot use *shift* yes with *tail* yes, since those are
 conflicting options.  You cannot use *tail* yes with 2d simulations.
+You cannot use *special* with pair styles from the GPU or
+USER-INTEL package.
 
 Related commands
 """"""""""""""""
diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst
index f6f686fc12..9b23266ca8 100644
--- a/doc/src/pair_style.rst
+++ b/doc/src/pair_style.rst
@@ -32,7 +32,7 @@ Description
 Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
 LAMMPS, pair potentials are defined between pairs of atoms that are
 within a cutoff distance and the set of active interactions typically
-changes over time.  See the :doc:`bond\_style <bond_style>` command to
+changes over time.  See the :doc:`bond_style <bond_style>` command to
 define potentials between pairs of bonded atoms, which typically
 remain in place for the duration of a simulation.
 
@@ -48,11 +48,11 @@ different pair potentials can be setup using the *hybrid* pair style.
 
 The coefficients associated with a pair style are typically set for
 each pair of atom types, and are specified by the
-:doc:`pair\_coeff <pair_coeff>` command or read from a file by the
-:doc:`read\_data <read_data>` or :doc:`read\_restart <read_restart>`
+:doc:`pair_coeff <pair_coeff>` command or read from a file by the
+:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
 commands.
 
-The :doc:`pair\_modify <pair_modify>` command sets options for mixing of
+The :doc:`pair_modify <pair_modify>` command sets options for mixing of
 type I-J interaction coefficients and adding energy offsets or tail
 corrections to Lennard-Jones potentials.  Details on these options as
 they pertain to individual potentials are described on the doc page
@@ -70,11 +70,11 @@ cutoffs for all pairs of atom types.  The distance(s) can be smaller
 or larger than the dimensions of the simulation box.
 
 Typically, the global cutoff value can be overridden for a specific
-pair of atom types by the :doc:`pair\_coeff <pair_coeff>` command.  The
+pair of atom types by the :doc:`pair_coeff <pair_coeff>` command.  The
 pair style settings (including global cutoffs) can be changed by a
 subsequent pair\_style command using the same style.  This will reset
 the cutoffs for all atom type pairs, including those previously set
-explicitly by a :doc:`pair\_coeff <pair_coeff>` command.  The exceptions
+explicitly by a :doc:`pair_coeff <pair_coeff>` command.  The exceptions
 to this are that pair\_style *table* and *hybrid* settings cannot be
 reset.  A new pair\_style command for these styles will wipe out all
 previously specified pair\_coeff values.
@@ -88,7 +88,7 @@ also listed in more compact form on the :doc:`Commands pair <Commands_pair>` doc
 
 Click on the style to display the formula it computes, any additional
 arguments specified in the pair\_style command, and coefficients
-specified by the associated :doc:`pair\_coeff <pair_coeff>` command.
+specified by the associated :doc:`pair_coeff <pair_coeff>` command.
 
 There are also additional accelerated pair styles included in the
 LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
@@ -170,6 +170,7 @@ accelerated styles exist.
 * :doc:`gauss <pair_gauss>` - Gaussian potential
 * :doc:`gauss/cut <pair_gauss>` - generalized Gaussian potential
 * :doc:`gayberne <pair_gayberne>` - Gay-Berne ellipsoidal potential
+* :doc:`granular <pair_granular>` - Generalized granular potential
 * :doc:`gran/hertz/history <pair_gran>` - granular potential with Hertzian interactions
 * :doc:`gran/hooke <pair_gran>` - granular potential with history effects
 * :doc:`gran/hooke/history <pair_gran>` - granular potential without history effects
@@ -231,7 +232,7 @@ accelerated styles exist.
 * :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
 * :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
 * :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential
-* `lj/switch3/coulgauss <pair_lj_switch3_coulgauss>`_ - smoothed LJ vdW potential with Gaussian electrostatics
+* :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed LJ vdW potential with Gaussian electrostatics
 * :doc:`lj96/cut <pair_lj96>` - Lennard-Jones 9/6 potential
 * :doc:`local/density <pair_local_density>` - generalized basic local density potential
 * :doc:`lubricate <pair_lubricate>` - hydrodynamic lubrication forces
@@ -245,7 +246,7 @@ accelerated styles exist.
 * :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
 * :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
 * :doc:`mie/cut <pair_mie>` - Mie potential
-* `mm3/switch3/coulgauss <pair_mm3_switch3_coulgauss>`_ - smoothed MM3 vdW potential with Gaussian electrostatics
+* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
 * :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
 * :doc:`morse <pair_morse>` - Morse potential
 * :doc:`morse/smooth/linear <pair_morse>` - linear smoothed Morse potential
@@ -267,6 +268,12 @@ accelerated styles exist.
 * :doc:`oxdna2/hbond <pair_oxdna2>` -
 * :doc:`oxdna2/stk <pair_oxdna2>` -
 * :doc:`oxdna2/xstk <pair_oxdna2>` -
+* :doc:`oxrna2/coaxstk <pair_oxrna2>` -
+* :doc:`oxrna2/dh <pair_oxrna2>` -
+* :doc:`oxrna2/excv <pair_oxrna2>` -
+* :doc:`oxrna2/hbond <pair_oxrna2>` -
+* :doc:`oxrna2/stk <pair_oxrna2>` -
+* :doc:`oxrna2/xstk <pair_oxrna2>` -
 * :doc:`peri/eps <pair_peri>` - peridynamic EPS potential
 * :doc:`peri/lps <pair_peri>` - peridynamic LPS potential
 * :doc:`peri/pmb <pair_peri>` - peridynamic PMB potential
@@ -280,7 +287,7 @@ accelerated styles exist.
 * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>` - smoothed dissipative particle dynamics for water at isothermal conditions
 * :doc:`smd/hertz <pair_smd_hertz>` -
 * :doc:`smd/tlsph <pair_smd_tlsph>` -
-* :doc:`smd/tri\_surface <pair_smd_triangulated_surface>` -
+* :doc:`smd/tri_surface <pair_smd_triangulated_surface>` -
 * :doc:`smd/ulsph <pair_smd_ulsph>` -
 * :doc:`smtbq <pair_smtbq>` -
 * :doc:`snap <pair_snap>` - SNAP quantum-accurate potential
@@ -328,8 +335,8 @@ Restrictions
 
 
 This command must be used before any coefficients are set by the
-:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`, or
-:doc:`read\_restart <read_restart>` commands.
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`, or
+:doc:`read_restart <read_restart>` commands.
 
 Some pair styles are part of specific packages.  They are only enabled
 if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.  The doc pages for
@@ -338,9 +345,9 @@ individual pair potentials tell if it is part of a package.
 Related commands
 """"""""""""""""
 
-:doc:`pair\_coeff <pair_coeff>`, :doc:`read\_data <read_data>`,
-:doc:`pair\_modify <pair_modify>`, :doc:`kspace\_style <kspace_style>`,
-:doc:`dielectric <dielectric>`, :doc:`pair\_write <pair_write>`
+:doc:`pair_coeff <pair_coeff>`, :doc:`read_data <read_data>`,
+:doc:`pair_modify <pair_modify>`, :doc:`kspace_style <kspace_style>`,
+:doc:`dielectric <dielectric>`, :doc:`pair_write <pair_write>`
 
 Default
 """""""
diff --git a/doc/src/server.rst b/doc/src/server.rst
index 463a67d356..f366639812 100644
--- a/doc/src/server.rst
+++ b/doc/src/server.rst
@@ -39,7 +39,7 @@ enables the two codes to work in tandem to perform a simulation.
 When this command is invoked, LAMMPS will run in server mode in an
 endless loop, waiting for messages from the client code.  The client
 signals when it is done sending messages to LAMMPS, at which point the
-loop will exit, and the remainder of the LAMMPS script will be
+loop will exit, and the remainder of the LAMMPS input script will be
 processed.
 
 The *protocol* argument defines the format and content of messages
diff --git a/doc/txt/Errors_warnings.txt b/doc/txt/Errors_warnings.txt
index 06474e1bb3..cb22b7ad0c 100644
--- a/doc/txt/Errors_warnings.txt
+++ b/doc/txt/Errors_warnings.txt
@@ -239,6 +239,13 @@ will be truncated to attempt to prevent the bond from blowing up. :dd
 
 You likely want to set this in your input script. :dd
 
+{ Fix bond/create is used multiple times or with fix bond/break - may not work as expected} :dt
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior. :dd
+
 {Fix bond/swap will ignore defined angles} :dt
 
