new library functions

Merge pull request #239 from akohlmey/static-analysis-fixes
Static analysis fixes
2016-10-27 09:34:04 -06:00 · 2016-10-25 10:32:55 -06:00 · 2016-10-25 10:32:41 -06:00 · 2016-10-25 10:30:34 -06:00 · 2016-10-25 12:12:48 -04:00 · 2016-10-25 11:58:42 -04:00
2009 changed files with 51776 additions and 131883 deletions
--- a/.gitignore
+++ b/.gitignore
@ -0,0 +1,34 @@
+*~
+*.o
+*.so
+*.cu_o
+*.ptx
+*_ptx.h
+*.a
+*.d
+*.x
+*.exe
+*.dll
+*.pyc
+__pycache__
+
+Obj_*
+log.lammps
+log.cite
+*.bz2
+*.gz
+*.tar
+.*.swp
+*.orig
+*.rej
+.vagrant
+\#*#
+.#*
+
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
--- a/doc/.gitignore
+++ b/doc/.gitignore
@ -0,0 +1,5 @@
+/html
+/LAMMPS.epub
+/LAMMPS.mobi
+/Manual.pdf
+/Developer.pdf
--- a/doc/Makefile
+++ b/doc/Makefile
@ -43,7 +43,7 @@ clean-all:
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe

 clean:
-	rm -rf $(RSTDIR) html
+	rm -rf $(RSTDIR)

 html: $(OBJECTS)
 	@(\
--- a/doc/src/Eqs/bond_oxdna_fene.jpg
+++ b/doc/src/Eqs/bond_oxdna_fene.jpg
--- a/doc/src/Eqs/bond_oxdna_fene.tex
+++ b/doc/src/Eqs/bond_oxdna_fene.tex
@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-$$ 
-  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]
-$$
-
-\end{document}
--- a/doc/src/Eqs/fix_grem.jpg
+++ b/doc/src/Eqs/fix_grem.jpg
--- a/doc/src/Eqs/fix_grem.tex
+++ b/doc/src/Eqs/fix_grem.tex
@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  T_{eff} = \lambda + \eta (H - H_0)
-$$
-
-\end{document}
--- a/doc/src/Eqs/pair_agni.jpg
+++ b/doc/src/Eqs/pair_agni.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.jpg
+++ b/doc/src/Eqs/pair_tersoff_mod_c.jpg
--- a/doc/src/Eqs/pair_tersoff_mod_c.tex
+++ b/doc/src/Eqs/pair_tersoff_mod_c.tex
@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-  V_{ij}  & =  & f_C(r_{ij}) \left[ f_R(r_{ij}) + b_{ij} f_A(r_{ij}) + c_0 \right]
-\end{eqnarray*}
-
-\end{document}
--- a/doc/src/Eqs/pressure.jpg
+++ b/doc/src/Eqs/pressure.jpg
--- a/doc/src/Eqs/pressure.tex
+++ b/doc/src/Eqs/pressure.tex
@ -3,7 +3,7 @@
 \begin{document}

 $$
-   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N'} r_i \bullet f_i}{dV}
+   P = \frac{N k_B T}{V} + \frac{\sum_{i}^{N} r_i \bullet f_i}{dV}
 $$

 \end{document}
--- a/doc/src/Eqs/pressure_tensor.jpg
+++ b/doc/src/Eqs/pressure_tensor.jpg
--- a/doc/src/Eqs/pressure_tensor.tex
+++ b/doc/src/Eqs/pressure_tensor.tex
@ -4,7 +4,7 @@

 $$
   P_{IJ} = \frac{\sum_{k}^{N} m_k v_{k_I} v_{k_J}}{V} + 
-   \frac{\sum_{k}^{N'} r_{k_I} f_{k_J}}{V}
+   \frac{\sum_{k}^{N} r_{k_I} f_{k_J}}{V}
 $$

 \end{document}
--- a/doc/src/JPG/pylammps_dihedral.jpg
+++ b/doc/src/JPG/pylammps_dihedral.jpg
--- a/doc/src/JPG/pylammps_mc_disordered.jpg
+++ b/doc/src/JPG/pylammps_mc_disordered.jpg
--- a/doc/src/JPG/pylammps_mc_energies_plot.jpg
+++ b/doc/src/JPG/pylammps_mc_energies_plot.jpg
--- a/doc/src/JPG/pylammps_mc_minimum.jpg
+++ b/doc/src/JPG/pylammps_mc_minimum.jpg
--- a/doc/src/JPG/tutorial_additional_changes.png
+++ b/doc/src/JPG/tutorial_additional_changes.png
--- a/doc/src/JPG/tutorial_automated_checks.png
+++ b/doc/src/JPG/tutorial_automated_checks.png
--- a/doc/src/JPG/tutorial_automated_checks_passed.png
+++ b/doc/src/JPG/tutorial_automated_checks_passed.png
--- a/doc/src/JPG/tutorial_branch.png
+++ b/doc/src/JPG/tutorial_branch.png
--- a/doc/src/JPG/tutorial_changes_others.png
+++ b/doc/src/JPG/tutorial_changes_others.png
--- a/doc/src/JPG/tutorial_create_new_pull_request1.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request1.png
--- a/doc/src/JPG/tutorial_create_new_pull_request2.png
+++ b/doc/src/JPG/tutorial_create_new_pull_request2.png
--- a/doc/src/JPG/tutorial_edits_maintainers.png
+++ b/doc/src/JPG/tutorial_edits_maintainers.png
--- a/doc/src/JPG/tutorial_fork.png
+++ b/doc/src/JPG/tutorial_fork.png
--- a/doc/src/JPG/tutorial_https_block.png
+++ b/doc/src/JPG/tutorial_https_block.png
--- a/doc/src/JPG/tutorial_merged.png
+++ b/doc/src/JPG/tutorial_merged.png
--- a/doc/src/JPG/tutorial_new_pull_request.png
+++ b/doc/src/JPG/tutorial_new_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request.png
--- a/doc/src/JPG/tutorial_reverse_pull_request2.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request2.png
--- a/doc/src/JPG/tutorial_reverse_pull_request3.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request3.png
--- a/doc/src/JPG/tutorial_reverse_pull_request4.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request4.png
--- a/doc/src/JPG/tutorial_reverse_pull_request5.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request5.png
--- a/doc/src/JPG/tutorial_reverse_pull_request6.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request6.png
--- a/doc/src/JPG/tutorial_reverse_pull_request7.png
+++ b/doc/src/JPG/tutorial_reverse_pull_request7.png
--- a/doc/src/JPG/tutorial_steve_assignee.png
+++ b/doc/src/JPG/tutorial_steve_assignee.png
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="26 Jan 2017 version">
+<META NAME="docnumber" CONTENT="27 Oct 2016 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-26 Jan 2017 version :c,h4
+27 Oct 2016 version :c,h4

 Version info: :h4

--- a/doc/src/PDF/USER-CGDNA-overview.pdf
+++ b/doc/src/PDF/USER-CGDNA-overview.pdf
--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -531,8 +531,7 @@ package"_Section_start.html#start_3.
 "dump nc"_dump_nc.html,
 "dump nc/mpiio"_dump_nc.html,
 "group2ndx"_group2ndx.html,
-"ndx2group"_group2ndx.html,
-"temper/grem"_temper_grem.html :tb(c=3,ea=c)
+"ndx2group"_group2ndx.html :tb(c=3,ea=c)

