Merge branch 'master' of https://github.com/lammps/lammps into bond/react-new-examples-and-package

doc/src/Build.rst

@@ -21,8 +21,3 @@ as described on the :doc:`Install <Install>` doc page.
    Build_extras
    Build_windows
    Build_development
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_basics.rst

@@ -430,8 +430,3 @@ you want to copy files to is protected.
 There is no "install" option in the src/Makefile for LAMMPS.  If you
 wish to do this you will need to first build LAMMPS, then manually
 copy the desired LAMMPS files to the appropriate system directories.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_cmake.rst

@@ -238,8 +238,3 @@ enough version, you can download the latest version at
 `https://cmake.org/download/ <https://cmake.org/download/>`_.
 Instructions on how to install it on various platforms can be found
 `on this page <https://cmake.org/install/>`_.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_development.rst

@@ -112,9 +112,3 @@ These reports require GCOVR to be installed. The easiest way to do this to insta
 .. parsed-literal::
 
    pip install git+https://github.com/gcovr/gcovr.git
-
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_extras.rst

@@ -177,7 +177,7 @@ KIM package
 
 To build with this package, the KIM library with API v2 must be downloaded
 and built on your system.  It must include the KIM models that you want to
-use with LAMMPS. If you want to use the :doc:`kim\_query <kim_commands>`
+use with LAMMPS. If you want to use the :doc:`kim_query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
@@ -203,7 +203,7 @@ inside the CMake build directory.  If the KIM library is already on
 your system (in a location CMake cannot find it), set the PKG\_CONFIG\_PATH
 environment variable so that libkim-api can be found.
 
-For using KIM web queries.
+For using OpenKIM web queries in LAMMPS.
 
 If LMP\_DEBUG\_CURL is set, the libcurl verbose mode will be on, and any
 libcurl calls within the KIM web query display a lot of information about
@@ -350,10 +350,12 @@ For NVIDIA GPUs using CUDA:
    KOKKOS_DEVICES = Cuda
    KOKKOS_ARCH = archCPU,archGPU    # archCPU = CPU from list above that is hosting the GPU
                                     # archGPU = GPU from list above
+   FFT_INC = -DFFT_CUFFT            # enable use of cuFFT (optional)
+   FFT_LIB = -lcufft                # link to cuFFT library
 
-For GPUs, you also need these 2 lines in your Makefile.machine before
-the CC line is defined, in this case for use with OpenMPI mpicxx.  The
-2 lines define a nvcc wrapper compiler, which will use nvcc for
+For GPUs, you also need the following 2 lines in your Makefile.machine
+before the CC line is defined, in this case for use with OpenMPI mpicxx.
+The 2 lines define a nvcc wrapper compiler, which will use nvcc for
 compiling CUDA files and use a C++ compiler for non-Kokkos, non-CUDA
 files.
 
@@ -878,6 +880,9 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `plumed installation instructions <plumedinstall_>`_.
+The USER-PLUMED package has been tested to work with Plumed versions
+2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
+with a different version of the Plumed kernel.
 
 
 PLUMED can be linked into MD codes in three different modes: static,
@@ -1412,8 +1417,3 @@ the settings are not valid for your system, check if one of the other
 lib/vtk/Makefile.lammps.\* files is compatible and copy it to
 Makefile.lammps.  If none of the provided files work, you will need to
 edit the Makefile.lammps file.  See lib/vtk/README for details.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_link.rst

@@ -84,8 +84,3 @@ See the sample codes in examples/COUPLE/simple for examples of C++ and
 C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the :doc:`Howto couple <Howto_couple>` doc page.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_make.rst

@@ -87,8 +87,3 @@ settings may become outdated:
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_package.rst

@@ -258,8 +258,3 @@ sub-directories with src files.
 
 Type "make package-diff" to list all differences between pairs of
 files in both the src dir and a package dir.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_settings.rst

@@ -5,11 +5,11 @@ LAMMPS can be built with several optional settings.  Each sub-section
 explain how to do this for building both with CMake and make.
 
 | :ref:`C++11 standard compliance test <cxx11>` when building all of LAMMPS
-| :ref:`FFT library <fft>` for use with the :doc:`kspace\_style pppm <kspace_style>` command
+| :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
 | :ref:`Size of LAMMPS data types <size>`
 | :ref:`Read or write compressed files <gzip>`
 | :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
-| :ref:`Output of movie files <graphics>` via the :doc:`dump\_movie <dump_image>` command
+| :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
 | :ref:`Memory allocation alignment <align>`
 | :ref:`Workaround for long long integers <longlong>`
 | :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library 
@@ -49,13 +49,19 @@ through the CMAKE\_CXX\_FLAGS variable. Example for CentOS 7:
 
    -D CMAKE_CXX_FLAGS="-O3 -g -fopenmp -DNDEBUG -std=c++11"
 
-**Makefile.machine setting**\ :
+**Makefile.machine setting**\ to bypass the C++11 test and compile in C++98 mode:
 
 
 .. parsed-literal::
 
    LMP_INC = -DLAMMPS_CXX98
 
+**Makefile.machine setting**\ to enable the C++11 with older (but not too old) GNU c++ (e.g. on CentOS 7):
+
+
+.. parsed-literal::
+
+   CCFLAGS = -g -O3 -std=c++11
 
 ----------
 
@@ -66,7 +72,7 @@ FFT library
 ---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
-:doc:`kspace\_style pppm <kspace_style>` command performs 3d FFTs which
+:doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
@@ -86,15 +92,21 @@ LAMMPS can use them if they are available on your system.
    an exception to the rule that all CMake variables can be specified
    with lower-case values.
 
