new Section package and start doc pages and build scripts

doc/src/Manual.txt

@@ -158,12 +158,11 @@ END_RST -->
   2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
   2.2 "Making LAMMPS"_start_2 :b
   2.3 "Making LAMMPS with optional packages"_start_3 :b
-  2.4 "Building LAMMPS via the Make.py script"_start_4 :b
+  2.4 "Building LAMMPS as a library"_start_4 :b
-  2.5 "Building LAMMPS as a library"_start_5 :b
+  2.5 "Running LAMMPS"_start_5 :b
-  2.6 "Running LAMMPS"_start_6 :b
+  2.6 "Command-line options"_start_6 :b
-  2.7 "Command-line options"_start_7 :b
+  2.7 "Screen output"_start_7 :b
-  2.8 "Screen output"_start_8 :b
+  2.8 "Tips for users of previous versions"_start_8 :ule,b
-  2.9 "Tips for users of previous versions"_start_9 :ule,b
 "Commands"_Section_commands.html :l
   3.1 "LAMMPS input script"_cmd_1 :ulb,b
   3.2 "Parsing rules"_cmd_2 :b

doc/src/Section_commands.txt

@@ -1052,7 +1052,7 @@ package"_Section_start.html#start_3.
 "oxdna2/excv"_pair_oxdna2.html,
 "oxdna2/stk"_pair_oxdna2.html,
 "quip"_pair_quip.html,
-"reax/c (k)"_pair_reax_c.html,
+"reax/c (k)"_pair_reaxc.html,
 "smd/hertz"_pair_smd_hertz.html,
 "smd/tlsph"_pair_smd_tlsph.html,
 "smd/triangulated/surface"_pair_smd_triangulated_surface.html,

doc/src/Section_intro.txt

@@ -249,8 +249,12 @@ Pizza.py WWW site"_pizza. :l
 
 Specialized features :h5
 
-These are LAMMPS capabilities which you may not think of as typical
+LAMMPS can be built with optional packages which implement a variety
-molecular dynamics options:
+of additional capabilities.  An overview of all the packages is "given
+here"_Section_packages.html.
+
+These are some LAMMPS capabilities which you may not think of as
+typical classical molecular dynamics options:
 
 "static"_balance.html and "dynamic load-balancing"_fix_balance.html
 "generalized aspherical particles"_body.html

doc/src/Section_start.txt

@@ -14,12 +14,11 @@ experienced users.
 2.1 "What's in the LAMMPS distribution"_#start_1
 2.2 "Making LAMMPS"_#start_2
 2.3 "Making LAMMPS with optional packages"_#start_3
-2.4 "Building LAMMPS via the Make.py script"_#start_4
+2.5 "Building LAMMPS as a library"_#start_4
-2.5 "Building LAMMPS as a library"_#start_5
+2.6 "Running LAMMPS"_#start_5
-2.6 "Running LAMMPS"_#start_6
+2.7 "Command-line options"_#start_6
-2.7 "Command-line options"_#start_7
+2.8 "Screen output"_#start_7
-2.8 "Screen output"_#start_8
+2.9 "Tips for users of previous versions"_#start_8 :all(b)
-2.9 "Tips for users of previous versions"_#start_9 :all(b)
 
 :line
 
@@ -80,7 +79,7 @@ This section has the following sub-sections:
 
 Read this first :h5,link(start_2_1)
 
-If you want to avoid building LAMMPS yourself, read the preceding
+If you want to avoid building LAMMPS yourself, read the preceeding
 section about options available for downloading and installing
 executables.  Details are discussed on the "download"_download page.
 
@@ -96,7 +95,7 @@ make serial :pre
 Note that on a facility supercomputer, there are often "modules"
 loaded in your environment that provide the compilers and MPI you
 should use.  In this case, the "mpicxx" compile/link command in
-Makefile.mpi should just work by accessing those modules.
+Makefile.mpi should simply work by accessing those modules.
 
 It may be the case that one of the other Makefile.machine files in the
 src/MAKE sub-directories is a better match to your system (type "make"
@@ -107,33 +106,35 @@ make stampede :pre
 If any of these builds (with an existing Makefile.machine) works on
 your system, then you're done!
 
+If you need to install an optional package with a LAMMPS command you
+want to use, and the package does not depend on an extra library, you
+can simply type
+
+make name :pre
+
+before invoking (or re-invoking) the above steps.  "Name" is the
+lower-case name of the package, e.g. replica or user-misc.
+
 If you want to do one of the following:
 
-use optional LAMMPS features that require additional libraries
+use a LAMMPS command that requires an extra library (e.g. "dump image"_dump_image.html)
-use optional packages that require additional libraries
+build with a package that requires an extra library
-use optional accelerator packages that require special compiler/linker settings
+build with an accelerator package that requires special compiler/linker settings
-run on a specialized platform that has its own compilers, settings, or other libs to use :ul
+run on a machine that has its own compilers, settings, or libraries :ul
 
 then building LAMMPS is more complicated.  You may need to find where
-auxiliary libraries exist on your machine or install them if they
+extra libraries exist on your machine or install them if they don't.
-don't.  You may need to build additional libraries that are part of
+You may need to build extra libraries that are included in the LAMMPS
-the LAMMPS package, before building LAMMPS.  You may need to edit a
+distribution, before building LAMMPS itself.  You may need to edit a
 Makefile.machine file to make it compatible with your system.
 
-Note that there is a Make.py tool in the src directory that automates
-several of these steps, but you still have to know what you are doing.
-"Section 2.4"_#start_4 below describes the tool.  It is a convenient
-way to work with installing/un-installing various packages, the
-Makefile.machine changes required by some packages, and the auxiliary
-libraries some of them use.
-
 Please read the following sections carefully.  If you are not
 comfortable with makefiles, or building codes on a Unix platform, or
 running an MPI job on your machine, please find a local expert to help
-you.  Many compilation, linking, and run problems that users have are
+you.  Many compilation, linking, and run problems users experience are
-often not really LAMMPS issues - they are peculiar to the user's
+often not LAMMPS issues - they are peculiar to the user's system,
-system, compilers, libraries, etc.  Such questions are better answered
+compilers, libraries, etc.  Such questions are better answered by a
-by a local expert.
+local expert.
 
 If you have a build problem that you are convinced is a LAMMPS issue
 (e.g. the compiler complains about a line of LAMMPS source code), then
@@ -251,7 +252,7 @@ re-compile, after typing "make clean" (which will describe different
 clean options).
 
 The LMP_INC variable is used to include options that turn on ifdefs
-within the LAMMPS code.  The options that are currently recognized are:
+within the LAMMPS code.  The options that are currently recogized are:
 
 -DLAMMPS_GZIP
 -DLAMMPS_JPEG
@@ -362,7 +363,7 @@ installed on your platform.  If MPI is installed on your system in the
 usual place (under /usr/local), you also may not need to specify these
 3 variables, assuming /usr/local is in your path.  On some large
 parallel machines which use "modules" for their compile/link
-environments, you may simply need to include the correct module in
+environements, you may simply need to include the correct module in
 your build environment, before building LAMMPS.  Or the parallel
 machine may have a vendor-provided MPI which the compiler has no
 trouble finding.
@@ -430,7 +431,7 @@ use the KISS library described above.
 You may also need to set the FFT_INC, FFT_PATH, and FFT_LIB variables,
 so the compiler and linker can find the needed FFT header and library
 files.  Note that on some large parallel machines which use "modules"
-for their compile/link environments, you may simply need to include
+for their compile/link environements, you may simply need to include
 the correct module in your build environment.  Or the parallel machine
 may have a vendor-provided FFT library which the compiler has no
 trouble finding.
@@ -450,12 +451,13 @@ you must also manually specify the correct library, namely -lsfftw or
 
 The FFT_INC variable also allows for a -DFFT_SINGLE setting that will
 use single-precision FFTs with PPPM, which can speed-up long-range
-calculations, particularly in parallel or on GPUs.  Fourier transform
+calulations, particularly in parallel or on GPUs.  Fourier transform
 and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
 accuracy for reduced memory use and parallel communication costs for
-transposing 3d FFT data.
+transposing 3d FFT data.  Note that single precision FFTs have only
+been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
 
 Step 7 :h6
 
@@ -507,13 +509,13 @@ You should get the executable lmp_foo when the build is complete.
 
 Errors that can occur when making LAMMPS: h5 :link(start_2_3)
 
-NOTE: If an error occurs when building LAMMPS, the compiler or linker
+If an error occurs when building LAMMPS, the compiler or linker will
-will state very explicitly what the problem is.  The error message
+state very explicitly what the problem is.  The error message should
-should give you a hint as to which of the steps above has failed, and
+give you a hint as to which of the steps above has failed, and what
-what you need to do in order to fix it.  Building a code with a
+you need to do in order to fix it.  Building a code with a Makefile is
-Makefile is a very logical process.  The compiler and linker need to
+a very logical process.  The compiler and linker need to find the
-find the appropriate files and those files need to be compatible with
+appropriate files and those files need to be compatible with LAMMPS
-LAMMPS source files.  When a make fails, there is usually a very
+settings and source files.  When a make fails, there is usually a very
 simple reason, which you or a local expert will need to fix.
 
 Here are two non-obvious errors that can occur:
@@ -556,7 +558,8 @@ Typing "make clean-all" or "make clean-machine" will delete *.o object
 files created when LAMMPS is built, for either all builds or for a
 particular machine.
 
-Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
+Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
+-DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :h6
 
 As explained above, any of these 3 settings can be specified on the
 LMP_INC line in your low-level src/MAKE/Makefile.foo.
@@ -655,11 +658,6 @@ This section has the following sub-sections:
 2.3.3 "Packages that require extra libraries"_#start_3_3
 2.3.4 "Packages that require Makefile.machine settings"_#start_3_4 :all(b)
 
-Note that the following "Section 2.4"_#start_4 describes the Make.py
-tool which can be used to install/un-install packages and build the
-auxiliary libraries which some of them use.  It can also auto-edit a
-Makefile.machine to add settings needed by some packages.
-
 :line
 
 Package basics: :h5,link(start_3_1)
@@ -669,235 +667,221 @@ are always included, plus optional packages.  Packages are groups of
 files that enable a specific set of features.  For example, force
 fields for molecular systems or granular systems are in packages.
 
-"Section 4"_Section_packages.html in the manual has details
+"Section 4"_Section_packages.html in the manual has details about all
-about all the packages, including specific instructions for building
+the packages, which come in two flavors: [standard] and [user]
-LAMMPS with each package, which are covered in a more general manner
+packages. It also has specific instructions for building LAMMPS with
+any package which requires an extra library.  General instructions are
 below.
 
 You can see the list of all packages by typing "make package" from
-within the src directory of the LAMMPS distribution.  This also lists
+within the src directory of the LAMMPS distribution.  It will also
-various make commands that can be used to manipulate packages.
+list various make commands that can be used to manage packages.
 
 If you use a command in a LAMMPS input script that is part of a
 package, you must have built LAMMPS with that package, else you will
 get an error that the style is invalid or the command is unknown.
-Every command's doc page specifies if it is part of a package.  You can
+Every command's doc page specfies if it is part of a package.  You can
-also type
+type
 
 lmp_machine -h :pre
 
 to run your executable with the optional "-h command-line
-switch"_#start_7 for "help", which will simply list the styles and
+switch"_#start_7 for "help", which will list the styles and commands
-commands known to your executable, and immediately exit.
+known to your executable, and immediately exit.
-
-There are two kinds of packages in LAMMPS, standard and user packages.
-More information about the contents of standard and user packages is
-given in "Section 4"_Section_packages.html of the manual.  The
-difference between standard and user packages is as follows:
-
-Standard packages, such as molecule or kspace, are supported by the
-LAMMPS developers and are written in a syntax and style consistent
-with the rest of LAMMPS.  This means we will answer questions about
-them, debug and fix them if necessary, and keep them compatible with
-future changes to LAMMPS.
-
-User packages, such as user-atc or user-omp, have been contributed by
-users, and always begin with the user prefix.  If they are a single
-command (single file), they are typically in the user-misc package.
-Otherwise, they are a set of files grouped together which add a
-specific functionality to the code.
-
-User packages don't necessarily meet the requirements of the standard
-packages.  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 either a standard or user-contributed package are given in
-"this section"_Section_modify.html#mod_15 of the documentation.
 
 :line
 
 Including/excluding packages :h5,link(start_3_2)
 
-To use (or not use) a package you must include it (or exclude it)
+To use (or not use) a package you must install it (or un-install it)
-before building LAMMPS.  From the src directory, this is typically as
+before building LAMMPS.  From the src directory, this is as simple as:
-simple as:
 
 make yes-colloid
 make mpi :pre
 
 or
 
-make no-manybody
+make no-user-omp
 make mpi :pre
 
-NOTE: You should NOT include/exclude packages and build LAMMPS in a
+NOTE: You should NOT install/un-install packages and build LAMMPS in a
 single make command using multiple targets, e.g. make yes-colloid mpi.
 This is because the make procedure creates a list of source files that
 will be out-of-date for the build if the package configuration changes
 within the same command.
 
-Some packages have individual files that depend on other packages
+Any package can be installed or not in a LAMMPS build, independent of
-being included.  LAMMPS checks for this and does the right thing.
+all other packages.  However, some packages include files derived from
-I.e. individual files are only included if their dependencies are
+files in other packages.  LAMMPS checks for this and does the right
-already included.  Likewise, if a package is excluded, other files
+thing.  I.e. individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
 dependent on that package are also excluded.
 
+NOTE: The one exception is that we do not recommend building with both
+the KOKKOS package installed and any of the other acceleration
+packages (GPU, OPT, USER-INTEL, USER-OMP) also installed.  This is
+because of how Kokkos sometimes builds using a wrapper compiler which
+can make it difficult to invoke all the compile/link flags correctly
+for both Kokkos and non-Kokkos files.
+
 If you will never run simulations that use the features in a
 particular packages, there is no reason to include it in your build.
-For some packages, this will keep you from having to build auxiliary
+For some packages, this will keep you from having to build extra
-libraries (see below), and will also produce a smaller executable
+libraries, and will also produce a smaller executable which may run a
-which may run a bit faster.
+bit faster.
 
-When you download a LAMMPS tarball, these packages are pre-installed
+When you download a LAMMPS tarball, three packages are pre-installed
-in the src directory: KSPACE, MANYBODY,MOLECULE, because they are so
+in the src directory -- KSPACE, MANYBODY, MOLECULE -- because they are
-commonly used.  When you download LAMMPS source files from the SVN or
+so commonly used.  When you download LAMMPS source files from the SVN
-Git repositories, no packages are pre-installed.
+or Git repositories, no packages are pre-installed.
 
-Packages are included or excluded by typing "make yes-name" or "make
+Packages are installed or un-installed by typing
-no-name", where "name" is the name of the package in lower-case, e.g.
-name = kspace for the KSPACE package or name = user-atc for the
-USER-ATC package.  You can also type "make yes-standard", "make
-no-standard", "make yes-std", "make no-std", "make yes-user", "make
-no-user", "make yes-lib", "make no-lib", "make yes-all", or "make
-no-all" to include/exclude various sets of packages.  Type "make
-package" to see all of the package-related make options.
 
-NOTE: Inclusion/exclusion of a package works by simply moving files
+make yes-name
-back and forth between the main src directory and sub-directories with
+make no-name :pre
-the package name (e.g. src/KSPACE, src/USER-ATC), so that the files
-are seen or not seen when LAMMPS is built.  After you have included or
-excluded a package, you must re-build LAMMPS.
 
-Additional package-related make options exist to help manage LAMMPS
+where "name" is the name of the package in lower-case, e.g.  name =
-files that exist in both the src directory and in package
+kspace for the KSPACE package or name = user-atc for the USER-ATC
-sub-directories.  You do not normally need to use these commands
+package.  You can also type any of these commands:
-unless you are editing LAMMPS files or have downloaded a patch from
-the LAMMPS WWW site.
 
-Typing "make package-update" or "make pu" will overwrite src files
+make yes-all | install all packages
-with files from the package sub-directories if the package has been
+make no-all | un-install all packages
-included.  It should be used after a patch is installed, since patches
+make yes-standard or make yes-std | install standard packages
-only update the files in the package sub-directory, but not the src
+make no-standard or make no-std| un-install standard packages
-files.  Typing "make package-overwrite" will overwrite files in the
+make yes-user | install user packages
-package sub-directories with src files.
+make no-user | un-install user packages
+make yes-lib | install packages that require extra libraries
+make no-lib | un-install packages that require extra libraries
+make yes-ext | install packages that require external libraries
+make no-ext | un-install packages that require external libraries :tb(s=|)
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+NOTE: Installing or un-installing a package works by simply moving
+files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are included or excluded when LAMMPS is built.
+After you have installed or un-installed a package, you must re-build
+LAMMPS for the action to take effect.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or have
+downloaded a patch from the LAMMPS web site.
 
 Typing "make package-status" or "make ps" will show which packages are
-currently included. For those that are included, it will list any
+currently installed. For those that are installed, it will list any
 files that are different in the src directory and package
-sub-directory.  Typing "make package-diff" lists all differences
+sub-directory.
-between these files.  Again, type "make package" to see all of the
+
-package-related make options.
+Typing "make package-update" or "make pu" will overwrite src files
+with files from the package sub-directories if the package is
+installed.  It should be used after a patch has been applied, since
+patches only update the files in the package sub-directory, but not
+the src files.
+
+Typing "make package-overwrite" will overwrite files in the package
+sub-directories with src files.
+
+Typing "make package-diff" lists all differences between these files.
+
+Again, just type "make package" to see all of the package-related make
+options.
 
 :line
 
 Packages that require extra libraries :h5,link(start_3_3)
 
-A few of the standard and user packages require additional auxiliary
+A few of the standard and user packages require extra libraries.  See
-libraries.  Many of them are provided with LAMMPS, in which case they
+"Section 4"_Section_packages.html for two tables of packages which
-must be compiled first, before LAMMPS is built, if you wish to include
+indicate which ones require libraries.  For each such package, the
-that package.  If you get a LAMMPS build error about a missing
+Section 4 doc page gives details on how to build the extra library,
-library, this is likely the reason.  See the
+including how to download it if necessary.  The basic ideas are
-"Section 4"_Section_packages.html doc page for a list of
+summarized here.
-packages that have these kinds of auxiliary libraries.
 
-The lib directory in the distribution has sub-directories with package
+[System libraries:]
-names that correspond to the needed auxiliary libs, e.g. lib/gpu.
-Each sub-directory has a README file that gives more details.  Code
-for most of the auxiliary libraries is included in that directory.
-Examples are the USER-ATC and MEAM packages.
 
-A few of the lib sub-directories do not include code, but do include
+Packages in the tables "Section 4"_Section_packages.html with a "sys"
-instructions (and sometimes scripts) that automate the process of
+in the last column link to system libraries that typically already
-downloading the auxiliary library and installing it so LAMMPS can link
+exist on your machine.  E.g. the python package links to a system
-to it.  Examples are the KIM, VORONOI, USER-MOLFILE, and USER-SMD
+Python library.  If your machine does not have the required library,
-packages.
+you will have to download and install it on your machine, in either
+the system or user space.
 
-The lib/python directory (for the PYTHON package) contains only a
+[Internal libraries:]
-choice of Makefile.lammps.* files.  This is because no auxiliary code
-or libraries are needed, only the Python library and other system libs
-that should already available on your system.  However, the
-Makefile.lammps file is needed to tell LAMMPS which libs to use and
-where to find them.
 
-For libraries with provided code, the sub-directory README file
+Packages in the tables "Section 4"_Section_packages.html with an "int"
-(e.g. lib/atc/README) has instructions on how to build that library.
+in the last column link to internal libraries whose source code is
-This information is also summarized in "Section
+included with LAMMPS, in the lib/name directory where name is the
-4"_Section_packages.html.  Typically this is done by typing
+package name.  You must first build the library in that directory
-something like:
+before building LAMMPS with that package installed.  E.g. the gpu
+package links to a library you build in the lib/gpu dir.  You can
+often do the build in one step by typing "make lib-name args=..."
+from the src dir, with appropriate arguments.  You can leave off the
+args to see a help message.  See "Section 4"_Section_packages.html for
+details for each package.
 
-make -f Makefile.g++ :pre
+[External libraries:]
 
-If one of the provided Makefiles is not appropriate for your system
+Packages in the tables "Section 4"_Section_packages.html with an "ext"
-you will need to edit or add one.  Note that all the Makefiles have a
+in the last column link to exernal libraries whose source code is not
-setting for EXTRAMAKE at the top that specifies a Makefile.lammps.*
+included with LAMMPS.  You must first download and install the library
-file.
+before building LAMMPS with that package installed.  E.g. the voronoi
+package links to the freely available "Voro++ library"_voronoi.  You
+can often do the download/build in one step by typing "make lib-name
+args=..." from the src dir, with appropriate arguments.  You can leave
+off the args to see a help message.  See "Section
+4"_Section_packages.html for details for each package.
 
