Merge pull request #4177 from lammps/maintenance

Fourth Set of Collected Bug Fixes and Maintenance Updates for 2 August 2023 Stable release

.github/workflows/unittest-macos.yml

@@ -15,7 +15,7 @@ jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-latest
+    runs-on: macos-13
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
@@ -43,6 +43,8 @@ jobs:
       working-directory: build
       run: |
         ccache -z
+        python3 -m venv macosenv
+        source macosenv/bin/activate
         python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \

cmake/CMakeLists.txt

@@ -12,6 +12,11 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
+# set policy to silence warnings about requiring execute permission for find_program
+# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
+if(POLICY CMP0109)
+  cmake_policy(SET CMP0109 OLD)
+endif()
 # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
@@ -29,6 +34,7 @@ project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -169,6 +175,22 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
+# warn about potentially problematic GCC compiler versions
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
+    endif()
+  endif()
+  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
+    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
+      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
+        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -211,7 +233,6 @@ else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
-include(GNUInstallDirs)
 file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,12 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.10.04.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+# PACE library support for ML-PACE package
 
-set(PACELIB_MD5 "70ff79f4e59af175e55d24f3243ad1ff" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)

cmake/Modules/Packages/ML-QUIP.cmake

@@ -25,7 +25,7 @@ if(DOWNLOAD_QUIP)
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")

cmake/Modules/Packages/PLUMED.cmake

@@ -1,5 +1,10 @@
 # Plumed2 support for PLUMED package
 
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
 if(BUILD_MPI)
   set(PLUMED_CONFIG_MPI "--enable-mpi")
   set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
@@ -21,9 +26,11 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.1/plumed-src-2.9.1.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
@@ -75,6 +82,9 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
     DEPENDS plumed_build
     COMMENT "Copying Plumed files"
   )
+  if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+    target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
+  endif()
 
 else()
 
@@ -149,6 +159,9 @@ else()
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
+    endif()
   else()
     find_package(PkgConfig REQUIRED)
     pkg_check_modules(PLUMED REQUIRED plumed)
@@ -163,7 +176,9 @@ else()
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
+    endif()
   endif()
 endif()
 
-target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/presets/mingw-cross.cmake

@@ -32,7 +32,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON

doc/src/Build_extras.rst

@@ -1450,6 +1450,11 @@ in lib/pace or somewhere else, which must be done before building
 LAMMPS with this package. The code for the library can be found
 at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
 
+Instead of including the ML-PACE package directly into LAMMPS, it
+is also possible to skip this step and build the ML-PACE package as
+a plugin using the CMake script files in the ``examples/PACKAGE/pace/plugin``
+folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
+
 .. tabs::
 
    .. tab:: CMake build
@@ -1614,6 +1619,11 @@ try a different one, switch to a different build system, consider a
 global PLUMED installation or consider downloading PLUMED during the
 LAMMPS build.
 
+Instead of including the PLUMED package directly into LAMMPS, it
+is also possible to skip this step and build the PLUMED package as
+a plugin using the CMake script files in the ``examples/PACKAGE/plumed/plugin``
+folder and then load this plugin at runtime with the :doc:`plugin command <plugin>`.
+
 .. tabs::
 
    .. tab:: CMake build

doc/src/Developer_plugins.rst

@@ -283,7 +283,7 @@ in the ``examples/kim/plugin`` folder.  No changes to the sources of the
 KIM package themselves are needed; only the plugin interface and loader
 code needs to be added.  This example only supports building with CMake,
 but is probably a more typical example. To compile you need to run CMake
-with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
+with ``-DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>``.  Other
 configuration setting are identical to those for compiling LAMMPS.
 
 A second example for a plugin from a package is in the

doc/src/Manual.rst

@@ -144,26 +144,28 @@ Indices and tables
    * :ref:`genindex`
    * :ref:`search`
 
-.. _webbrowser:
-.. admonition:: Web Browser Compatibility
-   :class: note
+.. only:: html
 
-   The HTML version of the manual makes use of advanced features present
-   in "modern" web browsers.  This leads to incompatibilities with older
-   web browsers and specific vendor browsers (e.g. Internet Explorer on Windows)
-   where parts of the pages are not rendered as expected (e.g. the layout is
-   broken or mathematical expressions not typeset).  In that case we
-   recommend to install/use a different/newer web browser or use
-   the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.
+  .. _webbrowser:
+  .. admonition:: Web Browser Compatibility
+     :class: note
 
-   The following web browser versions have been verified to work as
-   expected on Linux, macOS, and Windows where available:
+     The HTML version of the manual makes use of advanced features present
+     in "modern" web browsers.  This leads to incompatibilities with older
+     web browsers and specific vendor browsers (e.g. Internet Explorer on Windows)
+     where parts of the pages are not rendered as expected (e.g. the layout is
+     broken or mathematical expressions not typeset).  In that case we
+     recommend to install/use a different/newer web browser or use
+     the `PDF version of the manual <https://docs.lammps.org/Manual.pdf>`_.
 