-Usually these settings are all that is needed.  If CMake cannot find
-the FFT library, you can set these variables:
+Usually these settings are all that is needed.  If FFTW3 is selected,
+then CMake will try to detect, if threaded FFTW libraries are available
+and enable them by default.  This setting is independent of whether
+OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
+used.  If CMake cannot detect the FFT library, you can set these variables
+to assist:
 
 
 .. parsed-literal::
 
    -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
    -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
    -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
    -D MKL_LIBRARIES=path
 
 **Makefile.machine settings**\ :
@@ -105,6 +117,8 @@ the FFT library, you can set these variables:
    FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
                                  # default is KISS if not specified
    FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+   FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
    FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
 
 # default is FFT\_PACK\_ARRAY if not specified
@@ -115,27 +129,34 @@ the FFT library, you can set these variables:
    FFT_INC =       -I/usr/local/include
    FFT_PATH =      -L/usr/local/lib
    FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
    FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
-   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
 As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
-make can find the FFT header and library files.  You must specify
-FFT\_LIB with the appropriate FFT libraries to include in the link.
+the compiler can find the FFT header and library files in its default search path.
+You must specify FFT\_LIB with the appropriate FFT libraries to include in the link.
 
 **CMake and make info**\ :
 
 The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
-distribution.  It is portable across all platforms.  Depending on the
-size of the FFTs and the number of processors used, the other
-libraries listed here can be faster.
+distribution.  It is portable across all platforms.  Depending on the size
+of the FFTs and the number of processors used, the other libraries listed
+here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
 per-timestep CPU cost, FFTs are only a portion of long-range
 Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
 communication can be costly).  A breakdown of these timings is printed
-to the screen at the end of a run using the :doc:`kspace\_style pppm <kspace_style>` command.  The :doc:`Run output <Run_output>`
-doc page gives more details.
+to the screen at the end of a run when using the
+:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+doc page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
+:doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
 platform and can be faster than the KISS FFT library.  You can
@@ -166,7 +187,7 @@ When using -DFFT\_SINGLE with FFTW3 you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
-library libfftw3f.a
+library libfftw3f.a or libfftw3f.so.
 
 
 .. parsed-literal::
@@ -235,7 +256,7 @@ support 8-byte integers.  It allows for:
 
 Atom IDs are not required for atomic systems which do not store bond
 topology information, though IDs are enabled by default.  The
-:doc:`atom\_modify id no <atom_modify>` command will turn them off.  Atom
+:doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Thus if you model a molecular system with
 more than 2 billion atoms, you need the "bigbig" setting.
@@ -341,7 +362,7 @@ Read or write compressed files
 
 If this option is enabled, large files can be read or written with
 gzip compression by several LAMMPS commands, including
-:doc:`read\_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 **CMake variables**\ :
 
@@ -472,8 +493,3 @@ e.g. to Python.
 .. parsed-literal::
 
    LMP_INC = -DLAMMPS_EXCEPTIONS
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Build_windows.rst

@@ -17,9 +17,9 @@ General remarks
 
 LAMMPS is developed and tested primarily on Linux machines.  The vast
 majority of HPC clusters and supercomputers today runs on Linux as well.
-Thus portability to other platforms is desired, but not always achieved.
+While portability to other platforms is desired, it is not always achieved.
 The LAMMPS developers strongly rely on LAMMPS users giving feedback and
-providing assistance in resolving portability issues. This particularly
+providing assistance in resolving portability issues. This is particularly
 true for compiling LAMMPS on Windows, since this platform has significant
 differences with some low-level functionality.
 
@@ -31,18 +31,20 @@ Running Linux on Windows
 So before trying to build LAMMPS on Windows, please consider if using
 the pre-compiled Windows binary packages are sufficient for your needs
 (as an aside, those packages themselves are build on a Linux machine
-using cross-compilers).  If it is necessary for your to compile LAMMPS
+using cross-compilers).  If it is necessary for you to compile LAMMPS
 on a Windows machine (e.g. because it is your main desktop), please also
-consider using a virtual machine software and run a Linux virtual machine,
-or - if have a recently updated Windows 10 installation - consider using
-the Windows subsystem for Linux, which allows to run a bash shell from
-Ubuntu and from there on, you can pretty much use that shell like you
-are running on an Ubuntu Linux machine (e.g. installing software via
-apt-get). For more details on that, please see :doc:`this tutorial <Howto_bash>`
+consider using a virtual machine software and compile and run LAMMPS in
+a Linux virtual machine, or - if you have a recently updated Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows and from there on, you can pretty much use that
+shell like you are running on an Ubuntu Linux machine (e.g. installing
+software via apt-get and more). For more details on that, please
+see :doc:`this tutorial <Howto_bash>`
 
 .. _gnu:
 
-Using GNU GCC ported to Windows
+Using a GNU GCC ported to Windows
 -----------------------------------------
 
 One option for compiling LAMMPS on Windows natively, that has been known
@@ -83,13 +85,13 @@ traditional build system, but CMake has also been successfully tested
 using the mingw32-cmake and mingw64-cmake wrappers that are bundled
 with the cross-compiler environment on Fedora machines. A CMake preset
 selecting all packages compatible with this cross-compilation build
-is provided. You likely need to disable the GPU package unless you
+is provided. You will likely need to disable the GPU package unless you
 download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
 into your MinGW64 cross-compiler environment. The cross-compilation
 currently will only produce non-MPI serial binaries.
 
-Please keep in mind, though, that this only applies to compiling LAMMPS.
-Whether the resulting binaries do work correctly is no tested by the
+Please keep in mind, though, that this only applies to **compiling** LAMMPS.
+Whether the resulting binaries do work correctly is not tested by the
 LAMMPS developers.  We instead rely on the feedback of the users
 of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
@@ -104,8 +106,3 @@ Support for the Visual C++ compilers is currently not available. The
 CMake build system is capable of creating suitable a Visual Studio
 style build environment, but the LAMMPS code itself is not fully ported
 to support Visual C++. Volunteers to take on this task are welcome.
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_all.rst