 :line

@ -581,9 +580,8 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "indent"_fix_indent.html,
 "langevin (k)"_fix_langevin.html,
 "lineforce"_fix_lineforce.html,
-"momentum (k)"_fix_momentum.html,
+"momentum"_fix_momentum.html,
 "move"_fix_move.html,
-"mscg"_fix_mscg.html,
 "msst"_fix_msst.html,
 "neb"_fix_neb.html,
 "nph (ko)"_fix_nh.html,
@ -634,10 +632,10 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "rigid/nve (o)"_fix_rigid.html,
 "rigid/nvt (o)"_fix_rigid.html,
 "rigid/small (o)"_fix_rigid.html,
-"rigid/small/nph (o)"_fix_rigid.html,
-"rigid/small/npt (o)"_fix_rigid.html,
-"rigid/small/nve (o)"_fix_rigid.html,
-"rigid/small/nvt (o)"_fix_rigid.html,
+"rigid/small/nph"_fix_rigid.html,
+"rigid/small/npt"_fix_rigid.html,
+"rigid/small/nve"_fix_rigid.html,
+"rigid/small/nvt"_fix_rigid.html,
 "setforce (k)"_fix_setforce.html,
 "shake"_fix_shake.html,
 "spring"_fix_spring.html,
@ -689,7 +687,6 @@ package"_Section_start.html#start_3.
 "eos/table/rx"_fix_eos_table_rx.html,
 "flow/gauss"_fix_flow_gauss.html,
 "gle"_fix_gle.html,
-"grem"_fix_grem.html,
 "imd"_fix_imd.html,
 "ipi"_fix_ipi.html,
 "langevin/drude"_fix_langevin_drude.html,
@ -702,10 +699,7 @@ package"_Section_start.html#start_3.
 "meso"_fix_meso.html,
 "manifoldforce"_fix_manifoldforce.html,
 "meso/stationary"_fix_meso_stationary.html,
-"nve/dot"_fix_nve_dot.html,
-"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
 "nve/manifold/rattle"_fix_nve_manifold_rattle.html,
-"nvk"_fix_nvk.html,
 "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
 "nph/eff"_fix_nh_eff.html,
 "npt/eff"_fix_nh_eff.html,
@ -771,7 +765,6 @@ KOKKOS, o = USER-OMP, t = OPT.
 "erotate/sphere"_compute_erotate_sphere.html,
 "erotate/sphere/atom"_compute_erotate_sphere_atom.html,
 "event/displace"_compute_event_displace.html,
-"global/atom"_compute_global_atom.html,
 "group/group"_compute_group_group.html,
 "gyration"_compute_gyration.html,
 "gyration/chunk"_compute_gyration_chunk.html,
@ -893,8 +886,6 @@ KOKKOS, o = USER-OMP, t = OPT.
 "body"_pair_body.html,
 "bop"_pair_bop.html,
 "born (go)"_pair_born.html,
-"born/coul/dsf"_pair_born.html,
-"born/coul/dsf/cs"_pair_born.html,
 "born/coul/long (go)"_pair_born.html,
 "born/coul/long/cs"_pair_born.html,
 "born/coul/msm (o)"_pair_born.html,
@ -918,10 +909,10 @@ KOKKOS, o = USER-OMP, t = OPT.
 "coul/msm"_pair_coul.html,
 "coul/streitz"_pair_coul.html,
 "coul/wolf (ko)"_pair_coul.html,
-"dpd (go)"_pair_dpd.html,
-"dpd/tstat (go)"_pair_dpd.html,
+"dpd (o)"_pair_dpd.html,
+"dpd/tstat (o)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
-"eam (gkiot)"_pair_eam.html,
+"eam (gkot)"_pair_eam.html,
 "eam/alloy (gkot)"_pair_eam.html,
 "eam/fs (gkot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
@ -988,12 +979,11 @@ KOKKOS, o = USER-OMP, t = OPT.
 "table (gko)"_pair_table.html,
 "tersoff (gkio)"_pair_tersoff.html,
 "tersoff/mod (gko)"_pair_tersoff_mod.html,
-"tersoff/mod/c (o)"_pair_tersoff_mod.html,
 "tersoff/zbl (gko)"_pair_tersoff_zbl.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
 "tri/lj"_pair_tri_lj.html,
-"vashishta (ko)"_pair_vashishta.html,
+"vashishta (o)"_pair_vashishta.html,
 "vashishta/table (o)"_pair_vashishta.html,
 "yukawa (go)"_pair_yukawa.html,
 "yukawa/colloid (go)"_pair_yukawa_colloid.html,
@ -1003,7 +993,6 @@ These are additional pair styles in USER packages, which can be used
 if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

-"agni (o)"_pair_agni.html,
 "awpmd/cut"_pair_awpmd.html,
 "buck/mdf"_pair_mdf.html,
 "coul/cut/soft (o)"_pair_lj_soft.html,
@ -1037,11 +1026,6 @@ package"_Section_start.html#start_3.
 "morse/soft"_pair_morse.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx"_pair_multi_lucy_rx.html,
-"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,
 "quip"_pair_quip.html,
 "reax/c (k)"_pair_reax_c.html,
 "smd/hertz"_pair_smd_hertz.html,
@ -1090,8 +1074,7 @@ if "LAMMPS is built with the appropriate
 package"_Section_start.html#start_3.

 "harmonic/shift (o)"_bond_harmonic_shift.html,
-"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
-"oxdna/fene"_bond_oxdna_fene.html :tb(c=4,ea=c)
+"harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)

 :line

--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -55,13 +55,12 @@ LAMMPS errors are detected at setup time; others like a bond
 stretching too far may not occur until the middle of a run.

 LAMMPS tries to flag errors and print informative error messages so
-you can fix the problem.  For most errors it will also print the last
-input script command that it was processing.  Of course, LAMMPS cannot
-figure out your physics or numerical mistakes, like choosing too big a
-timestep, specifying erroneous force field coefficients, or putting 2
-atoms on top of each other!  If you run into errors that LAMMPS
-doesn't catch that you think it should flag, please send an email to
-the "developers"_http://lammps.sandia.gov/authors.html.
+you can fix the problem.  Of course, LAMMPS cannot figure out your
+physics or numerical mistakes, like choosing too big a timestep,
+specifying erroneous force field coefficients, or putting 2 atoms on
+top of each other!  If you run into errors that LAMMPS doesn't catch
+that you think it should flag, please send an email to the
+"developers"_http://lammps.sandia.gov/authors.html.

 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -1936,22 +1936,18 @@ documentation in the src/library.cpp file for details, including
 which quantities can be queried by name:

 void *lammps_extract_global(void *, char *)
-void lammps_extract_box(void *, double *, double *, 
-                        double *, double *, double *, int *, int *)
 void *lammps_extract_atom(void *, char *)
 void *lammps_extract_compute(void *, char *, int, int)
 void *lammps_extract_fix(void *, char *, int, int, int, int)
 void *lammps_extract_variable(void *, char *, char *) :pre

-void lammps_reset_box(void *, double *, double *, double, double, double)
-int lammps_set_variable(void *, char *, char *) :pre
+int lammps_set_variable(void *, char *, char *)
+double lammps_get_thermo(void *, char *) :pre

-double lammps_get_thermo(void *, char *)
 int lammps_get_natoms(void *)
 void lammps_gather_atoms(void *, double *)
 void lammps_scatter_atoms(void *, double *) :pre
-void lammps_create_atoms(void *, int, tagint *, int *, double *, double *,
-                         imageint *, int) :pre
+void lammps_create_atoms(void *, int, tagint *, int *, double *, double *) :pre

 The extract functions return a pointer to various global or per-atom
 quantities stored in LAMMPS or to values calculated by a compute, fix,
@ -1961,16 +1957,10 @@ the other extract functions, the underlying storage may be reallocated
 as LAMMPS runs, so you need to re-call the function to assure a
 current pointer or returned value(s).

-The lammps_reset_box() function resets the size and shape of the
-simulation box, e.g. as part of restoring a previously extracted and
-saved state of a simulation.
-
 The lammps_set_variable() function can set an existing string-style
 variable to a new string value, so that subsequent LAMMPS commands can
-access the variable.
-
-The lammps_get_thermo() function returns the current value of a thermo
-keyword as a double precision value.
+access the variable.  The lammps_get_thermo() function returns the
+current value of a thermo keyword as a double.

 The lammps_get_natoms() function returns the total number of atoms in
 the system and can be used by the caller to allocate space for the
@ -1983,13 +1973,10 @@ passed by the caller, to each atom owned by individual processors.

