patch 17Aug17

Merge pull request #613 from akohlmey/collected-small-changes
Collected small changes and bug fixes
2017-08-17 16:02:20 -06:00 · 2017-08-17 11:34:52 -06:00 · 2017-08-17 11:32:53 -06:00 · 2017-08-17 11:32:38 -06:00 · 2017-08-17 11:32:18 -06:00 · 2017-08-17 11:31:59 -06:00
405 changed files with 28555 additions and 7529 deletions
--- a/.github/CODEOWNERS
+++ b/.github/CODEOWNERS
@ -0,0 +1,21 @@
+# This file contains file patterns that triggers automatic
+# code review requests from users that are owners of these files
+# Order matters, the last match has the highest precedence
+
+# library folders
+lib/colvars/*         @giacomofiorin
+lib/compress/*        @akohlmey
+lib/kokkos/*          @stanmoore1
+lib/molfile/*         @akohlmey
+lib/qmmm/*            @akohlmey
+lib/vtk/*             @rbberger
+
+# packages
+src/KOKKOS            @stanmoore1
+src/USER-CGSDK        @akohlmey
+src/USER-COLVARS      @giacomofiorin
+src/USER-OMP          @akohlmey
+src/USER-QMMM         @akohlmey
+
+# tools
+tools/msi2lmp/*       @akohlmey
--- a/doc/src/JPG/bow_tutorial_01.png
+++ b/doc/src/JPG/bow_tutorial_01.png
--- a/doc/src/JPG/bow_tutorial_01_small.png
+++ b/doc/src/JPG/bow_tutorial_01_small.png
--- a/doc/src/JPG/bow_tutorial_02.png
+++ b/doc/src/JPG/bow_tutorial_02.png
--- a/doc/src/JPG/bow_tutorial_02_small.png
+++ b/doc/src/JPG/bow_tutorial_02_small.png
--- a/doc/src/JPG/bow_tutorial_03.png
+++ b/doc/src/JPG/bow_tutorial_03.png
--- a/doc/src/JPG/bow_tutorial_03_small.png
+++ b/doc/src/JPG/bow_tutorial_03_small.png
--- a/doc/src/JPG/bow_tutorial_04.png
+++ b/doc/src/JPG/bow_tutorial_04.png
--- a/doc/src/JPG/bow_tutorial_04_small.png
+++ b/doc/src/JPG/bow_tutorial_04_small.png
--- a/doc/src/JPG/bow_tutorial_05.png
+++ b/doc/src/JPG/bow_tutorial_05.png
--- a/doc/src/JPG/bow_tutorial_06.png
+++ b/doc/src/JPG/bow_tutorial_06.png
--- a/doc/src/JPG/bow_tutorial_07.png
+++ b/doc/src/JPG/bow_tutorial_07.png
--- a/doc/src/JPG/bow_tutorial_08.png
+++ b/doc/src/JPG/bow_tutorial_08.png
--- a/doc/src/JPG/bow_tutorial_09.png
+++ b/doc/src/JPG/bow_tutorial_09.png
--- a/doc/src/JPG/bow_tutorial_10.png
+++ b/doc/src/JPG/bow_tutorial_10.png
--- a/doc/src/JPG/user_intel.png
+++ b/doc/src/JPG/user_intel.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="24 Jul 2017 version">
+<META NAME="docnumber" CONTENT="17 Aug 2017 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
-24 Jul 2017 version :c,h4
+17 Aug 2017 version :c,h4

 Version info: :h4

@ -79,7 +79,7 @@ bug reports and feature requests are mainly coordinated through the
 "LAMMPS project on GitHub."_https://github.com/lammps/lammps
 The lammps.org domain, currently hosting "public continuous integration
 testing"_https://ci.lammps.org/job/lammps/ and "precompiled Linux
-RPM and Windows installer packages"_http://rpm.lammps.org is located
+RPM and Windows installer packages"_http://packages.lammps.org is located
 at Temple University and managed by Richard Berger,
 richard.berger at temple.edu.

--- a/doc/src/PDF/colvars-refman-lammps.pdf
+++ b/doc/src/PDF/colvars-refman-lammps.pdf
--- a/doc/src/Section_accelerate.txt
+++ b/doc/src/Section_accelerate.txt
@ -233,8 +233,8 @@ set any needed options for the package via "-pk" "command-line switch"_Section_s
 use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu
 :tb(c=2,s=|)

-Note that the first 4 steps can be done as a single command, using the
-src/Make.py tool.  This tool is discussed in "Section
+Note that the first 4 steps can be done as a single command with
+suitable make command invocations. This is discussed in "Section
 4"_Section_packages.html of the manual, and its use is
 illustrated in the individual accelerator sections.  Typically these
 steps only need to be done once, to create an executable that uses one
--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -734,8 +734,8 @@ package"_Section_start.html#start_3.
 "smd/wall/surface"_fix_smd_wall_surface.html,
 "temp/rescale/eff"_fix_temp_rescale_eff.html,
 "ti/spring"_fix_ti_spring.html,
-"ttm/mod"_fix_ttm.html
-"wall/ees"_fix_wall_ees.html
+"ttm/mod"_fix_ttm.html,
+"wall/ees"_fix_wall_ees.html,
 "wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c)

 :line
@ -892,8 +892,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "hybrid"_pair_hybrid.html,
 "hybrid/overlay"_pair_hybrid.html,
 "adp (o)"_pair_adp.html,
-"airebo (o)"_pair_airebo.html,
-"airebo/morse (o)"_pair_airebo.html,
+"airebo (oi)"_pair_airebo.html,
+"airebo/morse (oi)"_pair_airebo.html,
 "beck (go)"_pair_beck.html,
 "body"_pair_body.html,
 "bop"_pair_bop.html,
@ -927,8 +927,8 @@ KOKKOS, o = USER-OMP, t = OPT.
 "dpd/tstat (go)"_pair_dpd.html,
 "dsmc"_pair_dsmc.html,
 "eam (gkiot)"_pair_eam.html,
-"eam/alloy (gkot)"_pair_eam.html,
-"eam/fs (gkot)"_pair_eam.html,
+"eam/alloy (gkiot)"_pair_eam.html,
+"eam/fs (gkiot)"_pair_eam.html,
 "eim (o)"_pair_eim.html,
 "gauss (go)"_pair_gauss.html,
 "gayberne (gio)"_pair_gayberne.html,
@ -942,9 +942,9 @@ KOKKOS, o = USER-OMP, t = OPT.
 "kim"_pair_kim.html,
 "lcbop"_pair_lcbop.html,
 "line/lj"_pair_line_lj.html,
-"lj/charmm/coul/charmm (ko)"_pair_charmm.html,
+"lj/charmm/coul/charmm (kio)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
-"lj/charmm/coul/long (giko)"_pair_charmm.html,
+"lj/charmm/coul/long (gkio)"_pair_charmm.html,
 "lj/charmm/coul/msm"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
@ -990,7 +990,7 @@ KOKKOS, o = USER-OMP, t = OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "reax"_pair_reax.html,
-"rebo (o)"_pair_airebo.html,
+"rebo (oi)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
 "snap"_pair_snap.html,
 "soft (go)"_pair_soft.html,
--- a/doc/src/Section_errors.txt
+++ b/doc/src/Section_errors.txt
@ -7886,8 +7886,8 @@ keyword to allow for additional bonds to be formed :dd

 {New bond exceeded special list size in fix bond/create} :dt

-See the "special_bonds extra" command
-(or the "read_data extra/special/per/atom" command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd

@ -9666,8 +9666,8 @@ you are running. :dd

 {Special list size exceeded in fix bond/create} :dt

-See the special_bonds extra command
-(or the read_data extra/special/per/atom command)
+See the "read_data extra/special/per/atom" command
+(or the "create_box extra/special/per/atom" command)
 for info on how to leave space in the special bonds
 list to allow for additional bonds to be formed. :dd

--- a/doc/src/Section_example.txt
+++ b/doc/src/Section_example.txt
@ -49,6 +49,7 @@ Lists of both kinds of directories are given below.
 Lowercase directories :h4

 accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -25,6 +25,17 @@ There are two kinds of packages in LAMMPS, standard and user packages:
 "Table of standard packages"_#table_standard
 "Table of user packages"_#table_user :ul

+Either of these kinds of packages may work as is, may require some
+additional code compiled located in the lib folder, or may require
+an external library to be downloaded, compiled, installed, and LAMMPS
+configured to know about its location and additional compiler flags.
+You can often do the build of the internal or external libraries
+in one step by typing "make lib-name args='...'" from the src dir,
+with appropriate arguments included in args='...'. If you just type
+"make lib-name" you should see a help message about supported flags
+and some examples. For more details about this, please study the
+tables below and the sections about the individual packages.
+
 Standard packages are supported by the LAMMPS developers and are
 written in a syntax and style consistent with the rest of LAMMPS.
 This means the developers will answer questions about them, debug and
@ -34,7 +45,9 @@ LAMMPS.
 User packages have been contributed by users, and begin with the
 "user" prefix.  If they are a single command (single file), they are
 typically in the user-misc package.  User packages don't necessarily
-meet the requirements of the standard packages.  If you have problems
+meet the requirements of the standard packages. This means the
+developers will try to keep things working and usually can answer
+technical questions about compiling the package. If you have problems
 using a feature provided in a user package, you may need to contact
 the contributor directly to get help.  Information on how to submit
 additions you make to LAMMPS as single files or as a standard or user
@ -78,10 +91,10 @@ Package, Description, Doc page, Example, Library
 "COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys
 "CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, -
 "DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, -
-"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int
+"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int
 "GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, -
-"KIM"_#KIM, openKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
-"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, -
+"KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext
+"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, -
 "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, -
 "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, -
@ -90,7 +103,7 @@ Package, Description, Doc page, Example, Library
 "MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, -
 "MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, -
 "MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext
-"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, WWW bench, -
+"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, -
 "POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys
@ -101,8 +114,7 @@ Package, Description, Doc page, Example, Library
 "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, -
 "SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, -
 "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, -
-"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext
-:tb(ea=c,ca1=l)
+"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)

 [USER packages] :link(table_user),p

@ -118,7 +130,7 @@ Package, Description, Doc page, Example, Library
 "USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, -
 "USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, -
 "USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext
-"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, -
+"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, -
 "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, -
 "USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, -
@ -126,7 +138,7 @@ Package, Description, Doc page, Example, Library
 "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, -
 "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext
 "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext
-"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, -
+"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, -
 "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, -
 "USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext
 "USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, -
@ -136,8 +148,7 @@ Package, Description, Doc page, Example, Library
 "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, -
 "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, -
 "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, -
-"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext
-:tb(ea=c,ca1=l)
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)

 :line
 :line
@ -364,9 +375,12 @@ GPU package :link(GPU),h4
 [Contents:]

 Dozens of pair styles and a version of the PPPM long-range Coulombic
-solver optimized for NVIDIA GPUs.  All such styles have a "gpu" as a
-suffix in their style name.  "Section 5.3.1"_accelerate_gpu.html gives
-details of what hardware and Cuda software is required on your system,
+solver optimized for GPUs.  All such styles have a "gpu" as a
+suffix in their style name. The GPU code can be compiled with either
+CUDA or OpenCL, however the OpenCL variants are no longer actively
+maintained and only the CUDA versions are regularly tested.
+"Section 5.3.1"_accelerate_gpu.html gives details of what
+hardware and GPU software is required on your system,
 and details on how to build and use this package.  Its styles can be
 invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line
 switches"_Section_start.html#start_6.  See also the "KOKKOS"_#KOKKOS
@ -378,32 +392,41 @@ package, which has GPU-enabled styles.
 [Install or un-install:]

 Before building LAMMPS with this package, you must first build the GPU
-library in lib/gpu from a set of provided C and Cuda files.  You can
+library in lib/gpu from a set of provided C and CUDA files.  You can
 do this manually if you prefer; follow the instructions in
-lib/gpu/README.  You can also do it in one step from the lammps/src
+lib/gpu/README. Please note, that the GPU library uses MPI calls, so
+you have to make certain to use the same MPI library (or the STUBS
+library) settings as the main LAMMPS code. That same applies to the
+-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define.
+
+You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/gpu/Install.py script with the specified args:

-make lib-gpu                                # print help message
-make lib-gpu args="-m"                      # build GPU library with default Makefile.linux
-make lib-gpu args="-i xk7 -p single -o xk7.single"      # create new Makefile.xk7.single, altered for single-precision
-make lib-gpu args="-i xk7 -p single -o xk7.single -m"   # ditto, also build GPU library
+make lib-gpu               # print help message
+make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre

-Note that this procedure starts with one of the existing
-Makefile.machine files in lib/gpu.  It allows you to alter 4 important
-settings in that Makefile, via the -h, -a, -p, -e switches,
-and save the new Makefile, if desired:
+Note that this procedure through the '-m machine' flag starts with one of
+the existing Makefile.machine files in lib/gpu. For your convenience,
+machine makefiles for "mpi" and "serial" are provided, which have the
+same settings as the corresponding machine makefiles in the main LAMMPS
+source folder. In addition you can alter 4 important settings in that
+Makefile, via the -h, -a, -p, -e switches, and also save a copy of the
+new Makefile, if desired:

-CUDA_HOME = where NVIDIA Cuda software is installed on your system
+CUDA_HOME = where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = what GPU hardware you have (see help message for details)
 CUDA_PRECISION = precision (double, mixed, single)
 EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul

-If the library build is successful, 2 files should be created:
-lib/gpu/libgpu.a and lib/gpu/Makefile.lammps.  The latter has settings
-that enable LAMMPS to link with Cuda libraries.  If the settings in
-Makefile.lammps for your machine are not correct, the LAMMPS build
-will fail.
+If the library build is successful, at least 3 files should be created:
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
+The latter has settings that enable LAMMPS to link with CUDA libraries.
+If the settings in Makefile.lammps for your machine are not correct,
+the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to
+be edited.

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -492,14 +515,40 @@ Minnesota).

 [Install or un-install:]

-Using this package requires the KIM library and its models
-(interatomic potentials) to be downloaded and installed on your
-system.  The library can be downloaded and built in lib/kim or
-elsewhere on your system.  Details of the download, build, and install
-process for KIM are given in the lib/kim/README file.
+Before building LAMMPS with this package, you must first download and
+build the KIM library and include the KIM models that you want to
+use. You can do this manually if you prefer; follow the instructions
+in lib/kim/README.  You can also do it in one step from the lammps/src
+dir, using a command like these, which simply invoke the
+lib/kim/Install.py script with the specified args.

-Once that process is complete, you can then install/un-install the
-package and build LAMMPS in the usual manner:
+make lib-kim              # print help message
+make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b -a everything"     # install KIM API lib with all models
+make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.  Also note that installing the KIM API
+library with all its models, may take around 30 min to build.  Of
+course you only need to do that once.
+
+See the list of KIM model drivers here:
+https://openkim.org/kim-items/model-drivers/alphabetical
+
+See the list of all KIM models here:
+https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of example KIM models included by default here:
+https://openkim.org/kim-api in the "What is in the KIM API source
+package?" section
+
+You can then install/un-install the package and build LAMMPS in the
+usual manner:

 make yes-kim
 make machine :pre
@ -523,7 +572,7 @@ KOKKOS package :link(KOKKOS),h4

 Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute
 styles adapted to compile using the Kokkos library which can convert
-them to OpenMP or Cuda code so that they run efficiently on multicore
+them to OpenMP or CUDA code so that they run efficiently on multicore
 CPUs, KNLs, or GPUs.  All the styles have a "kk" as a suffix in their
 style name.  "Section 5.3.3"_accelerate_kokkos.html gives details of
 what hardware and software is required on your system, and how to
@ -553,28 +602,28 @@ files for examples.
 For multicore CPUs using OpenMP:

 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc
+KOKKOS_ARCH = HSW           # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre

 For Intel KNLs using OpenMP:

 KOKKOS_DEVICES = OpenMP
-KOKKOS_ARCH = KNL
+KOKKOS_ARCH = KNL :pre

-For NVIDIA GPUs using Cuda:
+For NVIDIA GPUs using CUDA:

 KOKKOS_DEVICES = Cuda
 KOKKOS_ARCH = Pascal60,Power8     # P100 hosted by an IBM Power8, etc
-KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc
+KOKKOS_ARCH = Kepler37,Power8     # K80 hosted by an IBM Power8, etc :pre

 For GPUs, you also need these 2 lines in your Makefile.machine before
 the CC line is defined, in this case for use with OpenMPI mpicxx.  The
 2 lines define a nvcc wrapper compiler, which will use nvcc for
-compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda
+compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA
 files.

 KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
 export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
-CC =		mpicxx
+CC =		mpicxx :pre

 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@ -710,6 +759,12 @@ MEAM package :link(MEAM),h4

 A pair style for the modified embedded atom (MEAM) potential.

+Please note that the MEAM package has been superseded by the
+"USER-MEAMC"_#USER-MEAMC package, which is a direct translation
+of the MEAM package to C++. USER-MEAMC contains additional
+optimizations making it run faster than MEAM on most machines,
+while providing the identical features and USER interface.
+
 [Author:] Greg Wagner (Northwestern U) while at Sandia.

 [Install or un-install:]
@ -720,9 +775,10 @@ follow the instructions in lib/meam/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/meam/Install.py script with the specified args:

-make lib-meam                      # print help message
-make lib-meam args="-m gfortran"   # build with GNU Fortran compiler
-make lib-meam args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-meam                  # print help message
+make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
+make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran)
+make lib-meam args="-m ifort"  # build with Intel Fortran compiler using Makefile.ifort :pre

 The build should produce two files: lib/meam/libmeam.a and
 lib/meam/Makefile.lammps.  The latter is copied from an existing
@ -765,6 +821,9 @@ A variety of compute, fix, pair, dump styles with specialized
 capabilities that don't align with other packages.  Do a directory
 listing, "ls src/MISC", to see the list of commands.

+NOTE: the MISC package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+
 [Install or un-install:]

 make yes-misc
@ -878,9 +937,9 @@ University of Chicago.

 Before building LAMMPS with this package, you must first download and
 build the MS-CG library.  Building the MS-CG library and using it from
-LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL
-(GNU Scientific Library) libraries be installed on your machine.  See
-the lib/mscg/README and MSCG/Install files for more details.
+LAMMPS requires a C++11 compatible compiler and that the GSL
+(GNU Scientific Library) headers and libraries are installed on your
+machine.  See the lib/mscg/README and MSCG/Install files for more details.

 Assuming these libraries are in place, you can do the download and
 build of MS-CG manually if you prefer; follow the instructions in
@ -888,15 +947,16 @@ lib/mscg/README.  You can also do it in one step from the lammps/src
 dir, using a command like these, which simply invoke the
 lib/mscg/Install.py script with the specified args:

-make lib-mscg                                # print help message
-make lib-mscg args="-g -b -l"                # download and build in default lib/mscg/MSCG-release-master
-make lib-mscg args="-h . MSCG -g -b -l"      # download and build in lib/mscg/MSCG
-make lib-mscg args="-h ~ MSCG -g -b -l"      # download and build in ~/mscg :pre
+make lib-mscg             # print help message
+make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make serial"
+make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                    # with the settings compatible with "make mpi"
+make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre

-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/mscg to point to the MS-CG src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/mscg/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
+to point to the MS-CG src/installation dir.  When LAMMPS is built in src it will use these links.
+You should not need to edit the lib/mscg/Makefile.lammps file.

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -942,11 +1002,11 @@ make no-opt
 make machine :pre

 NOTE: The compile flag "-restrict" must be used to build LAMMPS with
-the OPT package.  It should be added to the CCFLAGS line of your
-Makefile.machine.  See Makefile.opt in src/MAKE/OPTIONS for an
-example.
+the OPT package when using Intel compilers.  It should be added to
+the CCFLAGS line of your Makefile.machine.  See Makefile.opt in
+src/MAKE/OPTIONS for an example.