 See the doc page for fix bond/swap for more info on this
diff --git a/doc/txt/Examples.txt b/doc/txt/Examples.txt
index 86617e13df..04c211cb1d 100644
--- a/doc/txt/Examples.txt
+++ b/doc/txt/Examples.txt
@@ -94,6 +94,7 @@ python:   using embedded Python in a LAMMPS input script
 qeq:      use of the QEQ package for charge equilibration
 rdf-adf:  computing radial and angle distribution functions for water
 reax:     RDX and TATB models using the ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
 snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
diff --git a/doc/txt/Howto_client_server.txt b/doc/txt/Howto_client_server.txt
deleted file mode 100644
index 96939809dc..0000000000
--- a/doc/txt/Howto_client_server.txt
+++ /dev/null
@@ -1,131 +0,0 @@
-"Higher level section"_Howto.html - "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
-
-Using LAMMPS in client/server mode :h3
-
-Client/server coupling of two codes is where one code is the "client"
-and sends request messages to a "server" code.  The server responds to
-each request with a reply message.  This enables the two codes to work
-in tandem to perform a simulation.  LAMMPS can act as either a client
-or server code.
-
-Some advantages of client/server coupling are that the two codes run
-as stand-alone executables; they are not linked together.  Thus
-neither code needs to have a library interface.  This often makes it
-easier to run the two codes on different numbers of processors.  If a
-message protocol (format and content) is defined for a particular kind
-of simulation, then in principle any code that implements the
-client-side protocol can be used in tandem with any code that
-implements the server-side protocol, without the two codes needing to
-know anything more specific about each other.
-
-A simple example of client/server coupling is where LAMMPS is the
-client code performing MD timestepping.  Each timestep it sends a
-message to a server quantum code containing current coords of all the
-atoms.  The quantum code computes energy and forces based on the
-coords.  It returns them as a message to LAMMPS, which completes the
-timestep.
-
-Alternate methods for code coupling with LAMMPS are described on
-the "Howto couple"_Howto_couple.html doc page.
-
-LAMMPS support for client/server coupling is in its "MESSAGE
-package"_Packages_details.html#PKG-MESSAGE which implements several
-commands that enable LAMMPS to act as a client or server, as discussed
-below.  The MESSAGE package also wraps a client/server library called
-CSlib which enables two codes to exchange messages in different ways,
-either via files, sockets, or MPI.  The CSlib is provided with LAMMPS
-in the lib/message dir.  The CSlib has its own
-"website"_http://cslib.sandia.gov with documentation and test
-programs.
-
-NOTE: For client/server coupling to work between LAMMPS and another
-code, the other code also has to use the CSlib.  This can sometimes be
-done without any modifications to the other code by simply wrapping it
-with a Python script that exchanges CSlib messages with LAMMPS and
-prepares input for or processes output from the other code.  The other
-code also has to implement a matching protocol for the format and
-content of messages that LAMMPS exchanges with it.
-
-These are the commands currently in the MESSAGE package for two
-protocols, MD and MC (Monte Carlo).  New protocols can easily be
-defined and added to this directory, where LAMMPS acts as either the
-client or server.
-
-"message"_message.html
-"fix client md"_fix_client_md.html = LAMMPS is a client for running MD
-"server md"_server_md.html = LAMMPS is a server for computing MD forces
-"server mc"_server_mc.html = LAMMPS is a server for computing a Monte Carlo energy :ul
-
-The server doc files give details of the message protocols
-for data that is exchanged between the client and server.
-
-These example directories illustrate how to use LAMMPS as either a
-client or server code:
-
-examples/message
-examples/COUPLE/README
-examples/COUPLE/lammps_mc
-examples/COUPLE/lammps_vasp :ul
-
-The examples/message dir couples a client instance of LAMMPS to a
-server instance of LAMMPS.
-
-The lammps_mc dir shows how to couple LAMMPS as a server to a simple
-Monte Carlo client code as the driver.
-
-The lammps_vasp dir shows how to couple LAMMPS as a client code
-running MD timestepping to VASP acting as a server providing quantum
-DFT forces, through a Python wrapper script on VASP.
-
-Here is how to launch a client and server code together for any of the
-4 modes of message exchange that the "message"_message.html command
-and the CSlib support.  Here LAMMPS is used as both the client and
-server code.  Another code could be substituted for either.
-
-The examples below show launching both codes from the same window (or
-batch script), using the "&" character to launch the first code in the
-background.  For all modes except {mpi/one}, you could also launch the
-codes in separate windows on your desktop machine.  It does not
-matter whether you launch the client or server first.
-
-In these examples either code can be run on one or more processors.
-If running in a non-MPI mode (file or zmq) you can launch a code on a
-single processor without using mpirun.
-
-IMPORTANT: If you run in mpi/two mode, you must launch both codes via
-mpirun, even if one or both of them runs on a single processor.  This
-is so that MPI can figure out how to connect both MPI processes
-together to exchange MPI messages between them.
-
-For message exchange in {file}, {zmq}, or {mpi/two} modes:
-
-% mpirun -np 1 lmp_mpi -log log.client < in.client &
-% mpirun -np 2 lmp_mpi -log log.server < in.server :pre
-
-% mpirun -np 4 lmp_mpi -log log.client < in.client &
-% mpirun -np 1 lmp_mpi -log log.server < in.server :pre
-
-% mpirun -np 2 lmp_mpi -log log.client < in.client &
-% mpirun -np 4 lmp_mpi -log log.server < in.server :pre
-
-For message exchange in {mpi/one} mode:
-
-Launch both codes in a single mpirun command:
-
-mpirun -np 2 lmp_mpi -mpicolor 0 -in in.message.client -log log.client : -np 4 lmp_mpi -mpicolor 1 -in in.message.server -log log.server :pre
-
-The two -np values determine how many procs the client and the server
-run on.
-
-A LAMMPS executable run in this manner must use the -mpicolor color
-command-line option as their its option, where color is an integer
-label that will be used to distinguish one executable from another in
-the multiple executables that the mpirun command launches.  In this
-example the client was colored with a 0, and the server with a 1.
diff --git a/doc/txt/Packages_details.txt b/doc/txt/Packages_details.txt
deleted file mode 100644
index fc30c045cf..0000000000
--- a/doc/txt/Packages_details.txt
+++ /dev/null
@@ -1,2157 +0,0 @@
-"Higher level section"_Packages.html - "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
-
-Package details :h3
-
-Here is a brief description of all the standard and user packages in
-LAMMPS.  It lists authors (if applicable) and summarizes the package
-contents.  It has specific instructions on how to install the package,
-including, if necessary, info on how to download or build any extra
-library it requires.  It also gives links to documentation, example
-scripts, and pictures/movies (if available) that illustrate use of the
-package.
-
-The majority of packages can be included in a LAMMPS build with a
-single setting (-D PGK_NAME for CMake) or command ("make yes-name" for
-make).  See the "Build package"_Build_package.html doc page for more
-info.  A few packages may require additional steps; this is indicated
-in the descriptions below.  The "Build extras"_Build_extras.html doc
-page gives those details.
-
-NOTE: To see the complete list of commands a package adds to LAMMPS,
-you can examine the files in its src directory, e.g. "ls
-src/GRANULAR".  Files with names that start with fix, compute, atom,
-pair, bond, angle, etc correspond to commands with the same style name
-as contained in the file name.
-
-"ASPHERE"_#PKG-ASPHERE,
-"BODY"_#PKG-BODY,
-"CLASS2"_#PKG-CLASS2,
-"COLLOID"_#PKG-COLLOID,
-"COMPRESS"_#PKG-COMPRESS,
-"CORESHELL"_#PKG-CORESHELL,
-"DIPOLE"_#PKG-DIPOLE,
-"GPU"_#PKG-GPU,
-"GRANULAR"_#PKG-GRANULAR,
-"KIM"_#PKG-KIM,
-"KOKKOS"_#PKG-KOKKOS,
-"KSPACE"_#PKG-KSPACE,
-"LATTE"_#PKG-LATTE,
-"MANYBODY"_#PKG-MANYBODY,
-"MC"_#PKG-MC,
-"MESSAGE"_#PKG-MESSAGE,
-"MISC"_#PKG-MISC,
-"MOLECULE"_#PKG-MOLECULE,
-"MPIIO"_#PKG-MPIIO,
-"MSCG"_#PKG-MSCG,
-"OPT"_#PKG-OPT,
-"PERI"_#PKG-PERI,
-"POEMS"_#PKG-POEMS,
-"PYTHON"_#PKG-PYTHON,
-"QEQ"_#PKG-QEQ,
-"REPLICA"_#PKG-REPLICA2,
-"RIGID"_#PKG-RIGID,
-"SHOCK"_#PKG-SHOCK,
-"SNAP"_#PKG-SNAP,
-"SPIN"_#PKG-SPIN,
-"SRD"_#PKG-SRD,
-"VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
-
-"USER-ADIOS"_#PKG-USER-ADIOS,
-"USER-ATC"_#PKG-USER-ATC,
-"USER-AWPMD"_#PKG-USER-AWPMD,
-"USER-BOCS"_#PKG-USER-BOCS,
-"USER-CGDNA"_#PKG-USER-CGDNA,
-"USER-CGSDK"_#PKG-USER-CGSDK,
-"USER-COLVARS"_#PKG-USER-COLVARS,
-"USER-DIFFRACTION"_#PKG-USER-DIFFRACTION,
-"USER-DPD"_#PKG-USER-DPD,
-"USER-DRUDE"_#PKG-USER-DRUDE,
-"USER-EFF"_#PKG-USER-EFF,
-"USER-FEP"_#PKG-USER-FEP,
-"USER-H5MD"_#PKG-USER-H5MD,
-"USER-INTEL"_#PKG-USER-INTEL,
-"USER-LB"_#PKG-USER-LB,
-"USER-MANIFOLD"_#PKG-USER-MANIFOLD,
-"USER-MEAMC"_#PKG-USER-MEAMC,
-"USER-MESO"_#PKG-USER-MESO,
-"USER-MGPT"_#PKG-USER-MGPT,
-"USER-MISC"_#PKG-USER-MISC,
-"USER-MOFFF"_#PKG-USER-MOFFF,
-"USER-MOLFILE"_#PKG-USER-MOLFILE,
-"USER-NETCDF"_#PKG-USER-NETCDF,
-"USER-OMP"_#PKG-USER-OMP,
-"USER-PHONON"_#PKG-USER-PHONON,
-"USER-PLUMED"_#PKG-USER-PLUMED,
-"USER-PTM"_#PKG-USER-PTM,
-"USER-QMMM"_#PKG-USER-QMMM,
-"USER-QTB"_#PKG-USER-QTB,
-"USER-QUIP"_#PKG-USER-QUIP,
-"USER-REAXC"_#PKG-USER-REAXC,
-"USER-SCAFACOS"_#PKG-USER-SCAFACOS,
-"USER-SDPD"_#PKG-USER-SDPD,
-"USER-SMD"_#PKG-USER-SMD,
-"USER-SMTBQ"_#PKG-USER-SMTBQ,
-"USER-SPH"_#PKG-USER-SPH,
-"USER-TALLY"_#PKG-USER-TALLY,
-"USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK,
-"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
-
-:line
-
-ASPHERE package :link(PKG-ASPHERE),h4
-
-[Contents:]
-
-Computes, time-integration fixes, and pair styles for aspherical
-particle models including ellipsoids, 2d lines, and 3d triangles.
-
-[Supporting info:]
-
-src/ASPHERE: filenames -> commands
-"Howto spherical"_Howto_spherical.html
-"pair_style gayberne"_pair_gayberne.html
-"pair_style resquared"_pair_resquared.html
-"doc/PDF/pair_gayberne_extra.pdf"_PDF/pair_gayberne_extra.pdf
-"doc/PDF/pair_resquared_extra.pdf"_PDF/pair_resquared_extra.pdf
-examples/ASPHERE
-examples/ellipse
-http://lammps.sandia.gov/movies.html#line
-http://lammps.sandia.gov/movies.html#tri :ul
-
-:line
-
-BODY package :link(PKG-BODY),h4
-
-[Contents:]
-
-Body-style particles with internal structure.  Computes,
-time-integration fixes, pair styles, as well as the body styles
-themselves.  See the "Howto body"_Howto_body.html doc page for an
-overview.
-
-[Supporting info:]
-
-src/BODY filenames -> commands
-"Howto_body"_Howto_body.html
-"atom_style body"_atom_style.html
-"fix nve/body"_fix_nve_body.html
-"pair_style body/nparticle"_pair_body_nparticle.html
-examples/body :ul
-
-:line
-
-CLASS2 package :link(PKG-CLASS2),h4
-
-[Contents:]
-
-Bond, angle, dihedral, improper, and pair styles for the COMPASS
-CLASS2 molecular force field.
-
-[Supporting info:]
-
-src/CLASS2: filenames -> commands
-"bond_style class2"_bond_class2.html
-"angle_style class2"_angle_class2.html
-"dihedral_style class2"_dihedral_class2.html
-"improper_style class2"_improper_class2.html
-"pair_style lj/class2"_pair_class2.html :ul
-
-:line
-
-COLLOID package :link(PKG-COLLOID),h4
-
-[Contents:]
-
-Coarse-grained finite-size colloidal particles.  Pair styles and fix
-wall styles for colloidal interactions.  Includes the Fast Lubrication
-Dynamics (FLD) method for hydrodynamic interactions, which is a
-simplified approximation to Stokesian dynamics.
-
-[Authors:] This package includes Fast Lubrication Dynamics pair styles
-which were created by Amit Kumar and Michael Bybee from Jonathan
-Higdon's group at UIUC.
-
-[Supporting info:]
-
-src/COLLOID: filenames -> commands
-"fix wall/colloid"_fix_wall.html
-"pair_style colloid"_pair_colloid.html
-"pair_style yukawa/colloid"_pair_yukawa_colloid.html
-"pair_style brownian"_pair_brownian.html
-"pair_style lubricate"_pair_lubricate.html
-"pair_style lubricateU"_pair_lubricateU.html
-examples/colloid
-examples/srd :ul
-
-:line
-
-COMPRESS package :link(PKG-COMPRESS),h4
-
-[Contents:]
-
-Compressed output of dump files via the zlib compression library,
-using dump styles with a "gz" in their style name.
-
-To use this package you must have the zlib compression library
-available on your system.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#compress on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/COMPRESS: filenames -> commands
-src/COMPRESS/README
-lib/compress/README
-"dump atom/gz"_dump.html
-"dump cfg/gz"_dump.html
-"dump custom/gz"_dump.html
-"dump xyz/gz"_dump.html :ul
-
-:line
-
-CORESHELL package :link(PKG-CORESHELL),h4
-
-[Contents:]
-
-Compute and pair styles that implement the adiabatic core/shell model
-for polarizability.  The pair styles augment Born, Buckingham, and
-Lennard-Jones styles with core/shell capabilities.  The "compute
-temp/cs"_compute_temp_cs.html command calculates the temperature of a
-system with core/shell particles.  See the "Howto
-coreshell"_Howto_coreshell.html doc page for an overview of how to use
-this package.
-
-[Author:] Hendrik Heenen (Technical U of Munich).
-
-[Supporting info:]
-
-src/CORESHELL: filenames -> commands
-"Howto coreshell"_Howto_coreshell.html
-"Howto polarizable"_Howto_polarizable.html
-"compute temp/cs"_compute_temp_cs.html
-"pair_style born/coul/long/cs"_pair_cs.html
-"pair_style buck/coul/long/cs"_pair_cs.html
-"pair_style lj/cut/coul/long/cs"_pair_lj.html
-examples/coreshell :ul
-
-:line
-
-DIPOLE package :link(PKG-DIPOLE),h4
-
-[Contents:]
-
-An atom style and several pair styles for point dipole models with
-short-range or long-range interactions.
-
-[Supporting info:]
-
-src/DIPOLE: filenames -> commands
-"atom_style dipole"_atom_style.html
-"pair_style lj/cut/dipole/cut"_pair_dipole.html
-"pair_style lj/cut/dipole/long"_pair_dipole.html
-"pair_style lj/long/dipole/long"_pair_dipole.html
-examples/dipole :ul
-
-:line
-
-GPU package :link(PKG-GPU),h4
-
-[Contents:]
-
-Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for GPUs.  All such styles have a "gpu" as a suffix
-in their style name. The GPU code can be compiled with either CUDA or
-OpenCL, however the OpenCL variants are no longer actively maintained
-and only the CUDA versions are regularly tested.  The "Speed
-gpu"_Speed_gpu.html doc page gives details of what hardware and GPU
-software is required on your system, and details on how to build and
-use this package.  Its styles can be invoked at run time via the "-sf
-gpu" or "-suffix gpu" "command-line switches"_Run_options.html.  See
-also the "KOKKOS"_#PKG-KOKKOS package, which has GPU-enabled styles.
-
-[Authors:] Mike Brown (Intel) while at Sandia and ORNL and Trung Nguyen
-(Northwestern U) while at ORNL.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/GPU: filenames -> commands
-src/GPU/README
-lib/gpu/README
-"Speed packages"_Speed_packages.html
-"Speed gpu"_Speed_gpu.html
-"Section 2.6 -sf gpu"_Run_options.html
-"Section 2.6 -pk gpu"_Run_options.html
-"package gpu"_package.html
-"Commands all"_lc pages (pair,kspace) for styles followed by (g)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-GRANULAR package :link(PKG-GRANULAR),h4
-
-[Contents:]
-
-Pair styles and fixes for finite-size granular particles, which
-interact with each other and boundaries via frictional and dissipative
-potentials.
-
-[Supporting info:]
-
-src/GRANULAR: filenames -> commands
-"Howto granular"_Howto_granular.html
-"fix pour"_fix_pour.html
-"fix wall/gran"_fix_wall_gran.html
-"pair_style gran/hooke"_pair_gran.html
-"pair_style gran/hertz/history"_pair_gran.html
-examples/granregion
-examples/pour
-bench/in.chute
-http://lammps.sandia.gov/pictures.html#jamming
-http://lammps.sandia.gov/movies.html#hopper
-http://lammps.sandia.gov/movies.html#dem
-http://lammps.sandia.gov/movies.html#brazil
-http://lammps.sandia.gov/movies.html#granregion :ul
-
-:line
-
-KIM package :link(PKG-KIM),h4
-
-[Contents:]
-
-This package contains a set of commands that serve as a wrapper on the
-"Open Knowledgebase of Interatomic Models (OpenKIM)"_https://openkim.org
-repository of interatomic models (IMs)
-enabling compatible ones to be used in LAMMPS simulations.
-This includes "kim_init and kim_interactions"_kim_commands.html
-commands to select, initialize and instantiate the IM, and a
-"kim_query"_kim_commands.html command to perform web queries
-for material property predictions of OpenKIM IMs.
-Support for KIM IMs that conform to the
-"KIM Application Programming Interface (API)"_https://openkim.org/kim-api/
-is provided by the "pair_style kim"_pair_kim.html command.
-
-NOTE: The command {pair_style kim} is called by {kim_interactions} and
-is not recommended to be directly used in input scripts.
-
-To use this package you must have the KIM API library available on your
-system. The KIM API is available for download on the
-"OpenKIM website"_https://openkim.org/kim-api/.
-When installing LAMMPS from binary, the kim-api package
-is a dependency that is automatically downloaded and installed.
-
-Information about the KIM project can be found at its website:
-"https://openkim.org"_https://openkim.org.
-The KIM project is led by Ellad Tadmor and Ryan Elliott (U Minnesota)
-and is funded by the "National Science Foundation"_https://www.nsf.gov/.
-
-[Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
-API and the {pair_style kim} command. Axel Kohlmeyer (Temple U) and
-Ellad Tadmor (U Minnesota) contributed to the "kim_commands"_kim_commands.html
-interface in close collaboration with Ryan Elliott.
-
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#kim on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-"kim_commands"_kim_commands.html
-"pair_style kim"_pair_kim.html
-src/KIM: filenames -> commands
-src/KIM/README
-lib/kim/README
-examples/kim :ul
-
-:line
-
-KOKKOS package :link(PKG-KOKKOS),h4
-
-[Contents:]
-
-Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
-styles adapted to compile using the Kokkos library which can convert
-them to OpenMP or CUDA code so that they run efficiently on multicore
-CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
-style name.  The "Speed kokkos"_Speed_kokkos.html doc page gives
-details of what hardware and software is required on your system, and
-how to build and use this package.  Its styles can be invoked at run
-time via the "-sf kk" or "-suffix kk" "command-line
-switches"_Run_options.html.  Also see the "GPU"_#PKG-GPU, "OPT"_#PKG-OPT,
-"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
-have styles optimized for CPUs, KNLs, and GPUs.
-
-You must have a C++11 compatible compiler to use this package.
-KOKKOS makes extensive use of advanced C++ features, which can
-expose compiler bugs, especially when compiling for maximum
-performance at high optimization levels. Please see the file
-lib/kokkos/README for a list of compilers and their respective
-platforms, that are known to work.
-
-[Authors:] The KOKKOS package was created primarily by Christian Trott
-and Stan Moore (Sandia), with contributions from other folks as well.
-It uses the open-source "Kokkos library"_https://github.com/kokkos
-which was developed by Carter Edwards, Christian Trott, and others at
-Sandia, and which is included in the LAMMPS distribution in
-lib/kokkos.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#kokkos on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/KOKKOS: filenames -> commands
-src/KOKKOS/README
-lib/kokkos/README
-"Speed packages"_Speed_packages.html
-"Speed kokkos"_Speed_kokkos.html
-"Section 2.6 -k on ..."_Run_options.html
-"Section 2.6 -sf kk"_Run_options.html
-"Section 2.6 -pk kokkos"_Run_options.html
-"package kokkos"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (k)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-KSPACE package :link(PKG-KSPACE),h4
-
-[Contents:]
-
-A variety of long-range Coulombic solvers, as well as pair styles
-which compute the corresponding short-range pairwise Coulombic
-interactions.  These include Ewald, particle-particle particle-mesh
-(PPPM), and multilevel summation method (MSM) solvers.
-
-[Install:]
-
-Building with this package requires a 1d FFT library be present on
-your system for use by the PPPM solvers.  This can be the KISS FFT
-library provided with LAMMPS, 3rd party libraries like FFTW, or a
-vendor-supplied FFT library.  See the "Build
-settings"_Build_settings.html doc page for details on how to select
-different FFT options for your LAMPMS build.
-
-[Supporting info:]
-
-src/KSPACE: filenames -> commands
-"kspace_style"_kspace_style.html
-"doc/PDF/kspace.pdf"_PDF/kspace.pdf
-"Howto tip3p"_Howto_tip3p.html
-"Howto tip4p"_Howto_tip4p.html
-"Howto spc"_Howto_spc.html
-"pair_style coul"_pair_coul.html
-"Commands pair"_Commands_pair.html page for styles with "long" or "msm" in name
-examples/peptide
-bench/in.rhodo :ul
-
-:line
-
-LATTE package :link(PKG-LATTE),h4
-
-[Contents:]
-
-A fix command which wraps the LATTE DFTB code, so that molecular
-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
-description is given with the "fix latte"_fix_latte.html command.
-
-: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
-Cawkwell, Anders Niklasson, and Christian Negre.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#latte on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/LATTE: filenames -> commands
-src/LATTE/README
-lib/latte/README
-"fix latte"_fix_latte.html
-examples/latte
-"LAMMPS-LATTE tutorial"_https://github.com/lanl/LATTE/wiki/Using-LATTE-through-LAMMPS :ul
-
-:line
-
-MANYBODY package :link(PKG-MANYBODY),h4
-
-[Contents:]
-
-A variety of many-body and bond-order potentials.  These include
-(AI)REBO, BOP, EAM, EIM, Stillinger-Weber, and Tersoff potentials.
-
-[Supporting info:]
-
-src/MANYBODY: filenames -> commands
-"Commands pair"_Commands_pair.html page
-examples/comb
-examples/eim
-examples/nb3d
-examples/shear
-examples/streitz
-examples/vashishta
-bench/in.eam :ul
-
-:line
-
-MC package :link(PKG-MC),h4
-
-[Contents:]
-
-Several fixes and a pair style that have Monte Carlo (MC) or MC-like
-attributes.  These include fixes for creating, breaking, and swapping
-bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
-
-[Supporting info:]
-
-src/MC: filenames -> commands
-"fix atom/swap"_fix_atom_swap.html
-"fix bond/break"_fix_bond_break.html
-"fix bond/create"_fix_bond_create.html
-"fix bond/swap"_fix_bond_swap.html
-"fix gcmc"_fix_gcmc.html
-"pair_style dsmc"_pair_dsmc.html
-http://lammps.sandia.gov/movies.html#gcmc :ul
-
-:line
-
-MESSAGE package :link(PKG-MESSAGE),h4
-
-[Contents:]
-
-Commands to use LAMMPS as either a client or server and couple it to
-another application.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#message on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MESSAGE: filenames -> commands
-lib/message/README
-"message"_message.html
-"fix client/md"_fix_client_md.html
-"server md"_server_md.html
-"server mc"_server_mc.html
-examples/message :ul
-
-:line
-
-MISC package :link(PKG-MISC),h4
-
-[Contents:]
-
-A variety of compute, fix, pair, dump styles with specialized
-capabilities that don't align with other packages.  Do a directory
-listing, "ls src/MISC", to see the list of commands.
-
-NOTE: the MISC package contains styles that require using the
--restrict flag, when compiling with Intel compilers.
-
-[Supporting info:]
-
-src/MISC: filenames -> commands
-"compute ti"_compute_ti.html
-"fix evaporate"_fix_evaporate.html
-"fix orient/fcc"_fix_orient.html
-"fix ttm"_fix_ttm.html
-"fix thermal/conductivity"_fix_thermal_conductivity.html
-"fix viscosity"_fix_viscosity.html
-examples/KAPPA
-examples/VISCOSITY
-http://lammps.sandia.gov/pictures.html#ttm
-http://lammps.sandia.gov/movies.html#evaporation :ul
-
-:line
-
-MOLECULE package :link(PKG-MOLECULE),h4
-
-[Contents:]
-
-A large number of atom, pair, bond, angle, dihedral, improper styles
-that are used to model molecular systems with fixed covalent bonds.
-The pair styles include the Dreiding (hydrogen-bonding) and CHARMM
-force fields, and a TIP4P water model.
-
-[Supporting info:]
-
-src/MOLECULE: filenames -> commands
-"atom_style"_atom_style.html
-"bond_style"_bond_style.html
-"angle_style"_angle_style.html
-"dihedral_style"_dihedral_style.html
-"improper_style"_improper_style.html
-"pair_style hbond/dreiding/lj"_pair_hbond_dreiding.html
-"pair_style lj/charmm/coul/charmm"_pair_charmm.html
-"Howto bioFF"_Howto_bioFF.html
-examples/cmap
-examples/dreiding
-examples/micelle,
-examples/peptide
-bench/in.chain
-bench/in.rhodo :ul
-
-:line
-
-MPIIO package :link(PKG-MPIIO),h4
-
-[Contents:]
-
-Support for parallel output/input of dump and restart files via the
-MPIIO library.  It adds "dump styles"_dump.html with a "mpiio" in
-their style name.  Restart files with an ".mpiio" suffix are also
-written and read in parallel.
-
-[Supporting info:]
-
-src/MPIIO: filenames -> commands
-"dump"_dump.html
-"restart"_restart.html
-"write_restart"_write_restart.html
-"read_restart"_read_restart.html :ul
-
-:line
-
-MSCG package :link(PKG-mscg),h4
-
-[Contents:]
-
-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.
-
-: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.
-
-[Authors:] The fix was written by Lauren Abbott (Sandia).  The MS-CG
-library was developed by Jacob Wagner in Greg Voth's group at the
-University of Chicago.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#mscg on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MSCG: filenames -> commands
-src/MSCG/README
-lib/mscg/README
-examples/mscg :ul
-
-:line
-
-OPT package :link(PKG-OPT),h4
-
-[Contents:]
-
-A handful of pair styles which are optimized for improved CPU
-performance on single or multiple cores.  These include EAM, LJ,
-CHARMM, and Morse potentials.  The styles have an "opt" suffix in
-their style name.  The "Speed opt"_Speed_opt.html doc page gives
-details of how to build and use this package.  Its styles can be
-invoked at run time via the "-sf opt" or "-suffix opt" "command-line
-switches"_Run_options.html.  See also the "KOKKOS"_#PKG-KOKKOS,
-"USER-INTEL"_#PKG-USER-INTEL, and "USER-OMP"_#PKG-USER-OMP packages, which
-have styles optimized for CPU performance.
-
-[Authors:] James Fischer (High Performance Technologies), David Richie,
-and Vincent Natoli (Stone Ridge Technolgy).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#opt on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/OPT: filenames -> commands
-"Speed packages"_Speed_packages.html
-"Speed opt"_Speed_opt.html
-"Section 2.6 -sf opt"_Run_options.html
-"Commands pair"_Commands_pair.html for styles followed by (t)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-PERI package :link(PKG-PERI),h4
-
-[Contents:]
-
-An atom style, several pair styles which implement different
-Peridynamics materials models, and several computes which calculate
-diagnostics.  Peridynamics is a particle-based meshless continuum
-model.
-
-[Authors:] The original package was created by Mike Parks (Sandia).
-Additional Peridynamics models were added by Rezwanur Rahman and John
-Foster (UTSA).
-
-[Supporting info:]
-
-src/PERI: filenames -> commands
-"doc/PDF/PDLammps_overview.pdf"_PDF/PDLammps_overview.pdf
-"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf
-"doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf
-"atom_style peri"_atom_style.html
-"pair_style peri/*"_pair_peri.html
-"compute damage/atom"_compute_damage_atom.html
-"compute plasticity/atom"_compute_plasticity_atom.html
-examples/peri
-http://lammps.sandia.gov/movies.html#peri :ul
-
-:line
-
-POEMS package :link(PKG-POEMS),h4
-
-[Contents:]
-
-A fix that wraps the Parallelizable Open source Efficient Multibody
-Software (POEMS) library, which is able to simulate the dynamics of
-articulated body systems.  These are systems with multiple rigid
-bodies (collections of particles) whose motion is coupled by
-connections at hinge points.
-
-[Author:] Rudra Mukherjee (JPL) while at RPI.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#poems on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/POEMS: filenames -> commands
-src/POEMS/README
-lib/poems/README
-"fix poems"_fix_poems.html
-examples/rigid :ul
-
-:line
-
-PYTHON package :link(PKG-PYTHON),h4
-
-[Contents:]
-
-A "python"_python.html command which allow you to execute Python code
-from a LAMMPS input script.  The code can be in a separate file or
-embedded in the input script itself.  See the "Python
-call"_Python_call.html doc page for an overview of using Python from
-LAMMPS in this manner and all the "Python"_Python_head.html doc pages
-for other ways to use LAMMPS and Python together.
-
-NOTE: Building with the PYTHON package assumes you have a Python
-shared library available on your system, which needs to be a Python 2
-version, 2.6 or later.  Python 3 is not yet supported.  See the
-lib/python/README for more details.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#python on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/PYTHON: filenames -> commands
-"Python call"_Python_head.html
-lib/python/README
-examples/python :ul
-
-:line
-
-QEQ package :link(PKG-QEQ),h4
-
-[Contents:]
-
-Several fixes for performing charge equilibration (QEq) via different
-algorithms.  These can be used with pair styles that perform QEq as
-part of their formulation.
-
-[Supporting info:]
-
-src/QEQ: filenames -> commands
-"fix qeq/*"_fix_qeq.html
-examples/qeq
-examples/streitz :ul
-
-:line
-
-REPLICA package :link(PKG-REPLICA2),h4
-
-[Contents:]
-
-A collection of multi-replica methods which can be used when running
-multiple LAMMPS simulations (replicas).  See the "Howto
-replica"_Howto_replica.html doc page for an overview of how to run
-multi-replica simulations in LAMMPS.  Methods in the package include
-nudged elastic band (NEB), parallel replica dynamics (PRD),
-temperature accelerated dynamics (TAD), parallel tempering, and a
-verlet/split algorithm for performing long-range Coulombics on one set
-of processors, and the remainder of the force field calculation on
-another set.
-
-[Supporting info:]
-
-src/REPLICA: filenames -> commands
-"Howto replica"_Howto_replica.html
-"neb"_neb.html
-"prd"_prd.html
-"tad"_tad.html
-"temper"_temper.html,
-"run_style verlet/split"_run_style.html
-examples/neb
-examples/prd
-examples/tad :ul
-
-:line
-
-RIGID package :link(PKG-RIGID),h4
-
-[Contents:]
-
-Fixes which enforce rigid constraints on collections of atoms or
-particles.  This includes SHAKE and RATTLE, as well as various
-rigid-body integrators for a few large bodies or many small bodies.
-Also several computes which calculate properties of rigid bodies.
-
-[Supporting info:]
-
-src/RIGID: filenames -> commands
-"compute erotate/rigid"_compute_erotate_rigid.html
-fix shake"_fix_shake.html
-"fix rattle"_fix_shake.html
-"fix rigid/*"_fix_rigid.html
-examples/ASPHERE
-examples/rigid
-bench/in.rhodo
-http://lammps.sandia.gov/movies.html#box
-http://lammps.sandia.gov/movies.html#star :ul
-
-:line
-
-SHOCK package :link(PKG-SHOCK),h4
-
-[Contents:]
-
-Fixes for running impact simulations where a shock-wave passes through
-a material.
-
-[Supporting info:]
-
-src/SHOCK: filenames -> commands
-"fix append/atoms"_fix_append_atoms.html
-"fix msst"_fix_msst.html
-"fix nphug"_fix_nphug.html
-"fix wall/piston"_fix_wall_piston.html
-examples/hugoniostat
-examples/msst :ul
-
-:line
-
-SNAP package :link(PKG-SNAP),h4
-
-[Contents:]
-
-A pair style for the spectral neighbor analysis potential (SNAP).
-SNAP is methodology for deriving a highly accurate classical potential
-fit to a large archive of quantum mechanical (DFT) data. Also several
-computes which analyze attributes of the potential.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Supporting info:]
-
-src/SNAP: filenames -> commands
-"pair_style snap"_pair_snap.html
-"compute sna/atom"_compute_sna_atom.html
-"compute snad/atom"_compute_sna_atom.html
-"compute snav/atom"_compute_sna_atom.html
-examples/snap :ul
-
-:line
-
-SPIN package :link(PKG-SPIN),h4
-
-[Contents:]
-
-Model atomic magnetic spins classically, coupled to atoms moving in
-the usual manner via MD.  Various pair, fix, and compute styles.
-
-[Author:] Julien Tranchida (Sandia).
-
-[Supporting info:]
-
-src/SPIN: filenames -> commands
-"Howto spins"_Howto_spins.html
-"pair_style spin/dipole/cut"_pair_spin_dipole.html
-"pair_style spin/dipole/long"_pair_spin_dipole.html
-"pair_style spin/dmi"_pair_spin_dmi.html
-"pair_style spin/exchange"_pair_spin_exchange.html
-"pair_style spin/magelec"_pair_spin_magelec.html
-"pair_style spin/neel"_pair_spin_neel.html
-"fix nve/spin"_fix_nve_spin.html
-"fix precession/spin"_fix_precession_spin.html
-"compute spin"_compute_spin.html
-"neb/spin"_neb_spin.html
-examples/SPIN :ul
-
-:line
-
-SRD package :link(PKG-SRD),h4
-
-[Contents:]
-
-A pair of fixes which implement the Stochastic Rotation Dynamics (SRD)
-method for coarse-graining of a solvent, typically around large
-colloidal particles.
-
-[Supporting info:]
-
-src/SRD: filenames -> commands
-"fix srd"_fix_srd.html
-"fix wall/srd"_fix_wall_srd.html
-examples/srd
-examples/ASPHERE
-http://lammps.sandia.gov/movies.html#tri
-http://lammps.sandia.gov/movies.html#line
-http://lammps.sandia.gov/movies.html#poly :ul
-
-:line
-
-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
-can be used to calculate the local volume or each atoms or its near
-neighbors.
-
-:link(voro-home,http://math.lbl.gov/voro++)
-
-To use this package you must have the Voro++ library available on your
-system.
-
-[Author:] Daniel Schwen (INL) while at LANL.  The open-source Voro++
-library was written by Chris Rycroft (Harvard U) while at UC Berkeley
-and LBNL.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#voronoi on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/VORONOI: filenames -> commands
-src/VORONOI/README
-lib/voronoi/README
-"compute voronoi/atom"_compute_voronoi_atom.html
-examples/voronoi :ul
-
-:line
-
-USER-ADIOS package :link(PKG-USER-ADIOS),h4
-
-[Contents:]
-
-ADIOS is a high-performance I/O library. This package implements the
-dump "atom/adios" and dump "custom/adios" commands to write data using
-the ADIOS library.
-
-[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-adios on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-ADIOS: filenames -> commands
-src/USER-ADIOS/README
-examples/USER/adios
-https://github.com/ornladios/ADIOS2 :ul
-
-:line
-
-USER-ATC package :link(PKG-USER-ATC),h4
-
-[Contents:]
-
-ATC stands for atoms-to-continuum.  This package implements a "fix
-atc"_fix_atc.html command to either couple molecular dynamics with
-continuum finite element equations or perform on-the-fly conversion of
-atomic information to continuum fields.
-
-[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-atc on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-ATC: filenames -> commands
-src/USER-ATC/README
-"fix atc"_fix_atc.html
-examples/USER/atc
-http://lammps.sandia.gov/pictures.html#atc :ul
-
-:line
-
-USER-AWPMD package :link(PKG-USER-AWPMD),h4
-
-[Contents:]
-
-AWPMD stands for Antisymmetrized Wave Packet Molecular Dynamics.  This
-package implements an atom, pair, and fix style which allows electrons
-to be treated as explicit particles in a classical molecular dynamics
-model.
-
-[Author:] Ilya Valuev (JIHT, Russia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-awpmd on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-AWPMD: filenames -> commands
-src/USER-AWPMD/README
-"pair_style awpmd/cut"_pair_awpmd.html
-examples/USER/awpmd :ul
-
-:line
-
-USER-BOCS package :link(PKG-USER-BOCS),h4
-
-[Contents:]
-
-This package provides "fix bocs"_fix_bocs.html, a modified version
-of "fix npt"_fix_nh.html which includes the pressure correction to
-the barostat as outlined in:
-
-N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
-accurately describe the structure, pressure, and compressibility of
-molecular liquids," J. Chem. Phys. 143, 243148 (2015).
-
-[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The
-Pennsylvania State University)
-
-[Supporting info:]
-
-The USER-BOCS user package for LAMMPS is part of the BOCS software package:
-"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
-
-See the following reference for information about the entire package:
-
-Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
-"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
-J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
-
-Example inputs are in the examples/USER/bocs folder.
-
-:line
-
-USER-CGDNA package :link(PKG-USER-CGDNA),h4
-
-[Contents:]
-
-Several pair styles, a bond style, and integration fixes for
-coarse-grained models of single- and double-stranded DNA based on the
-oxDNA model of Doye, Louis and Ouldridge at the University of Oxford.
-This includes Langevin-type rigid-body integrators with improved
-stability.
-
-[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
-
-[Supporting info:]
-
-src/USER-CGDNA: filenames -> commands
-/src/USER-CGDNA/README
-"pair_style oxdna/*"_pair_oxdna.html
-"pair_style oxdna2/*"_pair_oxdna2.html
-"bond_style oxdna/*"_bond_oxdna.html
-"bond_style oxdna2/*"_bond_oxdna.html
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
-
-:line
-
-USER-CGSDK package :link(PKG-USER-CGSDK),h4
-
-[Contents:]
-
-Several pair styles and an angle style which implement the
-coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
-simulation of ionic liquids, electrolytes, lipids and charged amino
-acids.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Supporting info:]
-
-src/USER-CGSDK: filenames -> commands
-src/USER-CGSDK/README
-"pair_style lj/sdk/*"_pair_sdk.html
-"angle_style sdk"_angle_sdk.html
-examples/USER/cgsdk
-http://lammps.sandia.gov/pictures.html#cg :ul
-
-:line
-
-USER-COLVARS package :link(PKG-USER-COLVARS),h4
-
-[Contents:]
-
-COLVARS stands for collective variables, which can be used to
-implement various enhanced sampling methods, including Adaptive
-Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and
-Restraints.  A "fix colvars"_fix_colvars.html command is implemented
-which wraps a COLVARS library, which implements these methods.
-simulations.
-
-[Authors:] The COLVARS library is written and maintained by
-Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
-and Jerome Henin (LISM, CNRS, Marseille, France), originally for
-the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
-(Temple U) provided the interface to LAMMPS.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-colvars on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-COLVARS: filenames -> commands
-"doc/PDF/colvars-refman-lammps.pdf"_PDF/colvars-refman-lammps.pdf
-src/USER-COLVARS/README
-lib/colvars/README
-"fix colvars"_fix_colvars.html
-examples/USER/colvars :ul
-
-:line
-
-USER-PLUMED package :link(PKG-USER-PLUMED),h4
-
-[Contents:]
-
-The fix plumed command allows you to use the PLUMED free energy plugin
-for molecular dynamics to analyze and bias your LAMMPS trajectory on
-the fly.  The PLUMED library is called from within the LAMMPS input
-script by using the "fix plumed"_fix_plumed.html command.
-
-[Authors:] The "PLUMED library"_#PLUMED is written and maintained by
-Massimilliano Bonomi, Giovanni Bussi, Carlo Camiloni and Gareth
-Tribello.
-
-:link(PLUMED,http://www.plumed.org)
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-plumed on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-PLUMED/README
-lib/plumed/README
-"fix plumed"_fix_plumed.html
-examples/USER/plumed :ul
-
-:line
-
-USER-DIFFRACTION package :link(PKG-USER-DIFFRACTION),h4
-