 The lammps_create_atoms() function takes a list of N atoms as input
 with atom types and coords (required), an optionally atom IDs and
-velocities and image flags.  It uses the coords of each atom to assign
-it as a new atom to the processor that owns it.  This function is
-useful to add atoms to a simulation or (in tandem with
-lammps_reset_box()) to restore a previously extracted and saved state
-of a simulation.  Additional properties for the new atoms can then be
-assigned via the lammps_scatter_atoms() or lammps_extract_atom()
-functions.
+velocities.  It uses the coords of each atom to assign it as a new
+atom to the processor that owns it.  Additional properties for the new
+atoms can be assigned via the lammps_scatter_atoms() or
+lammps_extract_atom() functions.

 The examples/COUPLE and python directories have example C++ and C and
 Python codes which show how a driver code can link to LAMMPS as a
@ -2742,7 +2729,7 @@ production runs and is only required during equilibration. This way one
 is consistent with literature (based on the code packages DL_POLY or
 GULP for instance).

-The mentioned energy transfer will typically lead to a small drift
+The mentioned energy transfer will typically lead to a a small drift
 in total energy over time.  This internal energy can be monitored
 using the "compute chunk/atom"_compute_chunk_atom.html and "compute
 temp/chunk"_compute_temp_chunk.html commands.  The internal kinetic
@ -2843,7 +2830,7 @@ temp/drude"_compute_temp_drude.html. This requires also to use the
 command {comm_modify vel yes}.

 Short-range damping of the induced dipole interactions can be achieved
-using Thole functions through the "pair style
+using Thole functions through the the "pair style
 thole"_pair_thole.html in "pair_style hybrid/overlay"_pair_hybrid.html
 with a Coulomb pair style. It may be useful to use {coul/long/cs} or
 similar from the CORESHELL package if the core and Drude particle come
--- a/doc/src/Section_intro.txt
+++ b/doc/src/Section_intro.txt
@ -366,11 +366,11 @@ complementary modeling tasks.
 "DL_POLY"_dlpoly
 "Tinker"_tinker :ul

-:link(charmm,http://www.charmm.org)
-:link(amber,http://ambermd.org)
+:link(charmm,http://www.scripps.edu/brooks)
+:link(amber,http://amber.scripps.edu)
 :link(namd,http://www.ks.uiuc.edu/Research/namd/)
 :link(nwchem,http://www.emsl.pnl.gov/docs/nwchem/nwchem.html)
-:link(dlpoly,http://www.ccp5.ac.uk/DL_POLY_CLASSIC)
+:link(dlpoly,http://www.cse.clrc.ac.uk/msi/software/DL_POLY)
 :link(tinker,http://dasher.wustl.edu/tinker)

 CHARMM, AMBER, NAMD, NWCHEM, and Tinker are designed primarily for
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -84,7 +84,7 @@ Package, Description, Author(s), Doc page, Example, Library
 "PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems
 "PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python
-"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax, lib/reax
+"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax
 "REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -
 "RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -
 "SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -
@ -1140,7 +1140,6 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc
 "USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd
 "USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -
-"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -
 "USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars
 "USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -
 "USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -
@ -1154,7 +1153,7 @@ Package, Description, Author(s), Doc page, Example, Pic/movie, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER-MISC/README, -, -, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surface, Stefan Paquay (Eindhoven U of Technology), "fix manifoldforce"_fix_manifoldforce.html, USER/manifold, "manifold"_manifold, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_VMD molfile plug-ins, Axel Kohlmeyer (Temple U), "dump molfile"_dump_molfile.html, -, -, VMD-MOLFILE
-"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc / dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
+"USER-NC-DUMP"_#USER-NC-DUMP, dump output via NetCDF, Lars Pastewka (Karlsruhe Institute of Technology, KIT), "dump nc, dump nc/mpiio"_dump_nc.html, -, -, lib/netcdf
 "USER-OMP"_#USER-OMP, OpenMP threaded styles, Axel Kohlmeyer (Temple U), "Section 5.3.4"_accelerate_omp.html, -, -, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix, Ling-Ti Kong (Shanghai Jiao Tong U), "fix phonon"_fix_phonon.html, USER/phonon, -, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling, Axel Kohlmeyer (Temple U), "fix qmmm"_fix_qmmm.html, USER/qmmm, -, lib/qmmm
@ -1285,31 +1284,6 @@ him directly if you have questions.

 :line

-USER-CGDNA package :link(USER-CGDNA),h5
-
-Contents: The CGDNA package implements coarse-grained force fields for
-single- and double-stranded DNA. This is at the moment mainly the
-oxDNA model, developed by Doye, Louis and Ouldridge at the University
-of Oxford.  The package also contains Langevin-type rigid-body
-integrators with improved stability.
-
-See these doc pages to get started:
-
-"bond_style oxdna_fene"_bond_oxdna_fene.html
-"pair_style oxdna_excv"_pair_oxdna_excv.html
-"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html :ul
-
-Supporting info: /src/USER-CGDNA/README, "bond_style
-oxdna_fene"_bond_oxdna_fene.html, "pair_style
-oxdna_excv"_pair_oxdna_excv.html, "fix
-nve/dotc/langevin"_fix_nve_dotc_langevin.html
-
-Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich
-at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk).  Contact him directly if
-you have any questions.
-
-:line
-
 USER-COLVARS package :link(USER-COLVARS),h5

 Contents: COLVARS stands for collective variables which can be used to
@ -1636,12 +1610,11 @@ and a "dump nc/mpiio"_dump_nc.html command to output LAMMPS snapshots
 in this format.  See src/USER-NC-DUMP/README for more details.

 NetCDF files can be directly visualized with the following tools:
-
 Ovito (http://www.ovito.org/). Ovito supports the AMBER convention
-and all of the above extensions. :ulb,l
+  and all of the above extensions. :ulb,l
 VMD (http://www.ks.uiuc.edu/Research/vmd/) :l
 AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains
-a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule
+  a NetCDF reader that is not present in the standard distribution of AtomEye :l,ule

 The person who created these files is Lars Pastewka at
 Karlsruhe Institute of Technology (lars.pastewka at kit.edu).
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@ -8,26 +8,19 @@

 11. Python interface to LAMMPS :h3

-LAMMPS can work together with Python in three ways.  First, Python can
+LAMMPS can work together with Python in two ways.  First, Python can
 wrap LAMMPS through the "LAMMPS library
 interface"_Section_howto.html#howto_19, so that a Python script can
 create one or more instances of LAMMPS and launch one or more
 simulations.  In Python lingo, this is "extending" Python with LAMMPS.

-Second, the low-level Python interface can be used indirectly through the
-PyLammps and IPyLammps wrapper classes in Python. These wrappers try to
-simplify the usage of LAMMPS in Python by providing an object-based interface
-to common LAMMPS functionality. It also reduces the amount of code necessary to
-parameterize LAMMPS scripts through Python and makes variables and computes
-directly accessible. See "PyLammps interface"_#py_9 for more details.
-
-Third, LAMMPS can use the Python interpreter, so that a LAMMPS input
+Second, LAMMPS can use the Python interpreter, so that a LAMMPS input
 script can invoke Python code, and pass information back-and-forth
 between the input script and Python functions you write.  The Python
 code can also callback to LAMMPS to query or change its attributes.
 In Python lingo, this is "embedding" Python in LAMMPS.

-This section describes how to use these three approaches.
+This section describes how to do both.