-CCFLAGS: add -restrict :ul
+CCFLAGS: add -restrict for Intel compilers :ul

 [Supporting info:]

@ -1015,9 +1075,10 @@ follow the instructions in lib/poems/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/poems/Install.py script with the specified args:

-make lib-poems                      # print help message
-make lib-poems args="-m g++"        # build with GNU g++ compiler
-make lib-poems args="-m icc"        # build with Intel icc compiler :pre
+make lib-poems                   # print help message
+make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+make lib-poems args="-m icc"     # build with Intel icc compiler :pre

 The build should produce two files: lib/poems/libpoems.a and
 lib/poems/Makefile.lammps.  The latter is copied from an existing
@ -1127,9 +1188,10 @@ follow the instructions in lib/reax/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/reax/Install.py script with the specified args:

-make lib-reax                      # print help message
-make lib-reax args="-m gfortran"   # build with GNU Fortran compiler
-make lib-reax args="-m ifort"      # build with Intel ifort compiler :pre
+make lib-reax                    # print help message
+make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
+make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre

 The build should produce two files: lib/reax/libreax.a and
 lib/reax/Makefile.lammps.  The latter is copied from an existing
@ -1346,15 +1408,15 @@ one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/voronoi/Install.py script with the specified
 args:

-make lib-voronoi                                # print help message
-make lib-voronoi args="-g -b -l"                # download and build in default lib/voronoi/voro++-0.4.6
-make lib-voronoi args="-h . voro++ -g -b -l"    # download and build in lib/voronoi/voro++
-make lib-voronoi args="-h ~ voro++ -g -b -l"    # download and build in ~/voro++ :pre
+make lib-voronoi                          # print help message
+make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre

-Note that the final -l switch is to create 2 symbolic (soft) links,
-"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
-dir.  When LAMMPS builds it will use these links.  You should not need
-to edit the lib/voronoi/Makefile.lammps file.
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
+builds in src it will use these links.  You should not need to edit
+the lib/voronoi/Makefile.lammps file.

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -1396,7 +1458,8 @@ from the lammps/src dir, using a command like these, which simply
 invoke the lib/atc/Install.py script with the specified args:

 make lib-atc                      # print help message
-make lib-atc args="-m g++"        # build with GNU g++ compiler
+make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
 make lib-atc args="-m icc"        # build with Intel icc compiler :pre

 The build should produce two files: lib/atc/libatc.a and
@ -1413,8 +1476,10 @@ can either exist on your system, or you can use the files provided in
 lib/linalg.  In the latter case you also need to build the library
 in lib/linalg with a command like these:

-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -1454,9 +1519,10 @@ follow the instructions in lib/awpmd/README.  You can also do it in
 one step from the lammps/src dir, using a command like these, which
 simply invoke the lib/awpmd/Install.py script with the specified args:

-make lib-awpmd                      # print help message
-make lib-awpmd args="-m g++"        # build with GNU g++ compiler
-make lib-awpmd args="-m icc"        # build with Intel icc compiler :pre
+make lib-awpmd                   # print help message
+make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+make lib-awpmd args="-m icc"     # build with Intel icc compiler :pre

 The build should produce two files: lib/awpmd/libawpmd.a and
 lib/awpmd/Makefile.lammps.  The latter is copied from an existing
@ -1472,8 +1538,10 @@ these can either exist on your system, or you can use the files
 provided in lib/linalg.  In the latter case you also need to build the
 library in lib/linalg with a command like these:

-make lib-linalg                      # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+make lib-linalg                     # print help message
+make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler :pre

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -1566,9 +1634,11 @@ Restraints.  A "fix colvars"_fix_colvars.html command is implemented
 which wraps a COLVARS library, which implements these methods.
 simulations.

-[Authors:] Axel Kohlmeyer (Temple U).  The COLVARS library was written
-by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
-Jerome Henin (LISM, CNRS, Marseille, France).
+[Authors:] The COLVARS library is written and maintained by
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
+and Jerome Henin (LISM, CNRS, Marseille, France), originally for
+the NAMD MD code, but with portability in mind.  Axel Kohlmeyer
+(Temple U) provided the interface to LAMMPS.

 [Install or un-install:]

@ -1580,7 +1650,9 @@ which simply invoke the lib/colvars/Install.py script with the
 specified args:

 make lib-colvars                      # print help message
-make lib-colvars args="-m g++"        # build with GNU g++ compiler :pre
+make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled :pre

 The build should produce two files: lib/colvars/libcolvars.a and
 lib/colvars/Makefile.lammps.  The latter is copied from an existing
@ -1868,7 +1940,12 @@ Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP
 packages, which have styles optimized for CPUs and KNLs.

 You need to have an Intel compiler, version 14 or higher to take full
-advantage of this package.
+advantage of this package. While compilation with GNU compilers is
+supported, performance will be suboptimal.
+
+NOTE: the USER-INTEL package contains styles that require using the
+-restrict flag, when compiling with Intel compilers.
+

 [Author:] Mike Brown (Intel).

@ -1885,17 +1962,17 @@ For CPUs:

 OPTFLAGS =      -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc -ltbbmalloc_proxy
+LIB =           -ltbbmalloc -ltbbmalloc_proxy :pre

 For KNLs:

 OPTFLAGS =      -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits
 CCFLAGS =	-g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \
-                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+-fno-alias -ansi-alias -restrict $(OPTFLAGS)
 LINKFLAGS =	-g -qopenmp $(OPTFLAGS)
-LIB =           -ltbbmalloc
+LIB =           -ltbbmalloc :pre

 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner.
@ -2200,11 +2277,15 @@ CPUs.

 [Author:] Axel Kohlmeyer (Temple U).

-NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
-build LAMMPS with the USER-OMP package, as well as the link flag
-"-fopenmp".  They should be added to the CCFLAGS and LINKFLAGS lines
-of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.omp for an
-example.
+NOTE: To enable multi-threading support the compile flag "-fopenmp"
+and the link flag "-fopenmp" (for GNU compilers, you have to look up
+the equivalent flags for other compilers) must be used to build LAMMPS.
+When using Intel compilers, also the "-restrict" flag is required.
+The USER-OMP package can be compiled without enabling OpenMP; then
+all code will be compiled as serial and the only improvement over the
+regular styles are some data access optimization. These flags should
+be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine.
+See src/MAKE/OPTIONS/Makefile.omp for an example.

 Once you have an appropriate Makefile.machine, you can
 install/un-install the package and build LAMMPS in the usual manner:
@ -2217,7 +2298,7 @@ make machine :pre
 make no-user-omp
 make machine :pre

-CCFLAGS: add -fopenmp and -restrict
+CCFLAGS: add -fopenmp (and -restrict when using Intel compilers)
 LINKFLAGS: add -fopenmp :ul

 [Supporting info:]
@ -2286,12 +2367,14 @@ without changes to LAMMPS itself.

 Before building LAMMPS with this package, you must first build the
 QMMM library in lib/qmmm.  You can do this manually if you prefer;
-follow the first two steps explained in lib/colvars/README.  You can
+follow the first two steps explained in lib/qmmm/README.  You can
 also do it in one step from the lammps/src dir, using a command like
-these, which simply invoke the lib/colvars/Install.py script with the
+these, which simply invoke the lib/qmmm/Install.py script with the
 specified args:

 make lib-qmmm                      # print help message
+make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
 make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler :pre

 The build should produce two files: lib/qmmm/libqmmm.a and
@ -2468,15 +2551,13 @@ follow the instructions in lib/smd/README.  You can also do it in one
 step from the lammps/src dir, using a command like these, which simply
 invoke the lib/smd/Install.py script with the specified args:

-make lib-smd                            # print help message
-make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*
-make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen
-make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre
+make lib-smd                         # print help message
+make lib-smd args="-b"               # download and build in default lib/smd/eigen-eigen-...
+make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3 :pre

-Note that the final -l switch is to create a symbolic (soft) link
-named "includelink" in lib/smd to point to the Eigen dir.  When LAMMPS
-builds it will use this link.  You should not need to edit the
-lib/smd/Makefile.lammps file.
+Note that a symbolic (soft) link named "includelink" is created in
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
+this link.  You should not need to edit the lib/smd/Makefile.lammps file.

 You can then install/un-install the package and build LAMMPS in the
 usual manner:
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -587,8 +587,7 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.

-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6

 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@ -659,22 +658,29 @@ utilities.
 For Cygwin and the MinGW cross-compilers, suitable makefiles are
 provided in src/MAKE/MACHINES. When using other compilers, like
 Visual C++ or Intel compilers for Windows, you may have to implement
-your own build system. Since none of the current LAMMPS core developers
-has significant experience building executables on Windows, we are
-happy to distribute contributed instructions and modifications, but
-we cannot provide support for those.
+your own build system. Due to differences between the Windows OS
+and Windows system libraries to Unix-like environments like Linux
+or MacOS, when compiling for Windows a few adjustments may be needed:
+
+Do [not] set the -DLAMMPS_MEMALIGN define (see LMP_INC makefile variable)
+Add -lwsock32 -lpsapi to the linker flags (see LIB makefile variable)
+Try adding -static-libgcc or -static or both to the linker flags when your LAMMPS executable complains about missing .dll files  :ul
+
+Since none of the current LAMMPS core developers has significant
+experience building executables on Windows, we are happy to distribute
+contributed instructions and modifications to improve the situation,
+but we cannot provide support for those.

 With the so-called "Anniversary Update" to Windows 10, there is a
 Ubuntu Linux subsystem available for Windows, that can be installed
 and then used to compile/install LAMMPS as if you are running on a
 Ubuntu Linux system instead of Windows.

-As an alternative, you can download "daily builds" (and some older
-versions) of the installer packages from
-"rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html.
-These executables are built with most optional packages and the
-download includes documentation, potential files, some tools and
-many examples, but no source code.
+As an alternative, you can download pre-compiled installer packages from
+"packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html.
+These executables are built with most optional packages included and the
+download includes documentation, potential files, some tools and many
+examples, but no source code.

 :line

@ -909,7 +915,7 @@ src/MAKE/OPTIONS, which include the settings.  Note that the
 USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
 different hardware.  The USER-INTEL package can be compiled for Intel
 CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
-(Cuda), and Intel KNLs.
+(CUDA), and Intel KNLs.

 Makefile.intel_cpu
 Makefile.intel_phi
@ -1087,7 +1093,7 @@ LAMMPS to be built with one or more of its optional packages.
 :line

 On a Windows box, you can skip making LAMMPS and simply download an
-installer package from "here"_http://rpm.lammps.org/windows.html
+installer package from "here"_http://packages.lammps.org/windows.html

 For running the non-MPI executable, follow these steps:

@ -1099,18 +1105,27 @@ the [in.lj] input from the bench folder. (e.g. by typing: cd "Documents"). :l

 At the command prompt, type "lmp_serial -in in.lj", replacing [in.lj]
 with the name of your LAMMPS input script. :l
+
+The serial executable includes support for multi-threading
+parallelization from the styles in the USER-OMP packages.
+
+To run with, e.g. 4 threads, type "lmp_serial -in in.lj -pk omp 4 -sf omp"
 :ule

-For the MPI version, which allows you to run LAMMPS under Windows on
-multiple processors, follow these steps:
+For the MPI version, which allows you to run LAMMPS under Windows with
+the more general message passing parallel library (LAMMPS has been
+designed from ground up to use MPI efficiently), follow these steps:

-Download and install
-"MPICH2"_http://www.mcs.anl.gov/research/projects/mpich2/downloads/index.php?s=downloads
-for Windows. :ulb,l
+Download and install a compatible MPI library binary package:
+for 32-bit Windows
+"mpich2-1.4.1p1-win-ia32.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi
+and for 64-bit Windows
+"mpich2-1.4.1p1-win-x86-64.msi"_download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi
+:ulb,l

 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the installation
-of the MPICH software, it needs to be integrated into the system.
+of the MPICH2 software, it needs to be integrated into the system.
 For this you need to start a Command Prompt in {Administrator Mode}
 (right click on the icon and select it). Change into the MPICH2
 installation directory, then into the subdirectory [bin] and execute
@ -1129,7 +1144,7 @@ or

 mpiexec -np 4 lmp_mpi -in in.lj :pre

-replacing in.lj with the name of your LAMMPS input script. For the latter
+replacing [in.lj] with the name of your LAMMPS input script. For the latter
 case, you may be prompted to enter your password. :l

 In this mode, output may not immediately show up on the screen, so if
@ -1141,6 +1156,11 @@ something like:

 lmp_mpi -in in.lj :pre

+And the parallel executable also includes OpenMP multi-threading, which
+can be combined with MPI using something like:
+
+mpiexec -localonly 2 lmp_mpi -in in.lj -pk omp 2 -sf omp :pre
+
 :ule

 :line
--- a/doc/src/accelerate_gpu.txt
+++ b/doc/src/accelerate_gpu.txt
@ -62,7 +62,7 @@ respectively to your input script.
 [Required hardware/software:]

 To use this package, you currently need to have an NVIDIA GPU and
-install the NVIDIA Cuda software on your system:
+install the NVIDIA CUDA software on your system:

 Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/0/information
 Go to http://www.nvidia.com/object/cuda_get.html
@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t
 This requires two steps (a,b): build the GPU library, then build
 LAMMPS with the GPU package.

-You can do both these steps in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help.  If run from the src directory, this
-command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the
-starting Makefile.machine:
-
-Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre
+You can do both these steps in one line as described in
+"Section 4"_Section_packages.html of the manual.

 Or you can follow these two (a,b) steps:

@ -90,7 +85,7 @@ The GPU library is in lammps/lib/gpu.  Select a Makefile.machine (in
 lib/gpu) appropriate for your system.  You should pay special
 attention to 3 settings in this makefile.

-CUDA_HOME = needs to be where NVIDIA Cuda software is installed on your system
+CUDA_HOME = needs to be where NVIDIA CUDA software is installed on your system
 CUDA_ARCH = needs to be appropriate to your GPUs
 CUDA_PREC = precision (double, mixed, single) you desire :ul

--- a/doc/src/accelerate_intel.txt
+++ b/doc/src/accelerate_intel.txt
@ -29,8 +29,10 @@ 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,
-charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l
+Pair Styles: airebo, airebo/morse, buck/coul/cut, buck/coul/long, 
+buck, eam, eam/alloy, eam/fs, gayberne, lj/charmm/coul/charmm, 
+lj/charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, rebo,
+sw, tersoff :l
 K-Space Styles: pppm, pppm/disp :l
 :ule

@ -225,11 +227,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
 # or psxevars.csh for C-shell
 make intel_cpu_intelmpi :pre

-Alternatively, the build can be accomplished with the src/Make.py
-script, described in "Section 4"_Section_packages.html of the
-manual. Type "Make.py -h" for help. For an example:
-
-Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
+Alternatively this can be done as a single command with
+suitable make command invocations. This is discussed in "Section
+4"_Section_packages.html of the manual.

 Note that if you build with support for a Phi coprocessor, the same
 binary can be used on nodes with or without coprocessors installed.
@ -244,8 +244,7 @@ highly recommended for CCFLAGS and LINKFLAGS. LIB should include
 is required for CCFLAGS and "-qoffload" is required for LINKFLAGS.
 Other recommended CCFLAG options for best performance are
 "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2
-no-prec-div". The Make.py command will add all of these
-automatically.
+-no-prec-div".

 NOTE: The vectorization and math capabilities can differ depending on
 the CPU. For Intel compilers, the "-x" flag specifies the type of
--- a/doc/src/accelerate_kokkos.txt
+++ b/doc/src/accelerate_kokkos.txt
@ -60,8 +60,7 @@ More details follow.
 use a C++11 compatible compiler
 make yes-kokkos
 make mpi KOKKOS_DEVICES=OpenMP                 # build with the KOKKOS package
-make kokkos_omp                                # or Makefile.kokkos_omp already has variable set
-Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py :pre
+make kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre

 mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj              # 1 node, 16 MPI tasks/node, no threads
 mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj   # 2 nodes, 1 MPI task/node, 16 threads/task
@ -82,8 +81,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = Cuda, OpenMP
 KOKKOS_ARCH = Kepler35
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre
+make machine :pre

 mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj          # one MPI task, 6 threads on CPU
 mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj   # ditto on 4 nodes :pre
@ -98,8 +96,7 @@ use a C++11 compatible compiler
 KOKKOS_DEVICES = OpenMP
 KOKKOS_ARCH = KNC
 make yes-kokkos
-make machine
-Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre
+make machine :pre

 host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
 mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj           # 1 MPI task on 1 Phi, 1*240 = 240
@ -116,7 +113,7 @@ 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
+To build with Kokkos support for NVIDIA GPUs, NVIDIA CUDA software
 version 7.5 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.
@ -135,9 +132,9 @@ mode like the USER-INTEL package supports.
 You must choose at build time whether to build for CPUs (OpenMP),
 GPUs, or Phi.

-You can do any of these in one line, using the src/Make.py script,
-described in "Section 4"_Section_packages.html of the manual.
-Type "Make.py -h" for help.  If run from the src directory, these
+You can do any of these in one line, using the suitable make command
+line flags as described in "Section 4"_Section_packages.html of the
+manual. If run from the src directory, these
 commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and
 lmp_kokkos_phi.  Note that the OMP and PHI options use
 src/MAKE/Makefile.mpi as the starting Makefile.machine.  The CUDA
--- a/doc/src/accelerate_omp.txt
+++ b/doc/src/accelerate_omp.txt
@ -23,8 +23,7 @@ one or more 16-core nodes.  More details follow.
 use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine
 make yes-user-omp
 make mpi                                   # build with USER-OMP package, if settings added to Makefile.mpi
-make omp                                   # or Makefile.omp already has settings
-Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py :pre
+make omp                                   # or Makefile.omp already has settings :pre

 lmp_mpi -sf omp -pk omp 16 < in.script                         # 1 MPI task, 16 threads
 mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
@ -40,14 +39,11 @@ each MPI task running on a CPU.

 The lines above illustrate how to include/build with the USER-OMP
 package in two steps, using the "make" command.  Or how to do it with
-one command via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual.  Type "Make.py -h" for
-help.
+one command as described in "Section 4"_Section_packages.html of the manual.

 Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must
 include "-fopenmp".  Likewise, if you use an Intel compiler, the
-CCFLAGS setting must include "-restrict".  The Make.py command will
-add these automatically.
+CCFLAGS setting must include "-restrict".

 [Run with the USER-OMP package from the command line:]

--- a/doc/src/accelerate_opt.txt
+++ b/doc/src/accelerate_opt.txt
@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package.  More details
 follow.

 make yes-opt
-make mpi                               # build with the OPT package
-Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py :pre
+make mpi                               # build with the OPT package :pre

 lmp_mpi -sf opt -in in.script                # run in serial
 mpirun -np 4 lmp_mpi -sf opt -in in.script   # run in parallel :pre
@ -35,13 +34,10 @@ None.

 The lines above illustrate how to build LAMMPS with the OPT package in
 two steps, using the "make" command.  Or how to do it with one command
-via the src/Make.py script, described in "Section
-4"_Section_packages.html of the manual.  Type "Make.py -h" for
-help.
+as described in "Section 4"_Section_packages.html of the manual.

 Note that if you use an Intel compiler to build with the OPT package,
 the CCFLAGS setting in your Makefile.machine must include "-restrict".
-The Make.py command will add this automatically.

 [Run with the OPT package from the command line:]

--- a/doc/src/compute_voronoi_atom.txt
+++ b/doc/src/compute_voronoi_atom.txt
@ -217,7 +217,7 @@ This compute is part of the VORONOI package.  It is only enabled if
 LAMMPS was built with that package.  See the "Making
 LAMMPS"_Section_start.html#start_3 section for more info.

-It also requiers you have a copy of the Voro++ library built and
+It also requires you have a copy of the Voro++ library built and
 installed on your system.  See instructions on obtaining and
 installing the Voro++ software in the src/VORONOI/README file.