-If the library build is successful, it will produce 2 files in the lib
+:link(voronoi,http://math.lbl.gov/voro++)
-directory:
 
-libpackage.a
+[Possible errors:]
-Makefile.lammps :pre
 
-The Makefile.lammps file will typically be a copy of one of the
+There are various common errors which can occur when building extra
-Makefile.lammps.* files in the library directory.
+libraries or when building LAMMPS with packages that require the extra
+libraries.
 
-Note that you must insure that the settings in Makefile.lammps are
+If you cannot build the extra library itself successfully, you may
-appropriate for your system.  If they are not, the LAMMPS build may
+need to edit or create an appropriate Makefile for your machine, e.g.
-fail.  To fix this, you can edit or create a new Makefile.lammps.*
+with appropriate compiler or system settings.  Provided makefiles are
-file for your system, and copy it to Makefile.lammps.
+typically in the lib/name directory.  E.g. see the Makefile.* files in
+lib/gpu.
 
-As explained in the lib/package/README files, the settings in
+The LAMMPS build often uses settings in a lib/name/Makefile.lammps
-Makefile.lammps are used to specify additional system libraries and
+file which either exists in the LAMMPS distribution or is created or
-their locations so that LAMMPS can build with the auxiliary library.
+copied from a lib/name/Makefile.lammps.* file when the library is
-For example, if the MEAM package is used, the auxiliary library
+built.  If those settings are not correct for your machine you will
-consists of F90 code, built with a Fortran complier.  To link that
+need to edit or create an appropriate Makefile.lammps file.
-library with LAMMPS (a C++ code) via whatever C++ compiler LAMMPS is
-built with, typically requires additional Fortran-to-C libraries be
-included in the link.  Another example are the BLAS and LAPACK
-libraries needed to use the USER-ATC or USER-AWPMD packages.
 
-For libraries without provided code, the sub-directory README file has
+Package-specific details for these steps are given in "Section
-information on where to download the library and how to build it,
+4"_Section_packages.html an in README files in the lib/name
-e.g. lib/voronoi/README and lib/smd/README.  The README files also
+directories.
-describe how you must either (a) create soft links, via the "ln"
-command, in those directories to point to where you built or installed
-the packages, or (b) check or edit the Makefile.lammps file in the
-same directory to provide that information.
 
-Some of the sub-directories, e.g. lib/voronoi, also have an install.py
+[Compiler options needed for accelerator packages:]
-script which can be used to automate the process of
-downloading/building/installing the auxiliary library, and setting the
-needed soft links.  Type "python install.py" for further instructions.
 
-As with the sub-directories containing library code, if the soft links
+Several packages contain code that is optimized for specific hardware,
-or settings in the lib/package/Makefile.lammps files are not correct,
+e.g. CPU, KNL, or GPU.  These are the OPT, GPU, KOKKOS, USER-INTEL,
-the LAMMPS build will typically fail.
+and USER-OMP packages.  Compiling and linking the source files in
+these accelerator packages for optimal performance requires specific
+settings in the Makefile.machine file you use.
 
-:line
+A summary of the Makefile.machine settings needed for each of these
-
+packages is given in "Section 4"_Section_packages.html.  More info is
-Packages that require Makefile.machine settings :h5,link(start_3_4)
+given on the doc pages that describe each package in detail:
-
-A few packages require specific settings in Makefile.machine, to
-either build or use the package effectively.  These are the
-USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
-code performance on CPUs or other hardware, as discussed in "Section
-5.3"_Section_accelerate.html#acc_3.
-
-A summary of what Makefile.machine changes are needed for each of
-these packages is given in "Section 4"_Section_packages.html.
-The details are given on the doc pages that describe each of these
-accelerator packages in detail:
 
 5.3.1 "USER-INTEL package"_accelerate_intel.html
+5.3.2 "GPU package"_accelerate_intel.html
 5.3.3 "KOKKOS package"_accelerate_kokkos.html
 5.3.4 "USER-OMP package"_accelerate_omp.html
 5.3.5 "OPT package"_accelerate_opt.html :all(b)
 
-You can also look at the following machine Makefiles in
+You can also use or examine the following machine Makefiles in
-src/MAKE/OPTIONS, which include the changes.  Note that the USER-INTEL
+src/MAKE/OPTIONS, which include the settings.  Note that the
-and KOKKOS packages allow for settings that build LAMMPS for different
+USER-INTEL and KOKKOS packages can use settings that build LAMMPS for
-hardware.  The USER-INTEL package builds for CPU and the Xeon Phi, the
+different hardware.  The USER-INTEL package can be compiled for Intel
-KOKKOS package builds for OpenMP, GPUs (Cuda), and the Xeon Phi.
+CPUs and KNLs; the KOKKOS package builds for CPUs (OpenMP), GPUs
+(Cuda), and Intel KNLs.
 
 Makefile.intel_cpu
 Makefile.intel_phi
@@ -907,127 +891,9 @@ Makefile.kokkos_phi
 Makefile.omp
 Makefile.opt :ul
 
-Also note that the Make.py tool, described in the next "Section
-2.4"_#start_4 can automatically add the needed info to an existing
-machine Makefile, using simple command-line arguments.
-
 :line
 
-2.4 Building LAMMPS via the Make.py tool :h4,link(start_4)
+2.4 Building LAMMPS as a library :h4,link(start_4)
-
-The src directory includes a Make.py script, written in Python, which
-can be used to automate various steps of the build process.  It is
-particularly useful for working with the accelerator packages, as well
-as other packages which require auxiliary libraries to be built.
-
-The goal of the Make.py tool is to allow any complex multi-step LAMMPS
-build to be performed as a single Make.py command.  And you can
-archive the commands, so they can be re-invoked later via the -r
-(redo) switch.  If you find some LAMMPS build procedure that can't be
-done in a single Make.py command, let the developers know, and we'll
-see if we can augment the tool.
-
-You can run Make.py from the src directory by typing either:
-
-Make.py -h
-python Make.py -h :pre
-
-which will give you help info about the tool.  For the former to work,
-you may need to edit the first line of Make.py to point to your local
-Python.  And you may need to insure the script is executable:
-
-chmod +x Make.py :pre
-
-Here are examples of build tasks you can perform with Make.py:
-
-Install/uninstall packages: Make.py -p no-lib kokkos omp intel
-Build specific auxiliary libs: Make.py -a lib-atc lib-meam
-Build libs for all installed packages: Make.py -p cuda gpu -gpu mode=double arch=31 -a lib-all
-Create a Makefile from scratch with compiler and MPI settings: Make.py -m none -cc g++ -mpi mpich -a file
-Augment Makefile.serial with settings for installed packages: Make.py -p intel -intel cpu -m serial -a file
-Add JPG and FFTW support to Makefile.mpi: Make.py -m mpi -jpg -fft fftw -a file
-Build LAMMPS with a parallel make using Makefile.mpi: Make.py -j 16 -m mpi -a exe
-Build LAMMPS and libs it needs using Makefile.serial with accelerator settings: Make.py -p gpu intel -intel cpu -a lib-all file serial :tb(s=:)
-
-The bench and examples directories give Make.py commands that can be
-used to build LAMMPS with the various packages and options needed to
-run all the benchmark and example input scripts.  See these files for
-more details:
-
-bench/README
-bench/FERMI/README
-bench/KEPLER/README
-bench/PHI/README
-examples/README
-examples/accelerate/README
-examples/accelerate/make.list :ul
-
-All of the Make.py options and syntax help can be accessed by using
-the "-h" switch.
-
-E.g. typing "Make.py -h" gives
-
-Syntax: Make.py switch args ...
-  switches can be listed in any order
-  help switch:
-    -h prints help and syntax for all other specified switches
-  switch for actions:
-    -a lib-all, lib-dir, clean, file, exe or machine
-    list one or more actions, in any order
-    machine is a Makefile.machine suffix, must be last if used
-  one-letter switches:
-    -d (dir), -j (jmake), -m (makefile), -o (output),
-    -p (packages), -r (redo), -s (settings), -v (verbose)
-  switches for libs:
-    -atc, -awpmd, -colvars, -cuda
-    -gpu, -meam, -poems, -qmmm, -reax
-  switches for build and makefile options:
-    -intel, -kokkos, -cc, -mpi, -fft, -jpg, -png :pre
-
-Using the "-h" switch with other switches and actions gives additional
-info on all the other specified switches or actions.  The "-h" can be
-anywhere in the command-line and the other switches do not need their
-arguments.  E.g. type "Make.py -h -d -atc -intel" will print:
-
--d dir
-  dir = LAMMPS home dir
-  if -d not specified, working dir must be lammps/src :pre
-
--atc make=suffix lammps=suffix2
-  all args are optional and can be in any order
-  make = use Makefile.suffix (def = g++)
-  lammps = use Makefile.lammps.suffix2 (def = EXTRAMAKE in makefile) :pre
-
--intel mode
-  mode = cpu or phi (def = cpu)
-    build Intel package for CPU or Xeon Phi :pre
-
-Note that Make.py never overwrites an existing Makefile.machine.
-Instead, it creates src/MAKE/MINE/Makefile.auto, which you can save or
-rename if desired.  Likewise it creates an executable named
-src/lmp_auto, which you can rename using the -o switch if desired.
-
-The most recently executed Make.py command is saved in
-src/Make.py.last.  You can use the "-r" switch (for redo) to re-invoke
-the last command, or you can save a sequence of one or more Make.py
-commands to a file and invoke the file of commands using "-r".  You
-can also label the commands in the file and invoke one or more of them
-by name.
-
-A typical use of Make.py is to start with a valid Makefile.machine for
-your system, that works for a vanilla LAMMPS build, i.e. when optional
-packages are not installed.  You can then use Make.py to add various
-settings (FFT, JPG, PNG) to the Makefile.machine as well as change its
-compiler and MPI options.  You can also add additional packages to the
-build, as well as build the needed supporting libraries.
-
-You can also use Make.py to create a new Makefile.machine from
-scratch, using the "-m none" switch, if you also specify what compiler
-and MPI options to use, via the "-cc" and "-mpi" switches.
-
-:line
-
-2.5 Building LAMMPS as a library :h4,link(start_5)
 
 LAMMPS can be built as either a static or shared library, which can
 then be called from another application or a scripting language.  See
@@ -1063,7 +929,7 @@ src/MAKE/Makefile.foo and perform the build in the directory
 Obj_shared_foo.  This is so that each file can be compiled with the
 -fPIC flag which is required for inclusion in a shared library.  The
 build will create the file liblammps_foo.so which another application
-can link to dynamically.  It will also create a soft link liblammps.so,
+can link to dyamically.  It will also create a soft link liblammps.so,
 which will point to the most recently built shared library.  This is
 the file the Python wrapper loads by default.
 
@@ -1149,7 +1015,7 @@ interface and how to extend it for your needs.
 
 :line
 
-2.6 Running LAMMPS :h4,link(start_6)
+2.5 Running LAMMPS :h4,link(start_5)
 
 By default, LAMMPS runs by reading commands from standard input.  Thus
 if you run the LAMMPS executable by itself, e.g.
@@ -1281,7 +1147,7 @@ more processors or setup a smaller problem.
 
 :line
 
-2.7 Command-line options :h4,link(start_7)
+2.6 Command-line options :h4,link(start_6)
 
 At run time, LAMMPS recognizes several optional command-line switches
 which may be used in any order.  Either the full word or a one-or-two
@@ -1415,8 +1281,8 @@ LAMMPS is compiled with CUDA=yes.
 numa Nm :pre
 
 This option is only relevant when using pthreads with hwloc support.
-In this case Nm defines the number of NUMA regions (typically sockets)
+In this case Nm defines the number of NUMA regions (typicaly sockets)
-on a node which will be utilized by a single MPI rank.  By default Nm
+on a node which will be utilizied by a single MPI rank.  By default Nm
 = 1.  If this option is used the total number of worker-threads per
 MPI rank is threads*numa.  Currently it is always almost better to
 assign at least one MPI rank per NUMA region, and leave numa set to
@@ -1480,7 +1346,7 @@ replica runs on on one or a few processors.  Note that with MPI
 installed on a machine (e.g. your desktop), you can run on more
 (virtual) processors than you have physical processors.
 
-To run multiple independent simulations from one input script, using
+To run multiple independent simulatoins from one input script, using
 multiple partitions, see "Section 6.4"_Section_howto.html#howto_4
 of the manual.  World- and universe-style "variables"_variable.html
 are useful in this context.
@@ -1711,7 +1577,7 @@ negative numeric value.  It is OK if the first value1 starts with a
 
 :line
 
-2.8 LAMMPS screen output :h4,link(start_8)
+2.7 LAMMPS screen output :h4,link(start_7)
 
 As LAMMPS reads an input script, it prints information to both the
 screen and a log file about significant actions it takes to setup a
@@ -1759,7 +1625,7 @@ The first section provides a global loop timing summary. The {loop time}
 is the total wall time for the section.  The {Performance} line is
 provided for convenience to help predicting the number of loop
 continuations required and for comparing performance with other,
-similar MD codes.  The {CPU use} line provides the CPU utilization per
+similar MD codes.  The {CPU use} line provides the CPU utilzation per
 MPI task; it should be close to 100% times the number of OpenMP
 threads (or 1 of no OpenMP). Lower numbers correspond to delays due
 to file I/O or insufficient thread utilization.
@@ -1867,7 +1733,7 @@ communication, roughly 75% in the example above.
 
 :line
 
-2.9 Tips for users of previous LAMMPS versions :h4,link(start_9)
+2.8 Tips for users of previous LAMMPS versions :h4,link(start_8)
 
 The current C++ began with a complete rewrite of LAMMPS 2001, which
 was written in F90.  Features of earlier versions of LAMMPS are listed

doc/src/compute_sna_atom.txt

@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
   {diagonal} value = {0} or {1} or {2} or {3}
      {0} = all j1, j2, j <= twojmax, j2 <= j1
      {1} = subset satisfying j1 == j2
@@ -36,7 +36,10 @@ keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} :l
      {1} = use switching function
   {bzeroflag} value = {0} or {1}
      {0} = do not subtract B0
-     {1} = subtract B0 :pre
+     {1} = subtract B0
+  {quadraticflag} value = {0} or {1}
+     {0} = do not generate quadratic terms
+     {1} = generate quadratic terms :pre
 :ule
 
 [Examples:]
@@ -151,7 +154,7 @@ linear mapping from radial distance to polar angle {theta0} on the
 The argument {twojmax} and the keyword {diagonal} define which
 bispectrum components are generated. See section below on output for a
 detailed explanation of the number of bispectrum components and the
-ordered in which they are listed
+ordered in which they are listed.
 
 The keyword {switchflag} can be used to turn off the switching
 function.
@@ -162,6 +165,14 @@ the calculated bispectrum components. This optional keyword is only
 available for compute {sna/atom}, as {snad/atom} and {snav/atom}
 are unaffected by the removal of constant terms.
 
+The keyword {quadraticflag} determines whether or not the
+quadratic analogs to the bispectrum quantities are generated.
+These are formed by taking the outer product of the vector
+of bispectrum components with itself.
+See section below on output for a
+detailed explanation of the number of quadratic terms and the
+ordered in which they are listed.
+
 NOTE: If you have a bonded system, then the settings of
 "special_bonds"_special_bonds.html command can remove pairwise
 interactions between atoms in the same bond, angle, or dihedral.  This
@@ -180,7 +191,7 @@ command that includes all pairs in the neighbor list.
 
 Compute {sna/atom} calculates a per-atom array, each column
 corresponding to a particular bispectrum component.  The total number
-of columns and the identities of the bispectrum component contained in
+of columns and the identity of the bispectrum component contained in
 each column depend on the values of {twojmax} and {diagonal}, as
 described by the following piece of python code:
 
@@ -213,6 +224,19 @@ block contains six sub-blocks corresponding to the {xx}, {yy}, {zz},
 notation.  Each of these sub-blocks contains one column for each
 bispectrum component, the same as for compute {sna/atom}
 
+For example, if {K}=30 and ntypes=1, the number of columns in the per-atom
+arrays generated by {sna/atom}, {snad/atom}, and {snav/atom}
+are 30, 90, and 180, respectively. With {quadratic} value=1,
+the numbers of columns are 930, 2790, and 5580, respectively.
+
+If the {quadratic} keyword value is set to 1, then additional
+columns are appended to each per-atom array, corresponding to
+a matrix of quantities that are products of two bispectrum components. If the
+number of bispectrum components is {K}, then the number of matrix elements
+is {K}^2. These are output in subblocks of {K}^2 columns, using the same
+ordering of columns and sub-blocks as was used for the bispectrum
+components.
+
 These values can be accessed by any command that uses per-atom values
 from a compute as input.  See "Section
 6.15"_Section_howto.html#howto_15 for an overview of LAMMPS output
@@ -231,7 +255,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
 [Default:]
 
 The optional keyword defaults are {diagonal} = 0, {rmin0} = 0,
-{switchflag} = 1, {bzeroflag} = 0.
+{switchflag} = 1, {bzeroflag} = 1, {quadraticflag} = 0,
 
 :line
 

doc/src/dump.txt

@@ -7,12 +7,12 @@
 :line
 
 dump command :h3
-"dump custom/vtk"_dump_custom_vtk.html command :h3
+"dump vtk"_dump_vtk.html command :h3
 "dump h5md"_dump_h5md.html command :h3
+"dump molfile"_dump_molfile.html command :h3
+"dump netcdf"_dump_netcdf.html command :h3
 "dump image"_dump_image.html command :h3
 "dump movie"_dump_image.html command :h3
-"dump molfile"_dump_molfile.html command :h3
-"dump nc"_dump_nc.html command :h3
 
 [Syntax:]
 
@@ -20,7 +20,7 @@ dump ID group-ID style N file args :pre
 
 ID = user-assigned name for the dump :ulb,l
 group-ID = ID of the group of atoms to be dumped :l
-style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {dcd} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} or {h5md} or {image} or {movie} or {molfile} or {local} or {custom} or {custom/gz} or {custom/mpiio} :l
+style = {atom} or {atom/gz} or {atom/mpiio} or {cfg} or {cfg/gz} or {cfg/mpiio} or {custom} or {custom/gz} or {custom/mpiio} or {dcd} or {h5md} or {image} or or {local} or {molfile} or {movie} or {netcdf} or {netcdf/mpiio} or {vtk} or {xtc} or {xyz} or {xyz/gz} or {xyz/mpiio} :l
 N = dump every this many timesteps :l
 file = name of file to write dump info to :l
 args = list of arguments for a particular style :l
@@ -30,33 +30,22 @@ args = list of arguments for a particular style :l
   {cfg} args = same as {custom} args, see below
   {cfg/gz} args = same as {custom} args, see below
   {cfg/mpiio} args = same as {custom} args, see below
+  {custom}, {custom/gz}, {custom/mpiio} args = see below
   {dcd} args = none
+  {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page
+  {image} args = discussed on "dump image"_dump_image.html doc page
+  {local} args = see below
+  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
+  {movie} args = discussed on "dump image"_dump_image.html doc page
+  {netcdf} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+  {netcdf/mpiio} args = discussed on "dump netcdf"_dump_netcdf.html doc page
+  {vtk} args = same as {custom} args, see below, also "dump vtk"_dump_vtk.html doc page
   {xtc} args = none
-  {xyz} args = none :pre
+  {xyz} args = none
-  {xyz/gz} args = none :pre
+  {xyz/gz} args = none
   {xyz/mpiio} args = none :pre
 
-  {custom/vtk} args = similar to custom args below, discussed on "dump custom/vtk"_dump_custom_vtk.html doc page :pre
+{custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes :l
-
-  {h5md} args = discussed on "dump h5md"_dump_h5md.html doc page :pre
-
-  {image} args = discussed on "dump image"_dump_image.html doc page :pre
-
-  {movie} args = discussed on "dump image"_dump_image.html doc page :pre
-
-  {molfile} args = discussed on "dump molfile"_dump_molfile.html doc page
-
-  {nc} args = discussed on "dump nc"_dump_nc.html doc page :pre
-
-  {local} args = list of local attributes
-    possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
-      index = enumeration of local values
-      c_ID = local vector calculated by a compute with ID
-      c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
-      f_ID = local vector calculated by a fix with ID
-      f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
-
-  {custom} or {custom/gz} or {custom/mpiio} args = list of atom attributes
     possible attributes = id, mol, proc, procp1, type, element, mass,
                           x, y, z, xs, ys, zs, xu, yu, zu,
                           xsu, ysu, zsu, ix, iy, iz,
@@ -94,6 +83,15 @@ args = list of arguments for a particular style :l
       v_name = per-atom vector calculated by an atom-style variable with name
       d_name = per-atom floating point vector with name, managed by fix property/atom
       i_name = per-atom integer vector with name, managed by fix property/atom :pre
+
+{local} args = list of local attributes :l
+    possible attributes = index, c_ID, c_ID\[I\], f_ID, f_ID\[I\]
+      index = enumeration of local values
+      c_ID = local vector calculated by a compute with ID
+      c_ID\[I\] = Ith column of local array calculated by a compute with ID, I can include wildcard (see below)
+      f_ID = local vector calculated by a fix with ID
+      f_ID\[I\] = Ith column of local array calculated by a fix with ID, I can include wildcard (see below) :pre
+
 :ule
 