@@ -25,102 +25,105 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
    * :doc:`bond_coeff <bond_coeff>`
-   * :doc:`bond\_style <bond_style>`
-   * :doc:`bond\_write <bond_write>`
+   * :doc:`bond_style <bond_style>`
+   * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
    * :doc:`box <box>`
-   * :doc:`change\_box <change_box>`
+   * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
-   * :doc:`comm\_modify <comm_modify>`
-   * :doc:`comm\_style <comm_style>`
+   * :doc:`comm_modify <comm_modify>`
+   * :doc:`comm_style <comm_style>`
    * :doc:`compute <compute>`
-   * :doc:`compute\_modify <compute_modify>`
-   * :doc:`create\_atoms <create_atoms>`
-   * :doc:`create\_bonds <create_bonds>`
-   * :doc:`create\_box <create_box>`
-   * :doc:`delete\_atoms <delete_atoms>`
-   * :doc:`delete\_bonds <delete_bonds>`
+   * :doc:`compute_modify <compute_modify>`
+   * :doc:`create_atoms <create_atoms>`
+   * :doc:`create_bonds <create_bonds>`
+   * :doc:`create_box <create_box>`
+   * :doc:`delete_atoms <delete_atoms>`
+   * :doc:`delete_bonds <delete_bonds>`
    * :doc:`dielectric <dielectric>`
-   * :doc:`dihedral\_coeff <dihedral_coeff>`
-   * :doc:`dihedral\_style <dihedral_style>`
+   * :doc:`dihedral_coeff <dihedral_coeff>`
+   * :doc:`dihedral_style <dihedral_style>`
    * :doc:`dimension <dimension>`
-   * :doc:`displace\_atoms <displace_atoms>`
+   * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
-   * :doc:`dump adios <dump_adios>`
+   * :doc:`dump atom/adios <dump_adios>`
+   * :doc:`dump custom/adios <dump_adios>`
    * :doc:`dump image <dump_image>`
    * :doc:`dump movie <dump_image>`
    * :doc:`dump netcdf <dump_netcdf>`
    * :doc:`dump netcdf/mpiio <dump_netcdf>`
    * :doc:`dump vtk <dump_vtk>`
-   * :doc:`dump\_modify <dump_modify>`
-   * :doc:`dynamical\_matrix <dynamical_matrix>`
+   * :doc:`dump_modify <dump_modify>`
+   * :doc:`dynamical_matrix <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
-   * :doc:`fix\_modify <fix_modify>`
+   * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`if <if>`
-   * :doc:`improper\_coeff <improper_coeff>`
-   * :doc:`improper\_style <improper_style>`
+   * :doc:`improper_coeff <improper_coeff>`
+   * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
+   * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim\_init <kim_commands>`
-   * :doc:`kim\_interactions <kim_commands>`
-   * :doc:`kim\_query <kim_commands>`
-   * :doc:`kspace\_modify <kspace_modify>`
-   * :doc:`kspace\_style <kspace_style>`
+   * :doc:`kim_init <kim_commands>`
+   * :doc:`kim_interactions <kim_commands>`
+   * :doc:`kim_param <kim_commands>`
+   * :doc:`kim_query <kim_commands>`
+   * :doc:`kspace_modify <kspace_modify>`
+   * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
-   * :doc:`min\_modify <min_modify>`
-   * :doc:`min\_style <min_style>`
-   * :doc:`min\_style spin <min_spin>`
+   * :doc:`min_modify <min_modify>`
+   * :doc:`min_style <min_style>`
+   * :doc:`min_style spin <min_spin>`
    * :doc:`molecule <molecule>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`
    * :doc:`neb/spin <neb_spin>`
-   * :doc:`neigh\_modify <neigh_modify>`
+   * :doc:`neigh_modify <neigh_modify>`
    * :doc:`neighbor <neighbor>`
    * :doc:`newton <newton>`
    * :doc:`next <next>`
    * :doc:`package <package>`
-   * :doc:`pair\_coeff <pair_coeff>`
-   * :doc:`pair\_modify <pair_modify>`
-   * :doc:`pair\_write <pair_write>`
+   * :doc:`pair_coeff <pair_coeff>`
+   * :doc:`pair_modify <pair_modify>`
+   * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`
    * :doc:`python <python>`
    * :doc:`quit <quit>`
-   * :doc:`read\_data <read_data>`
-   * :doc:`read\_dump <read_dump>`
-   * :doc:`read\_restart <read_restart>`
+   * :doc:`read_data <read_data>`
+   * :doc:`read_dump <read_dump>`
+   * :doc:`read_restart <read_restart>`
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset\_ids <reset_ids>`
-   * :doc:`reset\_timestep <reset_timestep>`
+   * :doc:`reset_ids <reset_ids>`
+   * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
-   * :doc:`run\_style <run_style>`
+   * :doc:`run_style <run_style>`
    * :doc:`server <server>`
    * :doc:`set <set>`
    * :doc:`shell <shell>`
-   * :doc:`special\_bonds <special_bonds>`
+   * :doc:`special_bonds <special_bonds>`
    * :doc:`suffix <suffix>`
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
    * :doc:`temper/grem <temper_grem>`
    * :doc:`temper/npt <temper_npt>`
    * :doc:`thermo <thermo>`
-   * :doc:`thermo\_modify <thermo_modify>`
-   * :doc:`thermo\_style <thermo_style>`
-   * :doc:`third\_order <third_order>`
+   * :doc:`thermo_modify <thermo_modify>`
+   * :doc:`thermo_style <thermo_style>`
+   * :doc:`third_order <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -129,7 +132,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`units <units>`
    * :doc:`variable <variable>`
    * :doc:`velocity <velocity>`
-   * :doc:`write\_coeff <write_coeff>`
-   * :doc:`write\_data <write_data>`
-   * :doc:`write\_dump <write_dump>`
-   * :doc:`write\_restart <write_restart>`
+   * :doc:`write_coeff <write_coeff>`
+   * :doc:`write_data <write_data>`
+   * :doc:`write_dump <write_dump>`
+   * :doc:`write_restart <write_restart>`

doc/src/Commands_bond.rst

@@ -13,7 +13,7 @@
 
 .. _bond:
 
