Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17

2017-08-11 13:25:28 -04:00 · 2017-08-11 13:25:28 -04:00 · 4041db8d1a
parent 378989e065 52bec0f380
commit 4041db8d1a
151 changed files with 2662 additions and 2690 deletions
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--- a/doc/src/JPG/bow_tutorial_01_small.png
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--- a/doc/src/JPG/bow_tutorial_02.png
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--- a/doc/src/JPG/bow_tutorial_02_small.png
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--- a/doc/src/JPG/bow_tutorial_03.png
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--- a/doc/src/JPG/bow_tutorial_03_small.png
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--- a/doc/src/JPG/bow_tutorial_04.png
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--- a/doc/src/JPG/bow_tutorial_04_small.png
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--- a/doc/src/JPG/bow_tutorial_05.png
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--- a/doc/src/JPG/bow_tutorial_06.png
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--- 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/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="10 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
+10 Aug 2017 version :c,h4
 Version info: :h4
--- 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
+Note that the first 4 steps can be done as a single command with
-src/Make.py tool.  This tool is discussed in "Section
+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_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
+"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, -
+"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
+"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l)
 :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
+"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l)
 :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
+solver optimized for GPUs.  All such styles have a "gpu" as a
-suffix in their style name.  "Section 5.3.1"_accelerate_gpu.html gives
+suffix in their style name. The GPU code can be compiled with either
-details of what hardware and Cuda software is required on your system,
+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               # print help message
-make lib-gpu args="-m"                      # build GPU library with default Makefile.linux
+make lib-gpu args="-b"     # 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="-m 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 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
+Note that this procedure through the '-m machine' flag starts with one of
-Makefile.machine files in lib/gpu.  It allows you to alter 4 important
+the existing Makefile.machine files in lib/gpu. For your convenience,
-settings in that Makefile, via the -h, -a, -p, -e switches,
+machine makefiles for "mpi" and "serial" are provided, which have the
-and save the new Makefile, if desired:
+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:
+If the library build is successful, at least 3 files should be created:
-lib/gpu/libgpu.a and lib/gpu/Makefile.lammps.  The latter has settings
+lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps.
-that enable LAMMPS to link with Cuda libraries.  If the settings in
+The latter has settings that enable LAMMPS to link with CUDA libraries.
-Makefile.lammps for your machine are not correct, the LAMMPS build
+If the settings in Makefile.lammps for your machine are not correct,
-will fail.
+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:
@ -499,11 +522,13 @@ 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.
-make lib-kim                    # print help message
+make lib-kim              # print help message
-make lib-kim args="-b . none"   # install KIM API lib with only example models
+make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-make lib-kim args="-b . OpenKIM"   # install KIM API lib with all models
+make lib-kim args="-b -a everything"     # install KIM API lib with all models
-make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver :pre
+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
@ -547,7 +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
@ -577,28 +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.
@ -734,6 +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:]
@ -744,9 +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                  # print help message
-make lib-meam args="-m gfortran"   # build with GNU Fortran compiler
+make lib-meam args="-m mpi"    # build with default Fortran compiler compatible with your MPI library
-make lib-meam args="-m ifort"      # build with Intel ifort compiler :pre
+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
@ -789,6 +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
@ -902,9 +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
+LAMMPS requires a C++11 compatible compiler and that the GSL
-(GNU Scientific Library) libraries be installed on your machine.  See
+(GNU Scientific Library) headers and libraries are installed on your
-the lib/mscg/README and MSCG/Install files for more details.
+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
@ -912,15 +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             # print help message
-make lib-mscg args="-g -b -l"                # download and build in default lib/mscg/MSCG-release-master
+make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
-make lib-mscg args="-h . MSCG -g -b -l"      # download and build in lib/mscg/MSCG
+                                    # with the settings compatible with "make serial"
-make lib-mscg args="-h ~ MSCG -g -b -l"      # download and build in ~/mscg :pre
+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,
+Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg
-"includelink" and "liblink", in lib/mscg to point to the MS-CG src
+to point to the MS-CG src/installation dir.  When LAMMPS is built in src it will use these links.
-dir.  When LAMMPS builds it will use these links.  You should not need
+You should not need to edit the lib/mscg/Makefile.lammps file.
 to edit the lib/mscg/Makefile.lammps file.
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -966,11 +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
+the OPT package when using Intel compilers.  It should be added to
-Makefile.machine.  See Makefile.opt in src/MAKE/OPTIONS for an
+the CCFLAGS line of your Makefile.machine.  See Makefile.opt in
-example.
+src/MAKE/OPTIONS for an example.
-CCFLAGS: add -restrict :ul
+CCFLAGS: add -restrict for Intel compilers :ul
 [Supporting info:]
@ -1039,9 +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                   # print help message
-make lib-poems args="-m g++"        # build with GNU g++ compiler
+make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-make lib-poems args="-m icc"        # build with Intel icc compiler :pre
+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
@ -1151,9 +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                    # print help message
-make lib-reax args="-m gfortran"   # build with GNU Fortran compiler
+make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m ifort"      # build with Intel ifort compiler :pre
+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
@ -1370,15 +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                          # 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="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-make lib-voronoi args="-h . voro++ -g -b -l"    # download and build in lib/voronoi/voro++
+make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-make lib-voronoi args="-h ~ voro++ -g -b -l"    # download and build in ~/voro++ :pre
+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,
+Note that 2 symbolic (soft) links, "includelink" and "liblink", are
-"includelink" and "liblink", in lib/voronoi to point to the Voro++ src
+created in lib/voronoi to point to the Voro++ src dir.  When LAMMPS
-dir.  When LAMMPS builds it will use these links.  You should not need
+builds in src it will use these links.  You should not need to edit
-to edit the lib/voronoi/Makefile.lammps file.
+the lib/voronoi/Makefile.lammps file.
 You can then install/un-install the package and build LAMMPS in the
 usual manner:
@ -1420,7 +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
@ -1437,8 +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-linalg                     # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+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:
@ -1478,9 +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                   # print help message
-make lib-awpmd args="-m g++"        # build with GNU g++ compiler
+make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-make lib-awpmd args="-m icc"        # build with Intel icc compiler :pre
+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
@ -1496,8 +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-linalg                     # print help message
-make lib-atc args="-m gfortran"      # build with GNU Fortran compiler
+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:
@ -1590,9 +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
+[Authors:] The COLVARS library is written and maintained by
-by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
+Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA)
-Jerome Henin (LISM, CNRS, Marseille, France).