-[Contents:]
-
-Two computes and a fix for calculating x-ray and electron diffraction
-intensities based on kinematic diffraction theory.
-
-[Author:] Shawn Coleman while at the U Arkansas.
-
-[Supporting info:]
-
-src/USER-DIFFRACTION: filenames -> commands
-"compute saed"_compute_saed.html
-"compute xrd"_compute_xrd.html
-"fix saed/vtk"_fix_saed_vtk.html
-examples/USER/diffraction :ul
-
-:line
-
-USER-DPD package :link(PKG-USER-DPD),h4
-
-[Contents:]
-
-DPD stands for dissipative particle dynamics.  This package implements
-coarse-grained DPD-based models for energetic, reactive molecular
-crystalline materials.  It includes many pair styles specific to these
-systems, including for reactive DPD, where each particle has internal
-state for multiple species and a coupled set of chemical reaction ODEs
-are integrated each timestep.  Highly accurate time integrators for
-isothermal, isoenergetic, isobaric and isenthalpic conditions are
-included.  These enable long timesteps via the Shardlow splitting
-algorithm.
-
-[Authors:] Jim Larentzos (ARL), Tim Mattox (Engility Corp), and John
-Brennan (ARL).
-
-[Supporting info:]
-
-src/USER-DPD: filenames -> commands
-/src/USER-DPD/README
-"compute dpd"_compute_dpd.html
-"compute dpd/atom"_compute_dpd_atom.html
-"fix eos/cv"_fix_eos_table.html
-"fix eos/table"_fix_eos_table.html
-"fix eos/table/rx"_fix_eos_table_rx.html
-"fix shardlow"_fix_shardlow.html
-"fix rx"_fix_rx.html
-"pair_style table/rx"_pair_table_rx.html
-"pair_style dpd/fdt"_pair_dpd_fdt.html
-"pair_style dpd/fdt/energy"_pair_dpd_fdt.html
-"pair_style exp6/rx"_pair_exp6_rx.html
-"pair_style multi/lucy"_pair_multi_lucy.html
-"pair_style multi/lucy/rx"_pair_multi_lucy_rx.html
-examples/USER/dpd :ul
-
-:line
-
-USER-DRUDE package :link(PKG-USER-DRUDE),h4
-
-[Contents:]
-
-Fixes, pair styles, and a compute to simulate thermalized Drude
-oscillators as a model of polarization.  See the "Howto
-drude"_Howto_drude.html and "Howto drude2"_Howto_drude2.html doc pages
-for an overview of how to use the package.  There are auxiliary tools
-for using this package in tools/drude.
-
-[Authors:] Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
-Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
-
-[Supporting info:]
-
-src/USER-DRUDE: filenames -> commands
-"Howto drude"_Howto_drude.html
-"Howto drude2"_Howto_drude2.html
-"Howto polarizable"_Howto_polarizable.html
-src/USER-DRUDE/README
-"fix drude"_fix_drude.html
-"fix drude/transform/*"_fix_drude_transform.html
-"compute temp/drude"_compute_temp_drude.html
-"pair_style thole"_pair_thole.html
-"pair_style lj/cut/thole/long"_pair_thole.html
-examples/USER/drude
-tools/drude :ul
-
-:line
-
-USER-EFF package :link(PKG-USER-EFF),h4
-
-[Contents:]
-
-EFF stands for electron force field which allows a classical MD code
-to model electrons as particles of variable radius.  This package
-contains atom, pair, fix and compute styles which implement the eFF as
-described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III,
-JCC, 2010.  The eFF potential was first introduced by Su and Goddard,
-in 2007.  There are auxiliary tools for using this package in
-tools/eff; see its README file.
-
-[Author:] Andres Jaramillo-Botero (CalTech).
-
-[Supporting info:]
-
-src/USER-EFF: filenames -> commands
-src/USER-EFF/README
-"atom_style electron"_atom_style.html
-"fix nve/eff"_fix_nve_eff.html
-"fix nvt/eff"_fix_nh_eff.html
-"fix npt/eff"_fix_nh_eff.html
-"fix langevin/eff"_fix_langevin_eff.html
-"compute temp/eff"_compute_temp_eff.html
-"pair_style eff/cut"_pair_eff.html
-"pair_style eff/inline"_pair_eff.html
-examples/USER/eff
-tools/eff/README
-tools/eff
-http://lammps.sandia.gov/movies.html#eff :ul
-
-:line
-
-USER-FEP package :link(PKG-USER-FEP),h4
-
-[Contents:]
-
-FEP stands for free energy perturbation.  This package provides
-methods for performing FEP simulations by using a "fix
-adapt/fep"_fix_adapt_fep.html command with soft-core pair potentials,
-which have a "soft" in their style name.  There are auxiliary tools
-for using this package in tools/fep; see its README file.
-
-[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
-
-[Supporting info:]
-
-src/USER-FEP: filenames -> commands
-src/USER-FEP/README
-"fix adapt/fep"_fix_adapt_fep.html
-"compute fep"_compute_fep.html
-"pair_style */soft"_pair_fep_soft.html
-examples/USER/fep
-tools/fep/README
-tools/fep :ul
-
-:line
-
-USER-H5MD package :link(PKG-USER-H5MD),h4
-
-[Contents:]
-
-H5MD stands for HDF5 for MD.  "HDF5"_HDF5 is a portable, binary,
-self-describing file format, used by many scientific simulations.
-H5MD is a format for molecular simulations, built on top of HDF5.
-This package implements a "dump h5md"_dump_h5md.html command to output
-LAMMPS snapshots in this format.
-
-:link(HDF5,http://www.hdfgroup.org/HDF5)
-
-To use this package you must have the HDF5 library available on your
-system.
-
-[Author:] Pierre de Buyl (KU Leuven) created both the package and the
-H5MD format.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-h5md on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-H5MD: filenames -> commands
-src/USER-H5MD/README
-lib/h5md/README
-"dump h5md"_dump_h5md.html :ul
-
-:line
-
-USER-INTEL package :link(PKG-USER-INTEL),h4
-
-[Contents:]
-
-Dozens of pair, fix, bond, angle, dihedral, improper, and kspace
-styles which are optimized for Intel CPUs and KNLs (Knights Landing).
-All of them have an "intel" in their style name.  The "Speed
-intel"_Speed_intel.html doc page gives details of what hardware and
-compilers are required on your system, and how to build and use this
-package.  Its styles can be invoked at run time via the "-sf intel" or
-"-suffix intel" "command-line switches"_Run_options.html.  Also see
-the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-OMP"_#PKG-USER-OMP packages,
-which have styles optimized for CPUs and KNLs.
-
-You need to have an Intel compiler, version 14 or higher to take full
-advantage of this package. While compilation with GNU compilers is
-supported, performance will be sub-optimal.
-
-NOTE: the USER-INTEL package contains styles that require using the
--restrict flag, when compiling with Intel compilers.
-
-[Author:] Mike Brown (Intel).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-intel on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-INTEL: filenames -> commands
-src/USER-INTEL/README
-"Speed packages"_Speed_packages.html
-"Speed intel"_Speed_intel.html
-"Section 2.6 -sf intel"_Run_options.html
-"Section 2.6 -pk intel"_Run_options.html
-"package intel"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (i)
-src/USER-INTEL/TEST
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-USER-LB package :link(PKG-USER-LB),h4
-
-[Contents:]
-
-Fixes which implement a background Lattice-Boltzmann (LB) fluid, which
-can be used to model MD particles influenced by hydrodynamic forces.
-
-[Authors:] Frances Mackay and Colin Denniston (University of Western
-Ontario).
-
-[Supporting info:]
-
-src/USER-LB: filenames -> commands
-src/USER-LB/README
-"fix lb/fluid"_fix_lb_fluid.html
-"fix lb/momentum"_fix_lb_momentum.html
-"fix lb/viscous"_fix_lb_viscous.html
-examples/USER/lb :ul
-
-:line
-
-USER-MGPT package :link(PKG-USER-MGPT),h4
-
-[Contents:]
-
-A pair style which provides a fast implementation of the quantum-based
-MGPT multi-ion potentials.  The MGPT or model GPT method derives from
-first-principles DFT-based generalized pseudopotential theory (GPT)
-through a series of systematic approximations valid for mid-period
-transition metals with nearly half-filled d bands.  The MGPT method
-was originally developed by John Moriarty at LLNL.  The pair style in
-this package calculates forces and energies using an optimized
-matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
-
-[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
-
-[Supporting info:]
-
-src/USER-MGPT: filenames -> commands
-src/USER-MGPT/README
-"pair_style mgpt"_pair_mgpt.html
-examples/USER/mgpt :ul
-
-:line
-
-USER-MISC package :link(PKG-USER-MISC),h4
-
-[Contents:]
-
-A potpourri of (mostly) unrelated features contributed to LAMMPS by
-users.  Each feature is a single fix, compute, pair, bond, angle,
-dihedral, improper, or command style.
-
-[Authors:] The author for each style in the package is listed in the
-src/USER-MISC/README file.
-
-[Supporting info:]
-
-src/USER-MISC: filenames -> commands
-src/USER-MISC/README
-one doc page per individual command listed in src/USER-MISC/README
-examples/USER/misc :ul
-
-:line
-
-USER-MANIFOLD package :link(PKG-USER-MANIFOLD),h4
-
-[Contents:]
-
-Several fixes and a "manifold" class which enable simulations of
-particles constrained to a manifold (a 2D surface within the 3D
-simulation box).  This is done by applying the RATTLE constraint
-algorithm to formulate single-particle constraint functions
-g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold)
-n = grad(g).
-
-[Author:] Stefan Paquay (until 2017: Eindhoven University of
-Technology (TU/e), The Netherlands; since 2017: Brandeis University,
-Waltham, MA, USA)
-
-[Supporting info:]
-
-src/USER-MANIFOLD: filenames -> commands
-src/USER-MANIFOLD/README
-"Howto manifold"_Howto_manifold.html
-"fix manifoldforce"_fix_manifoldforce.html
-"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html
-"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
-examples/USER/manifold
-http://lammps.sandia.gov/movies.html#manifold :ul
-
-:line
-
-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 (obsolete) "MEAM" package
-to plain C++. The USER-MEAMC fully replaces the MEAM package, which
-has been removed from LAMMPS after the 12 December 2018 version.
-
-[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
-based on the Fortran version of Greg Wagner (Northwestern U) while at
-Sandia.
-
-[Supporting info:]
-
-src/USER-MEAMC: filenames -> commands
-src/USER-MEAMC/README
-"pair_style meam/c"_pair_meamc.html
-examples/meamc :ul
-
-:line
-
-USER-MESO package :link(PKG-USER-MESO),h4
-
-[Contents:]
-
-Several extensions of the dissipative particle dynamics (DPD)
-method.  Specifically, energy-conserving DPD (eDPD) that can model
-non-isothermal processes, many-body DPD (mDPD) for simulating
-vapor-liquid coexistence, and transport DPD (tDPD) for modeling
-advection-diffusion-reaction systems. The equations of motion of these
-DPD extensions are integrated through a modified velocity-Verlet (MVV)
-algorithm.
-
-[Author:] Zhen Li (Division of Applied Mathematics, Brown University)
-
-[Supporting info:]
-
-src/USER-MESO: filenames -> commands
-src/USER-MESO/README
-"atom_style edpd"_atom_style.html
-"pair_style edpd"_pair_meso.html
-"pair_style mdpd"_pair_meso.html
-"pair_style tdpd"_pair_meso.html
-"fix mvv/dpd"_fix_mvv_dpd.html
-examples/USER/meso
-http://lammps.sandia.gov/movies.html#mesodpd :ul
-
-:line
-
-USER-MOFFF package :link(PKG-USER-MOFFF),h4
-
-[Contents:]
-
-Pair, angle and improper styles needed to employ the MOF-FF
-force field by Schmid and coworkers with LAMMPS.
-MOF-FF is a first principles derived force field with the primary aim
-to simulate MOFs and related porous framework materials, using spherical
-Gaussian charges. It is described in S. Bureekaew et al., Phys. Stat. Sol. B
-2013, 250, 1128-1141.
-For the usage of MOF-FF see the example in the example directory as
-well as the "MOF+"_MOFplus website.
-
-:link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
-
-[Author:] Hendrik Heenen (Technical U of Munich),
-Rochus Schmid (Ruhr-University Bochum).
-
-[Supporting info:]
-
-src/USER-MOFFF: filenames -> commands
-src/USER-MOFFF/README
-"pair_style buck6d/coul/gauss"_pair_buck6d_coul_gauss.html
-"angle_style class2"_angle_class2.html
-"angle_style cosine/buck6d"_angle_cosine_buck6d.html
-"improper_style inversion/harmonic"_improper_inversion_harmonic.html
-examples/USER/mofff :ul
-
-:line
-
-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
-molecular visualization and analysis program, to enable LAMMPS to dump
-snapshots in formats compatible with various molecular simulation
-tools.
-
-To use this package you must have the desired VMD plugins available on
-your system.
-
-Note that this package only provides the interface code, not the
-plugins themselves, which will be accessed when requesting a specific
-plugin via the "dump molfile"_dump_molfile.html command.  Plugins can
-be obtained from a VMD installation which has to match the platform
-that you are using to compile LAMMPS for. By adding plugins to VMD,
-support for new file formats can be added to LAMMPS (or VMD or other
-programs that use them) without having to re-compile the application
-itself.  More information about the VMD molfile plugins can be found
-at
-"http://www.ks.uiuc.edu/Research/vmd/plugins/molfile"_http://www.ks.uiuc.edu/Research/vmd/plugins/molfile.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-molfile on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-MOLFILE: filenames -> commands
-src/USER-MOLFILE/README
-lib/molfile/README
-"dump molfile"_dump_molfile.html :ul
-
-:line
-
-USER-NETCDF package :link(PKG-USER-NETCDF),h4
-
-[Contents:]
-
-Dump styles for writing NetCDF formatted dump files.  NetCDF is a
-portable, binary, self-describing file format developed on top of
-HDF5. The file contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
-
-To use this package you must have the NetCDF library available on your
-system.
-
-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
-"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(atomeye,http://www.libatoms.org)
-
-[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-netcdf on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-NETCDF: filenames -> commands
-src/USER-NETCDF/README
-lib/netcdf/README
-"dump netcdf"_dump_netcdf.html :ul
-
-:line
-
-USER-OMP package :link(PKG-USER-OMP),h4
-
-[Contents:]
-
-Hundreds of pair, fix, compute, bond, angle, dihedral, improper, and
-kspace styles which are altered to enable threading on many-core CPUs
-via OpenMP directives.  All of them have an "omp" in their style name.
-The "Speed omp"_Speed_omp.html doc page gives details of what hardware
-and compilers are required on your system, and how to build and use
-this package.  Its styles can be invoked at run time via the "-sf omp"
-or "-suffix omp" "command-line switches"_Run_options.html.  Also see
-the "KOKKOS"_#PKG-KOKKOS, "OPT"_#PKG-OPT, and "USER-INTEL"_#PKG-USER-INTEL
-packages, which have styles optimized for CPUs.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-NOTE: To enable multi-threading support the compile flag "-fopenmp"
-and the link flag "-fopenmp" (for GNU compilers, you have to look up
-the equivalent flags for other compilers) must be used to build LAMMPS.
-When using Intel compilers, also the "-restrict" flag is required.
-The USER-OMP package can be compiled without enabling OpenMP; then
-all code will be compiled as serial and the only improvement over the
-regular styles are some data access optimization. These flags should
-be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
-See src/MAKE/OPTIONS/Makefile.omp for an example.
-
-Once you have an appropriate Makefile.machine, you can
-install/un-install the package and build LAMMPS in the usual manner:
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-omp on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-OMP: filenames -> commands
-src/USER-OMP/README
-"Speed packages"_Speed_packages.html
-"Speed omp"_Speed_omp.html
-"Section 2.6 -sf omp"_Run_options.html
-"Section 2.6 -pk omp"_Run_options.html
-"package omp"_package.html
-"Commands all"_lc pages (fix,compute,pair,etc) for styles followed by (o)
-"Benchmarks page"_http://lammps.sandia.gov/bench.html of web site :ul
-
-:line
-
-USER-PHONON package :link(PKG-USER-PHONON),h4
-
-[Contents:]
-
-A "fix phonon"_fix_phonon.html command that calculates dynamical
-matrices, which can then be used to compute phonon dispersion
-relations, directly from molecular dynamics simulations.
-And a "dynamical_matrix"_dynamical_matrix.html as well as a
-"third_order"_third_order.html command to compute the dynamical matrix
-and third order tensor from finite differences.
-
-[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
-and Charlie Sievers (UC Davis) for "dynamical_matrix" and "third_order"
-
-
-[Supporting info:]
-
-src/USER-PHONON: filenames -> commands
-src/USER-PHONON/README
-"fix phonon"_fix_phonon.html
-"dynamical_matrix"_dynamical_matrix.html
-"third_order"_third_order.html
-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:]
-
-A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
-QM/MM simulation, currently only in combination with the "Quantum
-ESPRESSO"_espresso package.
-
-:link(espresso,http://www.quantum-espresso.org)
-
-To use this package you must have Quantum ESPRESSO available on your
-system.
-
-The current implementation only supports an ONIOM style mechanical
-coupling to the Quantum ESPRESSO plane wave DFT package.
-Electrostatic coupling is in preparation and the interface has been
-written in a manner that coupling to other QM codes should be possible
-without changes to LAMMPS itself.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-qmmm on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-QMMM: filenames -> commands
-src/USER-QMMM/README
-lib/qmmm/README
-"fix phonon"_fix_phonon.html
-lib/qmmm/example-ec/README
-lib/qmmm/example-mc/README :ul
-
-:line
-
-USER-QTB package :link(PKG-USER-QTB),h4
-
-[Contents:]
-
-Two fixes which provide a self-consistent quantum treatment of
-vibrational modes in a classical molecular dynamics simulation.  By
-coupling the MD simulation to a colored thermostat, it introduces zero
-point energy into the system, altering the energy power spectrum and
-the heat capacity to account for their quantum nature. This is useful
-when modeling systems at temperatures lower than their classical
-limits or when temperatures ramp across the classical limits in a
-simulation.
-
-[Author:] Yuan Shen (Stanford U).
-
-[Supporting info:]
-
-src/USER-QTB: filenames -> commands
-src/USER-QTB/README
-"fix qtb"_fix_qtb.html
-"fix qbmsst"_fix_qbmsst.html
-examples/USER/qtb :ul
-
-:line
-
-USER-QUIP package :link(PKG-USER-QUIP),h4
-
-[Contents:]
-
-A "pair_style quip"_pair_quip.html command which wraps the "QUIP
-libAtoms library"_quip, which includes a variety of interatomic
-potentials, including Gaussian Approximation Potential (GAP) models
-developed by the Cambridge University group.
-
-:link(quip,https://github.com/libAtoms/QUIP)
-
-To use this package you must have the QUIP libAtoms library available
-on your system.
-
-[Author:] Albert Bartok (Cambridge University)
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-quip on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-QUIP: filenames -> commands
-src/USER-QUIP/README
-"pair_style quip"_pair_quip.html
-examples/USER/quip :ul
-
-:line
-
-USER-REAXC package :link(PKG-USER-REAXC),h4
-
-[Contents:]
-
-A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
-is a universal reactive force field.  See the src/USER-REAXC/README file
-for more info on differences between the two packages.  Also two fixes
-for monitoring molecules as bonds are created and destroyed.
-
-[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
-
-[Supporting info:]
-
-src/USER-REAXC: filenames -> commands
-src/USER-REAXC/README
-"pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reaxc_bonds.html
-"fix reax/c/species"_fix_reaxc_species.html
-examples/reax :ul
-
-:line
-
-USER-SCAFACOS package :link(PKG-USER-SCAFACOS),h4
-
-[Contents:]
-
-A KSpace style which wraps the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de to compute long-range Coulombic
-interactions.
-
-To use this package you must have the ScaFaCoS library available on
-your system.
-
-[Author:] Rene Halver (JSC) wrote the scafacos LAMMPS command.
-
-ScaFaCoS itself was developed by a consortium of German research
-facilities with a BMBF (German Ministry of Science and Education)
-funded project in 2009-2012. Participants of the consortium were the
-Universities of Bonn, Chemnitz, Stuttgart, and Wuppertal as well as
-the Forschungszentrum Juelich.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-scafacos on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-SCAFACOS: filenames -> commands
-src/USER-SCAFACOS/README
-"kspace_style scafacos"_kspace_style.html
-"kspace_modify"_kspace_modify.html
-examples/USER/scafacos :ul
-
-:line
-
-USER-SDPD package :link(PKG-USER-SDPD),h4
-
-[Contents:]
-
-A pair style for smoothed dissipative particle dynamics (SDPD), which
-is an extension of smoothed particle hydrodynamics (SPH) to mesoscale
-where thermal fluctuations are important (see the
-"USER-SPH package"_#PKG-USER-SPH).
-Also two fixes for moving and rigid body integration of SPH/SDPD particles
-(particles of atom_style meso).
-
-[Author:] Morteza Jalalvand (Institute for Advanced Studies in Basic
-Sciences, Iran).
-
-[Supporting info:]
-
-src/USER-SDPD: filenames -> commands
-src/USER-SDPD/README
-"pair_style sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html
-"fix meso/move"_fix_meso_move.html
-"fix rigid/meso"_fix_rigid_meso.html
-examples/USER/sdpd :ul
-
-:line
-
-USER-SMD package :link(PKG-USER-SMD),h4
-
-[Contents:]
-
-An atom style, fixes, computes, and several pair styles which
-implements smoothed Mach dynamics (SMD) for solids, which is a model
-related to smoothed particle hydrodynamics (SPH) for liquids (see the
-"USER-SPH package"_#PKG-USER-SPH).
-
-This package solves solids mechanics problems via a state of the art
-stabilized meshless method with hourglass control.  It can specify
-hydrostatic interactions independently from material strength models,
-i.e. pressure and deviatoric stresses are separated.  It provides many
-material models (Johnson-Cook, plasticity with hardening,
-Mie-Grueneisen, Polynomial EOS) and allows new material models to be
-added.  It implements rigid boundary conditions (walls) which can be
-specified as surface geometries from *.STL files.
-
-[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
-Dynamics, Ernst Mach Institute, Germany).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-smd on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-SMD: filenames -> commands
-src/USER-SMD/README
-doc/PDF/SMD_LAMMPS_userguide.pdf
-examples/USER/smd
-http://lammps.sandia.gov/movies.html#smd :ul
-
-:line
-
-USER-SMTBQ package :link(PKG-USER-SMTBQ),h4
-
-[Contents:]
-
-A pair style which implements a Second Moment Tight Binding model with
-QEq charge equilibration (SMTBQ) potential for the description of
-ionocovalent bonds in oxides.
-
-[Authors:] Nicolas Salles, Emile Maras, Olivier Politano, and Robert
-Tetot (LAAS-CNRS, France).
-
-[Supporting info:]
-
-src/USER-SMTBQ: filenames -> commands
-src/USER-SMTBQ/README
-"pair_style smtbq"_pair_smtbq.html
-examples/USER/smtbq :ul
-
-:line
-
-USER-SPH package :link(PKG-USER-SPH),h4
-
-[Contents:]
-
-An atom style, fixes, computes, and several pair styles which
-implements smoothed particle hydrodynamics (SPH) for liquids.  See the
-related "USER-SMD package"_#PKG-USER-SMD package for smooth Mach dynamics
-(SMD) for solids.
-
-This package contains ideal gas, Lennard-Jones equation of states,
-Tait, and full support for complete (i.e. internal-energy dependent)
-equations of state.  It allows for plain or Monaghans XSPH integration
-of the equations of motion.  It has options for density continuity or
-density summation to propagate the density field.  It has
-"set"_set.html command options to set the internal energy and density
-of particles from the input script and allows the same quantities to
-be output with thermodynamic output or to dump files via the "compute
-property/atom"_compute_property_atom.html command.
-
-[Author:] Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
-Dynamics, Ernst Mach Institute, Germany).
-
-[Supporting info:]
-
-src/USER-SPH: filenames -> commands
-src/USER-SPH/README
-doc/PDF/SPH_LAMMPS_userguide.pdf
-examples/USER/sph
-http://lammps.sandia.gov/movies.html#sph :ul
-
-:line
-
-USER-TALLY package :link(PKG-USER-TALLY),h4
-
-[Contents:]
-
-Several compute styles that can be called when pairwise interactions
-are calculated to tally information (forces, heat flux, energy,
-stress, etc) about individual interactions.
-
-[Author:] Axel Kohlmeyer (Temple U).
-
-[Supporting info:]
-
-src/USER-TALLY: filenames -> commands
-src/USER-TALLY/README
-"compute */tally"_compute_tally.html
-examples/USER/tally :ul
-
-:line
-
-USER-UEF package :link(PKG-USER-UEF),h4
-
-[Contents:]
-
-A fix style for the integration of the equations of motion under
-extensional flow with proper boundary conditions, as well as several
-supporting compute styles and an output option.
-
-[Author:] David Nicholson (MIT).
-
-[Supporting info:]
-
-src/USER-UEF: filenames -> commands
-src/USER-UEF/README
-"fix nvt/uef"_fix_nh_uef.html
-"fix npt/uef"_fix_nh_uef.html
-"compute pressure/uef"_compute_pressure_uef.html
-"compute temp/uef"_compute_temp_uef.html
-"dump cfg/uef"_dump_cfg_uef.html
-examples/uef :ul
-
-:line
-
-USER-VTK package :link(PKG-USER-VTK),h4
-
-[Contents:]
-
-A "dump vtk"_dump_vtk.html command which outputs snapshot info in the
-"VTK format"_vtk, enabling visualization by "Paraview"_paraview or
-other visualization packages.
-
-:link(vtk,http://www.vtk.org)
-:link(paraview,http://www.paraview.org)
-
-To use this package you must have VTK library available on your
-system.
-
-[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#user-vtk on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/USER-VTK: filenames -> commands
-src/USER-VTK/README
-lib/vtk/README
-"dump vtk"_dump_vtk.html :ul
-
-
-:line
-
-USER-YAFF package :link(PKG-USER-YAFF),h4
-
-[Contents:]
-
-Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
-The expressions and their use are discussed in the following papers
-
-Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
-Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
-
-which discuss the "QuickFF"_quickff methodology.
-
-
-:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
-:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
-:link(quickff,http://molmod.github.io/QuickFF)
-:link(yaff,https://github.com/molmod/yaff)
-
-
-[Author:] Steven Vandenbrande.
-
-[Supporting info:]
-
-src/USER-YAFF/README
-"angle_style cross"_angle_cross.html
-"angle_style mm3"_angle_mm3.html
-"bond_style mm3"_bond_mm3.html
-"improper_style distharm"_improper_distharm.html
-"improper_style sqdistharm"_improper_sqdistharm.html
-"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
-"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
-examples/USER/yaff :ul
diff --git a/doc/txt/fix.txt b/doc/txt/fix.txt
deleted file mode 100644
index fd281bce83..0000000000
--- a/doc/txt/fix.txt
+++ /dev/null
@@ -1,392 +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 command :h3
-
-[Syntax:]
-
-fix ID group-ID style args :pre
-
-ID = user-assigned name for the fix
-group-ID = ID of the group of atoms to apply the fix to
-style = one of a long list of possible style names (see below)
-args = arguments used by a particular style :ul
-
-[Examples:]
-
-fix 1 all nve
-fix 3 all nvt temp 300.0 300.0 0.01
-fix mine top setforce 0.0 NULL 0.0 :pre
-
-[Description:]
-
-Set a fix that will be applied to a group of atoms.  In LAMMPS, a
-"fix" is any operation that is applied to the system during
-timestepping or minimization.  Examples include updating of atom
-positions and velocities due to time integration, controlling
-temperature, applying constraint forces to atoms, enforcing boundary
-conditions, computing diagnostics, etc.  There are hundreds of fixes
-defined in LAMMPS and new ones can be added; see the
-"Modify"_Modify.html doc page for details.
-
-Fixes perform their operations at different stages of the timestep.
-If 2 or more fixes operate at the same stage of the timestep, they are
-invoked in the order they were specified in the input script.
-
-The ID of a fix can only contain alphanumeric characters and
-underscores.
-
-Fixes can be deleted with the "unfix"_unfix.html command.
-
-NOTE: The "unfix"_unfix.html command is the only way to turn off a
-fix; simply specifying a new fix with a similar style will not turn
-off the first one.  This is especially important to realize for
-integration fixes.  For example, using a "fix nve"_fix_nve.html
-command for a second run after using a "fix nvt"_fix_nh.html command
-for the first run, will not cancel out the NVT time integration
-invoked by the "fix nvt" command.  Thus two time integrators would be
-in place!
-
-If you specify a new fix with the same ID and style as an existing
-fix, the old fix is deleted and the new one is created (presumably
-with new settings).  This is the same as if an "unfix" command were
-first performed on the old fix, except that the new fix is kept in the
-same order relative to the existing fixes as the old one originally
-was.  Note that this operation also wipes out any additional changes
-made to the old fix via the "fix_modify"_fix_modify.html command.
-
-The "fix modify"_fix_modify.html command allows settings for some
-fixes to be reset.  See the doc page for individual fixes for details.
-
-Some fixes store an internal "state" which is written to binary
-restart files via the "restart"_restart.html or
-"write_restart"_write_restart.html commands.  This allows the fix to
-continue on with its calculations in a restarted simulation.  See the
-"read_restart"_read_restart.html command for info on how to re-specify
-a fix in an input script that reads a restart file.  See the doc pages
-for individual fixes for info on which ones can be restarted.
-
-:line
-
-Some fixes calculate one of three styles of quantities: global,
-per-atom, or local, which can be used by other commands or output as
-described below.  A global quantity is one or more system-wide values,
-e.g. the energy of a wall interacting with particles.  A per-atom
-quantity is one or more values per atom, e.g. the displacement vector
-for each atom since time 0.  Per-atom values are set to 0.0 for atoms
-not in the specified fix group.  Local quantities are calculated by
-each processor based on the atoms it owns, but there may be zero or
-more per atoms.
-
-Note that a single fix can produce either global or per-atom or local
-quantities (or none at all), but not both global and per-atom.  It can
-produce local quantities in tandem with global or per-atom quantities.
-The fix doc page will explain.
-
-Global, per-atom, and local quantities each come in three kinds: a
-single scalar value, a vector of values, or a 2d array of values.  The
-doc page for each fix describes the style and kind of values it
-produces, e.g. a per-atom vector.  Some fixes produce more than one
-kind of a single style, e.g. a global scalar and a global vector.
-
-When a fix quantity is accessed, as in many of the output commands
-discussed below, it can be referenced via the following bracket
-notation, where ID is the ID of the fix:
-
-f_ID | entire scalar, vector, or array
-f_ID\[I\] | one element of vector, one column of array
-f_ID\[I\]\[J\] | one element of array :tb(s=|)
-
-In other words, using one bracket reduces the dimension of the
-quantity once (vector -> scalar, array -> vector).  Using two brackets
-reduces the dimension twice (array -> scalar).  Thus a command that
-uses scalar fix values as input can also process elements of a vector
-or array.
-
-Note that commands and "variables"_variable.html which use fix
-quantities typically do not allow for all kinds, e.g. a command may
-require a vector of values, not a scalar.  This means there is no
-ambiguity about referring to a fix quantity as f_ID even if it
-produces, for example, both a scalar and vector.  The doc pages for
-various commands explain the details.
-
-:line
-
-In LAMMPS, the values generated by a fix can be used in several ways:
-
-Global values can be output via the "thermo_style
-custom"_thermo_style.html or "fix ave/time"_fix_ave_time.html command.
-Or the values can be referenced in a "variable equal"_variable.html or
-"variable atom"_variable.html command. :ulb,l
-
-Per-atom values can be output via the "dump custom"_dump.html command.
-Or they can be time-averaged via the "fix ave/atom"_fix_ave_atom.html
-command or reduced by the "compute reduce"_compute_reduce.html
-command.  Or the per-atom values can be referenced in an "atom-style
-variable"_variable.html. :l
-
-Local values can be reduced by the "compute
-reduce"_compute_reduce.html command, or histogrammed by the "fix
-ave/histo"_fix_ave_histo.html command. :l
-:ule
-
-See the "Howto output"_Howto_output.html doc page for a summary of
-various LAMMPS output options, many of which involve fixes.
-
-The results of fixes that calculate global quantities can be either
-"intensive" or "extensive" values.  Intensive means the value is
-independent of the number of atoms in the simulation,
-e.g. temperature.  Extensive means the value scales with the number of
-atoms in the simulation, e.g. total rotational kinetic energy.
-"Thermodynamic output"_thermo_style.html will normalize extensive
-values by the number of atoms in the system, depending on the
-"thermo_modify norm" setting.  It will not normalize intensive values.
-If a fix value is accessed in another way, e.g. by a
-"variable"_variable.html, you may want to know whether it is an
-intensive or extensive value.  See the doc page for individual fixes
-for further info.
-
-:line
-
-Each fix style has its own doc page which describes its arguments and
-what it does, as listed below.  Here is an alphabetic list of fix
-styles available in LAMMPS.  They are also listed in more compact form
-on the "Commands fix"_Commands_fix.html doc page.
-
-There are also additional accelerated fix styles included in the
-LAMMPS distribution for faster performance on CPUs, GPUs, and KNLs.
-The individual style names on the "Commands fix"_Commands_fix.html doc
-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 - enhanced version of fix adapt
-"addforce"_fix_addforce.html - add a force to each atom
-"addtorque"_fix_addtorque.html - add a torque to a group of atoms
-"append/atoms"_fix_append_atoms.html - append atoms to a running simulation
-"atc"_fix_atc.html - initiates a coupled MD/FE simulation
-"atom/swap"_fix_atom_swap.html - Monte Carlo atom type swapping
-"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 - weighted version of fix ave/histo
-"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 - NPT style time integration with pressure correction
-"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 - apply topology changes to model reactions
-"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 - MD client for client/server simulations
-"cmap"_fix_cmap.html - enables CMAP cross-terms of the CHARMM force field
-"colvars"_fix_colvars.html - interface to the collective variables "Colvars" library
-"controller"_fix_controller.html - apply control loop feedback mechanism
-"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 - constant energy dissipative particle dynamics
-"drag"_fix_drag.html - drag atoms towards a defined coordinate
-"drude"_fix_drude.html - part of Drude oscillator polarization model
-"drude/transform/direct"_fix_drude_transform.html -  part of Drude oscillator polarization model
-"drude/transform/inverse"_fix_drude_transform.html -  part of Drude oscillator polarization model
-"dt/reset"_fix_dt_reset.html - reset the timestep based on velocity, forces
-"edpd/source"_fix_dpd_source.html - add heat source to eDPD simulations
-"efield"_fix_efield.html - impose electric field on system
-"ehex"_fix_ehex.html - enhanced heat exchange algorithm
-"electron/stopping"_fix_electron_stopping.html - electronic stopping power as a friction force
-"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 - apply a Fast-Forward Langevin equation thermostat
-"filter/corotate"_fix_filter_corotate.html - implement corotation filter to allow larger timesteps with r-RESPA
-"flow/gauss"_fix_flow_gauss.html - Gaussian dynamics for constant mass flux
-"freeze"_fix_freeze.html - freeze atoms in a granular simulation
-"gcmc"_fix_gcmc.html - grand canonical insertions/deletions
-"gld"_fix_gld.html - generalized Langevin dynamics integrator
-"gle"_fix_gle.html - generalized Langevin equation thermostat
-"gravity"_fix_gravity.html - add gravity to atoms in a granular simulation
-"grem"_fix_grem.html - implements the generalized replica exchange method
-"halt"_fix_halt.html - terminate a dynamics run or minimization
-"heat"_fix_heat.html - add/subtract momentum-conserving heat
-"hyper/global"_fix_hyper_global.html - global hyperdynamics
-"hyper/local"_fix_hyper_local.html - local hyperdynamics
-"imd"_fix_imd.html - implements the "Interactive MD" (IMD) protocol
-"indent"_fix_indent.html - impose force due to an indenter
-"ipi"_fix_ipi.html - enable LAMMPS to run as a client for i-PI path-integral simulations
-"langevin"_fix_langevin.html - Langevin temperature control
-"langevin/drude"_fix_langevin_drude.html - Langevin temperature control of Drude oscillators
-"langevin/eff"_fix_langevin_eff.html - Langevin temperature control for the electron force field model
-"langevin/spin"_fix_langevin_spin.html - Langevin temperature control for a spin or spin-lattice system
-"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 - restrain atoms to a manifold during minimization
-"meso"_fix_meso.html - time integration for SPH/DPDE particles
-"meso/move"_fix_meso_move.html - move mesoscopic SPH/SDPD particles in a prescribed fashion
-"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 - apply MSCG method for force-matching to generate coarse grain models
-"msst"_fix_msst.html - multi-scale shock technique (MSST) integration
-"mvv/dpd"_fix_mvv_dpd.html - DPD using the modified velocity-Verlet integration algorithm
-"mvv/edpd"_fix_mvv_dpd.html - constant energy DPD using the modified velocity-Verlet algorithm
-"mvv/tdpd"_fix_mvv_dpd.html - constant temperature DPD using the modified velocity-Verlet algorithm
-"neb"_fix_neb.html - nudged elastic band (NEB) spring forces
-"nph"_fix_nh.html - constant NPH time integration via Nose/Hoover
-"nph/asphere"_fix_nph_asphere.html - NPH for aspherical particles
-"nph/body"_fix_nph_body.html - NPH for body particles
-"nph/eff"_fix_nh_eff.html - NPH for  nuclei and electrons in the electron force field model
-"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 for body particles
-"npt/eff"_fix_nh_eff.html - NPT for  nuclei and electrons in the electron force field model
-"npt/sphere"_fix_npt_sphere.html - NPT for spherical particles
-"npt/uef"_fix_nh_uef.html - NPT style time integration with diagonal flow
-"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 for the Antisymmetrized Wave Packet Molecular Dynamics model
-"nve/body"_fix_nve_body.html - NVE for body particles
-"nve/dot"_fix_nve_dot.html - rigid body constant energy time integrator for coarse grain models
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html - Langevin style rigid body time integrator for coarse grain models
-"nve/eff"_fix_nve_eff.html - NVE for  nuclei and electrons in the electron force field model
-"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 for a spin or spin-lattice system
-"nve/tri"_fix_nve_tri.html - NVE for triangles
-"nvk"_fix_nvk.html - constant kinetic energy time integration
-"nvt"_fix_nh.html - NVT time integration via Nose/Hoover
-"nvt/asphere"_fix_nvt_asphere.html - NVT for aspherical particles
-"nvt/body"_fix_nvt_body.html - NVT for body particles
-"nvt/eff"_fix_nh_eff.html - NVE for  nuclei and electrons in the electron force field model
-"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 for NEMD with SLLOD equations for the electron force field model
-"nvt/sphere"_fix_nvt_sphere.html - NVT for spherical particles
