diff --git a/doc/src/Build_manual.txt b/doc/src/Build_manual.txt
new file mode 100644
index 0000000000..695ac21a13
--- /dev/null
+++ b/doc/src/Build_manual.txt
@@ -0,0 +1,125 @@
+"Previous Section"_Errors.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Manual.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Building the LAMMPS Manual :h2
+
+Depending on how you obtained LAMMPS, the doc directory has
+2 or 3 sub-directories and optionally 2 PDF files and an ePUB file:
+
+src # content files for LAMMPS documentation
+html # HTML version of the LAMMPS manual (see html/Manual.html)
+tools # tools and settings for building the documentation
+Manual.pdf # large PDF version of entire manual
+Developer.pdf # small PDF with info about how LAMMPS is structured
+LAMMPS.epub # Manual in ePUB format :pre
+
+If you downloaded LAMMPS as a tarball from the web site, all these
+directories and files should be included.
+
+If you downloaded LAMMPS from the public SVN or Git repositories, then
+the HTML and PDF files are not included. Instead you need to create
+them, in one of three ways:
+
+(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
+site. Just type "make fetch". This should create a html_www dir and
+Manual_www.pdf/Developer_www.pdf files. Note that if new LAMMPS
+features have been added more recently than the date of your version,
+the fetched documentation will include those changes (but your source
+code will not, unless you update your local repository).
+
+(b) You can build the HTML and PDF files yourself, by typing "make
+html" followed by "make pdf". Note that the PDF make requires the
+HTML files already exist. This requires various tools including
+Sphinx, which the build process will attempt to download and install
+on your system, if not already available. See more details below.
+
+(c) You can genererate an older, simpler, less-fancy style of HTML
+documentation by typing "make old". This will create an "old"
+directory. This can be useful if (b) does not work on your box for
+some reason, or you want to quickly view the HTML version of a doc
+page you have created or edited yourself within the src directory.
+E.g. if you are planning to submit a new feature to LAMMPS.
+
+:line
+
+The generation of all documentation is managed by the Makefile in
+the doc dir.
+
+Documentation Build Options: :pre
+
+make html # generate HTML in html dir using Sphinx
+make pdf # generate 2 PDF files (Manual.pdf,Developer.pdf)
+ # in doc dir via htmldoc and pdflatex
+make old # generate old-style HTML pages in old dir via txt2html
+make fetch # fetch HTML doc pages and 2 PDF files from web site
+ # as a tarball and unpack into html dir and 2 PDFs
+make epub # generate LAMMPS.epub in ePUB format using Sphinx
+make clean # remove intermediate RST files created by HTML build
+make clean-all # remove entire build folder and any cached data :pre
+
+:line
+
+Installing prerequisites for HTML build :h3
+
+To run the HTML documention build toolchain, Python 3 and virtualenv
+have to be installed. Here are instructions for common setups:
+
+Ubuntu :h4
+
+sudo apt-get install python-virtualenv :pre
+
+Fedora (up to version 21) and Red Hat Enterprise Linux or CentOS (up to version 7.x) :h4
+
+sudo yum install python3-virtualenv :pre
+
+Fedora (since version 22) :h4
+
+sudo dnf install python3-virtualenv pre
+
+MacOS X :h4
+
+Python 3 :h5
+
+Download the latest Python 3 MacOS X package from
+"https://www.python.org"_https://www.python.org
+and install it. This will install both Python 3
+and pip3.
+
+virtualenv :h5
+
+Once Python 3 is installed, open a Terminal and type
+
+pip3 install virtualenv :pre
+
+This will install virtualenv from the Python Package Index.
+
+:line
+
+Installing prerequisites for PDF build
+
+[TBA]
+
+:line
+
+Installing prerequisites for epub build :h3
+
+ePUB :h4
+
+Same as for HTML. This uses the same tools and configuration
+files as the HTML tree.
+
+For converting the generated ePUB file to a mobi format file
+(for e-book readers like Kindle, that cannot read ePUB), you
+also need to have the 'ebook-convert' tool from the "calibre"
+software installed. "http://calibre-ebook.com/"_http://calibre-ebook.com/
+You first create the ePUB file with 'make epub' and then do:
+
+ebook-convert LAMMPS.epub LAMMPS.mobi :pre
+
diff --git a/doc/src/Commands_bond.txt b/doc/src/Commands_bond.txt
index 314260cb14..48069d3120 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/Errors_common.txt b/doc/src/Errors_common.txt
index 8f26b22b3a..d82114bd38 100644
--- a/doc/src/Errors_common.txt
+++ b/doc/src/Errors_common.txt
@@ -93,7 +93,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
-could be a bug (see "this section"_#err_2) or one of the following
+could be a bug (see "this section"_Errors_bugs.html) or one of the following
cases:
LAMMPS runs in the available memory a processor allows to be
diff --git a/doc/src/Howto_bioFF.txt b/doc/src/Howto_bioFF.txt
index afb8a84f2e..deb5b31441 100644
--- a/doc/src/Howto_bioFF.txt
+++ b/doc/src/Howto_bioFF.txt
@@ -96,6 +96,10 @@ documentation for the formula it computes.