 [Examples:]

doc/src/dump_custom_vtk.txt

@@ -1,347 +0,0 @@
- "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-dump custom/vtk command :h3
-
-[Syntax:]
-
-dump ID group-ID style N file args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be dumped :l
-style = {custom/vtk} :l
-N = dump every this many timesteps :l
-file = name of file to write dump info to :l
-args = list of arguments for a particular style :l
-  {custom/vtk} args = list of atom attributes
-    possible attributes = id, mol, proc, procp1, type, element, mass,
-                          x, y, z, xs, ys, zs, xu, yu, zu,
-                          xsu, ysu, zsu, ix, iy, iz,
-                          vx, vy, vz, fx, fy, fz,
-                          q, mux, muy, muz, mu,
-                          radius, diameter, omegax, omegay, omegaz,
-                          angmomx, angmomy, angmomz, tqx, tqy, tqz,
-                          c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :pre
-
-      id = atom ID
-      mol = molecule ID
-      proc = ID of processor that owns atom
-      procp1 = ID+1 of processor that owns atom
-      type = atom type
-      element = name of atom element, as defined by "dump_modify"_dump_modify.html command
-      mass = atom mass
-      x,y,z = unscaled atom coordinates
-      xs,ys,zs = scaled atom coordinates
-      xu,yu,zu = unwrapped atom coordinates
-      xsu,ysu,zsu = scaled unwrapped atom coordinates
-      ix,iy,iz = box image that the atom is in
-      vx,vy,vz = atom velocities
-      fx,fy,fz = forces on atoms
-      q = atom charge
-      mux,muy,muz = orientation of dipole moment of atom
-      mu = magnitude of dipole moment of atom
-      radius,diameter = radius,diameter of spherical particle
-      omegax,omegay,omegaz = angular velocity of spherical particle
-      angmomx,angmomy,angmomz = angular momentum of aspherical particle
-      tqx,tqy,tqz = torque on finite-size particles
-      c_ID = per-atom vector calculated by a compute with ID
-      c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
-      f_ID = per-atom vector calculated by a fix with ID
-      f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
-      v_name = per-atom vector calculated by an atom-style variable with name
-      d_name = per-atom floating point vector with name, managed by fix property/atom
-      i_name = per-atom integer vector with name, managed by fix property/atom :pre
-:ule
-
-[Examples:]
-
-dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
-dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre
-
-The style {custom/vtk} is similar to the "custom"_dump.html style but
-uses the VTK library to write data to VTK simple legacy or XML format
-depending on the filename extension specified. This can be either
-{*.vtk} for the legacy format or {*.vtp} and {*.vtu}, respectively,
-for the XML format; see the "VTK
-homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
-description of these formats.  Since this naming convention conflicts
-with the way binary output is usually specified (see below),
-"dump_modify binary"_dump_modify.html allows to set the binary
-flag for this dump style explicitly.
-
-[Description:]
-
-Dump a snapshot of atom quantities to one or more files every N
-timesteps in a format readable by the "VTK visualization
-toolkit"_http://www.vtk.org or other visualization tools that use it,
-e.g. "ParaView"_http://www.paraview.org.  The timesteps on which dump
-output is written can also be controlled by a variable; see the
-"dump_modify every"_dump_modify.html command for details.
-
-Only information for atoms in the specified group is dumped.  The
-"dump_modify thresh and region"_dump_modify.html commands can also
-alter what atoms are included; see details below.
-
-As described below, special characters ("*", "%") in the filename
-determine the kind of output.
-
-IMPORTANT NOTE: Because periodic boundary conditions are enforced only
-on timesteps when neighbor lists are rebuilt, the coordinates of an
-atom written to a dump file may be slightly outside the simulation
-box.
-
-IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html
-option is invoked, the lines of atom information written to dump files
-will be in an indeterminate order for each snapshot.  This is even
-true when running on a single processor, if the "atom_modify
-sort"_atom_modify.html option is on, which it is by default.  In this
-case atoms are re-ordered periodically during a simulation, due to
-spatial sorting.  It is also true when running in parallel, because
-data for a single snapshot is collected from multiple processors, each
-of which owns a subset of the atoms.
-
-For the {custom/vtk} style, sorting is off by default. See the
-"dump_modify"_dump_modify.html doc page for details.
-
-:line
-
-The dimensions of the simulation box are written to a separate file
-for each snapshot (either in legacy VTK or XML format depending on
-the format of the main dump file) with the suffix {_boundingBox}
-appended to the given dump filename.
-
-For an orthogonal simulation box this information is saved as a
-rectilinear grid (legacy .vtk or .vtr XML format).
-
-Triclinic simulation boxes (non-orthogonal) are saved as
-hexahedrons in either legacy .vtk or .vtu XML format.
-
-Style {custom/vtk} allows you to specify a list of atom attributes
-to be written to the dump file for each atom.  Possible attributes
-are listed above.  In contrast to the {custom} style, the attributes
-are rearranged to ensure correct ordering of vector components
-(except for computes and fixes - these have to be given in the right
-order) and duplicate entries are removed.
-
-You cannot specify a quantity that is not defined for a particular
-simulation - such as {q} for atom style {bond}, since that atom style
-doesn't assign charges.  Dumps occur at the very end of a timestep,
-so atom attributes will include effects due to fixes that are applied
-during the timestep.  An explanation of the possible dump custom/vtk attributes
-is given below. Since position data is required to write VTK files "x y z"
-do not have to be specified explicitly.
-
-The VTK format uses a single snapshot of the system per file, thus
-a wildcard "*" must be included in the filename, as discussed below.
-Otherwise the dump files will get overwritten with the new snapshot
-each time.
-
-:line
-
-Dumps are performed on timesteps that are a multiple of N (including
-timestep 0) and on the last timestep of a minimization if the
-minimization converges.  Note that this means a dump will not be
-performed on the initial timestep after the dump command is invoked,
-if the current timestep is not a multiple of N.  This behavior can be
-changed via the "dump_modify first"_dump_modify.html command, which
-can also be useful if the dump command is invoked after a minimization
-ended on an arbitrary timestep.  N can be changed between runs by
-using the "dump_modify every"_dump_modify.html command.
-The "dump_modify every"_dump_modify.html command
-also allows a variable to be used to determine the sequence of
-timesteps on which dump files are written.  In this mode a dump on the
-first timestep of a run will also not be written unless the
-"dump_modify first"_dump_modify.html command is used.
-
-Dump filenames can contain two wildcard characters.  If a "*"
-character appears in the filename, then one file per snapshot is
-written and the "*" character is replaced with the timestep value.
-For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
-tmp.dump20000.vtk, etc.  Note that the "dump_modify pad"_dump_modify.html
-command can be used to insure all timestep numbers are the same length
-(e.g. 00010), which can make it easier to read a series of dump files
-in order with some post-processing tools.
-
-If a "%" character appears in the filename, then each of P processors
-writes a portion of the dump file, and the "%" character is replaced
-with the processor ID from 0 to P-1 preceded by an underscore character.
-For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
-tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
-mode of output on parallel machines that support parallel I/O for output.
-
-By default, P = the number of processors meaning one file per
-processor, but P can be set to a smaller value via the {nfile} or
-{fileper} keywords of the "dump_modify"_dump_modify.html command.
-These options can be the most efficient way of writing out dump files
-when running on large numbers of processors.
-
-For the legacy VTK format "%" is ignored and P = 1, i.e., only
-processor 0 does write files.
-
-Note that using the "*" and "%" characters together can produce a
-large number of small dump files!
-
-If {dump_modify binary} is used, the dump file (or files, if "*" or
-"%" is also used) is written in binary format.  A binary dump file
-will be about the same size as a text version, but will typically
-write out much faster.
-
-:line
-
-This section explains the atom attributes that can be specified as
-part of the {custom/vtk} style.
-
-The {id}, {mol}, {proc}, {procp1}, {type}, {element}, {mass}, {vx},
-{vy}, {vz}, {fx}, {fy}, {fz}, {q} attributes are self-explanatory.
-
-{Id} is the atom ID.  {Mol} is the molecule ID, included in the data
-file for molecular systems.  {Proc} is the ID of the processor (0 to
-Nprocs-1) that currently owns the atom.  {Procp1} is the proc ID+1,
-which can be convenient in place of a {type} attribute (1 to Ntypes)
-for coloring atoms in a visualization program.  {Type} is the atom
-type (1 to Ntypes).  {Element} is typically the chemical name of an
-element, which you must assign to each type via the "dump_modify
-element"_dump_modify.html command.  More generally, it can be any
-string you wish to associated with an atom type.  {Mass} is the atom
-mass.  {Vx}, {vy}, {vz}, {fx}, {fy}, {fz}, and {q} are components of
-atom velocity and force and atomic charge.
-
-There are several options for outputting atom coordinates.  The {x},
-{y}, {z} attributes write atom coordinates "unscaled", in the
-appropriate distance "units"_units.html (Angstroms, sigma, etc).  Use
-{xs}, {ys}, {zs} if you want the coordinates "scaled" to the box size,
-so that each value is 0.0 to 1.0.  If the simulation box is triclinic
-(tilted), then all atom coords will still be between 0.0 and 1.0.
-I.e. actual unscaled (x,y,z) = xs*A + ys*B + zs*C, where (A,B,C) are
-the non-orthogonal vectors of the simulation box edges, as discussed
-in "Section 6.12"_Section_howto.html#howto_12.
-
-Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
-image flags for each atom.  Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
-printed for what the coordinate would be if it had not been wrapped
-back into the periodic box.  Note that using {xu}, {yu}, {zu} means
-that the coordinate values may be far outside the box bounds printed
-with the snapshot.  Using {xsu}, {ysu}, {zsu} is similar to using
-{xu}, {yu}, {zu}, except that the unwrapped coordinates are scaled by
-the box size. Atoms that have passed through a periodic boundary will
-have the corresponding coordinate increased or decreased by 1.0.
-
-The image flags can be printed directly using the {ix}, {iy}, {iz}
-attributes.  For periodic dimensions, they specify which image of the
-simulation box the atom is considered to be in.  An image of 0 means
-it is inside the box as defined.  A value of 2 means add 2 box lengths
-to get the true value.  A value of -1 means subtract 1 box length to
-get the true value.  LAMMPS updates these flags as atoms cross
-periodic boundaries during the simulation.
-
-The {mux}, {muy}, {muz} attributes are specific to dipolar systems
-defined with an atom style of {dipole}.  They give the orientation of
-the atom's point dipole moment.  The {mu} attribute gives the
-magnitude of the atom's dipole moment.
-
-The {radius} and {diameter} attributes are specific to spherical
-particles that have a finite size, such as those defined with an atom
-style of {sphere}.
-
-The {omegax}, {omegay}, and {omegaz} attributes are specific to
-finite-size spherical particles that have an angular velocity.  Only
-certain atom styles, such as {sphere} define this quantity.
-
-The {angmomx}, {angmomy}, and {angmomz} attributes are specific to
-finite-size aspherical particles that have an angular momentum.  Only
-the {ellipsoid} atom style defines this quantity.
-
-The {tqx}, {tqy}, {tqz} attributes are for finite-size particles that
-can sustain a rotational torque due to interactions with other
-particles.
-
-The {c_ID} and {c_ID\[I\]} attributes allow per-atom vectors or arrays
-calculated by a "compute"_compute.html to be output.  The ID in the
-attribute should be replaced by the actual ID of the compute that has
-been defined previously in the input script.  See the
-"compute"_compute.html command for details.  There are computes for
-calculating the per-atom energy, stress, centro-symmetry parameter,
-and coordination number of individual atoms.
-
-Note that computes which calculate global or local quantities, as
-opposed to per-atom quantities, cannot be output in a dump custom/vtk
-command.  Instead, global quantities can be output by the
-"thermo_style custom"_thermo_style.html command, and local quantities
-can be output by the dump local command.
-
-If {c_ID} is used as a attribute, then the per-atom vector calculated
-by the compute is printed.  If {c_ID\[I\]} is used, then I must be in
-the range from 1-M, which will print the Ith column of the per-atom
-array with M columns calculated by the compute.  See the discussion
-above for how I can be specified with a wildcard asterisk to
-effectively specify multiple values.
-
-The {f_ID} and {f_ID\[I\]} attributes allow vector or array per-atom
-quantities calculated by a "fix"_fix.html to be output.  The ID in the
-attribute should be replaced by the actual ID of the fix that has been
-defined previously in the input script.  The "fix
-ave/atom"_fix_ave_atom.html command is one that calculates per-atom
-quantities.  Since it can time-average per-atom quantities produced by
-any "compute"_compute.html, "fix"_fix.html, or atom-style
-"variable"_variable.html, this allows those time-averaged results to
-be written to a dump file.
-
-If {f_ID} is used as a attribute, then the per-atom vector calculated
-by the fix is printed.  If {f_ID\[I\]} is used, then I must be in the
-range from 1-M, which will print the Ith column of the per-atom array
-with M columns calculated by the fix.  See the discussion above for
-how I can be specified with a wildcard asterisk to effectively specify
-multiple values.
-
-The {v_name} attribute allows per-atom vectors calculated by a
-"variable"_variable.html to be output.  The name in the attribute
-should be replaced by the actual name of the variable that has been
-defined previously in the input script.  Only an atom-style variable
-can be referenced, since it is the only style that generates per-atom
-values.  Variables of style {atom} can reference individual atom
-attributes, per-atom atom attributes, thermodynamic keywords, or
-invoke other computes, fixes, or variables when they are evaluated, so
-this is a very general means of creating quantities to output to a
-dump file.
-
-The {d_name} and {i_name} attributes allow to output custom per atom
-floating point or integer properties that are managed by
-"fix property/atom"_fix_property_atom.html.
-
-See "Section 10"_Section_modify.html of the manual for information
-on how to add new compute and fix styles to LAMMPS to calculate
-per-atom quantities which could then be output into dump files.
-
-:line
-
-[Restrictions:]
-
-The {custom/vtk} style does not support writing of gzipped dump files.
-
-The {custom/vtk} dump style is part of the USER-VTK 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.
-
-To use this dump style, you also must link to the VTK library.  See
-the info in lib/vtk/README and insure the Makefile.lammps file in that
-directory is appropriate for your machine.
-
-The {custom/vtk} dump style neither supports buffering nor custom
-format strings.
-
-[Related commands:]
-
-"dump"_dump.html, "dump image"_dump_image.html,
-"dump_modify"_dump_modify.html, "undump"_undump.html
-
-[Default:]
-
-By default, files are written in ASCII format. If the file extension
-is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
-

doc/src/dump_h5md.txt

@@ -17,9 +17,7 @@ group-ID = ID of the group of atoms to be imaged :l
 h5md = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
 N = dump every this many timesteps :l
 file.h5 = name of file to write to :l
-args = list of data elements to dump, with their dump "subintervals".
+args = list of data elements to dump, with their dump "subintervals"
-At least one element must be given and image may only be present if
-position is specified first. :l
   position options
   image
   velocity options
@@ -29,16 +27,18 @@ position is specified first. :l
   box value = {yes} or {no}
   create_group value = {yes} or {no}
   author value = quoted string :pre
+:ule
 
-For the elements {position}, {velocity}, {force} and {species}, one
+Note that at least one element must be specified and image may only be
-may specify a sub-interval to write the data only every N_element
+present if position is specified first.
+
+For the elements {position}, {velocity}, {force} and {species}, a
+sub-interval may be specified to write the data only every N_element
 iterations of the dump (i.e. every N*N_element time steps). This is
-specified by the option
+specified by this option directly following the element declaration:
 
 every N_element :pre
 
-that follows directly the element declaration.
-
 :ule
 
 [Examples:]

doc/src/dump_nc.txt

@@ -1,66 +0,0 @@
-"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
-
-:link(lws,http://lammps.sandia.gov)
-:link(ld,Manual.html)
-:link(lc,Section_commands.html#comm)
-
-:line
-
-dump nc command :h3
-dump nc/mpiio command :h3
-
-[Syntax:]
-
-dump ID group-ID nc N file.nc args
-dump ID group-ID nc/mpiio N file.nc args :pre
-
-ID = user-assigned name for the dump :ulb,l
-group-ID = ID of the group of atoms to be imaged :l
-{nc} or {nc/mpiio}  = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
-N = dump every this many timesteps :l
-file.nc = name of file to write to :l
-args = list of per atom data elements to dump, same as for the 'custom' dump style. :l,ule
-
-[Examples:]
-
-dump 1 all nc 100 traj.nc type x y z vx vy vz
-dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press :pre
-
-dump 1 all nc/mpiio 1000 traj.nc id type x y z :pre
-
-[Description:]
-
-Dump a snapshot of atom coordinates every N timesteps in Amber-style
-NetCDF file format. NetCDF files are binary, portable and
-self-describing.  This dump style will write only one file on the root
-node.  The dump style {nc} uses the "standard NetCDF
-library"_netcdf-home all data is collected on one processor and then
-written to the dump file. Dump style {nc/mpiio} used the "parallel
-NetCDF library"_pnetcdf-home and MPI-IO; it has better performance on
-a larger number of processors. Note that 'nc' outputs all atoms sorted
-by atom tag while 'nc/mpiio' outputs in order of the MPI rank.
-
-In addition to per-atom data, also global (i.e. not per atom, but per
-frame) quantities can be included in the dump file. This can be
-variables, output from computes or fixes data prefixed with v_, c_ and
-f_, respectively.  These properties are included via
-"dump_modify"_dump_modify.html {global}.
-
-:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
-:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
-
-:line
-
-[Restrictions:]
-
-The {nc} and {nc/mpiio} dump styles are part of the USER-NC-DUMP
-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.
-
-:line
-
-[Related commands:]
-
-"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
-

doc/src/dump_netcdf.txt

@@ -0,0 +1,82 @@
+"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
+
+dump netcdf command :h3
+dump netcdf/mpiio command :h3
+
+[Syntax:]
+
+dump ID group-ID netcdf N file args
+dump ID group-ID netcdf/mpiio N file args :pre
+
+ID = user-assigned name for the dump :ulb,l
+group-ID = ID of the group of atoms to be imaged :l
+{netcdf} or {netcdf/mpiio}  = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
+N = dump every this many timesteps :l
+file = name of file to write dump info to :l
+args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule
+
+[Examples:]
+
+dump 1 all netcdf 100 traj.nc type x y z vx vy vz
+dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press
+dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre
+
+[Description:]
+
+Dump a snapshot of atom coordinates every N timesteps in Amber-style
+NetCDF file format.  NetCDF files are binary, portable and
+self-describing.  This dump style will write only one file on the root
+node.  The dump style {netcdf} uses the "standard NetCDF
+library"_netcdf-home.  All data is collected on one processor and then
+written to the dump file.  Dump style {netcdf/mpiio} uses the
+"parallel NetCDF library"_pnetcdf-home and MPI-IO to write to the dump
+file in parallel; it has better performance on a larger number of
+processors.  Note that style {netcdf} outputs all atoms sorted by atom
+tag while style {netcdf/mpiio} outputs atoms in order of their MPI
+rank.
+
+NetCDF files can be directly visualized via the following tools:
+
+Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and
+all of the above extensions. :ule,b
+
+VMD (http://www.ks.uiuc.edu/Research/vmd/). :l
+
+AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye
+contains a NetCDF reader that is not present in the standard
+distribution of AtomEye. :l,ule
+
+In addition to per-atom data, global data can be included in the dump
+file, which are the kinds of values output by the
+"thermo_style"_thermo_style.html command .  See "Section howto
+6.15"_Section_howto.html#howto_15 for an explanation of per-atom
+versus global data.  The global output written into the dump file can
+be from computes, fixes, or variables, by prefixing the compute/fix ID
+or variable name with "c_" or "f_" or "v_" respectively, as in the
+example above.  These global values are specified via the "dump_modify
+global"_dump_modify.html command.
+
+:link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/)
+:link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/)
+
+:line
+
+[Restrictions:]
+
+The {netcdf} and {netcdf/mpiio} dump styles are part of the
+USER-NETCDF package.  They are only enabled if LAMMPS was built with
+that package. See the "Making LAMMPS"_Section_start.html#start_3
+section for more info.
+
+:line
+
+[Related commands:]
+
+"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
+