-   - Safari version 11.1 and later
-   - Firefox version 54 and later
-   - Chrome version 54 and later
-   - Opera version 41 and later
-   - Edge version 80 and later
+     The following web browser versions have been verified to work as
+     expected on Linux, macOS, and Windows where available:
 
-   Also Android version 7.1 and later and iOS version 11 and later have
-   been verified to render this website as expected.
+     - Safari version 11.1 and later
+     - Firefox version 54 and later
+     - Chrome version 54 and later
+     - Opera version 41 and later
+     - Edge version 80 and later
+
+     Also Android version 7.1 and later and iOS version 11 and later have
+     been verified to render this website as expected.

doc/src/Packages_details.rst

@@ -1797,7 +1797,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-pace>` on the
-:doc:`Build extras <Build_extras>` page.
+:doc:`Build extras <Build_extras>` page.  This package may also be compiled
+as a plugin to avoid licensing conflicts when distributing binaries.
 
 **Supporting info:**
 
@@ -2357,7 +2358,9 @@ and Gareth Tribello.
 
 **Install:**
 
-This package has :ref:`specific installation instructions <plumed>` on the :doc:`Build extras <Build_extras>` page.
+This package has :ref:`specific installation instructions <plumed>` on the
+:doc:`Build extras <Build_extras>` page.  This package may also be compiled
+as a plugin to avoid licensing conflicts when distributing binaries.
 
 **Supporting info:**
 

doc/src/Tools.rst

@@ -802,7 +802,7 @@ and LAMMPS GUI can be launched from anywhere from the command line.
 
 The standard CMake build procedure can be applied and the
 ``mingw-cross.cmake`` preset used. By using ``mingw64-cmake`` the CMake
-command will automatically include a suitable CMake toolset file (the
+command will automatically include a suitable CMake toolchain file (the
 regular cmake command can be used after that).  After building the
 libraries and executables, you can build the target 'zip'
 (i.e. ``cmake --build <build dir> --target zip`` or ``make zip``

doc/src/commands_list.rst

@@ -31,15 +31,6 @@ Commands
    dihedral_write
    dimension
    displace_atoms
-   dump
-   dump_adios
-   dump_cfg_uef
-   dump_h5md
-   dump_image
-   dump_modify
-   dump_molfile
-   dump_netcdf
-   dump_vtk
    dynamical_matrix
    echo
    fix

doc/src/compute_smd_rho.rst

@@ -45,7 +45,8 @@ Restrictions
 """"""""""""
 
 This compute is part of the MACHDYN package. It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_smd_vol.rst

@@ -24,7 +24,7 @@ Description
 """""""""""
 
 Define a computation that provides the per-particle volume and the sum
-of the per-particle volumes of the group for which the fix is defined.
+of the per-particle volumes of the group for which the compute is defined.
 
 See `this PDF guide <PDF/MACHDYN_LAMMPS_userguide.pdf>`_ to using Smooth
 Mach Dynamics in LAMMPS.
@@ -41,13 +41,14 @@ The per-particle vector values will be given in :doc:`units <units>` of
 volume.
 
 Additionally, the compute returns a scalar, which is the sum of the
-per-particle volumes of the group for which the fix is defined.
+per-particle volumes of the group for which the compute is defined.
 
