diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 314260cb14bc582a5791912ac055ec50260878f1..48069d3120048e9d59ead6a3f2959be296d078de 100644
--- a/doc/src/Commands_bond.txt
+++ b/doc/src/Commands_bond.txt
@@ -9,7 +9,7 @@ Documentation"_ld - "LAMMPS Commands"_lc :c
"Fix styles"_Commands_fix.html,
"Compute styles"_Commands_compute.html,
"Pair styles"_Commands_pair.html,
-"Bond styles"_Commands_bond.html,
+"Bond styles"_Commands_bond.html#bond,
"Angle styles"_Commands_bond.html#angle,
"Dihedral styles"_Commands_bond.html#dihedral,
"Improper styles"_Commands_bond.html#improper,
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
index f9e548e26896c1143f1cead59e3c0a1effb015c3..9f7f1413147e9f13e9ce21b44457502d1d95fa87 100644
--- a/doc/src/Howto_tip4p.txt
+++ b/doc/src/Howto_tip4p.txt
@@ -31,7 +31,7 @@ using the "fix shake"_fix_shake.html command.
These are the additional parameters (in real units) to set for O and H
atoms and the water molecule to run a rigid TIP4P model with a cutoff
-"(Jorgensen)"_#Jorgensen1. Note that the OM distance is specified in
+"(Jorgensen)"_#Jorgensen5. Note that the OM distance is specified in
the "pair_style"_pair_style.html command, not as part of the pair
coefficients.
@@ -107,6 +107,6 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
-:link(Jorgensen1)
+:link(Jorgensen5)
[(Jorgensen)] Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
Phys, 79, 926 (1983).
diff --git a/doc/src/Intro_features.txt b/doc/src/Intro_features.txt
index 2bb7e25683be9bd90610193a3b265729b1eb9afa..07c549c1566a73c09d66b92b590c87d5654773d5 100644
--- a/doc/src/Intro_features.txt
+++ b/doc/src/Intro_features.txt
@@ -20,7 +20,7 @@ classes of functionality:
"Integrators"_#integrate
"Diagnostics"_#diag
"Output"_#output
-"Multi-replica models"_#replica
+"Multi-replica models"_#replica1
"Pre- and post-processing"_#prepost
"Specialized features (beyond MD itself)"_#special :ul
@@ -154,7 +154,7 @@ Output :h4,link(output)
time averaging of system-wide quantities
atom snapshots in native, XYZ, XTC, DCD, CFG formats :ul
-Multi-replica models :h4,link(replica)
+Multi-replica models :h4,link(replica1)
"nudged elastic band"_neb.html
"parallel replica dynamics"_prd.html
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index a5e8b63640be29f7212d66e1d6b42ceb66747a41..5a70be5c50a19726817af4bf25a60e5f1e0c85ea 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -8,6 +8,8 @@
<BODY>
+<H1></H1>
+
<!-- END_HTML_ONLY -->
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
@@ -18,8 +20,6 @@
:line
-<H1></H1>
-
LAMMPS Documentation :c,h1
2 Aug 2018 version :c,h2
@@ -71,6 +71,7 @@ every LAMMPS command.
:name: userdoc
:includehidden:
+ Manual_version
Intro
Section_start
Commands
@@ -82,6 +83,7 @@ every LAMMPS command.
Modify
Python
Errors
+ Build_manual
.. toctree::
:caption: Index
diff --git a/doc/src/Packages_details.txt b/doc/src/Packages_details.txt
index eb92fe4dc4c27506cf41b250f7a3dce49e159941..8b28002c2e51ce7fd23782cf78954eb105039df4 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -49,7 +49,7 @@ as contained in the file name.