+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:]
@ -1604,7 +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
@ -1892,7 +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).
@ -1909,17 +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.
@ -2224,11 +2277,15 @@ CPUs.
 [Author:] Axel Kohlmeyer (Temple U).
-NOTE: The compile flags "-restrict" and "-fopenmp" must be used to
+NOTE: To enable multi-threading support the compile flag "-fopenmp"
-build LAMMPS with the USER-OMP package, as well as the link flag
+and the link flag "-fopenmp" (for GNU compilers, you have to look up
-"-fopenmp".  They should be added to the CCFLAGS and LINKFLAGS lines
+the equivalent flags for other compilers) must be used to build LAMMPS.
-of your Makefile.machine.  See src/MAKE/OPTIONS/Makefile.omp for an
+When using Intel compilers, also the "-restrict" flag is required.
-example.
+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:
@ -2241,7 +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:]
@ -2310,12 +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
@ -2492,15 +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                         # print help message
-make lib-smd args="-g -l"               # download in default lib/smd/eigen-eigen-*
+make lib-smd args="-b"               # download and build in default lib/smd/eigen-eigen-...
-make lib-smd args="-h . eigen -g -l"    # download in lib/smd/eigen
+make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3 :pre
 make lib-smd args="-h ~ eigen -g -l"    # download and build in ~/eigen :pre
-Note that the final -l switch is to create a symbolic (soft) link
+Note that a symbolic (soft) link named "includelink" is created in
-named "includelink" in lib/smd to point to the Eigen dir.  When LAMMPS
+lib/smd to point to the Eigen dir.  When LAMMPS builds it will use
-builds it will use this link.  You should not need to edit the
+this link.  You should not need to edit the lib/smd/Makefile.lammps file.
 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
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 -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.
@ -659,7 +658,16 @@ 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
+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, but
 we cannot provide support for those.
@ -909,7 +917,7 @@ 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
--- 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,
+You can do both these steps in one line as described in
-described in "Section 4"_Section_packages.html of the manual.
+"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
 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
@ -225,11 +225,9 @@ 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
+Alternatively this can be done as a single command with
-script, described in "Section 4"_Section_packages.html of the
+suitable make command invocations. This is discussed in "Section
-manual. Type "Make.py -h" for help. For an example:
+4"_Section_packages.html of the manual.
 Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre
 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 +242,7 @@ 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
+-no-prec-div".
 automatically.
 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 kokkos_omp                                # or Makefile.kokkos_omp already has variable set :pre
 Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi   # or one-line build via Make.py :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 machine :pre
 Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :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 machine :pre
 Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :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,
+You can do any of these in one line, using the suitable make command
-described in "Section 4"_Section_packages.html of the manual.
+line flags as described in "Section 4"_Section_packages.html of the
-Type "Make.py -h" for help.  If run from the src directory, these
+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 omp                                   # or Makefile.omp already has settings :pre
 Make.py -v -p omp -o mpi -a file mpi       # or one-line build via Make.py :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
+one command as described in "Section 4"_Section_packages.html of the manual.
 4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 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
+CCFLAGS setting must include "-restrict".
 add these automatically.
 [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 mpi                               # build with the OPT package :pre
 Make.py -v -p opt -o mpi -a file mpi   # or one-line build via Make.py :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
+as described in "Section 4"_Section_packages.html of the manual.
 4"_Section_packages.html of the manual.  Type "Make.py -h" for
 help.
 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_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 =
+cluster = no, include = all (same as no include option defined),
-2000, and binsize = 0.0.
+exclude = none, page = 100000, one = 2000, and binsize = 0.0.
--- 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,
+Models (OpenKIM)"_https://openkim.org repository of interatomic
-so that they can be used by LAMMPS scripts.
+potentials, so that they can be used by LAMMPS scripts.
-In KIM lingo, a potential is a "model" and a model contains both the
+Note that in LAMMPS lingo, a KIM model driver is a pair style
-analytic formulas that define the potential as well as the parameters
+(e.g. EAM or Tersoff).  A KIM model is a pair style for a particular
-needed to run it for one or more materials, including coefficients and
+element or alloy and set of parameters, e.g. EAM for Cu with a
-cutoffs.
+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/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_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
+library is then loaded by the Python interface. In this example we enable the
-Make.py utility to create a Makefile with C++ exceptions, PNG, JPEG and FFMPEG
+MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG
-output support enabled. Finally, we also enable the MOLECULE package and compile
+output support enabled.
 using the generated {auto} Makefile.