-bond_style potentials
+Bond_style potentials
 =====================
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
@@ -44,16 +44,13 @@ OPT.
    * :doc:`nonlinear (o) <bond_nonlinear>`
    * :doc:`oxdna/fene <bond_oxdna>`
    * :doc:`oxdna2/fene <bond_oxdna>`
+   * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
    * :doc:`table (o) <bond_table>`
-   *
-   *
-
----
 
 .. _angle:
 
-angle_style potentials
+Angle_style potentials
 ======================
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
@@ -91,13 +88,10 @@ OPT.
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`sdk (o) <angle_sdk>`
    * :doc:`table (o) <angle_table>`
-   *
-
----
 
 .. _dihedral:
 
-dihedral_style potentials
+Dihedral_style potentials
 =========================
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
@@ -131,15 +125,13 @@ OPT.
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
    * :doc:`table/cut <dihedral_table_cut>`
-   *
-   *
 
 .. _improper:
 
-improper_style potentials
+Improper_style potentials
 =========================
 
-All LAMMPS :doc:`improper\_style <improper_style>` commands.  Some styles
+All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -166,4 +158,3 @@ OPT.
    * :doc:`ring (o) <improper_ring>`
    * :doc:`sqdistharm <improper_sqdistharm>`
    * :doc:`umbrella (o) <improper_umbrella>`
-   *

doc/src/Commands_category.rst

@@ -18,73 +18,73 @@ Setup simulation box:
 
 * :doc:`boundary <boundary>`,
 * :doc:`box <box>`,
-* :doc:`change\_box <change_box>`,
-* :doc:`create\_box <create_box>`,
+* :doc:`change_box <change_box>`,
+* :doc:`create_box <create_box>`,
 * :doc:`dimension <dimension>`,
 * :doc:`lattice <lattice>`,
 * :doc:`region <region>`
 
 Setup atoms:
 
-* :doc:`atom\_modify <atom_modify>`,
-* :doc:`atom\_style <atom_style>`,
+* :doc:`atom_modify <atom_modify>`,
+* :doc:`atom_style <atom_style>`,
 * :doc:`balance <balance>`,
-* :doc:`create\_atoms <create_atoms>`,
-* :doc:`create\_bonds <create_bonds>`,
-* :doc:`delete\_atoms <delete_atoms>`,
-* :doc:`delete\_bonds <delete_bonds>`,
-* :doc:`displace\_atoms <displace_atoms>`,
+* :doc:`create_atoms <create_atoms>`,
+* :doc:`create_bonds <create_bonds>`,
+* :doc:`delete_atoms <delete_atoms>`,
+* :doc:`delete_bonds <delete_bonds>`,
+* :doc:`displace_atoms <displace_atoms>`,
 * :doc:`group <group>`,
 * :doc:`mass <mass>`,
 * :doc:`molecule <molecule>`,
-* :doc:`read\_data <read_data>`,
-* :doc:`read\_dump <read_dump>`,
-* :doc:`read\_restart <read_restart>`,
+* :doc:`read_data <read_data>`,
+* :doc:`read_dump <read_dump>`,
+* :doc:`read_restart <read_restart>`,
 * :doc:`replicate <replicate>`,
 * :doc:`set <set>`,
 * :doc:`velocity <velocity>`
 
 Force fields:
 
-* :doc:`angle\_coeff <angle_coeff>`,
-* :doc:`angle\_style <angle_style>`,
-* :doc:`bond\_coeff <bond_coeff>`,
-* :doc:`bond\_style <bond_style>`,
-* :doc:`bond\_write <bond_write>`,
+* :doc:`angle_coeff <angle_coeff>`,
+* :doc:`angle_style <angle_style>`,
+* :doc:`bond_coeff <bond_coeff>`,
+* :doc:`bond_style <bond_style>`,
+* :doc:`bond_write <bond_write>`,
 * :doc:`dielectric <dielectric>`,
-* :doc:`dihedral\_coeff <dihedral_coeff>`,
-* :doc:`dihedral\_style <dihedral_style>`,
-* :doc:`improper\_coeff <improper_coeff>`,
-* :doc:`improper\_style <improper_style>`,
-* :doc:`kspace\_modify <kspace_modify>`,
-* :doc:`kspace\_style <kspace_style>`,
-* :doc:`pair\_coeff <pair_coeff>`,
-* :doc:`pair\_modify <pair_modify>`,
-* :doc:`pair\_style <pair_style>`,
-* :doc:`pair\_write <pair_write>`,
-* :doc:`special\_bonds <special_bonds>`
+* :doc:`dihedral_coeff <dihedral_coeff>`,
+* :doc:`dihedral_style <dihedral_style>`,
+* :doc:`improper_coeff <improper_coeff>`,
+* :doc:`improper_style <improper_style>`,
+* :doc:`kspace_modify <kspace_modify>`,
+* :doc:`kspace_style <kspace_style>`,
+* :doc:`pair_coeff <pair_coeff>`,
+* :doc:`pair_modify <pair_modify>`,
+* :doc:`pair_style <pair_style>`,
+* :doc:`pair_write <pair_write>`,
+* :doc:`special_bonds <special_bonds>`
 
 Settings:
 
-* :doc:`comm\_modify <comm_modify>`,
-* :doc:`comm\_style <comm_style>`,
+* :doc:`comm_modify <comm_modify>`,
+* :doc:`comm_style <comm_style>`,
 * :doc:`info <info>`,
-* :doc:`min\_modify <min_modify>`,
-* :doc:`min\_style <min_style>`,
-* :doc:`neigh\_modify <neigh_modify>`,
+* :doc:`min_modify <min_modify>`,
+* :doc:`min_style <min_style>`,
+* :doc:`neigh_modify <neigh_modify>`,
 * :doc:`neighbor <neighbor>`,
 * :doc:`partition <partition>`,
-* :doc:`reset\_timestep <reset_timestep>`,
-* :doc:`run\_style <run_style>`,
+* :doc:`reset_timestep <reset_timestep>`,
+* :doc:`run_style <run_style>`,
 * :doc:`timer <timer>`,
 * :doc:`timestep <timestep>`
 