doc/src/dump_vtk.txt

@@ -0,0 +1,179 @@
+ "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
+
+dump vtk command :h3
+
+[Syntax:]
+
+dump ID group-ID vtk N file args :pre
+
+ID = user-assigned name for the dump
+group-ID = ID of the group of atoms to be dumped
+vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
+N = dump every this many timesteps
+file = name of file to write dump info to 
+args = same as arguments for "dump_style custom"_dump.html :ul
+
+[Examples:]
+
+dump dmpvtk all vtk 100 dump*.myforce.vtk id type vx fx
+dump dmpvtp flow vtk 100 dump*.%.displace.vtp id type c_myD\[1\] c_myD\[2\] c_myD\[3\] v_ke :pre
+
+[Description:]
+
+Dump a snapshot of atom quantities to one or more files every N
+timesteps in a format readable by the "VTK visualization
+toolkit"_http://www.vtk.org or other visualization tools that use it,
+e.g. "ParaView"_http://www.paraview.org.  The timesteps on which dump
+output is written can also be controlled by a variable; see the
+"dump_modify every"_dump_modify.html command for details.
+
+This dump style is similar to "dump_style custom"_dump.html but uses
+the VTK library to write data to VTK simple legacy or XML format
+depending on the filename extension specified for the dump file.  This
+can be either {*.vtk} for the legacy format or {*.vtp} and {*.vtu},
+respectively, for XML format; see the "VTK
+homepage"_http://www.vtk.org/VTK/img/file-formats.pdf for a detailed
+description of these formats.  Since this naming convention conflicts
+with the way binary output is usually specified (see below), the
+"dump_modify binary"_dump_modify.html command allows setting of a
+binary option for this dump style explicitly.
+
+Only information for atoms in the specified group is dumped.  The
+"dump_modify thresh and region"_dump_modify.html commands can also
+alter what atoms are included; see details below.
+
+As described below, special characters ("*", "%") in the filename
+determine the kind of output.
+
+IMPORTANT NOTE: Because periodic boundary conditions are enforced only
+on timesteps when neighbor lists are rebuilt, the coordinates of an
+atom written to a dump file may be slightly outside the simulation
+box.
+
+IMPORTANT NOTE: Unless the "dump_modify sort"_dump_modify.html option
+is invoked, the lines of atom information written to dump files will
+be in an indeterminate order for each snapshot.  This is even true
+when running on a single processor, if the "atom_modify
+sort"_atom_modify.html option is on, which it is by default.  In this
+case atoms are re-ordered periodically during a simulation, due to
+spatial sorting.  It is also true when running in parallel, because
+data for a single snapshot is collected from multiple processors, each
+of which owns a subset of the atoms.
+
+For the {vtk} style, sorting is off by default. See the
+"dump_modify"_dump_modify.html doc page for details.
+
+:line
+
+The dimensions of the simulation box are written to a separate file
+for each snapshot (either in legacy VTK or XML format depending on the
+format of the main dump file) with the suffix {_boundingBox} appended
+to the given dump filename.
+
+For an orthogonal simulation box this information is saved as a
+rectilinear grid (legacy .vtk or .vtr XML format).
+
+Triclinic simulation boxes (non-orthogonal) are saved as
+hexahedrons in either legacy .vtk or .vtu XML format.
+
+Style {vtk} allows you to specify a list of atom attributes to be
+written to the dump file for each atom.  The list of possible attributes 
+is the same as for the "dump_style custom"_dump.html command; see
+its doc page for a listing and an explanation of each attribute.
+
+NOTE: Since position data is required to write VTK files the atom
+attributes "x y z" do not have to be specified explicitly; they will
+be included in the dump file regardless.  Also, in contrast to the
+{custom} style, the specified {vtk} attributes are rearranged to
+ensure correct ordering of vector components (except for computes and
+fixes - these have to be given in the right order) and duplicate
+entries are removed.
+
+The VTK format uses a single snapshot of the system per file, thus
+a wildcard "*" must be included in the filename, as discussed below.
+Otherwise the dump files will get overwritten with the new snapshot
+each time.
+
+:line
+
+Dumps are performed on timesteps that are a multiple of N (including
+timestep 0) and on the last timestep of a minimization if the
+minimization converges.  Note that this means a dump will not be
+performed on the initial timestep after the dump command is invoked,
+if the current timestep is not a multiple of N.  This behavior can be
+changed via the "dump_modify first"_dump_modify.html command, which
+can also be useful if the dump command is invoked after a minimization
+ended on an arbitrary timestep.  N can be changed between runs by
+using the "dump_modify every"_dump_modify.html command.
+The "dump_modify every"_dump_modify.html command
+also allows a variable to be used to determine the sequence of
+timesteps on which dump files are written.  In this mode a dump on the
+first timestep of a run will also not be written unless the
+"dump_modify first"_dump_modify.html command is used.
+
+Dump filenames can contain two wildcard characters.  If a "*"
+character appears in the filename, then one file per snapshot is
+written and the "*" character is replaced with the timestep value.
+For example, tmp.dump*.vtk becomes tmp.dump0.vtk, tmp.dump10000.vtk,
+tmp.dump20000.vtk, etc.  Note that the "dump_modify pad"_dump_modify.html
+command can be used to insure all timestep numbers are the same length
+(e.g. 00010), which can make it easier to read a series of dump files
+in order with some post-processing tools.
+
+If a "%" character appears in the filename, then each of P processors
+writes a portion of the dump file, and the "%" character is replaced
+with the processor ID from 0 to P-1 preceded by an underscore character.
+For example, tmp.dump%.vtp becomes tmp.dump_0.vtp, tmp.dump_1.vtp, ...
+tmp.dump_P-1.vtp, etc.  This creates smaller files and can be a fast
+mode of output on parallel machines that support parallel I/O for output.
+
+By default, P = the number of processors meaning one file per
+processor, but P can be set to a smaller value via the {nfile} or
+{fileper} keywords of the "dump_modify"_dump_modify.html command.
+These options can be the most efficient way of writing out dump files
+when running on large numbers of processors.
+
+For the legacy VTK format "%" is ignored and P = 1, i.e., only
+processor 0 does write files.
+
+Note that using the "*" and "%" characters together can produce a
+large number of small dump files!
+
+If {dump_modify binary} is used, the dump file (or files, if "*" or
+"%" is also used) is written in binary format.  A binary dump file
+will be about the same size as a text version, but will typically
+write out much faster.
+
+:line
+
+[Restrictions:]
+
+The {vtk} style does not support writing of gzipped dump files.
+
+The {vtk} dump style is part of the USER-VTK 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.
+
+To use this dump style, you also must link to the VTK library.  See
+the info in lib/vtk/README and insure the Makefile.lammps file in that
+directory is appropriate for your machine.
+
+The {vtk} dump style supports neither buffering or custom format
+strings.
+
+[Related commands:]
+
+"dump"_dump.html, "dump image"_dump_image.html,
+"dump_modify"_dump_modify.html, "undump"_undump.html
+
+[Default:]
+
+By default, files are written in ASCII format. If the file extension
+is not one of .vtk, .vtp or .vtu, the legacy VTK file format is used.
+

doc/src/fix_cmap.txt

@@ -87,8 +87,11 @@ the note below about how to include the CMAP energy when performing an
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
-No information about this fix is written to "binary restart
+This fix writes the list of CMAP crossterms to "binary restart
-files"_restart.html.
+files"_restart.html.  See the "read_restart"_read_restart.html command
+for info on how to re-specify a fix in an input script that reads a
+restart file, so that the operation of the fix continues in an
+uninterrupted fashion.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the potential "energy" of the CMAP interactions system's

doc/src/fix_gcmc.txt

@@ -317,7 +317,7 @@ solution is to start a new simulation after the equilibrium density
 has been reached.
 
 With some pair_styles, such as "Buckingham"_pair_buck.html,
-"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reax_c.html, two
+"Born-Mayer-Huggins"_pair_born.html and "ReaxFF"_pair_reaxc.html, two
 atoms placed close to each other may have an arbitrary large, negative
 potential energy due to the functional form of the potential.  While
 these unphysical configurations are inaccessible to typical dynamical

doc/src/fix_qeq.txt

@@ -74,7 +74,7 @@ NOTE: The "fix qeq/comb"_fix_qeq_comb.html command must still be used
 to perform charge equilibration with the "COMB
 potential"_pair_comb.html.  The "fix qeq/reax"_fix_qeq_reax.html
 command can be used to perform charge equilibration with the "ReaxFF
-force field"_pair_reax_c.html, although fix qeq/shielded yields the
+force field"_pair_reaxc.html, although fix qeq/shielded yields the
 same results as fix qeq/reax if {Nevery}, {cutoff}, and {tolerance}
 are the same.  Eventually the fix qeq/reax command will be deprecated.
 
@@ -116,7 +116,7 @@ the shielded Coulomb is given by equation (13) of the "ReaxFF force
 field"_#vanDuin paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
 as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
-reax/c"_pair_reax_c.html.  Only the {chi}, {eta}, and {gamma}
+reax/c"_pair_reaxc.html.  Only the {chi}, {eta}, and {gamma}
 parameters from the {qfile} file are used.  This style solves partial
 charges on atoms via the matrix inversion method.  A tolerance of
 1.0e-6 is usually a good number.

doc/src/fix_qeq_reax.txt

@@ -30,7 +30,7 @@ fix 1 all qeq/reax 1 0.0 10.0 1.0e-6 param.qeq :pre
 Perform the charge equilibration (QEq) method as described in "(Rappe
 and Goddard)"_#Rappe2 and formulated in "(Nakano)"_#Nakano2.  It is
 typically used in conjunction with the ReaxFF force field model as
-implemented in the "pair_style reax/c"_pair_reax_c.html command, but
+implemented in the "pair_style reax/c"_pair_reaxc.html command, but
 it can be used with any potential in LAMMPS, so long as it defines and
 uses charges on each atom.  The "fix qeq/comb"_fix_qeq_comb.html
 command should be used to perform charge equilibration with the "COMB
@@ -42,7 +42,7 @@ The QEq method minimizes the electrostatic energy of the system by
 adjusting the partial charge on individual atoms based on interactions
 with their neighbors.  It requires some parameters for each atom type.
 If the {params} setting above is the word "reax/c", then these are
-extracted from the "pair_style reax/c"_pair_reax_c.html command and
+extracted from the "pair_style reax/c"_pair_reaxc.html command and
 the ReaxFF force field file it reads in.  If a file name is specified
 for {params}, then the parameters are taken from the specified file
 and the file must contain one line for each atom type.  The latter
@@ -106,7 +106,7 @@ be used for periodic cell dimensions less than 10 angstroms.
 
 [Related commands:]
 
-"pair_style reax/c"_pair_reax_c.html
+"pair_style reax/c"_pair_reaxc.html
 
 [Default:] none
 

doc/src/fix_reax_bonds.txt

@@ -28,7 +28,7 @@ fix 1 all reax/c/bonds 100 bonds.reaxc :pre
 
 Write out the bond information computed by the ReaxFF potential
 specified by "pair_style reax"_pair_reax.html or "pair_style
-reax/c"_pair_reax_c.html in the exact same format as the original
+reax/c"_pair_reaxc.html in the exact same format as the original
 stand-alone ReaxFF code of Adri van Duin.  The bond information is
 written to {filename} on timesteps that are multiples of {Nevery},
 including timestep 0.  For time-averaged chemical species analysis,
@@ -80,7 +80,7 @@ reax"_pair_reax.html be invoked.  This fix is part of the REAX
 package.  It is only enabled if LAMMPS was built with that package,
 which also requires the REAX library be built and linked with LAMMPS.
 The fix reax/c/bonds command requires that the "pair_style
-reax/c"_pair_reax_c.html be invoked.  This fix is part of the
+reax/c"_pair_reaxc.html be invoked.  This fix is part of the
 USER-REAXC 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.
@@ -88,6 +88,6 @@ for more info.
 [Related commands:]
 
 "pair_style reax"_pair_reax.html, "pair_style
-reax/c"_pair_reax_c.html, "fix reax/c/species"_fix_reaxc_species.html
+reax/c"_pair_reaxc.html, "fix reax/c/species"_fix_reaxc_species.html
 
 [Default:] none

doc/src/fix_reaxc_species.txt

@@ -41,7 +41,7 @@ fix 1 all reax/c/species 1 100 100 species.out element Au O H position 1000 AuOH
 [Description:]
 
 Write out the chemical species information computed by the ReaxFF
-potential specified by "pair_style reax/c"_pair_reax_c.html.
+potential specified by "pair_style reax/c"_pair_reaxc.html.
 Bond-order values (either averaged or instantaneous, depending on
 value of {Nrepeat}) are used to determine chemical bonds.  Every
 {Nfreq} timesteps, chemical species information is written to
@@ -65,7 +65,7 @@ symbol printed for each LAMMPS atom type. The number of symbols must
 match the number of LAMMPS atom types and each symbol must consist of
 1 or 2 alphanumeric characters. Normally, these symbols should be
 chosen to match the chemical identity of each LAMMPS atom type, as
-specified using the "reax/c pair_coeff"_pair_reax_c.html command and
+specified using the "reax/c pair_coeff"_pair_reaxc.html command and
 the ReaxFF force field file.
 
 The optional keyword {position} writes center-of-mass positions of
@@ -158,8 +158,8 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]
 
 The fix species currently only works with
-"pair_style reax/c"_pair_reax_c.html and it requires that the "pair_style
+"pair_style reax/c"_pair_reaxc.html and it requires that the "pair_style
-reax/c"_pair_reax_c.html be invoked.  This fix is part of the
+reax/c"_pair_reaxc.html be invoked.  This fix is part of the
 USER-REAXC 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.
@@ -170,7 +170,7 @@ It should be possible to extend it to other reactive pair_styles (such as
 
 [Related commands:]
 
-"pair_style reax/c"_pair_reax_c.html, "fix
+"pair_style reax/c"_pair_reaxc.html, "fix
 reax/bonds"_fix_reax_bonds.html
 
 [Default:]

doc/src/lammps.book

@@ -469,7 +469,7 @@ pair_peri.html
 pair_polymorphic.html
 pair_quip.html
 pair_reax.html
-pair_reax_c.html
+pair_reaxc.html
 pair_resquared.html
 pair_sdk.html
 pair_smd_hertz.html

doc/src/pair_hybrid.txt

@@ -73,7 +73,7 @@ pair_coeff command to assign parameters for the different type pairs.
 NOTE: There are two exceptions to this option to list an individual
 pair style multiple times.  The first is for pair styles implemented
 as Fortran libraries: "pair_style meam"_pair_meam.html and "pair_style
-reax"_pair_reax.html ("pair_style reax/c"_pair_reax_c.html is OK).
+reax"_pair_reax.html ("pair_style reax/c"_pair_reaxc.html is OK).
 This is because unlike a C++ class, they can not be instantiated
 multiple times, due to the manner in which they were coded in Fortran.
 The second is for GPU-enabled pair styles in the GPU package.  This is

doc/src/pair_reax.txt

@@ -36,7 +36,7 @@ supplemental information of the following paper:
 the most up-to-date version of ReaxFF as of summer 2010.
 
 WARNING: pair style reax is now deprecated and will soon be retired. Users
-should switch to "pair_style reax/c"_pair_reax_c.html. The {reax} style
+should switch to "pair_style reax/c"_pair_reaxc.html. The {reax} style
 differs from the {reax/c} style in the lo-level implementation details.
 The {reax} style is a
 Fortran library, linked to LAMMPS.  The {reax/c} style was initially
@@ -82,7 +82,7 @@ be specified.
 
 Two examples using {pair_style reax} are provided in the examples/reax
 sub-directory, along with corresponding examples for
-"pair_style reax/c"_pair_reax_c.html. Note that while the energy and force
+"pair_style reax/c"_pair_reaxc.html. Note that while the energy and force
 calculated by both of these pair styles match very closely, the
 contributions due to the valence angles differ slightly due to
 the fact that with {pair_style reax/c} the default value of {thb_cutoff_sq}
@@ -201,7 +201,7 @@ appropriate units if your simulation doesn't use "real" units.
 
 [Related commands:]
 
-"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reax_c.html,
+"pair_coeff"_pair_coeff.html, "pair_style reax/c"_pair_reaxc.html,
 "fix_reax_bonds"_fix_reax_bonds.html
 
 [Default:]

doc/src/pair_reaxc.txt

@@ -17,6 +17,7 @@ cfile = NULL or name of a control file :ulb,l
 zero or more keyword/value pairs may be appended :l
 keyword = {checkqeq} or {lgvdw} or {safezone} or {mincap}
   {checkqeq} value = {yes} or {no} = whether or not to require qeq/reax fix
+  {enobonds} value = {yes} or {no} = whether or not to tally energy of atoms with no bonds
   {lgvdw} value = {yes} or {no} = whether or not to use a low gradient vdW correction
   {safezone} = factor used for array allocation
   {mincap} = minimum size for array allocation :pre
@@ -127,6 +128,13 @@ recommended value for parameter {thb} is 0.01, which can be set in the
 control file.  Note: Force field files are different for the original
 or lg corrected pair styles, using wrong ffield file generates an error message.
 
+Using the optional keyword {enobonds} with the value {yes}, the energy
+of atoms with no bonds (i.e. isolated atoms) is included in the total
+potential energy and the per-atom energy of that atom.  If the value
+{no} is specified then the energy of atoms with no bonds is set to zero.
+The latter behavior is usual not desired, as it causes discontinuities
+in the potential energy when the bonding of an atom drops to zero.
+
 Optional keywords {safezone} and {mincap} are used for allocating
 reax/c arrays.  Increasing these values can avoid memory problems, such
 as segmentation faults and bondchk failed errors, that could occur under
@@ -331,7 +339,7 @@ reax"_pair_reax.html
 
 [Default:]
 
-The keyword defaults are checkqeq = yes, lgvdw = no, safezone = 1.2,
+The keyword defaults are checkqeq = yes, enobonds = yes, lgvdw = no, safezone = 1.2,
 mincap = 50.
 
 :line

doc/src/pairs.txt

@@ -73,7 +73,7 @@ Pair Styles :h1
    pair_polymorphic
    pair_quip
    pair_reax
-   pair_reax_c
+   pair_reaxc
    pair_resquared
    pair_sdk
    pair_smd_hertz

examples/mscg/log.31Mar17.g++.1

@@ -0,0 +1,145 @@
+LAMMPS (13 Apr 2017)
+units real
+atom_style full
+pair_style zero 10.0
+
+read_data data.meoh
+  orthogonal box = (-20.6917 -20.6917 -20.6917) to (20.6917 20.6917 20.6917)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1000 atoms
+  0 = max # of 1-2 neighbors
+  0 = max # of 1-3 neighbors
+  0 = max # of 1-4 neighbors
+  1 = max # of special neighbors
+pair_coeff * *
+
+thermo 1
+thermo_style custom step
+
+# Test 1a: range finder functionality
+fix 1 all mscg 1 range on
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Neighbor list info ...
+  update every 1 steps, delay 10 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 12
+  ghost atom cutoff = 12
+  binsize = 6, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair zero, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d/newton
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 0.581537 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 2.823 ns/day, 8.502 hours/ns, 32.672 timesteps/s
+99.2% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.5815     |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1a mscg range finder"
+TEST_1a mscg range finder
+unfix 1
+
+# Test 1b: force matching functionality
+fix 1 all mscg 1
+rerun dump.meoh first 0 last 4500 every 250 dump x y z fx fy fz
+Per MPI rank memory allocation (min/avg/max) = 5.794 | 5.794 | 5.794 Mbytes
+Step 
+       0 
+     250 
+     500 
+     750 
+    1000 
+    1250 
+    1500 
+    1750 
+    2000 
+    2250 
+    2500 
+    2750 
+    3000 
+    3250 
+    3500 
+    3750 
+    4000 
+    4250 
+    4500 
+Loop time of 0.841917 on 1 procs for 19 steps with 1000 atoms
+
+Performance: 1.950 ns/day, 12.309 hours/ns, 22.568 timesteps/s
+99.8% CPU use with 1 MPI tasks x no OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0          | 0          | 0          |   0.0 |  0.00
+Bond    | 0          | 0          | 0          |   0.0 |  0.00
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0          | 0          | 0          |   0.0 |  0.00
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.8419     |            |       |100.00
+
+Nlocal:    1000 ave 1000 max 1000 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:    2934 ave 2934 max 2934 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    50654 ave 50654 max 50654 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 50654
+Ave neighs/atom = 50.654
+Ave special neighs/atom = 0
+Neighbor list builds = 0
+Dangerous builds = 0
+print "TEST_1b mscg force matching"
+TEST_1b mscg force matching
+
+print TEST_DONE
+TEST_DONE
+Total wall time: 0:00:01

lib/Install.py

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

lib/README

@@ -33,14 +33,16 @@ kokkos        Kokkos package for GPU and many-core acceleration
                 from Kokkos development team (Sandia)
 linalg        set of BLAS and LAPACK routines needed by USER-ATC package
 	        from Axel Kohlmeyer (Temple U)
-poems	      POEMS rigid-body integration package, POEMS package
-                from Rudranarayan Mukherjee (RPI)
 meam	      modified embedded atom method (MEAM) potential, MEAM package
                 from Greg Wagner (Sandia)
 molfile       hooks to VMD molfile plugins, used by the USER-MOLFILE package
                 from Axel Kohlmeyer (Temple U) and the VMD development team
 mscg          hooks to the MSCG library, used by fix_mscg command
                 from Jacob Wagner and Greg Voth group (U Chicago)
+netcdf        hooks to a NetCDF library installed on your system
+                from Lars Pastewka (Karlsruhe Institute of Technology)
+poems	      POEMS rigid-body integration package, POEMS package
+                from Rudranarayan Mukherjee (RPI)
 python        hooks to the system Python library, used by the PYTHON package
                 from the LAMMPS development team
 qmmm	      quantum mechanics/molecular mechanics coupling interface

lib/atc/Install.py

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

lib/atc/README

@@ -15,6 +15,11 @@ links against when using the USER-ATC package.
 This library must be built with a C++ compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-atc" from the src directory to see help on how
+to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 
@@ -44,16 +49,16 @@ user-atc_SYSINC = leave blank for this package
 user-atc_SYSLIB = BLAS and LAPACK libraries needed by this package
 user-atc_SYSPATH = path(s) to where those libraries are
 
-You have several choices for these settings:
+You have 3 choices for these settings:
 
-If the 2 libraries are already installed on your system, the settings
+a) If the 2 libraries are already installed on your system, the
-in Makefile.lammps.installed should work.
+settings in Makefile.lammps.installed should work.
 