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
+:link(howto-Cornell)
+[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
+Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
+
:link(howto-Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
diff --git a/doc/src/Howto_tip4p.txt b/doc/src/Howto_tip4p.txt
index f9e548e268..9f7f141314 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 2bb7e25683..07c549c156 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 a3747465cd..ec85547dec 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -8,6 +8,8 @@
+
+
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
@@ -18,8 +20,6 @@
:line
-
-
LAMMPS Documentation :c,h1
2 Aug 2018 version :c,h2
@@ -71,6 +71,7 @@ every LAMMPS command.
:name: userdoc
:includehidden:
+ Manual_version
Intro
Install
Build
@@ -84,6 +85,7 @@ 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 1dbde273b4..033e70dbc1 100644
--- a/doc/src/Packages_details.txt
+++ b/doc/src/Packages_details.txt
@@ -56,7 +56,7 @@ as contained in the file name.
"PYTHON"_#PYTHON,
"QEQ"_#QEQ,
"REAX"_#REAX,
-"REPLICA"_#REPLICA,
+"REPLICA"_#REPLICA2,
"RIGID"_#RIGID,
"SHOCK"_#SHOCK,
"SNAP"_#SNAP,
@@ -294,7 +294,7 @@ 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"_Run_options.html
"Section 2.6 -pk gpu"_Run_options.html
"package gpu"_package.html
@@ -831,7 +831,7 @@ examples/reax :ul
:line
-REPLICA package :link(REPLICA),h4
+REPLICA package :link(REPLICA2),h4
[Contents:]
@@ -937,7 +937,7 @@ the usual manner via MD. Various pair, fix, and compute styles.
[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 7e64345602..56ec693185 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 6591360ae2..85cf267de0 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/Tools.txt b/doc/src/Tools.txt
index 85ee531cfd..aa4adb7dc1 100644
--- a/doc/src/Tools.txt
+++ b/doc/src/Tools.txt
@@ -77,7 +77,7 @@ own sub-directories with their own Makefiles and/or README files.
:line
:line
-amber2lmp tool :h4,link(amber)
+amber2lmp tool :h3,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
@@ -92,7 +92,7 @@ necessary modifications yourself.
:line
-binary2txt tool :h4,link(binary)
+binary2txt tool :h3,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
@@ -105,7 +105,7 @@ since binary files are not compatible across all platforms.
:line
-ch2lmp tool :h4,link(charmm)
+ch2lmp tool :h3,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
@@ -130,7 +130,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
:line
-chain tool :h4,link(chain)
+chain tool :h3,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
@@ -147,7 +147,7 @@ for the "chain benchmark"_Speed_bench.html.
:line
-colvars tools :h4,link(colvars)
+colvars tools :h3,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
@@ -169,7 +169,7 @@ gmail.com) at ICTP, Italy.
:line
-createatoms tool :h4,link(createatoms)
+createatoms tool :h3,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
@@ -182,7 +182,7 @@ The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
-doxygen tool :h4,link(doxygen)
+doxygen tool :h3,link(doxygen)
The tools/doxygen directory contains a shell script called
doxygen.sh which can generate a call graph and API lists using
@@ -194,7 +194,7 @@ The tool is authored by Nandor Tamaskovics, numericalfreedom at googlemail.com.
:line
-drude tool :h4,link(drude)
+drude tool :h3,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
@@ -207,7 +207,7 @@ at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
-eam database tool :h4,link(eamdb)
+eam database tool :h3,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
@@ -223,7 +223,7 @@ X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
:line
-eam generate tool :h4,link(eamgn)
+eam generate tool :h3,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
@@ -236,7 +236,7 @@ The source files and potentials were provided by Gerolf Ziegenhain
:line
-eff tool :h4,link(eff)
+eff tool :h3,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
@@ -247,7 +247,7 @@ These tools were provided by Andres Jaramillo-Botero at CalTech
:line
-emacs tool :h4,link(emacs)
+emacs tool :h3,link(emacs)
The tools/emacs directory contains an Emacs Lisp add-on file for GNU Emacs
that enables a lammps-mode for editing input scripts when using GNU Emacs,
@@ -258,7 +258,7 @@ These tools were provided by Aidan Thompson at Sandia
:line
-fep tool :h4,link(fep)
+fep tool :h3,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
@@ -271,7 +271,7 @@ See README file in the tools/fep directory.
:line
-i-pi tool :h4,link(ipi)
+i-pi tool :h3,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
@@ -288,7 +288,7 @@ calculations with LAMMPS.