 Operations within timestepping (fixes) and diagnostics (computes):
 
 * :doc:`compute <compute>`,
-* :doc:`compute\_modify <compute_modify>`,
+* :doc:`compute_modify <compute_modify>`,
 * :doc:`fix <fix>`,
-* :doc:`fix\_modify <fix_modify>`,
+* :doc:`fix_modify <fix_modify>`,
 * :doc:`uncompute <uncompute>`,
 * :doc:`unfix <unfix>`
 
@@ -93,22 +93,22 @@ Output:
 * :doc:`dump image <dump_image>`,
 * :doc:`dump movie <dump_image>`,
 * :doc:`dump <dump>`,
-* :doc:`dump\_modify <dump_modify>`,
+* :doc:`dump_modify <dump_modify>`,
 * :doc:`restart <restart>`,
 * :doc:`thermo <thermo>`,
-* :doc:`thermo\_modify <thermo_modify>`,
-* :doc:`thermo\_style <thermo_style>`,
+* :doc:`thermo_modify <thermo_modify>`,
+* :doc:`thermo_style <thermo_style>`,
 * :doc:`undump <undump>`,
-* :doc:`write\_coeff <write_coeff>`,
-* :doc:`write\_data <write_data>`,
-* :doc:`write\_dump <write_dump>`,
-* :doc:`write\_restart <write_restart>`
+* :doc:`write_coeff <write_coeff>`,
+* :doc:`write_data <write_data>`,
+* :doc:`write_dump <write_dump>`,
+* :doc:`write_restart <write_restart>`
 
 Actions:
 
 * :doc:`minimize <minimize>`,
 * :doc:`neb <neb>`,
-* :doc:`neb\_spin <neb_spin>`,
+* :doc:`neb_spin <neb_spin>`,
 * :doc:`prd <prd>`,
 * :doc:`rerun <rerun>`,
 * :doc:`run <run>`,

doc/src/Commands_compute.rst

@@ -163,6 +163,3 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`
    * :doc:`xrd <compute_xrd>`
-   *
-   *
-   *

doc/src/Commands_fix.rst

@@ -105,16 +105,17 @@ OPT.
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
-   * :doc:`neb\_spin <fix_neb_spin>`
+   * :doc:`neb/spin <fix_neb_spin>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
-   * :doc:`nphug (o) <fix_nphug>`
+   * :doc:`nphug <fix_nphug>`
    * :doc:`npt (iko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
+   * :doc:`npt/cauchy <fix_npt_cauchy>`
    * :doc:`npt/eff <fix_nh_eff>`
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
@@ -155,6 +156,7 @@ OPT.
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
    * :doc:`print <fix_print>`
+   * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
    * :doc:`python/invoke <fix_python_invoke>`
    * :doc:`python/move <fix_python_move>`
@@ -188,15 +190,16 @@ OPT.
    * :doc:`rx (k) <fix_rx>`
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
+   * :doc:`setforce/spin <fix_setforce>`
    * :doc:`shake <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
-   * :doc:`smd/adjust\_dt <fix_smd_adjust_dt>`
-   * :doc:`smd/integrate\_tlsph <fix_smd_integrate_tlsph>`
-   * :doc:`smd/integrate\_ulsph <fix_smd_integrate_ulsph>`
-   * :doc:`smd/move\_tri\_surf <fix_smd_move_triangulated_surface>`
+   * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
+   * :doc:`smd/integrate_tlsph <fix_smd_integrate_tlsph>`
+   * :doc:`smd/integrate_ulsph <fix_smd_integrate_ulsph>`
+   * :doc:`smd/move_tri_surf <fix_smd_move_triangulated_surface>`
    * :doc:`smd/setvel <fix_smd_setvel>`
-   * :doc:`smd/wall\_surface <fix_smd_wall_surface>`
+   * :doc:`smd/wall_surface <fix_smd_wall_surface>`
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
@@ -233,8 +236,7 @@ OPT.
    * :doc:`wall/morse <fix_wall>`
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
+   * :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
-   *
-   *

doc/src/Commands_input.rst

@@ -45,7 +45,7 @@ belong to the group.
 (3) Sometimes command B will use values that can be set by command A.
 This means command A must precede command B in the input script if it
 is to have the desired effect.  For example, the
-:doc:`read\_data <read_data>` command initializes the system by setting
+:doc:`read_data <read_data>` command initializes the system by setting
 up the simulation box and assigning atoms to processors.  If default
 values are not desired, the :doc:`processors <processors>` and
 :doc:`boundary <boundary>` commands need to be used before read\_data to

doc/src/Commands_kspace.rst

@@ -14,7 +14,7 @@
 KSpace solvers
 ==============
 
-All LAMMPS :doc:`kspace\_style <kspace_style>` solvers.  Some styles have
+All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -24,13 +24,16 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/dipole <kspace_style>`
+   * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
-   * :doc:`pppm (gok) <kspace_style>`
+   * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
-   * :doc:`pppm/disp (i) <kspace_style>`
-   * :doc:`pppm/disp/tip4p <kspace_style>`
+   * :doc:`pppm/dipole <kspace_style>`
+   * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/disp (io) <kspace_style>`
+   * :doc:`pppm/disp/tip4p (o) <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
    * :doc:`scafacos <kspace_style>`
-   *