 Restrictions
 """"""""""""
 
 This compute is part of the MACHDYN package.  It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/dumps.rst

@@ -1,8 +1,9 @@
 Dump Styles
-###############
+###########
 
 .. toctree::
    :maxdepth: 1
    :glob:
 
-   dump*
+   dump
+   dump_*

doc/src/fix_ave_correlate.rst

@@ -65,7 +65,6 @@ Examples
    fix 1 all ave/correlate 1 50 10000 &
              c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
              type upper ave running title1 "My correlation data"
-
    fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]
 
 Description

doc/src/fix_ave_correlate_long.rst

@@ -20,11 +20,11 @@ Syntax
   .. parsed-literal::
 
        c_ID = global scalar calculated by a compute with ID
-       c_ID[I] = Ith component of global vector calculated by a compute with ID
+       c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
        f_ID = global scalar calculated by a fix with ID
-       f_ID[I] = Ith component of global vector calculated by a fix with ID
+       f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
        v_name = global value calculated by an equal-style variable with name
-       v_name[I] = Ith component of global vector calculated by a vector-style variable with name
+       v_name[I] = Ith component of a vector-style variable with name, I can include wildcard (see below)
 
 * zero or more keyword/arg pairs may be appended
 * keyword = *type* or *start* or *file* or *overwrite* or *title1* or *title2* or *ncorr* or *nlen* or *ncount*
@@ -63,6 +63,7 @@ Examples
    fix 1 all ave/correlate/long 1 10000 &
              c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &
              type upper title1 "My correlation data" nlen 15 ncount 3
+   fix 1 all ave/correlate/long 1 10000 c_thermo_press[*]
 
 Description
 """""""""""
@@ -80,8 +81,10 @@ specified values may represent calculations performed by computes and
 fixes which store their own "group" definitions.
 
 Each listed value can be the result of a compute or fix or the
-evaluation of an equal-style variable. See the
-:doc:`fix ave/correlate <fix_ave_correlate>` page for details.
+evaluation of an equal-style or vector-style variable.  For
+vector-style variables, the specified indices can include a wildcard
+character.  See the :doc:`fix ave/correlate <fix_ave_correlate>` page
+for details.
 
 The *Nevery* and *Nfreq* arguments specify on what time steps the input
 values will be used to calculate correlation data and the frequency

doc/src/neigh_modify.rst

@@ -267,6 +267,8 @@ The value of the *page* setting must be at least 10x larger than the
 *one* setting.  This ensures neighbor pages are not mostly empty
 space.
 
+The *exclude group* setting is currently not compatible with dynamic groups.
+
 Related commands
 """"""""""""""""
 

doc/src/pair_meam.rst

@@ -427,7 +427,7 @@ package. They are only enabled if LAMMPS was built with that package.
 See the :doc:`Build package <Build_package>` page for more info.
 
 The maximum number of elements, that can be read from the MEAM library
-file, is determined at compile time. The default is 5.  If you need
+file, is determined at compile time. The default is 8.  If you need
 support for more elements, you have to change the the constant 'maxelt'
 at the beginning of the file ``src/MEAM/meam.h`` and update/recompile
 LAMMPS.  There is no limit on the number of atoms types.

doc/utils/requirements.txt

@@ -1,4 +1,4 @@
-Sphinx >= 5.3.0, <7.2.0
+Sphinx >= 5.3.0, <7.5
 sphinxcontrib-spelling
 sphinxcontrib-jquery
 git+https://github.com/akohlmey/sphinx-fortran@parallel-read

doc/utils/sphinx-config/conf.py.in

@@ -68,7 +68,7 @@ images_config = {
 templates_path = ['_templates']
 
 # The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = {'.rst': 'restructuredtext'}
 
 # The encoding of source files.
 #source_encoding = 'utf-8-sig'
@@ -296,6 +296,7 @@ latex_elements = {
 \setcounter{tocdepth}{2}
 \renewcommand{\sfdefault}{ptm}  % Use Times New Roman font for \textrm
 \renewcommand{\sfdefault}{phv}  % Use Helvetica font for \textsf
+\usepackage[columns=1]{idxlayout} % create index with only one column
 % Set up math fonts to match text fonts
 \DeclareSymbolFont{operators}   {OT1}{ptm}{m}{n}
 \DeclareSymbolFont{bold}        {OT1}{ptm}{bx}{n}
@@ -340,6 +341,11 @@ latex_elements = {
 '''
 }
 
+# copy custom style file for tweaking index layout
+latex_additional_files = [
+    'latex/idxlayout.sty', 'latex/ellipse.sty',
+    'latex/pict2e.sty', 'latex/p2e-pdftex.def',
+]
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
@@ -382,6 +388,12 @@ man_pages = [
 #man_show_urls = False
 
 
+# strip off LAMMPS_NS:: from index entries
+cpp_index_common_prefix = [
+    'LAMMPS_NS::',
+    '_LMP_STYLE_CONST::', '_LMP_TYPE_CONST::', '_LMP_VAR_CONST::',
+]
+
 # -- Options for Texinfo output -------------------------------------------
 