--- a/doc/src/fix_bond_create.txt
+++ b/doc/src/fix_bond_create.txt
@ -150,10 +150,9 @@ atoms.  Note that adding a single bond always adds a new 1st neighbor
 but may also induce *many* new 2nd and 3rd neighbors, depending on the
 molecular topology of your system.  The "extra special per atom"
 parameter must typically be set to allow for the new maximum total
-size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 3
+size (1st + 2nd + 3rd neighbors) of this per-atom list.  There are 2
 ways to do this.  See the "read_data"_read_data.html or
-"create_box"_create_box.html or "special_bonds extra" commands for
-details.
+"create_box"_create_box.html commands for details.

 NOTE: Even if you do not use the {atype}, {dtype}, or {itype}
 keywords, the list of topological neighbors is updated for atoms
--- a/doc/src/fix_msst.txt
+++ b/doc/src/fix_msst.txt
@ -75,7 +75,7 @@ equations, but is used in calculating the deviation from the Hugoniot.
 The keyword {beta} is a scaling term that can be added to the MSST
 ionic equations of motion to account for drift in the conserved
 quantity during long timescale simulations, similar to a Berendson
-thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman for more
+thermostat. See "(Reed)"_#Reed and "(Goldman)"_#Goldman2 for more
 details.  The value of {beta} must be between 0.0 and 1.0 inclusive.
 A value of 0.0 means no contribution, a value of 1.0 means a full
 contribution.
@ -108,7 +108,7 @@ being driven by DFTB+, a density-functional tight-binding code. If the
 keyword {dftb} is used with a value of {yes}, then the MSST equations
 are altered to account for the electron entropy contribution to the
 Hugonio relations and total energy.  See "(Reed2)"_#Reed2 and
-"(Goldman)"_#Goldman for details on this contribution.  In this case,
+"(Goldman)"_#Goldman2 for details on this contribution.  In this case,
 you must define a "fix external"_fix_external.html command in your
 input script, which is used to callback to DFTB+ during the LAMMPS
 timestepping.  DFTB+ will communicate its info to LAMMPS via that fix.
@ -188,6 +188,6 @@ timestep.
 :link(Reed2)
 [(Reed2)] Reed, J. Phys. Chem. C, 116, 2205 (2012).

-:link(Goldman)
+:link(Goldman2)
 [(Goldman)] Goldman, Srinivasan, Hamel, Fried, Gaus, and Elstner,
 J. Phys. Chem. C, 117, 7885 (2013).
--- a/doc/src/fix_qbmsst.txt
+++ b/doc/src/fix_qbmsst.txt
@ -78,7 +78,7 @@ especially when the temperature of the initial state is below the
 classical limit or there is a great change in the zero point energies
 between the initial and final states. Theoretical post processing
 quantum corrections of shock compressed water and methane have been
-reported as much as 30% of the temperatures "(Goldman)"_#Goldman.  A
+reported as much as 30% of the temperatures "(Goldman)"_#Goldman1.  A
 self-consistent method that couples the shock to a quantum thermal
 bath described by a colored noise Langevin thermostat has been
 developed by Qi et al "(Qi)"_#Qi and applied to shocked methane.  The
@ -212,7 +212,7 @@ T_init=300.0. e0, p0, and v0 are calculated on the first step.

 :line

-:link(Goldman)
+:link(Goldman1)
 [(Goldman)] Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)

 :link(Qi)
--- a/doc/src/neigh_modify.txt
+++ b/doc/src/neigh_modify.txt
@ -109,7 +109,8 @@ atoms in the specified group.  This can be useful for models where a
 large portion of the simulation is particles that do not interact with
 other particles or with each other via pairwise interactions.  The
 group specified with this option must also be specified via the
-"atom_modify first"_atom_modify.html command.
+"atom_modify first"_atom_modify.html command.  Note that specifying
+"all" as the group-ID effectively turns off the {include} option.

 The {exclude} option turns off pairwise interactions between certain
 pairs of atoms, by not including them in the neighbor list.  These are
@ -213,5 +214,5 @@ space.
 [Default:]

 The option defaults are delay = 10, every = 1, check = yes, once = no,
-cluster = no, include = all, exclude = none, page = 100000, one =
-2000, and binsize = 0.0.
+cluster = no, include = all (same as no include option defined),
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.
--- a/doc/src/pair_airebo.txt
+++ b/doc/src/pair_airebo.txt
@ -7,10 +7,13 @@
 :line

 pair_style airebo command :h3
+pair_style airebo/intel command :h3
 pair_style airebo/omp command :h3
 pair_style airebo/morse command :h3
+pair_style airebo/morse/intel command :h3
 pair_style airebo/morse/omp command :h3
 pair_style rebo command :h3
+pair_style rebo/intel command :h3
 pair_style rebo/omp command :h3

 [Syntax:]
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@ -7,6 +7,7 @@
 :line

 pair_style lj/charmm/coul/charmm command :h3
+pair_style lj/charmm/coul/charmm/intel command :h3
 pair_style lj/charmm/coul/charmm/omp command :h3
 pair_style lj/charmm/coul/charmm/implicit command :h3
 pair_style lj/charmm/coul/charmm/implicit/omp command :h3
--- a/doc/src/pair_eam.txt
+++ b/doc/src/pair_eam.txt
@ -14,6 +14,7 @@ pair_style eam/omp command :h3
 pair_style eam/opt command :h3
 pair_style eam/alloy command :h3
 pair_style eam/alloy/gpu command :h3
+pair_style eam/alloy/intel command :h3
 pair_style eam/alloy/kk command :h3
 pair_style eam/alloy/omp command :h3
 pair_style eam/alloy/opt command :h3
@ -21,6 +22,7 @@ pair_style eam/cd command :h3
 pair_style eam/cd/omp command :h3
 pair_style eam/fs command :h3
 pair_style eam/fs/gpu command :h3
+pair_style eam/fs/intel command :h3
 pair_style eam/fs/kk command :h3
 pair_style eam/fs/omp command :h3
 pair_style eam/fs/opt command :h3
--- a/doc/src/pair_kim.txt
+++ b/doc/src/pair_kim.txt
@ -27,13 +27,34 @@ pair_coeff * * Ar Ar :pre
 [Description:]

 This pair style is a wrapper on the "Knowledge Base for Interatomic
-Models (KIM)"_https://openkim.org repository of interatomic potentials,
-so that they can be used by LAMMPS scripts.
+Models (OpenKIM)"_https://openkim.org repository of interatomic
+potentials, so that they can be used by LAMMPS scripts.

-In KIM lingo, a potential is a "model" and a model contains both the
-analytic formulas that define the potential as well as the parameters
-needed to run it for one or more materials, including coefficients and
-cutoffs.
+Note that in LAMMPS lingo, a KIM model driver is a pair style
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
+element or alloy and set of parameters, e.g. EAM for Cu with a
+specific EAM potential file.
+
+See the current list of "KIM model
+drivers"_https://openkim.org/kim-items/model-drivers/alphabetical.
+
+See the current list of all "KIM
+models"_https://openkim.org/kim-items/models/by-model-drivers
+
+See the list of "example KIM models"_https://openkim.org/kim-api which
+are included in the KIM library by default, in the "What is in the KIM
+API source package?" section.
+
+To use this pair style, you must first download and install the KIM
+API library from the "OpenKIM website"_https://openkim.org.  The "KIM
+section of Section packages"_Section_packages.html#KIM has
+instructions on how to do this with a simple make command, when
+building LAMMPS.
+
+See the examples/kim dir for an input script that uses a KIM model
+(potential) for Lennard-Jones.
+
+:line

 The argument {virialmode} determines how the global virial is
 calculated.  If {KIMvirial} is specified, the KIM model performs the
--- a/doc/src/special_bonds.txt
+++ b/doc/src/special_bonds.txt
@ -25,9 +25,7 @@ keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {c
  {coul} values = w1,w2,w3
    w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
  {angle} value = {yes} or {no}
-  {dihedral} value = {yes} or {no}
-  {extra} value = N
-    N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
+  {dihedral} value = {yes} or {no} :pre
 :ule

 Examples:
@ -36,8 +34,7 @@ special_bonds amber
 special_bonds charmm
 special_bonds fene dihedral no
 special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
-special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
-special_bonds lj/coul 0 1 1 extra 2 :pre
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes :pre

 [Description:]

@ -178,14 +175,6 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
 of 1.0).  If the {dihedral} keyword is specified as {no} which is the
 default, then the 2,5 interaction will also be weighted by 0.5.

-The {extra} keyword can be used when additional bonds will be created
-during a simulation run, e.g. by the "fix
-bond/create"_fix_bond_create.html command.  It can also be used if
-molecules will be added to the system, e.g. via the "fix
-deposit"_fix_deposit.html, or "fix pour"_fix_pour.html commands, which
-will have atoms with more special neighbors than any atom in the
-current system has.
-
 :line

 NOTE: LAMMPS stores and maintains a data structure with a list of the
@ -194,8 +183,9 @@ the system).  If new bonds are created (or molecules added containing
 atoms with more special neighbors), the size of this list needs to
 grow.  Note that adding a single bond always adds a new 1st neighbor
 but may also induce *many* new 2nd and 3rd neighbors, depending on the
-molecular topology of your system.  Using the {extra} keyword leaves
-empty space in the list for this N additional 1st, 2nd, or 3rd
+molecular topology of your system.  Using the {extra/special/per/atom}
+keyword to either "read_data"_read_data.html or "create_box"_create_box.html
+reserves empty space in the list for this N additional 1st, 2nd, or 3rd
 neighbors to be added.  If you do not do this, you may get an error
 when bonds (or molecules) are added.

@ -203,8 +193,7 @@ when bonds (or molecules) are added.

 NOTE: If you reuse this command in an input script, you should set all
 the options you need each time.  This command cannot be used a 2nd
-time incrementally, e.g. to add some extra storage locations via the
-{extra} keyword.  E.g. these two commands:
+time incrementally.  E.g. these two commands:

 special_bonds lj 0.0 1.0 1.0
 special_bonds coul 0.0 0.0 1.0
@ -221,25 +210,6 @@ Coul: coul 0.0 0.0 1.0
 because the LJ settings are reset to their default values
 each time the command is issued.

-Likewise
-
-special_bonds amber
-special_bonds extra 2 :pre
-
-is not the same as this single command:
-
-special_bonds amber extra 2 :pre
-
-since in the former case, the 2nd command will reset all the LJ and
-Coulombic weights to 0.0 (the default).
-
-One exception to this rule is the {extra} option itself.  It is not
-reset to its default value of 0 each time the special_bonds command is
-invoked.  This is because it can also be set by the
-"read_data"_read_data.html and "create_box"_create_box.html commands,
-so this command will not override those settings unless you explicitly
-use {extra} as an option.
-
 [Restrictions:] none

 [Related commands:]
--- a/doc/src/suffix.txt
+++ b/doc/src/suffix.txt
@ -50,7 +50,7 @@ Intel(R) Xeon Phi(TM) coprocessors. :l

 KOKKOS = a collection of atom, pair, and fix styles optimized to run
 using the Kokkos library on various kinds of hardware, including GPUs
-via Cuda and many-core chips via OpenMP or threading. :l
+via CUDA and many-core chips via OpenMP or threading. :l

 USER-OMP = a collection of pair, bond, angle, dihedral, improper,
 kspace, compute, and fix styles with support for OpenMP
--- a/doc/src/tutorial_bash_on_windows.txt
+++ b/doc/src/tutorial_bash_on_windows.txt
@ -0,0 +1,203 @@
+"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
+
+Using LAMMPS with Bash on Windows :h3
+[written by Richard Berger]
+
+:line
+Starting with Windows 10 you can install Linux tools directly in Windows. This
+allows you to compile LAMMPS following the same procedure as on a real Ubuntu
+Linux installation. Software can be easily installed using the package manager
+via apt-get and all files are accessible in both the Windows Explorer and your
+Linux shell (bash). This avoids switching to a different operating system or
+installing a virtual machine. Everything runs on Windows.
+
+Installing Bash on Windows :h4
+
+Prerequisites :h5
+
+Windows 10 (64bit only)
+Latest updates installed :ul
+
+Enable developer mode :h5
+You enable this feature by first opening Windows Settings and enabling
+Developer mode. Go to the Windows settings and search for "developer". This
+will allow you to install software which comes from outside of the Windows
+Store.  You might be prompted to reboot your compute. Please do so.
+
+:image(JPG/bow_tutorial_01_small.png,JPG/bow_tutorial_01.png)
+:image(JPG/bow_tutorial_02_small.png,JPG/bow_tutorial_02.png)
+:image(JPG/bow_tutorial_03_small.png,JPG/bow_tutorial_03.png)
+
+Install Windows Subsystem for Linux :h5
+
+Next you must ensure that the Window Subsystem for Linux is installed. Again,
+search for "enable windows features" in the Settings dialog. This opens a
+dialog with a list of features you can install. Add a checkmark to Windows
+Subsystem for Linux (Beta) and press OK.   
+
+:image(JPG/bow_tutorial_04_small.png,JPG/bow_tutorial_04.png)
+:image(JPG/bow_tutorial_05.png,JPG/bow_tutorial_05.png)
+
+Install Bash for Windows :h5
+
+After installation completes, type "bash" in the Windows Start menu search.
+Select the first found option. This will launch a command-line window which
+will prompt you about installing Ubuntu on Windows. Confirm with "y" and press
+enter. This will then download Ubuntu for Windows.
+
+:image(JPG/bow_tutorial_06.png)
+:image(JPG/bow_tutorial_07.png)
+  
+During installation, you will be asked for a new password. This will be used
+for installing new software and running commands with sudo.
+
+:image(JPG/bow_tutorial_08.png)
+ 
+Type exit to close the command-line window.
+
+Go to the Start menu and type "bash" again. This time you will see a "Bash on
+Ubuntu on Windows" Icon. Start this program.
+
+:image(JPG/bow_tutorial_09.png)
+
+Congratulations, you have installed [Bash on Ubuntu on Windows].
+
+:image(JPG/bow_tutorial_10.png)
+
+:line
+
+Compiling LAMMPS in Bash on Windows :h4
+
+The installation of LAMMPS in this environment is identical to working inside
+of a real Ubuntu Linux installation. At the time writing, it uses Ubuntu 16.04.
+
+Installing prerequisite packages :h5
+
+First upgrade all existing packages using
+
+sudo apt update
+sudo apt upgrade -y :pre
+
+Next install the following packages, which include compilers and libraries
+needed for various LAMMPS features:
+
+sudo apt install -y build-essential ccache gfortran openmpi-bin libopenmpi-dev libfftw3-dev libjpeg-dev libpng12-dev python-dev python-virtualenv libblas-dev liblapack-dev libhdf5-serial-dev hdf5-tools :pre
+
+Files in Ubuntu on Windows :h5
+
+When you launch "Bash on Ubuntu on Windows" you will start out in your Linux
+user home directory /home/[username]. You can access your Windows user directory
+using the /mnt/c/Users/[username] folder.
+
+
+Download LAMMPS :h5
+
+Obtain a copy of the LAMMPS code and go into it using "cd"
+
+Option 1: Downloading LAMMPS tarball using wget :h6
+
+wget http://lammps.sandia.gov/tars/lammps-stable.tar.gz
+tar xvzf lammps-stable.tar.gz
+cd lammps-31Mar17 :pre
+
+Option 2: Obtaining LAMMPS code from GitHub :h6
+
+git clone https://github.com/lammps/lammps.git
+cd lammps :pre
+
+Compiling LAMMPS :h5
+
+At this point you can compile LAMMPS like on Ubuntu Linux.
+
+Compiling serial version :h6
+
+cd src/
+make -j 4 serial :pre
+
+This will create an executable called lmp_serial in the src/ directory
+
+Compiling MPI version :h6
+
+cd src/
+make -j 4 mpi :pre
+
+This will create an executable called lmp_mpi in the src/ directory
+
+:line
+
+Finally, please note the absolute path of your src folder. You can get this using
+
+pwd :pre
+
+or
+
+echo $PWD :pre
+
+To run any examples you need the location of the executable. For now, let us
+save this location in a temporary variable
+
+LAMMPS_DIR=$PWD :pre
+
+:line
+
+Running an example script :h5
+
+Once compiled you can execute some of the LAMMPS examples. Switch into the
+examples/melt folder
+
+cd ../examples/melt :pre
+
+The full path of the serial executable is $LAMMPS_DIR/lmp_serial, while the mpi
+version is $LAMMPS_DIR/lmp_mpi. You can run the melt example with either
+version as follows:
+
+$LAMMPS_DIR/lmp_serial -in in.melt :pre
+
+or
+
+mpirun -np 4 $LAMMPS_DIR/lmp_mpi -in in.melt :pre
+
+Note the use of our variable $LAMMPS_DIR, which expands into the full path of
+the LAMMPS src folder we saved earlier.
+
+Adding your executable directory to your PATH :h6
+
+You can avoid having to type the full path of your LAMMPS binary by adding its
+parent folder to the PATH environment variable as follows:
+
+export PATH=$LAMMPS_DIR:$PATH :pre
+
+Input scripts can then be run like this:
+
+lmp_serial -in in.melt :pre
+
+or
+
+mpirun -np 4 lmp_mpi -in in.melt :pre
+
+However, this PATH variable will not persist if you close your bash window.
+To persist this setting edit the $HOME/.bashrc file using your favorite editor
+and add this line
+
+export PATH=/full/path/to/your/lammps/src:$PATH :pre
+
+[Example:]
+
+For an executable lmp_serial with a full path
+
+/home/richard/lammps/src/lmp_serial :pre
+
+the PATH variable should be
+
+export PATH=/home/richard/lammps/src:$PATH :pre
+
+NOTE: This should give you a jump start when trying to run LAMMPS on Windows.
+To become effective in this environment I encourage you to look into Linux
+tutorials explaining Bash and Basic Unix commands (e.g., "Linux
+Journey"_https://linuxjourney.com)
--- a/doc/src/tutorial_drude.txt
+++ b/doc/src/tutorial_drude.txt
@ -176,12 +176,13 @@ By recognizing the fix {drude}, LAMMPS will find and store matching
 DC-DP pairs and will treat DP as equivalent to their DC in the
 {special bonds} relations.  It may be necessary to extend the space
 for storing such special relations.  In this case extra space should
-be reserved by using the {extra} keyword of the {special_bonds}
+be reserved by using the {extra/special/per/atom} keyword of either
+the "read_data"_read_data.html or "create_box"_create_box.html
 command.  With our phenol, there is 1 more special neighbor for which
 space is required.  Otherwise LAMMPS crashes and gives the required
 value.