-"nvt/uef"_fix_nh_uef.html - NVT style time integration with diagonal flow
-"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 - calculate dynamical matrix from MD simulations
-"pimd"_fix_pimd.html - Feynman path integral molecular dynamics
-"planeforce"_fix_planeforce.html - constrain atoms to move in a plane
-"plumed"_fix_plumed.html - wrapper on PLUMED free energy library
-"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
-"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
-"python/invoke"_fix_python_invoke.html - call a Python function during a simulation
-"python/move"_fix_python_move.html -  call a Python function during a simulation run
-"qbmsst"_fix_qbmsst.html - quantum bath multi-scale shock technique time integrator
-"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 - charge equilibration for ReaxFF potential
-"qeq/shielded"_fix_qeq.html - charge equilibration via shielded method
-"qeq/slater"_fix_qeq.html - charge equilibration via Slater method
-"qmmm"_fix_qmmm.html - functionality to enable a quantum mechanics/molecular mechanics coupling
-"qtb"_fix_qtb.html - implement quantum thermal bath scheme
-"rattle"_fix_shake.html - RATTLE constraints on bonds and/or angles
-"reax/c/bonds"_fix_reaxc_bonds.html - write out ReaxFF bond information
-"reax/c/species"_fix_reaxc_species.html - write out ReaxFF molecule information
-"recenter"_fix_recenter.html - constrain the center-of-mass position of a group of atoms
-"restrain"_fix_restrain.html - constrain a bond, angle, dihedral
-"rhok"_fix_rhok.html - add bias potential for long-range ordered systems
-"rigid"_fix_rigid.html - constrain one or more clusters of atoms to move as a rigid body with NVE integration
-"rigid/meso"_fix_rigid_meso.html - constrain clusters of mesoscopic SPH/SDPD particles to move as a rigid body
-"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 - constrain many small 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/npt/small"_fix_rigid.html - constrain many small 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/nve/small"_fix_rigid.html - constrain many small 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/nvt/small"_fix_rigid.html - constrain many small 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
-"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 - integration of DPD equations of motion using the Shardlow splitting
-"smd"_fix_smd.html - applied a steered MD force to a group
-"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/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
-"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/eff"_fix_temp_rescale_eff.html - temperature control by velocity rescaling in the electron force field model
-"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
-"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 - enhanced two-temperature model with additional options
-"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
-"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 for ellipsoidal particles
-"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
-"wall/lj93"_fix_wall.html - Lennard-Jones 9-3 wall
-"wall/morse"_fix_wall.html - Morse potential wall
-"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 - use region surface as wall for ellipsoidal particles
-"wall/srd"_fix_wall_srd.html - slip/no-slip wall for SRD particles :ul
-
-[Restrictions:]
-
-Some fix styles are part of specific packages.  They are only enabled
-if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual fixes tell if it is part of a package.
-
-[Related commands:]
-
-"unfix"_unfix.html, "fix_modify"_fix_modify.html
-
-[Default:] none
diff --git a/doc/txt/fix_client_md.txt b/doc/txt/fix_client_md.txt
deleted file mode 100644
index 5fee8511fe..0000000000
--- a/doc/txt/fix_client_md.txt
+++ /dev/null
@@ -1,106 +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 client/md command :h3
-
-[Syntax:]
-
-fix ID group-ID client/md :pre
-
-ID, group-ID are documented in "fix"_fix.html command
-client/md = style name of this fix command :ul
-
-[Examples:]
-
-fix 1 all client/md :pre
-
-[Description:]
-
-This fix style enables LAMMPS to run as a "client" code and
-communicate each timestep with a separate "server" code to perform an
-MD simulation together.
-
-The "Howto client/server"_Howto_client_server.html doc page gives an
-overview of client/server coupling of LAMMPS with another code where
-one code is the "client" and sends request messages to a "server"
-code.  The server responds to each request with a reply message.  This
-enables the two codes to work in tandem to perform a simulation.
-
-When using this fix, LAMMPS (as the client code) passes the current
-coordinates of all particles to the server code each timestep, which
-computes their interaction, and returns the energy, forces, and virial
-for the interacting particles to LAMMPS, so it can complete the
-timestep.
-
-The server code could be a quantum code, or another classical MD code
-which encodes a force field (pair_style in LAMMPS lingo) which LAMMPS
-does not have.  In the quantum case, this fix is a mechanism for
-running {ab initio} MD with quantum forces.
-
-The group associated with this fix is ignored.
-
-The protocol and "units"_units.html for message format and content
-that LAMMPS exchanges with the server code is defined on the "server
-md"_server_md.html doc page.
-
-Note that when using LAMMPS as an MD client, your LAMMPS input script
-should not normally contain force field commands, like a
-"pair_style"_pair_style.html, "bond_style"_bond_style.html, or
-"kspace_style"_kspace_style.html command.  However it is possible for
-a server code to only compute a portion of the full force-field, while
-LAMMPS computes the remaining part.  Your LAMMPS script can also
-specify boundary conditions or force constraints in the usual way,
-which will be added to the per-atom forces returned by the server
-code.
-
-See the examples/message dir for example scripts where LAMMPS is both
-the "client" and/or "server" code for this kind of client/server MD
-simulation.  The examples/message/README file explains how to launch
-LAMMPS and another code in tandem to perform a coupled simulation.
-
-:line
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-No information about this fix is written to "binary restart
-files"_restart.html.
-
-The "fix_modify"_fix_modify.html {energy} option is supported by this
-fix to add the potential energy computed by the server application to
-the system's potential energy as part of "thermodynamic
-output"_thermo_style.html.
-
-The "fix_modify"_fix_modify.html {virial} option is supported by this
-fix to add the server application's contribution to the system's
-virial as part of "thermodynamic output"_thermo_style.html.  The
-default is {virial yes}
-
-This fix computes a global scalar which can be accessed by various
-"output commands"_Howto_output.html.  The scalar is the potential
-energy discussed above.  The scalar value calculated by this fix is
-"extensive".
-
-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 MESSAGE package.  It is only enabled if LAMMPS
-was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-A script that uses this command must also use the
-"message"_message.html command to setup the messaging protocol with
-the other server code.
-
-[Related commands:]
-
-"message"_message.html, "server"_server.html
-
-[Default:] none
diff --git a/doc/txt/fix_deposit.txt b/doc/txt/fix_deposit.txt
deleted file mode 100644
index 9ab125a55f..0000000000
--- a/doc/txt/fix_deposit.txt
+++ /dev/null
@@ -1,295 +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 deposit command :h3
-
-[Syntax:]
-
-fix ID group-ID deposit N type M seed keyword values ... :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-deposit = style name of this fix command :l
-N = # of atoms or molecules to insert :l
-type = atom type to assign to inserted atoms (offset for molecule insertion) :l
-M = insert a single atom or molecule every M steps :l
-seed = random # seed (positive integer) :l
-one or more keyword/value pairs may be appended to args :l
-keyword = {region} or {id} or {global} or {local} or {near} or {gaussian} or {attempt} or {rate} or {vx} or {vy} or {vz} or {mol} or {rigid} or {shake} or {units} :l
-  {region} value = region-ID
-    region-ID = ID of region to use as insertion volume
-  {id} value = {max} or {next}
-    max = atom ID for new atom(s) is max ID of all current atoms plus one
-    next = atom ID for new atom(s) increments by one for every deposition
-  {global} values = lo hi
-    lo,hi = put new atom/molecule a distance lo-hi above all other atoms (distance units)
-  {local} values = lo hi delta
-    lo,hi = put new atom/molecule a distance lo-hi above any nearby atom beneath it (distance units)
-    delta = lateral distance within which a neighbor is considered "nearby" (distance units)
-  {near} value = R
-    R = only insert atom/molecule if further than R from existing particles (distance units)
-  {gaussian} values = xmid ymid zmid sigma
-    xmid,ymid,zmid = center of the gaussian distribution (distance units)
-    sigma = width of gaussian distribution (distance units)
-  {attempt} value = Q
-    Q = attempt a single insertion up to Q times
-  {rate} value = V
-    V = z velocity (y in 2d) at which insertion volume moves (velocity units)
-  {vx} values = vxlo vxhi
-    vxlo,vxhi = range of x velocities for inserted atom/molecule (velocity units)
-  {vy} values = vylo vyhi
-    vylo,vyhi = range of y velocities for inserted atom/molecule (velocity units)
-  {vz} values = vzlo vzhi
-    vzlo,vzhi = range of z velocities for inserted atom/molecule (velocity units)
-  {target} values = tx ty tz
-    tx,ty,tz = location of target point (distance units)
-  {mol} value = template-ID
-    template-ID = ID of molecule template specified in a separate "molecule"_molecule.html command
-  {molfrac} values = f1 f2 ... fN
-    f1 to fN = relative probability of creating each of N molecules in template-ID
-  {rigid} value = fix-ID
-    fix-ID = ID of "fix rigid/small"_fix_rigid.html command
-  {shake} value = fix-ID
-    fix-ID = ID of "fix shake"_fix_shake.html command
-  {units} value = {lattice} or {box}
-    lattice = the geometry is defined in lattice units
-    box = the geometry is defined in simulation box units :pre
-:ule
-
-[Examples:]
-
-fix 3 all deposit 1000 2 100 29494 region myblock local 1.0 1.0 1.0 units box
-fix 2 newatoms deposit 10000 1 500 12345 region disk near 2.0 vz -1.0 -0.8
-fix 4 sputter deposit 1000 2 500 12235 region sphere vz -1.0 -1.0 target 5.0 5.0 0.0 units lattice
-fix 5 insert deposit 200 2 100 777 region disk gaussian 5.0 5.0 9.0 1.0 units box :pre
-
-[Description:]
-
-Insert a single atom or molecule into the simulation domain every M
-timesteps until N atoms or molecules have been inserted.  This is
-useful for simulating deposition onto a surface.  For the remainder of
-this doc page, a single inserted atom or molecule is referred to as a
-"particle".
-
-If inserted particles are individual atoms, they are assigned the
-specified atom type.  If they are molecules, the type of each atom in
-the inserted molecule is specified in the file read by the
-"molecule"_molecule.html command, and those values are added to the
-specified atom type.  E.g. if the file specifies atom types 1,2,3, and
-those are the atom types you want for inserted molecules, then specify
-{type} = 0.  If you specify {type} = 2, the in the inserted molecule
-will have atom types 3,4,5.
-
-All atoms in the inserted particle are assigned to two groups: the
-default group "all" and the group specified in the fix deposit command
-(which can also be "all").
-
-If you are computing temperature values which include inserted
-particles, you will want to use the
-"compute_modify"_compute_modify.html dynamic option, which insures the
-current number of atoms is used as a normalizing factor each time the
-temperature is computed.
-
-Care must be taken that inserted particles are not too near existing
-atoms, using the options described below.  When inserting particles
-above a surface in a non-periodic box (see the
-"boundary"_boundary.html command), the possibility of a particle
-escaping the surface and flying upward should be considered, since the
-particle may be lost or the box size may grow infinitely large.  A
-"fix wall/reflect"_fix_wall_reflect.html command can be used to
-prevent this behavior.  Note that if a shrink-wrap boundary is used,
-it is OK to insert the new particle outside the box, however the box
-will immediately be expanded to include the new particle. When
-simulating a sputtering experiment it is probably more realistic to
-ignore those atoms using the "thermo_modify"_thermo_modify.html
-command with the {lost ignore} option and a fixed
-"boundary"_boundary.html.
-
-The fix deposit command must use the {region} keyword to define an
-insertion volume.  The specified region must have been previously
-defined with a "region"_region.html command.  It must be defined with
-side = {in}.
-
-NOTE: LAMMPS checks that the specified region is wholly inside the
-simulation box.  It can do this correctly for orthonormal simulation
-boxes.  However for "triclinic boxes"_Howto_triclinic.html, it only
-tests against the larger orthonormal box that bounds the tilted
-simulation box.  If the specified region includes volume outside the
-tilted box, then an insertion will likely fail, leading to a "lost
-atoms" error.  Thus for triclinic boxes you should insure the
-specified region is wholly inside the simulation box.
-
-The locations of inserted particles are taken from uniform distributed
-random numbers, unless the {gaussian} keyword is used. Then the
-individual coordinates are taken from a gaussian distribution of
-width {sigma} centered on {xmid,ymid,zmid}.
-
-Individual atoms are inserted, unless the {mol} keyword is used.  It
-specifies a {template-ID} previously defined using the
-"molecule"_molecule.html command, which reads files that define one or
-more molecules.  The coordinates, atom types, charges, etc, as well as
-any bond/angle/etc and special neighbor information for the molecule
-can be specified in the molecule file.  See the
-"molecule"_molecule.html command for details.  The only settings
-required to be in each file are the coordinates and types of atoms in
-the molecule.
-
-If the molecule template contains more than one molecule, the relative
-probability of depositing each molecule can be specified by the
-{molfrac} keyword.  N relative probabilities, each from 0.0 to 1.0, are
-specified, where N is the number of molecules in the template.  Each
-time a molecule is deposited, a random number is used to sample from
-the list of relative probabilities.  The N values must sum to 1.0.
-
-If you wish to insert molecules via the {mol} keyword, that will be
-treated as rigid bodies, use the {rigid} keyword, specifying as its
-value the ID of a separate "fix rigid/small"_fix_rigid.html
-command which also appears in your input script.
-
-NOTE: If you wish the new rigid molecules (and other rigid molecules)
-to be thermostatted correctly via "fix rigid/small/nvt"_fix_rigid.html
-or "fix rigid/small/npt"_fix_rigid.html, then you need to use the
-"fix_modify dynamic/dof yes" command for the rigid fix.  This is to
-inform that fix that the molecule count will vary dynamically.
-
-If you wish to insert molecules via the {mol} keyword, that will have
-their bonds or angles constrained via SHAKE, use the {shake} keyword,
-specifying as its value the ID of a separate "fix
-shake"_fix_shake.html command which also appears in your input script.
-
-Each timestep a particle is inserted, the coordinates for its atoms
-are chosen as follows.  For insertion of individual atoms, the
-"position" referred to in the following description is the coordinate
-of the atom.  For insertion of molecule, the "position" is the
-geometric center of the molecule; see the "molecule"_molecule.html doc
-page for details.  A random rotation of the molecule around its center
-point is performed, which determines the coordinates all the
-individual atoms.
-
-A random position within the region insertion volume is generated.  If
-neither the {global} or {local} keyword is used, the random position
-is the trial position.  If the {global} keyword is used, the random
-x,y values are used, but the z position of the new particle is set
-above the highest current atom in the simulation by a distance
-randomly chosen between lo/hi.  (For a 2d simulation, this is done for
-the y position.)  If the {local} keyword is used, the z position is
-set a distance between lo/hi above the highest current atom in the
-simulation that is "nearby" the chosen x,y position.  In this context,
-"nearby" means the lateral distance (in x,y) between the new and old
-particles is less than the {delta} setting.
-
-Once a trial x,y,z position has been selected, the insertion is only
-performed if no current atom in the simulation is within a distance R
-of any atom in the new particle, including the effect of periodic
-boundary conditions if applicable.  R is defined by the {near}
-keyword.  Note that the default value for R is 0.0, which will allow
-atoms to strongly overlap if you are inserting where other atoms are
-present.  This distance test is performed independently for each atom
-in an inserted molecule, based on the randomly rotated configuration
-of the molecule.  If this test fails, a new random position within the
-insertion volume is chosen and another trial is made.  Up to Q
-attempts are made.  If the particle is not successfully inserted,
-LAMMPS prints a warning message.
-
-NOTE: If you are inserting finite size particles or a molecule or
-rigid body consisting of finite-size particles, then you should
-typically set R larger than the distance at which any inserted
-particle may overlap with either a previously inserted particle or an
-existing particle.  LAMMPS will issue a warning if R is smaller than
-this value, based on the radii of existing and inserted particles.
-
-The {rate} option moves the insertion volume in the z direction (3d)
-or y direction (2d).  This enables particles to be inserted from a
-successively higher height over time.  Note that this parameter is
-ignored if the {global} or {local} keywords are used, since those
-options choose a z-coordinate for insertion independently.
-
-The vx, vy, and vz components of velocity for the inserted particle
-are set using the values specified for the {vx}, {vy}, and {vz}
-keywords.  Note that normally, new particles should be a assigned a
-negative vertical velocity so that they move towards the surface.  For
-molecules, the same velocity is given to every particle (no rotation
-or bond vibration).
-
-If the {target} option is used, the velocity vector of the inserted
-particle is changed so that it points from the insertion position
-towards the specified target point.  The magnitude of the velocity is
-unchanged.  This can be useful, for example, for simulating a
-sputtering process.  E.g. the target point can be far away, so that
-all incident particles strike the surface as if they are in an
-incident beam of particles at a prescribed angle.
-
-The {id} keyword determines how atom IDs and molecule IDs are assigned
-to newly deposited particles.  Molecule IDs are only assigned if
-molecules are being inserted.  For the {max} setting, the atom and
-molecule IDs of all current atoms are checked.  Atoms in the new
-particle are assigned IDs starting with the current maximum plus one.
-If a molecule is inserted it is assigned an ID = current maximum plus
-one.  This means that if particles leave the system, the new IDs may
-replace the lost ones.  For the {next} setting, the maximum ID of any
-atom and molecule is stored at the time the fix is defined.  Each time
-a new particle is added, this value is incremented to assign IDs to
-the new atom(s) or molecule.  Thus atom and molecule IDs for deposited
-particles will be consecutive even if particles leave the system over
-time.
-
-The {units} keyword determines the meaning of the distance units used
-for the other deposition parameters.  A {box} value selects standard
-distance units as defined by the "units"_units.html command,
-e.g. Angstroms for units = real or metal.  A {lattice} value means the
-distance units are in lattice spacings.  The "lattice"_lattice.html
-command must have been previously used to define the lattice spacing.
-Note that the units choice affects all the keyword values that have
-units of distance or velocity.
-
-NOTE: If you are monitoring the temperature of a system where the atom
-count is changing due to adding particles, you typically should use
-the "compute_modify dynamic yes"_compute_modify.html command for the
-temperature compute you are using.
-
-[Restart, fix_modify, output, run start/stop, minimize info:]
-
-This fix writes the state of the deposition to "binary restart
-files"_restart.html.  This includes information about how many
-particles have been deposited, the random number generator seed, the
-next timestep for deposition, etc.  See the
-"read_restart"_read_restart.html command for info on how to re-specify
-a fix in an input script that reads a restart file, so that the
-operation of the fix continues in an uninterrupted fashion.
-
-NOTE: For this to work correctly, the timestep must [not] be changed
-after reading the restart with "reset_timestep"_reset_timestep.html.
-The fix will try to detect it and stop with an error.
-
-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 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.
-
-The specified insertion region cannot be a "dynamic" region, as
-defined by the "region"_region.html command.
-
-[Related commands:]
-
-"fix pour"_fix_pour.html, "region"_region.html
-
-[Default:]
-
-Insertions are performed for individual atoms, i.e. no {mol} setting
-is defined.  If the {mol} keyword is used, the default for {molfrac}
-is an equal probabilities for all molecules in the template.
-Additional option defaults are id = max, delta = 0.0, near = 0.0,
-attempt = 10, rate = 0.0, vx = 0.0 0.0, vy = 0.0 0.0, vz = 0.0 0.0,
-and units = lattice.
diff --git a/doc/txt/fix_nve_dot.txt b/doc/txt/fix_nve_dot.txt
deleted file mode 100644
index fcd8926c13..0000000000
--- a/doc/txt/fix_nve_dot.txt
+++ /dev/null
@@ -1,63 +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 nve/dot command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dot :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dot = style name of this fix command :l
-:ule
-
-[Examples:]
-
-fix 1 all nve/dot :pre
-
-[Description:]
-
-Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
-to a group of atoms, but without Langevin dynamics.
-This command performs Molecular dynamics (MD)
-via a velocity-Verlet algorithm and an evolution operator that rotates
-the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
-
-This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-without damping and noise and can be used to determine the stability range
-in a NVE ensemble prior to using the Langevin-type DOTC-integrator
-(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
-The command is equivalent to the "fix nve"_fix_nve.html.
-The particles are always considered to have a finite size.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex1/.
-Further details of the implementation and stability of the integrator are contained in "(Henrich)"_#Henrich3.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack1)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller1)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Henrich3)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/txt/fix_nve_dotc_langevin.txt b/doc/txt/fix_nve_dotc_langevin.txt
deleted file mode 100644
index 898ca5132b..0000000000
--- a/doc/txt/fix_nve_dotc_langevin.txt
+++ /dev/null
@@ -1,143 +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 nve/dotc/langevin command :h3
-
-[Syntax:]
-
-fix ID group-ID nve/dotc/langevin Tstart Tstop damp seed keyword value :pre
-
-ID, group-ID are documented in "fix"_fix.html command :ulb,l
-nve/dotc/langevin = style name of this fix command :l
-Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
-damp = damping parameter (time units) :l
-seed = random number seed to use for white noise (positive integer) :l
-keyword = {angmom} :l
-  {angmom} value = factor
-    factor = do thermostat rotational degrees of freedom via the angular momentum and apply numeric scale factor as discussed below :pre
-:ule
-
-[Examples:]
-
-fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10
-fix 1 all nve/dotc/langevin 0.1 0.1 78.9375 457145 angmom 10 :pre
-
-[Description:]
-
-Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
-as described in "(Davidchack)"_#Davidchack2
-to a group of atoms, which models an interaction with an implicit background
-solvent.  This command performs Brownian dynamics (BD)
-via a technique that splits the integration into a deterministic Hamiltonian
-part and the Ornstein-Uhlenbeck process for noise and damping.
-The quaternion degrees of freedom are updated though an evolution
-operator which performs a rotation in quaternion space, preserves
-the quaternion norm and is akin to "(Miller)"_#Miller2.
-
-In terms of syntax this command has been closely modelled on the
-"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
-the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
-one single command. The main feature is improved stability
-over the standard integrator, permitting slightly larger timestep sizes.
-
-NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
-also time integration of the translational and quaternion degrees of freedom.
-
-The total force on each atom will have the form:
-
-F = Fc + Ff + Fr
-Ff = - (m / damp) v
-Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
-
-Fc is the conservative force computed via the usual inter-particle
-interactions ("pair_style"_pair_style.html,
-"bond_style"_bond_style.html, etc).
-
-The Ff and Fr terms are implicitly taken into account by this fix
-on a per-particle basis.
-
-Ff is a frictional drag or viscous damping term proportional to the
-particle's velocity.  The proportionality constant for each atom is
-computed as m/damp, where m is the mass of the particle and damp is
-the damping factor specified by the user.
-
-Fr is a force due to solvent atoms at a temperature T randomly bumping
-into the particle.  As derived from the fluctuation/dissipation
-theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
-dt damp), where Kb is the Boltzmann constant, T is the desired
-temperature, m is the mass of the particle, dt is the timestep size,
-and damp is the damping factor.  Random numbers are used to randomize
-the direction and magnitude of this force as described in
-"(Dunweg)"_#Dunweg3, where a uniform random number is used (instead of
-a Gaussian random number) for speed.
-
-:line
-
-{Tstart} and {Tstop} have to be constant values, i.e. they cannot
-be variables. If used together with the oxDNA force field for
-coarse-grained simulation of DNA please note that T = 0.1 in oxDNA units
-corresponds to T = 300 K.
-
-The {damp} parameter is specified in time units and determines how
-rapidly the temperature is relaxed.  For example, a value of 0.03
-means to relax the temperature in a timespan of (roughly) 0.03 time
-units tau (see the "units"_units.html command).
-The damp factor can be thought of as inversely related to the
-viscosity of the solvent, i.e. a small relaxation time implies a
-hi-viscosity solvent and vice versa.  See the discussion about gamma
-and viscosity in the documentation for the "fix
-viscous"_fix_viscous.html command for more details.
-Note that the value 78.9375 in the second example above corresponds
-to a diffusion constant, which is about an order of magnitude larger
-than realistic ones. This has been used to sample configurations faster
-in Brownian dynamics simulations.
-
-The random # {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 keyword/value option has to be used in the following way:
-
-This fix has to be used together with the {angmom} keyword. The
-particles are always considered to have a finite size.
-The keyword {angmom} enables thermostatting of the rotational degrees of
-freedom in addition to the usual translational degrees of freedom.
-
-The scale factor after the {angmom} keyword gives the ratio of the rotational to
-the translational friction coefficient.
-
-An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
-Further details of the implementation and stability of the integrators are contained in "(Henrich)"_#Henrich4.
-The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
-
-:line
-
-[Restrictions:]
-
-These pair styles can only be used if LAMMPS was built with the
-"USER-CGDNA"_Package_details.html#PKG-USER-CGDNA package and the MOLECULE and ASPHERE package.
-See the "Build package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, "bond_style oxdna/fene"_bond_oxdna.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Davidchack2)
-[(Davidchack)] R.L Davidchack, T.E. Ouldridge, M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).
-:link(Miller2)
-[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
-:link(Dunweg3)
-[(Dunweg)] B. Dunweg, W. Paul, Int. J. Mod. Phys. C, 2, 817-27 (1991).
-:link(Henrich4)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
diff --git a/doc/txt/kspace_style.txt b/doc/txt/kspace_style.txt
deleted file mode 100644
index 04b845acaa..0000000000
--- a/doc/txt/kspace_style.txt
+++ /dev/null
@@ -1,495 +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
-
-kspace_style command :h3
-
-[Syntax:]
-
-kspace_style style value :pre
-
-style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} or {pppm/disp} or {pppm/tip4p} or {pppm/stagger} or {pppm/disp/tip4p} or {pppm/gpu} or {pppm/kk} or {pppm/omp} or {pppm/cg/omp} or {pppm/tip4p/omp} or {msm} or {msm/cg} or {msm/omp} or {msm/cg/omp} or {scafacos} :ulb,l
-  {none} value = none
-  {ewald} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {ewald/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg} values = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {pppm/disp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/tip4p} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/gpu} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/kk} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/cg/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/disp/intel} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/tip4p/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/stagger} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole} value = accuracy
-    accuracy = desired relative error in forces
-  {pppm/dipole/spin} value = accuracy
-    accuracy = desired relative error in forces
-  {msm} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {msm/omp} value = accuracy
-    accuracy = desired relative error in forces
-  {msm/cg/omp} value = accuracy (smallq)
-    accuracy = desired relative error in forces
-    smallq = cutoff for charges to be considered (optional) (charge units)
-  {scafacos} values = method accuracy
-    method = fmm or p2nfft or p3m or ewald or direct
-    accuracy = desired relative error in forces :pre
-:ule
-
-[Examples:]
-
-kspace_style pppm 1.0e-4
-kspace_style pppm/cg 1.0e-5 1.0e-6
-kspace style msm 1.0e-4
-kspace style scafacos fmm 1.0e-4
-kspace_style none :pre
-
-[Description:]
-
-Define a long-range solver for LAMMPS to use each timestep to compute
-long-range Coulombic interactions or long-range 1/r^6 interactions.
-Most of the long-range solvers perform their computation in K-space,
-hence the name of this command.
-
-When such a solver is used in conjunction with an appropriate pair
-style, the cutoff for Coulombic or 1/r^N interactions is effectively
-infinite.  If the Coulombic case, this means each charge in the system
-interacts with charges in an infinite array of periodic images of the
-simulation domain.
-
-Note that using a long-range solver requires use of a matching "pair
-style"_pair_style.html to perform consistent short-range pairwise
-calculations.  This means that the name of the pair style contains a
-matching keyword to the name of the KSpace style, as in this table:
-
-Pair style : KSpace style
-coul/long : ewald or pppm
-coul/msm : msm
-lj/long or buck/long : disp (for dispersion)
-tip4p/long : tip4p :tb(s=:,ea=c)
-
-:line
-
-The {ewald} style performs a standard Ewald summation as described in
-any solid-state physics text.
-
-The {ewald/disp} style adds a long-range dispersion sum option for
-1/r^6 potentials and is useful for simulation of interfaces
-"(Veld)"_#Veld.  It also performs standard Coulombic Ewald summations,
-but in a more efficient manner than the {ewald} style.  The 1/r^6
-capability means that Lennard-Jones or Buckingham potentials can be
-used without a cutoff, i.e. they become full long-range potentials.
-The {ewald/disp} style can also be used with point-dipoles, see
-"(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole} style adds long-range standard Ewald summations
-for dipole-dipole interactions, see "(Toukmaji)"_#Toukmaji.
-
-The {ewald/dipole/spin} style adds long-range standard Ewald
-summations for magnetic dipole-dipole interactions between
-magnetic spins.
-
-:line
-
-The {pppm} style invokes a particle-particle particle-mesh solver
-"(Hockney)"_#Hockney which maps atom charge to a 3d mesh, uses 3d FFTs
-to solve Poisson's equation on the mesh, then interpolates electric
-fields on the mesh points back to the atoms.  It is closely related to
-the particle-mesh Ewald technique (PME) "(Darden)"_#Darden used in
-AMBER and CHARMM.  The cost of traditional Ewald summation scales as
-N^(3/2) where N is the number of atoms in the system.  The PPPM solver
-scales as Nlog(N) due to the FFTs, so it is almost always a faster
-choice "(Pollock)"_#Pollock.
-
-The {pppm/cg} style is identical to the {pppm} style except that it
-has an optimization for systems where most particles are uncharged.
-Similarly the {msm/cg} style implements the same optimization for {msm}.
-The optional {smallq} argument defines the cutoff for the absolute
-charge value which determines whether a particle is considered charged
-or not.  Its default value is 1.0e-5.
-
-The {pppm/dipole} style invokes a particle-particle particle-mesh solver
-for dipole-dipole interactions, following the method of "(Cerda)"_#Cerda2008.
-
-The {pppm/dipole/spin} style invokes a particle-particle particle-mesh solver
-for magnetic dipole-dipole interactions between magnetic spins.
-
-The {pppm/tip4p} style is identical to the {pppm} style except that it
-adds a charge at the massless 4th site in each TIP4P water molecule.
-It should be used with "pair styles"_pair_style.html with a
-{tip4p/long} in their style name.
-
-The {pppm/stagger} style performs calculations using two different
-meshes, one shifted slightly with respect to the other.  This can
-reduce force aliasing errors and increase the accuracy of the method
-for a given mesh size.  Or a coarser mesh can be used for the same
-target accuracy, which saves CPU time.  However, there is a trade-off
-since FFTs on two meshes are now performed which increases the
-computation required.  See "(Cerutti)"_#Cerutti, "(Neelov)"_#Neelov,
-and "(Hockney)"_#Hockney for details of the method.
-
-For high relative accuracy, using staggered PPPM allows the mesh size
-to be reduced by a factor of 2 in each dimension as compared to
-regular PPPM (for the same target accuracy).  This can give up to a 4x
-speedup in the KSpace time (8x less mesh points, 2x more expensive).
-However, for low relative accuracy, the staggered PPPM mesh size may
-be essentially the same as for regular PPPM, which means the method
-will be up to 2x slower in the KSpace time (simply 2x more expensive).
-For more details and timings, see the "Speed tips"_Speed_tips.html doc
-page.
-
-NOTE: Using {pppm/stagger} may not give the same increase in the
-accuracy of energy and pressure as it does in forces, so some caution
-must be used if energy and/or pressure are quantities of interest,
-such as when using a barostat.
-
-:line
-
-The {pppm/disp} and {pppm/disp/tip4p} styles add a mesh-based long-range
-dispersion sum option for 1/r^6 potentials "(Isele-Holder)"_#Isele-Holder2012,
-similar to the {ewald/disp} style. The 1/r^6 capability means
-that Lennard-Jones or Buckingham potentials can be used without a cutoff,
-i.e. they become full long-range potentials.
-
-For these styles, you will possibly want to adjust the default choice
-of parameters by using the "kspace_modify"_kspace_modify.html command.
-This can be done by either choosing the Ewald and grid parameters, or
-by specifying separate accuracies for the real and kspace
-calculations. When not making any settings, the simulation will stop
-with an error message. Further information on the influence of the
-parameters and how to choose them is described in
-"(Isele-Holder)"_#Isele-Holder2012,
-"(Isele-Holder2)"_#Isele-Holder2013 and the "Howto
-dispersion"_Howto_dispersion.html doc page.
-
-:line
-
-NOTE: All of the PPPM styles can be used with single-precision FFTs by
-using the compiler switch -DFFT_SINGLE for the FFT_INC setting in your
-lo-level Makefile.  This setting also changes some of the PPPM
-operations (e.g. mapping charge to mesh and interpolating electric
-fields to particles) to be performed in single precision.  This option
-can speed-up long-range calculations, particularly in parallel or on
-GPUs.  The use of the -DFFT_SINGLE flag is discussed on the "Build
-settings"_Build_settings.html doc page. MSM does not currently support
-the -DFFT_SINGLE compiler switch.
-
-:line
-
-The {msm} style invokes a multi-level summation method MSM solver,
-"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
-to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
-meshes on which direct Coulomb solvers are done.  This method does not
-use FFTs and scales as N. It may therefore be faster than the other
-K-space solvers for relatively large problems when running on large
-core counts. MSM can also be used for non-periodic boundary conditions
-and for mixed periodic and non-periodic boundaries.
-
-MSM is most competitive versus Ewald and PPPM when only relatively
-low accuracy forces, about 1e-4 relative error or less accurate,
-are needed. Note that use of a larger Coulombic cutoff (i.e. 15
-angstroms instead of 10 angstroms) provides better MSM accuracy for
-both the real space and grid computed forces.
-
-Currently calculation of the full pressure tensor in MSM is expensive.
-Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes}
-command provides a less expensive way to compute the scalar pressure
-(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example,
-to run an isotropic barostat. If the full pressure tensor is needed,
-then calculating the pressure at every timestep or using a fixed
-pressure simulation with MSM will cause the code to run slower.
-
-:line
-
-The {scafacos} style is a wrapper on the "ScaFaCoS Coulomb solver
-library"_http://www.scafacos.de which provides a variety of solver
-methods which can be used with LAMMPS.  The paper by "(Who)"_#Who2012
-gives an overview of ScaFaCoS.
-
-ScaFaCoS was developed by a consortium of German research facilities
-with a BMBF (German Ministry of Science and Education) funded project
-in 2009-2012. Participants of the consortium were the Universities of
-Bonn, Chemnitz, Stuttgart, and Wuppertal as well as the
-Forschungszentrum Juelich.
-
-The library is available for download at "http://scafacos.de" or can
-be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
-
-In order to use this KSpace style, you must download and build the