-If they are not, you can install them yourself, and speficy the
+b) If they are not, you can install them yourself, and specify the
-appropriate settings accordingly.
+appropriate settings accordingly in a Makefile.lammps.* file
+and set the EXTRAMAKE setting in Makefile.* to that file.
 
-If you want to use the minimalist version of these libraries provided
+c) Use the minimalist version of these libraries provided with LAMMPS
-with LAMMPS in lib/linalg, then the settings in Makefile.lammps.linalg
+in lib/linalg, by using Makefile.lammps.linalg.  In this case you also
-should work.  Note that in this case you also need to build the
+need to build the library in lib/linalg; see the lib/linalg/README
-linear-algebra in lib/linalg; see the lib/linalg/README for more
+file for more details.
-details.

lib/awpmd/Install.py

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

lib/awpmd/README

@@ -19,6 +19,11 @@ links against when using the USER-AWPMD package.
 This library must be built with a C++ compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-awpmd" from the src directory to see help on
+how to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 
@@ -47,16 +52,16 @@ user-awpmd_SYSINC = leave blank for this package
 user-awpmd_SYSLIB = BLAS and LAPACK libraries needed by this package
 user-awpmd_SYSPATH = path(s) to where those libraries are
 
-You have several choices for these settings:
+You have 3 choices for these settings:
 
-If the 2 libraries are already installed on your system, the settings
+a) If the 2 libraries are already installed on your system, the
-in Makefile.lammps.installed should work.
+settings in Makefile.lammps.installed should work.
 
-If they are not, you can install them yourself, and speficy the
+b) If they are not, you can install them yourself, and specify the
-appropriate settings accordingly.
+appropriate settings accordingly in a Makefile.lammps.* file
+and set the EXTRAMAKE setting in Makefile.* to that file.
 
-If you want to use the minimalist version of these libraries provided
+c) Use the minimalist version of these libraries provided with LAMMPS
-with LAMMPS in lib/linalg, then the settings in Makefile.lammps.linalg
+in lib/linalg, by using Makefile.lammps.linalg.  In this case you also
-should work.  Note that in this case you also need to build the
+need to build the library in lib/linalg; see the lib/linalg/README
-linear-algebra in lib/linalg; see the lib/linalg/README for more
+file for more details.
-details.

lib/colvars/Install.py

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

lib/colvars/README

@@ -35,6 +35,11 @@ links against when using the USER-COLVARS package.
 This library must be built with a C++ compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-colvars" from the src directory to see help on
+how to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 

lib/gpu/Install.py

@@ -0,0 +1,146 @@
+#!/usr/bin/env python
+
+# 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
+
+# help message
+
+help = """
+Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix
+  specify one or more options, order does not matter
+  copies an existing Makefile.isuffix in lib/gpu to Makefile.auto 
+  optionally edits these variables in Makefile.auto:
+    CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE
+  optionally uses Makefile.auto to build the GPU library -> libgpu.a
+    and to copy a Makefile.lammps.esuffix -> Makefile.lammps
+  optionally copies Makefile.auto to a new Makefile.osuffix
+
+  -i = use Makefile.isuffix as starting point, copy to Makefile.auto
+       default isuffix = linux
+  -h = set CUDA_HOME variable in Makefile.auto to hdir
+       hdir = path to NVIDIA Cuda software, e.g. /usr/local/cuda
+  -a = set CUDA_ARCH variable in Makefile.auto to arch
+       use arch = ?? for K40 (Tesla)
+       use arch = 37 for dual K80 (Tesla)
+       use arch = 60 for P100 (Pascal)
+  -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
+       first performs a "make clean"
+       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
+"""
+
+# 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()
+
+isuffix = "linux"
+hflag = aflag = pflag = eflag = 0
+makeflag = 0
+outflag = 0
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-i":
+    if iarg+2 > nargs: error()
+    isuffix = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-h":
+    if iarg+2 > nargs: error()
+    hflag = 1
+    hdir = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-a":
+    if iarg+2 > nargs: error()
+    aflag = 1
+    arch = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-p":
+    if iarg+2 > nargs: error()
+    pflag = 1
+    precision = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-e":
+    if iarg+2 > nargs: error()
+    eflag = 1
+    lmpsuffix = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-m":
+    makeflag = 1
+    iarg += 1
+  elif args[iarg] == "-o":
+    if iarg+2 > nargs: error()
+    outflag = 1
+    osuffix = args[iarg+1]
+    iarg += 2
+  else: error()
+
+if pflag:
+  if precision == "double": precstr = "-D_DOUBLE_DOUBLE"
+  elif precision == "mixed": precstr = "-D_SINGLE_DOUBLE"
+  elif precision == "single": precstr = "-D_SINGLE_SINGLE"
+  else: error("Invalid precision setting")
+  
+# create Makefile.auto
+# reset EXTRAMAKE, CUDA_HOME, CUDA_ARCH, CUDA_PRECISION if requested
+  
+if not os.path.exists("Makefile.%s" % isuffix):
+  error("lib/gpu/Makefile.%s does not exist" % isuffix)
+
+lines = open("Makefile.%s" % isuffix,'r').readlines()
+fp = open("Makefile.auto",'w')
+
+for line in lines:
+  words = line.split()
+  if len(words) != 3:
+    print >>fp,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] == '=':
+    line = line.replace(words[2],"-arch=sm_%s" % arch)
+  if pflag and words[0] == "CUDA_PRECISION" and words[1] == '=':
+    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.close()
+
+# perform make
+# make operations copies EXTRAMAKE file to Makefile.lammps
+
+if makeflag:
+  print "Building libgpu.a ..."
+  cmd = "rm -f libgpu.a"
+  commands.getoutput(cmd)
+  cmd = "make -f Makefile.auto clean; make -f Makefile.auto"
+  commands.getoutput(cmd)
+  if not os.path.exists("libgpu.a"):
+    error("Build of lib/gpu/libgpu.a was NOT successful")
+  if not os.path.exists("Makefile.lammps"):
+    error("lib/gpu/Makefile.lammps was NOT created")
+
+# copy new Makefile.auto to Makefile.osuffix
+
+if outflag:
+  print "Creating new Makefile.%s" % osuffix
+  cmd = "cp Makefile.auto Makefile.%s" % osuffix
+  commands.getoutput(cmd)

lib/gpu/README

@@ -17,6 +17,11 @@ links against when using the GPU package.
 This library must be built with a C++ compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-gpu" from the src directory to see help on how
+to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 
@@ -164,9 +169,9 @@ this directory).
 The gpu library supports 3 precision modes as determined by 
 the CUDA_PRECISION variable:
 
-  CUDA_PREC = -D_SINGLE_SINGLE  # Single precision for all calculations
+  CUDA_PRECISION = -D_SINGLE_SINGLE  # Single precision for all calculations
-  CUDA_PREC = -D_DOUBLE_DOUBLE  # Double precision for all calculations
+  CUDA_PRECISION = -D_DOUBLE_DOUBLE  # Double precision for all calculations
-  CUDA_PREC = -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
+  CUDA_PRECISION = -D_SINGLE_DOUBLE  # Accumulation of forces, etc. in double
 
 NOTE: PPPM acceleration can only be run on GPUs with compute capability>=1.1.
       You will get the error "GPU library not compiled for this accelerator."

lib/h5md/Install.py

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

lib/h5md/Makefile.h5cc

@@ -19,7 +19,7 @@ build/ch5md.o: src/ch5md.c | build
 	$(CC) $(INC) $(CFLAGS) -c $< -o $@
 
 Makefile.lammps:
-	cp Makefile.lammps.empty $@
+	cp $(EXTRAMAKE) $@
 
 .PHONY: all lib clean
 

lib/h5md/README

@@ -3,6 +3,11 @@ LAMMPS under its own BSD license; see below.  This library is used
 when the USER-H5MD package is included in a LAMMPS build and the dump
 h5md command is invoked in a LAMMPS input script.
 
+You can type "make lib-h5md" from the src directory to see help on how
+to 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.
+
 ---------------------
 
 ch5md : Read and write H5MD files in C
@@ -17,8 +22,14 @@ molecular data, whose development is found at <http://nongnu.org/h5md/>.
 ch5md is developped by Pierre de Buyl and is released under the 3-clause BSD
 license that can be found in the file LICENSE.
 
-To use the h5md dump style in lammps, execute make in this directory then 'make
+To use the h5md dump style in lammps, execute
-yes-user-h5md' in the src directory of lammps. Rebuild lammps. 
+make -f Makefile.h5cc
+in this directory then
+make yes-user-h5md
+in the src directory of LAMMPS to rebuild LAMMPS. 
+
+Note that you must have the h5cc compiler installed to use
+Makefile.h5cc.  It should be part
 
 If HDF5 is not in a standard system location, edit Makefile.lammps accordingly.
 

lib/linalg/Install.py

@@ -0,0 +1,52 @@
+#!/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))

lib/linalg/README

@@ -3,11 +3,16 @@ USER-AWPMD packages, and possibly by other packages in the future.
 
 Note that this is an *incomplete* subset of full BLAS/LAPACK.
 
-You should only need to build and use the resulting library in this
+You should only need to build and use the library in this directory if
-directory if you want to build LAMMPS with the USER-ATC and/or
+you want to build LAMMPS with the USER-ATC and/or USER-AWPMD packages
-USER-AWPMD packages AND you do not have any other suitable BLAS and
+AND you do not have any other suitable BLAS and LAPACK libraries
-LAPACK libraries installed on your system.  E.g. ATLAS, GOTO-BLAS,
+installed on your system.  E.g. ATLAS, GOTO-BLAS, OpenBLAS, ACML, or
-OpenBLAS, ACML, or MKL.
+MKL.
+
+You can type "make lib-linalg" from the src directory to see help on
+how to 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.
 
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
@@ -20,4 +25,5 @@ directory:
 liblinalg.a		the library LAMMPS will link against
 
 You can then include this library and its path in the Makefile.lammps
-file of any packages that need it, e.g. in lib/atc/Makefile.lammps.
+file of any packages that need it.  As an example, see the
+lib/atc/Makefile.lammps.linalg file.

lib/meam/Install.py

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

lib/meam/README

@@ -15,6 +15,11 @@ links against when using the MEAM package.
 This library must be built with a F90 compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-meam" from the src directory to see help on how
+to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 

lib/mscg/Install.py

@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, build, and link to the MS-CG library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,commands
+
+# help message
+
+help = """
+Syntax: python Install.py -h hpath hdir -g -b [suffix] -l
+  specify one or more options, order does not matter
+  -h = set home dir of MS-CG to be hpath/hdir
+       hpath can be full path, contain '~' or '.' chars
+       default hpath = . = lib/mscg
+       default hdir = MSCG-release-master = what GitHub zipfile unpacks to
+  -g = grab (download) zipfile from MS-CG GitHub website
+       unpack it to hpath/hdir
+       hpath must already exist
+       if hdir already exists, it will be deleted before unpack
+  -b = build MS-CG library in its src dir
+       optional suffix specifies which src/Make/Makefile.suffix to use
+       default suffix = g++_simple
+  -l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir
+"""
+
+# settings
+
+url = "https://github.com/uchicago-voth/MSCG-release/archive/master.zip"
+zipfile = "MS-CG-master.zip"
+zipdir = "MSCG-release-master"
+
+# print error message or help
+
+def error(str=None):
+  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))
+  
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+homepath = "."
+homedir = zipdir
+
+grabflag = 0
+buildflag = 0
+msuffix = "g++_simple"
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-h":
+    if iarg+3 > nargs: error()
+    homepath = args[iarg+1]
+    homedir = args[iarg+2]
+    iarg += 3
+  elif args[iarg] == "-g":
+    grabflag = 1
+    iarg += 1
+  elif args[iarg] == "-b":
+    buildflag = 1
+    if iarg+1 < nargs and args[iarg+1][0] != '-':
+      msuffix = args[iarg+1]
+      iarg += 1
+    iarg += 1
+  elif args[iarg] == "-l":
+    linkflag = 1
+    iarg += 1
+  else: error()
+
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("MS-CG path does not exist")
+homedir = "%s/%s" % (homepath,homedir)
+
+# download and unpack MS-CG zipfile
+
+if grabflag:
+  print "Downloading MS-CG ..."
+  cmd = "curl -L %s > %s/%s" % (url,homepath,zipfile)
+  print cmd
+  print commands.getoutput(cmd)
+
+  print "Unpacking MS-CG zipfile ..."
+  if os.path.exists("%s/%s" % (homepath,zipdir)):
+    commands.getoutput("rm -rf %s/%s" % (homepath,zipdir))
+  cmd = "cd %s; unzip %s" % (homepath,zipfile)
+  commands.getoutput(cmd)
+  if os.path.basename(homedir) != zipdir:
+    if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+    os.rename("%s/%s" % (homepath,zipdir),homedir)
+
+# build MS-CG
+
+if buildflag:
+  print "Building MS-CG ..."
+  cmd = "cd %s/src; cp Make/Makefile.%s .; make -f Makefile.%s" % \
+      (homedir,msuffix,msuffix)
+  txt = commands.getoutput(cmd)
+  print txt
+
+# create 2 links in lib/mscg to MS-CG src dir
+
+if linkflag:
+  print "Creating links to MS-CG include and lib files"
+  if os.path.isfile("includelink") or os.path.islink("includelink"):
+    os.remove("includelink")
+  if os.path.isfile("liblink") or os.path.islink("liblink"):
+    os.remove("liblink")
+  cmd = "ln -s %s/src includelink" % homedir
+  commands.getoutput(cmd)
+  cmd = "ln -s %s/src liblink" % homedir
+  commands.getoutput(cmd)

lib/mscg/Makefile.lammps

@@ -1,5 +1,5 @@
 # Settings that the LAMMPS build will import when this package library is used
 
-mscg_SYSINC = 
+mscg_SYSINC = -std=c++11
-mscg_SYSLIB = -lm -lgsl -llapack -lcblas
+mscg_SYSLIB = -lm -lgsl -llapack -lgslcblas
 mscg_SYSPATH = 

lib/mscg/README

@@ -6,6 +6,15 @@ The MS-CG library is available at
 https://github.com/uchicago-voth/MSCG-release and was developed by
 Jacob Wagner in Greg Voth's group at the University of Chicago.
 
+This library requires a compiler with C++11 support (e.g., g++ v4.9+),
+LAPACK, and the GNU scientific library (GSL v 2.1+).
+
+You can type "make lib-mscg" from the src directory to see help on 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.
+
 -----------------
 
 You must perform the following steps yourself.
@@ -14,16 +23,21 @@ You must perform the following steps yourself.
     either as a tarball or via SVN, and unpack the tarball either in
     this /lib/mscg directory or somewhere else on your system.
 
-2.  Compile MS-CG from within its home directory using your makefile choice:
+2.  Ensure that you have LAPACK and GSL (or Intel MKL) as well as a compiler
-    % make -f Makefile."name" libmscg.a
+    with support for C++11.
     
-3.  There is no need to install MS-CG if you only wish 
+3.  Compile MS-CG from within its home directory using your makefile of choice:
+    % make -f Makefile."name" libmscg.a
+	It is recommended that you start with Makefile.g++_simple
+        for most machines
+
+4.  There is no need to install MS-CG if you only wish 
     to use it from LAMMPS.
 
-4.  Create two soft links in this dir (lib/mscg) to the MS-CG src
+5.  Create two soft links in this dir (lib/mscg) to the MS-CG src
     directory.  E.g if you built MS-CG in this dir:
-      % ln -s mscgfm-master/src includelink
+      % ln -s src includelink
-      % ln -s mscgfm-master/src liblink
+      % ln -s src liblink
     These links could instead be set to the include and lib
     directories created by a MS-CG install, e.g.
       % ln -s /usr/local/include includelink
@@ -46,8 +60,8 @@ somewhere else, you will also need to repeat steps 1,2,3.
 
 The Makefile.lammps file in this directory is there for compatibility
 with the way other libraries under the lib dir are linked with by
-LAMMPS.  MS-CG requires the GSL, LAPACK, and BLAS libraries as listed
+LAMMPS.  MS-CG requires the GSL and LAPACK libraries as listed in
-in Makefile.lammps.  If they are not in default locations where your
+Makefile.lammps.  If they are not in default locations where your
 LD_LIBRARY_PATH environment settings can find them, then you should
 add the approrpriate -L paths to the mscg_SYSPATH variable in
 Makefile.lammps.

lib/netcdf/README

@@ -1,6 +1,9 @@
 The Makefile.lammps file in this directory is used when building
 LAMMPS with packages that make use of the NetCDF library or its
-parallel version.  The file has several settings needed to compile
+parallel version.  For example, the USER-NETCDF package which adds
+dump netcdf and dump netcdf/mpiio commands.
+
+The file has several settings needed to compile
 and link LAMMPS with the NetCDF and parallel NetCDF support.
 For any regular NetCDF installation, all required flags should be
 autodetected. Please note that parallel NetCDF support is

lib/poems/Install.py

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

lib/poems/README

@@ -40,6 +40,11 @@ links against when using the POEMA package.
 This library must be built with a C++ compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-poems" from the src directory to see help on
+how to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 

lib/qmmm/Install.py

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

lib/qmmm/README

@@ -18,6 +18,15 @@ the only option. Adding support for a different QM code will require
 to write a new version of the top-level wrapper code, pwqmmm.c, and
 also an interface layer into the QM code similar to the one in QE.
 
+You can type "make lib-qmmm" from the src directory to see help on how
+to build this library (steps 1 and 2 below) 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.
+
+However you perform steps 1 and 2, you will need to perform steps 3
+and 4 manually, as outlined below.
+
 -------------------------------------------------
 
 WARNING: This is experimental code under developement and is provided

lib/reax/Install.py

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

lib/reax/README

@@ -17,6 +17,11 @@ links against when using the REAX package.
 This library must be built with a F90 compiler, before LAMMPS is
 built, so LAMMPS can link against it.
 
+You can type "make lib-reax" from the src directory to see help on how
+to 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.
+
 Build the library using one of the provided Makefile.* files or create
 your own, specific to your compiler and system.  For example:
 

lib/smd/Install.py

@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+
+# Install.py tool to download, unpack, and point to the Eigen library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,glob,commands
+
+# help message
+
+help = """
+Syntax: python Install.py -h hpath hdir -g -l
+  specify one or more options, order does not matter
+  -h = set home dir of Eigen to be hpath/hdir
+       hpath can be full path, contain '~' or '.' chars
+       default hpath = . = lib/smd
+       default hdir = "ee" = what tarball unpacks to (eigen-eigen-*)
+  -g = grab (download) tarball from http://eigen.tuxfamily.org website
+       unpack it to hpath/hdir
+       hpath must already exist
+       if hdir already exists, it will be deleted before unpack
+  -l = create softlink (includelink) in lib/smd to Eigen src dir
+"""
+
+# settings
+
+url = "http://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz"
+tarball = "eigen.tar.gz"
+
+# print error message or help
+
+def error(str=None):
+  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))
+  
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+homepath = "."
+homedir = "ee"
+
+grabflag = 0
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-h":
+    if iarg+3 > nargs: error()
+    homepath = args[iarg+1]
+    homedir = args[iarg+2]
+    iarg += 3
+  elif args[iarg] == "-g":
+    grabflag = 1
+    iarg += 1
+  elif args[iarg] == "-l":
+    linkflag = 1
+    iarg += 1
+  else: error()
+
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("Eigen path does not exist")
+
+# download and unpack Eigen tarball
+# glob to find name of dir it unpacks to
+
+if grabflag:
+  print "Downloading Eigen ..."
+  cmd = "curl -L %s > %s/%s" % (url,homepath,tarball)
+  print cmd
+  print commands.getoutput(cmd)
+
+  print "Unpacking Eigen tarball ..."
+  edir = glob.glob("%s/eigen-eigen-*" % homepath)
+  for one in edir:
+    if os.path.isdir(one): commands.getoutput("rm -rf %s" % one)
+  cmd = "cd %s; tar zxvf %s" % (homepath,tarball)
+  commands.getoutput(cmd)
+  if homedir != "ee":
+    if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+    edir = glob.glob("%s/eigen-eigen-*" % homepath)
+    os.rename(edir[0],"%s/%s" % (homepath,homedir))
+
+# create link in lib/smd to Eigen src dir
+
+if linkflag:
+  print "Creating link to Eigen files"
+  if os.path.isfile("includelink") or os.path.islink("includelink"):
+    os.remove("includelink")
+  if homedir == "ee":
+    edir = glob.glob("%s/eigen-eigen-*" % homepath)
+    linkdir = edir[0]
+  else: linkdir = "%s/%s" % (homepath,homedir)
+  cmd = "ln -s %s includelink" % linkdir
+  commands.getoutput(cmd)

lib/smd/README

@@ -4,9 +4,12 @@ to use the USER-SMD package in a LAMMPS input script.
 The Eigen library is available at http://eigen.tuxfamily.org.  It's
 a general C++ template library for linear algebra.
 