 11.1 "Overview of running LAMMPS from Python"_#py_1
 11.2 "Overview of using Python from a LAMMPS script"_#py_2
@ -36,8 +29,7 @@ This section describes how to use these three approaches.
 11.5 "Extending Python with MPI to run in parallel"_#py_5
 11.6 "Testing the Python-LAMMPS interface"_#py_6
 11.7 "Using LAMMPS from Python"_#py_7
-11.8 "Example Python scripts that use LAMMPS"_#py_8
-11.9 "PyLammps interface"_#py_9 :ul
+11.8 "Example Python scripts that use LAMMPS"_#py_8 :ul

 If you are not familiar with it, "Python"_http://www.python.org is a
 powerful scripting and programming language which can essentially do
@ -832,7 +824,3 @@ different visualization package options.  Click to see larger images:
 :image(JPG/screenshot_atomeye_small.jpg,JPG/screenshot_atomeye.jpg)
 :image(JPG/screenshot_pymol_small.jpg,JPG/screenshot_pymol.jpg)
 :image(JPG/screenshot_vmd_small.jpg,JPG/screenshot_vmd.jpg)
-
-11.9 PyLammps interface :link(py_9),h4
-
-Please see the "PyLammps Tutorial"_tutorial_pylammps.html.
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -706,7 +706,7 @@ future changes to LAMMPS.
 User packages, such as user-atc or user-omp, have been contributed by
 users, and always begin with the user prefix.  If they are a single
 command (single file), they are typically in the user-misc package.
-Otherwise, they are a set of files grouped together which add a
+Otherwise, they are a a set of files grouped together which add a
 specific functionality to the code.

 User packages don't necessarily meet the requirements of the standard
@ -1727,7 +1727,7 @@ thermodynamic state and a total run time for the simulation.  It then
 appends statistics about the CPU time and storage requirements for the
 simulation.  An example set of statistics is shown here:

-Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms :pre
+Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms

 Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
 97.0% CPU use with 4 MPI tasks x no OpenMP threads :pre
@ -1757,14 +1757,14 @@ Ave special neighs/atom = 2.34032
 Neighbor list builds = 26
 Dangerous builds = 0 :pre

-The first section provides a global loop timing summary. The {loop time}
+The first section provides a global loop timing summary. The loop time
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
-continuations required and for comparing performance with other,
-similar MD codes.  The {CPU use} line provides the CPU utilzation per
+continuations required and for comparing performance with other
+similar MD codes.  The CPU use line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
-threads (or 1 of no OpenMP). Lower numbers correspond to delays due
-to file I/O or insufficient thread utilization.
+threads (or 1). Lower numbers correspond to delays due to file I/O or
+insufficient thread utilization.

 The MPI task section gives the breakdown of the CPU run time (in
 seconds) into major categories:
@ -1791,7 +1791,7 @@ is present that also prints the CPU utilization in percent. In
 addition, when using {timer full} and the "package omp"_package.html
 command are active, a similar timing summary of time spent in threaded
 regions to monitor thread utilization and load balance is provided. A
-new entry is the {Reduce} section, which lists the time spent in
+new entry is the {Reduce} section, which lists the time spend in
 reducing the per-thread data elements to the storage for non-threaded
 computation. These thread timings are taking from the first MPI rank
 only and and thus, as the breakdown for MPI tasks can change from MPI
--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,7 +29,7 @@ Bond Styles: fene, harmonic :l
 Dihedral Styles: charmm, harmonic, opls :l
 Fixes: nve, npt, nvt, nvt/sllod :l
 Improper Styles: cvff, harmonic :l
-Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne,
+Pair Styles: buck/coul/cut, buck/coul/long, buck, gayberne,
 charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l
 K-Space Styles: pppm :l
 :ule
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -110,14 +110,14 @@ mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj   # ditto on 8 Phis :p
 [Required hardware/software:]

 Kokkos support within LAMMPS must be built with a C++11 compatible
-compiler.  If using gcc, version 4.7.2 or later is required.
+compiler.  If using gcc, version 4.8.1 or later is required.

 To build with Kokkos support for CPUs, your compiler must support the
 OpenMP interface.  You should have one or more multi-core CPUs so that
 multiple threads can be launched by each MPI task running on a CPU.

 To build with Kokkos support for NVIDIA GPUs, NVIDIA Cuda software
-version 7.5 or later must be installed on your system.  See the
+version 6.5 or later must be installed on your system.  See the
 discussion for the "GPU"_accelerate_gpu.html package for details of
 how to check and do this.

--- a/doc/src/angle_charmm.txt
+++ b/doc/src/angle_charmm.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine.txt
+++ b/doc/src/angle_cosine.txt
@ -61,7 +61,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_delta.txt
+++ b/doc/src/angle_cosine_delta.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_periodic.txt
+++ b/doc/src/angle_cosine_periodic.txt
@ -74,7 +74,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_cosine_squared.txt
+++ b/doc/src/angle_cosine_squared.txt
@ -66,7 +66,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/angle_harmonic.txt
+++ b/doc/src/angle_harmonic.txt
@ -65,11 +65,11 @@ more instructions on how to use the accelerated styles effectively.

 :line

-[Restrictions:]
+[Restrictions:] none

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+MOLECULE package (which it is by default).  See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]

--- a/doc/src/angle_hybrid.txt
+++ b/doc/src/angle_hybrid.txt
@ -76,7 +76,7 @@ for specific angle types.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other angle styles, the hybrid angle style does not store angle
--- a/doc/src/angle_table.txt
+++ b/doc/src/angle_table.txt
@ -147,7 +147,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This angle style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_fene.txt
+++ b/doc/src/bond_fene.txt
@ -70,7 +70,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_fene_expand.txt
+++ b/doc/src/bond_fene_expand.txt
@ -73,7 +73,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 You typically should specify "special_bonds fene"_special_bonds.html
--- a/doc/src/bond_harmonic.txt
+++ b/doc/src/bond_harmonic.txt
@ -65,7 +65,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_hybrid.txt
+++ b/doc/src/bond_hybrid.txt
@ -59,7 +59,7 @@ bond types.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Unlike other bond styles, the hybrid bond style does not store bond
--- a/doc/src/bond_morse.txt
+++ b/doc/src/bond_morse.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_nonlinear.txt
+++ b/doc/src/bond_nonlinear.txt
@ -64,7 +64,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bond_oxdna_fene.txt
+++ b/doc/src/bond_oxdna_fene.txt
@ -1,70 +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,Section_commands.html#comm)
-
-:line
-
-bond_style oxdna_fene command :h3
-
-[Syntax:]
-
-bond_style oxdna_fene :pre
-
-[Examples:]
-
-bond_style oxdna_fene
-bond_coeff * 2.0 0.25 0.7525 :pre
-
-[Description:]
-
-The {oxdna_fene} bond style uses the potential
-
-:c,image(Eqs/bond_oxdna_fene.jpg)
-
-to define a modified finite extensible nonlinear elastic (FENE) potential
-"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
-in the oxDNA force field for coarse-grained modelling of DNA. 
-
-The following coefficients must be defined for the bond type via the
-"bond_coeff"_bond_coeff.html command as given in the above example, or in
-the data file or restart files read by the "read_data"_read_data.html
-or "read_restart"_read_restart.html commands:
-
-epsilon (energy)
-Delta (distance)
-r0 (distance) :ul
-
-NOTE: This bond style has to be used together with the corresponding oxDNA pair styles
-for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}
-and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 
-"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
-
-Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.
-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/.
-A technical report with more information on the model, the structure of the input file,
-the setup tool and the performance of the LAMMPS-implementation of oxDNA
-can be found "here"_PDF/USER-CGDNA-overview.pdf.
-
-:line
-
-[Restrictions:]
-
-This bond style can only be used if LAMMPS was built with the
-USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making
-LAMMPS"_Section_start.html#start_3 section for more info on packages.
-
-
-[Related commands:]
-
-"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 
-
-[Default:] none
-
-:line
-
-:link(oxdna_fene)
-[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).
--- a/doc/src/bond_quartic.txt
+++ b/doc/src/bond_quartic.txt
@ -99,7 +99,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 The {quartic} style requires that "special_bonds"_special_bonds.html
--- a/doc/src/bond_table.txt
+++ b/doc/src/bond_table.txt
@ -144,7 +144,7 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 This bond style can only be used if LAMMPS was built with the
-MOLECULE package.  See the "Making
+MOLECULE package (which it is by default).  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info on packages.