-special_bonds lj/coul 0.0 0.0 0.5 extra 1 :pre
+read_data data-p.lmp extra/special/per/atom 1 :pre

 Let us assume we want to run a simple NVT simulation at 300 K.  Note
 that Drude oscillators need to be thermalized at a low temperature in
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@ -48,21 +48,17 @@ System-wide Installation :h3
 Step 1: Building LAMMPS as a shared library :h4

 To use LAMMPS inside of Python it has to be compiled as shared library. This
-library is then loaded by the Python interface. In this example, we use the
-Make.py utility to create a Makefile with C++ exceptions, PNG, JPEG and FFMPEG
-output support enabled. Finally, we also enable the MOLECULE package and compile
-using the generated {auto} Makefile.
+library is then loaded by the Python interface. In this example we enable the
+MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
+output support enabled.

 cd $LAMMPS_DIR/src :pre

-# generate custom Makefile
-python Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre
-
 # add packages if necessary
 make yes-MOLECULE :pre

 # compile shared library using Makefile
-make mode=shlib auto :pre
+make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG -DLAMMPS_EXCEPTIONS" JPG_LIB="-lpng -ljpeg" :pre

 Step 2: Installing the LAMMPS Python package :h4

--- a/doc/src/tutorials.txt
+++ b/doc/src/tutorials.txt
@ -8,6 +8,7 @@ Tutorials :h1
   tutorial_drude
   tutorial_github
   tutorial_pylammps
+   tutorial_bash_on_windows
   body
   manifolds

--- a/examples/README
+++ b/examples/README
@ -58,7 +58,7 @@ These are the sample problems and their output in the various
 sub-directories:

 accelerate: use of all the various accelerator packages
-airebo:   example for using AIREBO and AIREBO-M
+airebo:   polyethylene with AIREBO potential
 balance:  dynamic load balancing, 2d system
 body:     body particles, 2d system
 cmap:     CMAP 5-body contributions to CHARMM force field
--- a/examples/USER/quip/in.gap
+++ b/examples/USER/quip/in.gap
@ -17,6 +17,6 @@ fix		1 all nve
 thermo		10
 timestep	0.001

-dump		1 all custom 10 dump.gap id fx fy fz
+#dump		1 all custom 10 dump.gap id fx fy fz

 run		40
--- a/examples/USER/quip/in.molecular
+++ b/examples/USER/quip/in.molecular
@ -1,7 +1,6 @@
 units metal
 atom_style full
 boundary p p p
-processors 1 1 1
 timestep 0.0001 # 0.1 fs

 read_data methane-box-8.data
@ -28,7 +27,7 @@ pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0

 # Intramolecular
 # Tell QUIP to pretend this is silane (which is covered by the parameter file)
-pair_coeff * * quip ip.parms.SW.xml "IP SW" 14 1
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
 bond_style none
 angle_style none

--- a/examples/USER/quip/in.sw
+++ b/examples/USER/quip/in.sw
@ -10,6 +10,7 @@ read_data	data_sw
 pair_style	quip
 pair_coeff	* * sw_example.xml "IP SW" 14

+velocity        all create 10.0 355311
 neighbor	0.3 bin
 neigh_modify	delay 10

@ -17,6 +18,6 @@ fix		1 all nve
 thermo		10
 timestep	0.001

-dump		1 all custom 10 dump.sw id fx fy fz
+#dump		1 all custom 10 dump.sw id fx fy fz

-run		1
+run		100
--- a/examples/USER/quip/log.24Jul17.gap.g++.1
+++ b/examples/USER/quip/log.24Jul17.gap.g++.1
@ -0,0 +1,76 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of GAP potential for Si system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data_gap
+  orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  64 atoms
+
+pair_style	quip
+pair_coeff	* * gap_example.xml "Potential xml_label=GAP_2015_2_20_0_10_54_35_765" 14
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all custom 10 dump.gap id fx fy fz
+
+run		40
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.689 | 2.689 | 2.689 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -10412.677            0   -10412.677   -107490.01 
+      10    173.98393   -10414.096            0   -10412.679   -91270.969 
+      20    417.38493    -10416.08            0   -10412.681   -42816.133 
+      30    434.34789   -10416.217            0    -10412.68      2459.83 
+      40    423.05899   -10416.124            0   -10412.679    22936.209 
+Loop time of 1.83555 on 1 procs for 40 steps with 64 atoms
+
+Performance: 1.883 ns/day, 12.747 hours/ns, 21.792 timesteps/s
+98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8349     | 1.8349     | 1.8349     |   0.0 | 99.96
+Neigh   | 0.00022817 | 0.00022817 | 0.00022817 |   0.0 |  0.01
+Comm    | 0.00013709 | 0.00013709 | 0.00013709 |   0.0 |  0.01
+Output  | 9.8228e-05 | 9.8228e-05 | 9.8228e-05 |   0.0 |  0.01
+Modify  | 8.6308e-05 | 8.6308e-05 | 8.6308e-05 |   0.0 |  0.00
+Other   |            | 0.0001223  |            |       |  0.01
+
+Nlocal:    64 ave 64 max 64 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    303 ave 303 max 303 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  1080 ave 1080 max 1080 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 1080
+Ave neighs/atom = 16.875
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:01
--- a/examples/USER/quip/log.24Jul17.gap.g++.4
+++ b/examples/USER/quip/log.24Jul17.gap.g++.4
@ -0,0 +1,76 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of GAP potential for Si system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data_gap
+  orthogonal box = (0 0 0) to (10.9685 10.9685 10.9685)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  64 atoms
+
+pair_style	quip
+pair_coeff	* * gap_example.xml "Potential xml_label=GAP_2015_2_20_0_10_54_35_765" 14
+
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all custom 10 dump.gap id fx fy fz
+
+run		40
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.3
+  ghost atom cutoff = 4.3
+  binsize = 2.15, bins = 6 6 6
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.685 | 2.779 | 3.06 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0            0   -10412.677            0   -10412.677   -107490.01 
+      10    173.98393   -10414.096            0   -10412.679   -91270.969 
+      20    417.38493    -10416.08            0   -10412.681   -42816.133 
+      30    434.34789   -10416.217            0    -10412.68      2459.83 
+      40    423.05899   -10416.124            0   -10412.679    22936.209 
+Loop time of 0.837345 on 4 procs for 40 steps with 64 atoms
+
+Performance: 4.127 ns/day, 5.815 hours/ns, 47.770 timesteps/s
+96.0% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.73144    | 0.79214    | 0.83586    |   4.3 | 94.60
+Neigh   | 5.7936e-05 | 6.5327e-05 | 7.1049e-05 |   0.0 |  0.01
+Comm    | 0.00085807 | 0.044631   | 0.10532    |  18.0 |  5.33
+Output  | 0.00013208 | 0.00013494 | 0.00013733 |   0.0 |  0.02
+Modify  | 6.0558e-05 | 7.8678e-05 | 9.5129e-05 |   0.0 |  0.01
+Other   |            | 0.0002971  |            |       |  0.04
+
+Nlocal:    16 ave 18 max 14 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:    174 ave 182 max 167 min
+Histogram: 1 0 0 0 2 0 0 0 0 1
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  270 ave 294 max 237 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+
+Total # of neighbors = 1080
+Ave neighs/atom = 16.875
+Neighbor list builds = 2
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/quip/log.24Jul17.molecular.g++.1
+++ b/examples/USER/quip/log.24Jul17.molecular.g++.1
@ -0,0 +1,130 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+units metal
+atom_style full
+boundary p p p
+timestep 0.0001 # 0.1 fs
+
+read_data methane-box-8.data
+  orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  40 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  reading bonds ...
+  32 bonds
+  reading angles ...
+  48 angles
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  3 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+# DISCLAIMER: This potential mixes parameters from methane and silane
+# potentials and is NOT intended to be a realistic representation of either
+# system.  It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
+# including the use of separate 'special_bonds' settings.
+
+pair_style hybrid/overlay lj/cut 8.0 quip
+
+# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
+# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
+special_bonds lj/coul 0.999999999 0.999999999 0.999999999
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  3 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
+# Coulomb interactions ommitted for simplicity
+pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
+pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
+pair_coeff 1 2 lj/cut 0.0019295487 2.95
+pair_modify shift no
+# change exclusion settings for lj/cut only: exclude bonded pairs
+pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
+
+# Intramolecular
+# Tell QUIP to pretend this is silane (which is covered by the parameter file)
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
+bond_style none
+angle_style none
+
+fix 1 all nve
+
+# Include diagnostics that allow us to compare to a pure QUIP run
+compute equip all pair quip
+compute evdw all pair lj/cut
+compute vir all pressure NULL virial
+
+thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
+thermo 1
+
+# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
+# dump_modify 1 sort id
+
+run 10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 2 2 2
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.288 | 8.288 | 8.288 Mbytes
+Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip 
+       0   -5.3530213            0   -5.3530213            0    518847.56    518847.56  -0.10904079   -5.2439805 
+       1   -5.9384459   0.58384822   -5.3545977    115.81657     517370.5    516488.87  -0.10783656   -5.8306093 
+       2    -7.669616    2.3104051   -5.3592109    458.30954    512986.36    509497.58  -0.10422283   -7.5653932 
+       3   -10.473314    5.1069211   -5.3663924    1013.0477    505833.04    498121.43 -0.098049469   -10.375264 
+       4   -14.234705     8.859182   -5.3755227    1757.3747    496127.44    482749.79 -0.089147485   -14.145557 
+       5   -18.806851    13.420941   -5.3859098      2662.28    484148.76    463882.72 -0.077305196   -18.729546 
+       6   -24.021727    18.625147   -5.3965797    3694.6259    470219.95    442095.39  -0.06194509   -23.959782 
+       7   -29.702647    24.295529   -5.4071176     4819.446    454683.57    417996.56 -0.042859727   -29.659787 
+       8    -35.67405    30.257258   -5.4167913    6002.0599    437887.03    392197.62 -0.019248651   -35.654801 
+       9   -41.771047    36.345757   -5.4252893    7209.8209    420163.51    365280.27 0.0096063065   -41.780653 
+      10   -47.845522    42.413161   -5.4323614    8413.3973    401821.91     337776.7  0.044743702   -47.890266 
+Loop time of 0.0537777 on 1 procs for 10 steps with 40 atoms
+
+Performance: 1.607 ns/day, 14.938 hours/ns, 185.951 timesteps/s
+90.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.053478   | 0.053478   | 0.053478   |   0.0 | 99.44
+Bond    | 1.9073e-06 | 1.9073e-06 | 1.9073e-06 |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 7.7724e-05 | 7.7724e-05 | 7.7724e-05 |   0.0 |  0.14
+Output  | 0.00018263 | 0.00018263 | 0.00018263 |   0.0 |  0.34
+Modify  | 1.5974e-05 | 1.5974e-05 | 1.5974e-05 |   0.0 |  0.03
+Other   |            | 2.122e-05  |            |       |  0.04
+
+Nlocal:    40 ave 40 max 40 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    1175 ave 1175 max 1175 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4768 ave 4768 max 4768 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  9536 ave 9536 max 9536 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 9536
+Ave neighs/atom = 238.4
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/quip/log.24Jul17.molecular.g++.4
+++ b/examples/USER/quip/log.24Jul17.molecular.g++.4
@ -0,0 +1,130 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+units metal
+atom_style full
+boundary p p p
+timestep 0.0001 # 0.1 fs
+
+read_data methane-box-8.data
+  orthogonal box = (-0.499095 -0.270629 0.131683) to (8.4109 8.63937 9.04168)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  40 atoms
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  reading bonds ...
+  32 bonds
+  reading angles ...
+  48 angles
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  3 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+# DISCLAIMER: This potential mixes parameters from methane and silane
+# potentials and is NOT intended to be a realistic representation of either
+# system.  It is meant to demonstrate the use of hybrid QUIP/LAMMPS potentials,
+# including the use of separate 'special_bonds' settings.
+
+pair_style hybrid/overlay lj/cut 8.0 quip
+
+# exclusion setting for quip; cannot be exactly 1.0 1.0 1.0,
+# since that would not flag 1-2, 1-3, and 1-4 pairs in lj/cut
+special_bonds lj/coul 0.999999999 0.999999999 0.999999999
+  4 = max # of 1-2 neighbors
+  3 = max # of 1-3 neighbors
+  3 = max # of 1-4 neighbors
+  4 = max # of special neighbors
+
+# Intermolecular: OPLS (JACS 118 (45), p. 11225 (1996))
+# Coulomb interactions ommitted for simplicity
+pair_coeff 1 1 lj/cut 0.0028619844 3.5 # CT
+pair_coeff 2 2 lj/cut 0.0013009018 2.5 # HC
+pair_coeff 1 2 lj/cut 0.0019295487 2.95
+pair_modify shift no
+# change exclusion settings for lj/cut only: exclude bonded pairs
+pair_modify pair lj/cut special lj/coul 0.0 0.0 0.0
+
+# Intramolecular
+# Tell QUIP to pretend this is silane (which is covered by the parameter file)
+pair_coeff * * quip sw_example.xml "IP SW" 14 1
+bond_style none
+angle_style none
+
+fix 1 all nve
+
+# Include diagnostics that allow us to compare to a pure QUIP run
+compute equip all pair quip
+compute evdw all pair lj/cut
+compute vir all pressure NULL virial
+
+thermo_style custom step epair ke etotal temp press c_vir c_evdw c_equip
+thermo 1
+
+# dump 1 all custom 1 dump.molecular id type x y z fx fy fz
+# dump_modify 1 sort id
+
+run 10
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 10
+  ghost atom cutoff = 10
+  binsize = 5, bins = 2 2 2
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair lj/cut, perpetual, half/full from (2)
+      attributes: half, newton on
+      pair build: halffull/newton
+      stencil: none
+      bin: none
+  (2) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 8.26 | 8.386 | 8.762 Mbytes
+Step E_pair KinEng TotEng Temp Press c_vir c_evdw c_equip 
+       0   -5.3530213            0   -5.3530213            0    518847.56    518847.56  -0.10904079   -5.2439805 
+       1   -5.9384459   0.58384822   -5.3545977    115.81657     517370.5    516488.87  -0.10783656   -5.8306093 
+       2    -7.669616    2.3104051   -5.3592109    458.30954    512986.36    509497.58  -0.10422283   -7.5653932 
+       3   -10.473314    5.1069211   -5.3663924    1013.0477    505833.04    498121.43 -0.098049469   -10.375264 
+       4   -14.234705     8.859182   -5.3755227    1757.3747    496127.44    482749.79 -0.089147485   -14.145557 
+       5   -18.806851    13.420941   -5.3859098      2662.28    484148.76    463882.72 -0.077305196   -18.729546 
+       6   -24.021727    18.625147   -5.3965797    3694.6259    470219.95    442095.39  -0.06194509   -23.959782 
+       7   -29.702647    24.295529   -5.4071176     4819.446    454683.57    417996.56 -0.042859727   -29.659787 
+       8    -35.67405    30.257258   -5.4167913    6002.0599    437887.03    392197.62 -0.019248651   -35.654801 
+       9   -41.771047    36.345757   -5.4252893    7209.8209    420163.51    365280.27 0.0096063065   -41.780653 
+      10   -47.845522    42.413161   -5.4323614    8413.3973    401821.91     337776.7  0.044743702   -47.890266 
+Loop time of 0.0506847 on 4 procs for 10 steps with 40 atoms
+
+Performance: 1.705 ns/day, 14.079 hours/ns, 197.298 timesteps/s
+94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.04216    | 0.045656   | 0.049349   |   1.2 | 90.08
+Bond    | 1.9073e-06 | 2.4438e-06 | 2.861e-06  |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00068545 | 0.004438   | 0.0079191  |   3.9 |  8.76
+Output  | 0.00048304 | 0.00053334 | 0.00060964 |   0.0 |  1.05
+Modify  | 1.1444e-05 | 1.4424e-05 | 1.9312e-05 |   0.0 |  0.03
+Other   |            | 4.047e-05  |            |       |  0.08
+
+Nlocal:    10 ave 15 max 6 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+Nghost:    878 ave 948 max 812 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:    1192 ave 1764 max 731 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+FullNghs:  2384 ave 3527 max 1439 min
+Histogram: 1 0 0 1 1 0 0 0 0 1
+
+Total # of neighbors = 9536
+Ave neighs/atom = 238.4
+Ave special neighs/atom = 4
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/quip/log.24Jul17.sw.g++.1
+++ b/examples/USER/quip/log.24Jul17.sw.g++.1
@ -0,0 +1,83 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of SW potential for Si system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data_sw
+  orthogonal box = (0 0 0) to (5.431 5.431 5.431)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8 atoms
+
+pair_style	quip
+pair_coeff	* * sw_example.xml "IP SW" 14
+
+velocity        all create 10.0 355311
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all custom 10 dump.sw id fx fy fz
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2258
+  ghost atom cutoff = 4.2258
+  binsize = 2.1129, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.684 | 2.684 | 2.684 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0           10       -34.68            0   -34.670952    32.206289 
+      10    4.5659178   -34.675073            0   -34.670942    46.253731 
+      20     1.606683   -34.672391            0   -34.670937    44.736892 
+      30    6.7007748   -34.677011            0   -34.670948    16.403049 
+      40     5.682757   -34.676087            0   -34.670945    18.696408 
+      50    2.2140716   -34.672942            0   -34.670939    37.592282 
+      60    5.0475382   -34.675512            0   -34.670944    37.331666 
+      70    7.0990979   -34.677369            0   -34.670946    40.533757 
+      80    5.7306189   -34.676128            0   -34.670943    47.748813 
+      90    5.0895648   -34.675549            0   -34.670944    38.092721 
+     100    4.1070919   -34.674659            0   -34.670943    28.737864 
+Loop time of 0.384233 on 1 procs for 100 steps with 8 atoms
+
+Performance: 22.486 ns/day, 1.067 hours/ns, 260.259 timesteps/s
+94.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.38365    | 0.38365    | 0.38365    |   0.0 | 99.85
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.00017333 | 0.00017333 | 0.00017333 |   0.0 |  0.05
+Output  | 0.00014162 | 0.00014162 | 0.00014162 |   0.0 |  0.04
+Modify  | 7.081e-05  | 7.081e-05  | 7.081e-05  |   0.0 |  0.02
+Other   |            | 0.0001957  |            |       |  0.05
+
+Nlocal:    8 ave 8 max 8 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    162 ave 162 max 162 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+FullNghs:  128 ave 128 max 128 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/examples/USER/quip/log.24Jul17.sw.g++.4
+++ b/examples/USER/quip/log.24Jul17.sw.g++.4
@ -0,0 +1,83 @@
+LAMMPS (24 Jul 2017)
+  using 1 OpenMP thread(s) per MPI task
+# Test of SW potential for Si system
+
+units		metal
+boundary	p p p
+
+atom_style	atomic
+
+read_data	data_sw
+  orthogonal box = (0 0 0) to (5.431 5.431 5.431)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  8 atoms
+
+pair_style	quip
+pair_coeff	* * sw_example.xml "IP SW" 14
+
+velocity        all create 10.0 355311
+neighbor	0.3 bin
+neigh_modify	delay 10
+
+fix		1 all nve
+thermo		10
+timestep	0.001
+
+#dump		1 all custom 10 dump.sw id fx fy fz
+
+run		100
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 4.2258
+  ghost atom cutoff = 4.2258
+  binsize = 2.1129, bins = 3 3 3
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair quip, perpetual
+      attributes: full, newton on
+      pair build: full/bin/atomonly
+      stencil: full/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 2.698 | 2.698 | 2.698 Mbytes
+Step Temp E_pair E_mol TotEng Press 
+       0           10       -34.68            0   -34.670952    32.206289 
+      10    4.5659178   -34.675073            0   -34.670942    46.253731 
+      20     1.606683   -34.672391            0   -34.670937    44.736892 
+      30    6.7007748   -34.677011            0   -34.670948    16.403049 
+      40     5.682757   -34.676087            0   -34.670945    18.696408 
+      50    2.2140716   -34.672942            0   -34.670939    37.592282 
+      60    5.0475382   -34.675512            0   -34.670944    37.331666 
+      70    7.0990979   -34.677369            0   -34.670946    40.533757 
+      80    5.7306189   -34.676128            0   -34.670943    47.748813 
+      90    5.0895648   -34.675549            0   -34.670944    38.092721 
+     100    4.1070919   -34.674659            0   -34.670943    28.737864 
+Loop time of 0.423803 on 4 procs for 100 steps with 8 atoms
+
+Performance: 20.387 ns/day, 1.177 hours/ns, 235.959 timesteps/s
+90.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.39332    | 0.40011    | 0.40704    |   0.8 | 94.41
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.015632   | 0.022605   | 0.029425   |   3.3 |  5.33
+Output  | 0.00025702 | 0.00028491 | 0.00035429 |   0.0 |  0.07
+Modify  | 7.3671e-05 | 8.1897e-05 | 8.9884e-05 |   0.0 |  0.02
+Other   |            | 0.0007259  |            |       |  0.17
+
+Nlocal:    2 ave 2 max 2 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Nghost:    113 ave 113 max 113 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+Neighs:    0 ave 0 max 0 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+FullNghs:  32 ave 32 max 32 min
+Histogram: 4 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 128
+Ave neighs/atom = 16
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:00
--- a/lib/.gitignore
+++ b/lib/.gitignore
@ -1 +1,3 @@
 Makefile.lammps
+.depend
+Makefile.auto
--- a/lib/Install.py
+++ b/lib/Install.py
@ -4,24 +4,35 @@
 # soft linked to by many of the lib/Install.py files
 # used to automate the steps described in the corresponding lib/README