"PYTHON"_#PYTHON,
"QEQ"_#QEQ,
"REAX"_#REAX,
-"REPLICA"_#REPLICA,
+"REPLICA"_#REPLICA2,
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
@@ -392,7 +392,7 @@ src/GPU: filenames -> commands
src/GPU/README
lib/gpu/README
"Speed packages"_Speed_packages.html
-"Speed gpu"_Speed_gpu.html.html
+"Speed gpu"_Speed_gpu.html
"Section 2.6 -sf gpu"_Section_start.html#start_6
"Section 2.6 -pk gpu"_Section_start.html#start_6
"package gpu"_package.html
@@ -1225,7 +1225,7 @@ examples/reax :ul
:line
-REPLICA package :link(REPLICA),h4
+REPLICA package :link(REPLICA2),h4
[Contents:]
@@ -1373,7 +1373,7 @@ make machine :pre
[Supporting info:]
src/SPIN: filenames -> commands
-"Howto spin"_Howto_spin.html
+"Howto spins"_Howto_spins.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
diff --git a/doc/src/Packages_standard.txt b/doc/src/Packages_standard.txt
index 7e6434560244abfce710c182af2c4fb6cad31da6..56ec693185ec715a40ac7b3b03085b000ab8cba8 100644
--- a/doc/src/Packages_standard.txt
+++ b/doc/src/Packages_standard.txt
@@ -57,9 +57,9 @@ Package, Description, Doc page, Example, Library
"PYTHON"_Packages_details.html#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
"QEQ"_Packages_details.html#QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, -
"REAX"_Packages_details.html#REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
-"REPLICA"_Packages_details.html#REPLICA, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
+"REPLICA"_Packages_details.html#REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, -
"RIGID"_Packages_details.html#RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, -
"SHOCK"_Packages_details.html#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
"SNAP"_Packages_details.html#SNAP, quantum-fitted potential, "pair_style snap"_pair_snap.html, snap, -
-"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spin"_Howto_spin.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
+"SPIN"_#SPIN, magnetic atomic spin dynamics, "Howto spins"_Howto_spins.html, SPIN, -"SRD"_Packages_details.html#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
"VORONOI"_Packages_details.html#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
diff --git a/doc/src/Python_install.txt b/doc/src/Python_install.txt
index 6591360ae2535935f0c9e88e8bf6bc2c830f6cb0..85cf267de06f543d092114e473eff44aa3149006 100644
--- a/doc/src/Python_install.txt
+++ b/doc/src/Python_install.txt
@@ -68,7 +68,7 @@ need to prefix this with "sudo". In this mode you cannot control
which Python is invoked by root.
Note that if you want Python to be able to load different versions of
-the LAMMPS shared library (see "this section"_#py_5 below), you will
+the LAMMPS shared library (see "this section"_Python_shlib.html), you will
need to manually copy files like liblammps_g++.so into the appropriate
system directory. This is not needed if you set the LD_LIBRARY_PATH
environment variable as described above.
diff --git a/doc/src/Python_shlib.txt b/doc/src/Python_shlib.txt
index 1a921e4025cde5cc1376c603a4beb2cf5c4c58fb..c3b81fa342328c388d3158ba049f4ffa9ff9126a 100644
--- a/doc/src/Python_shlib.txt
+++ b/doc/src/Python_shlib.txt
@@ -31,4 +31,5 @@ extra libraries must also be shared libraries. If the LAMMPS
shared-library build fails with an error complaining about this, see
"Section 2.4"_Section_start.html#start_4 for more details.
-Also include CMake info on this
+TODO: Also include CMake info on this
+
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index aa32a875bfe2f77de00cdbee7f87085af8443a94..2159d6211ae27aa20967e1b02601f10412bfc733 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -24,7 +24,7 @@ fix constrain all manifoldforce sphere 5.0
[Description:]
-This fix subtracts each time step from the force the component along the normal of the specified "manifold"_manifolds.html.
+This fix subtracts each time step from the force the component along the normal of the specified "manifold"_Howto_manifold.html.
This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 136ed6c15e6ecb9de65599eb41a821d6487bbf69..8a70cd8213ccc223c279e6961bf31b059c2dbf1d 100644
--- a/doc/src/fix_property_atom.txt
+++ b/doc/src/fix_property_atom.txt
@@ -200,7 +200,8 @@ added classes.
:line
-:link(isotopes) Example for using per-atom masses with TIP4P water to
+:link(isotopes)
+Example for using per-atom masses with TIP4P water to
study isotope effects. When setting up simulations with the "TIP4P
pair styles"_Howto_tip4p.html for water, you have to provide exactly
one atom type each to identify the water oxygen and hydrogen
diff --git a/doc/src/fix_wall_reflect.txt b/doc/src/fix_wall_reflect.txt
index 78be84eb638224ec631841fabc022bf0700a5162..e35fac6eeb8093dad0fa1d3ea89f5ccbf27de11d 100644
--- a/doc/src/fix_wall_reflect.txt
+++ b/doc/src/fix_wall_reflect.txt
@@ -51,7 +51,7 @@ corresponding component of its velocity is flipped.
When used in conjunction with "fix nve"_fix_nve.html and "run_style
verlet"_run_style.html, the resultant time-integration algorithm is
equivalent to the primitive splitting algorithm (PSA) described by
-"Bond"_#Bond. Because each reflection event divides
+"Bond"_#Bond1. Because each reflection event divides
the corresponding timestep asymmetrically, energy conservation is only
satisfied to O(dt), rather than to O(dt^2) as it would be for
velocity-Verlet integration without reflective walls.
@@ -179,5 +179,5 @@ error.
:line
-:link(Bond)
+:link(Bond1)
[(Bond)] Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).