 [Related commands:]
--- a/doc/src/bonds.txt
+++ b/doc/src/bonds.txt
@ -15,7 +15,6 @@ Bond Styles :h1
   bond_morse
   bond_none
   bond_nonlinear
-   bond_oxdna_fene
   bond_quartic
   bond_table
   bond_zero
--- a/doc/src/commands.txt
+++ b/doc/src/commands.txt
@ -91,7 +91,6 @@ Commands :h1
   suffix
   tad
   temper
-   temper_grem
   thermo
   thermo_modify
   thermo_style
--- a/doc/src/compute_bond_local.txt
+++ b/doc/src/compute_bond_local.txt
@ -51,12 +51,12 @@ relative to the center of mass (COM) velocity of the 2 atoms in the
 bond.

 The value {engvib} is the vibrational kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms along the bond
 direction, after the COM velocity has been subtracted from each.

 The value {engrot} is the rotationsl kinetic energy of the two atoms
-in the bond, which is simply 1/2 m1 v1^2 + 1/2 m2 v2^2, where v1 and
+in the bond, which is simply 1/2 m1 v1^2 + 1/2 m1 v2^2, where v1 and
 v2 are the magnitude of the velocity of the 2 atoms perpendicular to
 the bond direction, after the COM velocity has been subtracted from
 each.
@ -67,7 +67,7 @@ Vcm^2 where Vcm = magnitude of the velocity of the COM.

 Note that these 3 kinetic energy terms are simply a partitioning of
 the summed kinetic energy of the 2 atoms themselves.  I.e. total KE =
-1/2 m1 v1^2 + 1/2 m2 v2^2 = engvib + engrot + engtrans, where v1,v2
+1/2 m1 v1^2 + 1/2 m2 v3^2 = engvib + engrot + engtrans, where v1,v2
 are the magnitude of the velocities of the 2 atoms, without any
 adjustment for the COM velocity.

--- a/doc/src/compute_centro_atom.txt
+++ b/doc/src/compute_centro_atom.txt
@ -114,7 +114,7 @@ local defects surrounding the central atom, as described above.  For
 the {axes yes} case, the vector components are also unitless, since
 they represent spatial directions.

-Here are typical centro-symmetry values, from a nanoindentation
+Here are typical centro-symmetry values, from a a nanoindentation
 simulation into gold (FCC).  These were provided by Jon Zimmerman
 (Sandia):

--- a/doc/src/compute_chunk_atom.txt
+++ b/doc/src/compute_chunk_atom.txt
@ -536,7 +536,7 @@ For the {bin/cylinder} style the details are as follows.  If {discard}
 is set to {yes}, an out-of-domain atom will have its chunk ID set to
 0.  If {discard} is set to {no}, the atom will have its chunk ID set
 to the first or last bin in both the radial and axis dimensions.  If
-{discard} is set to {mixed}, which is the default, the radial
+{discard} is set to {mixed}, which is the default, the the radial
 dimension is treated the same as for {discard} = no.  But for the axis
 dimensinon, it will only have its chunk ID set to the first or last
 bin if bins extend to the simulation box boundary in the axis
@ -641,8 +641,7 @@ the restarted simulation begins.

 [Related commands:]

-"fix ave/chunk"_fix_ave_chunk.html,
-"compute global/atom"_compute_global_atom.html
+"fix ave/chunk"_fix_ave_chunk.html

 [Default:]

--- a/doc/src/compute_cluster_atom.txt
+++ b/doc/src/compute_cluster_atom.txt
@ -37,7 +37,7 @@ The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
 is dumped).  Thus it can be inefficient to compute/dump this quantity
 too frequently or to have multiple compute/dump commands, each of a
-{cluster/atom} style.
+{clsuter/atom} style.

 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
--- a/doc/src/compute_coord_atom.txt
+++ b/doc/src/compute_coord_atom.txt
@ -10,43 +10,34 @@ compute coord/atom command :h3

 [Syntax:]

-compute ID group-ID coord/atom cstyle args ... :pre
+compute ID group-ID coord/atom cutoff type1 type2 ... :pre

-ID, group-ID are documented in "compute"_compute.html command :ulb,l
-coord/atom = style name of this compute command :l
-cstyle = {cutoff} or {orientorder} :l
-  {cutoff} args = cutoff typeN
-    cutoff = distance within which to count coordination neighbors (distance units)
-    typeN = atom type for Nth coordination count (see asterisk form below)
-  {orientorder} args = orientorderID threshold
-    orientorderID = ID of an orientorder/atom compute
-    threshold = minimum value of the product of two "connected" atoms :pre
-:ule
+ID, group-ID are documented in "compute"_compute.html command
+coord/atom = style name of this compute command
+cutoff = distance within which to count coordination neighbors (distance units)
+typeN = atom type for Nth coordination count (see asterisk form below) :ul

 [Examples:]

-compute 1 all coord/atom cutoff 2.0
-compute 1 all coord/atom cutoff 6.0 1 2
-compute 1 all coord/atom cutoff 6.0 2*4 5*8 *
-compute 1 all coord/atom orientorder 2 0.5 :pre
+compute 1 all coord/atom 2.0
+compute 1 all coord/atom 6.0 1 2
+compute 1 all coord/atom 6.0 2*4 5*8 * :pre

 [Description:]

-This compute performs calculations between neighboring atoms to
-determine a coordination value.  The specific calculation and the
-meaning of the resulting value depend on the {cstyle} keyword used.
+Define a computation that calculates one or more coordination numbers
+for each atom in a group.

-The {cutoff} cstyle calculates one or more traditional coordination
-numbers for each atom.  A coordination number is defined as the number
-of neighbor atoms with specified atom type(s) that are within the
-specified cutoff distance from the central atom.  Atoms not in the
-specified group are included in the coordination number tally.
+A coordination number is defined as the number of neighbor atoms with
+specified atom type(s) that are within the specified cutoff distance
+from the central atom.  Atoms not in the group are included in a
+coordination number of atoms in the group.

-The {typeN} keywords allow specification of which atom types
-contribute to each coordination number.  One coordination number is
-computed for each of the {typeN} keywords listed.  If no {typeN}
-keywords are listed, a single coordination number is calculated, which
-includes atoms of all types (same as the "*" format, see below).
+The {typeN} keywords allow you to specify which atom types contribute
+to each coordination number.  One coordination number is computed for
+each of the {typeN} keywords listed.  If no {typeN} keywords are
+listed, a single coordination number is calculated, which includes
+atoms of all types (same as the "*" format, see below).

 The {typeN} keywords can be specified in one of two ways.  An explicit
 numeric value can be used, as in the 2nd example above.  Or a
@ -58,27 +49,8 @@ from 1 to N.  A leading asterisk means all types from 1 to n
 (inclusive).  A middle asterisk means all types from m to n
 (inclusive).

-The {orientorder} cstyle calculates the number of "connected" neighbor
-atoms J around each central atom I.  For this {cstyle}, connected is
-defined by the orientational order parameter calculated by the
-"compute orientorder/atom"_compute_orientorder_atom.html command.
-This {cstyle} thus allows one to apply the ten Wolde's criterion to
-identify crystal-like atoms in a system, as discussed in "ten
-Wolde"_#tenWolde.
-
-The ID of the previously specified "compute
-orientorder/atom"_compute_orientorder/atom command is specified as
-{orientorderID}.  The compute must invoke its {components} option to
-calculate components of the {Ybar_lm} vector for each atoms, as
-described in its documenation.  Note that orientorder/atom compute
-defines its own criteria for identifying neighboring atoms.  If the
-scalar product ({Ybar_lm(i)},{Ybar_lm(j)}), calculated by the
-orientorder/atom compute is larger than the specified {threshold},
-then I and J are connected, and the coordination value of I is
-incremented by one.
-
-For all {cstyle} settings, all coordination values will be 0.0 for
-atoms not in the specified compute group.
+The value of all coordination numbers will be 0.0 for atoms not in the
+specified compute group.