 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
+Syntax from src dir: make lib-libname args="-m machine -e suffix"
-  specify -m and optionally -e, order does not matter
+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
+  if not str: print(help)
-  else: print "ERROR",str
+  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 \
+  if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
-        words[0] == "EXTRAMAKE" and words[1] == '=':
+    has_extramake = True
-    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)
+    if extraflag:
-  print >>fp,line,
+      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
+try:
-cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+  import multiprocessing
-txt = commands.getoutput(cmd)
+  n_cpus = multiprocessing.cpu_count()
-print txt
+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"):
+if has_extramake and not os.path.exists("Makefile.lammps"):
-  print "lib/%s/Makefile.lammps was NOT created" % lib
+  print("lib/%s/Makefile.lammps was NOT created" % lib)
--- a/lib/atc/Install.py
+++ b/lib/atc/Install.py
@ -1 +1 @@
-Install.py
+../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 $<
+	$(CC) $(CPPFLAGS) $(CCFLAGS) -c $<
 %.d:%.cpp
 	$(CC) $(CCFLAGS) $(DEPFLAGS) $< > $@		
 # ------ 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 +1 @@
-Install.py
+../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
+SRC = \
-vpath %.cpp ivutils/src
+    ivutils/src/logexc.cpp \
-vpath %.cpp systems/interact/TCP
+    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
+LIB = libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
+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++
+CC =	    mpicxx
-CCFLAGS =  -O3 -march=core2 -mtune=core2 -mpc64 -msse2    \
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
-                -ffast-math -funroll-loops -fstrict-aliasing		\
+	  -DMPICH_IGNORE_CXX_SEEK -DOMPI_SKIP_MPICXX=1
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+
-ARCHIVE =	x86_64-w64-mingw32-ar
+ARCHIVE =	ar
-ARCHFLAG =	-rscv
+ARCHFLAG =	-rc
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
@ -50,23 +50,15 @@ SYSLIB =
 # ------ MAKE PROCEDURE ------
-default: $(DIR) $(LIB) Makefile.lammps
+lib: 	$(OBJ)
 $(DIR):
 	mkdir $(DIR)
 Makefile.lammps:
 	@cp $(EXTRAMAKE) Makefile.lammps
 $(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++ 
+CC =	    mpicxx
-CCFLAGS = -O -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+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
+SRC = \
-vpath %.cpp ivutils/src
+    ivutils/src/logexc.cpp \
-vpath %.cpp systems/interact/TCP
+    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
+LIB = libawpmd.a
-OBJ =  $(SRC:%.cpp=$(DIR)%.o)
+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++
+CC =	    g++
-CCFLAGS = 	-O2 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
+CCFLAGS = -O3 -fPIC -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include \
-		-finline-functions		\
+	  -I../../src/STUBS
-                -ffast-math -funroll-loops -fstrict-aliasing		\
+
-                -Wall -W -Wno-uninitialized -Isystems/interact/TCP/ -Isystems/interact -Iivutils/include
+ARCHIVE =	ar
-ARCHIVE =	i686-w64-mingw32-ar
+ARCHFLAG =	-rc
 ARCHFLAG =	-rscv
 DEPFLAGS =  -M
 #LINK =         
 #LINKFLAGS =	
@ -51,23 +50,15 @@ SYSLIB =
 # ------ MAKE PROCEDURE ------
-default: $(DIR) $(LIB) Makefile.lammps
+lib: 	$(OBJ)
 $(DIR):
 	mkdir $(DIR)
 Makefile.lammps:
 	@cp $(EXTRAMAKE) Makefile.lammps
 $(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
@ -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/gpu/.gitignore
+++ b/lib/gpu/.gitignore
@ -1,4 +1,6 @@
-obj
+/obj
-obj_ocl
+/obj_ocl
-ocl_get_devices
+/ocl_get_devices
-nvc_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
+Syntax from src dir: make lib-gpu args="-m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix"
-  specify one or more options, order does not matter
+Syntax from lib dir: python Install.py -m machine -h hdir -a arch -p precision -e esuffix -m -o osuffix
  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
-  -i = use Makefile.isuffix as starting point, copy to Makefile.auto
+specify one or more options, order does not matter
-       default isuffix = linux
+
 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 = 20 for Tesla C2050/C2070 (Fermi) (deprecated as of CUDA 8.0) 
-       use arch = 37 for dual K80 (Tesla)
+                     or GeForce GTX 580 or similar
-       use arch = 60 for P100 (Pascal)
+       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
+  if not str: print(help)
-  else: print "ERROR",str
+  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":
@ -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 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
 BIN_DIR = ./
--- a/lib/gpu/Makefile.mingw32-cross
+++ b/lib/gpu/Makefile.mingw32-cross
@ -1,17 +0,0 @@
 CUDA_HOME = ../../tools/mingw-cross/OpenCL
 OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
        -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
        -I$(CUDA_HOME)/include
 OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic -L../../src/STUBS -lmpi_mingw32
 OCL_PREC = -D_SINGLE_DOUBLE
 OCL_TUNE = -DFERMI_OCL
 EXTRAMAKE = Makefile.lammps.mingw-cross
 BIN_DIR = Obj_mingw32
 OBJ_DIR = Obj_mingw32
 LIB_DIR = Obj_mingw32
 AR = i686-w64-mingw32-ar
 BSH = /bin/sh
 include Opencl.makefile
--- a/lib/gpu/Makefile.mingw32-cross-mpi
+++ b/lib/gpu/Makefile.mingw32-cross-mpi
@ -1,19 +0,0 @@
 CUDA_HOME = ../../tools/mingw-cross/OpenCL
 OCL_CPP = i686-w64-mingw32-g++ -O2 -march=i686 -mtune=generic -mfpmath=387 \
        -mpc64 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
 	-I../../tools/mingw-cross/mpich2-win32/include/ \
        -DMPICH_IGNORE_CXX_SEEK
 OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw32 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
 	-L../../tools/mingw-cross/mpich2-win32/lib -lmpi
 OCL_PREC = -D_SINGLE_DOUBLE
 OCL_TUNE = -DFERMI_OCL
 EXTRAMAKE = Makefile.lammps.mingw-cross
 BIN_DIR = Obj_mingw32-mpi
 OBJ_DIR = Obj_mingw32-mpi