:line
-ipp tool :h4,link(ipp)
+ipp tool :h3,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
@@ -302,7 +302,7 @@ tools/createatoms tool's input file.
:line
-kate tool :h4,link(kate)
+kate tool :h3,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
@@ -313,7 +313,7 @@ The file was provided by Alessandro Luigi Sellerio
:line
-lmp2arc tool :h4,link(arc)
+lmp2arc tool :h3,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
@@ -329,7 +329,7 @@ Greathouse at Sandia (jagreat at sandia.gov).
:line
-lmp2cfg tool :h4,link(cfg)
+lmp2cfg tool :h3,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
@@ -340,7 +340,7 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
-matlab tool :h4,link(matlab)
+matlab tool :h3,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
@@ -358,7 +358,7 @@ These scripts were written by Arun Subramaniyan at Purdue Univ
:line
-micelle2d tool :h4,link(micelle)
+micelle2d tool :h3,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
@@ -375,7 +375,7 @@ definition file. This tool was used to create the system for the
:line
-moltemplate tool :h4,link(moltemplate)
+moltemplate tool :h3,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
@@ -389,7 +389,7 @@ supports it. It has its own WWW page at
:line
-msi2lmp tool :h4,link(msi)
+msi2lmp tool :h3,link(msi)
The msi2lmp sub-directory contains a tool for creating LAMMPS template
input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
@@ -406,7 +406,7 @@ See the README file in the tools/msi2lmp folder for more information.
:line
-phonon tool :h4,link(phonon)
+phonon tool :h3,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
@@ -421,7 +421,7 @@ University.
:line
-polybond tool :h4,link(polybond)
+polybond tool :h3,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
@@ -435,7 +435,7 @@ This tool was written by Zachary Kraus at Georgia Tech.
:line
-pymol_asphere tool :h4,link(pymol)
+pymol_asphere tool :h3,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
@@ -453,7 +453,7 @@ This tool was written by Mike Brown at Sandia.
:line
-python tool :h4,link(pythontools)
+python tool :h3,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
@@ -469,7 +469,7 @@ README for more info on Pizza.py and how to use these scripts.
:line
-reax tool :h4,link(reax_tool)
+reax tool :h3,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
@@ -480,7 +480,7 @@ These tools were written by Aidan Thompson at Sandia.
:line
-smd tool :h4,link(smd)
+smd tool :h3,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
@@ -496,7 +496,7 @@ Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
-vim tool :h4,link(vim)
+vim tool :h3,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
@@ -507,7 +507,7 @@ ziegenhain.com)
:line
-xmgrace tool :h4,link(xmgrace)
+xmgrace tool :h3,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
diff --git a/doc/src/fix_manifoldforce.txt b/doc/src/fix_manifoldforce.txt
index 8dd992170b..a25b9f0b2e 100644
--- a/doc/src/fix_manifoldforce.txt
+++ b/doc/src/fix_manifoldforce.txt
@@ -25,7 +25,7 @@ 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 can be
+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
diff --git a/doc/src/fix_property_atom.txt b/doc/src/fix_property_atom.txt
index 136ed6c15e..8a70cd8213 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 e4dd7e2fb9..d43cafbf09 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).
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index 88ef6d77cb..c45a930bbc 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -1,6 +1,7 @@
#HTMLDOC 1.8.28
-t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=9 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont Sans --bodyfont Serif --headfootsize 11.0 --headfootfont Sans-Bold --charset iso-8859-15 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow
Manual.html
+Manual_version.html
Intro.html
Intro_overview.html
Intro_features.html
@@ -126,6 +127,7 @@ Errors_common.html
Errors_bugs.html
Errors_messages.html
Errors_warnings.html
+Build_manual.html
lammps_commands.html
atom_modify.html