 The neighbor list needed to compute this quantity is constructed each
 time the calculation is performed (i.e. each time a snapshot of atoms
@ -100,16 +72,11 @@ the neighbor list.

 [Output info:]

-For {cstyle} cutoff, this compute can calculate a per-atom vector or
-array.  If single {type1} keyword is specified (or if none are
-specified), this compute calculates a per-atom vector.  If multiple
-{typeN} keywords are specified, this compute calculates a per-atom
-array, with N columns.
-
-For {cstyle} orientorder, this compute calculates a per-atom vector.
-
-These values can be accessed by any command that uses per-atom values
-from a compute as input.  See "Section
+If single {type1} keyword is specified (or if none are specified),
+this compute calculates a per-atom vector.  If multiple {typeN}
+keywords are specified, this compute calculates a per-atom array, with
+N columns.  These values can be accessed by any command that uses
+per-atom values from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
 options.

@ -121,12 +88,5 @@ explained above.
 [Related commands:]

 "compute cluster/atom"_compute_cluster_atom.html
-"compute orientorder/atom"_compute_orientorder_atom.html

 [Default:] none
-
-:line
-
-:link(tenWolde)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
-J. Chem. Phys. 104, 9932 (1996).
--- a/doc/src/compute_global_atom.txt
+++ b/doc/src/compute_global_atom.txt
@ -1,220 +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,Section_commands.html#comm)
-
-:line
-
-compute global/atom command :h3
-
-[Syntax:]
-
-compute ID group-ID style index input1 input2 ... :pre
-
-ID, group-ID are documented in "compute"_compute.html command :ulb,l
-global/atom = style name of this compute command :l
-index = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
-  c_ID = per-atom vector calculated by a compute with ID
-  c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
-  f_ID = per-atom vector calculated by a fix with ID
-  f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
-  v_name = per-atom vector calculated by an atom-style variable with name :pre
-one or more inputs can be listed :l
-input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
-  c_ID = global vector calculated by a compute with ID
-  c_ID\[I\] = Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
-  f_ID = global vector calculated by a fix with ID
-  f_ID\[I\] = Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
-  v_name = global vector calculated by a vector-style variable with name :pre
-:ule
-
-[Examples:]
-
-compute 1 all global/atom c_chunk c_com\[1\\] c_com\[2\\] c_com\[3\\]
-compute 1 all global/atom c_chunk c_com\[*\\] :pre
-
-[Description:]
-
-Define a calculation that assigns global values to each atom from
-vectors or arrays of global values.  The specified {index} parameter
-is used to determine which global value is assigned to each atom.
-
-The {index} parameter must reference a per-atom vector or array from a
-"compute"_compute.html or "fix"_fix.html or the evaluation of an
-atom-style "variable"_variable.html.  Each {input} value must
-reference a global vector or array from a "compute"_compute.html or
-"fix"_fix.html or the evaluation of an vector-style
-"variable"_variable.html.  Details are given below.
-
-The {index} value for an atom is used as a index I (from 1 to N) into
-the vector associated with each of the input values.  The Ith value
-from the input vector becomes one output value for that atom.  If the
-atom is not in the specified group, or the index I < 1 or I > M, where
-M is the actual length of the input vector, then an output value of
-0.0 is assigned to the atom.
-
-An example of how this command is useful, is in the context of
-"chunks" which are static or dyanmic subsets of atoms.  The "compute
-chunk/atom"_compute_chunk_atom.html command assigns unique chunk IDs
-to each atom.  It's output can be used as the {index} parameter for
-this command.  Various other computes with "chunk" in their style
-name, such as "compute com/chunk"_compute_com_chunk.html or "compute
-msd/chunk"_compute_msd_chunk.html, calculate properties for each
-chunk.  The output of these commands are global vectors or arrays,
-with one or more values per chunk, and can be used as input values for
-this command.  This command will then assign the global chunk value to
-each atom in the chunk, producing a per-atom vector or per-atom array
-as output.  The per-atom values can then be output to a dump file or
-used by any command that uses per-atom values from a compute as input,
-as discussed in "Section 6.15"_Section_howto.html#howto_15.
-
-As a concrete example, these commands will calculate the displacement
-of each atom from the center-of-mass of the molecule it is in, and
-dump those values to a dump file.  In this case, each molecule is a
-chunk.
-
-compute cc1 all chunk/atom molecule
-compute myChunk all com/chunk cc1
-compute prop all property/atom xu yu zu
-compute glob all global/atom c_cc1 c_myChunk\[*\]
-variable dx atom c_prop\[1\]-c_glob\[1\]
-variable dy atom c_prop\[2\]-c_glob\[2\]
-variable dz atom c_prop\[3\]-c_glob\[3\]
-variable dist atom sqrt(v_dx*v_dx+v_dy*v_dy+v_dz*v_dz)
-dump 1 all custom 100 tmp.dump id xu yu zu c_glob\[1\] c_glob\[2\] c_glob\[3\] &
-     v_dx v_dy v_dz v_dist
-dump_modify 1 sort id :pre
-
-You can add these commands to the bench/in.chain script to see how
-they work.
-
-:line
-
-Note that for input values from a compute or fix, the bracketed index
-I can be specified using a wildcard asterisk with the index to
-effectively specify multiple values.  This takes the form "*" or "*n"
-or "n*" or "m*n".  If N = the size of the vector (for {mode} = scalar)
-or the number of columns in the array (for {mode} = vector), then an
-asterisk with no numeric values means all indices from 1 to N.  A
-leading asterisk means all indices from 1 to n (inclusive).  A
-trailing asterisk means all indices from n to N (inclusive).  A middle
-asterisk means all indices from m to n (inclusive).
-
-Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  E.g. these 2 compute global/atom commands
-are equivalent, since the "compute com/chunk"_compute_com_chunk.html
-command creates a global array with 3 columns:
-
-compute cc1 all chunk/atom molecule
-compute com all com/chunk cc1
-compute 1 all global/atom c_cc1 c_com\[1\] c_com\[2\] c_com\[3\]
-compute 1 all global/atom c_cc1 c_com\[*\] :pre
-
-:line
-
-This section explains the {index} parameter.  Note that it must
-reference per-atom values, as contrasted with the {input} values which
-must reference global values.
-
-Note that all of these options generate floating point values.  When
-they are used as an index into the specified input vectors, they
-simple rounded down to convert the value to integer indices.  The
-final values should range from 1 to N (inclusive), since they are used
-to access values from N-length vectors.
-
-If {index} begins with "c_", a compute ID must follow which has been
-previously defined in the input script.  The compute must generate
-per-atom quantities.  See the individual "compute"_compute.html doc
-page for details.  If no bracketed integer is appended, the per-atom
-vector calculated by the compute is used.  If a bracketed integer is
-appended, the Ith column of the per-atom array calculated by the
-compute is used.  Users can also write code for their own compute
-styles and "add them to LAMMPS"_Section_modify.html.  See the
-discussion above for how I can be specified with a wildcard asterisk
-to effectively specify multiple values.
-
-If {index} begins with "f_", a fix ID must follow which has been
-previously defined in the input script.  The Fix must generate
-per-atom quantities.  See the individual "fix"_fix.html doc page for
-details.  Note that some fixes only produce their values on certain
-timesteps, which must be compatible with when compute global/atom
-references the values, else an error results.  If no bracketed integer
-is appended, the per-atom vector calculated by the fix is used.  If a
-bracketed integer is appended, the Ith column of the per-atom array
-calculated by the fix is used.  Users can also write code for their
-own fix style and "add them to LAMMPS"_Section_modify.html.  See the
-discussion above for how I can be specified with a wildcard asterisk
-to effectively specify multiple values.
-
-If {index} begins with "v_", a variable name must follow which has
-been previously defined in the input script.  It must be an
-"atom-style variable"_variable.html.  Atom-style variables can
-reference thermodynamic keywords and various per-atom attributes, or
-invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of generating per-atom quantities to use
-as {index}.
-
-:line
-
-This section explains the kinds of {input} values that can be used.
-Note that inputs reference global values, as contrasted with the
-{index} parameter which must reference per-atom values.
-
-If a value begins with "c_", a compute ID must follow which has been
-previously defined in the input script.  The compute must generate a
-global vector or array.  See the individual "compute"_compute.html doc
-page for details.  If no bracketed integer is appended, the vector
-calculated by the compute is used.  If a bracketed integer is
-appended, the Ith column of the array calculated by the compute is
-used.  Users can also write code for their own compute styles and "add
-them to LAMMPS"_Section_modify.html.  See the discussion above for how
-I can be specified with a wildcard asterisk to effectively specify
-multiple values.
-
-If a value begins with "f_", a fix ID must follow which has been
-previously defined in the input script.  The fix must generate a
-global vector or array.  See the individual "fix"_fix.html doc page
-for details.  Note that some fixes only produce their values on
-certain timesteps, which must be compatible with when compute
-global/atom references the values, else an error results.  If no
-bracketed integer is appended, the vector calculated by the fix is
-used.  If a bracketed integer is appended, the Ith column of the array
-calculated by the fix is used.  Users can also write code for their
-own fix style and "add them to LAMMPS"_Section_modify.html.  See the
-discussion above for how I can be specified with a wildcard asterisk
-to effectively specify multiple values.
-
-If a value begins with "v_", a variable name must follow which has
-been previously defined in the input script.  It must be a
-"vector-style variable"_variable.html.  Vector-style variables can
-reference thermodynamic keywords and various other attributes of
-atoms, or invoke other computes, fixes, or variables when they are
-evaluated, so this is a very general means of generating a vector of
-global quantities which the {index} parameter will reference for
-assignement of global values to atoms.
-
-:line
-
-[Output info:]
-
-If a single input is specified this compute produces a per-atom
-vector.  If multiple inputs are specified, this compute produces a
-per-atom array values, where the number of columns is equal to the
-number of inputs specified.  These values can be used by any command
-that uses per-atom vector or array values from a compute as input.
-See "Section 6.15"_Section_howto.html#howto_15 for an overview of
-LAMMPS output options.
-
-The per-atom vector or array values will be in whatever units the
-corresponsing input values are in.
-
-[Restrictions:] none
-
-[Related commands:]
-
-"compute"_compute.html, "fix"_fix.html, "variable"_variable.html,
-"compute chunk/atom"_compute_chunk_atom.html, "compute
-reduce"_compute_reduce.html
-
-[Default:] none
--- a/doc/src/compute_orientorder_atom.txt
+++ b/doc/src/compute_orientorder_atom.txt
@ -15,19 +15,17 @@ compute ID group-ID orientorder/atom keyword values ... :pre
 ID, group-ID are documented in "compute"_compute.html command :ulb,l
 orientorder/atom = style name of this compute command :l
 one or more keyword/value pairs may be appended :l
-keyword = {cutoff} or {nnn} or {degrees} or {components}
+keyword = {cutoff} or {nnn} or {degrees}
  {cutoff} value = distance cutoff
  {nnn} value = number of nearest neighbors
-  {degrees} values = nlvalues, l1, l2,...
-  {components} value = ldegree  :pre
+  {degrees} values = nlvalues, l1, l2,...  :pre