 # Grouping the document tree into Texinfo files. List of tuples

doc/utils/sphinx-config/false_positives.txt

@@ -790,6 +790,7 @@ dispersionflag
 dissipative
 Dissipative
 distharm
+distutils
 dl
 dlabel
 dlambda

doc/utils/sphinx-config/latex/ellipse.sty

@@ -0,0 +1,318 @@
+%%
+%% This is file `ellipse.sty',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% ellipse.dtx  (with options: `package')
+%% 
+%% Copyright (C) 2015
+%% Daan Leijen
+%% 
+%% This work may be distributed and/or modified under the
+%% conditions of the LaTeX Project Public License, either version 1.3
+%% of this license or (at your option) any later version.
+%% The latest version of this license is in
+%%   http://www.latex-project.org/lppl.txt
+%% and version 1.3 or later is part of all distributions of LaTeX
+%% version 2003/12/01 or later.
+%% 
+%% This work has the LPPL maintenance status "author-maintained".
+%% 
+\NeedsTeXFormat{LaTeX2e}[1999/12/01]
+\ProvidesPackage{ellipse}
+    [2004/11/05 v1.0 .dtx ellipse file]
+\RequirePackage{pict2e}
+
+\providecommand*\pIIe@csedef[1]{\expandafter\edef\csname #1\endcsname}
+\newcommand*\pIIe@ellip@csqrt[3]{%
+  \@ovxx=#1\relax
+  \ifdim\@ovxx<\z@\@ovxx-\@ovxx\fi
+  \@ovyy=#2\relax
+  \ifdim\@ovyy<\z@\@ovyy-\@ovyy\fi
+  \edef\pIIe@csname{@csqrt(\number\@ovxx,\number\@ovyy)}%
+  \expandafter\ifx\csname\pIIe@csname\endcsname\relax
+    \pIIe@ellip@csqrt@%
+    \pIIe@csedef{\pIIe@csname}{\the\dimen@}%
+    #3\dimen@
+  \else
+    #3\dimexpr\csname\pIIe@csname\endcsname\relax
+  \fi
+}
+\newcommand*\pIIe@ellip@csqrt@{%
+  \@ovdx\@ovxx
+  \advance\@ovdx by \@ovyy
+  \dimen@0.7071067\@ovdx
+  \ifdim\dimen@<\@ovyy\dimen@\@ovyy\fi
+  \ifdim\dimen@<\@ovxx\dimen@\@ovxx\fi
+  \ifdim\@ovdx<128\p@
+    \edef\@tempa{\strip@pt\@ovxx}%
+    \@ovxx\@tempa\@ovxx
+    \edef\@tempa{\strip@pt\@ovyy}%
+    \@ovyy\@tempa\@ovyy
+    \advance\@ovxx by \@ovyy
+    \advance\dimen@ by \dimexpr1pt * \@ovxx/\dimen@\relax
+    \divide\dimen@ by 2%
+    \advance\dimen@ by \dimexpr1pt * \@ovxx/\dimen@\relax
+    \divide\dimen@ by 2%
+  \fi
+}
+
+\newcommand*\pIIe@atan@{%
+  \@tempdima\dimen@
+  \@tempdimb\@tempdima
+  \ifdim\@tempdimb<\z@\@tempdimb-\@tempdimb\fi
+  \dimen@0.0663\@tempdimb
+  \advance\dimen@ 0.2447pt\relax
+  \advance\@tempdimb -1pt\relax
+  \edef\@tempa{\strip@pt\@tempdimb}%
+  \dimen@\@tempa\dimen@
+  \edef\@tempa{\strip@pt\@tempdima}%
+  \dimen@\@tempa\dimen@
+  \dimen@-\dimen@
+  \advance\dimen@ 0.7853\@tempdima
+}
+
+\newcommand*\pIIe@atantwo[3]{%
+  \edef\pIIe@csname{@atan2(\number\dimexpr#1\relax,\number\dimexpr#2\relax)}%
+  \expandafter\ifx\csname\pIIe@csname\endcsname\relax
+    \pIIe@atantwo@{#1}{#2}{#3}%