diff --git a/lib/gpu/geryon/ocl_timer.h b/lib/gpu/geryon/ocl_timer.h
index 1f56aeb364..bdfec64f54 100644
--- a/lib/gpu/geryon/ocl_timer.h
+++ b/lib/gpu/geryon/ocl_timer.h
@@ -38,8 +38,8 @@ namespace ucl_opencl {
/// Class for timing OpenCL events
class UCL_Timer {
public:
- inline UCL_Timer() : _total_time(0.0f), _initialized(false) { }
- inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false)
+ inline UCL_Timer() : _total_time(0.0f), _initialized(false), has_measured_time(false) { }
+ inline UCL_Timer(UCL_Device &dev) : _total_time(0.0f), _initialized(false), has_measured_time(false)
{ init(dev); }
inline ~UCL_Timer() { clear(); }
@@ -52,6 +52,7 @@ class UCL_Timer {
_initialized=false;
_total_time=0.0;
}
+ has_measured_time = false;
}
/// Initialize default command queue for timing
@@ -64,25 +65,39 @@ class UCL_Timer {
_cq=cq;
clRetainCommandQueue(_cq);
_initialized=true;
+ has_measured_time = false;
}
/// Start timing on default command queue
- inline void start() { UCL_OCL_MARKER(_cq,&start_event); }
+ inline void start() {
+ UCL_OCL_MARKER(_cq,&start_event);
+ has_measured_time = false;
+ }
/// Stop timing on default command queue
- inline void stop() { UCL_OCL_MARKER(_cq,&stop_event); }
+ inline void stop() {
+ UCL_OCL_MARKER(_cq,&stop_event);
+ has_measured_time = true;
+ }
/// Block until the start event has been reached on device
- inline void sync_start()
- { CL_SAFE_CALL(clWaitForEvents(1,&start_event)); }
+ inline void sync_start() {
+ CL_SAFE_CALL(clWaitForEvents(1,&start_event));
+ has_measured_time = false;
+ }
/// Block until the stop event has been reached on device
- inline void sync_stop()
- { CL_SAFE_CALL(clWaitForEvents(1,&stop_event)); }
+ inline void sync_stop() {
+ CL_SAFE_CALL(clWaitForEvents(1,&stop_event));
+ has_measured_time = true;
+ }
/// Set the time elapsed to zero (not the total_time)
- inline void zero()
- { UCL_OCL_MARKER(_cq,&start_event); UCL_OCL_MARKER(_cq,&stop_event); }
+ inline void zero() {
+ has_measured_time = false;
+ UCL_OCL_MARKER(_cq,&start_event);
+ UCL_OCL_MARKER(_cq,&stop_event);
+ }
/// Set the total time to zero
inline void zero_total() { _total_time=0.0; }
@@ -97,6 +112,7 @@ class UCL_Timer {
/// Return the time (ms) of last start to stop - Forces synchronization
inline double time() {
+ if(!has_measured_time) return 0.0;
cl_ulong tstart,tend;
CL_SAFE_CALL(clWaitForEvents(1,&stop_event));
CL_SAFE_CALL(clGetEventProfilingInfo(stop_event,
@@ -107,6 +123,7 @@ class UCL_Timer {
sizeof(cl_ulong), &tstart, NULL));
clReleaseEvent(start_event);
clReleaseEvent(stop_event);
+ has_measured_time = false;
return (tend-tstart)*t_factor;
}
@@ -123,8 +140,9 @@ class UCL_Timer {
cl_event start_event, stop_event;
cl_command_queue _cq;
double _total_time;
- bool _initialized;
double t_factor;
+ bool _initialized;
+ bool has_measured_time;
};
} // namespace
diff --git a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
index 49b11f3ae0..11aa695f08 100644
--- a/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
+++ b/lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp
@@ -292,7 +292,8 @@ public:
#if ! defined( KOKKOS_ENABLE_CUDA_LDG_INTRINSIC )
if ( 0 == r ) {
- Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory");
+ //Kokkos::abort("Cuda const random access View using Cuda texture memory requires Kokkos to allocate the View's memory");
+ return handle_type();
}
#endif
diff --git a/src/.gitignore b/src/.gitignore
index 058833ffb3..df3a22a5cd 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -729,6 +729,8 @@
/pair_eam.h
/pair_eam_alloy.cpp
/pair_eam_alloy.h
+/pair_eam_cd.cpp
+/pair_eam_cd.h
/pair_eam_fs.cpp
/pair_eam_fs.h
/pair_edip.cpp
diff --git a/src/USER-UEF/fix_nh_uef.cpp b/src/USER-UEF/fix_nh_uef.cpp
index cd0b2ba268..bfa4549286 100644
--- a/src/USER-UEF/fix_nh_uef.cpp
+++ b/src/USER-UEF/fix_nh_uef.cpp
@@ -536,10 +536,26 @@ void FixNHUef::pre_exchange()
rotate_x(rot);
rotate_f(rot);
- // put all atoms in the new box
- double **x = atom->x;
+ // this is a generalization of what is done in domain->image_flip(...)