 :ule

 [Examples:]

 compute 1 all orientorder/atom
-compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5
-compute 1 all orientorder/atom degrees 4 6 components 6 nnn NULL cutoff 3.0 :pre
+compute 1 all orientorder/atom degrees 5 4 6 8 10 12 nnn NULL cutoff 1.5 :pre

 [Description:]

@ -64,21 +62,14 @@ specified distance cutoff are used.
 The optional keyword {degrees} defines the list of order parameters to
 be computed.  The first argument {nlvalues} is the number of order
 parameters. This is followed by that number of integers giving the
-degree of each order parameter. Because {Q}2 and all odd-degree order
-parameters are zero for atoms in cubic crystals (see
-"Steinhardt"_#Steinhardt), the default order parameters are {Q}4,
-{Q}6, {Q}8, {Q}10, and {Q}12. For the FCC crystal with {nnn}=12, {Q}4
-= sqrt(7/3)/8 = 0.19094....  The numerical values of all order
-parameters up to {Q}12 for a range of commonly encountered
-high-symmetry structures are given in Table I of "Mickel et
-al."_#Mickel.
-
-The optional keyword {components} will output the components of the
-normalized complex vector {Ybar_lm} of degree {ldegree}, which must be
-explicitly included in the keyword {degrees}. This option can be used
-in conjunction with "compute coord_atom"_compute_coord_atom.html to
-calculate the ten Wolde's criterion to identify crystal-like
-particles, as discussed in "ten Wolde"_#tenWolde.
+degree of each order parameter. Because {Q}2 and all odd-degree
+order parameters are zero for atoms in cubic crystals
+(see "Steinhardt"_#Steinhardt), the default order parameters
+are {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12. For the
+FCC crystal with {nnn}=12, {Q}4 = sqrt(7/3)/8 = 0.19094....
+The numerical values of all order parameters up to {Q}12
+for a range of commonly encountered high-symmetry structures are given
+in Table I of "Mickel et al."_#Mickel.

 The value of {Ql} is set to zero for atoms not in the
 specified compute group, as well as for atoms that have less than
@ -104,16 +95,8 @@ the neighbor list.

 [Output info:]

-This compute calculates a per-atom array with {nlvalues} columns,
-giving the {Ql} values for each atom, which are real numbers on the
-range 0 <= {Ql} <= 1.
-
-If the keyword {components} is set, then the real and imaginary parts
-of each component of (normalized) {Ybar_lm} will be added to the
-output array in the following order: Re({Ybar_-m}) Im({Ybar_-m})
-Re({Ybar_-m+1}) Im({Ybar_-m+1}) ... Re({Ybar_m}) Im({Ybar_m}).  This
-way, the per-atom array will have a total of {nlvalues}+2*(2{l}+1)
-columns.
+This compute calculates a per-atom array with {nlvalues} columns, giving the
+{Ql} values for each atom, which are real numbers on the range 0 <= {Ql} <= 1.

 These values can be accessed by any command that uses
 per-atom values from a compute as input.  See "Section
@ -124,25 +107,15 @@ options.

 [Related commands:]

-"compute coord/atom"_compute_coord_atom.html, "compute
-centro/atom"_compute_centro_atom.html, "compute
-hexorder/atom"_compute_hexorder_atom.html
+"compute coord/atom"_compute_coord_atom.html, "compute centro/atom"_compute_centro_atom.html, "compute hexorder/atom"_compute_hexorder_atom.html

 [Default:]

-The option defaults are {cutoff} = pair style cutoff, {nnn} = 12,
-{degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.
+The option defaults are {cutoff} = pair style cutoff, {nnn} = 12, {degrees} = 5 4 6 8 10 12 i.e. {Q}4, {Q}6, {Q}8, {Q}10, and {Q}12.

 :line

 :link(Steinhardt)
-[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti,
-Phys. Rev. B 28, 784 (1983).
-
+[(Steinhardt)] P. Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
 :link(Mickel)
-[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke,
-J. Chem. Phys. 138, 044501 (2013).
-
-:link(tenWolde)
-[(tenWolde)] P. R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel,
-J. Chem. Phys. 104, 9932 (1996).
+[(Mickel)] W. Mickel, S. C. Kapfer, G. E. Schroeder-Turkand, K. Mecke, J. Chem. Phys. 138, 044501 (2013).
--- a/doc/src/compute_pressure.txt
+++ b/doc/src/compute_pressure.txt
@ -37,18 +37,12 @@ The pressure is computed by the formula

 where N is the number of atoms in the system (see discussion of DOF
 below), Kb is the Boltzmann constant, T is the temperature, d is the
-dimensionality of the system (2 or 3 for 2d/3d), and V is the system
-volume (or area in 2d).  The second term is the virial, equal to
-dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
-manybody, and long-range interactions, where r_i and f_i are the
-position and force vector of atom i, and the black dot indicates a dot
-product.  When periodic boundary conditions are used, N' necessarily
-includes periodic image (ghost) atoms outside the central box, and the
-position and force vectors of ghost atoms are thus included in the
-summation.  When periodic boundary conditions are not used, N' = N =
-the number of atoms in the system.  "Fixes"_fix.html that impose
-constraints (e.g. the "fix shake"_fix_shake.html command) also
-contribute to the virial term.
+dimensionality of the system (2 or 3 for 2d/3d), V is the system
+volume (or area in 2d), and the second term is the virial, computed
+within LAMMPS for all pairwise as well as 2-body, 3-body, and 4-body,
+and long-range interactions.  "Fixes"_fix.html that impose constraints
+(e.g. the "fix shake"_fix_shake.html command) also contribute to the
+virial term.