-You must perform the following steps yourself, or you can use the
+You can type "make lib-smd" from the src directory to see help on how
-install.py Python script to automate any or all steps of the process.
+to download build this library via make commands, or you can do the
-Type "python install.py" for instructions.
+same thing by typing "python Install.py" from within this directory,
+or you can do it manually by following the instructions below.
+
+Instructions:
 
 1.  Download the Eigen tarball at http://eigen.tuxfamily.org and
     unpack the tarball either in this /lib/smd directory or somewhere

lib/voronoi/Install.py

@@ -1,6 +1,6 @@
 #!/usr/bin/env python
 
-# install.py tool to download, unpack, build, and link to the Voro++ library
+# Install.py tool to download, unpack, build, and link to the Voro++ library
 # used to automate the steps described in the README file in this dir
 
 import sys,os,re,urllib,commands
@@ -8,19 +8,20 @@ import sys,os,re,urllib,commands
 # help message
 
 help = """
-Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir
+Syntax: python Install.py -v version -h hpath hdir -g -b -l
   specify one or more options, order does not matter
-  gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~
   -v = version of Voro++ to download and build
-       default = voro++-0.4.6 (current as of Jan 2015)
+       default version = voro++-0.4.6 (current as of Jan 2015)
-  -g = grab (download) from math.lbl.gov/voro++ website
+  -h = set home dir of Voro++ to be hpath/hdir
-       unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6)
+       hpath can be full path, contain '~' or '.' chars
-       if optional gname specified, rename version dir to gname within gdir
+       default hpath = . = lib/voronoi
-  -b = build Voro++, bdir = Voro++ home directory
+       default hdir = voro++-0.4.6 = what tarball unpacks to
-       note that bdir must include the version suffix unless renamed
+  -g = grab (download) tarball from math.lbl.gov/voro++ website
-  -l = create 2 softlinks (includelink,liblink)
+       unpack it to hpath/hdir
-         in lib/voronoi to src dir of ldir = Voro++ home directory
+       hpath must already exist
-       note that ldir must include the version suffix unless renamed
+       if hdir already exists, it will be deleted before unpack
+  -b = build Voro++ library in its src dir
+  -l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir
 """
 
 # settings
@@ -47,6 +48,9 @@ args = sys.argv[1:]
 nargs = len(args)
 if nargs == 0: error()
 
+homepath = "."
+homedir = version
+
 grabflag = 0
 buildflag = 0
 linkflag = 0
@@ -57,48 +61,46 @@ while iarg < nargs:
     if iarg+2 > nargs: error()
     version = args[iarg+1]
     iarg += 2
+  elif args[iarg] == "-h":
+    if iarg+3 > nargs: error()
+    homepath = args[iarg+1]
+    homedir = args[iarg+2]
+    iarg += 3
   elif args[iarg] == "-g":
-    if iarg+2 > nargs: error()
     grabflag = 1
-    grabdir = args[iarg+1]
-    grabname = None
-    if iarg+2 < nargs and args[iarg+2][0] != '-':
-      grabname = args[iarg+2]
     iarg += 1
-    iarg += 2
   elif args[iarg] == "-b":
-    if iarg+2 > nargs: error()
     buildflag = 1
-    builddir = args[iarg+1]
+    iarg += 1
-    iarg += 2
   elif args[iarg] == "-l":
-    if iarg+2 > nargs: error()
     linkflag = 1
-    linkdir = args[iarg+1]
+    iarg += 1
-    iarg += 2
   else: error()
 
+homepath = fullpath(homepath)
+if not os.path.isdir(homepath): error("Voro++ path does not exist")
+homedir = "%s/%s" % (homepath,homedir)
+
 # download and unpack Voro++ tarball
 
 if grabflag:
   print "Downloading Voro++ ..."
-  grabdir = fullpath(grabdir)
+  urllib.urlretrieve(url,"%s/%s.tar.gz" % (homepath,version))
-  if not os.path.isdir(grabdir): error("Grab directory does not exist")
-  urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version))
   
   print "Unpacking Voro++ tarball ..."
-  tardir = "%s/%s" % (grabdir,version)
+  if os.path.exists("%s/%s" % (homepath,version)):
-  if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir)
+    commands.getoutput("rm -rf %s/%s" % (homepath,version))
-  cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version)
+  cmd = "cd %s; tar zxvf %s.tar.gz" % (homepath,version)
-  txt = commands.getoutput(cmd)
+  commands.getoutput(cmd)
-  print tardir,grabdir,grabname
+  if os.path.basename(homedir) != version:
-  if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname))
+    if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir)
+    os.rename("%s/%s" % (homepath,version),homedir)
 
 # build Voro++
 
 if buildflag:
   print "Building Voro++ ..."
-  cmd = "cd %s; make" % builddir
+  cmd = "cd %s; make" % homedir
   txt = commands.getoutput(cmd)
   print txt
 
@@ -110,7 +112,7 @@ if linkflag:
     os.remove("includelink")
   if os.path.isfile("liblink") or os.path.islink("liblink"):
     os.remove("liblink")
-  cmd = "ln -s %s/src includelink" % linkdir
+  cmd = "ln -s %s/src includelink" % homedir
   commands.getoutput(cmd)
-  cmd = "ln -s %s/src liblink" % linkdir
+  cmd = "ln -s %s/src liblink" % homedir
   commands.getoutput(cmd)

lib/voronoi/README

@@ -6,11 +6,15 @@ The Voro++ library is available at http://math.lbl.gov/voro++ and was
 developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
 Laboratory.
 
+You can type "make lib-voronoi" from the src directory to see help on
+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.
+
 -----------------
 
-You must perform the following steps yourself, or you can use the
+Instructions:
-Install.py Python script to automate any or all steps of the process.
-Type "python Install.py" for instructions.
 
 1.  Download Voro++ at http://math.lbl.gov/voro++/download
     either as a tarball or via SVN, and unpack the

lib/vtk/Makefile.lammps

@@ -1,13 +1,12 @@
 # Settings that the LAMMPS build will import when this package library is used
-#
+
 # settings for VTK-5.8.0 on RHEL/CentOS 6.x
  vtk_SYSINC = -I/usr/include/vtk
  vtk_SYSLIB = -lvtkCommon -lvtkIO 
  vtk_SYSPATH = -L/usr/lib64/vtk
-#
+
 # settings for VTK 6.2.0 on Fedora 23
 #vtk_SYSINC = -I/usr/include/vtk
 #vtk_SYSLIB = -lvtkCommonCore -lvtkIOCore -lvtkCommonDataModel -lvtkIOXML -lvtkIOLegacy -lvtkIOParallelXML
 #vtk_SYSPATH = -L/usr/lib64/vtk
-#
 

lib/vtk/README

@@ -1,14 +1,15 @@
-The Makefile.lammps file in this directory is used when building LAMMPS with
+The Makefile.lammps file in this directory is used when building
-its USER-VTK package installed.  The file has several settings needed to
+LAMMPS with its USER-VTK package installed.  The file has several
-compile and link LAMMPS with the VTK library.  You should choose a
+settings needed to compile and link LAMMPS with the VTK library.  You
-Makefile.lammps.* file compatible with your system and your version of VTK, and
+should choose a Makefile.lammps.* file compatible with your system and
-copy it to Makefile.lammps before building LAMMPS itself.  You may need to edit
+your version of VTK, and copy it to Makefile.lammps before building
-one of the provided files to match your system.
+LAMMPS itself.  You may need to edit one of the provided files to
+match your system.
 
-If you create a new Makefile.lammps file suitable for some version of VTK on
+If you create a new Makefile.lammps file suitable for some version of
-some system, that is not a match to one of the provided Makefile.lammps.*
+VTK on some system, that is not a match to one of the provided
-files, you can send it to the developers, and we can include it in the
+Makefile.lammps.* files, you can send it to the developers, and we can
-distribution for others to use.
+include it in the distribution for others to use.
 
 To illustrate, these are example settings from the
 Makefile.lammps.ubuntu14.04_vtk6 file:
@@ -19,10 +20,11 @@ vtk_SYSPATH =
 
 vtk_SYSINC refers to the include directory of the installed VTK library
 
-vtk_SYSLIB refers to the libraries needed to link to from an application
+vtk_SYSLIB refers to the libraries needed to link to from an
-(LAMMPS in this case) to "embed" VTK in the application. VTK consists of
+application (LAMMPS in this case) to "embed" VTK in the
-multiple shared libraries which are needed when using the USER-VTK package.
+application. VTK consists of multiple shared libraries which are
+needed when using the USER-VTK package.
 
-vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK library
+vtk_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the VTK
-can be found.  You may not need this setting if the path is already included in
+library can be found.  You may not need this setting if the path is
-your LD_LIBRARY_PATH environment variable.
+already included in your LD_LIBRARY_PATH environment variable.

src/KOKKOS/pair_reax_c_kokkos.cpp

@@ -2294,12 +2294,12 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
   int numbonds = d_bo_num[i];
 
   e_lp = 0.0;
-  if (numbonds > 0)
+  if (numbonds > 0 || control->enobondsflag)
     e_lp = p_lp2 * d_Delta_lp[i] * inv_expvd2;
   const F_FLOAT dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * d_Delta_lp[i] * expvd2 * inv_expvd2*inv_expvd2;
   const F_FLOAT CElp = dElp * d_dDelta_lp[i];
 
-  if (numbonds > 0)
+  if (numbonds > 0 || control->enobondsflag)
     a_CdDelta[i] += CElp;
 
   if (eflag) ev.ereax[0] += e_lp;
@@ -2336,7 +2336,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
   const F_FLOAT inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);
 
   e_un = 0;
-  if (numbonds > 0)
+  if (numbonds > 0 || control->enobondsflag)
     e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
 
   if (eflag) ev.ereax[2] += e_un;
@@ -2356,7 +2356,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
   // multibody forces
 
   a_CdDelta[i] += CEover3;
-  if (numbonds > 0)
+  if (numbonds > 0 || control->enobondsflag)
     a_CdDelta[i] += CEunder3;
 
   const int j_start = d_bo_first[i];

src/KSPACE/pair_lj_charmmfsw_coul_long.cpp

@@ -57,6 +57,10 @@ PairLJCharmmfswCoulLong::PairLJCharmmfswCoulLong(LAMMPS *lmp) : Pair(lmp)
   implicit = 0;
   mix_flag = ARITHMETIC;
   writedata = 1;
+
+  // short-range/long-range flag accessed by DihedralCharmmfsw
+
+  dihedflag = 1;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -669,10 +673,6 @@ void PairLJCharmmfswCoulLong::settings(int narg, char **arg)
   cut_lj = force->numeric(FLERR,arg[1]);
   if (narg == 2) cut_coul = cut_lj;
   else cut_coul = force->numeric(FLERR,arg[2]);
-
-  // indicates pair_style being used for dihedral_charmm
-
-  dihedflag = 1;
 }
 
 /* ----------------------------------------------------------------------

src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp

@@ -42,6 +42,10 @@ PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
   implicit = 0;
   mix_flag = ARITHMETIC;
   writedata = 1;
+
+  // short-range/long-range flag accessed by DihedralCharmmfsw
+
+  dihedflag = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -235,10 +239,6 @@ void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg)
   } else {
     cut_coul = force->numeric(FLERR,arg[2]);
   }
-
-  // indicates pair_style being used for dihedral_charmm
-
-  dihedflag = 0;
 }
 
 /* ----------------------------------------------------------------------
@@ -535,7 +535,7 @@ void *PairLJCharmmfswCoulCharmmfsh::extract(const char *str, int &dim)
   dim = 0;
   if (strcmp(str,"implicit") == 0) return (void *) &implicit;
 
-  // info extracted by dihedral_charmmf
+  // info extracted by dihedral_charmmfsw
 
   if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
   if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner;

src/Makefile

@@ -46,39 +46,37 @@ endif
 # PACKAGE    = standard packages
 # PACKUSER   = user packagse
 # PACKLIB    = all packages that require an additional lib
+#              should be PACKSYS + PACKINT + PACKEXT
 # PACKSYS    = subset that reqiure a common system library
+#              include MPIIO and LB b/c require full MPI, not just STUBS
 # PACKINT    = subset that require an internal (provided) library
 # PACKEXT    = subset that require an external (downloaded) library
-# PACKLIB    = PACKSYS + PACKING + PACKEXT
-# PACKSCRIPT = libs under lammps/lib that have an Install.py script
 
 PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  granular kim kokkos kspace manybody mc meam misc molecule \
 	  mpiio mscg opt peri poems \
 	  python qeq reax replica rigid shock snap srd voronoi
 
-PACKUSER = user-atc user-awpmd user-cgsdk user-cgdna user-colvars \
+PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
 	   user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
 	   user-intel user-lb user-manifold user-mgpt user-misc user-molfile \
-	   user-nc-dump user-omp user-phonon user-qmmm user-qtb \
+	   user-netcdf user-omp user-phonon user-qmmm user-qtb \
 	   user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
 	   user-vtk
 
 PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
 	  python reax voronoi \
-	  user-atc user-awpmd user-colvars user-h5md user-molfile \
+	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
-	  user-nc-dump user-qmmm user-quip user-smd user-vtk
+	  user-netcdf user-qmmm user-quip user-smd user-vtk
 
-PACKSYS = compress mpiio python
+PACKSYS = compress mpiio python user-lb
 
 PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
 
 PACKEXT = kim mscg voronoi \
-	  user-h5md user-molfile user-nc-dump user-qmmm user-quip \
+	  user-h5md user-molfile user-netcdf user-qmmm user-quip \
 	  user-smd user-vtk
 
-PACKSCRIPT = voronoi
-
 PACKALL = $(PACKAGE) $(PACKUSER)
 
 PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
@@ -87,6 +85,7 @@ PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)
 YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
 NODIR  = $(shell echo $(@:no-%=%) | tr a-z A-Z)
 LIBDIR = $(shell echo $(@:lib-%=%))
+LIBUSERDIR = $(shell echo $(@:lib-user-%=%))
 
 # List of all targets
 
@@ -108,7 +107,7 @@ help:
 	@echo 'make no-standard (no-std)    remove all standard pkgs'
 	@echo 'make yes-user                install all user pkgs'
 	@echo 'make no-user                 remove all user pkgs'
-	@echo 'make yes-lib       install all pkgs with libs (incldued or ext)'
+	@echo 'make yes-lib       install all pkgs with libs (included or ext)'
 	@echo 'make no-lib        remove all pkgs with libs (included or ext)'
 	@echo 'make yes-ext                 install all pkgs with external libs'
 	@echo 'make no-ext                  remove all pkgs with external libs'
@@ -273,7 +272,7 @@ package:
 	@echo 'make package-overwrite    replace package files with src files'
 	@echo 'make package-diff (pd)    diff src files against package file'
 	@echo ''
-	@echo 'make lib-package      download/build/install a package library'
+	@echo 'make lib-package      build and/or download a package library'
 
 yes-all:
 	@for p in $(PACKALL); do $(MAKE) yes-$$p; done
@@ -338,11 +337,14 @@ no-%:
 # download/build/install a package library
 
 lib-%:
-	@if [ ! -e ../lib/$(LIBDIR)/Install.py ]; then \
+	@if [ -e ../lib/$(LIBDIR)/Install.py ]; then \
-	  echo "Install script for lib $(@:lib-%=%) does not exist"; \
+	  echo "Installing lib $(@:lib-%=%)"; \
-	else \
-	  echo "Installing lib for package $(@:lib-%=%)"; \
 	  cd ../lib/$(LIBDIR); python Install.py $(args); \
+	elif [ -e ../lib/$(LIBUSERDIR)/Install.py ]; then \
+	  echo "Installing lib $(@:lib-user-%=%)"; \
+	  cd ../lib/$(LIBUSERDIR); python Install.py $(args); \
+	else \
+	  echo "Install script for lib $(@:lib-%=%) does not exist"; \
 	fi;
 
 # status = list src files that differ from package files

src/RIGID/fix_shake.cpp

@@ -1419,12 +1419,14 @@ void FixShake::shake(int m)
   domain->minimum_image(r01);
 
   // s01 = distance vec after unconstrained update, with PBC
+  // use Domain::minimum_image_once(), not minimum_image()
+  // b/c xshake values might be huge, due to e.g. fix gcmc
 
   double s01[3];
   s01[0] = xshake[i0][0] - xshake[i1][0];
   s01[1] = xshake[i0][1] - xshake[i1][1];
   s01[2] = xshake[i0][2] - xshake[i1][2];
-  domain->minimum_image(s01);
+  domain->minimum_image_once(s01);
 
   // scalar distances between atoms
 
@@ -1526,18 +1528,20 @@ void FixShake::shake3(int m)
   domain->minimum_image(r02);
 
   // s01,s02 = distance vec after unconstrained update, with PBC
+  // use Domain::minimum_image_once(), not minimum_image()
+  // b/c xshake values might be huge, due to e.g. fix gcmc
 
   double s01[3];
   s01[0] = xshake[i0][0] - xshake[i1][0];
   s01[1] = xshake[i0][1] - xshake[i1][1];
   s01[2] = xshake[i0][2] - xshake[i1][2];
-  domain->minimum_image(s01);
+  domain->minimum_image_once(s01);
 
   double s02[3];
   s02[0] = xshake[i0][0] - xshake[i2][0];
   s02[1] = xshake[i0][1] - xshake[i2][1];
   s02[2] = xshake[i0][2] - xshake[i2][2];
-  domain->minimum_image(s02);
+  domain->minimum_image_once(s02);
 
   // scalar distances between atoms
 
@@ -1699,24 +1703,26 @@ void FixShake::shake4(int m)
   domain->minimum_image(r03);
 
   // s01,s02,s03 = distance vec after unconstrained update, with PBC
+  // use Domain::minimum_image_once(), not minimum_image()
+  // b/c xshake values might be huge, due to e.g. fix gcmc
 
   double s01[3];
   s01[0] = xshake[i0][0] - xshake[i1][0];
   s01[1] = xshake[i0][1] - xshake[i1][1];
   s01[2] = xshake[i0][2] - xshake[i1][2];
-  domain->minimum_image(s01);
+  domain->minimum_image_once(s01);
 
   double s02[3];
   s02[0] = xshake[i0][0] - xshake[i2][0];
   s02[1] = xshake[i0][1] - xshake[i2][1];
   s02[2] = xshake[i0][2] - xshake[i2][2];
-  domain->minimum_image(s02);
+  domain->minimum_image_once(s02);
 
   double s03[3];
   s03[0] = xshake[i0][0] - xshake[i3][0];
   s03[1] = xshake[i0][1] - xshake[i3][1];
   s03[2] = xshake[i0][2] - xshake[i3][2];
-  domain->minimum_image(s03);
+  domain->minimum_image_once(s03);
 
   // scalar distances between atoms
 
@@ -1941,24 +1947,26 @@ void FixShake::shake3angle(int m)
   domain->minimum_image(r12);
 
   // s01,s02,s12 = distance vec after unconstrained update, with PBC
+  // use Domain::minimum_image_once(), not minimum_image()
+  // b/c xshake values might be huge, due to e.g. fix gcmc
 
   double s01[3];
   s01[0] = xshake[i0][0] - xshake[i1][0];
   s01[1] = xshake[i0][1] - xshake[i1][1];
   s01[2] = xshake[i0][2] - xshake[i1][2];
-  domain->minimum_image(s01);
+  domain->minimum_image_once(s01);
 
   double s02[3];
   s02[0] = xshake[i0][0] - xshake[i2][0];
   s02[1] = xshake[i0][1] - xshake[i2][1];
   s02[2] = xshake[i0][2] - xshake[i2][2];
-  domain->minimum_image(s02);
+  domain->minimum_image_once(s02);
 
   double s12[3];
   s12[0] = xshake[i1][0] - xshake[i2][0];
   s12[1] = xshake[i1][1] - xshake[i2][1];
   s12[2] = xshake[i1][2] - xshake[i2][2];
-  domain->minimum_image(s12);
+  domain->minimum_image_once(s12);
 