 LIB_DIR = Obj_mingw32-mpi
 AR = i686-w64-mingw32-ar
 BSH = /bin/sh
 include Opencl.makefile
--- a/lib/gpu/Makefile.mingw64-cross
+++ b/lib/gpu/Makefile.mingw64-cross
@ -1,18 +0,0 @@
 CUDA_HOME = ../../tools/mingw-cross/OpenCL
 OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
 	-msse2 -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS \
        -I$(CUDA_HOME)/include
 OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
 	-L../../src/STUBS -lmpi_mingw64
 OCL_PREC = -D_SINGLE_DOUBLE
 OCL_TUNE = -DFERMI_OCL
 EXTRAMAKE = Makefile.lammps.mingw-cross
 BIN_DIR = Obj_mingw64
 OBJ_DIR = Obj_mingw64
 LIB_DIR = Obj_mingw64
 AR = x86_64-w64-mingw32-ar
 BSH = /bin/sh
 include Opencl.makefile
--- a/lib/gpu/Makefile.mingw64-cross-mpi
+++ b/lib/gpu/Makefile.mingw64-cross-mpi
@ -1,20 +0,0 @@
 CUDA_HOME = ../../tools/mingw-cross/OpenCL
 OCL_CPP = x86_64-w64-mingw32-g++ -O3 -march=core2 -mtune=core2 -mpc64 \
 	-msse2 -DMPI_GERYON -DUCL_NO_EXIT -I$(CUDA_HOME)/include \
 	-I../../tools/mingw-cross/mpich2-win64/include/ \
        -DMPICH_IGNORE_CXX_SEEK
 OCL_LINK = -static -Wl,--enable-stdcall-fixup -L$(CUDA_HOME)/../Obj_mingw64 -Wl,-Bdynamic,-lOpenCL,-Bstatic \
 	-L../../tools/mingw-cross/mpich2-win64/lib -lmpi
 OCL_PREC = -D_SINGLE_DOUBLE
 OCL_TUNE = -DFERMI_OCL
 EXTRAMAKE = Makefile.lammps.mingw-cross
 BIN_DIR = Obj_mingw64-mpi
 OBJ_DIR = Obj_mingw64-mpi
 LIB_DIR = Obj_mingw64-mpi
 AR = x86_64-w64-mingw32-ar
 BSH = /bin/sh
 include Opencl.makefile
--- a/lib/gpu/Makefile.mpi
+++ b/lib/gpu/Makefile.mpi
@ -0,0 +1 @@
 Makefile.linux
--- a/lib/gpu/Makefile.serial
+++ b/lib/gpu/Makefile.serial
@ -1,5 +1,5 @@
 # /* ----------------------------------------------------------------------   
-#  Generic Makefile for CUDA using MPI STUBS library
+#  Generic Linux Makefile for CUDA 
 #     - Change CUDA_ARCH for your GPU
 # ------------------------------------------------------------------------- */
@ -7,23 +7,38 @@
 EXTRAMAKE = Makefile.lammps.standard
-CUDA_HOME = $(HOME)/cuda
+ifeq ($(CUDA_HOME),)
 CUDA_HOME = /usr/local/cuda
 endif
 NVCC = nvcc
 # Tesla CUDA
-CUDA_ARCH = -arch=sm_20
+CUDA_ARCH = -arch=sm_21
 # newer CUDA
 #CUDA_ARCH = -arch=sm_13
 # older CUDA
 #CUDA_ARCH = -arch=sm_10 -DCUDA_PRE_THREE
 CUDA_ARCH = -arch=sm_35
 # this setting should match LAMMPS Makefile
 # one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
 LMP_INC = -DLAMMPS_SMALLBIG
 # precision for GPU calculations
 # -D_SINGLE_SINGLE  # Single precision for all calculations
 # -D_DOUBLE_DOUBLE  # Double precision for all calculations
 # -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
 CUDA_PRECISION = -D_SINGLE_DOUBLE
 CUDA_INCLUDE = -I$(CUDA_HOME)/include
 CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi
 CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math
-CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -I../../src/STUBS
+CUDA_INCLUDE = -I$(CUDA_HOME)/include
-CUDR_OPTS = -O2 
+CUDA_LIB = -L$(CUDA_HOME)/lib64 -L../../src/STUBS -lmpi_stubs
 CUDA_OPTS = -DUNIX -O3 -Xptxas -v --use_fast_math $(LMP_INC)
 CUDR_CPP = g++ -DMPI_GERYON -DUCL_NO_EXIT -fPIC -I../../src/STUBS
 CUDR_OPTS = -O2 $(LMP_INC) # -xHost -no-prec-div -ansi-alias
 BIN_DIR = ./
 OBJ_DIR = ./
@ -31,5 +46,7 @@ LIB_DIR = ./
 AR = ar
 BSH = /bin/sh
 CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini
 include Nvidia.makefile
--- a/lib/h5md/Install.py
+++ b/lib/h5md/Install.py
@ -1 +1 @@
-Install.py
+../Install.py
--- a/lib/h5md/Makefile.h5cc
+++ b/lib/h5md/Makefile.h5cc
@ -9,12 +9,14 @@ HDF5_PATH=/usr
 INC=-I include
 AR=ar
 ARFLAGS=rc
-LIB=libch5md.a
+# need to build two libraries to not break compatibility and to support Install.py
 LIB=libh5md.a libch5md.a
 all: lib Makefile.lammps
 build:
 	mkdir -p build
 build/ch5md.o: src/ch5md.c | build
 	$(CC) $(INC) $(CFLAGS) -c $< -o $@
@ -23,8 +25,11 @@ Makefile.lammps:
 .PHONY: all lib clean
-$(LIB): build/ch5md.o
+libch5md.a : build/ch5md.o
-	$(AR) $(ARFLAGS) $(LIB) build/ch5md.o
+	$(AR) $(ARFLAGS) $@ build/ch5md.o
 libh5md.a : build/ch5md.o
 	$(AR) $(ARFLAGS) $@ build/ch5md.o
 lib: $(LIB)
--- a/lib/h5md/Makefile.mpi
+++ b/lib/h5md/Makefile.mpi
@ -0,0 +1 @@
 Makefile.h5cc
--- a/lib/h5md/Makefile.serial
+++ b/lib/h5md/Makefile.serial
@ -0,0 +1 @@
 Makefile.h5cc
--- a/lib/kim/.gitignore
+++ b/lib/kim/.gitignore
@ -1,2 +1,3 @@
 /Makefile.KIM_DIR
 /Makefile.KIM_Config
 /installed-kim-api-*
--- a/lib/kim/Install.py
+++ b/lib/kim/Install.py
@ -1,150 +1,301 @@
 #!/usr/bin/env python
-# install.py tool to setup the kim-api library
+# install.py tool to download, compile, and setup the kim-api library
 # used to automate the steps described in the README file in this dir
-import sys,os,re,urllib,commands
+from __future__ import print_function
 import sys,os,re,subprocess
 help = """
-Syntax: install.py -v version -c kim-dir -b kim-model-name -a kim-name
+Syntax from src dir: make lib-kim args="-b -v version  -a kim-name"
-        specify one or more options, order does not matter
+                 or: make lib-kim args="-b -a everything"
-        -v = version of kim-api to download and work with
+                 or: make lib-kim args="-n -a kim-name"
-             default = kim-api-v1.8.2 (current as of June 2017)
+                 or: make lib-kim args="-p /usr/local/open-kim -a kim-name"
-        -c = create Makefile.KIM_DIR within lammps lib/kim to configure lammps
+Syntax from lib dir: python Install.py -b -v version  -a kim-name
-             for use with the kim-api library installed at "kim-dir" (absolute
+                 or: python Install.py -b -a everything
-             path).  default = this dir
+                 or: python Install.py -n -a kim-name
-        -b = build kim-api and kim model where kim-model-name can be a specific
+                 or: python Install.py -p /usr/local/open-kim -a kim-name
-             openkim.org model name (such as
+
-             "EAM_Dynamo_Ackland_W__MO_141627196590_002") or the keyword
+specify one or more options, order does not matter
-             "OpenKIM" to install all compatible models from the openkim.org
+
-             site.