+ int ri[3][3];
+ uefbox->get_inverse_cob(ri);
imageint *image = atom->image;
int nlocal = atom->nlocal;
+ for (int i=0; i> IMGBITS & IMGMASK) - IMGMAX;
+ iold[2] = (image[i] >> IMG2BITS) - IMGMAX;
+ inew[0] = ri[0][0]*iold[0] + ri[0][1]*iold[1] + ri[0][2]*iold[2];
+ inew[1] = ri[1][0]*iold[0] + ri[1][1]*iold[1] + ri[1][2]*iold[2];
+ inew[2] = ri[2][0]*iold[0] + ri[2][1]*iold[1] + ri[2][2]*iold[2];
+ image[i] = ((imageint) (inew[0] + IMGMAX) & IMGMASK) |
+ (((imageint) (inew[1] + IMGMAX) & IMGMASK) << IMGBITS) |
+ (((imageint) (inew[2] + IMGMAX) & IMGMASK) << IMG2BITS);
+ }
+
+ // put all atoms in the new box
+ double **x = atom->x;
for (int i=0; iremap(x[i],image[i]);
// move atoms to the right processors
diff --git a/src/USER-UEF/uef_utils.cpp b/src/USER-UEF/uef_utils.cpp
index a5498d605f..a2e6cb291e 100644
--- a/src/USER-UEF/uef_utils.cpp
+++ b/src/USER-UEF/uef_utils.cpp
@@ -30,47 +30,54 @@ namespace LAMMPS_NS {
UEFBox::UEFBox()
{
+
// initial box (also an inverse eigenvector matrix of automorphisms)
+
double x = 0.327985277605681;
double y = 0.591009048506103;
double z = 0.736976229099578;
l0[0][0]= z; l0[0][1]= y; l0[0][2]= x;
l0[1][0]=-x; l0[1][1]= z; l0[1][2]=-y;
l0[2][0]=-y; l0[2][1]= x; l0[2][2]= z;
+
// spectra of the two automorpisms (log of eigenvalues)
+
w1[0]=-1.177725211523360;
w1[1]=-0.441448620566067;
w1[2]= 1.619173832089425;
w2[0]= w1[1];
w2[1]= w1[2];
w2[2]= w1[0];
+
// initialize theta
// strain = w1 * theta1 + w2 * theta2
+
theta[0]=theta[1]=0;
-
//set up the initial box l and change of basis matrix r
+
for (int k=0;k<3;k++)
- for (int j=0;j<3;j++)
- {
+ for (int j=0;j<3;j++) {
l[k][j] = l0[k][j];
r[j][k]=(j==k);
+ ri[j][k]=(j==k);
}
// get the initial rotation and upper triangular matrix
+
rotation_matrix(rot, lrot ,l);
// this is just a way to calculate the automorphisms
// themselves, which play a minor role in the calculations
// it's overkill, but only called once
+
double t1[3][3];
double t1i[3][3];
double t2[3][3];
double t2i[3][3];
double l0t[3][3];
for (int k=0; k<3; ++k)
- for (int j=0; j<3; ++j)
- {
+ for (int j=0; j<3; ++j) {
t1[k][j] = exp(w1[k])*l0[k][j];
t1i[k][j] = exp(-w1[k])*l0[k][j];
t2[k][j] = exp(w2[k])*l0[k][j];
@@ -82,8 +89,7 @@ UEFBox::UEFBox()
mul_m2(l0t,t2);
mul_m2(l0t,t2i);
for (int k=0; k<3; ++k)
- for (int j=0; j<3; ++j)
- {
+ for (int j=0; j<3; ++j) {
a1[k][j] = round(t1[k][j]);
a1i[k][j] = round(t1i[k][j]);
a2[k][j] = round(t2[k][j]);
@@ -92,6 +98,7 @@ UEFBox::UEFBox()
// winv used to transform between
// strain increments and theta increments
+
winv[0][0] = w2[1];
winv[0][1] = -w2[0];
winv[1][0] = -w1[1];
@@ -102,7 +109,9 @@ UEFBox::UEFBox()
winv[k][j] /= d;
}
-// get volume-correct r basis in: basis*cbrt(vol) = q*r
+/* ----------------------------------------------------------------------
+ get volume-correct r basis in: basis*cbrt(vol) = q*r
+------------------------------------------------------------------------- */
void UEFBox::get_box(double x[3][3], double v)
{
v = cbrtf(v);
@@ -111,7 +120,9 @@ void UEFBox::get_box(double x[3][3], double v)
x[k][j] = lrot[k][j]*v;
}
-// get rotation matrix q in: basis = q*r
+/* ----------------------------------------------------------------------
+ get rotation matrix q in: basis = q*r
+------------------------------------------------------------------------- */
void UEFBox::get_rot(double x[3][3])
{
for (int k=0;k<3;k++)
@@ -119,20 +130,32 @@ void UEFBox::get_rot(double x[3][3])
x[k][j]=rot[k][j];
}
-// diagonal, incompressible deformation
+/* ----------------------------------------------------------------------
+ get inverse change of basis matrix
+------------------------------------------------------------------------- */
+void UEFBox::get_inverse_cob(int x[3][3])
+{
+ for (int k=0;k<3;k++)
+ for (int j=0;j<3;j++)
+ x[k][j]=ri[k][j];
+}
+
+/* ----------------------------------------------------------------------