-ScaFaCoS library, then build LAMMPS with the USER-SCAFACOS package
-installed package which links LAMMPS to the ScaFaCoS library.
-See details on "this page"_Section_packages.html#USER-SCAFACOS.
-
-NOTE: Unlike other KSpace solvers in LAMMPS, ScaFaCoS computes all
-Coulombic interactions, both short- and long-range.  Thus you should
-NOT use a Coulombic pair style when using kspace_style scafacos.  This
-also means the total Coulombic energy (short- and long-range) will be
-tallied for "thermodynamic output"_thermo_style.html command as part
-of the {elong} keyword; the {ecoul} keyword will be zero.
-
-NOTE: See the current restriction below about use of ScaFaCoS in
-LAMMPS with molecular charged systems or the TIP4P water model.
-
-The specified {method} determines which ScaFaCoS algorithm is used.
-These are the ScaFaCoS methods currently available from LAMMPS:
-
-{fmm} = Fast Multi-Pole method
-{p2nfft} = FFT-based Coulomb solver
-{ewald} = Ewald summation
-{direct} = direct O(N^2) summation
-{p3m} = PPPM :ul
-
-We plan to support additional ScaFaCoS solvers from LAMMPS in the
-future.  For an overview of the included solvers, refer to
-"(Sutmann)"_#Sutmann2013
-
-The specified {accuracy} is similar to the accuracy setting for other
-LAMMPS KSpace styles, but is passed to ScaFaCoS, which can interpret
-it in different ways for different methods it supports.  Within the
-ScaFaCoS library the {accuracy} is treated as a tolerance level
-(either absolute or relative) for the chosen quantity, where the
-quantity can be either the Columic field values, the per-atom Columic
-energy or the total Columic energy.  To select from these options, see
-the "kspace_modify scafacos accuracy"_kspace_modify.html doc page.
-
-The "kspace_modify scafacos"_kspace_modify.html command also explains
-other ScaFaCoS options currently exposed to LAMMPS.
-
-:line
-
-The specified {accuracy} determines the relative RMS error in per-atom
-forces calculated by the long-range solver.  It is set as a
-dimensionless number, relative to the force that two unit point
-charges (e.g. 2 monovalent ions) exert on each other at a distance of
-1 Angstrom.  This reference value was chosen as representative of the
-magnitude of electrostatic forces in atomic systems.  Thus an accuracy
-value of 1.0e-4 means that the RMS error will be a factor of 10000
-smaller than the reference force.
-
-The accuracy setting is used in conjunction with the pairwise cutoff
-to determine the number of K-space vectors for style {ewald} or the
-grid size for style {pppm} or {msm}.
-
-Note that style {pppm} only computes the grid size at the beginning of
-a simulation, so if the length or triclinic tilt of the simulation
-cell increases dramatically during the course of the simulation, the
-accuracy of the simulation may degrade.  Likewise, if the
-"kspace_modify slab"_kspace_modify.html option is used with
-shrink-wrap boundaries in the z-dimension, and the box size changes
-dramatically in z.  For example, for a triclinic system with all three
-tilt factors set to the maximum limit, the PPPM grid should be
-increased roughly by a factor of 1.5 in the y direction and 2.0 in the
-z direction as compared to the same system using a cubic orthogonal
-simulation cell.  One way to handle this issue if you have a long
-simulation where the box size changes dramatically, is to break it
-into shorter simulations (multiple "run"_run.html commands).  This
-works because the grid size is re-computed at the beginning of each
-run.  Another way to ensure the described accuracy requirement is met
-is to run a short simulation at the maximum expected tilt or length,
-note the required grid size, and then use the
-"kspace_modify"_kspace_modify.html {mesh} command to manually set the
-PPPM grid size to this value for the long run.  The simulation then
-will be "too accurate" for some portion of the run.
-
-RMS force errors in real space for {ewald} and {pppm} are estimated
-using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as
-equation 9 of "(Petersen)"_#Petersen. RMS force errors in K-space for
-{ewald} are estimated using equation 11 of "(Petersen)"_#Petersen,
-which is similar to equation 32 of "(Kolafa)"_#Kolafa. RMS force
-errors in K-space for {pppm} are estimated using equation 38 of
-"(Deserno)"_#Deserno. RMS force errors for {msm} are estimated
-using ideas from chapter 3 of "(Hardy)"_#Hardy2006, with equation 3.197
-of particular note. When using {msm} with non-periodic boundary
-conditions, it is expected that the error estimation will be too
-pessimistic. RMS force errors for dipoles when using {ewald/disp}
-or {ewald/dipole} are estimated using equations 33 and 46 of
-"(Wang)"_#Wang. The RMS force errors for {pppm/dipole} are estimated
-using the equations in "(Cerda)"_#Cerda2008.
-
-
-See the "kspace_modify"_kspace_modify.html command for additional
-options of the K-space solvers that can be set, including a {force}
-option for setting an absolute RMS error in forces, as opposed to a
-relative RMS error.
-
-: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.
-
-More specifically, the {pppm/gpu} style performs charge assignment and
-force interpolation calculations on the GPU.  These processes are
-performed either in single or double precision, depending on whether
-the -DFFT_SINGLE setting was specified in your lo-level Makefile, as
-discussed above.  The FFTs themselves are still calculated on the CPU.
-If {pppm/gpu} is used with a GPU-enabled pair style, part of the PPPM
-calculation can be performed concurrently on the GPU while other
-calculations for non-bonded and bonded force calculation are performed
-on the CPU.
-
-The {pppm/kk} style also performs charge assignment and force
-interpolation calculations on the GPU while the FFTs themselves are
-calculated on the CPU in non-threaded mode.
-
-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.
-
-See the "Speed packages"_Speed_packages.html doc page for more
-instructions on how to use the accelerated styles effectively.
-
-:line
-
-[Restrictions:]
-
-Note that the long-range electrostatic solvers in LAMMPS assume conducting
-metal (tinfoil) boundary conditions for both charge and dipole
-interactions. Vacuum boundary conditions are not currently supported.
-
-The {ewald/disp}, {ewald}, {pppm}, and {msm} styles support
-non-orthogonal (triclinic symmetry) simulation boxes. However,
-triclinic simulation cells may not yet be supported by suffix versions
-of these styles.
-
-All of the kspace styles are part of the KSPACE package.  They are
-only enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-For MSM, a simulation must be 3d and one can use any combination of
-periodic, non-periodic, or shrink-wrapped boundaries (specified using
-the "boundary"_boundary.html command).
-
-For Ewald and PPPM, a simulation must be 3d and periodic in all
-dimensions.  The only exception is if the slab option is set with
-"kspace_modify"_kspace_modify.html, in which case the xy dimensions
-must be periodic and the z dimension must be non-periodic.
-
-The scafacos KSpace style will only be enabled if LAMMPS is built with
-the USER-SCAFACOS package.  See the "Build package"_Build_package.html
-doc page for more info.
-
-The use of ScaFaCos in LAMMPS does not yet support molecular charged
-systems where the short-range Coulombic interactions between atoms in
-the same bond/angle/dihedral are weighted by the
-"special_bonds"_special_bonds.html command.  Likewise it does not
-support the "TIP4P water style" where a fictitious charge site is
-introduced in each water molecule.
-Finally, the methods {p3m} and {ewald} do not support computing the
-virial, so this contribution is not included.
-
-[Related commands:]
-
-"kspace_modify"_kspace_modify.html, "pair_style
-lj/cut/coul/long"_pair_lj.html, "pair_style
-lj/charmm/coul/long"_pair_charmm.html, "pair_style
-lj/long/coul/long"_pair_lj_long.html, "pair_style
-buck/coul/long"_pair_buck.html
-
-[Default:]
-
-kspace_style none :pre
-
-:line
-
-:link(Darden)
-[(Darden)] Darden, York, Pedersen, J Chem Phys, 98, 10089 (1993).
-
-:link(Deserno)
-[(Deserno)] Deserno and Holm, J Chem Phys, 109, 7694 (1998).
-
-:link(Hockney)
-[(Hockney)] Hockney and Eastwood, Computer Simulation Using Particles,
-Adam Hilger, NY (1989).
-
-:link(Kolafa)
-[(Kolafa)] Kolafa and Perram, Molecular Simulation, 9, 351 (1992).
-
-:link(Petersen)
-[(Petersen)] Petersen, J Chem Phys, 103, 3668 (1995).
-
-:link(Wang)
-[(Wang)] Wang and Holm, J Chem Phys, 115, 6277 (2001).
-
-:link(Pollock)
-[(Pollock)] Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
-
-:link(Cerutti)
-[(Cerutti)] Cerutti, Duke, Darden, Lybrand, Journal of Chemical Theory
-and Computation 5, 2322 (2009)
-
-:link(Neelov)
-[(Neelov)] Neelov, Holm, J Chem Phys 132, 234103 (2010)
-
-:link(Veld)
-[(Veld)] In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
-
-:link(Toukmaji)
-[(Toukmaji)] Toukmaji, Sagui, Board, and Darden, J Chem Phys, 113,
-10913 (2000).
-
-:link(Isele-Holder2012)
-[(Isele-Holder)] Isele-Holder, Mitchell, Ismail, J Chem Phys, 137,
-174107 (2012).
-
-:link(Isele-Holder2013)
-[(Isele-Holder2)] Isele-Holder, Mitchell, Hammond, Kohlmeyer, Ismail,
-J Chem Theory Comput 9, 5412 (2013).
-
-:link(Hardy2006)
-[(Hardy)] David Hardy thesis: Multilevel Summation for the Fast
-Evaluation of Forces for the Simulation of Biomolecules, University of
-Illinois at Urbana-Champaign, (2006).
-
-:link(Hardy2009)
-[(Hardy2)] Hardy, Stone, Schulten, Parallel Computing, 35, 164-177
-(2009).
-
-:link(Sutmann2013)
-[(Sutmann)] Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
-
-:link(Cerda2008)
-[(Cerda)] Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
-
-:link(Who2012)
-[(Who)] Who, Author2, Author3, J of Long Range Solvers, 35, 164-177
-(2012).
diff --git a/doc/txt/message.txt b/doc/txt/message.txt
deleted file mode 100644
index 0c10af4ac6..0000000000
--- a/doc/txt/message.txt
+++ /dev/null
@@ -1,162 +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,Command_all.html)
-
-:line
-
-message command :h3
-
-[Syntax:]
-
-message which protocol mode arg :pre
-
-which = {client} or {server} :ulb,l
-protocol = {md} or {mc} :l
-mode = {file} or {zmq} or {mpi/one} or {mpi/two} :l
-  {file} arg = filename
-    filename = file used for message exchanges
-  {zmq} arg = socket-ID
-    socket-ID for client = localhost:5555, see description below
-    socket-ID for server = *:5555, see description below
-  {mpi/one} arg = none
-  {mpi/two} arg = filename
-    filename = file used to establish communication between 2 MPI jobs :pre
-:ule
-
-[Examples:]
-
-message client md file tmp.couple
-message server md file tmp.couple :pre
-
-message client md zmq localhost:5555
-message server md zmq *:5555 :pre
-
-message client md mpi/one
-message server md mpi/one :pre
-
-message client md mpi/two tmp.couple
-message server md mpi/two tmp.couple :pre
-
-[Description:]
-
-Establish a messaging protocol between LAMMPS and another code for the
-purpose of client/server coupling.
-
-The "Howto client/server"_Howto_client_server.html doc page gives an
-overview of client/server coupling of LAMMPS with another code where
-one code is the "client" and sends request messages to a "server"
-code.  The server responds to each request with a reply message.  This
-enables the two codes to work in tandem to perform a simulation.
-
-:line
-
-The {which} argument defines LAMMPS to be the client or the server.
-
-:line
-
-The {protocol} argument defines the format and content of messages
-that will be exchanged between the two codes.  The current options
-are:
-
-md = run dynamics with another code
-mc = perform Monte Carlo moves with another code :ul
-
-For protocol {md}, LAMMPS can be either a client or server.  See the
-"server md"_server_md.html doc page for details on the protocol.
-
-For protocol {mc}, LAMMPS can be the server.  See the "server
-mc"_server_mc.html doc page for details on the protocol.
-
-:line
-
-The {mode} argument specifies how messages are exchanged between the
-client and server codes.  Both codes must use the same mode and use
-consistent parameters.
-
-For mode {file}, the 2 codes communicate via binary files.  They must
-use the same filename, which is actually a file prefix.  Several files
-with that prefix will be created and deleted as a simulation runs.
-The filename can include a path.  Both codes must be able to access
-the path/file in a common filesystem.
-
-For mode {zmq}, the 2 codes communicate via a socket on the server
-code's machine.  Support for socket messaging is provided by the
-open-source "ZeroMQ library"_http://zeromq.org, which must be
-installed on your system.  The client specifies an IP address (IPv4
-format) or the DNS name of the machine the server code is running on,
-followed by a 4-digit port ID for the socket, separated by a colon.
-E.g.
-
-localhost:5555        # client and server running on same machine
-192.168.1.1:5555      # server is 192.168.1.1
-deptbox.uni.edu:5555  # server is deptbox.uni.edu :pre
-
-The server specifies "*:5555" where "*" represents all available
-interfaces on the server's machine, and the port ID must match
-what the client specifies.
-
-NOTE: What are allowed port IDs?
-
-NOTE: Additional explanation is needed here about how to use the {zmq}
-mode on a parallel machine, e.g. a cluster with many nodes.
-
-For mode {mpi/one}, the 2 codes communicate via MPI and are launched
-by the same mpirun command, e.g. with this syntax for OpenMPI:
-
-mpirun -np 2 lmp_mpi -mpicolor 0 -in in.client -log log.client : -np 4 othercode args  # LAMMPS is client
-mpirun -np 2 othercode args : -np 4 lmp_mpi -mpicolor 1 -in in.server  # LAMMPS is server :pre
-
-Note the use of the "-mpicolor color" command-line argument with
-LAMMPS.  See the "command-line args"_Run_options.html doc page for
-further explanation.
-
-For mode {mpi/two}, the 2 codes communicate via MPI, but are launched
-be 2 separate mpirun commands.  The specified {filename} argument is a
-file the 2 MPI processes will use to exchange info so that an MPI
-inter-communicator can be established to enable the 2 codes to send
-MPI messages to each other.  Both codes must be able to access the
-path/file in a common filesystem.
-
-:line
-
-Normally, the message command should be used at the top of a LAMMPS
-input script.  It performs an initial handshake with the other code to
-setup messaging and to verify that both codes are using the same
-message protocol and mode.  Assuming both codes are launched at
-(nearly) the same time, the other code should perform the same kind of
-initialization.
-
-If LAMMPS is the client code, it will begin sending messages when a
-LAMMPS client command begins its operation.  E.g. for the "fix
-client/md"_fix_client_md.html command, it is when a "run"_run.html
-command is executed.
-
-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.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.
-
-If both codes do something similar, this means a new round of
-client/server messaging can be initiated after termination by re-using
-a 2nd message command in your LAMMPS input script, followed by a new
-fix client or server command.
-
-:line
-
-[Restrictions:]
-
-This command is part of the MESSAGE 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:]
-
-"server"_server.html, "fix client/md"_fix_client_md.html
-
-[Default:] none
diff --git a/doc/txt/pair_lj_switch3_coulgauss.txt b/doc/txt/pair_lj_switch3_coulgauss.txt
deleted file mode 100644
index 1277cff9aa..0000000000
--- a/doc/txt/pair_lj_switch3_coulgauss.txt
+++ /dev/null
@@ -1,86 +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
-
-pair_style lj/switch3/coulgauss/long command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = {lj/switch3/coulgauss/long}
-args = list of arguments for a particular style :ul
-  {lj/switch3/coulgauss/long} args = cutoff (cutoff2) width
-    cutoff  = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-    width  = width parameter of the smoothing function (distance units) :pre
-
-[Examples:]
-
-pair_style lj/switch3/coulgauss/long    12.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-pair_style lj/switch3/coulgauss/long   12.0 10.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-[Description:]
-
-The {lj/switch3/coulgauss} style evaluates the LJ
-vdW potential
-
-:c,image(Eqs/pair_lj_switch3.jpg)
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-:c,image(Eqs/pair_switch3.jpg)
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-:c,image(Eqs/pair_coulgauss.jpg)
-
-where qi and qj are the
-charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
-are the widths of the Gaussian charge distribution and erf() is the error-function.
-This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-sigma (distance)
-gamma (distance) :ul
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-
-[Restrictions:]
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-
diff --git a/doc/txt/pair_meamc.txt b/doc/txt/pair_meamc.txt
deleted file mode 100644
index 2831600e08..0000000000
--- a/doc/txt/pair_meamc.txt
+++ /dev/null
@@ -1,402 +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
-
-pair_style meam/c command :h3
-
-[Syntax:]
-
-pair_style style :pre
-
-style = {meam/c}
-
-[Examples:]
-
-pair_style meam/c
-pair_coeff * * ../potentials/library.meam Si ../potentials/si.meam Si
-pair_coeff * * ../potentials/library.meam Ni Al NULL Ni Al Ni Ni :pre
-
-[Description:]
-
-NOTE: The behavior of the MEAM potential for alloy systems has changed
-as of November 2010; see description below of the mixture_ref_t
-parameter
-
-Style {meam/c} computes pairwise interactions for a variety of materials
-using modified embedded-atom method (MEAM) potentials
-"(Baskes)"_#Baskes.  Conceptually, it is an extension to the original
-"EAM potentials"_pair_eam.html which adds angular forces.  It is
-thus suitable for modeling metals and alloys with fcc, bcc, hcp and
-diamond cubic structures, as well as covalently bonded materials like
-silicon and carbon. Style {meam/c} is a translation of the (now obsolete)
-{meam} code from Fortran to C++. It is functionally equivalent to {meam}
-but more efficient, and thus {meam} has been removed from LAMMPS after
-the 12 December 2018 release.
-
-In the MEAM formulation, the total energy E of a system of atoms is
-given by:
-
-:c,image(Eqs/pair_meam.jpg)
-
-where F is the embedding energy which is a function of the atomic
-electron density rho, and phi is a pair potential interaction.  The
-pair interaction is summed over all neighbors J of atom I within the
-cutoff distance.  As with EAM, the multi-body nature of the MEAM
-potential is a result of the embedding energy term.  Details of the
-computation of the embedding and pair energies, as implemented in
-LAMMPS, are given in "(Gullet)"_#Gullet and references therein.
-
-The various parameters in the MEAM formulas are listed in two files
-which are specified by the "pair_coeff"_pair_coeff.html command.
-These are ASCII text files in a format consistent with other MD codes
-that implement MEAM potentials, such as the serial DYNAMO code and
-Warp.  Several MEAM potential files with parameters for different
-materials are included in the "potentials" directory of the LAMMPS
-distribution with a ".meam" suffix.  All of these are parameterized in
-terms of LAMMPS "metal units"_units.html.
-
-Note that unlike for other potentials, cutoffs for MEAM potentials are
-not set in the pair_style or pair_coeff command; they are specified in
-the MEAM potential files themselves.
-
-Only a single pair_coeff command is used with the {meam} style which
-specifies two MEAM files and the element(s) to extract information
-for.  The MEAM elements are mapped to LAMMPS atom types by specifying
-N additional arguments after the 2nd filename in the pair_coeff
-command, where N is the number of LAMMPS atom types:
-
-MEAM library file
-Elem1, Elem2, ...
-MEAM parameter file
-N element names = mapping of MEAM elements to atom types :ul
-
-See the "pair_coeff"_pair_coeff.html doc page for alternate ways
-to specify the path for the potential files.
-
-As an example, the potentials/library.meam file has generic MEAM
-settings for a variety of elements.  The potentials/SiC.meam file has
-specific parameter settings for a Si and C alloy system.  If your
-LAMMPS simulation has 4 atoms types and you want the 1st 3 to be Si,
-and the 4th to be C, you would use the following pair_coeff command:
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-The 1st 2 arguments must be * * so as to span all LAMMPS atom types.
-The two filenames are for the library and parameter file respectively.
-The Si and C arguments (between the file names) are the two elements
-for which info will be extracted from the library file.  The first
-three trailing Si arguments map LAMMPS atom types 1,2,3 to the MEAM Si
-element.  The final C argument maps LAMMPS atom type 4 to the MEAM C
-element.
-
-If the 2nd filename is specified as NULL, no parameter file is read,
-which simply means the generic parameters in the library file are
-used.  Use of the NULL specification for the parameter file is
-discouraged for systems with more than a single element type
-(e.g. alloys), since the parameter file is expected to set element
-interaction terms that are not captured by the information in the
-library file.
-
-If a mapping value is specified as NULL, the mapping is not performed.
-This can be used when a {meam} potential is used as part of the
-{hybrid} pair style.  The NULL values are placeholders for atom types
-that will be used with other potentials.
-
-NOTE: If the 2nd filename is NULL, the element names between the two
-filenames can appear in any order, e.g. "Si C" or "C Si" in the
-example above.  However, if the 2nd filename is not NULL (as in the
-example above), it contains settings that are Fortran-indexed for the
-elements that preceed it.  Thus you need to insure you list the
-elements between the filenames in an order consistent with how the
-values in the 2nd filename are indexed.  See details below on the
-syntax for settings in the 2nd file.
-
-The MEAM library file provided with LAMMPS has the name
-potentials/library.meam.  It is the "meamf" file used by other MD
-codes.  Aside from blank and comment lines (start with #) which can
-appear anywhere, it is formatted as a series of entries, each of which
-has 19 parameters and can span multiple lines:
-
-elt, lat, z, ielement, atwt, alpha, b0, b1, b2, b3, alat, esub, asub,
-t0, t1, t2, t3, rozero, ibar
-
-The "elt" and "lat" parameters are text strings, such as elt = Si or
-Cu and lat = dia or fcc.  Because the library file is used by Fortran
-MD codes, these strings may be enclosed in single quotes, but this is
-not required.  The other numeric parameters match values in the
-formulas above.  The value of the "elt" string is what is used in the
-pair_coeff command to identify which settings from the library file
-you wish to read in.  There can be multiple entries in the library
-file with the same "elt" value; LAMMPS reads the 1st matching entry it
-finds and ignores the rest.
-
-Other parameters in the MEAM library file correspond to single-element
-potential parameters:
-
-lat      = lattice structure of reference configuration
-z        = number of nearest neighbors in the reference structure
-             This field is only read for compatibility, the correct
-             value is inferred from the lattice structure
-ielement = atomic number
-atwt     = atomic weight
-alat     = lattice constant of reference structure
-esub     = energy per atom (eV) in the reference structure at equilibrium
-asub     = "A" parameter for MEAM (see e.g. "(Baskes)"_#Baskes) :pre
-
-The alpha, b0, b1, b2, b3, t0, t1, t2, t3 parameters correspond to the
-standard MEAM parameters in the literature "(Baskes)"_#Baskes (the b
-parameters are the standard beta parameters). Note that only parameters
-normalized to t0 = 1.0 are supported.  The rozero parameter is
-an element-dependent density scaling that weights the reference
-background density (see e.g. equation 4.5 in "(Gullet)"_#Gullet) and
-is typically 1.0 for single-element systems.  The ibar parameter
-selects the form of the function G(Gamma) used to compute the electron
-density; options are
-
-   0 => G = sqrt(1+Gamma)
-   1 => G = exp(Gamma/2)
-   2 => not implemented
-   3 => G = 2/(1+exp(-Gamma))
-   4 => G = sqrt(1+Gamma)
-  -5 => G = +-sqrt(abs(1+Gamma)) :pre
-
-If used, the MEAM parameter file contains settings that override or
-complement the library file settings.  Examples of such parameter
-files are in the potentials directory with a ".meam" suffix.  Their
-format is the same as is read by other Fortran MD codes.  Aside from
-blank and comment lines (start with #) which can appear anywhere, each
-line has one of the following forms.  Each line can also have a
-trailing comment (starting with #) which is ignored.
-
-keyword = value
-keyword(I) = value
-keyword(I,J) = value
-keyword(I,J,K) = value :pre
-
-The indices I, J, K correspond to the elements selected from the
-MEAM library file numbered in the order of how those elements were
-selected starting from 1. Thus for the example given below
-
-pair_coeff * * library.meam Si C sic.meam Si Si Si C :pre
-
-an index of 1 would refer to Si and an index of 2 to C.
-
-The recognized keywords for the parameter file are as follows:
-
-Ec, alpha, rho0, delta, lattce, attrac, repuls, nn2, Cmin, Cmax, rc, delr,
-augt1, gsmooth_factor, re
-
-where
-
-rc          = cutoff radius for cutoff function; default = 4.0
-delr        = length of smoothing distance for cutoff function; default = 0.1
-rho0(I)     = relative density for element I (overwrites value
-              read from meamf file)
-Ec(I,J)     = cohesive energy of reference structure for I-J mixture
-delta(I,J)  = heat of formation for I-J alloy; if Ec_IJ is input as
-              zero, then LAMMPS sets Ec_IJ = (Ec_II + Ec_JJ)/2 - delta_IJ
-alpha(I,J)  = alpha parameter for pair potential between I and J (can
-              be computed from bulk modulus of reference structure
-re(I,J)     = equilibrium distance between I and J in the reference
-              structure
-Cmax(I,J,K) = Cmax screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.8
-Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened
-              by K (I<=J); default = 2.0
-lattce(I,J) = lattice structure of I-J reference structure:
-                dia = diamond (interlaced fcc for alloy)
-                fcc = face centered cubic
-                bcc = body centered cubic
-                dim = dimer
-                b1  = rock salt (NaCl structure)
-                hcp = hexagonal close-packed
-                c11 = MoSi2 structure
-                l12 = Cu3Au structure (lower case L, followed by 12)
-                b2  = CsCl structure (interpenetrating simple cubic)
-nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for
-              I-J pair (see for example "(Lee)"_#Lee).
-                0 = second-nearest neighbor formulation off
-                1 = second-nearest neighbor formulation on
-                default = 0
-attrac(I,J) = additional cubic attraction term in Rose energy I-J pair potential
-                default = 0
-repuls(I,J) = additional cubic repulsive term in Rose energy I-J pair potential
-                default = 0
-zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small
-              atom separations "(ZBL)"_#ZBL
-                default = 1
-gsmooth_factor  = factor determining the length of the G-function smoothing
-                  region; only significant for ibar=0 or ibar=4.
-                      99.0 = short smoothing region, sharp step
-                      0.5  = long smoothing region, smooth step
-                      default = 99.0
-augt1           = integer flag for whether to augment t1 parameter by
-                  3/5*t3 to account for old vs. new meam formulations;
-                    0 = don't augment t1
-                    1 = augment t1
-                    default = 1
-ialloy          = integer flag to use alternative averaging rule for t parameters,
-                  for comparison with the DYNAMO MEAM code
-                    0 = standard averaging (matches ialloy=0 in DYNAMO)
-                    1 = alternative averaging (matches ialloy=1 in DYNAMO)
-                    2 = no averaging of t (use single-element values)
-                    default = 0
-mixture_ref_t   = integer flag to use mixture average of t to compute the background
-                  reference density for alloys, instead of the single-element values
-                  (see description and warning elsewhere in this doc page)
-                    0 = do not use mixture averaging for t in the reference density
-                    1 = use mixture averaging for t in the reference density
-                    default = 0
-erose_form      = integer value to select the form of the Rose energy function
-                  (see description below).
-                    default = 0
-emb_lin_neg     = integer value to select embedding function for negative densities
-                    0 = F(rho)=0
-                    1 = F(rho) = -asub*esub*rho (linear in rho, matches DYNAMO)
-                    default = 0
-bkgd_dyn        = integer value to select background density formula
-                    0 = rho_bkgd = rho_ref_meam(a) (as in the reference structure)
-                    1 = rho_bkgd = rho0_meam(a)*Z_meam(a) (matches DYNAMO)
-                    default = 0 :pre
-
-Rc, delr, re are in distance units (Angstroms in the case of metal
-units).  Ec and delta are in energy units (eV in the case of metal
-units).
-
-Each keyword represents a quantity which is either a scalar, vector,
-2d array, or 3d array and must be specified with the correct
-corresponding array syntax.  The indices I,J,K each run from 1 to N
-where N is the number of MEAM elements being used.
-
-Thus these lines
-
-rho0(2) = 2.25
-alpha(1,2) = 4.37 :pre
-
-set rho0 for the 2nd element to the value 2.25 and set alpha for the
-alloy interaction between elements 1 and 2 to 4.37.
-
-The augt1 parameter is related to modifications in the MEAM
-formulation of the partial electron density function.  In recent
-literature, an extra term is included in the expression for the
-third-order density in order to make the densities orthogonal (see for
-example "(Wang)"_#Wang2, equation 3d); this term is included in the
-MEAM implementation in lammps.  However, in earlier published work
-this term was not included when deriving parameters, including most of
-those provided in the library.meam file included with lammps, and to
-account for this difference the parameter t1 must be augmented by
-3/5*t3.  If augt1=1, the default, this augmentation is done
-automatically.  When parameter values are fit using the modified
-density function, as in more recent literature, augt1 should be set to
-0.
-
-The mixture_ref_t parameter is available to match results with those
-of previous versions of lammps (before January 2011).  Newer versions
-of lammps, by default, use the single-element values of the t
-parameters to compute the background reference density.  This is the
-proper way to compute these parameters.  Earlier versions of lammps
-used an alloy mixture averaged value of t to compute the background
-reference density.  Setting mixture_ref_t=1 gives the old behavior.
-WARNING: using mixture_ref_t=1 will give results that are demonstrably
-incorrect for second-neighbor MEAM, and non-standard for
-first-neighbor MEAM; this option is included only for matching with
-previous versions of lammps and should be avoided if possible.
-
-The parameters attrac and repuls, along with the integer selection
-parameter erose_form, can be used to modify the Rose energy function
-used to compute the pair potential.  This function gives the energy of
-the reference state as a function of interatomic spacing.  The form of
-this function is:
-
-astar = alpha * (r/re - 1.d0)
-if erose_form = 0: erose = -Ec*(1+astar+a3*(astar**3)/(r/re))*exp(-astar)
-if erose_form = 1: erose = -Ec*(1+astar+(-attrac+repuls/r)*(astar**3))*exp(-astar)
-if erose_form = 2: erose = -Ec*(1 +astar + a3*(astar**3))*exp(-astar)
-a3 = repuls, astar < 0
-a3 = attrac, astar >= 0 :pre
-
-Most published MEAM parameter sets use the default values attrac=repulse=0.
-Setting repuls=attrac=delta corresponds to the form used in several
-recent published MEAM parameter sets, such as "(Valone)"_#Valone
-
-NOTE: The default form of the erose expression in LAMMPS was corrected
-in March 2009.  The current version is correct, but may show different
-behavior compared with earlier versions of lammps with the attrac
-and/or repuls parameters are non-zero.  To obtain the previous default
-form, use erose_form = 1 (this form does not seem to appear in the
-literature).  An alternative form (see e.g. "(Lee2)"_#Lee2) is
-available using erose_form = 2.
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-For atom type pairs I,J and I != J, where types I and J correspond to
-two different element types, mixing is performed by LAMMPS with
-user-specifiable parameters as described above.  You never need to
-specify a pair_coeff command with I != J arguments for this style.
-
-This pair style does not support the "pair_modify"_pair_modify.html
-shift, table, and tail options.
-
-This pair style does not write its information to "binary restart
-files"_restart.html, since it is stored in potential files.  Thus, you
-need to re-specify the pair_style and pair_coeff commands in an input
-script that reads a restart file.
-
-This pair style can only be used via the {pair} keyword of the
-"run_style respa"_run_style.html command.  It does not support the
-{inner}, {middle}, {outer} keywords.
-
-:line
-
-[Restrictions:]
-
-The {meam/c} style is provided in the USER-MEAMC package. It is
-only enabled if LAMMPS was built with that package.
-See the "Build package"_Build_package.html doc page for more info.
-
-The maximum number of elements, that can be read from the MEAM
-library file, is determined at compile time. The default is 5.
-If you need support for more elements, you have to change the
-define for the constant 'maxelt' at the beginning of the file
-src/USER-MEAMC/meam.h and update/recompile LAMMPS. There is no
-limit on the number of atoms types.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "pair_style eam"_pair_eam.html,
-"pair_style meam/spline"_pair_meam_spline.html
-
-[Default:] none
-
-:line
-
-:link(Baskes)
-[(Baskes)] Baskes, Phys Rev B, 46, 2727-2742 (1992).
-
-:link(Gullet)
-[(Gullet)] Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
-This report may be accessed on-line via "this link"_sandreport.
-
-:link(sandreport,http://infoserve.sandia.gov/sand_doc/2003/038782.pdf)
-
-:link(Lee)
-[(Lee)] Lee, Baskes, Phys. Rev. B, 62, 8564-8567 (2000).
-
-:link(Lee2)
-[(Lee2)] Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
-
-:link(Valone)
-[(Valone)] Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
-
-:link(Wang2)
-[(Wang)] Wang, Van Hove, Ross, Baskes, J. Chem. Phys., 121, 5410 (2004).
-
-:link(ZBL)
-[(ZBL)] J.F. Ziegler, J.P. Biersack, U. Littmark, "Stopping and Ranges
-of Ions in Matter", Vol 1, 1985, Pergamon Press.
diff --git a/doc/txt/pair_mm3_switch3_coulgauss.txt b/doc/txt/pair_mm3_switch3_coulgauss.txt
deleted file mode 100644
index 86e6a0d1d9..0000000000
--- a/doc/txt/pair_mm3_switch3_coulgauss.txt
+++ /dev/null
@@ -1,88 +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
-
-pair_style mm3/switch3/coulgauss/long command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = {mm3/switch3/coulgauss/long}
-args = list of arguments for a particular style :ul
-  {mm3/switch3/coulgauss/long} args = cutoff (cutoff2) width
-    cutoff  = global cutoff for MM3 (and Coulombic if only 1 arg) (distance units)
-    cutoff2 = global cutoff for Coulombic (optional) (distance units)
-    width  = width parameter of the smoothing function (distance units) :pre
-
-[Examples:]
-
-pair_style mm3/switch3/coulgauss/long    12.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-pair_style mm3/switch3/coulgauss/long   12.0 10.0 3.0
-pair_coeff 1  0.2 2.5 1.2 :pre
-
-[Description:]
-
-The {mm3/switch3/coulgauss} style evaluates the MM3
-vdW potential "(Allinger)"_#mm3-allinger1989
-
-:c,image(Eqs/pair_mm3_switch3.jpg)
-
-, which goes smoothly to zero at the cutoff r_c as defined
-by the switching function
-
-:c,image(Eqs/pair_switch3.jpg)
-
-where w is the width defined in the arguments. This potential
-is combined with Coulomb interaction between Gaussian charge densities:
-
-:c,image(Eqs/pair_coulgauss.jpg)
-
-where qi and qj are the
-charges on the 2 atoms, epsilon is the dielectric constant which
-can be set by the "dielectric"_dielectric.html command, gamma_i and gamma_j
-are the widths of the Gaussian charge distribution and erf() is the error-function.
-This style has to be used in conjunction with the "kspace_style"_kspace_style.html command
-
-If one cutoff is specified it is used for both the vdW and Coulomb
-terms.  If two cutoffs are specified, the first is used as the cutoff
-for the vdW terms, and the second is the cutoff for the Coulombic term.
-
-The following coefficients must be defined for each pair of atoms
-types via the "pair_coeff"_pair_coeff.html command as in the examples
-above, or in the data file or restart files read by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands:
-
-epsilon (energy)
-r_v (distance)
-gamma (distance) :ul
-
-:line
-
-[Mixing, shift, table, tail correction, restart, rRESPA info]:
-
-Mixing rules are fixed for this style as defined above.
-
-Shifting the potential energy is not necessary because the switching
-function ensures that the potential is zero at the cut-off.
-
-
-[Restrictions:]
-
-These styles are part of the USER-YAFF package.  They are only
-enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html
-
-[Default:] none
-
diff --git a/doc/txt/pair_modify.txt b/doc/txt/pair_modify.txt
deleted file mode 100644
index c446aa29d0..0000000000
--- a/doc/txt/pair_modify.txt
+++ /dev/null
@@ -1,281 +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
-
-pair_modify command :h3
-
-[Syntax:]
-
-pair_modify keyword values ... :pre
-
-one or more keyword/value pairs may be listed :ulb,l
-keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner}
-or {tabinner/disp} or {tail} or {compute} or {nofdotr} :l
-  {pair} values = sub-style N {special} which wt1 wt2 wt3
-               or sub-style N {compute/tally} flag
-    sub-style = sub-style of "pair hybrid"_pair_hybrid.html
-    N = which instance of sub-style (only if sub-style is used multiple times)
-      {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional)
-        which = {lj/coul} or {lj} or {coul}
-        w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
-      {compute/tally} flag = {yes} or {no}
-  {mix} value = {geometric} or {arithmetic} or {sixthpower}
-  {shift} value = {yes} or {no}
-  {table} value = N
-    2^N = # of values in table
-  {table/disp} value = N
-    2^N = # of values in table
-  {tabinner} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tabinner/disp} value = cutoff
-    cutoff = inner cutoff at which to begin table (distance units)
-  {tail} value = {yes} or {no}
-  {compute} value = {yes} or {no}
-  {nofdotr} :pre
-:ule
-
-[Examples:]
-
-pair_modify shift yes mix geometric
-pair_modify tail yes
-pair_modify table 12
-pair_modify pair lj/cut compute no
-pair_modify pair tersoff compute/tally no
-pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre
-
-[Description:]
-
-Modify the parameters of the currently defined pair style.  Not all
-parameters are relevant to all pair styles.
-
-If used, the {pair} keyword must appear first in the list of keywords.