+  -v = version of KIM API library to use
-        -a = add kim-name openkim.org item (model driver or model) to existing
+       default = kim-api-v1.8.2 (current as of June 2017)
-             kim-api instalation.
+  -b = download and build base KIM API library with example Models
       this will delete any previous installation in the current folder
  -n = do NOT download and build base KIM API library.
       Use an existing installation 
  -p = specify location of KIM API installation (implies -n)
  -a = add single KIM model or model driver with kim-name
       to existing KIM API lib (see example below).
       If kim-name = everything, then rebuild KIM API library with
       *all* available OpenKIM Models (make take a long time).
  -vv = be more verbose about what is happening while the script runs
 Examples:
 make lib-kim args="-b" # install KIM API lib with only example models
 make lib-kim args="-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"   # only add one model or model driver
 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
 """
-def error():
+def error(str=None):
-  print help
+  if not str: print(help)
  else: print("ERROR",str)
  sys.exit()
 # expand to full path name
 # process leading '~' or relative path
 def fullpath(path):
  return os.path.abspath(os.path.expanduser(path))
 def which(program):
  def is_exe(fpath):
    return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
  fpath, fname = os.path.split(program)
  if fpath:
    if is_exe(program):
      return program
  else:
    for path in os.environ["PATH"].split(os.pathsep):
      path = path.strip('"')
      exe_file = os.path.join(path, program)
      if is_exe(exe_file):
        return exe_file
  return None
 def geturl(url,fname):
  if which('curl') != None:
    cmd = 'curl -L -o "%s" %s' % (fname,url)
  elif which('wget') != None:
    cmd = 'wget -O "%s" %s' % (fname,url)
  else: error("cannot find 'wget' or 'curl' to download source code")
  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
  return txt
 # parse args
-args = sys.argv
+args = sys.argv[1:]
 nargs = len(args)
 if nargs == 0: error()
 thisdir = os.environ['PWD']
 dir = thisdir
 version = "kim-api-v1.8.2"
-dirflag = 0
+buildflag = False
-buildflag = 0
+everythingflag = False
-addflag = 0
+addflag = False
 verboseflag = False
 pathflag = False
-iarg = 1
+iarg = 0
 while iarg < len(args):
  if args[iarg] == "-v":
    if iarg+2 > len(args): error()
    version = args[iarg+1]
    iarg += 2
  elif args[iarg] == "-c":
    dirflag = 1
    if iarg+2 > len(args): error()
    dir = args[iarg+1]
    iarg += 2
  elif args[iarg] == "-b":
-    buildflag = 1
+    buildflag = True
    iarg += 1
  elif args[iarg] == "-n":
    buildflag = False
    iarg += 1
  elif args[iarg] == "-p":
    if iarg+2 > len(args): error()
-    modelname = args[iarg+1]
+    kimdir = fullpath(args[iarg+1])
    pathflag = True
    buildflag = False
    iarg += 2
  elif args[iarg] == "-a":
-    addflag = 1
+    addflag = True
    if iarg+2 > len(args): error()
    addmodelname = args[iarg+1]
    if addmodelname == "everything":
      buildflag = True
      everythingflag = True
      addflag = False
    iarg += 2
  elif args[iarg] == "-vv":
    verboseflag = True
    iarg += 1
  else: error()
 thisdir = os.path.abspath(thisdir)
 dir = os.path.abspath(dir)
 url = "https://s3.openkim.org/kim-api/%s.tgz" % version
-# download and unpack tarball
+# set KIM API directory
 if pathflag:
  if not os.path.isdir(kimdir):
    print("\nkim-api is not installed at %s" % kimdir)
    error()
-if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir):
+  # configure LAMMPS to use existing kim-api installation
-  open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
+  with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
-  open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
+    mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
-  print "Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
+    mkfile.write(".DUMMY: print_dir\n\n")
    mkfile.write("print_dir:\n")
    mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
 else:
-  if dirflag == 1:
+  kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
    open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir)
    open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir)
    print "Updated %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)
 # download KIM tarball, unpack, build KIM
 if buildflag:
-if buildflag == 1:
+  # check to see if an installed kim-api already exists and wipe it out.
-  # download kim-api
+
-  print "Downloading kim-api tarball ..."
+  if os.path.isdir(kimdir):
-  urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,version))
+    print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir)
-  print "Unpacking kim-api tarball ..."
+    cmd = 'rm -rf "%s"' % kimdir
-  cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version)
+    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  txt = commands.getstatusoutput(cmd)
+
-  if txt[0] != 0: error()
+  # configure LAMMPS to use kim-api to be installed
  with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
    mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
    mkfile.write(".DUMMY: print_dir\n\n")
    mkfile.write("print_dir:\n")
    mkfile.write("	@printf $(KIM_INSTALL_DIR)\n")
  with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
    cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
  print("Created %s/Makefile.KIM_DIR\n  using %s" % (thisdir,kimdir))
  # download entire kim-api tarball
  print("Downloading kim-api tarball ...")
  geturl(url,"%s/%s.tgz" % (thisdir,version))
  print("Unpacking kim-api tarball ...")
  cmd = 'cd "%s"; rm -rf "%s"; tar -xzvf %s.tgz' % (thisdir,version,version)
  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
  # configure kim-api
-  print "Configuring kim-api ..."
+
-  cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,dir)
+  print("Configuring kim-api ...")
-  txt = commands.getstatusoutput(cmd)
+  cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir,version,kimdir)
-  print txt[1]
+  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
  if txt[0] != 0: error()
  # build kim-api
-  print "Configuring model : %s" % modelname
+
-  cmd = "cd %s/%s; make add-%s" % (thisdir,version,modelname)
+  print("Configuring example Models")
-  txt = commands.getstatusoutput(cmd)
+  cmd = 'cd "%s/%s"; make add-examples' % (thisdir,version)
-  print txt[1]
+  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  if txt[0] != 0: error()
+  if verboseflag: print (txt.decode("UTF-8"))
-  #
+
-  print "Building kim-api ..."
+  if everythingflag:
-  cmd = "cd %s/%s; make" % (thisdir,version)
+    print("Configuring all OpenKIM models, this will take a while ...")
-  txt = commands.getstatusoutput(cmd)
+    cmd = 'cd "%s/%s"; make add-OpenKIM' % (thisdir,version)
-  print txt[1]
+    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  if txt[0] != 0: error()
+    if verboseflag: print(txt.decode("UTF-8"))
  print("Building kim-api ...")
  cmd = 'cd "%s/%s"; make' % (thisdir,version)
  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
  if verboseflag: print(txt.decode("UTF-8"))
  # install kim-api
-  print "Installing kim-api ..."