doc/src/Commands_pair.rst

@@ -11,10 +11,10 @@
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
 
-Pair\_style potentials
+Pair_style potentials
 ======================
 
-All LAMMPS :doc:`pair\_style <pair_style>` commands.  Some styles have
+All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
 parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
 OPT.
@@ -146,7 +146,7 @@ OPT.
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/thole/long (o) <pair_thole>`
    * :doc:`lj/cut/tip4p/cut (o) <pair_lj>`
-   * :doc:`lj/cut/tip4p/long (ot) <pair_lj>`
+   * :doc:`lj/cut/tip4p/long (got) <pair_lj>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
    * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
@@ -162,7 +162,7 @@ OPT.
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (o) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
-   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss>`
+   * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
    * :doc:`local/density <pair_local_density>`
    * :doc:`lubricate (o) <pair_lubricate>`
@@ -174,8 +174,10 @@ OPT.
    * :doc:`meam/c <pair_meamc>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
+   * :doc:`mesocnt <pair_mesocnt>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -197,10 +199,17 @@ OPT.
    * :doc:`oxdna2/hbond <pair_oxdna2>`
    * :doc:`oxdna2/stk <pair_oxdna2>`
    * :doc:`oxdna2/xstk <pair_oxdna2>`
+   * :doc:`oxrna2/excv <pair_oxrna2>`
+   * :doc:`oxrna2/hbond <pair_oxrna2>`
+   * :doc:`oxrna2/dh <pair_oxrna2>`
+   * :doc:`oxrna2/stk <pair_oxrna2>`
+   * :doc:`oxrna2/xstk <pair_oxrna2>`
+   * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
    * :doc:`peri/ves <pair_peri>`
+   * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
    * :doc:`reax/c (ko) <pair_reaxc>`
@@ -209,7 +218,7 @@ OPT.
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`
    * :doc:`smd/hertz <pair_smd_hertz>`
    * :doc:`smd/tlsph <pair_smd_tlsph>`
-   * :doc:`smd/tri\_surface <pair_smd_triangulated_surface>`
+   * :doc:`smd/tri_surface <pair_smd_triangulated_surface>`
    * :doc:`smd/ulsph <pair_smd_ulsph>`
    * :doc:`smtbq <pair_smtbq>`
    * :doc:`snap (k) <pair_snap>`
@@ -248,5 +257,3 @@ OPT.
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`
-   *
-   *

doc/src/Commands_removed.rst

@@ -57,11 +57,6 @@ restart2data tool
 
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read\_restart <read_restart>` and
-:doc:`write\_data <write_data>` can be used to the same effect.  For added
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For added
 convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`
-
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/Commands_structure.rst

@@ -26,23 +26,23 @@ read-in from a file.
 The relevant commands are :doc:`units <units>`,
 :doc:`dimension <dimension>`, :doc:`newton <newton>`,
 :doc:`processors <processors>`, :doc:`boundary <boundary>`,
-:doc:`atom\_style <atom_style>`, :doc:`atom\_modify <atom_modify>`.
+:doc:`atom_style <atom_style>`, :doc:`atom_modify <atom_modify>`.
 
 If force-field parameters appear in the files that will be read, these
 commands tell LAMMPS what kinds of force fields are being used:
-:doc:`pair\_style <pair_style>`, :doc:`bond\_style <bond_style>`,
-:doc:`angle\_style <angle_style>`, :doc:`dihedral\_style <dihedral_style>`,
-:doc:`improper\_style <improper_style>`.
+:doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`,
+:doc:`angle_style <angle_style>`, :doc:`dihedral_style <dihedral_style>`,
+:doc:`improper_style <improper_style>`.
 
 (2) Atom definition
 
 There are 3 ways to define atoms in LAMMPS.  Read them in from a data
-or restart file via the :doc:`read\_data <read_data>` or
-:doc:`read\_restart <read_restart>` commands.  These files can contain
+or restart file via the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands.  These files can contain
 molecular topology information.  Or create atoms on a lattice (with no
 molecular topology), using these commands: :doc:`lattice <lattice>`,
-:doc:`region <region>`, :doc:`create\_box <create_box>`,
-:doc:`create\_atoms <create_atoms>`.  The entire set of atoms can be
+:doc:`region <region>`, :doc:`create_box <create_box>`,
+:doc:`create_atoms <create_atoms>`.  The entire set of atoms can be
 duplicated to make a larger simulation using the
 :doc:`replicate <replicate>` command.
 
@@ -53,25 +53,25 @@ can be specified: force field coefficients, simulation parameters,
 output options, etc.
 
 Force field coefficients are set by these commands (they can also be
-set in the read-in files): :doc:`pair\_coeff <pair_coeff>`,
-:doc:`bond\_coeff <bond_coeff>`, :doc:`angle\_coeff <angle_coeff>`,
-:doc:`dihedral\_coeff <dihedral_coeff>`,
-:doc:`improper\_coeff <improper_coeff>`,
-:doc:`kspace\_style <kspace_style>`, :doc:`dielectric <dielectric>`,
-:doc:`special\_bonds <special_bonds>`.
+set in the read-in files): :doc:`pair_coeff <pair_coeff>`,
+:doc:`bond_coeff <bond_coeff>`, :doc:`angle_coeff <angle_coeff>`,
+:doc:`dihedral_coeff <dihedral_coeff>`,
+:doc:`improper_coeff <improper_coeff>`,
+:doc:`kspace_style <kspace_style>`, :doc:`dielectric <dielectric>`,
+:doc:`special_bonds <special_bonds>`.
 
 Various simulation parameters are set by these commands:
-:doc:`neighbor <neighbor>`, :doc:`neigh\_modify <neigh_modify>`,
+:doc:`neighbor <neighbor>`, :doc:`neigh_modify <neigh_modify>`,
 :doc:`group <group>`, :doc:`timestep <timestep>`,
-:doc:`reset\_timestep <reset_timestep>`, :doc:`run\_style <run_style>`,
-:doc:`min\_style <min_style>`, :doc:`min\_modify <min_modify>`.
+:doc:`reset_timestep <reset_timestep>`, :doc:`run_style <run_style>`,
+:doc:`min_style <min_style>`, :doc:`min_modify <min_modify>`.
 
 Fixes impose a variety of boundary conditions, time integration, and
 diagnostic options.  The :doc:`fix <fix>` command comes in many flavors.
 
 Various computations can be specified for execution during a
 simulation using the :doc:`compute <compute>`,
-:doc:`compute\_modify <compute_modify>`, and :doc:`variable <variable>`
+:doc:`compute_modify <compute_modify>`, and :doc:`variable <variable>`
 commands.
 