-import sys,commands,os
+from __future__ import print_function
+import sys,os,subprocess

 # help message

 help = """
-Syntax: python Install.py -m machine -e suffix
-  specify -m and optionally -e, order does not matter
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
+Syntax from lib dir: python Install.py -m machine -e suffix
+
+libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
+specify -m and optionally -e, order does not matter
+
  -m = peform a clean followed by "make -f Makefile.machine"
       machine = suffix of a lib/Makefile.* file
  -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
       does not alter existing Makefile.machine
+
+Examples:
+
+make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
+make lib-colvars args="-m mpi"  # build USER-COLVARS lib with same settings as in the mpi Makefile in src
+make lib-meam args="-m ifort"   # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
 """

 # print error message or help

 def error(str=None):
-  if not str: print help
-  else: print "ERROR",str
+  if not str: print(help)
+  else: print("ERROR",str)
  sys.exit()

 # parse args
@ -38,12 +49,12 @@ while iarg < nargs:
  if args[iarg] == "-m":
    if iarg+2 > nargs: error()
    machine = args[iarg+1]
-    iarg += 2  
+    iarg += 2
  elif args[iarg] == "-e":
    if iarg+2 > nargs: error()
    extraflag = 1
    suffix = args[iarg+1]
-    iarg += 2  
+    iarg += 2
  else: error()

 # set lib from working dir
@ -53,30 +64,38 @@ lib = os.path.basename(cwd)

 # create Makefile.auto as copy of Makefile.machine
 # reset EXTRAMAKE if requested
-  
+
 if not os.path.exists("Makefile.%s" % machine):
  error("lib/%s/Makefile.%s does not exist" % (lib,machine))

 lines = open("Makefile.%s" % machine,'r').readlines()
 fp = open("Makefile.auto",'w')

+has_extramake = False
 for line in lines:
  words = line.split()
-  if len(words) == 3 and extraflag and \
-        words[0] == "EXTRAMAKE" and words[1] == '=':
-    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
-  print >>fp,line,
+  if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
+    has_extramake = True
+    if extraflag:
+      line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+  fp.write(line)

 fp.close()

-# make the library via Makefile.auto
+# make the library via Makefile.auto optionally with parallel make

-print "Building lib%s.a ..." % lib
-cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
-txt = commands.getoutput(cmd)
-print txt
+try:
+  import multiprocessing
+  n_cpus = multiprocessing.cpu_count()
+except:
+  n_cpus = 1

-if os.path.exists("lib%s.a" % lib): print "Build was successful"
+print("Building lib%s.a ..." % lib)
+cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
+txt = subprocess.check_output(cmd,shell=True,stderr=subprocess.STDOUT)
+print(txt.decode('UTF-8'))
+
+if os.path.exists("lib%s.a" % lib): print("Build was successful")
 else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
-if not os.path.exists("Makefile.lammps"):
-  print "lib/%s/Makefile.lammps was NOT created" % lib
+if has_extramake and not os.path.exists("Makefile.lammps"):
+  print("lib/%s/Makefile.lammps was NOT created" % lib)
--- a/lib/atc/Install.py
+++ b/lib/atc/Install.py
@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-# install.py tool to do a generic build of a library
-# soft linked to by many of the lib/Install.py files
-# used to automate the steps described in the corresponding lib/README
-
-import sys,commands,os
-
-# help message
-
-help = """
-Syntax: python Install.py -m machine -e suffix
-  specify -m and optionally -e, order does not matter
-  -m = peform a clean followed by "make -f Makefile.machine"
-       machine = suffix of a lib/Makefile.* file
-  -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
-       does not alter existing Makefile.machine
-"""
-
-# print error message or help
-
-def error(str=None):
-  if not str: print help
-  else: print "ERROR",str
-  sys.exit()
-
-# parse args
-
-args = sys.argv[1:]
-nargs = len(args)
-if nargs == 0: error()
-
-machine = None
-extraflag = 0
-
-iarg = 0
-while iarg < nargs:
-  if args[iarg] == "-m":
-    if iarg+2 > nargs: error()
-    machine = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-e":
-    if iarg+2 > nargs: error()
-    extraflag = 1
-    suffix = args[iarg+1]
-    iarg += 2  
-  else: error()
-
-# set lib from working dir
-
-cwd = os.getcwd()
-lib = os.path.basename(cwd)
-
-# create Makefile.auto as copy of Makefile.machine
-# reset EXTRAMAKE if requested
-  
-if not os.path.exists("Makefile.%s" % machine):
-  error("lib/%s/Makefile.%s does not exist" % (lib,machine))
-
-lines = open("Makefile.%s" % machine,'r').readlines()
-fp = open("Makefile.auto",'w')
-
-for line in lines:
-  words = line.split()
-  if len(words) == 3 and extraflag and \
-        words[0] == "EXTRAMAKE" and words[1] == '=':
-    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
-  print >>fp,line,
-
-fp.close()
-
-# make the library via Makefile.auto
-
-print "Building lib%s.a ..." % lib
-cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
-txt = commands.getoutput(cmd)
-print txt
-
-if os.path.exists("lib%s.a" % lib): print "Build was successful"
-else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
-if not os.path.exists("Makefile.lammps"):
-  print "lib/%s/Makefile.lammps was NOT created" % lib
--- a/lib/atc/Install.py
+++ b/lib/atc/Install.py
@ -0,0 +1 @@
+../Install.py
--- a/lib/atc/Makefile.g++
+++ b/lib/atc/Makefile.g++
@ -1,3 +1,4 @@
+# library build -*- makefile -*-
 SHELL = /bin/sh

 # which file will be copied to Makefile.lammps
@ -5,6 +6,7 @@ SHELL = /bin/sh
 EXTRAMAKE = Makefile.lammps.installed

 # ------ FILES ------
+
 SRC = $(wildcard *.cpp)
 INC = $(wildcard *.h)

@ -47,5 +49,9 @@ DEPENDS = $(OBJ:.o=.d)

 # ------ CLEAN ------

+.PHONY: clean lib
+
 clean:
 	-rm *.o *.d *~ $(LIB)
+
+sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mingw32-cross
+++ b/lib/atc/Makefile.mingw32-cross
@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		i686-w64-mingw32-g++
-CCFLAGS =	-I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-                -ffast-math -funroll-loops -fstrict-aliasing 	\
-		-DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mingw32-cross-mpi
+++ b/lib/atc/Makefile.mingw32-cross-mpi
@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw32-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		i686-w64-mingw32-g++
-CCFLAGS =	-I../../tools/mingw-cross/mpich2-win32/include/		\
-		-I../../src -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-                -ffast-math -funroll-loops -fstrict-aliasing 	\
-		-DLAMMPS_SMALLSMALL -Wno-uninitialized
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mingw64-cross
+++ b/lib/atc/Makefile.mingw64-cross
@ -1,67 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		  x86_64-w64-mingw32-g++
-CCFLAGS =	-I../../src -I../../src/STUBS -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-		-DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mingw64-cross-mpi
+++ b/lib/atc/Makefile.mingw64-cross-mpi
@ -1,68 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.linalg
-
-# ------ FILES ------
-
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-
-# ------ DEFINITIONS ------
-
-DIR = Obj_mingw64-mpi/
-LIB = $(DIR)libatc.a
-OBJ = $(SRC:%.cpp=$(DIR)%.o)
-
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# the same MPI library that LAMMPS is built with
-
-CC =		  x86_64-w64-mingw32-g++
-CCFLAGS =	-I../../tools/mingw-cross/mpich2-win64/include/		\
-		-I../../src -DMPICH_IGNORE_CXX_SEEK	\
-		-O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-		-DLAMMPS_SMALLBIG -Wno-uninitialized
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rcs
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-USRLIB =
-SYSLIB =
-
-# ------ MAKE PROCEDURE ------
-
-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): $(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-# ------ COMPILE RULES ------
-
-$(DIR)%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-
-# ------ DEPENDENCIES ------
-
-DEPENDS = $(OBJ:.o=.d)
-
-# ------ CLEAN ------
-
-clean:
-	-rm $(DIR)*.o $(DIR)*.d *~ $(LIB)
-
-$(DEPENDS) : $(DIR)
-sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mpi
+++ b/lib/atc/Makefile.mpi
@ -0,0 +1,55 @@
+# library build -*- makefile -*-
+SHELL = /bin/sh
+
+# which file will be copied to Makefile.lammps
+EXTRAMAKE = Makefile.lammps.linalg
+
+# ------ FILES ------
+
+SRC = $(wildcard *.cpp)
+INC = $(wildcard *.h)
+
+# ------ DEFINITIONS ------
+
+LIB = libatc.a
+OBJ =   $(SRC:.cpp=.o)
+
+default: lib
+
+# ------ SETTINGS ------
+
+.PHONY: clean lib depend
+
+# include any MPI settings needed for the ATC library to build with
+# must be the same MPI library that LAMMPS is built with
+
+CC =	        mpicxx
+CCFLAGS =       -O3 -Wall -g -fPIC
+CPPFLAGS = -I../../src -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+ARCHIVE =	ar
+ARCHFLAG =	-rc
+# ------ MAKE PROCEDURE ------
+
+lib: 	$(OBJ)
+	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
+	@cp $(EXTRAMAKE) Makefile.lammps
+
+# ------ COMPILE RULES ------
+
+%.o:%.cpp
+	$(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
+
+# ------ DEPENDENCIES ------
+
+depend .depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+	@cc -O -o $@ $<
+
+# ------ CLEAN ------
+
+clean:
+	-rm -f *.o *~ .depend $(LIB) fastdep.exe
+
+sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mpic++
+++ b/lib/atc/Makefile.mpic++
@ -1,39 +0,0 @@
-# library build -*- makefile -*-
-SHELL = /bin/sh
-
-# which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.installed
-# ------ FILES ------
-SRC = $(wildcard *.cpp)
-INC = $(wildcard *.h)
-# ------ DEFINITIONS ------
-LIB = libatc.a
-OBJ =   $(SRC:.cpp=.o)
-# ------ SETTINGS ------
-
-# include any MPI settings needed for the ATC library to build with
-# must be the same MPI library that LAMMPS is built with
-
-CC =	        mpic++
-CCFLAGS =       -O3 -Wall -g -I../../src -fPIC -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
-ARCHIVE =	ar
-ARCHFLAG =	-rc
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
-# ------ MAKE PROCEDURE ------
-lib: 	$(OBJ)
-	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
-	@cp $(EXTRAMAKE) Makefile.lammps
-# ------ COMPILE RULES ------
-%.o:%.cpp
-	$(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
-# ------ DEPENDENCIES ------
-DEPENDS = $(OBJ:.o=.d)
-# ------ CLEAN ------
-clean:
-	-rm *.o *.d *~ $(LIB)
-
-sinclude $(DEPENDS)
--- a/lib/atc/Makefile.mpic++
+++ b/lib/atc/Makefile.mpic++
@ -0,0 +1 @@
+Makefile.mpi
--- a/lib/atc/Makefile.serial
+++ b/lib/atc/Makefile.serial
@ -14,18 +14,20 @@ INC = $(wildcard *.h)
 LIB = libatc.a
 OBJ =   $(SRC:.cpp=.o)

+default: lib
+
 # ------ SETTINGS ------

+.PHONY: clean lib depend
+
 # include any MPI settings needed for the ATC library to build with
 # must be the same MPI library that LAMMPS is built with

 CC =	        g++
-CCFLAGS =       -O -g -fPIC -I../../src -I../../src/STUBS
+CCFLAGS =       -O3 -g -fPIC
+CPPFLAGS = -I../../src -I../../src/STUBS
 ARCHIVE =	ar
 ARCHFLAG =	-rc
-DEPFLAGS =      -M
-LINK =         	$(CC)
-LINKFLAGS =	-O
 # ------ MAKE PROCEDURE ------

 lib: 	$(OBJ)
@ -35,17 +37,19 @@ lib: 	$(OBJ)
 # ------ COMPILE RULES ------

 %.o:%.cpp
-	$(CC) $(CCFLAGS) -c $<
-%.d:%.cpp
-	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
+	$(CC) $(CPPFLAGS) $(CCFLAGS) -c $<

 # ------ DEPENDENCIES ------

-DEPENDS = $(OBJ:.o=.d)
+depend .depend : fastdep.exe $(SRC)
+	@./fastdep.exe $(INCFLAGS) -- $^ > .depend || exit 1
+
+fastdep.exe: ../../src/DEPEND/fastdep.c
+	@cc -O -o $@ $<

 # ------ CLEAN ------

 clean:
-	-rm *.o *.d *~ $(LIB)
+	-rm -f *.o *~ .depend $(LIB) fastdep.exe

-sinclude $(DEPENDS)
+sinclude .depend
--- a/lib/awpmd/Install.py
+++ b/lib/awpmd/Install.py
@ -1,82 +0,0 @@
-#!/usr/bin/env python
-
-# install.py tool to do a generic build of a library
-# soft linked to by many of the lib/Install.py files
-# used to automate the steps described in the corresponding lib/README
-
-import sys,commands,os
-
-# help message
-
-help = """
-Syntax: python Install.py -m machine -e suffix
-  specify -m and optionally -e, order does not matter
-  -m = peform a clean followed by "make -f Makefile.machine"
-       machine = suffix of a lib/Makefile.* file
-  -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
-       does not alter existing Makefile.machine
-"""
-
-# print error message or help
-
-def error(str=None):
-  if not str: print help
-  else: print "ERROR",str
-  sys.exit()
-
-# parse args
-
-args = sys.argv[1:]
-nargs = len(args)
-if nargs == 0: error()
-
-machine = None
-extraflag = 0
-
-iarg = 0
-while iarg < nargs:
-  if args[iarg] == "-m":
-    if iarg+2 > nargs: error()
-    machine = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-e":
-    if iarg+2 > nargs: error()
-    extraflag = 1
-    suffix = args[iarg+1]
-    iarg += 2  
-  else: error()
-
-# set lib from working dir
-
-cwd = os.getcwd()
-lib = os.path.basename(cwd)
-
-# create Makefile.auto as copy of Makefile.machine
-# reset EXTRAMAKE if requested
-  
-if not os.path.exists("Makefile.%s" % machine):
-  error("lib/%s/Makefile.%s does not exist" % (lib,machine))
-
-lines = open("Makefile.%s" % machine,'r').readlines()
-fp = open("Makefile.auto",'w')
-
-for line in lines:
-  words = line.split()
-  if len(words) == 3 and extraflag and \
-        words[0] == "EXTRAMAKE" and words[1] == '=':
-    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
-  print >>fp,line,
-
-fp.close()
-
-# make the library via Makefile.auto
-
-print "Building lib%s.a ..." % lib
-cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
-txt = commands.getoutput(cmd)
-print txt
-
-if os.path.exists("lib%s.a" % lib): print "Build was successful"
-else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
-if not os.path.exists("Makefile.lammps"):
-  print "lib/%s/Makefile.lammps was NOT created" % lib
--- a/lib/awpmd/Install.py
+++ b/lib/awpmd/Install.py
@ -0,0 +1 @@
+../Install.py
--- a/lib/awpmd/Makefile.mingw32-cross-mpi
+++ b/lib/awpmd/Makefile.mingw32-cross-mpi
@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw32-cross
-	rm -f Obj_mingw32-mpi
-	ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	rm -f Obj_mingw32-mpi
-
--- a/lib/awpmd/Makefile.mingw64-cross-mpi
+++ b/lib/awpmd/Makefile.mingw64-cross-mpi
@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw64-cross
-	rm -f Obj_mingw64-mpi
-	ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	rm -f Obj_mingw64-mpi
-
--- a/lib/awpmd/Makefile.mingw64-cross
+++ b/lib/awpmd/Makefile.mingw64-cross
@ -1,4 +1,3 @@
-# library build -*- makefile -*-
 SHELL = /bin/sh

 # which file will be copied to Makefile.lammps
@ -7,9 +6,10 @@ EXTRAMAKE = Makefile.lammps.linalg

 # ------ FILES ------

-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
+SRC = \
+    ivutils/src/logexc.cpp \
+    systems/interact/TCP/wpmd.cpp \
+    systems/interact/TCP/wpmd_split.cpp

 INC = \
    cerf.h \
@ -27,21 +27,21 @@ INC = \
    wpmd_split.h

 # ------ DEFINITIONS ------
-DIR = Obj_mingw64/
-LIB = $(DIR)libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
+
+LIB = libawpmd.a
+OBJ =   $(SRC:.cpp=.o)

 # ------ SETTINGS ------

 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with

-CC =	  x86_64-w64-mingw32-g++
-CCFLAGS =  -O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE =	x86_64-w64-mingw32-ar
-ARCHFLAG =	-rscv
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
@ -50,23 +50,15 @@ SYSLIB =

 # ------ MAKE PROCEDURE ------

-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): 	$(OBJ)
+lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps

 # ------ COMPILE RULES ------

-$(DIR)%.o:%.cpp
+%.o:%.cpp
 	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
+%.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		

 # ------ DEPENDENCIES ------
@ -76,4 +68,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------

 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
--- a/lib/awpmd/Makefile.mpicc
+++ b/lib/awpmd/Makefile.mpicc
@ -36,8 +36,10 @@ OBJ =   $(SRC:.cpp=.o)
 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with

-CC =	    mpic++ 
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+CC =	    mpicxx
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
+
 ARCHIVE =	ar
 ARCHFLAG =	-rc
 DEPFLAGS =  -M
@ -66,4 +68,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------

 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
--- a/lib/awpmd/Makefile.mingw32-cross
+++ b/lib/awpmd/Makefile.mingw32-cross
@ -1,4 +1,3 @@
-# library build -*- makefile -*-
 SHELL = /bin/sh

 # which file will be copied to Makefile.lammps
@ -7,9 +6,10 @@ EXTRAMAKE = Makefile.lammps.linalg

 # ------ FILES ------

-SRC = logexc.cpp wpmd.cpp wpmd_split.cpp
-vpath %.cpp ivutils/src
-vpath %.cpp systems/interact/TCP
+SRC = \
+    ivutils/src/logexc.cpp \
+    systems/interact/TCP/wpmd.cpp \
+    systems/interact/TCP/wpmd_split.cpp

 INC = \
    cerf.h \
@ -27,22 +27,21 @@ INC = \
    wpmd_split.h

 # ------ DEFINITIONS ------
-DIR = Obj_mingw32/
-LIB = $(DIR)libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
+
+LIB = libawpmd.a
+OBJ =   $(SRC:.cpp=.o)

 # ------ SETTINGS ------

 # include any MPI settings needed for the ATC library to build with
 # the same MPI library that LAMMPS is built with

-CC =	  i686-w64-mingw32-g++
-CCFLAGS = 	-O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
-ARCHIVE =	i686-w64-mingw32-ar
-ARCHFLAG =	-rscv
+CC =	    g++
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
+	  -I../../src/STUBS
+
+ARCHIVE =	ar
+ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
@ -51,23 +50,15 @@ SYSLIB =

 # ------ MAKE PROCEDURE ------

-default: $(DIR) $(LIB) Makefile.lammps
-
-$(DIR):
-	mkdir $(DIR)
-
-Makefile.lammps:
-	@cp $(EXTRAMAKE) Makefile.lammps
-
-$(LIB): 	$(OBJ)
+lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps

 # ------ COMPILE RULES ------

-$(DIR)%.o:%.cpp
+%.o:%.cpp
 	$(CC) $(CCFLAGS) -c $< -o $@
-$(DIR)%.d:%.cpp
+%.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		