+ apply diagonal, incompressible deformation
+------------------------------------------------------------------------- */
void UEFBox::step_deform(const double ex, const double ey)
{
// increment theta values used in the reduction
+
theta[0] +=winv[0][0]*ex + winv[0][1]*ey;
theta[1] +=winv[1][0]*ex + winv[1][1]*ey;
- // deformation of the box. reduce() needs to
- // be called regularly or calculation will become
- // unstable
+ // deformation of the box. reduce() needs to be called regularly or
+ // calculation will become unstable
+
double eps[3];
eps[0]=ex; eps[1] = ey; eps[2] = -ex-ey;
- for (int k=0;k<3;k++)
- {
+ for (int k=0;k<3;k++) {
eps[k] = exp(eps[k]);
l[k][0] = eps[k]*l[k][0];
l[k][1] = eps[k]*l[k][1];
@@ -140,68 +163,84 @@ void UEFBox::step_deform(const double ex, const double ey)
}
rotation_matrix(rot,lrot, l);
}
-// reuduce the current basis
+
+/* ----------------------------------------------------------------------
+ reduce the current basis
+------------------------------------------------------------------------- */
bool UEFBox::reduce()
{
- // determine how many times to apply the automorphisms
- // and find new theta values
+ // determine how many times to apply the automorphisms and find new theta
+ // values
+
int f1 = round(theta[0]);
int f2 = round(theta[1]);
theta[0] -= f1;
theta[1] -= f2;
- // store old change or basis matrix to determine if it
- // changes
+ // store old change or basis matrix to determine if it changes
+
int r0[3][3];
for (int k=0;k<3;k++)
for (int j=0;j<3;j++)
r0[k][j]=r[k][j];
- // this modifies the old change basis matrix to
- // handle the case where the automorphism transforms
- // the box but the reduced basis doesn't change
+ // this modifies the old change basis matrix to handle the case where the
+ // automorphism transforms the box but the reduced basis doesn't change
// (r0 should still equal r at the end)
+
if (f1 > 0) for (int k=0;k 0) for (int k=0;k (-q)*m = (-r) will hold row-wise
+
if (r[0][0] < 0){ neg_row(q,0); neg_row(r,0); }
if (r[1][1] < 0){ neg_row(q,1); neg_row(r,1); }
if (r[2][2] < 0){ neg_row(q,2); neg_row(r,2); }
}
-
-
-//sort columns in order of increasing length
-void col_sort(double b[3][3],int r[3][3])
+/* ----------------------------------------------------------------------
+ sort columns of b in order of increasing length
+ mimic column operations on ri and r
+------------------------------------------------------------------------- */
+void col_sort(double b[3][3],int r[3][3],int ri[3][3])
{
- if (col_prod(b,0,0)>col_prod(b,1,1))
- {
+ if (col_prod(b,0,0)>col_prod(b,1,1)) {
col_swap(b,0,1);
col_swap(r,0,1);
+ col_swap(ri,0,1);
}
- if (col_prod(b,0,0)>col_prod(b,2,2))
- {
+ if (col_prod(b,0,0)>col_prod(b,2,2)) {
col_swap(b,0,2);
col_swap(r,0,2);
+ col_swap(ri,0,2);
}
- if (col_prod(b,1,1)>col_prod(b,2,2))
- {
+ if (col_prod(b,1,1)>col_prod(b,2,2)) {
col_swap(b,1,2);
col_swap(r,1,2);
+ col_swap(ri,1,2);
}
}
-
-// 1-2 reduction (Graham-Schmidt)
-void red12(double b[3][3],int r[3][3])
+/* ----------------------------------------------------------------------
+ 1-2 reduction (Graham-Schmidt)
+------------------------------------------------------------------------- */
+void red12(double b[3][3],int r[3][3],int ri[3][3])
{
int y = round(col_prod(b,0,1)/col_prod(b,0,0));
b[0][1] -= y*b[0][0];
@@ -276,16 +318,23 @@ void red12(double b[3][3],int r[3][3])
r[0][1] -= y*r[0][0];
r[1][1] -= y*r[1][0];
r[2][1] -= y*r[2][0];
- if (col_prod(b,1,1) < col_prod(b,0,0))
- {
+
+ ri[0][0] += y*ri[0][1];
+ ri[1][0] += y*ri[1][1];
+ ri[2][0] += y*ri[2][1];
+
+ if (col_prod(b,1,1) < col_prod(b,0,0)) {
col_swap(b,0,1);
col_swap(r,0,1);
- red12(b,r);
+ col_swap(ri,0,1);
+ red12(b,r,ri);
}
}
-// The Semaev condition for a 3-reduced basis
-void red3(double b[3][3], int r[3][3])
+/* ----------------------------------------------------------------------
+ Apply the Semaev condition for a 3-reduced basis