 Output options are set by the :doc:`thermo <thermo>`, :doc:`dump <dump>`,

doc/src/Eqs/angle_class2_p6.tex

@@ -1,15 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-$$
-  E_{a} = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
-$$
-
-\end{document}
-
-%%% Local Variables:
-%%% mode: latex
-%%% TeX-master: t
-%%% End:

doc/src/Eqs/box.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-a &=& {\rm lx} \\
-b^2 &=&  {\rm ly}^2 +  {\rm xy}^2 \\
-c^2 &=&  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
-\cos{\alpha} &=& \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
-\cos{\beta} &=& \frac{\rm xz}{c} \\
-\cos{\gamma} &=& \frac{\rm xy}{b} \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/box_inverse.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-{\rm lx} &=& a \\
-{\rm xy} &=& b \cos{\gamma}  \\
-{\rm xz} &=& c \cos{\beta}\\
-{\rm ly}^2 &=&   b^2 - {\rm xy}^2 \\
-{\rm yz} &=& \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
-{\rm lz}^2 &=&  c^2 - {\rm xz}^2 - {\rm yz}^2 \\
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/centro_symmetry.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   CS = \sum_{i = 1}^{N/2} | \vec{R}_i + \vec{R}_{i+N/2} |^2
-$$
-
-\end{document}

doc/src/Eqs/cna_cutoff1.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cna_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_cutoff.tex

@@ -1,14 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-\begin{eqnarray*}
-  r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\
-  r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\
-  r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/cnp_cutoff2.tex

@@ -1,12 +0,0 @@
-\documentclass[12pt,article]{article}
-
-\usepackage{indentfirst}
-\usepackage{amsmath}
-
-\begin{document}
-
-$$
-  Rc + Rs > 2*{\rm cutoff}
-$$
-
-\end{document}

doc/src/Eqs/cnp_eq.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-   Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}}  \vec{R}_{ik} + \vec{R}_{jk} |^2
-$$
-
-\end{document}

doc/src/Eqs/compute_dpd.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
-   U^{cond} = \displaystyle\sum_{i=1}^{N} u_{i}^{cond} \\ 
-   U^{mech} = \displaystyle\sum_{i=1}^{N} u_{i}^{mech} \\
-   U^{chem} = \displaystyle\sum_{i=1}^{N} u_{i}^{chem} \\
-   U = \displaystyle\sum_{i=1}^{N} (u_{i}^{cond} + u_{i}^{mech} + u_{i}^{chem}) \\
-   \theta_{avg} = (\frac{1}{N}\displaystyle\sum_{i=1}^{N} \frac{1}{\theta_{i}})^{-1} \\
-\end{eqnarray*}                           
-
-\end{document}

doc/src/Eqs/compute_fep_bar.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \left< \frac{1}{1 + \exp\left[\left(U_1 - U_0 - \Delta_0^1A \right) /kT \right]} \right>_0 = \left< \frac{1}{1 + \exp\left[\left(U_0 - U_1 + \Delta_0^1A \right) /kT \right]} \right>_1 \]
-
-\end{document}

doc/src/Eqs/compute_fep_fdti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left( \frac{\partial
-    A(\lambda)}{\partial\lambda} \right)_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \frac{A(\lambda_{i} + \delta) -
-  A(\lambda_i)}{\delta} \]
-
-\end{document}

doc/src/Eqs/compute_fep_fep.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \sum_{i=0}^{n-1} \Delta_{\lambda_i}^{\lambda_{i+1}} A =
-- kT \sum_{i=0}^{n-1} \ln \left< \exp \left( - \frac{U(\lambda_{i+1}) -
-      U(\lambda_i)}{kT} \right) \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_lambda.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  \lambda = 0 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_0 \\
-  \lambda = 1 \quad\Rightarrow\quad U = U_{\mathrm{bg}} + U_1 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_fep_ti.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = \int_{\lambda=0}^{\lambda=1} \left< \frac{\partial
-    U(\lambda)}{\partial\lambda} \right>_\lambda \mathrm{d}\lambda
-\approx \sum_{i=0}^{n-1} w_i \left< \frac{U(\lambda_{i} + \delta) -
-    U(\lambda_i)}{\delta} \right>_{\lambda_i} \]
-
-\end{document}

doc/src/Eqs/compute_fep_u.tex

@@ -1,7 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[  U(\lambda) = U_{\mathrm{bg}} + U_1(\lambda) + U_0(\lambda) \]
-
-\end{document}

doc/src/Eqs/compute_fep_vol.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-\[ \Delta_0^1 A = - kT \sum_{i=0}^{n-1} \ln \frac{\left< V \exp \left( -
-    \frac{U(\lambda_{i+1}) - U(\lambda_i)}{kT} \right)
-\right>_{\lambda_i}}{\left< V \right>_{\lambda_i}} \]
-
-\end{document}

doc/src/Eqs/compute_gyration.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- {R_g}^2 = \frac{1}{M} \sum_i m_i (r_i - r_{cm})^2
-$$
-
-\end{document}

doc/src/Eqs/compute_msd_nongauss.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
- NGP(t) = 3<(r(t)-r(0))^4>/(5<(r(t)-r(0))^2>^2) - 1
-$$
-
-\end{document}

doc/src/Eqs/compute_saed1.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  I=\frac{F^{*}F}{N}
-$$
-
-\end{document}
-

doc/src/Eqs/compute_saed2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-

doc/src/Eqs/compute_saed3.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{5}
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )
-$$
-\end{document}
-

doc/src/Eqs/compute_shape_parameters.tex

@@ -1,13 +0,0 @@
-\documentclass[12pt]{article}
-
-\pagestyle{empty}
-\begin{document}
-
-\begin{eqnarray*}
- c = l_z - 0.5(l_y+l_x) \\
- b = l_y - l_x \\
- k = \frac{3}{2} \frac{l_x^2+l_y^2+l_z^2}{(l_x+l_y+l_z)^2} - \frac{1}{2} 
-\end{eqnarray*}
-
-\end{document}
-

doc/src/Eqs/compute_sna_atom1.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\theta_0 = {\tt rfac0} \frac{r-r_{min0}}{R_{ii'}-r_{min0}} \pi
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom2.tex