+    \pIIe@csedef{\pIIe@csname}{\the\dimexpr#3\relax}%
+  \else
+    #3\dimexpr\csname\pIIe@csname\endcsname\relax
+  \fi
+}
+
+\newcommand*\pIIe@atantwo@[3]{%
+  \@tempdima\dimexpr#2\relax
+  \@tempdimb\dimexpr#1\relax
+  \ifdim\@tempdima=\z@\relax
+    \ifdim\@tempdimb>\z@\relax\dimen@90\p@
+    \else\ifdim\@tempdimb<\z@\relax\dimen@-90\p@
+    \else\dimen@0\p@
+    \fi\fi
+  \else
+    \@tempdimd\z@
+    \ifdim\@tempdima<\z@\relax
+      \ifdim\@tempdimb<\z@\relax\@tempdimd-180\p@
+      \else\@tempdimd180\p@
+      \fi
+    \fi
+    \dimen@\dimexpr1pt * \@tempdimb/\@tempdima\relax
+    \@tempdimc\dimen@
+    \ifdim\@tempdimc<\z@\relax\@tempdimc-\@tempdimc\fi
+    \ifdim\@tempdimc>\p@\relax
+      \dimen@\dimexpr1pt * \@tempdima/\@tempdimb\relax
+      \ifdim\dimen@<\z@\relax\def\@tempsign{-}\else\def\@tempsign{}\fi
+      \pIIe@atan@
+      \dimen@-\dimen@
+      \advance\dimen@ by \@tempsign1.5707pt\relax
+    \else
+      \pIIe@atan@
+    \fi
+    \dimen@57.29578\dimen@
+    \advance\dimen@ by \@tempdimd
+  \fi
+  #3\dimen@%
+}
+
+\newcommand*\pIIe@noneto[2]{}
+\newcommand*\pIIe@ellip@sincost@[2]{%
+  \CalculateSin{#1}%
+  \CalculateCos{#1}%
+  \@tempdima\UseSin{#1}\p@
+  \@tempdimb\UseCos{#1}\p@
+  \ifdim\@tempdima=\p@\relax
+    \pIIe@csedef{@ellipsin#2}{1}%
+    \pIIe@csedef{@ellipcos#2}{0}%
+  \else\ifdim\@tempdima=-\p@\relax
+    \pIIe@csedef{@ellipsin#2}{-1}%
+    \pIIe@csedef{@ellipcos#2}{0}%
+  \else
+    \@tempdimc\@ellipratio\dimexpr1pt * \@tempdima/\@tempdimb\relax
+    %\typeout{ i#2=\the\@tempdimc, sin(#1)=\the\@tempdima}%
+    \pIIe@ellip@csqrt{\p@}{\@tempdimc}\@tempdimd
+    \ifdim\@tempdimb<\z@\relax\@tempdimd-\@tempdimd\fi
+    \pIIe@csedef{@ellipsin#2}{\strip@pt\dimexpr1pt * \@tempdimc/\@tempdimd\relax}%
+    \pIIe@csedef{@ellipcos#2}{\strip@pt\dimexpr1pt * \p@/\@tempdimd\relax}%
+  \fi\fi
+}
+
+\newcommand*\pIIe@ellip@sincost[2]{%
+  %\typeout{ calc sin cos: angles (#1,#2), radii: (\the\@ovro,\the\@ovri)}%
+  \edef\@ellipratio{\strip@pt\dimexpr1pt * \@ovro/\@ovri\relax}%
+  \pIIe@ellip@sincost@{#1}{one}%
+  \pIIe@ellip@sincost@{#2}{two}%
+  %\typeout{ sincos(a=#1)=(\@ellipsinone,\@ellipcosone), sincos(a=#2)=(\@ellipsintwo,\@ellipcostwo), }%
+}
+\newcommand*\pIIe@omega[3]{%
+  \@tempdima\csname @ellipcos#3\endcsname\@ovro
+  \advance\@tempdima by #1\relax
+  \@tempdimb\csname @ellipsin#3\endcsname\@ovri
+  \advance\@tempdimb by #2\relax
+}
+
+\newcommand*\pIIe@omegai[1]{%
+  \@tempdimc\csname @ellipsin#1\endcsname\@ovro
+  \@tempdimc-\@tempdimc
+  \@tempdimd\csname @ellipcos#1\endcsname\@ovri
+}
+
+\newcommand*\pIIe@ellip@kappa{%
+  \@ovyy\@ellipsinone\p@
+  \@ovxx\@ellipcosone\p@
+  \@tempdima\@ellipcostwo\@ovyy
+  \@tempdima-\@tempdima