-It can only be used with the "hybrid and
-hybrid/overlay"_pair_hybrid.html pair styles.  It means that all the
-following parameters will only be modified for the specified
-sub-style.  If the sub-style is defined multiple times, then an
-additional numeric argument {N} must also be specified, which is a
-number from 1 to M where M is the number of times the sub-style was
-listed in the "pair_style hybrid"_pair_hybrid.html command.  The extra
-number indicates which instance of the sub-style the remaining
-keywords will be applied to.  Note that if the {pair} keyword is not
-used, and the pair style is {hybrid} or {hybrid/overlay}, then all the
-specified keywords will be applied to all sub-styles.
-
-The {special} and {compute/tally} keywords can [only] be used in
-conjunction with the {pair} keyword and must directly follow it.
-{special} allows to override the
-"special_bonds"_special_bonds.html settings for the specified sub-style.
-{compute/tally} allows to disable or enable registering
-"compute */tally"_compute_tally.html computes for a given sub-style.
-More details are given below.
-
-The {mix} keyword affects pair coefficients for interactions between
-atoms of type I and J, when I != J and the coefficients are not
-explicitly set in the input script.  Note that coefficients for I = J
-must be set explicitly, either in the input script via the
-"pair_coeff" command or in the "Pair Coeffs" section of the "data
-file"_read_data.html.  For some pair styles it is not necessary to
-specify coefficients when I != J, since a "mixing" rule will create
-them from the I,I and J,J settings.  The pair_modify {mix} value
-determines what formulas are used to compute the mixed coefficients.
-In each case, the cutoff distance is mixed the same way as sigma.
-
-Note that not all pair styles support mixing.  Also, some mix options
-are not available for certain pair styles.  See the doc page for
-individual pair styles for those restrictions.  Note also that the
-"pair_coeff"_pair_coeff.html command also can be to directly set
-coefficients for a specific I != J pairing, in which case no mixing is
-performed.
-
-mix {geometric}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = sqrt(sigma_i * sigma_j) :pre
-
-mix {arithmetic}
-
-epsilon_ij = sqrt(epsilon_i * epsilon_j)
-sigma_ij = (sigma_i + sigma_j) / 2 :pre
-
-mix {sixthpower}
-
-epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
-             (sigma_i^6 + sigma_j^6)
-sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre
-
-The {shift} keyword determines whether a Lennard-Jones potential is
-shifted at its cutoff to 0.0.  If so, this adds an energy term to each
-pairwise interaction which will be included in the thermodynamic
-output, but does not affect pair forces or atom trajectories.  See the
-doc page for individual pair styles to see which ones support this
-option.
-
-The {table} and {table/disp} keywords apply to pair styles with a
-long-range Coulombic term or long-range dispersion term respectively;
-see the doc page for individual styles to see which potentials support
-these options.  If N is non-zero, a table of length 2^N is
-pre-computed for forces and energies, which can shrink their
-computational cost by up to a factor of 2.  The table is indexed via a
-bit-mapping technique "(Wolff)"_#Wolff1 and a linear interpolation is
-performed between adjacent table values.  In our experiments with
-different table styles (lookup, linear, spline), this method typically
-gave the best performance in terms of speed and accuracy.
-
-The choice of table length is a tradeoff in accuracy versus speed.  A
-larger N yields more accurate force computations, but requires more
-memory which can slow down the computation due to cache misses.  A
-reasonable value of N is between 8 and 16.  The default value of 12
-(table of length 4096) gives approximately the same accuracy as the
-no-table (N = 0) option.  For N = 0, forces and energies are computed
-directly, using a polynomial fit for the needed erfc() function
-evaluation, which is what earlier versions of LAMMPS did.  Values
-greater than 16 typically slow down the simulation and will not
-improve accuracy; values from 1 to 8 give unreliable results.
-
-The {tabinner} and {tabinner/disp} keywords set an inner cutoff above
-which the pairwise computation is done by table lookup (if tables are
-invoked), for the corresponding Coulombic and dispersion tables
-discussed with the {table} and {table/disp} keywords.  The smaller the
-cutoff is set, the less accurate the table becomes (for a given number
-of table values), which can require use of larger tables.  The default
-cutoff value is sqrt(2.0) distance units which means nearly all
-pairwise interactions are computed via table lookup for simulations
-with "real" units, but some close pairs may be computed directly
-(non-table) for simulations with "lj" units.
-
-When the {tail} keyword is set to {yes}, certain pair styles will add
-a long-range VanderWaals tail "correction" to the energy and pressure.
-These corrections are bookkeeping terms which do not affect dynamics,
-unless a constant-pressure simulation is being performed.  See the doc
-page for individual styles to see which support this option.  These
-corrections are included in the calculation and printing of
-thermodynamic quantities (see the "thermo_style"_thermo_style.html
-command).  Their effect will also be included in constant NPT or NPH
-simulations where the pressure influences the simulation box
-dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html
-commands).  The formulas used for the long-range corrections come from
-equation 5 of "(Sun)"_#Sun.
-
-NOTE: The tail correction terms are computed at the beginning of each
-run, using the current atom counts of each atom type.  If atoms are
-deleted (or lost) or created during a simulation, e.g. via the "fix
-gcmc"_fix_gcmc.html command, the correction factors are not
-re-computed.  If you expect the counts to change dramatically, you can
-break a run into a series of shorter runs so that the correction
-factors are re-computed more frequently.
-
-Several additional assumptions are inherent in using tail corrections,
-including the following:
-
-The simulated system is a 3d bulk homogeneous liquid. This option
-should not be used for systems that are non-liquid, 2d, have a slab
-geometry (only 2d periodic), or inhomogeneous. :ulb,l
-
-G(r), the radial distribution function (rdf), is unity beyond the
-cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an
-LJ fluid), and it is probably a good idea to verify this assumption by
-checking the rdf.  The rdf is not exactly unity beyond the cutoff for
-each pair of interaction types, so the tail correction is necessarily
-an approximation. :l
-
-The tail corrections are computed at the beginning of each simulation
-run.  If the number of atoms changes during the run, e.g. due to atoms
-leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html
-command, then the corrections are not updated to reflect the changed
-atom count.  If this is a large effect in your simulation, you should
-break the long run into several short runs, so that the correction
-factors are re-computed multiple times.
-
-Thermophysical properties obtained from calculations with this option
-enabled will not be thermodynamically consistent with the truncated
-force-field that was used.  In other words, atoms do not feel any LJ
-pair interactions beyond the cutoff, but the energy and pressure
-reported by the simulation include an estimated contribution from
-those interactions. :l
-:ule
-
-The {compute} keyword allows pairwise computations to be turned off,
-even though a "pair_style"_pair_style.html is defined.  This is not
-useful for running a real simulation, but can be useful for debugging
-purposes or for performing a "rerun"_rerun.html simulation, when you
-only wish to compute partial forces that do not include the pairwise
-contribution.
-
-Two examples are as follows.  First, this option allows you to perform
-a simulation with "pair_style hybrid"_pair_hybrid.html with only a
-subset of the hybrid sub-styles enabled.  Second, this option allows
-you to perform a simulation with only long-range interactions but no
-short-range pairwise interactions.  Doing this by simply not defining
-a pair style will not work, because the
-"kspace_style"_kspace_style.html command requires a Kspace-compatible
-pair style be defined.
-
-The {nofdotr} keyword allows to disable an optimization that computes
-the global stress tensor from the total forces and atom positions rather
-than from summing forces between individual pairs of atoms.
-
-:line
-
-The {special} keyword allows to override the 1-2, 1-3, and 1-4
-exclusion settings for individual sub-styles of a
-"hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar
-to the "special_bonds"_special_bonds.html command, {which} and
-wt1,wt2,wt3.  The {which} argument can be {lj} to change the
-Lennard-Jones settings, {coul} to change the Coulombic settings,
-or {lj/coul} to change both to the same set of 3 values.  The wt1,wt2,wt3
-values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2,
-1-3, and 1-4 bond topology neighbors, respectively. The {special}
-keyword can only be used in conjunction with the {pair} keyword
-and has to directly follow it.
-
-NOTE: The global settings specified by the
-"special_bonds"_special_bonds.html command affect the construction of
-neighbor lists.  Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors)
-exclude those pairs from the neighbor list entirely.  Weights of 1.0
-store the neighbor with no weighting applied. Thus only global values
-different from exactly 0.0 or 1.0 can be overridden and an error is
-generated if the requested setting is not compatible with the global
-setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is
-usually a sufficient workaround in this case without causing a
-significant error.
-
-The {compute/tally} keyword takes exactly 1 argument ({no} or {yes}),
-and allows to selectively disable or enable processing of the various
-"compute */tally"_compute_tally.html styles for a given
-"pair hybrid or hybrid/overlay"_pair_hybrid.html sub-style.
-
-NOTE: Any "pair_modify pair compute/tally" command must be issued
-[before] the corresponding compute style is defined.
-
-:line
-
-[Restrictions:] none
-
-You cannot use {shift} yes with {tail} yes, since those are
-conflicting options.  You cannot use {tail} yes with 2d simulations.
-
-[Related commands:]
-
-"pair_style"_pair_style.html, "pair_style hybrid"_pair_hybrid.html,
-pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html,
-"compute */tally"_compute_tally.html
-
-[Default:]
-
-The option defaults are mix = geometric, shift = no, table = 12,
-tabinner = sqrt(2.0), tail = no, and compute = yes.
-
-Note that some pair styles perform mixing, but only a certain style of
-mixing.  See the doc pages for individual pair styles for details.
-
-:line
-
-:link(Wolff1)
-[(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).
-
-:link(Sun)
-[(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998).
diff --git a/doc/txt/pair_oxdna.txt b/doc/txt/pair_oxdna.txt
deleted file mode 100644
index 8f3f9933e6..0000000000
--- a/doc/txt/pair_oxdna.txt
+++ /dev/null
@@ -1,112 +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
-
-pair_style oxdna/excv command :h3
-pair_style oxdna/stk command :h3
-pair_style oxdna/hbond command :h3
-pair_style oxdna/xstk command :h3
-pair_style oxdna/coaxstk command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk} :ul
-
-style2 = {oxdna/excv} or {oxdna/stk} or {oxdna/hbond} or {oxdna/xstk} or {oxdna/coaxstk}
-args = list of arguments for these particular styles :ul
-
-  {oxdna/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength
-    kappa = coefficient of linear temperature dependence in stacking strength
-  {oxdna/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.077 (between base pairs A-T and C-G) or 0 (all other pairs) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna/excv oxdna/stk oxdna/hbond oxdna/xstk oxdna/coaxstk
-pair_coeff * * oxdna/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna/stk     seqdep 0.1 1.3448 2.6568 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna/hbond   seqdep 1.077 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 -0.65 2.0 -0.65 :pre
-
-[Description:]
-
-The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
-and coaxial stacking interaction {oxdna/coaxstk} as well
-as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc1. Quasi-unique base-pairing between nucleotides can be achieved by using 
-more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
-This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
-up and down along the backbone.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
-for a detailed description of the oxDNA force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA bond style
-{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna/stk} (seq=seqdep, T=0.1, xi=1.3448 and kappa=2.6568 in the above example)
-and the first coefficient after {oxdna/hbond} (seq=seqdep in the above example).
-When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
-or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-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)"_#Henrich1 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
-
-[Restrictions:]
-
-These pair styles 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:]
-
-"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
-
-[Default:] none
-
-:line
-
-:link(Henrich1)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc1)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Ouldridge-DPhil1)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge1)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/txt/pair_oxdna2.txt b/doc/txt/pair_oxdna2.txt
deleted file mode 100644
index 64a686d5d9..0000000000
--- a/doc/txt/pair_oxdna2.txt
+++ /dev/null
@@ -1,121 +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
-
-pair_style oxdna2/excv command :h3
-pair_style oxdna2/stk command :h3
-pair_style oxdna2/hbond command :h3
-pair_style oxdna2/xstk command :h3
-pair_style oxdna2/coaxstk command :h3
-pair_style oxdna2/dh command :h3
-
-[Syntax:]
-
-pair_style style1 :pre
-
-pair_coeff * * style2 args :pre
-
-style1 = {hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh} :ul
-
-style2 = {oxdna2/excv} or {oxdna2/stk} or {oxdna2/hbond} or {oxdna2/xstk} or {oxdna2/coaxstk} or {oxdna2/dh}
-args = list of arguments for these particular styles :ul
-
-  {oxdna2/stk} args = seq T xi kappa 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-    seq = seqav (for average sequence stacking strength) or seqdep (for sequence-dependent stacking strength)
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    xi = temperature-independent coefficient in stacking strength
-    kappa = coefficient of linear temperature dependence in stacking strength
-  {oxdna2/hbond} args = seq eps 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-    seq = seqav (for average sequence base-pairing strength) or seqdep (for sequence-dependent base-pairing strength)
-    eps = 1.0678 (between base pairs A-T and C-G) or 0 (all other pairs)
-  {oxdna2/dh} args = T rhos qeff
-    T = temperature (oxDNA units, 0.1 = 300 K)
-    rhos = salt concentration (mole per litre)
-    qeff = effective charge (elementary charges) :pre
-
-[Examples:]
-
-pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh
-pair_coeff * * oxdna2/excv    2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32
-pair_coeff * * oxdna2/stk     seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65
-pair_coeff * * oxdna2/hbond   seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 1 4 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff 2 3 oxdna2/hbond   seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45
-pair_coeff * * oxdna2/xstk    47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68
-pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793
-pair_coeff * * oxdna2/dh      0.1 1.0 0.815 :pre
-
-[Description:]
-
-The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
-for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
-excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
-and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
-as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
-opposite strands. Average sequence or sequence-dependent stacking and base-pairing strengths
-are supported "(Sulc)"_#Sulc2. Quasi-unique base-pairing between nucleotides can be achieved by using 
-more complementary pairs of atom types like 5-8 and 6-7, 9-12 and 10-11, 13-16 and 14-15, etc. 
-This prevents the hybridization of in principle complementary bases within Ntypes/4 bases 
-up and down along the backbone.
-
-The exact functional form of the pair styles is rather complex.
-The individual potentials consist of products of modulation factors,
-which themselves are constructed from a number of more basic potentials
-(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
-We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
-and  "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
-
-NOTE: These pair styles have to be used together with the related oxDNA2 bond style
-{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
-"bond_style oxdna2/fene"_bond_oxdna.html). Most of the coefficients
-in the above example have to be kept fixed and cannot be changed without reparameterizing the entire model.
-Exceptions are the first four coefficients after {oxdna2/stk} (seq=seqdep, T=0.1, xi=1.3523 and kappa=2.6717 in the above example),
-the first coefficient after {oxdna2/hbond} (seq=seqdep in the above example) and the three coefficients
-after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
-e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
-the temperature coefficients have to be matched to the one used in the fix.
-
-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)"_#Henrich 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
-
-[Restrictions:]
-
-These pair styles 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:]
-
-"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
-"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
-
-[Default:] none
-
-:line
-
-:link(Henrich)
-[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
-
-:link(Sulc2)
-[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).
-
-:link(Snodin)
-[(Snodin)] B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
-
-:link(Ouldridge-DPhil2)
-[(Ouldrigde-DPhil)] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA self-assembly, DPhil. University of Oxford (2011).
-
-:link(Ouldridge2)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
diff --git a/doc/txt/pair_style.txt b/doc/txt/pair_style.txt
deleted file mode 100644
index 7ba982cd2d..0000000000
--- a/doc/txt/pair_style.txt
+++ /dev/null
@@ -1,338 +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
-
-pair_style command :h3
-
-[Syntax:]
-
-pair_style style args :pre
-
-style = one of the styles from the list below
-args = arguments used by a particular style :ul
-
-[Examples:]
-
-pair_style lj/cut 2.5
-pair_style eam/alloy
-pair_style hybrid lj/charmm/coul/long 10.0 eam
-pair_style table linear 1000
-pair_style none :pre
-
-[Description:]
-
-Set the formula(s) LAMMPS uses to compute pairwise interactions.  In
-LAMMPS, pair potentials are defined between pairs of atoms that are
-within a cutoff distance and the set of active interactions typically
-changes over time.  See the "bond_style"_bond_style.html command to
-define potentials between pairs of bonded atoms, which typically
-remain in place for the duration of a simulation.
-
-In LAMMPS, pairwise force fields encompass a variety of interactions,
-some of which include many-body effects, e.g. EAM, Stillinger-Weber,
-Tersoff, REBO potentials.  They are still classified as "pairwise"
-potentials because the set of interacting atoms changes with time
-(unlike molecular bonds) and thus a neighbor list is used to find
-nearby interacting atoms.
-
-Hybrid models where specified pairs of atom types interact via
-different pair potentials can be setup using the {hybrid} pair style.
-
-The coefficients associated with a pair style are typically set for
-each pair of atom types, and are specified by the
-"pair_coeff"_pair_coeff.html command or read from a file by the
-"read_data"_read_data.html or "read_restart"_read_restart.html
-commands.
-
-The "pair_modify"_pair_modify.html command sets options for mixing of
-type I-J interaction coefficients and adding energy offsets or tail
-corrections to Lennard-Jones potentials.  Details on these options as
-they pertain to individual potentials are described on the doc page
-for the potential.  Likewise, info on whether the potential
-information is stored in a "restart file"_write_restart.html is listed
-on the potential doc page.
-
-In the formulas listed for each pair style, {E} is the energy of a
-pairwise interaction between two atoms separated by a distance {r}.
-The force between the atoms is the negative derivative of this
-expression.
-
-If the pair_style command has a cutoff argument, it sets global
-cutoffs for all pairs of atom types.  The distance(s) can be smaller
-or larger than the dimensions of the simulation box.
-
-Typically, the global cutoff value can be overridden for a specific
-pair of atom types by the "pair_coeff"_pair_coeff.html command.  The
-pair style settings (including global cutoffs) can be changed by a
-subsequent pair_style command using the same style.  This will reset
-the cutoffs for all atom type pairs, including those previously set
-explicitly by a "pair_coeff"_pair_coeff.html command.  The exceptions
-to this are that pair_style {table} and {hybrid} settings cannot be
-reset.  A new pair_style command for these styles will wipe out all
-previously specified pair_coeff values.
-
-:line
-
-Here is an alphabetic list of pair styles defined in LAMMPS.  They are
-also listed in more compact form on the "Commands
-pair"_Commands_pair.html doc page.
-
-Click on the style to display the formula it computes, any additional
-arguments specified in the pair_style command, and coefficients
-specified by the associated "pair_coeff"_pair_coeff.html command.
-
-There are also additional accelerated pair styles included in the
-LAMMPS distribution for faster performance on CPUs, 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.
-
-"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
-
-"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
-"cosine/squared"_pair_cosine_squared.html - Cooke-Kremer-Deserno membrane model potential
-"coul/cut"_pair_coul.html - cutoff Coulombic potential
-"coul/cut/soft"_pair_fep_soft.html - Coulombic potential with a soft core
-"coul/debye"_pair_coul.html - cutoff Coulombic potential with Debye screening
-"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_fep_soft.html - long-range Coulombic potential with a soft core
-"coul/msm"_pair_coul.html - long-range MSM Coulombics
-"coul/shield"_pair_coul_shield.html - Coulombics for boron nitride for use with "ilp/graphene/hbn"_pair_ilp_graphene_hbn.html potential
-"coul/streitz"_pair_coul.html - Coulombics via Streitz/Mintmire Slater orbitals
-"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)
-"e3b"_pair_e3b.html - Explicit-three body (E3B) water model
-"drip"_pair_drip.html - Dihedral-angle-corrected registry-dependent interlayer potential (DRIP)
-"eam"_pair_eam.html - embedded atom method (EAM)
-"eam/alloy"_pair_eam.html - alloy EAM
-"eam/cd"_pair_eam.html - concentration-dependent EAM
-"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)
-"lebedeva/z"_pair_lebedeva_z.html - Lebedeva interlayer potential for graphene with normals along z-axis
-"lennard/mdf"_pair_mdf.html - LJ potential in A/B form with a taper function
-"line/lj"_pair_line_lj.html - LJ potential between line segments
-"list"_pair_list.html - potential between pairs of atoms explicitly listed in an input file
-"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_fep_soft.html - CHARMM with long-range Coulomb and a soft core
-"lj/charmm/coul/msm"_pair_charmm.html - CHARMM with long-range MSM Coulombics
-"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html - CHARMM with force switching and shifting
-"lj/charmmfsw/coul/long"_pair_charmm.html - CHARMM with force switching and long-rnage Coulombics
-"lj/class2"_pair_class2.html - COMPASS (class 2) force field with no Coulomb
-"lj/class2/coul/cut"_pair_class2.html - COMPASS with cutoff Coulomb
-"lj/class2/coul/cut/soft"_pair_fep_soft.html - COMPASS with cutoff Coulomb with a soft core
-"lj/class2/coul/long"_pair_class2.html - COMPASS with long-range Coulomb
-"lj/class2/coul/long/soft"_pair_fep_soft.html - COMPASS with long-range Coulomb with a soft core
-"lj/class2/soft"_pair_fep_soft.html - COMPASS (class 2) force field with no Coulomb with a soft core
-"lj/cubic"_pair_lj_cubic.html - LJ with cubic after inflection point
-"lj/cut"_pair_lj.html - cutoff Lennard-Jones potential with no Coulomb
-"lj/cut/coul/cut"_pair_lj.html - LJ with cutoff Coulomb
-"lj/cut/coul/cut/soft"_pair_fep_soft.html - LJ with cutoff Coulomb with a soft core
-"lj/cut/coul/debye"_pair_lj.html - LJ with Debye screening added to Coulomb
-"lj/cut/coul/dsf"_pair_lj.html - LJ with Coulombics via damped shifted forces
-"lj/cut/coul/long"_pair_lj.html - LJ with long-range Coulombics
-"lj/cut/coul/long/cs"_pair_cs.html - ditto with core/shell adjustments
-"lj/cut/coul/long/soft"_pair_fep_soft.html - LJ with long-range Coulombics with a soft core
-"lj/cut/coul/msm"_pair_lj.html - LJ with long-range MSM Coulombics
-"lj/cut/coul/wolf"_pair_lj.html - LJ with Coulombics via Wolf potential
-"lj/cut/dipole/cut"_pair_dipole.html - point dipoles with cutoff
-"lj/cut/dipole/long"_pair_dipole.html - point dipoles with long-range Ewald
-"lj/cut/soft"_pair_fep_soft.html - LJ with a soft core
-"lj/cut/thole/long"_pair_thole.html - LJ with Coulombics with thole damping
-"lj/cut/tip4p/cut"_pair_lj.html - LJ with cutoff Coulomb for TIP4P water
-"lj/cut/tip4p/long"_pair_lj.html - LJ with long-range Coulomb for TIP4P water
-"lj/cut/tip4p/long/soft"_pair_fep_soft.html - LJ with cutoff Coulomb for TIP4P water with a soft core
-"lj/expand"_pair_lj_expand.html - Lennard-Jones for variable size particles
-"lj/expand/coul/long"_pair_lj_expand.html - Lennard-Jones for variable size particles with long-range Coulombics
-"lj/gromacs"_pair_gromacs.html - GROMACS-style Lennard-Jones potential
-"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
-"lj/switch3/coulgauss"_pair_lj_switch3_coulgauss - smoothed LJ vdW potential with Gaussian electrostatics
-"lj96/cut"_pair_lj96.html - Lennard-Jones 9/6 potential
-"local/density"_pair_local_density.html - generalized basic local density 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/c"_pair_meamc.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
-"mm3/switch3/coulgauss"_pair_mm3_switch3_coulgauss - smoothed MM3 vdW potential with Gaussian electrostatics
-"momb"_pair_momb.html - Many-Body Metal-Organic (MOMB) force field
-"morse"_pair_morse.html - Morse potential
-"morse/smooth/linear"_pair_morse.html - linear smoothed Morse potential
-"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 - non-bonded 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/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
-"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html - smoothed dissipative particle dynamics for water at isothermal conditions
-"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/dipole/cut"_pair_spin_dipole.html -
-"spin/dipole/long"_pair_spin_dipole.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_fep_soft.html -
-"tri/lj"_pair_tri_lj.html - LJ potential between triangles
-"ufm"_pair_ufm.html -
-"vashishta"_pair_vashishta.html - Vashishta 2-body and 3-body potential
-"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
-
-[Restrictions:]
-
-This command must be used before any coefficients are set by the
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html, or
-"read_restart"_read_restart.html commands.
-
-Some pair styles are part of specific packages.  They are only enabled
-if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  The doc pages for
-individual pair potentials tell if it is part of a package.
-
-[Related commands:]
-
-"pair_coeff"_pair_coeff.html, "read_data"_read_data.html,
-"pair_modify"_pair_modify.html, "kspace_style"_kspace_style.html,
-"dielectric"_dielectric.html, "pair_write"_pair_write.html
-
-[Default:]
-
-pair_style none :pre
diff --git a/doc/txt/server.txt b/doc/txt/server.txt
deleted file mode 100644
index 8f87b5c76b..0000000000
--- a/doc/txt/server.txt
+++ /dev/null
@@ -1,71 +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
-
-server command :h3
-
-[Syntax:]
-
-server protocol :pre
-
-protocol = {md} or {mc} :ul
-
-[Examples:]
-
-server md :pre
-
-[Description:]
-
-This command starts LAMMPS running in "server" mode, where it receives
-messages from a separate "client" code and responds by sending a reply
-message back to the client.  The specified {protocol} determines the
-format and content of messages LAMMPS expects to receive and how it
-responds.
-
-The "Howto client/server"_Howto_client_server.html doc page gives an
-overview of client/server coupling of LAMMPS with another code where
-one code is the "client" and sends request messages to a "server"
-code.  The server responds to each request with a reply message.  This
-enables the two codes to work in tandem to perform a simulation.
-
-When this command is invoked, LAMMPS will run in server mode in an
-endless loop, waiting for messages from the client code.  The client
-signals when it is done sending messages to LAMMPS, at which point the
-loop will exit, and the remainder of the LAMMPS script will be
-processed.
-
-The {protocol} argument defines the format and content of messages
-that will be exchanged between the two codes.  The current options
-are:
-
-"md"_server_md.html = run dynamics with another code
-"mc"_server_mc.html = perform Monte Carlo moves with another code :ul
-
-For protocol {md}, LAMMPS can be either a client (via the "fix
-client/md"_fix_client_md.html command) or server.  See the "server
-md"_server_md.html doc page for details on the protocol.
-
-For protocol {mc}, LAMMPS can be the server.  See the "server
-mc"_server_mc.html doc page for details on the protocol.
-
-:line
-
-[Restrictions:]
-
-This command is part of the MESSAGE package.  It is only enabled if
-LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.
-
-A script that uses this command must also use the
-"message"_message.html command to setup the messaging protocol with
-the other client code.
-
-[Related commands:]
-
-"message"_message.html, "fix client/md"_fix_client_md.html
-
-[Default:] none
diff --git a/doc/utils/check-styles.py b/doc/utils/check-styles.py
new file mode 100755
index 0000000000..a5bf31801c
--- /dev/null
+++ b/doc/utils/check-styles.py
@@ -0,0 +1,244 @@
+#!/usr/bin/env python3
+
+from __future__ import print_function
+from glob import glob
+from argparse import ArgumentParser
+import os, re, sys
+
+parser = ArgumentParser(prog='check-styles.py',
+                        description="Check style table completeness")
+
+parser.add_argument("-v", "--verbose",
+                    action='store_const',
+                    const=True, default=False,
+                    help="Enable verbose output")
+
+parser.add_argument("-d", "--doc",
+                    help="Path to LAMMPS documentation sources")
+parser.add_argument("-s", "--src",
+                    help="Path to LAMMPS sources")
+
+args = parser.parse_args()
+verbose = args.verbose
+src = args.src
+doc = args.doc
+
+if not args.src or not args.doc:
+  parser.print_help()
+  sys.exit(1)
+
+if not os.path.isdir(src):
+    sys.exit("LAMMPS source path %s does not exist" % src)
+
+if not os.path.isdir(doc):
+    sys.exit("LAMMPS documentation source path %s does not exist" % doc)
+
+headers = glob(os.path.join(src, '*', '*.h'))
+headers += glob(os.path.join(src, '*.h'))
+
+angle = {}
+atom = {}
+body = {}
+bond = {}
+command = {}
+compute = {}
+dihedral = {}
+dump = {}
+fix = {}
+improper = {}
+integrate = {}
+kspace = {}
+minimize = {}
+pair = {}
+reader = {}
+region = {}
+
+upper = re.compile("[A-Z]+")
+gpu = re.compile("(.+)/gpu$")
+intel = re.compile("(.+)/intel$")
+kokkos = re.compile("(.+)/kk$")
+kokkos_skip = re.compile("(.+)/kk/(host|device)$")
+omp = re.compile("(.+)/omp$")
+opt = re.compile("(.+)/opt$")
+removed = re.compile("(.+)Deprecated$")
+
+def register_style(list,style,info):
+    if style in list.keys():
+        list[style]['gpu'] += info['gpu']
+        list[style]['intel'] += info['intel']
+        list[style]['kokkos'] += info['kokkos']
+        list[style]['omp'] += info['omp']
+        list[style]['opt'] += info['opt']
+        list[style]['removed'] += info['removed']
+    else:
+        list[style] = info
+
+def add_suffix(list,style):
+    suffix = ""
+    if list[style]['gpu']:
+        suffix += 'g'
+    if list[style]['intel']:
+        suffix += 'i'
+    if list[style]['kokkos']:
+        suffix += 'k'
+    if list[style]['omp']:
+        suffix += 'o'
+    if list[style]['opt']:
+        suffix += 't'
+    if suffix:
+        return style + ' (' + suffix + ')'
+    else:
+        return style
+
+def check_style(file,dir,pattern,list,name,suffix=False,skip=()):
+    f = os.path.join(dir, file)
+    fp = open(f)
+    text = fp.read()
+    fp.close()
+    matches = re.findall(pattern,text,re.MULTILINE)
+    counter = 0
+    for c in list.keys():
+        # known undocumented aliases we need to skip
+        if c in skip: continue
+        s = c
+        if suffix: s = add_suffix(list,c)
+        if not s in matches:
+            if not list[c]['removed']:
+                print("%s style entry %s" % (name,s),
+                      "is missing or incomplete in %s" % file)
+                counter += 1
+    return counter
+
+for h in headers:
+    if verbose: print("Checking ", h)
+    fp = open(h)
+    text = fp.read()
+    fp.close()
+    matches = re.findall("(.+)Style\((.+),(.+)\)",text,re.MULTILINE)
+    for m in matches:
+
+        # skip over internal styles w/o explicit documentation
+        style = m[1]
+        if upper.match(style):
+            continue
+
+        # detect, process, and flag suffix styles:
+        info = { 'kokkos':  0, 'gpu':     0, 'intel':   0, \
+                 'omp':     0, 'opt':     0, 'removed': 0 }
+        suffix = kokkos_skip.match(style)
+        if suffix:
+            continue
+        suffix = gpu.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['gpu'] = 1
+        suffix = intel.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['intel'] = 1
+        suffix = kokkos.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['kokkos'] = 1
+        suffix = omp.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['omp'] = 1
+        suffix = opt.match(style)
+        if suffix:
+            style = suffix.groups()[0]
+            info['opt'] = 1
+        deprecated = removed.match(m[2])
+        if deprecated:
+            info['removed'] = 1
+
+        # register style and suffix flags
+        if m[0] == 'Angle':
+            register_style(angle,style,info)
+        elif m[0] == 'Atom':
+            register_style(atom,style,info)
+        elif m[0] == 'Body':
+            register_style(body,style,info)
+        elif m[0] == 'Bond':
+            register_style(bond,style,info)
+        elif m[0] == 'Command':
+            register_style(command,style,info)
+        elif m[0] == 'Compute':
+            register_style(compute,style,info)
+        elif m[0] == 'Dihedral':
+            register_style(dihedral,style,info)
+        elif m[0] == 'Dump':
+            register_style(dump,style,info)
+        elif m[0] == 'Fix':
+            register_style(fix,style,info)
+        elif m[0] == 'Improper':
+            register_style(improper,style,info)
+        elif m[0] == 'Integrate':
+            register_style(integrate,style,info)
+        elif m[0] == 'KSpace':
+            register_style(kspace,style,info)
+        elif m[0] == 'Minimize':
+            register_style(minimize,style,info)
+        elif m[0] == 'Pair':
+            register_style(pair,style,info)
+        elif m[0] == 'Reader':
+            register_style(reader,style,info)
+        elif m[0] == 'Region':
+            register_style(region,style,info)
+        else:
+            print("Skipping over: ",m)
+
+
+print("""Parsed style names w/o suffixes from C++ tree in %s:
+   Angle styles:     %3d    Atom styles:      %3d
+   Body styles:      %3d    Bond styles:      %3d
+   Command styles:   %3d    Compute styles:   %3d
+   Dihedral styles:  %3d    Dump styles:      %3d
+   Fix styles:       %3d    Improper styles:  %3d
+   Integrate styles: %3d    Kspace styles:    %3d
+   Minimize styles:  %3d    Pair styles:      %3d
+   Reader styles:    %3d    Region styles:    %3d""" \
+      % (src, len(angle), len(atom), len(body), len(bond),   \
+       len(command), len(compute), len(dihedral), len(dump), \
+       len(fix), len(improper), len(integrate), len(kspace), \
+       len(minimize), len(pair), len(reader), len(region)))
+
+
+counter = 0
+
+counter += check_style('Commands_all.rst',doc,":doc:`(.+) <.+>`",
+                       command,'Command',suffix=False)
+counter += check_style('Commands_compute.rst',doc,":doc:`(.+) <compute.+>`",
+                       compute,'Compute',suffix=True)
+counter += check_style('compute.rst',doc,":doc:`(.+) <compute.+>` -",
+                       compute,'Compute',suffix=False)
+counter += check_style('Commands_fix.rst',doc,":doc:`(.+) <fix.+>`",
+                       fix,'Fix',skip=('python'),suffix=True)
+counter += check_style('fix.rst',doc,":doc:`(.+) <fix.+>` -",
+                       fix,'Fix',skip=('python'),suffix=False)
+counter += check_style('Commands_pair.rst',doc,":doc:`(.+) <pair.+>`",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=True)
+counter += check_style('pair_style.rst',doc,":doc:`(.+) <pair.+>` -",
+                       pair,'Pair',skip=('meam','lj/sf'),suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <bond.+>`",
+                       bond,'Bond',suffix=True)
+counter += check_style('bond_style.rst',doc,":doc:`(.+) <bond.+>` -",
+                       bond,'Bond',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <angle.+>`",
+                       angle,'Angle',suffix=True)
+counter += check_style('angle_style.rst',doc,":doc:`(.+) <angle.+>` -",
+                       angle,'Angle',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <dihedral.+>`",
+                       dihedral,'Dihedral',suffix=True)
+counter += check_style('dihedral_style.rst',doc,":doc:`(.+) <dihedral.+>` -",
+                       dihedral,'Dihedral',suffix=False)
+counter += check_style('Commands_bond.rst',doc,":doc:`(.+) <improper.+>`",
+                       improper,'Improper',suffix=True)
+counter += check_style('improper_style.rst',doc,":doc:`(.+) <improper.+>` -",
+                       improper,'Improper',suffix=False)
+counter += check_style('Commands_kspace.rst',doc,":doc:`(.+) <kspace_style>`",
+                       kspace,'KSpace',suffix=True)
+
+if counter:
+    print("Found %d issue(s) with style lists" % counter)
+
diff --git a/doc/utils/converters/lammpsdoc/rst_anchor_check.py b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
index 9c097e7d0e..64a1308601 100644
--- a/doc/utils/converters/lammpsdoc/rst_anchor_check.py
+++ b/doc/utils/converters/lammpsdoc/rst_anchor_check.py
@@ -42,7 +42,7 @@ def main():
                     else:
                         anchors[label] = [(filename, line_number+1)]
 