+------------------------------------------------------------------------- */
+void red3(double b[3][3], int r[3][3], int ri[3][3])
{
double b11 = col_prod(b,0,0);
double b22 = col_prod(b,1,1);
@@ -304,63 +353,97 @@ void red3(double b[3][3], int r[3][3])
x1v[0] = floor(y1); x1v[1] = x1v[0]+1;
x2v[0] = floor(y2); x2v[1] = x2v[0]+1;
for (int k=0;k<2;k++)
- for (int j=0;j<2;j++)
- {
+ for (int j=0;j<2;j++) {
double a[3];
a[0] = b[0][2] + x1v[k]*b[0][0] + x2v[j]*b[0][1];
a[1] = b[1][2] + x1v[k]*b[1][0] + x2v[j]*b[1][1];
a[2] = b[2][2] + x1v[k]*b[2][0] + x2v[j]*b[2][1];
double val=a[0]*a[0]+a[1]*a[1]+a[2]*a[2];
- if (val
T col_prod(T x[3][3], int c1, int c2)
{
@@ -56,8 +57,7 @@ T col_prod(T x[3][3], int c1, int c2)
template
void col_swap(T x[3][3], int c1, int c2)
{
- for (int k=0;k<3;k++)
- {
+ for (int k=0;k<3;k++) {
T t = x[k][c2];
x[k][c2]=x[k][c1];
x[k][c1]=t;
@@ -101,9 +101,21 @@ bool mat_same(T x1[3][3], T x2[3][3])
}
template
-void mul_m1(T m1[3][3], const T m2[3][3])
+void transpose(T m[3][3])
{
T t[3][3];
+ for (int k=0;k<3;k++)
+ for (int j=k+1;j<3;j++) {
+ T x = m[k][j];
+ m[k][j] = m[j][k];
+ m[j][k] = x;
+ }
+}
+
+template
+void mul_m1(T1 m1[3][3], const T2 m2[3][3])
+{
+ T1 t[3][3];
for (int k=0;k<3;k++)
for (int j=0;j<3;j++)
t[k][j]=m1[k][j];
@@ -113,10 +125,10 @@ void mul_m1(T m1[3][3], const T m2[3][3])
m1[k][j] = t[k][0]*m2[0][j] + t[k][1]*m2[1][j] + t[k][2]*m2[2][j];
}
-template
-void mul_m2(const T m1[3][3], T m2[3][3])
+template
+void mul_m2(const T1 m1[3][3], T2 m2[3][3])
{
- T t[3][3];
+ T2 t[3][3];
for (int k=0;k<3;k++)
for (int j=0;j<3;j++)
t[k][j]=m2[k][j];
diff --git a/src/compute_cluster_atom.cpp b/src/compute_cluster_atom.cpp
index 146f8fd1b3..85934c5e6d 100644
--- a/src/compute_cluster_atom.cpp
+++ b/src/compute_cluster_atom.cpp
@@ -31,6 +31,8 @@
using namespace LAMMPS_NS;
+enum{CLUSTER,MASK,COORDS};
+
/* ---------------------------------------------------------------------- */
ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
@@ -44,7 +46,7 @@ ComputeClusterAtom::ComputeClusterAtom(LAMMPS *lmp, int narg, char **arg) :
peratom_flag = 1;
size_peratom_cols = 0;
- comm_forward = 1;
+ comm_forward = 3;
nmax = 0;
}
@@ -122,10 +124,19 @@ void ComputeClusterAtom::compute_peratom()
numneigh = list->numneigh;
firstneigh = list->firstneigh;
+ // if update->post_integrate set:
+ // a dynamic group in FixGroup is invoking a variable with this compute
+ // thus ghost atom coords need to be up-to-date after initial_integrate()
+
+ if (update->post_integrate) {
+ commflag = COORDS;
+ comm->forward_comm_compute(this);
+ }
+
// if group is dynamic, insure ghost atom masks are current
if (group->dynamic[igroup]) {
- commflag = 0;
+ commflag = MASK;
comm->forward_comm_compute(this);
}
@@ -147,7 +158,7 @@ void ComputeClusterAtom::compute_peratom()
// iterate until no changes in my atoms
// then check if any proc made changes
- commflag = 1;
+ commflag = CLUSTER;
double **x = atom->x;
int change,done,anychange;
@@ -203,17 +214,25 @@ int ComputeClusterAtom::pack_forward_comm(int n, int *list, double *buf,
int i,j,m;
m = 0;
- if (commflag) {
+ if (commflag == CLUSTER) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = clusterID[j];
}
- } else {
+ } else if (commflag == MASK) {
int *mask = atom->mask;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(mask[j]).d;
}
+ } else if (commflag == COORDS) {
+ double **x = atom->x;
+ for (i = 0; i < n; i++) {
+ j = list[i];
+ buf[m++] = x[j][0];
+ buf[m++] = x[j][1];
+ buf[m++] = x[j][2];
+ }
}
return m;
@@ -227,11 +246,18 @@ void ComputeClusterAtom::unpack_forward_comm(int n, int first, double *buf)
m = 0;
last = first + n;
- if (commflag)
+ if (commflag == CLUSTER) {
for (i = first; i < last; i++) clusterID[i] = buf[m++];
- else {
+ } else if (commflag == MASK) {
int *mask = atom->mask;
for (i = first; i < last; i++) mask[i] = (int) ubuf(buf[m++]).i;