@@ -1,11 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-u^j_{m,m'} = U^j_{m,m'}(0,0,0) + \sum_{r_{ii'} < R_{ii'}}{f_c(r_{ii'}) w_{i'} U^j_{m,m'}(\theta_0,\theta,\phi)} 
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_sna_atom3.tex

@@ -1,16 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\newcommand{\hcoeff}[9]{H\!\!{\tiny\begin{array}{l}#1 #2 #3 \\ #4 #5 #6 \\ #7 #8 #9 \end{array}}}
-
-\begin{equation}
-B_{j_1,j_2,j}  = \\
-\sum_{m_1,m'_1=-j_1}^{j_1}\sum_{m_2,m'_2=-j_2}^{j_2}\sum_{m,m'=-j}^{j} (u^j_{m,m'})^*
-\hcoeff{j}{m}{m'}{j_1}{\!m_1}{\!m'_1}{j_2}{m_2}{m'_2}
-u^{j_1}_{m_1,m'_1} u^{j_2}_{m_2,m'_2}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom4.tex

@@ -1,14 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-\begin{eqnarray*}
-\label{eqn:f_c}
-f_c(r)  & = & \frac{1}{2}(\cos(\pi \frac{r-r_{min0}}{R_{ii'}-r_{min0}}) + 1), r \leq R_{ii'} \\
-& = & 0,  r > R_{ii'}
-\end{eqnarray*}
-
-
-\end{document}

doc/src/Eqs/compute_sna_atom5.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{equation}
-- \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}  }}{\partial {\bf r}_i}
-\end{equation}
-
-\end{document}

doc/src/Eqs/compute_sna_atom6.tex

@@ -1,12 +0,0 @@
-\documentclass[24pt]{article}
-
-\pagestyle{empty}
-
-\begin{document}
-
-
-\begin{eqnarray*}
-- {\bf r}_i \otimes \sum_{i' \in I} \frac{\partial {B^{i'}_{j_1,j_2,j}}}{\partial {\bf r}_i}
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/compute_xrd1.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  I=Lp(\theta)\frac{F^{*}F}{N}
-$$
-
-\end{document}
-

doc/src/Eqs/compute_xrd2.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  F(\mathbf{k})=\sum_{j=1}^{N}f_j(\theta)exp(2\pi i \mathbf{k}\cdot \mathbf{r}_j)
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd3.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  Lp(\theta)=\frac{1+cos^{2}(2\theta)}{cos(\theta)sin^{2}(\theta)}
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd4.tex

@@ -1,9 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  \frac{sin(\theta)}{\lambda}=\frac{\left | \mathbf{k} \right |}{2}
-$$
-\end{document}
-

doc/src/Eqs/compute_xrd5.tex

@@ -1,10 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$ 
-  f_j\left ( \frac{sin(\theta)}{\lambda} \right )=\sum_{i}^{4} 
-a_i exp\left ( -b_i \frac{sin^{2}(\theta)}{\lambda^{2}} \right )+c
-$$
-\end{document}
-

doc/src/Eqs/dihedral_charmm.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = K [ 1 + \cos (n \phi - d) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_class2.tex

@@ -1,17 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-\begin{eqnarray*}
-  E & = & E_d + E_{mbt} + E_{ebt} + E_{at} + E_{aat} + E_{bb13} \\
-  E_d & = & \sum_{n=1}^{3} K_n [ 1 - \cos (n \phi - \phi_n) ] \\
-  E_{mbt} & = & (r_{jk} - r_2) [ A_1 \cos (\phi) + A_2 \cos (2\phi) + A_3 \cos (3\phi) ] \\
-  E_{ebt} & = & (r_{ij} - r_1) [ B_1 \cos (\phi) + B_2 \cos (2\phi) + B_3 \cos (3\phi) ] + \\
-  & & (r_{kl} - r_3) [ C_1 \cos (\phi) + C_2 \cos (2\phi) + C_3 \cos (3\phi) ] \\
-  E_{at} & = & (\theta_{ijk} - \theta_1) [ D_1 \cos (\phi) + D_2 \cos (2\phi) + D_3 \cos (3\phi) ] + \\
-  & & (\theta_{jkl} - \theta_2) [ E_1 \cos (\phi) + E_2 \cos (2\phi) + E_3 \cos (3\phi) ] \\
-  E_{aat} & = & M (\theta_{ijk} - \theta_1) (\theta_{jkl} - \theta_2) \cos (\phi) \\
-  E_{bb13} & = & N (r_{ij} - r_1) (r_{kl} - r_3)
-\end{eqnarray*}
-
-\end{document}

doc/src/Eqs/dihedral_cosine_shift_exp.tex

@@ -1,13 +0,0 @@
-\documentstyle[12pt]{article}
-
-\begin{document}
-
-$$
-E=-U_{min} 
-\frac{e^{-a U(\theta,\theta_0)}-1}{e^a-1}
-\quad\mbox{with}\quad
-U(\theta,\theta_0)
-=-0.5 \left(1+\cos(\theta-\theta_0) \right)
-$$
-
-\end{document}

doc/src/Eqs/dihedral_fourier.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$  
-  E = \sum_{i=1,m} K_i  [ 1.0 + \cos ( n_i \phi - d_i ) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_harmonic.tex

@@ -1,9 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = K [ 1 + d  \cos (n \phi) ]
-$$
-
-\end{document}

doc/src/Eqs/dihedral_helix.tex

@@ -1,10 +0,0 @@
-\documentclass[12pt]{article}
-
-\begin{document}
-
-$$
-  E = A [1 - \cos(\theta)] + B [1 + \cos(3 \theta)] + 
-      C [1 + \cos(\theta + \frac{\pi}{4})]
-$$
-
-\end{document}