-    print("found %d anchor labels" % len(anchors))
+    print("Found %d anchor labels" % len(anchors))
 
     count = 0
 
diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt
index 3182c8605e..b0e80b485a 100644
--- a/doc/utils/sphinx-config/false_positives.txt
+++ b/doc/utils/sphinx-config/false_positives.txt
@@ -1141,6 +1141,7 @@ ico
 icosahedral
 idealgas
 IDR
+idx
 ielement
 ieni
 ifdefs
@@ -2475,6 +2476,8 @@ Runge
 runtime
 Rutuparna
 rx
+ry
+rz
 Ryckaert
 Rycroft
 Rydbergs
diff --git a/examples/COUPLE/lammps_vasp/in.client.W b/examples/COUPLE/lammps_vasp/in.client.W
index 3eaf99dcbb..1af1c312e4 100644
--- a/examples/COUPLE/lammps_vasp/in.client.W
+++ b/examples/COUPLE/lammps_vasp/in.client.W
@@ -32,3 +32,4 @@ fix_modify      2 energy yes
 thermo          1
 run		3
 
+message         quit
diff --git a/examples/README b/examples/README
index 47463a85d8..a0f27e2c05 100644
--- a/examples/README
+++ b/examples/README
@@ -101,6 +101,7 @@ prd:      parallel replica dynamics of vacancy diffusion in bulk Si
 python:   use of PYTHON package to invoke Python code from input script
 qeq:      use of QEQ package for charge equilibration
 reax:     RDX and TATB and several other models using ReaxFF
+rerun:    use of rerun and read_dump commands
 rigid:    rigid bodies modeled as independent or coupled
 shear:    sideways shear applied to 2d solid, with and without a void
 snap:     examples for using several bundled SNAP potentials
@@ -164,6 +165,9 @@ The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.
 
+The TIP4P directory has an example for testing forces computed on a
+GPU.
+
 The UNITS directory contains examples of input scripts modeling the
 same Lennard-Jones liquid model, written in 3 different unit systems:
 lj, real, and metal.  So that you can see how to scale/unscale input
diff --git a/examples/message/in.message.client b/examples/message/in.message.client
index f1ec644a80..cd0a40367a 100644
--- a/examples/message/in.message.client
+++ b/examples/message/in.message.client
@@ -39,3 +39,5 @@ fix_modify      2 energy yes
 
 thermo          10
 run             50
+
+message         quit
diff --git a/examples/message/in.message.tilt.client b/examples/message/in.message.tilt.client
index b55bc6585b..d178c801f5 100644
--- a/examples/message/in.message.tilt.client
+++ b/examples/message/in.message.tilt.client
@@ -40,3 +40,5 @@ thermo_style    custom step temp epair etotal press xy
 
 thermo		1000
 run		50000
+
+message         quit
diff --git a/examples/rerun/README b/examples/rerun/README
new file mode 100644
index 0000000000..66db685d92
--- /dev/null
+++ b/examples/rerun/README
@@ -0,0 +1,17 @@
+Examples of how to use the rerun and read_dump commands
+
+in.first - run on any number of procs for any size problem
+in.rerun - run on same or different proc count for same size problem
+in.read_dump - ditto to in.rerun
+
+The thermo output on the same timesteps should be identical
+to within round-off errors.
+
+in.rdf.first - produces RDF in rdf.first, 50 bins out to 2.5 sigma
+in.rdf.rerun - produces RDF in rdf.rerun, 100 bins out to 5 sigma
+
+In both bases the time averaged RDF is computed 10x times, every 100
+steps for 1000 total.  In the rerun, the pair style cutoff is changed
+so the RDF can be computed to a longer distance without re-running the
+simulation.  The RDF values in the 2 files should be the same (within
+round-off) for the first 50 bins.
diff --git a/examples/rerun/in.first b/examples/rerun/in.first
new file mode 100644
index 0000000000..2aa4c1974c
--- /dev/null
+++ b/examples/rerun/in.first
@@ -0,0 +1,33 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.rdf.first b/examples/rerun/in.rdf.first
new file mode 100644
index 0000000000..f9d1ecf55e
--- /dev/null
+++ b/examples/rerun/in.rdf.first
@@ -0,0 +1,36 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
diff --git a/examples/rerun/in.rdf.rerun b/examples/rerun/in.rdf.rerun
new file mode 100644
index 0000000000..5562cac74d
--- /dev/null
+++ b/examples/rerun/in.rdf.rerun
@@ -0,0 +1,31 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+
diff --git a/examples/rerun/in.read_dump b/examples/rerun/in.read_dump
new file mode 100644
index 0000000000..3c1310b305
--- /dev/null
+++ b/examples/rerun/in.read_dump
@@ -0,0 +1,37 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 800 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 600 x y z vx vy vz
+run             0 post no
+
+read_dump       lj.dump 400 x y z vx vy vz
+run             0 post no
diff --git a/examples/rerun/in.rerun b/examples/rerun/in.rerun
new file mode 100644
index 0000000000..a695006f26
--- /dev/null
+++ b/examples/rerun/in.rerun
@@ -0,0 +1,29 @@
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	yy equal 20*$y
+variable	zz equal 20*$z
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200 &
+                dump x y z vx vy vz
+
diff --git a/examples/rerun/log.09Jan20.first.g++.4 b/examples/rerun/log.09Jan20.first.g++.4
new file mode 100644
index 0000000000..cabc17c851
--- /dev/null
+++ b/examples/rerun/log.09Jan20.first.g++.4
@@ -0,0 +1,97 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00173283 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z vx vy vz
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 7.869 | 7.869 | 7.869 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 6.3349 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 68193.673 tau/day, 157.856 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 4.3538     | 4.6712     | 5.0021     |  12.8 | 73.74
+Neigh   | 0.59378    | 0.65229    | 0.75202    |   8.0 | 10.30
+Comm    | 0.28101    | 0.69839    | 1.0586     |  38.5 | 11.02
+Output  | 0.21601    | 0.21682    | 0.21718    |   0.1 |  3.42
+Modify  | 0.074002   | 0.074803   | 0.075779   |   0.2 |  1.18
+Other   |            | 0.0214     |            |       |  0.34
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:06
diff --git a/examples/rerun/log.09Jan20.rdf.first.g++.4 b/examples/rerun/log.09Jan20.rdf.first.g++.4
new file mode 100644
index 0000000000..7d029f23d4
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rdf.first.g++.4
@@ -0,0 +1,105 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+velocity	all create 1.44 87287 loop geom
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+neigh_modify	delay 0 every 20 check no
+
+fix		1 all nve
+
+dump            1 all custom 100 lj.dump id type x y z
+
+compute         myRDF all rdf 50 cutoff 2.5
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.first mode vector
+
+thermo          100
+run		1000
+Neighbor list info ...
+  update every 20 steps, delay 0 steps, check no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 2.8
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.487 | 8.487 | 8.487 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0         1.44   -6.7733681            0   -4.6134356   -5.0197073 
+     100    0.7574531   -5.7585055            0   -4.6223613   0.20726105 
+     200   0.75953175   -5.7618892            0   -4.6226272   0.20910575 
+     300   0.74624286    -5.741962            0   -4.6226327   0.32016436 
+     400   0.74155675   -5.7343359            0   -4.6220356    0.3777989 
+     500   0.73249345   -5.7206946            0   -4.6219887   0.44253023 
+     600   0.72087255   -5.7029314            0   -4.6216563   0.55730354 
+     700   0.71489947    -5.693532            0   -4.6212164   0.61322381 
+     800   0.70876958   -5.6840594            0   -4.6209382   0.66822293 
+     900   0.70799522   -5.6828388            0   -4.6208791   0.66961272 
+    1000   0.70325878   -5.6750833            0   -4.6202281    0.7112575 
+Loop time of 7.44016 on 4 procs for 1000 steps with 32000 atoms
+
+Performance: 58063.267 tau/day, 134.406 timesteps/s
+99.7% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.3881     | 5.5809     | 5.7111     |   5.4 | 75.01
+Neigh   | 0.80101    | 0.82776    | 0.85702    |   2.2 | 11.13
+Comm    | 0.31801    | 0.48426    | 0.72201    |  22.5 |  6.51
+Output  | 0.17801    | 0.17801    | 0.17801    |   0.0 |  2.39
+Modify  | 0.31201    | 0.33076    | 0.33701    |   1.9 |  4.45
+Other   |            | 0.0385     |            |       |  0.52
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    8632.5 ave 8685 max 8591 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Neighs:    299934 ave 303105 max 295137 min
+Histogram: 1 0 0 0 0 0 1 1 0 1
+
+Total # of neighbors = 1199738
+Ave neighs/atom = 37.4918
+Neighbor list builds = 50
+Dangerous builds not checked
+Total wall time: 0:00:07
diff --git a/examples/rerun/log.09Jan20.rdf.rerun.g++.4 b/examples/rerun/log.09Jan20.rdf.rerun.g++.4
new file mode 100644
index 0000000000..7c5137bb08
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rdf.rerun.g++.4
@@ -0,0 +1,100 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00183487 secs
+mass		1 1.0
+
+pair_style	lj/cut 5.0
+pair_coeff	1 1 1.0 1.0
+
+neighbor	0.3 bin
+
+compute         myRDF all rdf 100 cutoff 5.0
+fix             2 all ave/time 100 10 1000 c_myRDF[*] file rdf.rerun mode vector
+
+thermo          100
+
+rerun           lj.dump dump x y z
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 5.3
+  ghost atom cutoff = 5.3
+  binsize = 2.65, bins = 13 13 13
+  2 neighbor lists, perpetual/occasional/extra = 1 1 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+  (2) compute rdf, occasional
+      attributes: half, newton on, cut 5.3
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 15.19 | 15.19 | 15.19 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -7.1616928            0   -7.1616928   -6.8899898 
+     100            0   -6.1442754            0   -6.1442754   -1.0825318 
+     200            0   -6.1472483            0   -6.1472483   -1.0817213 
+     300            0   -6.1274033            0   -6.1274033  -0.95961014 
+     400            0   -6.1202956            0   -6.1202956   -0.8988851 
+     500            0   -6.1067136            0   -6.1067136  -0.82660368 
+     600            0   -6.0893179            0   -6.0893179  -0.70264528 
+     700            0   -6.0803044            0   -6.0803044  -0.64232743 
+     800            0   -6.0710303            0   -6.0710303   -0.5824798 
+     900            0   -6.0698963            0   -6.0698963  -0.58057929 
+    1000            0   -6.0627642            0   -6.0627642  -0.53599799 
+Loop time of 3.07661 on 4 procs for 11 steps with 32000 atoms
+
+Performance: 1544.558 tau/day, 3.575 timesteps/s
+99.8% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 3.077      |            |       |100.00
+
+Nlocal:    8000 ave 8049 max 7942 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Nghost:    20028 ave 20060 max 19988 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:    2.10417e+06 ave 2.12604e+06 max 2.07878e+06 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+
+Total # of neighbors = 8416685
+Ave neighs/atom = 263.021
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:03
diff --git a/examples/rerun/log.09Jan20.read_dump.g++.4 b/examples/rerun/log.09Jan20.read_dump.g++.4
new file mode 100644
index 0000000000..874309aaa3
--- /dev/null
+++ b/examples/rerun/log.09Jan20.read_dump.g++.4
@@ -0,0 +1,118 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.001724 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+read_dump       lj.dump 200 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+Loop time of 2.26498e-06 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 800 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 600 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+Loop time of 7.7486e-07 on 4 procs for 0 steps with 32000 atoms
+
+
+read_dump       lj.dump 400 x y z vx vy vz
+  orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  32000 atoms before read
+  32000 atoms in snapshot
+  0 atoms purged
+  32000 atoms replaced
+  0 atoms trimmed
+  0 atoms added
+  32000 atoms after read
+run             0 post no
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Per MPI rank memory allocation (min/avg/max) = 6.841 | 6.843 | 6.846 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+Loop time of 5.36442e-07 on 4 procs for 0 steps with 32000 atoms
+
+Total wall time: 0:00:00
diff --git a/examples/rerun/log.09Jan20.rerun.g++.4 b/examples/rerun/log.09Jan20.rerun.g++.4
new file mode 100644
index 0000000000..f654e2c777
--- /dev/null
+++ b/examples/rerun/log.09Jan20.rerun.g++.4
@@ -0,0 +1,86 @@
+LAMMPS (09 Jan 2020)
+# 3d Lennard-Jones melt
+
+variable	x index 1
+variable	y index 1
+variable	z index 1
+
+variable	xx equal 20*$x
+variable	xx equal 20*1
+variable	yy equal 20*$y
+variable	yy equal 20*1
+variable	zz equal 20*$z
+variable	zz equal 20*1
+
+units		lj
+atom_style	atomic
+
+lattice		fcc 0.8442
+Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
+region		box block 0 ${xx} 0 ${yy} 0 ${zz}
+region		box block 0 20 0 ${yy} 0 ${zz}
+region		box block 0 20 0 20 0 ${zz}
+region		box block 0 20 0 20 0 20
+create_box	1 box
+Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919)
+  1 by 2 by 2 MPI processor grid
+create_atoms	1 box
+Created 32000 atoms
+  create_atoms CPU = 0.00100017 secs
+mass		1 1.0
+
+pair_style	lj/cut 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+
+thermo          100
+
+rerun           lj.dump first 200 last 800 every 200                 dump x y z vx vy vz
+WARNING: No fixes defined, atoms won't move (../verlet.cpp:52)
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 2.8
+  ghost atom cutoff = 2.8
+  binsize = 1.4, bins = 24 24 24
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/cut, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 6.716 | 6.718 | 6.721 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+     200   0.75953173   -5.7618854            0   -4.6226234   0.20912952 
+     400   0.74155677   -5.7343336            0   -4.6220332   0.37780193 
+     600   0.72087256   -5.7029306            0   -4.6216556   0.55729873 
+     800   0.70876957   -5.6840545            0   -4.6209334   0.66823926 
+Loop time of 0.375898 on 4 procs for 4 steps with 32000 atoms
+
+Performance: 4596.990 tau/day, 10.641 timesteps/s
+98.0% CPU use with 4 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.3759     |            |       |100.00
+
+Nlocal:    8000 ave 8073 max 7933 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Nghost:    8693.25 ave 8731 max 8658 min
+Histogram: 1 1 0 0 0 0 0 0 1 1
+Neighs:    299786 ave 302947 max 293888 min
+Histogram: 1 0 0 0 0 0 0 1 1 1
+
+Total # of neighbors = 1199142
+Ave neighs/atom = 37.4732
+Neighbor list builds = 0
+Dangerous builds = 0
+
+Total wall time: 0:00:00
diff --git a/examples/rerun/rdf.09Jan20.first.g++.4 b/examples/rerun/rdf.09Jan20.first.g++.4
new file mode 100644
index 0000000000..d78e0ce2c1
--- /dev/null
+++ b/examples/rerun/rdf.09Jan20.first.g++.4
@@ -0,0 +1,54 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 50
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.0217263 0.00986875
+20 0.975 0.506735 0.265431
+21 1.025 1.92083 1.33605
+22 1.075 2.8749 3.09855
+23 1.125 2.7805 4.96541
+24 1.175 2.21879 6.59047
+25 1.225 1.67622 7.92484
+26 1.275 1.25407 9.00629
+27 1.325 0.963413 9.90353
+28 1.375 0.774441 10.6802
+29 1.425 0.656196 11.3871
+30 1.475 0.589364 12.0672
+31 1.525 0.560681 12.7589
+32 1.575 0.560195 13.4961
+33 1.625 0.587995 14.3197
+34 1.675 0.632155 15.2605
+35 1.725 0.706585 16.3758
+36 1.775 0.805303 17.7216
+37 1.825 0.925415 19.3565
+38 1.875 1.05672 21.3271
+39 1.925 1.17634 23.6394
+40 1.975 1.2557 26.2375
+41 2.025 1.30009 29.0653
+42 2.075 1.30889 32.0546
+43 2.125 1.27704 35.1135
+44 2.175 1.21808 38.17
+45 2.225 1.13622 41.1536
+46 2.275 1.05072 44.0382
+47 2.325 0.973786 46.8303
+48 2.375 0.910095 49.5533
+49 2.425 0.866474 52.256
+50 2.475 0.841724 54.991
diff --git a/examples/rerun/rdf.09Jan20.rerun.g++.4 b/examples/rerun/rdf.09Jan20.rerun.g++.4
new file mode 100644
index 0000000000..3fa6acc461
--- /dev/null
+++ b/examples/rerun/rdf.09Jan20.rerun.g++.4
@@ -0,0 +1,104 @@
+# Time-averaged data for fix 2
+# TimeStep Number-of-rows
+# Row c_myRDF[1] c_myRDF[2] c_myRDF[3]
+1000 100
+1 0.025 0 0
+2 0.075 0 0
+3 0.125 0 0
+4 0.175 0 0
+5 0.225 0 0
+6 0.275 0 0
+7 0.325 0 0
+8 0.375 0 0
+9 0.425 0 0
+10 0.475 0 0
+11 0.525 0 0
+12 0.575 0 0
+13 0.625 0 0
+14 0.675 0 0
+15 0.725 0 0
+16 0.775 0 0
+17 0.825 0 0
+18 0.875 1.53863e-05 6.25e-06
+19 0.925 0.021685 0.00985
+20 0.975 0.506834 0.265463
+21 1.025 1.92047 1.33588
+22 1.075 2.87514 3.09853
+23 1.125 2.78062 4.96547
+24 1.175 2.21869 6.59046
+25 1.225 1.67626 7.92486
+26 1.275 1.25409 9.00633
+27 1.325 0.963245 9.90341
+28 1.375 0.774535 10.6802
+29 1.425 0.65626 11.3871
+30 1.475 0.58925 12.0672
+31 1.525 0.560782 12.759
+32 1.575 0.560133 13.496
+33 1.625 0.588008 14.3197
+34 1.675 0.632185 15.2605
+35 1.725 0.706541 16.3757
+36 1.775 0.805341 17.7216
+37 1.825 0.925351 19.3565
+38 1.875 1.05677 21.3271
+39 1.925 1.17639 23.6395
+40 1.975 1.25571 26.2376
+41 2.025 1.30011 29.0655
+42 2.075 1.30883 32.0547
+43 2.125 1.27702 35.1134
+44 2.175 1.21813 38.17
+45 2.225 1.13617 41.1536
+46 2.275 1.05073 44.0382
+47 2.325 0.97376 46.8302
+48 2.375 0.91012 49.5533
+49 2.425 0.866556 52.2563
+50 2.475 0.841651 54.991
+51 2.525 0.839516 57.8301
+52 2.575 0.848795 60.8153
+53 2.625 0.868861 63.991
+54 2.675 0.896335 67.393
+55 2.725 0.925794 71.0395
+56 2.775 0.961909 74.9685
+57 2.825 0.999727 79.2005
+58 2.875 1.03745 83.749
+59 2.925 1.07355 88.6208
+60 2.975 1.10406 93.8039
+61 3.025 1.11993 99.2397
+62 3.075 1.12062 104.86
+63 3.125 1.10531 110.586
+64 3.175 1.07711 116.345
+65 3.225 1.04268 122.097
+66 3.275 1.00838 127.834
+67 3.325 0.974855 133.55
+68 3.375 0.949817 139.289
+69 3.425 0.936519 145.116
+70 3.475 0.92942 151.069
+71 3.525 0.930926 157.205
+72 3.575 0.940561 163.581
+73 3.625 0.94956 170.199
+74 3.675 0.964202 177.107
+75 3.725 0.97905 184.312
+76 3.775 0.991906 191.81
+77 3.825 1.00093 199.577
+78 3.875 1.01248 207.641
+79 3.925 1.02301 216.001
+80 3.975 1.03474 224.673
+81 4.025 1.04171 233.624
+82 4.075 1.04725 242.849
+83 4.125 1.04997 252.325
+84 4.175 1.04758 262.01
+85 4.225 1.03985 271.856
+86 4.275 1.02755 281.817
+87 4.325 1.00883 291.826
+88 4.375 0.99045 301.882
+89 4.425 0.97287 311.986
+90 4.475 0.958469 322.166
+91 4.525 0.952552 332.512
+92 4.575 0.948064 343.037
+93 4.625 0.952592 353.845
+94 4.675 0.958837 364.96
+95 4.725 0.970831 376.457
+96 4.775 0.985248 388.372
+97 4.825 0.998873 400.707
+98 4.875 1.0119 413.462
+99 4.925 1.02446 426.643
+100 4.975 1.03613 440.245
diff --git a/src/GPU/pair_beck_gpu.cpp b/src/GPU/pair_beck_gpu.cpp
index d4d36a5837..f4b73ba5a6 100644
--- a/src/GPU/pair_beck_gpu.cpp
+++ b/src/GPU/pair_beck_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_special.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathSpecial;
@@ -68,6 +69,7 @@ PairBeckGPU::PairBeckGPU(LAMMPS *lmp) : PairBeck(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 7314024d71..bab66e0351 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -90,6 +91,7 @@ PairBornCoulLongCSGPU::PairBornCoulLongCSGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index 79c0d5f147..39d34420a8 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -85,6 +86,7 @@ PairBornCoulLongGPU::PairBornCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 5f74d3fc7c..b00b5a0b56 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -78,6 +79,7 @@ PairBornCoulWolfCSGPU::PairBornCoulWolfCSGPU(LAMMPS *lmp) : PairBornCoulWolfCS(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_coul_wolf_gpu.cpp b/src/GPU/pair_born_coul_wolf_gpu.cpp
index 693c2abffb..c5243dc443 100644
--- a/src/GPU/pair_born_coul_wolf_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -76,6 +77,7 @@ PairBornCoulWolfGPU::PairBornCoulWolfGPU(LAMMPS *lmp) : PairBornCoulWolf(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_born_gpu.cpp b/src/GPU/pair_born_gpu.cpp
index e9edc4f1c2..b71a296d66 100644
--- a/src/GPU/pair_born_gpu.cpp
+++ b/src/GPU/pair_born_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairBornGPU::PairBornGPU(LAMMPS *lmp) : PairBorn(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_cut_gpu.cpp b/src/GPU/pair_buck_coul_cut_gpu.cpp
index 182673fb0d..5d27ee8c51 100644
--- a/src/GPU/pair_buck_coul_cut_gpu.cpp
+++ b/src/GPU/pair_buck_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairBuckCoulCutGPU::PairBuckCoulCutGPU(LAMMPS *lmp) : PairBuckCoulCut(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 75e784fafa..e30230d5a0 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -81,6 +82,7 @@ PairBuckCoulLongGPU::PairBuckCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_buck_gpu.cpp b/src/GPU/pair_buck_gpu.cpp
index 1559c45b88..b4d5677d53 100644
--- a/src/GPU/pair_buck_gpu.cpp
+++ b/src/GPU/pair_buck_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairBuckGPU::PairBuckGPU(LAMMPS *lmp) : PairBuck(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 4db18dbc52..230adb3db0 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairColloidGPU::PairColloidGPU(LAMMPS *lmp) : PairColloid(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_cut_gpu.cpp b/src/GPU/pair_coul_cut_gpu.cpp
index 8a3eb12f8d..0242c98343 100644
--- a/src/GPU/pair_coul_cut_gpu.cpp
+++ b/src/GPU/pair_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairCoulCutGPU::PairCoulCutGPU(LAMMPS *lmp) : PairCoulCut(lmp), gpu_mode(GPU_FOR
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_debye_gpu.cpp b/src/GPU/pair_coul_debye_gpu.cpp
index 1fc07f8dac..198f7f5f67 100644
--- a/src/GPU/pair_coul_debye_gpu.cpp
+++ b/src/GPU/pair_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairCoulDebyeGPU::PairCoulDebyeGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_dsf_gpu.cpp b/src/GPU/pair_coul_dsf_gpu.cpp
index 408be036dd..67d025ff70 100644
--- a/src/GPU/pair_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -81,6 +82,7 @@ PairCoulDSFGPU::PairCoulDSFGPU(LAMMPS *lmp) : PairCoulDSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index c70424e472..afd0d6cf56 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -83,6 +84,7 @@ PairCoulLongCSGPU::PairCoulLongCSGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 9623c25f2f..485e45ddc6 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -78,6 +79,7 @@ PairCoulLongGPU::PairCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_gpu.cpp b/src/GPU/pair_dpd_gpu.cpp
index 5fcad6a350..9e14164c57 100644
--- a/src/GPU/pair_dpd_gpu.cpp
+++ b/src/GPU/pair_dpd_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -209,6 +210,7 @@ PairDPDGPU::PairDPDGPU(LAMMPS *lmp) : PairDPD(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_dpd_tstat_gpu.cpp b/src/GPU/pair_dpd_tstat_gpu.cpp
index 2d6798a12d..920eb8dd8a 100644
--- a/src/GPU/pair_dpd_tstat_gpu.cpp
+++ b/src/GPU/pair_dpd_tstat_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -212,6 +213,7 @@ PairDPDTstatGPU::PairDPDTstatGPU(LAMMPS *lmp) : PairDPDTstat(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index bc55c66676..e7503839f6 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -30,7 +30,7 @@
 #include "gpu_extra.h"
 #include "domain.h"
 #include "utils.h"
-
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +72,7 @@ PairEAMAlloyGPU::PairEAMAlloyGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index ac379a9ce6..6edfa69359 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -29,6 +29,7 @@
 #include "neigh_request.h"
 #include "gpu_extra.h"
 #include "domain.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairEAMFSGPU::PairEAMFSGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index 57106f48a4..fb851770f9 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -30,6 +30,7 @@
 #include "error.h"
 #include "neigh_request.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MAXLINE 1024
 