+
-  cmd = "cd %s/%s; make install" % (thisdir,version)
+  print("Installing kim-api ...")
-  txt = commands.getstatusoutput(cmd)
+  cmd = 'cd "%s/%s"; make install' % (thisdir,version)
-  print txt[1]
+  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  if txt[0] != 0: error()
+  if verboseflag: print(txt.decode("UTF-8"))
-  #
+
-  cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version)
+  cmd = 'cd "%s/%s"; make install-set-default-to-v1' %(thisdir,version)
-  txt = commands.getstatusoutput(cmd)
+  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  print txt[1]
+  if verboseflag: print(txt.decode("UTF-8"))
  if txt[0] != 0: error()
  # remove source files
  print "Removing kim-api source and build files ..."
  cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version)
  txt = commands.getstatusoutput(cmd)
  print txt[1]
  if txt[0] != 0: error()
-if addflag == 1:
+  print("Removing kim-api source and build files ...")
-  # download model
+  cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' % (thisdir,version,version)
  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
 # add a single model (and possibly its driver) to existing KIM installation
 if addflag:
  if not os.path.isdir(kimdir):
    print("\nkim-api is not installed")
    error()
  # download single model
  print("Downloading tarball for %s..." % addmodelname)
  url = "https://openkim.org/download/%s.tgz" % addmodelname
-  print "Downloading item tarball ..."
+  geturl(url,"%s/%s.tgz" % (thisdir,addmodelname))
-  urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,addmodelname))
+
-  print "Unpacking item tarball ..."
+  print("Unpacking item tarball ...")
-  cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname)
+  cmd = 'cd "%s"; tar -xzvf %s.tgz' % (thisdir,addmodelname)
-  txt = commands.getstatusoutput(cmd)
+  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  if txt[0] != 0: error()
+
-  #
+  print("Building item ...")
-  print "Building item ..."
+  cmd = 'cd "%s/%s"; make; make install' %(thisdir,addmodelname)
-  cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname)
+  try:
-  txt = commands.getstatusoutput(cmd)
+    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  print txt[1]
+  except subprocess.CalledProcessError as e:
-  if txt[0] != 0: error()
+
-  #
+    # Error: but first, check to see if it needs a driver
-  print "Removing kim item source and build files ..."
+    firstRunOutput = e.output.decode("UTF-8")
-  cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname)
+
-  txt = commands.getstatusoutput(cmd)
+    cmd = 'cd "%s/%s"; make kim-item-type' % (thisdir,addmodelname)
-  print txt[1]
+    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
-  if txt[0] != 0: error()
+    txt = txt.decode("UTF-8")
    if txt == "ParameterizedModel":
      # Get and install driver
      cmd = 'cd "%s/%s"; make model-driver-name' % (thisdir,addmodelname)
      txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
      adddrivername = txt.decode("UTF-8").strip()
      print("First installing model driver: %s..." % adddrivername)
      cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,adddrivername)
      try:
        txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
      except subprocess.CalledProcessError as e:
        print(e.output)
        sys.exit()
      if verboseflag: print(txt.decode("UTF-8"))
      # now install the model that needed the driver
      print("Now installing model : %s" % addmodelname)
      cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,addmodelname)
      try:
        txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
      except subprocess.CalledProcessError as e:
        print(e.output)
        sys.exit()
      print(txt.decode("UTF-8"))
      sys.exit()
    else:
      print(firstRunOutput)
      print("Error, unable to build and install OpenKIM item: %s" \
            % addmodelname)
      sys.exit()
  # success the first time
  if verboseflag: print(txt.decode("UTF-8"))
  print("Removing kim item source and build files ...")
  cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' %(thisdir,addmodelname,addmodelname)
  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
--- a/lib/kim/README
+++ b/lib/kim/README
@ -8,14 +8,16 @@ James Sethna (Cornell U).  Ryan Elliott is the main developer for the
 KIM API and he also maintains the code that implements the pair_style
 kim command.
-To download, build, and install the KIM API on your system, follow
+You can type "make lib-kim" from the src directory to see help on
-these steps.  You can use the install.py script to automate these steps.
+how to download and build this library via make commands, or you can
 do the same thing by typing "python Install.py" from within this
 directory, or you can do it manually by following the instructions
 below.