 # ------ DEPENDENCIES ------
@ -77,4 +68,4 @@ DEPENDS = $(OBJ:.o=.d)
 # ------ CLEAN ------

 clean:
-	-rm *.d *~ $(OBJ) $(LIB)
+	-rm -f *.d *~ $(OBJ) $(LIB)
--- a/lib/colvars/Install.py
+++ b/lib/colvars/Install.py
@ -13,7 +13,7 @@ Syntax from lib/colvars dir: python Install.py -m machine -e suffix

 specify -m and optionally -e, order does not matter

-  -m = peform a clean followed by "make -f Makefile.machine"
+  -m = delete all existing objects, followed by "make -f Makefile.machine"
       machine = suffix of a lib/colvars/Makefile.* or of a
         src/MAKE/MACHINES/Makefile.* file
  -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix
@ -21,14 +21,14 @@ specify -m and optionally -e, order does not matter

 Examples:

-make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler
+make lib-colvars args="-m mpi"     # build COLVARS lib with default mpi compiler wrapper
 """

 # print error message or help

 def error(str=None):
  if not str: print(help)
-  else: print("ERROR"),str
+  else: print("ERROR",str)
  sys.exit()

 # parse args
@ -45,12 +45,12 @@ while iarg < nargs:
  if args[iarg] == "-m":
    if iarg+2 > len(args): error()
    machine = args[iarg+1]
-    iarg += 2  
+    iarg += 2
  elif args[iarg] == "-e":
    if iarg+2 > len(args): error()
    extraflag = True
    suffix = args[iarg+1]
-    iarg += 2  
+    iarg += 2
  else: error()

 # set lib from working dir
@ -122,7 +122,7 @@ for line in lines:
  fp.write(line)
 fp.close()

-# make the library via Makefile.auto
+# make the library via Makefile.auto optionally with parallel make

 try:
  import multiprocessing
@ -132,9 +132,9 @@ except:

 print("Building lib%s.a ..." % lib)
 cmd = ["make -f Makefile.auto clean"]
-print(subprocess.check_output(cmd, shell=True).decode())
+print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))
 cmd = ["make -f Makefile.auto -j%d" % n_cpus]
-print(subprocess.check_output(cmd, shell=True).decode())
+print(subprocess.check_output(cmd, shell=True).decode('UTF-8'))

 if os.path.exists("lib%s.a" % lib): print("Build was successful")
 else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))
--- a/lib/colvars/Makefile.mingw32-cross
+++ b/lib/colvars/Makefile.mingw32-cross
@ -1,31 +0,0 @@
-# -*- makefile -*- to build Colvars module with MinGW 32-bit
-
-EXTRAMAKE = Makefile.lammps.empty
-
-COLVARS_LIB = libcolvars.a
-COLVARS_OBJ_DIR = Obj_mingw64/
-
-CXX =		i686-w64-mingw32-g++
-CXXFLAGS =	-O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
-		-fno-rtti -fno-exceptions -finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized
-AR =		i686-w64-mingw32-ar
-ARFLAGS =	-rscv
-SHELL =		/bin/sh
-
-.PHONY: default clean
-
-default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
-
-include Makefile.common
-
-$(COLVARS_OBJ_DIR):
-	mkdir $(COLVARS_OBJ_DIR)
-
-clean:
-	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-	-rmdir $(COLVARS_OBJ_DIR)
-
-Makefile.lammps:
-	-cp $(EXTRAMAKE) Makefile.lammps
--- a/lib/colvars/Makefile.mingw32-cross-mpi
+++ b/lib/colvars/Makefile.mingw32-cross-mpi
@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw32-cross
-	-rm -f Obj_mingw32-mpi
-	ln -s Obj_mingw32 Obj_mingw32-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw32-cross
-	-rm -f Obj_mingw32-mpi
-
--- a/lib/colvars/Makefile.mingw64-cross
+++ b/lib/colvars/Makefile.mingw64-cross
@ -1,31 +0,0 @@
-# -*- makefile -*- to build Colvars module with MinGW 32-bit
-
-EXTRAMAKE = Makefile.lammps.empty
-
-COLVARS_LIB = libcolvars.a
-COLVARS_OBJ_DIR = Obj_mingw32/
-
-CXX =		x86_64-w64-mingw32-g++
-CXXFLAGS =	-O2 -march=core2 -mtune=core2 -mpc64 -msse2		\
-		-fno-rtti -fno-exceptions -finline-functions		\
-                -ffast-math -funroll-loops -fstrict-aliasing		\
-                -Wall -W -Wno-uninitialized
-AR =		x86_64-w64-mingw32-ar
-ARFLAGS =	-rscv
-SHELL =		/bin/sh
-
-.PHONY: default clean
-
-default: $(COLVARS_OBJ_DIR) $(COLVARS_LIB) Makefile.lammps
-
-include Makefile.common
-
-$(COLVARS_OBJ_DIR):
-	mkdir $(COLVARS_OBJ_DIR)
-
-clean:
-	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
-	-rmdir $(COLVARS_OBJ_DIR)
-
-Makefile.lammps:
-	-cp $(EXTRAMAKE) Makefile.lammps
--- a/lib/colvars/Makefile.mingw64-cross-mpi
+++ b/lib/colvars/Makefile.mingw64-cross-mpi
@ -1,13 +0,0 @@
-# -*- makefile -*- wrapper for non-MPI libraries
-
-SHELL=/bin/sh
-
-all:
-	$(MAKE) $(MFLAGS) mingw64-cross
-	-rm -f Obj_mingw64-mpi
-	ln -s Obj_mingw64 Obj_mingw64-mpi
-
-clean:
-	$(MAKE) $(MFLAGS) clean-mingw64-cross
-	-rm -f Obj_mingw64-mpi
-
--- a/lib/colvars/Makefile.mpi
+++ b/lib/colvars/Makefile.mpi
@ -0,0 +1,25 @@
+# -*- makefile -*- to build Colvars module with default MPI compiler wrapper
+
+EXTRAMAKE = Makefile.lammps.empty
+
+COLVARS_LIB = libcolvars.a
+COLVARS_OBJ_DIR =
+
+CXX =		mpicxx
+CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops
+AR =		ar
+ARFLAGS =	-rscv
+SHELL =		/bin/sh
+
+.PHONY: default clean
+
+default: $(COLVARS_LIB) Makefile.lammps
+
+include Makefile.common
+
+clean:
+	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
+
+Makefile.lammps:
+	-cp $(EXTRAMAKE) Makefile.lammps
+
--- a/lib/colvars/Makefile.serial
+++ b/lib/colvars/Makefile.serial
@ -0,0 +1,25 @@
+# -*- makefile -*- to build Colvars module with GNU compiler
+
+EXTRAMAKE = Makefile.lammps.empty
+
+COLVARS_LIB = libcolvars.a
+COLVARS_OBJ_DIR =
+
+CXX =		g++
+CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops
+AR =		ar
+ARFLAGS =	-rscv
+SHELL =		/bin/sh
+
+.PHONY: default clean
+
+default: $(COLVARS_LIB) Makefile.lammps
+
+include Makefile.common
+
+clean:
+	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)
+
+Makefile.lammps:
+	-cp $(EXTRAMAKE) Makefile.lammps
+
--- a/lib/colvars/README
+++ b/lib/colvars/README
@ -32,7 +32,7 @@ where Makefile.g++ uses the GNU C++ compiler and is a good template to start.

 **Optional**: if you use the Install.py script provided in this folder, you
 can give the machine name as the '-m' argument.  This can be the suffix of one
-of the files from either this folder, or from src/MAKE.
+of the files from either this folder, or from src/MAKE/MACHINES.
 *This is only supported by the Install.py within the lib/colvars folder*.

 When you are done building this library, two files should
@ -53,10 +53,10 @@ settings in Makefile.common should work.
 For the reference manual see:
  http://colvars.github.io/colvars-refman-lammps

-A copy of reference manual is also in:
+A copy of the reference manual is also in:
  doc/PDF/colvars-refman-lammps.pdf

-Also included is a Doxygen-based developer documentation:
+Also available is a Doxygen-based developer documentation:
  http://colvars.github.io/doxygen/html/

 The reference article is:
--- a/lib/colvars/colvar.h
+++ b/lib/colvars/colvar.h
@ -88,7 +88,12 @@ public:
  static std::vector<feature *> cv_features;

  /// \brief Implementation of the feature list accessor for colvar
-  std::vector<feature *> &features() {
+  virtual const std::vector<feature *> &features()
+  {
+    return cv_features;
+  }
+  virtual std::vector<feature *> &modify_features()
+  {
    return cv_features;
  }

--- a/lib/colvars/colvaratoms.h
+++ b/lib/colvars/colvaratoms.h
@ -206,7 +206,12 @@ public:
  static std::vector<feature *> ag_features;

  /// \brief Implementation of the feature list accessor for atom group
-  virtual std::vector<feature *> &features() {
+  virtual const std::vector<feature *> &features()
+  {
+    return ag_features;
+  }
+  virtual std::vector<feature *> &modify_features()
+  {
    return ag_features;
  }

--- a/lib/colvars/colvarbias.cpp
+++ b/lib/colvars/colvarbias.cpp
@ -384,6 +384,7 @@ std::ostream & colvarbias::write_traj(std::ostream &os)
  os << " ";
  if (b_output_energy)
    os << " "
+       << std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
       << bias_energy;
  return os;
 }
--- a/lib/colvars/colvarbias.h
+++ b/lib/colvars/colvarbias.h
@ -175,7 +175,11 @@ public:
  static std::vector<feature *> cvb_features;

  /// \brief Implementation of the feature list accessor for colvarbias
-  virtual std::vector<feature *> &features()
+  virtual const std::vector<feature *> &features()
+  {
+    return cvb_features;
+  }
+  virtual std::vector<feature *> &modify_features()
  {
    return cvb_features;
  }
--- a/lib/colvars/colvarbias_restraint.cpp
+++ b/lib/colvars/colvarbias_restraint.cpp
@ -99,12 +99,9 @@ int colvarbias_restraint_centers::init(std::string const &conf)
  if (null_centers) {
    // try to initialize the restraint centers for the first time
    colvar_centers.resize(num_variables());
-    colvar_centers_raw.resize(num_variables());
    for (i = 0; i < num_variables(); i++) {
      colvar_centers[i].type(variables(i)->value());
      colvar_centers[i].reset();
-      colvar_centers_raw[i].type(variables(i)->value());
-      colvar_centers_raw[i].reset();
    }
  }

@ -113,7 +110,6 @@ int colvarbias_restraint_centers::init(std::string const &conf)
      if (cvm::debug()) {
        cvm::log("colvarbias_restraint: parsing initial centers, i = "+cvm::to_str(i)+".\n");
      }
-      colvar_centers_raw[i] = colvar_centers[i];
      colvar_centers[i].apply_constraints();
    }
    null_centers = false;
@ -141,8 +137,6 @@ int colvarbias_restraint_centers::change_configuration(std::string const &conf)
    for (size_t i = 0; i < num_variables(); i++) {
      colvar_centers[i].type(variables(i)->value());
      colvar_centers[i].apply_constraints();
-      colvar_centers_raw[i].type(variables(i)->value());
-      colvar_centers_raw[i] = colvar_centers[i];
    }
  }
  return COLVARS_OK;
@ -232,7 +226,6 @@ int colvarbias_restraint_moving::set_state_params(std::string const &conf)
 {
  if (b_chg_centers || b_chg_force_k) {
    if (target_nstages) {
-      //    cvm::log ("Reading current stage from the restart.\n");
      if (!get_keyval(conf, "stage", stage))
        cvm::error("Error: current stage is missing from the restart.\n");
    }
@ -265,100 +258,127 @@ int colvarbias_restraint_centers_moving::init(std::string const &conf)

  size_t i;
  if (get_keyval(conf, "targetCenters", target_centers, colvar_centers)) {
-    if (colvar_centers.size() != num_variables()) {
+    if (target_centers.size() != num_variables()) {
      cvm::error("Error: number of target centers does not match "
-                 "that of collective variables.\n");
+                 "that of collective variables.\n", INPUT_ERROR);
    }
    b_chg_centers = true;
    for (i = 0; i < target_centers.size(); i++) {
      target_centers[i].apply_constraints();
+      centers_incr.push_back(colvar_centers[i]);
+      centers_incr[i].reset();
    }
  }

  if (b_chg_centers) {
-    // parse moving restraint options
+    // parse moving schedule options
    colvarbias_restraint_moving::init(conf);
+    if (initial_centers.size() == 0) {
+      // One-time init
+      initial_centers = colvar_centers;
+    }
+    // Call to check that the definition is correct
+    for (i = 0; i < num_variables(); i++) {
+      colvarvalue const midpoint =
+        colvarvalue::interpolate(initial_centers[i],
+                                 target_centers[i],
+                                 0.5);
+    }
  } else {
    target_centers.clear();
    return COLVARS_OK;
  }

  get_keyval(conf, "outputCenters", b_output_centers, b_output_centers);
-  get_keyval(conf, "outputAccumulatedWork", b_output_acc_work, b_output_acc_work);
+  get_keyval(conf, "outputAccumulatedWork", b_output_acc_work,
+             b_output_acc_work); // TODO this conflicts with stages

  return COLVARS_OK;
 }


+int colvarbias_restraint_centers_moving::update_centers(cvm::real lambda)
+{
+  if (cvm::debug()) {
+    cvm::log("Updating centers for the restraint bias \""+
+             this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
+  }
+  size_t i;
+  for (i = 0; i < num_variables(); i++) {
+    colvarvalue const c_new = colvarvalue::interpolate(initial_centers[i],
+                                                       target_centers[i],
+                                                       lambda);
+    centers_incr[i] = (c_new).dist2_grad(colvar_centers[i]);
+    colvar_centers[i] = c_new;
+    variables(i)->wrap(colvar_centers[i]);
+  }
+  if (cvm::debug()) {
+    cvm::log("New centers for the restraint bias \""+
+             this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
+  }
+  return cvm::get_error();
+}
+
+
 int colvarbias_restraint_centers_moving::update()
 {
  if (b_chg_centers) {

-    if (cvm::debug()) {
-      cvm::log("Updating centers for the restraint bias \""+
-               this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
-    }
-
-    if (!centers_incr.size()) {
-      // if this is the first calculation, calculate the advancement
-      // at each simulation step (or stage, if applicable)
-      // (take current stage into account: it can be non-zero
-      //  if we are restarting a staged calculation)
-      centers_incr.resize(num_variables());
-      for (size_t i = 0; i < num_variables(); i++) {
-        centers_incr[i].type(variables(i)->value());
-        centers_incr[i] = (target_centers[i] - colvar_centers_raw[i]) /
-          cvm::real( target_nstages ? (target_nstages - stage) :
-                     (target_nsteps - cvm::step_absolute()));
-      }
-      if (cvm::debug()) {
-        cvm::log("Center increment for the restraint bias \""+
-                 this->name+"\": "+cvm::to_str(centers_incr)+" at stage "+cvm::to_str(stage)+ ".\n");
-      }
-    }
-
    if (target_nstages) {
-      if ((cvm::step_relative() > 0)
-          && (cvm::step_absolute() % target_nsteps) == 0
-          && stage < target_nstages) {
-
-        for (size_t i = 0; i < num_variables(); i++) {
-          colvar_centers_raw[i] += centers_incr[i];
-          colvar_centers[i] = colvar_centers_raw[i];
-          variables(i)->wrap(colvar_centers[i]);
-          colvar_centers[i].apply_constraints();
+      // Staged update
+      if (stage <= target_nstages) {
+        if ((cvm::step_relative() > 0) &&
+            ((cvm::step_absolute() % target_nsteps) == 1)) {
+          cvm::real const lambda =
+            cvm::real(stage)/cvm::real(target_nstages);
+          update_centers(lambda);
+          stage++;
+          cvm::log("Moving restraint \"" + this->name +
+                   "\" stage " + cvm::to_str(stage) +
+                   " : setting centers to " + cvm::to_str(colvar_centers) +
+                   " at step " +  cvm::to_str(cvm::step_absolute()));
+        } else {
+          for (size_t i = 0; i < num_variables(); i++) {
+            centers_incr[i].reset();
+          }
        }
-        stage++;
-        cvm::log("Moving restraint \"" + this->name +
-                 "\" stage " + cvm::to_str(stage) +
-                 " : setting centers to " + cvm::to_str(colvar_centers) +
-                 " at step " +  cvm::to_str(cvm::step_absolute()));
      }
-    } else if ((cvm::step_relative() > 0) && (cvm::step_absolute() <= target_nsteps)) {
-      // move the restraint centers in the direction of the targets
-      // (slow growth)
+    } else {
+      // Continuous update
+      if (cvm::step_absolute() <= target_nsteps) {
+        cvm::real const lambda =
+          cvm::real(cvm::step_absolute())/cvm::real(target_nsteps);
+        update_centers(lambda);
+      } else {
+        for (size_t i = 0; i < num_variables(); i++) {
+          centers_incr[i].reset();
+        }
+      }
+    }
+
+    if (cvm::step_relative() == 0) {
      for (size_t i = 0; i < num_variables(); i++) {
-        colvar_centers_raw[i] += centers_incr[i];
-        colvar_centers[i] = colvar_centers_raw[i];
-        variables(i)->wrap(colvar_centers[i]);
-        colvar_centers[i].apply_constraints();
+        // finite differences are undefined when restarting
+        centers_incr[i].reset();
      }
    }

    if (cvm::debug()) {
-      cvm::log("New centers for the restraint bias \""+
-               this->name+"\": "+cvm::to_str(colvar_centers)+".\n");
+      cvm::log("Center increment for the restraint bias \""+
+               this->name+"\": "+cvm::to_str(centers_incr)+
+               " at stage "+cvm::to_str(stage)+ ".\n");
    }
  }

-  return COLVARS_OK;
+  return cvm::get_error();
 }


 int colvarbias_restraint_centers_moving::update_acc_work()
 {
  if (b_output_acc_work) {
-    if ((cvm::step_relative() > 0) || (cvm::step_absolute() == 0)) {
+    if ((cvm::step_relative() > 0) &&
+        (cvm::step_absolute() <= target_nsteps)) {
      for (size_t i = 0; i < num_variables(); i++) {
        // project forces on the calculated increments at this step
        acc_work += colvar_forces[i] * centers_incr[i];
@ -383,13 +403,6 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const
         << colvar_centers[i];
    }
    os << "\n";
-    os << "centers_raw ";
-    for (i = 0; i < num_variables(); i++) {
-      os << " "
-         << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
-         << colvar_centers_raw[i];
-    }
-    os << "\n";

    if (b_output_acc_work) {
      os << "accumulatedWork "
@ -398,7 +411,7 @@ std::string const colvarbias_restraint_centers_moving::get_state_params() const
    }
  }

-  return colvarbias_restraint_moving::get_state_params() + os.str();
+  return os.str();
 }


@ -410,8 +423,6 @@ int colvarbias_restraint_centers_moving::set_state_params(std::string const &con
    //    cvm::log ("Reading the updated restraint centers from the restart.\n");
    if (!get_keyval(conf, "centers", colvar_centers))
      cvm::error("Error: restraint centers are missing from the restart.\n");
-    if (!get_keyval(conf, "centers_raw", colvar_centers_raw))
-      cvm::error("Error: \"raw\" restraint centers are missing from the restart.\n");
    if (b_output_acc_work) {
      if (!get_keyval(conf, "accumulatedWork", acc_work))
        cvm::error("Error: accumulatedWork is missing from the restart.\n");
@ -609,7 +620,7 @@ std::string const colvarbias_restraint_k_moving::get_state_params() const
       << std::setprecision(cvm::en_prec)
       << std::setw(cvm::en_width) << force_k << "\n";
  }
-  return colvarbias_restraint_moving::get_state_params() + os.str();
+  return os.str();
 }