+ } else if (commflag == COORDS) {
+ double **x = atom->x;
+ for (i = first; i < last; i++) {
+ x[i][0] = buf[m++];
+ x[i][1] = buf[m++];
+ x[i][2] = buf[m++];
+ }
}
}
diff --git a/src/fix_group.cpp b/src/fix_group.cpp
index 2447002bc5..10736964e7 100644
--- a/src/fix_group.cpp
+++ b/src/fix_group.cpp
@@ -84,7 +84,7 @@ idregion(NULL), idvar(NULL), idprop(NULL)
idprop = new char[n];
strcpy(idprop,arg[iarg+1]);
iarg += 2;
- } else if (strcmp(arg[iarg],"every") == 0) {
+ } else if (strcmp(arg[iarg],"every") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal group command");
nevery = force->inumeric(FLERR,arg[iarg+1]);
if (nevery <= 0) error->all(FLERR,"Illegal group command");
@@ -204,17 +204,22 @@ void FixGroup::set_group()
int nlocal = atom->nlocal;
// invoke atom-style variable if defined
+ // set post_integrate flag to 1, then unset after
+ // this is for any compute to check if it needs to
+ // operate differently due to invocation this early in timestep
+ // e.g. perform ghost comm update due to atoms having just moved
double *var = NULL;
int *ivector = NULL;
double *dvector = NULL;
-
if (varflag) {
+ update->post_integrate = 1;
modify->clearstep_compute();
memory->create(var,nlocal,"fix/group:varvalue");
input->variable->compute_atom(ivar,igroup,var,1,0);
modify->addstep_compute(update->ntimestep + nevery);
+ update->post_integrate = 0;
}
// invoke per-atom property if defined
diff --git a/src/group.cpp b/src/group.cpp
index 9d33da9acb..dd5e53bb3c 100644
--- a/src/group.cpp
+++ b/src/group.cpp
@@ -754,6 +754,18 @@ void Group::read_restart(FILE *fp)
// computations on a group of atoms
// ----------------------------------------------------------------------
+/* ----------------------------------------------------------------------
+ count atoms in group all
+------------------------------------------------------------------------- */
+
+bigint Group::count_all()
+{
+ bigint nme = atom->nlocal;
+ bigint nall;
+ MPI_Allreduce(&nme,&nall,1,MPI_LMP_BIGINT,MPI_SUM,world);
+ return nall;
+}
+
/* ----------------------------------------------------------------------
count atoms in group
------------------------------------------------------------------------- */
diff --git a/src/group.h b/src/group.h
index 6b6cbb1def..962d37b32a 100644
--- a/src/group.h
+++ b/src/group.h
@@ -37,6 +37,7 @@ class Group : protected Pointers {
void write_restart(FILE *);
void read_restart(FILE *);
+ bigint count_all(); // count atoms in group all
bigint count(int); // count atoms in group
bigint count(int,int); // count atoms in group & region
double mass(int); // total mass of atoms in group
diff --git a/src/thermo.cpp b/src/thermo.cpp
index ade7a3c333..ddbbd0f496 100644
--- a/src/thermo.cpp
+++ b/src/thermo.cpp
@@ -1698,7 +1698,7 @@ void Thermo::compute_timeremain()
void Thermo::compute_atoms()
{
- bivalue = atom->natoms;
+ bivalue = group->count_all();
}
/* ---------------------------------------------------------------------- */
diff --git a/src/update.cpp b/src/update.cpp
index aa152a8508..6f9c2c9a07 100644
--- a/src/update.cpp
+++ b/src/update.cpp
@@ -46,10 +46,10 @@ Update::Update(LAMMPS *lmp) : Pointers(lmp)
whichflag = 0;
firststep = laststep = 0;
beginstep = endstep = 0;
- setupflag = 0;
- multireplica = 0;
-
restrict_output = 0;
+ setupflag = 0;
+ post_integrate = 0;
+ multireplica = 0;
eflag_global = vflag_global = -1;
diff --git a/src/update.h b/src/update.h
index 7996440318..d3602ef21e 100644
--- a/src/update.h
+++ b/src/update.h
@@ -35,6 +35,7 @@ class Update : protected Pointers {
int max_eval; // max force evaluations for minimizer
int restrict_output; // 1 if output should not write dump/restart
int setupflag; // set when setup() is computing forces
+ int post_integrate; // 1 if now at post_integrate() in timestep
int multireplica; // 1 if min across replicas, else 0
bigint eflag_global,eflag_atom; // timestep global/peratom eng is tallied on