 -----------------
 Instructions:
 1. Configure lammps for use with the kim-api library installed in this directory
 $ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR
@ -65,7 +67,7 @@ $ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz
 When these steps are complete you can build LAMMPS with the KIM
 package installed:
-$ cd ../../src
+$ cd lammpos/src
 $ make yes-kim
 $ make g++ (or whatever target you wish)
--- a/lib/linalg/Install.py
+++ b/lib/linalg/Install.py
@ -1,52 +0,0 @@
 #!/usr/bin/env python
 # install.py tool to do build of the linear algebra library
 # used to automate the steps described in the README file in this dir
 import sys,commands,os
 # help message
 help = """
 Syntax: python Install.py -m machine
  -m = peform a clean followed by "make -f Makefile.machine"
       machine = suffix of a lib/Makefile.* file
 """
 # 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
 iarg = 0
 while iarg < nargs:
  if args[iarg] == "-m":
    if iarg+2 > nargs: error()
    machine = args[iarg+1]
    iarg += 2  
  else: error()
 # set lib from working dir
 cwd = os.getcwd()
 lib = os.path.basename(cwd)
 # make the library
 print "Building lib%s.a ..." % lib
 cmd = "make -f Makefile.%s clean; make -f Makefile.%s" % (machine,machine)
 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))
--- a/lib/linalg/Install.py
+++ b/lib/linalg/Install.py
@ -0,0 +1 @@
 ../Install.py
--- a/lib/linalg/Makefile.gfortran
+++ b/lib/linalg/Makefile.gfortran
@ -18,10 +18,8 @@ OBJ =   $(SRC:.f=.o)
 # ------ SETTINGS ------
 FC =           gfortran
-FFLAGS =      -O3 -fPIC -march=native -mpc64  \
+FFLAGS =      -O3 -fPIC -ffast-math -fstrict-aliasing -fno-second-underscore
-         -ffast-math -funroll-loops -fstrict-aliasing -Wall -W -Wno-uninitialized -fno-second-underscore
+FFLAGS0 =     -O0 -fPIC -fno-second-underscore
 FFLAGS0 =      -O0 -fPIC -march=native -mpc64  \
         -Wall -W -Wno-uninitialized -fno-second-underscore
 ARCHIVE =	ar
 AR =	ar
 ARCHFLAG =	-rcs
@ -47,7 +45,7 @@ dlamch.o: dlamch.f
 # ------ CLEAN ------
 clean:
-	-rm *.o *.mod *~ $(LIB)
+	-rm -f *.o *.mod *~ $(LIB)
 tar:
 	-tar -czvf ../linalg.tar.gz $(FILES)
--- a/lib/linalg/Makefile.mingw32-cross
+++ b/lib/linalg/Makefile.mingw32-cross
@ -1,67 +0,0 @@
 # -*- makefile -*-
 # *_________________________________________________________________________*
 # *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
 SHELL = /bin/sh
 # ------ FILES ------
 SRC =	$(wildcard *.f)
 FILES = $(SRC) Makefile.* README
 # ------ DEFINITIONS ------
 DIR = Obj_mingw32/
 LIB = $(DIR)liblinalg.a
 OBJ =   $(SRC:%.f=$(DIR)%.o)
 # ------ SETTINGS ------
 FC =    	i686-w64-mingw32-gfortran
 FFLAGS =	-O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
 		-ffast-math -funroll-loops -fstrict-aliasing -Wall -W	\
 		-Wno-uninitialized -fno-second-underscore
 FFLAGS0 =	-O0 -march=i686 -mtune=generic -mfpmath=387 -mpc64	\
 		-Wall -W -Wno-uninitialized -fno-second-underscore
 ARCHIVE =	i686-w64-mingw32-ar
 AR =		i686-w64-mingw32-ar
 ARCHFLAG =	-rcs
 USRLIB =
 SYSLIB =
 .PHONY: default clean tar
 .SUFFIXES:
 .SUFFIXES: .F .f .o
 # ------ MAKE PROCEDURE ------
 default: $(DIR) $(LIB)
 $(LIB): $(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 $(DIR):
 	mkdir $(DIR)
 # ------ COMPILE RULES ------
 $(DIR)%.o:%.F
 	$(F90) $(F90FLAGS) -c $< -o $@
 $(DIR)%.o:%.f
 	$(FC) $(FFLAGS) -c $< -o $@
 $(DIR)dlamch.o: dlamch.f
 	$(FC) $(FFLAGS0) -c $< -o $@
 # ------ CLEAN ------
 clean:
 	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
 	-rmdir $(DIR)
 tar:
 	-tar -czvf ../linalg.tar.gz $(FILES)
--- a/lib/linalg/Makefile.mingw32-cross-mpi
+++ b/lib/linalg/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/linalg/Makefile.mingw64-cross
+++ b/lib/linalg/Makefile.mingw64-cross
@ -1,67 +0,0 @@
 # -*- makefile -*-
 # *_________________________________________________________________________*
 # *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
 SHELL = /bin/sh
 # ------ FILES ------
 SRC =	$(wildcard *.f)
 FILES = $(SRC) Makefile.* README
 # ------ DEFINITIONS ------
 DIR = Obj_mingw64/
 LIB = $(DIR)liblinalg.a
 OBJ =   $(SRC:%.f=$(DIR)%.o)
 # ------ SETTINGS ------
 FC =    	x86_64-w64-mingw32-gfortran
 FFLAGS =	-O3 -march=core2 -mtune=generic -msse2 -mpc64	\
 		-ffast-math -funroll-loops -fstrict-aliasing -Wall -W	\
 		-Wno-uninitialized -fno-second-underscore
 FFLAGS0 =	-O0 -march=core2 -mtune=generic -msse2 -mpc64	\
 		-Wall -W -Wno-uninitialized -fno-second-underscore
 ARCHIVE =	x86_64-w64-mingw32-ar
 AR =		x86_64-w64-mingw32-ar
 ARCHFLAG =	-rcs
 USRLIB =
 SYSLIB =
 .PHONY: default clean tar
 .SUFFIXES:
 .SUFFIXES: .F .f .o
 # ------ MAKE PROCEDURE ------
 default: $(DIR) $(LIB)
 $(LIB): $(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 $(DIR):
 	mkdir $(DIR)
 # ------ COMPILE RULES ------
 $(DIR)%.o:%.F
 	$(F90) $(F90FLAGS) -c $< -o $@
 $(DIR)%.o:%.f
 	$(FC) $(FFLAGS) -c $< -o $@
 $(DIR)dlamch.o: dlamch.f
 	$(FC) $(FFLAGS0) -c $< -o $@
 # ------ CLEAN ------
 clean:
 	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
 	-rmdir $(DIR)
 tar:
 	-tar -czvf ../linalg.tar.gz $(FILES)
--- a/lib/linalg/Makefile.mingw64-cross-mpi
+++ b/lib/linalg/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/linalg/Makefile.mpi
+++ b/lib/linalg/Makefile.mpi
@ -0,0 +1,52 @@