@@ -71,6 +72,7 @@ PairEAMGPU::PairEAMGPU(LAMMPS *lmp) : PairEAM(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gauss_gpu.cpp b/src/GPU/pair_gauss_gpu.cpp
index 842b84acf2..17125f9875 100644
--- a/src/GPU/pair_gauss_gpu.cpp
+++ b/src/GPU/pair_gauss_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairGaussGPU::PairGaussGPU(LAMMPS *lmp) : PairGauss(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index f00accda15..445c74487f 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -74,6 +75,7 @@ PairGayBerneGPU::PairGayBerneGPU(LAMMPS *lmp) : PairGayBerne(lmp),
   quat_nmax = 0;
   reinitflag = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj96_cut_gpu.cpp b/src/GPU/pair_lj96_cut_gpu.cpp
index 16b6b835c0..f6f9bd379b 100644
--- a/src/GPU/pair_lj96_cut_gpu.cpp
+++ b/src/GPU/pair_lj96_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -66,6 +67,7 @@ PairLJ96CutGPU::PairLJ96CutGPU(LAMMPS *lmp) : PairLJ96Cut(lmp), gpu_mode(GPU_FOR
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index bacbb400b1..6eda677928 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCharmmCoulLongGPU::PairLJCharmmCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index e34dbb0f99..4ee776b4ff 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -80,6 +81,7 @@ PairLJClass2CoulLongGPU::PairLJClass2CoulLongGPU(LAMMPS *lmp) :
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_class2_gpu.cpp b/src/GPU/pair_lj_class2_gpu.cpp
index 68f27598f3..643e3ff090 100644
--- a/src/GPU/pair_lj_class2_gpu.cpp
+++ b/src/GPU/pair_lj_class2_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairLJClass2GPU::PairLJClass2GPU(LAMMPS *lmp) : PairLJClass2(lmp), gpu_mode(GPU_
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cubic_gpu.cpp b/src/GPU/pair_lj_cubic_gpu.cpp
index 542de37840..64fd6119c3 100644
--- a/src/GPU/pair_lj_cubic_gpu.cpp
+++ b/src/GPU/pair_lj_cubic_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 using namespace PairLJCubicConstants;
@@ -70,6 +71,7 @@ PairLJCubicGPU::PairLJCubicGPU(LAMMPS *lmp) : PairLJCubic(lmp),
   respa_enable = 0;
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
index cf3dd711dc..e52a971786 100644
--- a/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJCutCoulCutGPU::PairLJCutCoulCutGPU(LAMMPS *lmp) : PairLJCutCoulCut(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
index 20354e732c..4c8920450f 100644
--- a/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_debye_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutCoulDebyeGPU::PairLJCutCoulDebyeGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
index ccaf86efa6..acfbcd847e 100644
--- a/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_dsf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define MY_PIS 1.77245385090551602729
 #define EWALD_F   1.12837917
@@ -82,6 +83,7 @@ PairLJCutCoulDSFGPU::PairLJCutCoulDSFGPU(LAMMPS *lmp) : PairLJCutCoulDSF(lmp), g
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 36c72f1143..24ce118c6d 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJCutCoulLongGPU::PairLJCutCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 79ca90698a..0e700f6fb2 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJCutCoulMSMGPU::PairLJCutCoulMSMGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
index e2c8b8d686..6c53b02227 100644
--- a/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairLJCutDipoleCutGPU::PairLJCutDipoleCutGPU(LAMMPS *lmp) : PairLJCutDipoleCut(l
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index fb76376d34..0535735820 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -84,6 +85,7 @@ PairLJCutDipoleLongGPU::PairLJCutDipoleLongGPU(LAMMPS *lmp) : PairLJCutDipoleLon
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_gpu.cpp b/src/GPU/pair_lj_cut_gpu.cpp
index 809e5cf05e..c6f61a7e96 100644
--- a/src/GPU/pair_lj_cut_gpu.cpp
+++ b/src/GPU/pair_lj_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairLJCutGPU::PairLJCutGPU(LAMMPS *lmp) : PairLJCut(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
index 99668d26b8..a7875f15c4 100644
--- a/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_tip4p_long_gpu.cpp
@@ -37,6 +37,7 @@
 #include "angle.h"
 #include "bond.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -91,6 +92,7 @@ PairLJCutTIP4PLongGPU::PairLJCutTIP4PLongGPU(LAMMPS *lmp)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index a530f7ff9a..a906f57707 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -83,6 +84,7 @@ PairLJExpandCoulLongGPU::PairLJExpandCoulLongGPU(LAMMPS *lmp) :
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_expand_gpu.cpp b/src/GPU/pair_lj_expand_gpu.cpp
index 86f8a76b52..db88e8dae8 100644
--- a/src/GPU/pair_lj_expand_gpu.cpp
+++ b/src/GPU/pair_lj_expand_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairLJExpandGPU::PairLJExpandGPU(LAMMPS *lmp) : PairLJExpand(lmp), gpu_mode(GPU_
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_gromacs_gpu.cpp b/src/GPU/pair_lj_gromacs_gpu.cpp
index 78f8b8b461..6989d73d50 100644
--- a/src/GPU/pair_lj_gromacs_gpu.cpp
+++ b/src/GPU/pair_lj_gromacs_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJGromacsGPU::PairLJGromacsGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
index 24ff8a4f28..3bcaa78d46 100644
--- a/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_coul_long_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "kspace.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define EWALD_F   1.12837917
 #define EWALD_P   0.3275911
@@ -86,6 +87,7 @@ PairLJSDKCoulLongGPU::PairLJSDKCoulLongGPU(LAMMPS *lmp) :
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sdk_gpu.cpp b/src/GPU/pair_lj_sdk_gpu.cpp
index 2621f49aeb..c0a3e8ec39 100644
--- a/src/GPU/pair_lj_sdk_gpu.cpp
+++ b/src/GPU/pair_lj_sdk_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,6 +72,7 @@ PairLJSDKGPU::PairLJSDKGPU(LAMMPS *lmp) : PairLJSDK(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
index cf26cdf3b4..d001c282e2 100644
--- a/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
+++ b/src/GPU/pair_lj_sf_dipole_sf_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairLJSFDipoleSFGPU::PairLJSFDipoleSFGPU(LAMMPS *lmp) : PairLJSFDipoleSF(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index f3a384113f..84cc903dee 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairMIECutGPU::PairMIECutGPU(LAMMPS *lmp) : PairMIECut(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index dcad227045..5bcda54d85 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -65,6 +66,7 @@ PairMorseGPU::PairMorseGPU(LAMMPS *lmp) : PairMorse(lmp), gpu_mode(GPU_FORCE)
 {
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index b12a790c81..b03834d5d1 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -36,6 +36,7 @@
 #include "domain.h"
 #include "update.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ PairRESquaredGPU::PairRESquaredGPU(LAMMPS *lmp) : PairRESquared(lmp),
     error->all(FLERR,"Pair resquared/gpu requires atom style ellipsoid");
   quat_nmax = 0;
   quat = NULL;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index 0efcb20c8d..04efb1e96a 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -35,6 +35,7 @@
 #include "domain.h"
 #include "gpu_extra.h"
 #include "math_const.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairSoftGPU::PairSoftGPU(LAMMPS *lmp) : PairSoft(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_sw_gpu.cpp b/src/GPU/pair_sw_gpu.cpp
index 906f8a7e83..8e75aff545 100644
--- a/src/GPU/pair_sw_gpu.cpp
+++ b/src/GPU/pair_sw_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairSWGPU::PairSWGPU(LAMMPS *lmp) : PairSW(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
   reinitflag = 0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index 4432265874..563b070bda 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 #define LOOKUP 0
 #define LINEAR 1
@@ -73,6 +74,7 @@ PairTableGPU::PairTableGPU(LAMMPS *lmp) : PairTable(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_tersoff_gpu.cpp b/src/GPU/pair_tersoff_gpu.cpp
index 15fc5c95da..33bac49e5e 100644
--- a/src/GPU/pair_tersoff_gpu.cpp
+++ b/src/GPU/pair_tersoff_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -76,6 +77,7 @@ extern double lmp_gpu_forces(double **f, double **tor, double *eatom,
 PairTersoffGPU::PairTersoffGPU(LAMMPS *lmp) : PairTersoff(lmp), gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_tersoff_mod_gpu.cpp b/src/GPU/pair_tersoff_mod_gpu.cpp
index 2ff09c3248..ebcdf0f7dd 100644
--- a/src/GPU/pair_tersoff_mod_gpu.cpp
+++ b/src/GPU/pair_tersoff_mod_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -69,6 +70,7 @@ PairTersoffMODGPU::PairTersoffMODGPU(LAMMPS *lmp) : PairTersoffMOD(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_tersoff_zbl_gpu.cpp b/src/GPU/pair_tersoff_zbl_gpu.cpp
index b8d02f09ab..09b5a7f838 100644
--- a/src/GPU/pair_tersoff_zbl_gpu.cpp
+++ b/src/GPU/pair_tersoff_zbl_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -77,6 +78,7 @@ PairTersoffZBLGPU::PairTersoffZBLGPU(LAMMPS *lmp) : PairTersoffZBL(lmp),
   gpu_mode(GPU_FORCE)
 {
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 97c2eebf24..49ed6289e1 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -36,6 +36,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -72,6 +73,7 @@ PairUFMGPU::PairUFMGPU(LAMMPS *lmp) : PairUFM(lmp), gpu_mode(GPU_FORCE)
 {
   respa_enable = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 56199f7e54..6f0d938440 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -32,6 +32,7 @@
 #include "error.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -73,6 +74,7 @@ PairVashishtaGPU::PairVashishtaGPU(LAMMPS *lmp) : PairVashishta(lmp), gpu_mode(G
   cpu_time = 0.0;
   reinitflag = 0;
   gpu_allocated = false;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 
   cutghost = NULL;
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 51c7e683db..7bbed7d89b 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -68,6 +69,7 @@ PairYukawaColloidGPU::PairYukawaColloidGPU(LAMMPS *lmp) : PairYukawaColloid(lmp)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index 5dc13c7750..9d702daf20 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -34,6 +34,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -67,6 +68,7 @@ PairYukawaGPU::PairYukawaGPU(LAMMPS *lmp) : PairYukawa(lmp),
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index 5e24281145..23c3c077fa 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -35,6 +35,7 @@
 #include "update.h"
 #include "domain.h"
 #include "gpu_extra.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -70,6 +71,7 @@ PairZBLGPU::PairZBLGPU(LAMMPS *lmp) : PairZBL(lmp), gpu_mode(GPU_FORCE)
   respa_enable = 0;
   reinitflag = 0;
   cpu_time = 0.0;
+  suffix_flag |= Suffix::GPU;
   GPU_EXTRA::gpu_ready(lmp->modify, lmp->error);
 }
 
diff --git a/src/MC/fix_bond_break.cpp b/src/MC/fix_bond_break.cpp
index 2ff0e4126f..2e8200f751 100644
--- a/src/MC/fix_bond_break.cpp
+++ b/src/MC/fix_bond_break.cpp
@@ -33,7 +33,8 @@ using namespace FixConst;
 
 FixBondBreak::FixBondBreak(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL), broken(NULL), copy(NULL), random(NULL)
+  partner(NULL), finalpartner(NULL), distsq(NULL), probability(NULL),
+  broken(NULL), copy(NULL), random(NULL)
 {
   if (narg < 6) error->all(FLERR,"Illegal fix bond/break command");
 
diff --git a/src/MC/fix_bond_create.cpp b/src/MC/fix_bond_create.cpp
index 3f63a22d60..629e6defff 100644
--- a/src/MC/fix_bond_create.cpp
+++ b/src/MC/fix_bond_create.cpp
@@ -18,6 +18,7 @@
 #include "respa.h"
 #include "atom.h"
 #include "force.h"
+#include "modify.h"
 #include "pair.h"
 #include "comm.h"
 #include "neighbor.h"
@@ -216,6 +217,19 @@ void FixBondCreate::init()
   if (force->pair == NULL || cutsq > force->pair->cutsq[iatomtype][jatomtype])
     error->all(FLERR,"Fix bond/create cutoff is longer than pairwise cutoff");
 
+  // warn if more than one fix bond/create or also a fix bond/break
+  // because this fix stores per-atom state in bondcount
+  //   if other fixes create/break bonds, this fix will not know about it
+
+  int count = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (strcmp(modify->fix[i]->style,"bond/create") == 0) count++;
+    if (strcmp(modify->fix[i]->style,"bond/break") == 0) count++;
+  }
+  if (count > 1 && me == 0)
+    error->warning(FLERR,"Fix bond/create is used multiple times "
+                   " or with fix bond/break - may not work as expected");
+
   // enable angle/dihedral/improper creation if atype/dtype/itype
   //   option was used and a force field has been specified
 
diff --git a/src/MC/fix_bond_create.h b/src/MC/fix_bond_create.h
index 403b1ae340..1e4b9a11c1 100644
--- a/src/MC/fix_bond_create.h
+++ b/src/MC/fix_bond_create.h
@@ -170,4 +170,11 @@ See the read_data command for info on setting the "extra special per
 atom" header value to allow for additional special values to be
 stored.
 
+W: Fix bond/create is used multiple times or with fix bond/break - may not work as expected
+
+When using fix bond/create multiple times or in combination with
+fix bond/break, the individual fix instances do not share information
+about changes they made at the same time step and thus it may result
+in unexpected behavior.
+
 */
diff --git a/src/MESSAGE/fix_client_md.cpp b/src/MESSAGE/fix_client_md.cpp
index 7d4ae13f0f..1a9437ebe2 100644
--- a/src/MESSAGE/fix_client_md.cpp
+++ b/src/MESSAGE/fix_client_md.cpp
@@ -80,21 +80,6 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
 FixClientMD::~FixClientMD()
 {
   memory->destroy(xpbc);
-
-  CSlib *cs = (CSlib *) lmp->cslib;
-
-  // all-done message to server
-
-  cs->send(-1,0);
-
-  int nfield;
-  int *fieldID,*fieldtype,*fieldlen;
-  cs->recv(nfield,fieldID,fieldtype,fieldlen);
-
-  // clean-up
-
-  delete cs;
-  lmp->cslib = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/MESSAGE/message.cpp b/src/MESSAGE/message.cpp
index 214025be63..b83be0339c 100644
--- a/src/MESSAGE/message.cpp
+++ b/src/MESSAGE/message.cpp
@@ -26,16 +26,31 @@ using namespace CSLIB_NS;
 
 void Message::command(int narg, char **arg)
 {
-  if (narg < 3) error->all(FLERR,"Illegal message command");
+  if (narg < 1) error->all(FLERR,"Illegal message command");
 
   int clientserver=0;
   if (strcmp(arg[0],"client") == 0) clientserver = 1;
   else if (strcmp(arg[0],"server") == 0) clientserver = 2;
+  else if (strcmp(arg[0],"quit") == 0) clientserver = 0;
   else error->all(FLERR,"Illegal message command");
+
+  // shutdown current client mode
+
+  if (clientserver == 0) {
+    if (lmp->clientserver != 1)
+      error->all(FLERR,"Cannot message quit if not in client mode");
+    quit();
+    return;
+  }
+
+  // setup client or server mode
+
   lmp->clientserver = clientserver;
 
   // validate supported protocols
 
+  if (narg < 3) error->all(FLERR,"Illegal message command");
+
   if ((strcmp(arg[1],"md") != 0) && (strcmp(arg[1],"mc") != 0))
     error->all(FLERR,"Unknown message protocol");
 
@@ -82,3 +97,25 @@ void Message::command(int narg, char **arg)
     cs->send(0,0);
   }
 }
+
+/* ---------------------------------------------------------------------- */
+
+void Message::quit()
+{
+  CSlib *cs = (CSlib *) lmp->cslib;
+
+  // send all-done message to server
+  // receive acknowledgement back
+
+  cs->send(-1,0);
+
+  int nfield;
+  int *fieldID,*fieldtype,*fieldlen;
+  cs->recv(nfield,fieldID,fieldtype,fieldlen);
+
+  // clean-up
+
+  delete cs;
+  lmp->cslib = NULL;
+  lmp->clientserver = 0;
+}
diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h
index c384a5a7b7..f8b2d47a21 100644
--- a/src/MESSAGE/message.h
+++ b/src/MESSAGE/message.h
@@ -28,6 +28,9 @@ class Message : protected Pointers {
  public:
   Message(class LAMMPS *lmp) : Pointers(lmp) {};
   void command(int, char **);
+
+ private:
+  void quit();
 };
 
 }
diff --git a/src/MISC/fix_deposit.cpp b/src/MISC/fix_deposit.cpp
index b33d58aab1..5279b2df36 100644
--- a/src/MISC/fix_deposit.cpp
+++ b/src/MISC/fix_deposit.cpp
@@ -421,9 +421,15 @@ void FixDeposit::pre_exchange()
       while (rng > molfrac[imol]) imol++;
       natom = onemols[imol]->natoms;
       if (dimension == 3) {
-        r[0] = random->uniform() - 0.5;
-        r[1] = random->uniform() - 0.5;
-        r[2] = random->uniform() - 0.5;
+        if (orientflag) {
+          r[0] = rx;
+          r[1] = ry;
+          r[2] = rz;
+        } else {
+          r[0] = random->uniform() - 0.5;
+          r[1] = random->uniform() - 0.5;
+          r[2] = random->uniform() - 0.5;
+        }
       } else {
         r[0] = r[1] = 0.0;
         r[2] = 1.0;
@@ -662,6 +668,10 @@ void FixDeposit::options(int narg, char **arg)
   xmid = ymid = zmid = 0.0;
   scaleflag = 1;
   targetflag = 0;
+  orientflag = 0;
+  rx = 0.0;
+  ry = 0.0;
+  rz = 0.0;
 
   int iarg = 0;
   while (iarg < narg) {
@@ -769,6 +779,17 @@ void FixDeposit::options(int narg, char **arg)
       vzlo = force->numeric(FLERR,arg[iarg+1]);
       vzhi = force->numeric(FLERR,arg[iarg+2]);
       iarg += 3;
+    } else if (strcmp(arg[iarg],"orient") == 0) {
+      if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
+      orientflag = 1;
+      rx = force->numeric(FLERR,arg[iarg+1]);
+      ry = force->numeric(FLERR,arg[iarg+2]);
+      rz = force->numeric(FLERR,arg[iarg+3]);
+      if (domain->dimension == 2 && (rx != 0.0 || ry != 0.0))
+        error->all(FLERR,"Illegal fix deposit orient settings");
+      if (rx == 0.0 && ry == 0.0 && rz == 0.0)
+        error->all(FLERR,"Illegal fix deposit orient settings");
+      iarg += 4;
     } else if (strcmp(arg[iarg],"units") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
       if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
diff --git a/src/MISC/fix_deposit.h b/src/MISC/fix_deposit.h
index e3104c890d..92ecdd9efd 100644
--- a/src/MISC/fix_deposit.h
+++ b/src/MISC/fix_deposit.h
@@ -38,11 +38,11 @@ class FixDeposit : public Fix {
  private:
   int ninsert,ntype,nfreq,seed;
   int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
-  int mode,rigidflag,shakeflag,idnext,distflag;
+  int mode,rigidflag,shakeflag,idnext,distflag,orientflag;
   double lo,hi,deltasq,nearsq,rate,sigma;
   double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
   double xlo,xhi,ylo,yhi,zlo,zhi,xmid,ymid,zmid;
-  double tx,ty,tz;
+  double rx,ry,rz,tx,ty,tz;
   char *idregion;
   char *idrigid,*idshake;
 
diff --git a/src/pair_hybrid.cpp b/src/pair_hybrid.cpp
index eb9423aa57..b88fa49a85 100644
--- a/src/pair_hybrid.cpp
+++ b/src/pair_hybrid.cpp
@@ -27,6 +27,7 @@
 #include "error.h"
 #include "respa.h"
 #include "utils.h"
+#include "suffix.h"
 
 using namespace LAMMPS_NS;
 
@@ -919,6 +920,12 @@ void PairHybrid::modify_special(int m, int /*narg*/, char **arg)
   special[2] = force->numeric(FLERR,arg[2]);
   special[3] = force->numeric(FLERR,arg[3]);
 
+  // have to cast to PairHybrid to work around C++ access restriction
+
+  if (((PairHybrid *)styles[m])->suffix_flag & (Suffix::INTEL|Suffix::GPU))
+    error->all(FLERR,"Pair_modify special is not compatible with "
+                     "suffix version of hybrid substyle");
+
   if (strcmp(arg[0],"lj/coul") == 0) {
     if (!special_lj[m]) special_lj[m] = new double[4];
     if (!special_coul[m]) special_coul[m] = new double[4];
diff --git a/src/suffix.h b/src/suffix.h
index 817600dfd5..88629aa796 100644
--- a/src/suffix.h
+++ b/src/suffix.h
@@ -16,13 +16,14 @@
 
 namespace LAMMPS_NS {
 
-namespace Suffix {
-  static const int NONE = 0;
-  static const int OPT  = 1<<0;
-  static const int GPU  = 1<<1;
-  static const int OMP  = 1<<2;
-  static const int INTEL  = 1<<3;
-}
+enum Suffix {
+  NONE   = 0,
+  OPT    = 1<<0,
+  GPU    = 1<<1,
+  OMP    = 1<<2,
+  INTEL  = 1<<3,
+  KOKKOS = 1<<4
+};
 
 }