   // scalar distances between atoms
 
@@ -2055,6 +2063,7 @@ void FixShake::shake3angle(int m)
   double quad1,quad2,quad3,b1,b2,b3,lamda01_new,lamda02_new,lamda12_new;
 
   while (!done && niter < max_iter) {
+
     quad1 = quad1_0101 * lamda01*lamda01 +
       quad1_0202 * lamda02*lamda02 +
       quad1_1212 * lamda12*lamda12 +

src/SNAP/compute_sna_atom.cpp

@@ -48,7 +48,8 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
   diagonalstyle = 0;
   rmin0 = 0.0;
   switchflag = 1;
-  bzeroflag = 0;
+  bzeroflag = 1;
+  quadraticflag = 0;
 
   // offset by 1 to match up with types
 
@@ -106,6 +107,11 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
 	error->all(FLERR,"Illegal compute sna/atom command");
       bzeroflag = atoi(arg[iarg+1]);
       iarg += 2;
+    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+      if (iarg+2 > narg)
+	error->all(FLERR,"Illegal compute sna/atom command");
+      quadraticflag = atoi(arg[iarg+1]);
+      iarg += 2;
     } else error->all(FLERR,"Illegal compute sna/atom command");
   }
 
@@ -122,8 +128,9 @@ ComputeSNAAtom::ComputeSNAAtom(LAMMPS *lmp, int narg, char **arg) :
   }
 
   ncoeff = snaptr[0]->ncoeff;
-  peratom_flag = 1;
   size_peratom_cols = ncoeff;
+  if (quadraticflag) size_peratom_cols += ncoeff*ncoeff;
+  peratom_flag = 1;
 
   nmax = 0;
   njmax = 0;
@@ -264,8 +271,16 @@ void ComputeSNAAtom::compute_peratom()
       snaptr[tid]->copy_bi2bvec();
       for (int icoeff = 0; icoeff < ncoeff; icoeff++)
 	sna[i][icoeff] = snaptr[tid]->bvec[icoeff];
+      if (quadraticflag) {
+        int ncount = ncoeff;
+        for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+          double bi = snaptr[tid]->bvec[icoeff];
+          for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++)
+            sna[i][ncount++] = bi*snaptr[tid]->bvec[jcoeff];
+        }
+      }
     } else {
-      for (int icoeff = 0; icoeff < ncoeff; icoeff++)
+      for (int icoeff = 0; icoeff < size_peratom_cols; icoeff++)
 	sna[i][icoeff] = 0.0;
     }
   }

src/SNAP/compute_sna_atom.h

@@ -44,7 +44,7 @@ class ComputeSNAAtom : public Compute {
   double *wjelem;
   class SNA** snaptr;
   double cutmax;
-
+  int quadraticflag;
 };
 
 }

src/SNAP/compute_snad_atom.cpp

@@ -48,9 +48,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
   diagonalstyle = 0;
   rmin0 = 0.0;
   switchflag = 1;
-  bzeroflag = 0;
+  bzeroflag = 1;
+  quadraticflag = 0;
   
   // process required arguments
+  
   memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
   memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
   rcutfac = atof(arg[3]);
@@ -60,11 +62,15 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
     radelem[i+1] = atof(arg[6+i]);
   for(int i = 0; i < ntypes; i++)
     wjelem[i+1] = atof(arg[6+ntypes+i]);
+
   // construct cutsq
+
   double cut;
+  cutmax = 0.0;
   memory->create(cutsq,ntypes+1,ntypes+1,"sna/atom:cutsq");
   for(int i = 1; i <= ntypes; i++) {
     cut = 2.0*radelem[i]*rcutfac;
+    if (cut > cutmax) cutmax = cut;
     cutsq[i][i] = cut*cut;
     for(int j = i+1; j <= ntypes; j++) {
       cut = (radelem[i]+radelem[j])*rcutfac;
@@ -94,6 +100,11 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
 	error->all(FLERR,"Illegal compute snad/atom command");
       switchflag = atoi(arg[iarg+1]);
       iarg += 2;
+    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+      if (iarg+2 > narg)
+	error->all(FLERR,"Illegal compute snad/atom command");
+      quadraticflag = atoi(arg[iarg+1]);
+      iarg += 2;
     } else error->all(FLERR,"Illegal compute snad/atom command");
   }
 
@@ -110,9 +121,19 @@ ComputeSNADAtom::ComputeSNADAtom(LAMMPS *lmp, int narg, char **arg) :
   }
 
   ncoeff = snaptr[0]->ncoeff;
-  peratom_flag = 1;
+  twoncoeff = 2*ncoeff;
-  size_peratom_cols = 3*ncoeff*atom->ntypes;
+  threencoeff = 3*ncoeff;
+  size_peratom_cols = threencoeff*atom->ntypes;
+  if (quadraticflag) {
+    ncoeffsq = ncoeff*ncoeff;
+    twoncoeffsq = 2*ncoeffsq;
+    threencoeffsq = 3*ncoeffsq;
+    size_peratom_cols +=
+      threencoeffsq*atom->ntypes;
+  }
   comm_reverse = size_peratom_cols;
+  peratom_flag = 1;
+
   nmax = 0;
   njmax = 0;
   snad = NULL;
@@ -136,10 +157,9 @@ void ComputeSNADAtom::init()
 {
   if (force->pair == NULL)
     error->all(FLERR,"Compute snad/atom requires a pair style be defined");
-  // TODO: Not sure what to do with this error check since cutoff radius is not
+
-  // a single number
+  if (cutmax > force->pair->cutforce)
-  //if (sqrt(cutsq) > force->pair->cutforce)
+    error->all(FLERR,"Compute sna/atom cutoff is longer than pairwise cutoff");
-    //error->all(FLERR,"Compute snad/atom cutoff is longer than pairwise cutoff");
 
   // need an occasional full neighbor list
 
@@ -228,7 +248,9 @@ void ComputeSNADAtom::compute_peratom()
       const int* const jlist = firstneigh[i];
       const int jnum = numneigh[i];
 
-      const int typeoffset = 3*ncoeff*(atom->type[i]-1);
+      const int typeoffset = threencoeff*(atom->type[i]-1);
+      const int quadraticoffset = threencoeff*atom->ntypes +
+        threencoeffsq*(atom->type[i]-1);
 
       // insure rij, inside, and typej  are of size jnum
 
@@ -262,6 +284,10 @@ void ComputeSNADAtom::compute_peratom()
 
       snaptr[tid]->compute_ui(ninside);
       snaptr[tid]->compute_zi();
+      if (quadraticflag) {
+        snaptr[tid]->compute_bi();
+        snaptr[tid]->copy_bi2bvec();
+      }
       
       for (int jj = 0; jj < ninside; jj++) {
 	const int j = snaptr[tid]->inside[jj];
@@ -279,10 +305,37 @@ void ComputeSNADAtom::compute_peratom()
 	for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
 	  snadi[icoeff] += snaptr[tid]->dbvec[icoeff][0];
 	  snadi[icoeff+ncoeff] += snaptr[tid]->dbvec[icoeff][1];
-	  snadi[icoeff+2*ncoeff] += snaptr[tid]->dbvec[icoeff][2];
+	  snadi[icoeff+twoncoeff] += snaptr[tid]->dbvec[icoeff][2];
 	  snadj[icoeff] -= snaptr[tid]->dbvec[icoeff][0];
 	  snadj[icoeff+ncoeff] -= snaptr[tid]->dbvec[icoeff][1];
-	  snadj[icoeff+2*ncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+	  snadj[icoeff+twoncoeff] -= snaptr[tid]->dbvec[icoeff][2];
+	}
+
+        if (quadraticflag) {
+          double *snadi = snad[i]+quadraticoffset;
+          double *snadj = snad[j]+quadraticoffset;
+          int ncount = 0;
+          for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+            double bi = snaptr[tid]->bvec[icoeff];
+            double bix = snaptr[tid]->dbvec[icoeff][0];
+            double biy = snaptr[tid]->dbvec[icoeff][1];
+            double biz = snaptr[tid]->dbvec[icoeff][2];
+            for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++) {
+              double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+                + bix*snaptr[tid]->bvec[jcoeff];
+              double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+                + biy*snaptr[tid]->bvec[jcoeff];
+              double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+                + biz*snaptr[tid]->bvec[jcoeff];
+              snadi[ncount] += dbxtmp;
+              snadi[ncount+ncoeffsq] += dbytmp;
+              snadi[ncount+twoncoeffsq] += dbztmp;
+              snadj[ncount] -= dbxtmp;
+              snadj[ncount+ncoeffsq] -= dbytmp;
+              snadj[ncount+twoncoeffsq] -= dbztmp;
+              ncount++;
+            }
+          }
         }
       }
     }
@@ -331,7 +384,8 @@ double ComputeSNADAtom::memory_usage()
   double bytes = nmax*size_peratom_cols * sizeof(double);
   bytes += 3*njmax*sizeof(double);
   bytes += njmax*sizeof(int);
-  bytes += ncoeff*3;
+  bytes += threencoeff*atom->ntypes;
+  if (quadraticflag) bytes += threencoeffsq*atom->ntypes;
   bytes += snaptr[0]->memory_usage()*comm->nthreads;
   return bytes;
 }

src/SNAP/compute_snad_atom.h

@@ -37,7 +37,7 @@ class ComputeSNADAtom : public Compute {
 
  private:
   int nmax, njmax, diagonalstyle;
-  int ncoeff;
+  int ncoeff, twoncoeff, threencoeff, ncoeffsq, twoncoeffsq, threencoeffsq;
   double **cutsq;
   class NeighList *list;
   double **snad;
@@ -45,7 +45,8 @@ class ComputeSNADAtom : public Compute {
   double *radelem;
   double *wjelem;
   class SNA** snaptr;
-
+  double cutmax;
+  int quadraticflag;
 };
 
 }

src/SNAP/compute_snav_atom.cpp

@@ -38,8 +38,6 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
   radelem = NULL;
   wjelem = NULL;
 
-  nvirial = 6;
-
   int ntypes = atom->ntypes;
   int nargmin = 6+2*ntypes;
 
@@ -50,9 +48,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
   diagonalstyle = 0;
   rmin0 = 0.0;
   switchflag = 1;
-  bzeroflag = 0;
+  bzeroflag = 1;
+  quadraticflag = 0;
 
   // process required arguments
+  
   memory->create(radelem,ntypes+1,"sna/atom:radelem"); // offset by 1 to match up with types
   memory->create(wjelem,ntypes+1,"sna/atom:wjelem");
   rcutfac = atof(arg[3]);
@@ -96,6 +96,11 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
 	error->all(FLERR,"Illegal compute snav/atom command");
       switchflag = atoi(arg[iarg+1]);
       iarg += 2;
+    } else if (strcmp(arg[iarg],"quadraticflag") == 0) {
+      if (iarg+2 > narg)
+	error->all(FLERR,"Illegal compute snav/atom command");
+      quadraticflag = atoi(arg[iarg+1]);
+      iarg += 2;
     } else error->all(FLERR,"Illegal compute snav/atom command");
   }
 
@@ -112,9 +117,24 @@ ComputeSNAVAtom::ComputeSNAVAtom(LAMMPS *lmp, int narg, char **arg) :
   }
 
   ncoeff = snaptr[0]->ncoeff;
-  peratom_flag = 1;
+  twoncoeff = 2*ncoeff;
-  size_peratom_cols = nvirial*ncoeff*atom->ntypes;
+  threencoeff = 3*ncoeff;
+  fourncoeff = 4*ncoeff;
+  fivencoeff = 5*ncoeff;
+  sixncoeff = 6*ncoeff;
+  size_peratom_cols = sixncoeff*atom->ntypes;
+  if (quadraticflag) {
+    ncoeffsq = ncoeff*ncoeff;
+    twoncoeffsq = 2*ncoeffsq;
+    threencoeffsq = 3*ncoeffsq;
+    fourncoeffsq = 4*ncoeffsq;
+    fivencoeffsq = 5*ncoeffsq;
+    sixncoeffsq = 6*ncoeffsq;
+    size_peratom_cols +=
+      sixncoeffsq*atom->ntypes;
+  }
   comm_reverse = size_peratom_cols;
+  peratom_flag = 1;
 
   nmax = 0;
   njmax = 0;
@@ -231,7 +251,9 @@ void ComputeSNAVAtom::compute_peratom()
       const int* const jlist = firstneigh[i];
       const int jnum = numneigh[i];
 
-      const int typeoffset = nvirial*ncoeff*(atom->type[i]-1);
+      const int typeoffset = sixncoeff*(atom->type[i]-1);
+      const int quadraticoffset = sixncoeff*atom->ntypes +
+        sixncoeffsq*(atom->type[i]-1);
 
       // insure rij, inside, and typej  are of size jnum
 
@@ -265,6 +287,10 @@ void ComputeSNAVAtom::compute_peratom()
 
       snaptr[tid]->compute_ui(ninside);
       snaptr[tid]->compute_zi();
+      if (quadraticflag) {
+        snaptr[tid]->compute_bi();
+        snaptr[tid]->copy_bi2bvec();
+      }
 
       for (int jj = 0; jj < ninside; jj++) {
 	const int j = snaptr[tid]->inside[jj];
@@ -283,16 +309,49 @@ void ComputeSNAVAtom::compute_peratom()
 	for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
 	  snavi[icoeff]             += snaptr[tid]->dbvec[icoeff][0]*xtmp;
 	  snavi[icoeff+ncoeff]      += snaptr[tid]->dbvec[icoeff][1]*ytmp;
-	  snavi[icoeff+2*ncoeff] += snaptr[tid]->dbvec[icoeff][2]*ztmp;
+	  snavi[icoeff+twoncoeff]   += snaptr[tid]->dbvec[icoeff][2]*ztmp;
-	  snavi[icoeff+3*ncoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
+	  snavi[icoeff+threencoeff] += snaptr[tid]->dbvec[icoeff][1]*ztmp;
-	  snavi[icoeff+4*ncoeff] += snaptr[tid]->dbvec[icoeff][0]*ztmp;
+	  snavi[icoeff+fourncoeff]  += snaptr[tid]->dbvec[icoeff][0]*ztmp;
-	  snavi[icoeff+5*ncoeff] += snaptr[tid]->dbvec[icoeff][0]*ytmp;
+	  snavi[icoeff+fivencoeff]  += snaptr[tid]->dbvec[icoeff][0]*ytmp;
 	  snavj[icoeff]             -= snaptr[tid]->dbvec[icoeff][0]*x[j][0];
 	  snavj[icoeff+ncoeff]      -= snaptr[tid]->dbvec[icoeff][1]*x[j][1];
-	  snavj[icoeff+2*ncoeff] -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
+	  snavj[icoeff+twoncoeff]   -= snaptr[tid]->dbvec[icoeff][2]*x[j][2];
-	  snavj[icoeff+3*ncoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
+	  snavj[icoeff+threencoeff] -= snaptr[tid]->dbvec[icoeff][1]*x[j][2];
-	  snavj[icoeff+4*ncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
+	  snavj[icoeff+fourncoeff]  -= snaptr[tid]->dbvec[icoeff][0]*x[j][2];
-	  snavj[icoeff+5*ncoeff] -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+	  snavj[icoeff+fivencoeff]  -= snaptr[tid]->dbvec[icoeff][0]*x[j][1];
+	}
+
+        if (quadraticflag) {
+          double *snavi = snav[i]+quadraticoffset;
+          double *snavj = snav[j]+quadraticoffset;
+          int ncount = 0;
+          for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
+            double bi = snaptr[tid]->bvec[icoeff];
+            double bix = snaptr[tid]->dbvec[icoeff][0];
+            double biy = snaptr[tid]->dbvec[icoeff][1];
+            double biz = snaptr[tid]->dbvec[icoeff][2];
+            for (int jcoeff = 0; jcoeff < ncoeff; jcoeff++) {
+              double dbxtmp = bi*snaptr[tid]->dbvec[jcoeff][0]
+                + bix*snaptr[tid]->bvec[jcoeff];
+              double dbytmp = bi*snaptr[tid]->dbvec[jcoeff][1]
+                + biy*snaptr[tid]->bvec[jcoeff];
+              double dbztmp = bi*snaptr[tid]->dbvec[jcoeff][2]
+                + biz*snaptr[tid]->bvec[jcoeff];
+              snavi[ncount] +=               dbxtmp*xtmp;
+              snavi[ncount+ncoeffsq] +=      dbytmp*ytmp;
+              snavi[ncount+twoncoeffsq] +=   dbztmp*ztmp;
+              snavi[ncount+threencoeffsq] += dbytmp*ztmp;
+              snavi[ncount+fourncoeffsq] +=  dbxtmp*ztmp;
+              snavi[ncount+fivencoeffsq] +=  dbxtmp*ytmp;
+              snavj[ncount] -=               dbxtmp*x[j][0];
+              snavj[ncount+ncoeffsq] -=      dbytmp*x[j][1];
+              snavj[ncount+twoncoeffsq] -=   dbztmp*x[j][2];
+              snavj[ncount+threencoeffsq] -= dbytmp*x[j][2];
+              snavj[ncount+fourncoeffsq] -=  dbxtmp*x[j][2];
+              snavj[ncount+fivencoeffsq] -=  dbxtmp*x[j][1];
+              ncount++;
+            }
+          }
         }
       }
     }
@@ -341,7 +400,8 @@ double ComputeSNAVAtom::memory_usage()
   double bytes = nmax*size_peratom_cols * sizeof(double);
   bytes += 3*njmax*sizeof(double);
   bytes += njmax*sizeof(int);
-  bytes += ncoeff*nvirial;
+  bytes += sixncoeff*atom->ntypes;
+  if (quadraticflag) bytes += sixncoeffsq*atom->ntypes;
   bytes += snaptr[0]->memory_usage()*comm->nthreads;
   return bytes;
 }

src/SNAP/compute_snav_atom.h

@@ -37,16 +37,17 @@ class ComputeSNAVAtom : public Compute {
 
  private:
   int nmax, njmax, diagonalstyle;
-  int ncoeff,nvirial;
+  int ncoeff, twoncoeff, threencoeff, fourncoeff, fivencoeff, sixncoeff;
+  int ncoeffsq, twoncoeffsq, threencoeffsq, fourncoeffsq, fivencoeffsq, sixncoeffsq;
   double **cutsq;
   class NeighList *list;
   double **snav;
   double rcutfac;
   double *radelem;
   double *wjelem;
-
   class SNA** snaptr;
-
+  double cutmax;
+  int quadraticflag;
 };
 
 }

src/SNAP/pair_snap.cpp

@@ -1635,7 +1635,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
   rmin0 = 0.0;
   diagonalstyle = 3;
   switchflag = 1;
-  bzeroflag = 0;
+  bzeroflag = 1;
+  
   // open SNAP parameter file on proc 0
 
   FILE *fpparam;

src/USER-NETCDF/README

@@ -1,7 +1,7 @@
-USER-NC-DUMP
+USER-NETCDF
 ============
 
-This package provides the nc and (optionally) the nc/mpiio dump styles.
+This package provides the netcf and netcdf/mpiio dump styles.
 See the doc page for dump nc or dump nc/mpiio command for how to use them.
 Compiling these dump styles requires having the netCDF library installed
 on your system. See lib/netcdf/README for additional details.

src/USER-NETCDF/dump_netcdf.cpp

@@ -32,14 +32,14 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
+
 #if defined(LMP_HAS_NETCDF)
 
 #include <unistd.h>
 #include <stdlib.h>
 #include <string.h>
-
 #include <netcdf.h>
-
+#include "dump_netcdf.h"
 #include "atom.h"
 #include "comm.h"
 #include "compute.h"
@@ -56,8 +56,6 @@
 #include "variable.h"
 #include "force.h"
 
-#include "dump_nc.h"
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
@@ -91,7 +89,7 @@ const int THIS_IS_A_BIGINT   = -4;
 
 /* ---------------------------------------------------------------------- */
 
-DumpNC::DumpNC(LAMMPS *lmp, int narg, char **arg) :
+DumpNetCDF::DumpNetCDF(LAMMPS *lmp, int narg, char **arg) :
   DumpCustom(lmp, narg, arg)
 {
   // arrays for data rearrangement
@@ -224,7 +222,7 @@ DumpNC::DumpNC(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-DumpNC::~DumpNC()
+DumpNetCDF::~DumpNetCDF()
 {
   closefile();
 
@@ -238,7 +236,7 @@ DumpNC::~DumpNC()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::openfile()
+void DumpNetCDF::openfile()
 {
   // now the computes and fixes have been initialized, so we can query
   // for the size of vector quantities
@@ -594,12 +592,12 @@ void DumpNC::openfile()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::closefile()
+void DumpNetCDF::closefile()
 {
   if (filewriter && singlefile_opened) {
     NCERR( nc_close(ncid) );
     singlefile_opened = 0;
-    // append next time DumpNC::openfile is called
+    // append next time DumpNetCDF::openfile is called
     append_flag = 1;
     // write to next frame upon next open
     framei++;
@@ -608,7 +606,7 @@ void DumpNC::closefile()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::write()
+void DumpNetCDF::write()
 {
   // open file
 
@@ -678,7 +676,7 @@ void DumpNC::write()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::write_header(bigint n)
+void DumpNetCDF::write_header(bigint n)
 {
   size_t start[2];
 