@ -770,6 +781,7 @@ cvm::real colvarbias_restraint_harmonic::d_restraint_potential_dk(size_t i) cons
 std::string const colvarbias_restraint_harmonic::get_state_params() const
 {
  return colvarbias_restraint::get_state_params() +
+    colvarbias_restraint_moving::get_state_params() +
    colvarbias_restraint_centers_moving::get_state_params() +
    colvarbias_restraint_k_moving::get_state_params();
 }
@ -779,6 +791,7 @@ int colvarbias_restraint_harmonic::set_state_params(std::string const &conf)
 {
  int error_code = COLVARS_OK;
  error_code |= colvarbias_restraint::set_state_params(conf);
+  error_code |= colvarbias_restraint_moving::set_state_params(conf);
  error_code |= colvarbias_restraint_centers_moving::set_state_params(conf);
  error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
  return error_code;
@ -1037,6 +1050,7 @@ cvm::real colvarbias_restraint_harmonic_walls::d_restraint_potential_dk(size_t i
 std::string const colvarbias_restraint_harmonic_walls::get_state_params() const
 {
  return colvarbias_restraint::get_state_params() +
+    colvarbias_restraint_moving::get_state_params() +
    colvarbias_restraint_k_moving::get_state_params();
 }

@ -1045,6 +1059,7 @@ int colvarbias_restraint_harmonic_walls::set_state_params(std::string const &con
 {
  int error_code = COLVARS_OK;
  error_code |= colvarbias_restraint::set_state_params(conf);
+  error_code |= colvarbias_restraint_moving::set_state_params(conf);
  error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
  return error_code;
 }
@ -1164,6 +1179,7 @@ cvm::real colvarbias_restraint_linear::d_restraint_potential_dk(size_t i) const
 std::string const colvarbias_restraint_linear::get_state_params() const
 {
  return colvarbias_restraint::get_state_params() +
+    colvarbias_restraint_moving::get_state_params() +
    colvarbias_restraint_centers_moving::get_state_params() +
    colvarbias_restraint_k_moving::get_state_params();
 }
@ -1173,6 +1189,7 @@ int colvarbias_restraint_linear::set_state_params(std::string const &conf)
 {
  int error_code = COLVARS_OK;
  error_code |= colvarbias_restraint::set_state_params(conf);
+  error_code |= colvarbias_restraint_moving::set_state_params(conf);
  error_code |= colvarbias_restraint_centers_moving::set_state_params(conf);
  error_code |= colvarbias_restraint_k_moving::set_state_params(conf);
  return error_code;
--- a/lib/colvars/colvarbias_restraint.h
+++ b/lib/colvars/colvarbias_restraint.h
@ -74,9 +74,6 @@ protected:

  /// \brief Restraint centers
  std::vector<colvarvalue> colvar_centers;
-
-  /// \brief Restraint centers outside the domain of the colvars (no wrapping or constraints applied)
-  std::vector<colvarvalue> colvar_centers_raw;
 };


@ -156,10 +153,16 @@ protected:
  /// \brief New restraint centers
  std::vector<colvarvalue> target_centers;

+  /// \brief Initial value of the restraint centers
+  std::vector<colvarvalue> initial_centers;
+
  /// \brief Amplitude of the restraint centers' increment at each step
-  /// (or stage) towards the new values (calculated from target_nsteps)
+  /// towards the new values (calculated from target_nsteps)
  std::vector<colvarvalue> centers_incr;

+  /// \brief Update the centers by interpolating between initial and target
+  virtual int update_centers(cvm::real lambda);
+
  /// Whether to write the current restraint centers to the trajectory file
  bool b_output_centers;

--- a/lib/colvars/colvarcomp.h
+++ b/lib/colvars/colvarcomp.h
@ -132,9 +132,15 @@ public:
  static std::vector<feature *> cvc_features;

  /// \brief Implementation of the feature list accessor for colvar
-  virtual std::vector<feature *> &features() {
+  virtual const std::vector<feature *> &features()
+  {
    return cvc_features;
  }
+  virtual std::vector<feature *> &modify_features()
+  {
+    return cvc_features;
+  }
+

  /// \brief Obtain data needed for the calculation for the backend
  virtual void read_data();
--- a/lib/colvars/colvardeps.cpp
+++ b/lib/colvars/colvardeps.cpp
@ -374,8 +374,8 @@ int colvardeps::decr_ref_count(int feature_id) {
 }

 void colvardeps::init_feature(int feature_id, const char *description, feature_type type) {
-  features()[feature_id]->description = description;
-  features()[feature_id]->type = type;
+  modify_features()[feature_id]->description = description;
+  modify_features()[feature_id]->type = type;
 }

 // Shorthand macros for describing dependencies
@ -401,7 +401,7 @@ void colvardeps::init_cvb_requires() {
  int i;
  if (features().size() == 0) {
    for (i = 0; i < f_cvb_ntot; i++) {
-      features().push_back(new feature);
+      modify_features().push_back(new feature);
    }

    init_feature(f_cvb_active, "active", f_type_dynamic);
@ -438,7 +438,7 @@ void colvardeps::init_cv_requires() {
  size_t i;
  if (features().size() == 0) {
    for (i = 0; i < f_cv_ntot; i++) {
-      features().push_back(new feature);
+      modify_features().push_back(new feature);
    }

    init_feature(f_cv_active, "active", f_type_dynamic);
@ -554,7 +554,7 @@ void colvardeps::init_cvc_requires() {
  // Initialize static array once and for all
  if (features().size() == 0) {
    for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
-      features().push_back(new feature);
+      modify_features().push_back(new feature);
    }

    init_feature(f_cvc_active, "active", f_type_dynamic);
@ -633,7 +633,7 @@ void colvardeps::init_ag_requires() {
  // Initialize static array once and for all
  if (features().size() == 0) {
    for (i = 0; i < f_ag_ntot; i++) {
-      features().push_back(new feature);
+      modify_features().push_back(new feature);
    }

    init_feature(f_ag_active, "active", f_type_dynamic);
--- a/lib/colvars/colvardeps.h
+++ b/lib/colvars/colvardeps.h
@ -135,7 +135,8 @@ public:
  // with a non-static array
  // Intermediate classes (colvarbias and colvarcomp, which are also base classes)
  // implement this as virtual to allow overriding
-  virtual std::vector<feature *>&features() = 0;
+  virtual const std::vector<feature *>&features() = 0;
+  virtual std::vector<feature *>&modify_features() = 0;

  void add_child(colvardeps *child);

--- a/lib/colvars/colvars_version.h
+++ b/lib/colvars/colvars_version.h
@ -1,4 +1,5 @@
-#define COLVARS_VERSION "2017-07-15"
+#ifndef COLVARS_VERSION
+#define COLVARS_VERSION "2017-08-06"
 // This file is part of the Collective Variables module (Colvars).
 // The original version of Colvars and its updates are located at:
 // https://github.com/colvars/colvars
@ -6,3 +7,4 @@
 // If you wish to distribute your changes, please submit them to the
 // Colvars repository at GitHub.

+#endif
--- a/lib/colvars/colvarscript.cpp
+++ b/lib/colvars/colvarscript.cpp
@ -472,7 +472,7 @@ int colvarscript::proc_features(colvardeps *obj,
  }

  if ((subcmd == "get") || (subcmd == "set")) {
-    std::vector<colvardeps::feature *> &features = obj->features();
+    std::vector<colvardeps::feature *> const &features = obj->features();
    std::string const req_feature(obj_to_str(objv[3]));
    colvardeps::feature *f = NULL;
    int fid = 0;
--- a/lib/colvars/colvartypes.cpp
+++ b/lib/colvars/colvartypes.cpp
@ -19,6 +19,17 @@ bool      colvarmodule::rotation::monitor_crossings = false;
 cvm::real colvarmodule::rotation::crossing_threshold = 1.0E-02;


+/// Numerical recipes diagonalization
+static int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot);
+
+/// Eigenvector sort
+static int eigsrt(cvm::real *d, cvm::real **v);
+
+/// Transpose the matrix
+static int transpose(cvm::real **v);
+
+
+
 std::string cvm::rvector::to_simple_string() const
 {
  std::ostringstream os;
@ -286,7 +297,12 @@ void colvarmodule::rotation::diagonalize_matrix(cvm::matrix2d<cvm::real> &S,

  // diagonalize
  int jac_nrot = 0;
-  jacobi(S.c_array(), S_eigval.c_array(), S_eigvec.c_array(), &jac_nrot);
+  if (jacobi(S.c_array(), S_eigval.c_array(), S_eigvec.c_array(), &jac_nrot) !=
+      COLVARS_OK) {
+    cvm::error("Too many iterations in routine jacobi.\n"
+               "This is usually the result of an ill-defined set of atoms for "
+               "rotational alignment (RMSD, rotateReference, etc).\n");
+  }
  eigsrt(S_eigval.c_array(), S_eigvec.c_array());
  // jacobi saves eigenvectors by columns
  transpose(S_eigvec.c_array());
@ -528,7 +544,7 @@ void colvarmodule::rotation::calc_optimal_rotation(std::vector<cvm::atom_pos> co

 #define n 4

-void jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot)
+int jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot)
 {
  int j,iq,ip,i;
  cvm::real tresh,theta,tau,t,sm,s,h,g,c;
@ -554,7 +570,7 @@ void jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot)
        sm += std::fabs(a[ip][iq]);
    }
    if (sm == 0.0) {
-      return;
+      return COLVARS_OK;
    }
    if (i < 4)
      tresh=0.2*sm/(n*n);
@ -606,10 +622,11 @@ void jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot)
      z[ip]=0.0;
    }
  }
-  cvm::error("Too many iterations in routine jacobi.\n");
+  return COLVARS_ERROR;
 }

-void eigsrt(cvm::real *d, cvm::real **v)
+
+int eigsrt(cvm::real *d, cvm::real **v)
 {
  int k,j,i;
  cvm::real p;
@ -628,9 +645,11 @@ void eigsrt(cvm::real *d, cvm::real **v)
      }
    }
  }
+  return COLVARS_OK;
 }

-void transpose(cvm::real **v)
+
+int transpose(cvm::real **v)
 {
  cvm::real p;
  int i,j;
@ -641,6 +660,7 @@ void transpose(cvm::real **v)
      v[j][i]=p;
    }
  }
+  return COLVARS_OK;
 }

 #undef n
--- a/lib/colvars/colvartypes.h
+++ b/lib/colvars/colvartypes.h
@ -1020,16 +1020,6 @@ inline cvm::rvector operator * (cvm::rmatrix const &m,
 }


-/// Numerical recipes diagonalization
-void jacobi(cvm::real **a, cvm::real *d, cvm::real **v, int *nrot);
-
-/// Eigenvector sort
-void eigsrt(cvm::real *d, cvm::real **v);
-
-/// Transpose the matrix
-void transpose(cvm::real **v);
-
-


 /// \brief 1-dimensional vector of real numbers with four components and
--- a/lib/colvars/colvarvalue.cpp
+++ b/lib/colvars/colvarvalue.cpp
@ -570,6 +570,50 @@ colvarvalue colvarvalue::dist2_grad(colvarvalue const &x2) const
 }


+/// Return the midpoint between x1 and x2, optionally weighted by lambda
+/// (which must be between 0.0 and 1.0)
+colvarvalue const colvarvalue::interpolate(colvarvalue const &x1,
+                                           colvarvalue const &x2,
+                                           cvm::real const lambda)
+{
+  colvarvalue::check_types(x1, x2);
+
+  if ((lambda < 0.0) || (lambda > 1.0)) {
+    cvm::error("Error: trying to interpolate between two colvarvalues with a "
+               "lamdba outside [0:1].\n", BUG_ERROR);
+  }
+
+  colvarvalue interp = ((1.0-lambda)*x1 + lambda*x2);
+  cvm::real const d2 = x1.dist2(x2);
+
+  switch (x1.type()) {
+  case colvarvalue::type_scalar:
+  case colvarvalue::type_3vector:
+  case colvarvalue::type_vector:
+  case colvarvalue::type_unit3vectorderiv:
+  case colvarvalue::type_quaternionderiv:
+    return interp;
+    break;
+  case colvarvalue::type_unit3vector:
+  case colvarvalue::type_quaternion:
+    if (interp.norm()/std::sqrt(d2) < 1.0e-6) {
+      cvm::error("Error: interpolation between "+cvm::to_str(x1)+" and "+
+                 cvm::to_str(x2)+" with lambda = "+cvm::to_str(lambda)+
+                 " is undefined: result = "+cvm::to_str(interp)+"\n",
+                 INPUT_ERROR);
+    }
+    interp.apply_constraints();
+    return interp;
+    break;
+  case colvarvalue::type_notset:
+  default:
+    x1.undef_op();
+    break;
+  }
+  return colvarvalue(colvarvalue::type_notset);
+}
+
+
 std::string colvarvalue::to_simple_string() const
 {
  switch (type()) {
--- a/lib/colvars/colvarvalue.h
+++ b/lib/colvars/colvarvalue.h
@ -193,6 +193,12 @@ public:
  /// Derivative with respect to this \link colvarvalue \endlink of the square distance
  colvarvalue dist2_grad(colvarvalue const &x2) const;

+  /// Return the midpoint between x1 and x2, optionally weighted by lambda
+  /// (which must be between 0.0 and 1.0)
+  static colvarvalue const interpolate(colvarvalue const &x1,
+                                       colvarvalue const &x2,
+                                       cvm::real const lambda = 0.5);
+
  /// Assignment operator (type of x is checked)
  colvarvalue & operator = (colvarvalue const &x);

@ -285,10 +291,10 @@ public:
  cvm::real & operator [] (int const i);

  /// Ensure that the two types are the same within a binary operator
-  int static check_types(colvarvalue const &x1, colvarvalue const &x2);
+  static int check_types(colvarvalue const &x1, colvarvalue const &x2);

  /// Ensure that the two types are the same within an assignment, or that the left side is type_notset
-  int static check_types_assign(Type const &vt1, Type const &vt2);
+  static int check_types_assign(Type const &vt1, Type const &vt2);

  /// Undefined operation
  void undef_op() const;
@ -317,14 +323,14 @@ public:

  /// \brief Optimized routine for the inner product of one collective
  /// variable with an array
-  void static inner_opt(colvarvalue const                        &x,
+  static void inner_opt(colvarvalue const                        &x,
                        std::vector<colvarvalue>::iterator       &xv,
                        std::vector<colvarvalue>::iterator const &xv_end,
                        std::vector<cvm::real>::iterator         &result);

  /// \brief Optimized routine for the inner product of one collective
  /// variable with an array
-  void static inner_opt(colvarvalue const                        &x,
+  static void inner_opt(colvarvalue const                        &x,
                        std::list<colvarvalue>::iterator         &xv,
                        std::list<colvarvalue>::iterator const   &xv_end,
                        std::vector<cvm::real>::iterator         &result);
@ -332,14 +338,14 @@ public:
  /// \brief Optimized routine for the second order Legendre
  /// polynomial, (3cos^2(w)-1)/2, of one collective variable with an
  /// array
-  void static p2leg_opt(colvarvalue const                        &x,
+  static void p2leg_opt(colvarvalue const                        &x,
                        std::vector<colvarvalue>::iterator       &xv,
                        std::vector<colvarvalue>::iterator const &xv_end,
                        std::vector<cvm::real>::iterator         &result);

  /// \brief Optimized routine for the second order Legendre
  /// polynomial of one collective variable with an array
-  void static p2leg_opt(colvarvalue const                        &x,
+  static void p2leg_opt(colvarvalue const                        &x,
                        std::list<colvarvalue>::iterator         &xv,
                        std::list<colvarvalue>::iterator const   &xv_end,
                        std::vector<cvm::real>::iterator         &result);
--- a/lib/gpu/.gitignore
+++ b/lib/gpu/.gitignore
@ -1,4 +1,6 @@
-obj
-obj_ocl
-ocl_get_devices
-nvc_get_devices
+/obj
+/obj_ocl
+/ocl_get_devices
+/nvc_get_devices
+/*.cubin
+/*_cubin.h
--- a/lib/gpu/Install.py
+++ b/lib/gpu/Install.py
@ -3,44 +3,57 @@
 # Install.py tool to build the GPU library
 # used to automate the steps described in the README file in this dir

-import sys,os,re,commands
+from __future__ import print_function
+import sys,os,subprocess

 # help message

 help = """
-Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
-  specify one or more options, order does not matter
-  copies an existing Makefile.isuffix in lib/gpu to Makefile.auto 
-  optionally edits these variables in Makefile.auto:
-    CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
-  optionally uses Makefile.auto to build the GPU library -> libgpu.a
-    and to copy a Makefile.lammps.esuffix -> Makefile.lammps
-  optionally copies Makefile.auto to a new Makefile.osuffix
+Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix"
+Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix

-  -i = use Makefile.isuffix as starting point, copy to Makefile.auto
-       default isuffix = linux
+specify one or more options, order does not matter
+
+copies an existing Makefile.machine in lib/gpu to Makefile.auto
+optionally edits these variables in Makefile.auto:
+  CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
+optionally uses Makefile.auto to build the GPU library -> libgpu.a
+  and to copy a Makefile.lammps.esuffix -> Makefile.lammps
+optionally copies Makefile.auto to a new Makefile.osuffix
+
+  -m = use Makefile.machine as starting point, copy to Makefile.auto
+       default machine = linux
  -h = set CUDA_HOME variable in Makefile.auto to hdir
       hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda
  -a = set CUDA_ARCH variable in Makefile.auto to arch
-       use arch = ?? for K40 (Tesla)
-       use arch = 37 for dual K80 (Tesla)
-       use arch = 60 for P100 (Pascal)
+       use arch = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0)
+                     or GeForce GTX 580 or similar
+       use arch = 30 for Tesla K10 (Kepler)
+       use arch = 35 for Tesla K40 (Kepler) or GeForce GTX Titan or similar
+       use arch = 37 for Tesla dual K80 (Kepler)
+       use arch = 60 for Tesla P100 (Pascal)
  -p = set CUDA_PRECISION variable in Makefile.auto to precision
       use precision = double or mixed or single
  -e = set EXTRAMAKE variable in Makefile.auto to Makefile.lammps.esuffix
-  -m = make the GPU library using Makefile.auto
+  -b = make the GPU library using Makefile.auto
       first performs a "make clean"
-       produces libgpu.a if successful
+       then produces libgpu.a if successful
       also copies EXTRAMAKE file -> Makefile.lammps
         -e can set which Makefile.lammps.esuffix file is copied
  -o = copy final Makefile.auto to Makefile.osuffix
+
+Examples:
+
+make lib-gpu args="-b"      # build GPU lib with default Makefile.linux
+make lib-gpu args="-m xk7 -p single -o xk7.single"      # create new Makefile.xk7.single, altered for single-precision
+make lib-gpu args="-m mpi -a 35 -p single -o mpi.mixed -b" # create new Makefile.mpi.mixed, also build GPU lib with these settings
 """

 # print error message or help

 def error(str=None):
-  if not str: print help
-  else: print "ERROR",str
+  if not str: print(help)
+  else: print("ERROR",str)
  sys.exit()

 # parse args
@ -56,7 +69,7 @@ outflag = 0

 iarg = 0
 while iarg < nargs:
-  if args[iarg] == "-i":
+  if args[iarg] == "-m":
    if iarg+2 > nargs: error()
    isuffix = args[iarg+1]
    iarg += 2
@ -80,7 +93,7 @@ while iarg < nargs:
    eflag = 1
    lmpsuffix = args[iarg+1]
    iarg += 2
-  elif args[iarg] == "-m":
+  elif args[iarg] == "-b":
    makeflag = 1
    iarg += 1
  elif args[iarg] == "-o":
@ -95,10 +108,10 @@ if pflag:
  elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
  elif precision == "single": precstr = "-D_SINGLE_SINGLE"
  else: error("Invalid precision setting")
-  
+
 # create Makefile.auto
 # reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested
-  
+
 if not os.path.exists("Makefile.%s" % isuffix):
  error("lib/gpu/Makefile.%s does not exist" % isuffix)