 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are
@ -68,9 +62,8 @@ compute temperature or ke and/or the virial.  The {virial} keyword
 means include all terms except the kinetic energy {ke}.

 Details of how LAMMPS computes the virial efficiently for the entire
-system, including for manybody potentials and accounting for the
-effects of periodic boundary conditions are discussed in
-"(Thompson)"_#Thompson.
+system, including the effects of periodic boundary conditions is
+discussed in "(Thompson)"_#Thompson.

 The temperature and kinetic energy tensor is not calculated by this
 compute, but rather by the temperature compute specified with the
--- a/doc/src/compute_smd_contact_radius.txt
+++ b/doc/src/compute_smd_contact_radius.txt
@ -27,7 +27,7 @@ contact radius is used only to prevent particles belonging to
 different physical bodies from penetrating each other. It is used by
 the contact pair styles, e.g., smd/hertz and smd/tri_surface.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 The value of the contact radius will be 0.0 for particles not in the
--- a/doc/src/compute_smd_damage.txt
+++ b/doc/src/compute_smd_damage.txt
@ -24,7 +24,7 @@ compute 1 all smd/damage :pre
 Define a computation that calculates the damage status of SPH particles
 according to the damage model which is defined via the SMD SPH pair styles, e.g., the maximum plastic strain failure criterion.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth Mach Dynamics in LAMMPS.

 [Output Info:]

--- a/doc/src/compute_smd_hourglass_error.txt
+++ b/doc/src/compute_smd_hourglass_error.txt
@ -32,7 +32,7 @@ configuration.  This compute is only really useful for debugging the
 hourglass control mechanim which is part of the Total-Lagrangian SPH
 pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_internal_energy.txt
+++ b/doc/src/compute_smd_internal_energy.txt
@ -24,7 +24,7 @@ compute 1 all smd/internal/energy :pre
 Define a computation which outputs the per-particle enthalpy, i.e.,
 the sum of potential energy and heat.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_plastic_strain.txt
+++ b/doc/src/compute_smd_plastic_strain.txt
@ -25,7 +25,7 @@ Define a computation that outputs the equivalent plastic strain per
 particle.  This command is only meaningful if a material model with
 plasticity is defined.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_plastic_strain_rate.txt
+++ b/doc/src/compute_smd_plastic_strain_rate.txt
@ -25,7 +25,7 @@ Define a computation that outputs the time rate of the equivalent
 plastic strain.  This command is only meaningful if a material model
 with plasticity is defined.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output Info:]
--- a/doc/src/compute_smd_rho.txt
+++ b/doc/src/compute_smd_rho.txt
@ -26,7 +26,7 @@ The mass density is the mass of a particle which is constant during
 the course of a simulation, divided by its volume, which can change
 due to mechanical deformation.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_defgrad.txt
+++ b/doc/src/compute_smd_tlsph_defgrad.txt
@ -25,7 +25,7 @@ Define a computation that calculates the deformation gradient.  It is
 only meaningful for particles which interact according to the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_dt.txt
+++ b/doc/src/compute_smd_tlsph_dt.txt
@ -30,7 +30,7 @@ time step.  This calculation is performed automatically in the
 relevant SPH pair styles and this compute only serves to make the
 stable time increment accessible for output purposes.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_num_neighs.txt
+++ b/doc/src/compute_smd_tlsph_num_neighs.txt
@ -25,7 +25,7 @@ Define a computation that calculates the number of particles inside of
 the smoothing kernel radius for particles interacting via the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_shape.txt
+++ b/doc/src/compute_smd_tlsph_shape.txt
@ -26,7 +26,7 @@ associated with a particle as a rotated ellipsoid.  It is only
 meaningful for particles which interact according to the
 Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to use Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to use Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_strain.txt
+++ b/doc/src/compute_smd_tlsph_strain.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain :pre
 Define a computation that calculates the Green-Lagrange strain tensor
 for particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_strain_rate.txt
+++ b/doc/src/compute_smd_tlsph_strain_rate.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/strain/rate :pre
 Define a computation that calculates the rate of the strain tensor for
 particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_tlsph_stress.txt
+++ b/doc/src/compute_smd_tlsph_stress.txt
@ -24,7 +24,7 @@ compute 1 all smd/tlsph/stress :pre
 Define a computation that outputs the Cauchy stress tensor for
 particles interacting via the Total-Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_triangle_mesh_vertices.txt
+++ b/doc/src/compute_smd_triangle_mesh_vertices.txt
@ -25,7 +25,7 @@ Define a computation that returns the coordinates of the vertices
 corresponding to the triangle-elements of a mesh created by the "fix
 smd/wall_surface"_fix_smd_wall_surface.html.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_num_neighs.txt
+++ b/doc/src/compute_smd_ulsph_num_neighs.txt
@ -25,7 +25,7 @@ Define a computation that returns the number of neighbor particles
 inside of the smoothing kernel radius for particles interacting via
 the updated Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_strain.txt
+++ b/doc/src/compute_smd_ulsph_strain.txt
@ -24,7 +24,7 @@ compute 1 all smd/ulsph/strain :pre
 Define a computation that outputs the logarithmic strain tensor.  for
 particles interacting via the updated Lagrangian SPH pair style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_strain_rate.txt
+++ b/doc/src/compute_smd_ulsph_strain_rate.txt
@ -25,7 +25,7 @@ Define a computation that outputs the rate of the logarithmic strain
 tensor for particles interacting via the updated Lagrangian SPH pair
 style.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_ulsph_stress.txt
+++ b/doc/src/compute_smd_ulsph_stress.txt
@ -23,7 +23,7 @@ compute 1 all smd/ulsph/stress :pre

 Define a computation that outputs the Cauchy stress tensor.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_smd_vol.txt
+++ b/doc/src/compute_smd_vol.txt
@ -24,7 +24,7 @@ compute 1 all smd/vol :pre
 Define a computation that provides the per-particle volume and the sum
 of the per-particle volumes of the group for which the fix is defined.

-See "this PDF guide"_PDF/SMD_LAMMPS_userguide.pdf to using Smooth
+See "this PDF guide"_USER/smd/SMD_LAMMPS_userguide.pdf to using Smooth
 Mach Dynamics in LAMMPS.

 [Output info:]
--- a/doc/src/compute_stress_atom.txt
+++ b/doc/src/compute_stress_atom.txt
@ -60,7 +60,7 @@ produced by a small set of atoms (e.g. 4 atoms in a dihedral or 3
 atoms in a Tersoff 3-body interaction) is assigned in equal portions
 to each atom in the set.  E.g. 1/4 of the dihedral virial to each of
 the 4 atoms, or 1/3 of the fix virial due to SHAKE constraints applied
-to atoms in a water molecule via the "fix shake"_fix_shake.html
+to atoms in a a water molecule via the "fix shake"_fix_shake.html
 command.

 If no extra keywords are listed, all of the terms in this formula are
--- a/doc/src/compute_temp_asphere.txt
+++ b/doc/src/compute_temp_asphere.txt
--- a/doc/src/compute_temp_body.txt
+++ b/doc/src/compute_temp_body.txt
--- a/Show More
+++ b/Show More