@@ -753,7 +751,7 @@ void DumpNC::write_header(bigint n)
    write head of block (mass & element name) only if has atoms of the type
 ------------------------------------------------------------------------- */
 
-void DumpNC::write_data(int n, double *mybuf)
+void DumpNetCDF::write_data(int n, double *mybuf)
 {
   size_t start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
   ptrdiff_t stride[NC_MAX_VAR_DIMS];
@@ -761,18 +759,17 @@ void DumpNC::write_data(int n, double *mybuf)
   if (!int_buffer) {
     n_buffer = n;
     int_buffer = (int *)
-      memory->smalloc(n*sizeof(int), "DumpNC::int_buffer");
+      memory->smalloc(n*sizeof(int),"dump::int_buffer");
     double_buffer = (double *)
-      memory->smalloc(n*sizeof(double), "DumpNC::double_buffer");
+      memory->smalloc(n*sizeof(double),"dump::double_buffer");
   }
 
   if (n > n_buffer) {
     n_buffer = n;
     int_buffer = (int *)
-      memory->srealloc(int_buffer, n*sizeof(int), "DumpNC::int_buffer");
+      memory->srealloc(int_buffer, n*sizeof(int),"dump::int_buffer");
     double_buffer = (double *)
-      memory->srealloc(double_buffer, n*sizeof(double),
+      memory->srealloc(double_buffer, n*sizeof(double),"dump::double_buffer");
-                       "DumpNC::double_buffer");
   }
 
   start[0] = framei-1;
@@ -887,7 +884,7 @@ void DumpNC::write_data(int n, double *mybuf)
 
 /* ---------------------------------------------------------------------- */
 
-int DumpNC::modify_param(int narg, char **arg)
+int DumpNetCDF::modify_param(int narg, char **arg)
 {
   int iarg = 0;
   if (strcmp(arg[iarg],"double") == 0) {
@@ -925,17 +922,17 @@ int DumpNC::modify_param(int narg, char **arg)
 
       if (!strcmp(arg[iarg],"step")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNC::compute_step;
+        perframe[i].compute = &DumpNetCDF::compute_step;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else if (!strcmp(arg[iarg],"elapsed")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNC::compute_elapsed;
+        perframe[i].compute = &DumpNetCDF::compute_elapsed;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else if (!strcmp(arg[iarg],"elaplong")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNC::compute_elapsed_long;
+        perframe[i].compute = &DumpNetCDF::compute_elapsed_long;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else {
@@ -1036,7 +1033,7 @@ int DumpNC::modify_param(int narg, char **arg)
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::write_prmtop()
+void DumpNetCDF::write_prmtop()
 {
   char fn[1024];
   char tmp[81];
@@ -1098,7 +1095,7 @@ void DumpNC::write_prmtop()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::ncerr(int err, const char *descr, int line)
+void DumpNetCDF::ncerr(int err, const char *descr, int line)
 {
   if (err != NC_NOERR) {
     char errstr[1024];
@@ -1122,21 +1119,21 @@ void DumpNC::ncerr(int err, const char *descr, int line)
    customize a new keyword by adding a method
 ------------------------------------------------------------------------- */
 
-void DumpNC::compute_step(void *r)
+void DumpNetCDF::compute_step(void *r)
 {
   *((bigint *) r) = update->ntimestep;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::compute_elapsed(void *r)
+void DumpNetCDF::compute_elapsed(void *r)
 {
   *((bigint *) r) = update->ntimestep - update->firststep;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNC::compute_elapsed_long(void *r)
+void DumpNetCDF::compute_elapsed_long(void *r)
 {
   *((bigint *) r) = update->ntimestep - update->beginstep;
 }

src/USER-NETCDF/dump_netcdf.h

@@ -32,16 +32,17 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
+
 #if defined(LMP_HAS_NETCDF)
 
 #ifdef DUMP_CLASS
 
-DumpStyle(nc,DumpNC)
+DumpStyle(netcdf,DumpNetCDF)
 
 #else
 
-#ifndef LMP_DUMP_NC_H
+#ifndef LMP_DUMP_NETCDF_H
-#define LMP_DUMP_NC_H
+#define LMP_DUMP_NETCDFC_H
 
 #include "dump_custom.h"
 
@@ -50,10 +51,10 @@ namespace LAMMPS_NS {
 const int NC_FIELD_NAME_MAX = 100;
 const int DUMP_NC_MAX_DIMS  = 100;
 
-class DumpNC : public DumpCustom {
+class DumpNetCDF : public DumpCustom {
  public:
-  DumpNC(class LAMMPS *, int, char **);
+  DumpNetCDF(class LAMMPS *, int, char **);
-  virtual ~DumpNC();
+  virtual ~DumpNetCDF();
   virtual void write();
 
  private:
@@ -68,7 +69,7 @@ class DumpNC : public DumpCustom {
     int ndumped;                  // number of enties written for this prop.
   };
 
-  typedef void (DumpNC::*funcptr_t)(void *);
+  typedef void (DumpNetCDF::*funcptr_t)(void *);
 
   // per-frame quantities (variables, fixes or computes)
   struct nc_perframe_t {

src/USER-NETCDF/dump_netcdf_mpiio.cpp

@@ -32,14 +32,14 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
+
 #if defined(LMP_HAS_PNETCDF)
 
 #include <unistd.h>
 #include <stdlib.h>
 #include <string.h>
-
 #include <pnetcdf.h>
-
+#include "dump_netcdf_mpiio.h"
 #include "atom.h"
 #include "comm.h"
 #include "compute.h"
@@ -56,8 +56,6 @@
 #include "variable.h"
 #include "force.h"
 
-#include "dump_nc_mpiio.h"
-
 using namespace LAMMPS_NS;
 using namespace MathConst;
 
@@ -91,7 +89,7 @@ const int THIS_IS_A_BIGINT   = -4;
 
 /* ---------------------------------------------------------------------- */
 
-DumpNCMPIIO::DumpNCMPIIO(LAMMPS *lmp, int narg, char **arg) :
+DumpNetCDFMPIIO::DumpNetCDFMPIIO(LAMMPS *lmp, int narg, char **arg) :
   DumpCustom(lmp, narg, arg)
 {
   // arrays for data rearrangement
@@ -217,7 +215,7 @@ DumpNCMPIIO::DumpNCMPIIO(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-DumpNCMPIIO::~DumpNCMPIIO()
+DumpNetCDFMPIIO::~DumpNetCDFMPIIO()
 {
   closefile();
 
@@ -231,7 +229,7 @@ DumpNCMPIIO::~DumpNCMPIIO()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::openfile()
+void DumpNetCDFMPIIO::openfile()
 {
   // now the computes and fixes have been initialized, so we can query
   // for the size of vector quantities
@@ -570,12 +568,12 @@ void DumpNCMPIIO::openfile()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::closefile()
+void DumpNetCDFMPIIO::closefile()
 {
   if (singlefile_opened) {
     NCERR( ncmpi_close(ncid) );
     singlefile_opened = 0;
-    // append next time DumpNCMPIIO::openfile is called
+    // append next time DumpNetCDFMPIIO::openfile is called
     append_flag = 1;
     // write to next frame upon next open
     framei++;
@@ -584,7 +582,7 @@ void DumpNCMPIIO::closefile()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::write()
+void DumpNetCDFMPIIO::write()
 {
   // open file
 
@@ -687,7 +685,7 @@ void DumpNCMPIIO::write()
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::write_time_and_cell()
+void DumpNetCDFMPIIO::write_time_and_cell()
 {
   MPI_Offset start[2];
 
@@ -759,7 +757,7 @@ void DumpNCMPIIO::write_time_and_cell()
    write head of block (mass & element name) only if has atoms of the type
 ------------------------------------------------------------------------- */
 
-void DumpNCMPIIO::write_data(int n, double *mybuf)
+void DumpNetCDFMPIIO::write_data(int n, double *mybuf)
 {
   MPI_Offset start[NC_MAX_VAR_DIMS], count[NC_MAX_VAR_DIMS];
   MPI_Offset stride[NC_MAX_VAR_DIMS];
@@ -767,19 +765,18 @@ void DumpNCMPIIO::write_data(int n, double *mybuf)
   if (!int_buffer) {
     n_buffer = std::max(1, n);
     int_buffer = (int *)
-      memory->smalloc(n_buffer*sizeof(int), "DumpNCMPIIO::int_buffer");
+      memory->smalloc(n_buffer*sizeof(int),"dump::int_buffer");
     double_buffer = (double *)
-      memory->smalloc(n_buffer*sizeof(double), "DumpNCMPIIO::double_buffer");
+      memory->smalloc(n_buffer*sizeof(double),"dump::double_buffer");
   }
 
   if (n > n_buffer) {
     n_buffer = std::max(1, n);
     int_buffer = (int *)
-      memory->srealloc(int_buffer, n_buffer*sizeof(int),
+      memory->srealloc(int_buffer, n_buffer*sizeof(int),"dump::int_buffer");
-                       "DumpNCMPIIO::int_buffer");
     double_buffer = (double *)
       memory->srealloc(double_buffer, n_buffer*sizeof(double),
-                       "DumpNCMPIIO::double_buffer");
+                       "dump::double_buffer");
   }
 
   start[0] = framei-1;
@@ -882,7 +879,7 @@ void DumpNCMPIIO::write_data(int n, double *mybuf)
 
 /* ---------------------------------------------------------------------- */
 
-int DumpNCMPIIO::modify_param(int narg, char **arg)
+int DumpNetCDFMPIIO::modify_param(int narg, char **arg)
 {
   int iarg = 0;
   if (strcmp(arg[iarg],"double") == 0) {
@@ -920,17 +917,17 @@ int DumpNCMPIIO::modify_param(int narg, char **arg)
 
       if (!strcmp(arg[iarg],"step")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNCMPIIO::compute_step;
+        perframe[i].compute = &DumpNetCDFMPIIO::compute_step;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else if (!strcmp(arg[iarg],"elapsed")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNCMPIIO::compute_elapsed;
+        perframe[i].compute = &DumpNetCDFMPIIO::compute_elapsed;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else if (!strcmp(arg[iarg],"elaplong")) {
         perframe[i].type = THIS_IS_A_BIGINT;
-        perframe[i].compute = &DumpNCMPIIO::compute_elapsed_long;
+        perframe[i].compute = &DumpNetCDFMPIIO::compute_elapsed_long;
         strcpy(perframe[i].name, arg[iarg]);
       }
       else {
@@ -1031,7 +1028,7 @@ int DumpNCMPIIO::modify_param(int narg, char **arg)
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::ncerr(int err, const char *descr, int line)
+void DumpNetCDFMPIIO::ncerr(int err, const char *descr, int line)
 {
   if (err != NC_NOERR) {
     char errstr[1024];
@@ -1055,21 +1052,21 @@ void DumpNCMPIIO::ncerr(int err, const char *descr, int line)
    customize a new keyword by adding a method
 ------------------------------------------------------------------------- */
 
-void DumpNCMPIIO::compute_step(void *r)
+void DumpNetCDFMPIIO::compute_step(void *r)
 {
   *((bigint *) r) = update->ntimestep;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::compute_elapsed(void *r)
+void DumpNetCDFMPIIO::compute_elapsed(void *r)
 {
   *((bigint *) r) = update->ntimestep - update->firststep;
 }
 
 /* ---------------------------------------------------------------------- */
 
-void DumpNCMPIIO::compute_elapsed_long(void *r)
+void DumpNetCDFMPIIO::compute_elapsed_long(void *r)
 {
   *((bigint *) r) = update->ntimestep - update->beginstep;
 }

src/USER-NETCDF/dump_netcdf_mpiio.h

@@ -32,16 +32,17 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
+
 #if defined(LMP_HAS_PNETCDF)
 
 #ifdef DUMP_CLASS
 
-DumpStyle(nc/mpiio,DumpNCMPIIO)
+DumpStyle(netcdf/mpiio,DumpNetCDFMPIIO)
 
 #else
 
-#ifndef LMP_DUMP_NC_MPIIO_H
+#ifndef LMP_DUMP_NETCDF_MPIIO_H
-#define LMP_DUMP_NC_MPIIO_H
+#define LMP_DUMP_NETCDF_MPIIO_H
 
 #include "dump_custom.h"
 
@@ -50,10 +51,10 @@ namespace LAMMPS_NS {
 const int NC_MPIIO_FIELD_NAME_MAX = 100;
 const int DUMP_NC_MPIIO_MAX_DIMS  = 100;
 
-class DumpNCMPIIO : public DumpCustom {
+class DumpNetCDFMPIIO : public DumpCustom {
  public:
-  DumpNCMPIIO(class LAMMPS *, int, char **);
+  DumpNetCDFMPIIO(class LAMMPS *, int, char **);
-  virtual ~DumpNCMPIIO();
+  virtual ~DumpNetCDFMPIIO();
   virtual void write();
 
  private:

src/USER-REAXC/compute_spec_atom.cpp

@@ -24,7 +24,7 @@
 
 #include "reaxc_defs.h"
 #include "reaxc_types.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 
 using namespace LAMMPS_NS;
 
@@ -71,7 +71,7 @@ ComputeSpecAtom::ComputeSpecAtom(LAMMPS *lmp, int narg, char **arg) :
     } else if (strcmp(arg[iarg],"vz") == 0) {
       pack_choice[i] = &ComputeSpecAtom::pack_vz;
 
-    // from pair_reax_c
+    // from pair_reaxc
     } else if (strcmp(arg[iarg],"abo01") == 0) {
       pack_choice[i] = &ComputeSpecAtom::pack_abo01;
     } else if (strcmp(arg[iarg],"abo02") == 0) {

src/USER-REAXC/fix_qeq_reax.cpp

@@ -23,7 +23,7 @@
 #include <stdlib.h>
 #include <string.h>
 #include "fix_qeq_reax.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "atom.h"
 #include "comm.h"
 #include "domain.h"

src/USER-REAXC/fix_reaxc.cpp

@@ -21,7 +21,7 @@
    Algorithmic Techniques", Parallel Computing, in press.
 ------------------------------------------------------------------------- */
 
-#include "fix_reax_c.h"
+#include "fix_reaxc.h"
 #include "atom.h"
 #include "pair.h"
 #include "comm.h"

src/USER-REAXC/fix_reaxc_bonds.cpp

@@ -21,7 +21,7 @@
 #include "fix_reaxc_bonds.h"
 #include "atom.h"
 #include "update.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "neigh_list.h"

src/USER-REAXC/fix_reaxc_species.cpp

@@ -24,7 +24,7 @@
 #include "fix_reaxc_species.h"
 #include "domain.h"
 #include "update.h"
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "modify.h"
 #include "neighbor.h"
 #include "neigh_list.h"

src/USER-REAXC/fix_reaxc_species.h

@@ -23,7 +23,7 @@ FixStyle(reax/c/species,FixReaxCSpecies)
 #include "fix.h"
 #include "pointers.h"
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_types.h"
 #include "reaxc_defs.h"
 

src/USER-REAXC/pair_reaxc.cpp

@@ -20,7 +20,7 @@
    Hybrid and hybrid/overlay compatibility added by Ray Shan (Sandia)
 ------------------------------------------------------------------------- */
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "atom.h"
 #include "update.h"
 #include "force.h"
@@ -30,7 +30,7 @@
 #include "neigh_request.h"
 #include "modify.h"
 #include "fix.h"
-#include "fix_reax_c.h"
+#include "fix_reaxc.h"
 #include "citeme.h"
 #include "memory.h"
 #include "error.h"
@@ -223,6 +223,7 @@ void PairReaxC::settings(int narg, char **arg)
 
   qeqflag = 1;
   control->lgflag = 0;
+  control->enobondsflag = 1;
   system->mincap = MIN_CAP;
   system->safezone = SAFE_ZONE;
   system->saferzone = SAFER_ZONE;
@@ -238,6 +239,12 @@ void PairReaxC::settings(int narg, char **arg)
       else if (strcmp(arg[iarg+1],"no") == 0) qeqflag = 0;
       else error->all(FLERR,"Illegal pair_style reax/c command");
       iarg += 2;
+    } else if (strcmp(arg[iarg],"enobonds") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
+      if (strcmp(arg[iarg+1],"yes") == 0) control->enobondsflag = 1;
+      else if (strcmp(arg[iarg+1],"no") == 0) control->enobondsflag = 0;
+      else error->all(FLERR,"Illegal pair_style reax/c command");
+      iarg += 2;
   } else if (strcmp(arg[iarg],"lgvdw") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal pair_style reax/c command");
       if (strcmp(arg[iarg+1],"yes") == 0) control->lgflag = 1;

src/USER-REAXC/reaxc_allocate.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_allocate.h"
 #include "reaxc_list.h"
 #include "reaxc_reset_tools.h"

src/USER-REAXC/reaxc_bond_orders.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_types.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"

src/USER-REAXC/reaxc_bonds.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_bonds.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"

src/USER-REAXC/reaxc_control.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_control.h"
 #include "reaxc_tool_box.h"
 

src/USER-REAXC/reaxc_defs.h

@@ -116,8 +116,8 @@
 
 #define MAX_BOND 20
 
-#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reax_c.cpp */
+#define MAXREAXBOND 24 /* used in fix_reaxc_bonds.cpp and pair_reaxc.cpp */
-#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reax_c.cpp */
+#define MAXSPECBOND 24 /* used in fix_reaxc_species.cpp and pair_reaxc.cpp */
 
 /******************* ENUMERATIONS *************************/
 enum geo_formats { CUSTOM, PDB, ASCII_RESTART, BINARY_RESTART, GF_N };

src/USER-REAXC/reaxc_ffield.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "error.h"
 #include "reaxc_ffield.h"
 #include "reaxc_tool_box.h"

src/USER-REAXC/reaxc_forces.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_forces.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_bonds.h"

src/USER-REAXC/reaxc_hydrogen_bonds.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_hydrogen_bonds.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"

src/USER-REAXC/reaxc_init_md.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_init_md.h"
 #include "reaxc_allocate.h"
 #include "reaxc_forces.h"

src/USER-REAXC/reaxc_io_tools.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "update.h"
 #include "reaxc_io_tools.h"
 #include "reaxc_list.h"

src/USER-REAXC/reaxc_list.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_list.h"
 #include "reaxc_tool_box.h"
 

src/USER-REAXC/reaxc_lookup.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_lookup.h"
 #include "reaxc_nonbonded.h"
 #include "reaxc_tool_box.h"

src/USER-REAXC/reaxc_multi_body.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_multi_body.h"
 #include "reaxc_bond_orders.h"
 #include "reaxc_list.h"
@@ -79,7 +79,7 @@ void Atom_Energy( reax_system *system, control_params *control,
       numbonds ++;
 
     /* calculate the energy */
-    if (numbonds > 0)
+    if (numbonds > 0 || control->enobondsflag)
       data->my_en.e_lp += e_lp =
         p_lp2 * workspace->Delta_lp[i] * inv_expvd2;
 
@@ -87,7 +87,8 @@ void Atom_Energy( reax_system *system, control_params *control,
       75 * p_lp2 * workspace->Delta_lp[i] * expvd2 * SQR(inv_expvd2);
     CElp = dElp * workspace->dDelta_lp[i];
 
-    if (numbonds > 0) workspace->CdDelta[i] += CElp;  // lp - 1st term
+    if (numbonds > 0 || control->enobondsflag)
+      workspace->CdDelta[i] += CElp;  // lp - 1st term
 
     /* tally into per-atom energy */
     if( system->pair_ptr->evflag)
@@ -187,7 +188,7 @@ void Atom_Energy( reax_system *system, control_params *control,
     for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj )
       numbonds ++;
 
-    if (numbonds > 0)
+    if (numbonds > 0 || control->enobondsflag)
       data->my_en.e_un += e_un =
         -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;
 
@@ -202,13 +203,15 @@ void Atom_Energy( reax_system *system, control_params *control,
     /* tally into per-atom energy */
     if( system->pair_ptr->evflag) {
       eng_tmp = e_ov;
-      if (numbonds > 0) eng_tmp += e_un;
+      if (numbonds > 0 || control->enobondsflag)
+        eng_tmp += e_un;
       system->pair_ptr->ev_tally(i,i,system->n,1,eng_tmp,0.0,0.0,0.0,0.0,0.0);
     }
 
     /* forces */
     workspace->CdDelta[i] += CEover3;   // OvCoor - 2nd term
-    if (numbonds > 0) workspace->CdDelta[i] += CEunder3;  // UnCoor - 1st term
+    if (numbonds > 0 || control->enobondsflag)
+      workspace->CdDelta[i] += CEunder3;  // UnCoor - 1st term
 
     for( pj = Start_Index(i, bonds); pj < End_Index(i, bonds); ++pj ) {
       pbond = &(bonds->select.bond_list[pj]);

src/USER-REAXC/reaxc_nonbonded.cpp

@@ -24,7 +24,7 @@
   <http://www.gnu.org/licenses/>.
   ----------------------------------------------------------------------*/
 
-#include "pair_reax_c.h"
+#include "pair_reaxc.h"
 #include "reaxc_types.h"
 #include "reaxc_nonbonded.h"
 #include "reaxc_bond_orders.h"