@ -108,9 +121,9 @@ fp = open("Makefile.auto",'w')
 for line in lines:
  words = line.split()
  if len(words) != 3:
-    print >>fp,line,
+    fp.write(line)
    continue
-  
+
  if hflag and words[0] == "CUDA_HOME" and words[1] == '=':
    line = line.replace(words[2],hdir)
  if aflag and words[0] == "CUDA_ARCH" and words[1] == '=':
@ -119,20 +132,20 @@ for line in lines:
    line = line.replace(words[2],precstr)
  if eflag and words[0] == "EXTRAMAKE" and words[1] == '=':
    line = line.replace(words[2],"Makefile.lammps.%s" % lmpsuffix)
-    
-  print >>fp,line,

+  fp.write(line)
 fp.close()

 # perform make
 # make operations copies EXTRAMAKE file to Makefile.lammps

 if makeflag:
-  print "Building libgpu.a ..."
+  print("Building libgpu.a ...")
  cmd = "rm -f libgpu.a"
-  commands.getoutput(cmd)
+  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
  cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
-  commands.getoutput(cmd)
+  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
+  print(txt.decode('UTF-8'))
  if not os.path.exists("libgpu.a"):
    error("Build of lib/gpu/libgpu.a was NOT successful")
  if not os.path.exists("Makefile.lammps"):
@ -141,6 +154,6 @@ if makeflag:
 # copy new Makefile.auto to Makefile.osuffix

 if outflag:
-  print "Creating new Makefile.%s" % osuffix
+  print("Creating new Makefile.%s" % osuffix)
  cmd = "cp Makefile.auto Makefile.%s" % osuffix
-  commands.getoutput(cmd)
+  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
--- a/lib/gpu/Makefile.linux
+++ b/lib/gpu/Makefile.linux
@ -37,7 +37,7 @@ CUDA_INCLUDE = -I$(CUDA_HOME)/include
 CUDA_LIB = -L$(CUDA_HOME)/lib64
 CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC)

-CUDR_CPP = mpic++ -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
+CUDR_CPP = mpicxx -DMPI_GERYON -DUCL_NO_EXIT -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1 -fPIC
 CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias

 BIN_DIR = ./
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
Steve Plimpton	7ddcb6812b	patch 17Aug17	2017-08-17 16:02:20 -06:00
Steve Plimpton	76cd61350d	Merge pull request #613 from akohlmey/collected-small-changes Collected small changes and bug fixes	2017-08-17 11:34:52 -06:00
Steve Plimpton	fa3c0c61d6	Merge pull request #618 from lammps/intel USER-INTEL add-ons from Mike	2017-08-17 11:32:53 -06:00
Steve Plimpton	c46d5ff422	Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10 Minor fixes to Colvars module	2017-08-17 11:32:38 -06:00
Steve Plimpton	dd67989c76	Merge pull request #601 from stanmoore1/kokkos_update Update Kokkos library to v2.03.13	2017-08-17 11:32:18 -06:00
Steve Plimpton	00aafef1a8	Merge pull request #597 from ndtrung81/three-body-short-nlist Implementing short neighbor lists for three-body gpu styles	2017-08-17 11:31:59 -06:00
Axel Kohlmeyer	7175abcc71	flag more pair styles as supporting USER-INTEL to match newly added code	2017-08-16 13:58:46 -04:00
Axel Kohlmeyer	e34b20405c	Fix a couple of typos in the docs	2017-08-15 21:10:05 -04:00
Steve Plimpton	1d4d2155a2	USER-INTEL add-ons from Mike	2017-08-15 17:12:07 -06:00
Axel Kohlmeyer	cee87d7a54	update manual to point to packages.lammps.org instead of rpm.lammps.org	2017-08-15 16:19:09 -04:00
Axel Kohlmeyer	60e14f1490	add comment to msi2lmp README about symmetry limitations	2017-08-14 08:54:26 -04:00
Axel Kohlmeyer	81e7d4a942	fix incorrect preprocessor define for windows	2017-08-12 00:35:50 -04:00
Steve Plimpton	0b3f1b8a15	patch 11Aug17	2017-08-11 12:19:02 -06:00
Steve Plimpton	b209a4e246	Merge pull request #614 from akohlmey/fixes-for-stable Fixes for stable	2017-08-11 08:35:20 -06:00
Axel Kohlmeyer	27553283c3	fix bug with pair_modify <style> compute not triggering the correct global change	2017-08-11 08:28:37 -04:00
Axel Kohlmeyer	df56b2d6a4	trigger relink after package library build through updating the time stamp on main.cpp	2017-08-11 08:16:20 -04:00
Axel Kohlmeyer	c6d923b6c8	make download function more resilient by also catching failed execution	2017-08-10 21:15:35 -04:00
Axel Kohlmeyer	6d24be8bb7	whitespace cleanup	2017-08-10 21:14:40 -04:00
Steve Plimpton	52bec0f380	patch 10Aug17	2017-08-10 16:44:09 -06:00
Axel Kohlmeyer	8c16ea1bfc	add automatic triggering of review requests with a code owners file	2017-08-10 15:58:51 -04:00
Axel Kohlmeyer	c8741f3a01	remove special_bonds extra keyword and refer to read_data and create_box instead	2017-08-10 15:12:56 -04:00
Axel Kohlmeyer	2a7d2dee36	add more strict checking of data when parsing molecule files to detect format errors	2017-08-10 14:49:51 -04:00
Steve Plimpton	f68c6254d4	Merge pull request #611 from akohlmey/final-tweaks More tweaks for stable release	2017-08-10 08:02:55 -06:00
Giacomo Fiorin	da01be7c18	More robust change from initial to target restraint centers in Colvars	2017-08-10 09:22:53 -04:00
Axel Kohlmeyer	146aa4cdbd	fall back to wget when curl is not available	2017-08-10 09:05:23 -04:00
Axel Kohlmeyer	2f3747eb6e	we need to override compiler flags in lib/voronoi/Install.py The default compiler flags in voro++'s config.mk file do not include -fPIC, which makes it incompatible with building the shared object for the python wrapper.	2017-08-10 08:34:46 -04:00
Axel Kohlmeyer	2bc6ad80d4	avoid writable string and deprecated implicit conversion warning	2017-08-10 07:45:21 -04:00
Axel Kohlmeyer	f9a515efd3	add some remarks about makefile settings on windows	2017-08-10 07:24:24 -04:00
Axel Kohlmeyer	5b55744209	fix a header line formatting issue	2017-08-10 07:21:39 -04:00
Axel Kohlmeyer	0dc3cbaa8a	Revert "remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability" This reverts commit `4e97b57508`.	2017-08-10 06:51:57 -04:00
Axel Kohlmeyer	ce62c41252	when recomputing special bonds, make certain we do not shrink atom->maxspecial and add force->special_extra only once	2017-08-10 06:47:26 -04:00
Axel Kohlmeyer	4e97b57508	remove -DLAMMPS_MEMALIGN from "make mpi" and "make serial" for increased portability	2017-08-10 05:46:42 -04:00
Steve Plimpton	7f437d7690	Merge pull request #609 from akohlmey/doc-changes-for-stable Final tweaks and doc changes for stable release	2017-08-09 17:37:35 -06:00
Axel Kohlmeyer	77a628e4ef	make the deprecation warning nicer looking	2017-08-09 19:13:40 -04:00
Axel Kohlmeyer	f01103dd08	correctly use the term CUDA (instead of Cuda) when not referring to the KOKKOS device flag (which is Cuda)	2017-08-09 19:08:23 -04:00
Axel Kohlmeyer	81f4d7ecb5	rework section 4 (Packages) in the manual to match Install.py scripts	2017-08-09 19:07:20 -04:00
Axel Kohlmeyer	210a77c5a0	add a deprecation warning to pair style meam and make the reax one consistent with it	2017-08-09 16:36:51 -04:00
Trung Nguyen	3e9b41c6b7	Added references to GPU package citations	2017-08-09 10:09:40 -05:00
Axel Kohlmeyer	6780c73907	restore mpic++ makefile to resolve regression test failure	2017-08-09 07:10:08 -04:00
Axel Kohlmeyer	be25a7d9a4	updated comment for fix neb by steve	2017-08-08 20:37:20 -04:00
Steve Plimpton	691d1b730d	Merge pull request #607 from akohlmey/final-changes-for-stable Final build system changes for stable release	2017-08-08 17:26:22 -06:00
Axel Kohlmeyer	95ece8a6c0	consistently use $(PYTHON) in the master makefile (which defaults to "python")	2017-08-08 17:03:52 -04:00
Axel Kohlmeyer	b7b1257b01	remove attempts to use urllib and use curl for all downloading. restore printing help with no flags.	2017-08-08 17:00:09 -04:00
Axel Kohlmeyer	30431d4edb	rework Install.py for gpu library. make it consistent with other lib folders and support python3	2017-08-08 16:57:27 -04:00
Stan Moore	8a7a831bd6	Remove redundant check in Makefile.kokkos	2017-08-08 12:57:22 -06:00
Axel Kohlmeyer	c53a84a967	update README file for lib/mscg	2017-08-08 13:55:12 -04:00
Axel Kohlmeyer	b7b62f6893	do not pollute global namespace by including mscg header in fix header	2017-08-08 13:20:25 -04:00
Axel Kohlmeyer	d2b0c287d2	add local makefile overrides to be compatible with standard suffixes	2017-08-08 13:19:44 -04:00
Axel Kohlmeyer	b3244f9c98	more lib compilation updates	2017-08-08 07:20:33 -04:00
Axel Kohlmeyer	8bba29d91e	more lib installation cleanup	2017-08-07 17:21:45 -04:00
Axel Kohlmeyer	135b1650f1	revamp of library builds - remove cross compiler stuff - make use of Install.py consistent - provide options for Makefile.serial and Makefile.mpi that match those in src	2017-08-07 17:13:01 -04:00
Steve Plimpton	0a54c34e34	Merge pull request #600 from akohlmey/install-and-docs-reviewed Installation scripts and docs reviewed for release	2017-08-07 08:02:04 -06:00
Steve Plimpton	a8f6a95cba	Merge pull request #605 from rbberger/bash_on_windows Adds tutorial for using LAMMPS in Bash on Windows	2017-08-07 08:00:56 -06:00
Richard Berger	e0f9a7c34c	Adds BOW tutorial link in main menu	2017-08-07 00:06:53 -04:00
Richard Berger	aaf17bde3f	Added tutorial for using LAMMPS in Bash on Windows	2017-08-07 00:06:12 -04:00
Axel Kohlmeyer	5ad8a3332d	Merge pull request #55 from GarrettTow/patch-1 Fixed typo in "compute_voronoi_atom.txt"	2017-08-04 19:18:57 -04:00
GarrettTow	ca7a3a6316	Fixed typo in "compute_voronoi_atom.txt" There was the typo "requiers" in the Restrictions section of compute_voronoi_atom.txt.	2017-08-04 17:48:27 -04:00
Axel Kohlmeyer	163ed27618	update .gitignore	2017-08-04 16:10:59 -04:00
Axel Kohlmeyer	23ca0099f7	more updates to kim/Install.py to restore missing functionality and align with other scripts - build into local directory to replace existing installation is now default - add wrapper function that calls curl in case python package has not ssl support - have to specify -n flag to avoid wiping out the existing installation - can specify -p to point to an existing kim-api installation (implies -n)	2017-08-04 14:47:32 -04:00
Axel Kohlmeyer	59ac6ef573	correct a link and a name for OpenKIM	2017-08-04 11:19:09 -04:00
Axel Kohlmeyer	2fa16bcd4c	make overlapping links to references unique to avoid anchor label errors	2017-08-04 11:11:41 -04:00
sjplimp	e84b6d8067	Merge pull request #602 from rbberger/pylammps_fixes PyLammps corrections	2017-08-04 08:35:00 -06:00
Richard Berger	96d3712817	Add missing link flag	2017-07-31 15:52:44 -06:00
Richard Berger	b395ef00b4	Update tutorial_pylammps.txt	2017-07-31 15:50:14 -06:00
Richard Berger	d3169eeab3	Remove Make.py reference in PyLammps examples Also fixes some regressions due to command syntax changes	2017-07-31 13:56:20 -06:00
Richard Berger	71553cf732	Fix PyLammps regression after output.cpp change	2017-07-31 13:53:41 -06:00
Stan Moore	8431ca5fec	Remove tpls directory	2017-07-31 10:54:07 -06:00
Stan Moore	13f2d39f55	Update Kokkos library to v2.03.13	2017-07-31 10:34:21 -06:00
Axel Kohlmeyer	9bfd9267fa	update and automate the QUIP configuration so that no environment variables are needed	2017-07-28 16:11:13 -04:00
Axel Kohlmeyer	7d0d701eaf	add reference outputs for QUIP/GAP example	2017-07-28 16:05:16 -04:00
Axel Kohlmeyer	841a92c7fa	remove unused variable	2017-07-28 16:03:24 -04:00
Axel Kohlmeyer	85120842dd	update QUIP examples to closer match typical LAMMPS examples	2017-07-28 15:20:33 -04:00
Axel Kohlmeyer	3ebf561e0d	remove tarball after unpacking	2017-07-28 14:25:47 -04:00
Axel Kohlmeyer	ffb778cf9b	make Install.py for lib/smd and lib/voronoi consistent	2017-07-28 14:03:29 -04:00
Axel Kohlmeyer	f3850da9fe	clean up makefiles provide "serial" and "mpi" targets for atc and awpmd	2017-07-28 13:36:06 -04:00
Axel Kohlmeyer	e7d9aabca6	Merge branch 'kim-install' into install-and-docs-reviewed	2017-07-28 11:25:08 -04:00
Axel Kohlmeyer	e3973796ba	fix bug in power operator in LAMMPS variable expressions	2017-07-27 15:51:45 -04:00
Axel Kohlmeyer	c494ec35e2	correct symbolic links to shared Install.py file	2017-07-27 12:48:32 -04:00
sjplimp	6d0a228624	Merge pull request #599 from lammps/kim-doc restore lost KIM doc section in Section packages	2017-07-27 10:34:44 -06:00
Axel Kohlmeyer	acf6d54ec1	python3 port, yet untested	2017-07-27 09:25:39 -04:00
Axel Kohlmeyer	0427f6205e	fix typo	2017-07-27 09:25:02 -04:00
Axel Kohlmeyer	72419b6313	Merge remote-tracking branch 'github/kim-doc' into install-and-docs-reviewed	2017-07-26 19:35:15 -04:00
Axel Kohlmeyer	da7a5f55d3	Merge branch 'kim-install' into install-and-docs-reviewed	2017-07-26 19:32:55 -04:00
Steve Plimpton	934cbbbeca	restore lost KIM doc section in Section packages	2017-07-26 16:07:08 -06:00
sjplimp	2806f070a4	Merge pull request #598 from akohlmey/last-minute-changes last minute changes for stable release	2017-07-26 15:46:51 -06:00
Axel Kohlmeyer	715c797df0	simplify Install.py for voronoi	2017-07-26 15:14:12 -04:00
Axel Kohlmeyer	fd6e11f821	convert copies of Install.py files to symlinks	2017-07-26 14:29:52 -04:00
Axel Kohlmeyer	f7a243a4d9	convert explicit copies back into symbolic links	2017-07-26 14:20:03 -04:00
Axel Kohlmeyer	f0d286358e	must not include system headers within 'extern "C"' blocks. breaks with MPICH	2017-07-26 14:02:02 -04:00
Axel Kohlmeyer	51a06334ad	avoid invalid calls to memcpy(): when ndot == 0, pointers may be NULL	2017-07-26 12:08:42 -04:00
Axel Kohlmeyer	aa5ea95a0f	avoid integer overflow and remove unused function argument causing it	2017-07-26 11:55:50 -04:00
Axel Kohlmeyer	60c67b07dc	import updated fix msst file with some additional cleanup and simplification	2017-07-26 10:45:11 -04:00
Trung Nguyen	aa60ef6ed8	Cleaned up 3-body kernels, reverted some mistaken changes to vashishta	2017-07-23 00:08:55 -05:00
Trung Nguyen	a71f5a0c20	Enabled again neigh no with tpa > 1 for 3-body gpu styles for backward compatibility, could be slower than neigh no tpa 1 in many cases	2017-07-22 22:57:37 -05:00
Trung Nguyen	3d1d0c58c7	Cleaned up 3-body gpu styles, and fixed a bug for tersoff/zbl/gpu. There is a unresolved bug for neigh no with tpa > 1 with BaseThree, enforce tpa = 1 for neigh no in BaseThree for now.	2017-07-21 12:08:04 -05:00
Axel Kohlmeyer	3449d42267	include pair style kim doc changes that were accidentally included in PR #590	2017-07-20 17:58:49 -04:00
Axel Kohlmeyer	d2f76ae394	Merge pull request #586 from ellio167/kim-install Refactor lib/kim/Install.py; works with python 3 and 2.7	2017-07-20 14:40:57 -04:00
Ryan S. Elliott	84065dde21	Refactor lib/kim/Install.py; works with phtyon 3 2.7	2017-07-20 12:02:50 -05:00
Axel Kohlmeyer	355aad9691	restore python3 support. this now can run with python 2.7.13 and 3.5.3.	2017-07-19 17:19:44 -04:00
Axel Kohlmeyer	ec42a60587	Merge pull request #584 from ellio167/kim-install Update lib/kim/Install.py for phthon 2.7 conversion	2017-07-19 16:21:04 -04:00
Ryan S. Elliott	f181a0bfab	Update lib/kim/Install.py for phthon 2.7 conversion	2017-07-19 12:54:33 -05:00
Axel Kohlmeyer	81f342aafa	fix variable name bug and synchronize with other ported Install.py files	2017-07-18 18:06:18 -04:00
Axel Kohlmeyer	7ccb0d37cd	port USER-SMD folder. make voronoi consistent with it	2017-07-18 17:37:48 -04:00
Axel Kohlmeyer	03cd4c5255	ported lib/voronoi/Install.py to python 3.x and tested with 2.7	2017-07-18 17:16:10 -04:00
Axel Kohlmeyer	5cbaf7ca1d	correct commands table format issue	2017-07-18 14:47:54 -04:00
Axel Kohlmeyer	49b4cf9a77	remove references to Make.py and USER-CUDA	2017-07-18 13:24:32 -04:00
Axel Kohlmeyer	49e6c2eb7d	remove references to Make.py from the manual and instead refer to section 4	2017-07-18 13:14:03 -04:00
Axel Kohlmeyer	a92d792537	update manual links that got broken when removing and renumbering a section	2017-07-18 12:55:55 -04:00
Richard Berger	d7355801df	Make KIM Install.py Python 3 compatible	2017-07-15 12:03:04 -05:00
Steve Plimpton	296e572e69	better Install.py script for KIM from Ryan Elliott	2017-07-14 16:25:16 -06:00
Trung Nguyen	cdac5f496c	Built 3-body short neighbor list for the 3-body kernels using per-pair cutoffs for vashishta gpu style	2017-07-11 00:13:56 -05:00
Trung Nguyen	8c9db3ea00	Built 2-body short neighbor list and used for 2-body kernels in tersoff gpu styles	2017-07-10 23:50:21 -05:00
Trung Nguyen	ea2b01e83b	Refactored 3-body gpu styles to remove code duplication	2017-07-08 20:17:31 -05:00
Trung Nguyen	34fe2273f6	Added short neighbor list implementation for tersoff/zbl/gpu and tersoff/mod/gpu	2017-07-08 14:59:48 -05:00
Trung Nguyen	77c60189b8	Minor cleanups for tersoff/gpu	2017-07-08 14:43:53 -05:00
Trung Nguyen	1c6533e53d	Working on short neighbor list for tersoff/gpu	2017-07-08 14:15:26 -05:00
Trung Nguyen	68206079da	Supported short neighbor lists for 3-body kernels in sw/gpu and vashishta/gpu	2017-07-07 16:47:24 -05:00