 # -*- makefile -*-
 # *_________________________________________________________________________*
 # *      Minimal BLAS/LAPACK Library for use by other LAMMPS packages
 SHELL = /bin/sh
 # ------ FILES ------
 SRC =	$(wildcard *.f)
 FILES = $(SRC) Makefile.* README
 # ------ DEFINITIONS ------
 LIB = liblinalg.a
 OBJ =   $(SRC:.f=.o)
 # ------ SETTINGS ------
 FC =          mpifort
 FFLAGS =      -O3 -fPIC
 FFLAGS0 =     -O0 -fPIC
 ARCHIVE =	ar
 AR =	ar
 ARCHFLAG =	-rcs
 USRLIB =
 SYSLIB =
 # ------ MAKE PROCEDURE ------
 lib: 	$(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 # ------ COMPILE RULES ------
 %.o:%.F
 	$(F90) $(F90FLAGS) -c $<
 %.o:%.f
 	$(FC) $(FFLAGS) -c $<
 dlamch.o: dlamch.f
 	$(FC) $(FFLAGS0) -c $<
 # ------ CLEAN ------
 clean:
 	-rm -f *.o *.mod *~ $(LIB)
 tar:
 	-tar -czvf ../linalg.tar.gz $(FILES)
--- a/lib/linalg/Makefile.serial
+++ b/lib/linalg/Makefile.serial
@ -0,0 +1 @@
 Makefile.gfortran
--- a/lib/meam/Install.py
+++ b/lib/meam/Install.py
@ -1 +1 @@
-Install.py
+../Install.py
--- a/lib/meam/Makefile.lammps.empty
+++ b/lib/meam/Makefile.lammps.empty
@ -1,5 +1,5 @@
 # Settings that the LAMMPS build will import when this package library is used
-colvars_SYSINC =
+meam_SYSINC =
-colvars_SYSLIB =
+meam_SYSLIB = 
-colvars_SYSPATH =
+meam_SYSPATH =
--- a/lib/meam/Makefile.mingw32-cross
+++ b/lib/meam/Makefile.mingw32-cross
@ -1,69 +0,0 @@
 # * -*- makefile -*-
 # *_________________________________________________________________________*
 # *      MEAM: MODEFIED EMBEDDED ATOM METHOD                                *
 # *      DESCRIPTION: SEE READ-ME                                           *
 # *      FILE NAME: Makefile                                                *
 # *      AUTHORS: Greg Wagner, Sandia National Laboratories                 * 
 # *      CONTACT: gjwagne@sandia.gov                                        *
 # *_________________________________________________________________________*/
 SHELL = /bin/sh
 # which file will be copied to Makefile.lammps
 EXTRAMAKE = Makefile.lammps.gfortran
 # ------ FILES ------
 SRC = meam_data.F meam_setup_done.F meam_setup_global.F meam_setup_param.F meam_dens_init.F meam_dens_final.F meam_force.F meam_cleanup.F
 FILES = $(SRC) Makefile 
 # ------ DEFINITIONS ------
 DIR = Obj_mingw32/
 LIB = $(DIR)libmeam.a
 OBJ = $(SRC:%.F=$(DIR)%.o) $(DIR)fm_exp.o
 # ------ SETTINGS ------
 F90 =           i686-w64-mingw32-gfortran
 F90FLAGS =      -O3 -march=i686 -mtune=generic -mfpmath=387 -mpc64  \
 		-ffast-math -funroll-loops -fstrict-aliasing -J$(DIR) \
 		-Wall -W -Wno-uninitialized -fno-second-underscore
 #F90FLAGS =      -O 
 ARCHIVE =	i686-w64-mingw32-ar
 ARCHFLAG =	-rcs
 LINK =         	i686-w64-mingw32-g++
 LINKFLAGS =	-O
 USRLIB =
 SYSLIB =
 # ------ MAKE PROCEDURE ------
 default: $(DIR) $(LIB)
 $(DIR):
 	-mkdir $(DIR)
 $(LIB):  $(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
 # ------ COMPILE RULES ------
 $(DIR)%.o:%.F
 	$(F90) $(F90FLAGS) -c $< -o $@
 $(DIR)%.o:%.c
 	$(F90) $(F90FLAGS) -c $< -o $@
 include .depend
 # ------ CLEAN ------
 clean:
 	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
 	-rmdir $(DIR)
 tar:
 	-tar -cvf ../MEAM.tar $(FILES)
--- a/lib/meam/Makefile.mingw32-cross-mpi
+++ b/lib/meam/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/meam/Makefile.mingw64-cross-mpi
+++ b/lib/meam/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/meam/Makefile.mingw64-cross
+++ b/lib/meam/Makefile.mingw64-cross
@ -1,4 +1,4 @@
-# * -*- makefile -*-
+# *
 # *_________________________________________________________________________*
 # *      MEAM: MODEFIED EMBEDDED ATOM METHOD                                *
 # *      DESCRIPTION: SEE READ-ME                                           *
@ -11,7 +11,7 @@ SHELL = /bin/sh
 # which file will be copied to Makefile.lammps
-EXTRAMAKE = Makefile.lammps.gfortran
+EXTRAMAKE = Makefile.lammps.empty
 # ------ FILES ------
@ -21,49 +21,41 @@ FILES = $(SRC) Makefile
 # ------ DEFINITIONS ------
-DIR = Obj_mingw64/
+LIB = libmeam.a
-LIB = $(DIR)libmeam.a
+OBJ =   $(SRC:.F=.o) fm_exp.o
 OBJ = $(SRC:%.F=$(DIR)%.o) $(DIR)fm_exp.o
 # ------ SETTINGS ------
-F90 =           x86_64-w64-mingw32-gfortran
+F90 =           mpifort
-F90FLAGS =      -O3 -march=core2 -mtune=core2 -msse2 -mpc64  \
+CC  =		mpicc
-		-ffast-math -funroll-loops -fstrict-aliasing -J$(DIR) \
+F90FLAGS =      -O3 -fPIC
 		-Wall -W -Wno-uninitialized -fno-second-underscore
 #F90FLAGS =      -O 
-ARCHIVE =	x86_64-w64-mingw32-ar
+ARCHIVE =	ar
-ARCHFLAG =	-rcs
+ARCHFLAG =	-rc
-LINK =         	x86_64-w64-mingw32-g++
+LINK =         	mpicxx
 LINKFLAGS =	-O
 USRLIB =
 SYSLIB =
 # ------ MAKE PROCEDURE ------
-default: $(DIR) $(LIB)
+lib: 	$(OBJ)
 $(DIR):
 	-mkdir $(DIR)
 $(LIB):  $(OBJ)
 	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
 	@cp $(EXTRAMAKE) Makefile.lammps
 # ------ COMPILE RULES ------
-$(DIR)%.o:%.F
+%.o:%.F
-	$(F90) $(F90FLAGS) -c $< -o $@
+	$(F90) $(F90FLAGS) -c $<
-$(DIR)%.o:%.c
+%.o:%.c
-	$(F90) $(F90FLAGS) -c $< -o $@
+	$(CC) $(F90FLAGS) -c $<
 include .depend
 # ------ CLEAN ------
 clean:
-	-rm $(DIR)*.o $(DIR)*.mod *~ $(LIB)
+	-rm *.o *.mod *~ $(LIB)
 	-rmdir $(DIR)
 tar:
 	-tar -cvf ../MEAM.tar $(FILES)
--- a/lib/meam/Makefile.serial
+++ b/lib/meam/Makefile.serial
@ -0,0 +1 @@
 Makefile.gfortran
--- a/Show More
+++ b/Show More