+  \advance\@tempdima by \@ellipsintwo\@ovxx
+  \@tempdimb\@ellipcostwo\@ovxx
+  \advance\@tempdimb by \@ellipsintwo\@ovyy
+  \ifdim\@tempdima=\z@\relax
+    \edef\@ellipkappa{0}%
+  \else
+    \dimen@\dimexpr1pt - \@tempdimb\relax
+    \dimen@\dimexpr1pt * \dimen@/\@tempdima\relax
+    \pIIe@ellip@csqrt{2\p@}{1.73205\dimen@}{\dimen@}%
+    \advance\dimen@ by -\p@
+    \divide\dimen@ by 3%
+    \edef\@tempa{\strip@pt\@tempdima}%
+    \dimen@\@tempa\dimen@
+    \edef\@ellipkappa{\strip@pt\dimen@}%
+  \fi
+  %\typeout{ calculated kappa: \@ellipkappa}%
+}
+
+\newcommand*\pIIe@elliparc@[5]{%
+  %\typeout{elliparc: #1, center: (#2, #3), radius (\the\@ovro, \the\@ovri),angle (#4, #5)}%
+  \ifcase #1\relax
+      \let\@ellip@startto\pIIe@lineto
+  \or \let\@ellip@startto\pIIe@moveto
+  \or \let\@ellip@startto\pIIe@noneto%
+  \else\PackageWarning{ellipse}{Illegal initial action in \protect\elliparc: %
+          must be one of 0 (lineto), 1 (moveto) or 2 (do nothing) but I got: #1}%
+  \fi
+  \ifdim\@ovro=\z@\relax\@ovri\z@\fi
+  \ifdim\@ovri=\z@\relax
+    \@ellip@startto{#2}{#3}%
+  \else
+    \pIIe@ellip@sincost{#4}{#5}%
+    \pIIe@elliparc@draw{#2}{#3}%
+  \fi
+}
+\newcommand*\pIIe@elliparc@t[5]{%
+  \ifcase #1\relax
+      \let\@ellip@startto\pIIe@lineto
+  \or \let\@ellip@startto\pIIe@moveto
+  \or \let\@ellip@startto\pIIe@noneto%
+  \else\PackageWarning{ellipse}{Illegal initial action in \protect\elliparc: %
+          must be one of 0 (lineto), 1 (moveto) or 2 (do nothing) but I got: #1}%
+  \fi
+  \ifdim\@ovro=\z@\relax\@ovri\z@\fi
+  \ifdim\@ovri=\z@\relax
+    \@ellip@startto{#2}{#3}%
+  \else
+    \CalculateSin{#4}\CalculateCos{#4}%
+    \edef\@ellipsinone{\UseSin{#4}}%
+    \edef\@ellipcosone{\UseCos{#4}}%
+    \CalculateSin{#5}\CalculateCos{#5}%
+    \edef\@ellipsintwo{\UseSin{#5}}%
+    \edef\@ellipcostwo{\UseCos{#5}}%
+    \pIIe@elliparc@draw{#2}{#3}%
+  \fi
+}
+\newcommand*\pIIe@elliparc@draw[2]{%
+  \pIIe@ellip@kappa%
+  \pIIe@omega{#1}{#2}{one}%
+  %\typeout{ point one: (\the\@tempdima,\the\@tempdimb)}%
+  \@ellip@startto\@tempdima\@tempdimb
+  \pIIe@omegai{one}%
+  \advance\@tempdima by \@ellipkappa\@tempdimc
+  \advance\@tempdimb by \@ellipkappa\@tempdimd
+  \pIIe@add@nums\@tempdima\@tempdimb
+  %\typeout{ control one: (\the\@tempdima,\the\@tempdimb)}%
+  \pIIe@omega{#1}{#2}{two}%
+  \pIIe@omegai{two}%
+  \@tempdimc\@ellipkappa\@tempdimc
+  \@tempdimd\@ellipkappa\@tempdimd
+  \@tempdimc-\@tempdimc
+  \@tempdimd-\@tempdimd
+  \advance\@tempdimc by \@tempdima
+  \advance\@tempdimd by \@tempdimb
+  \pIIe@add@nums\@tempdimc\@tempdimd
+  %\typeout{ control two: (\the\@tempdimc,\the\@tempdimd)}%
+  \pIIe@add@CP\@tempdima\@tempdimb
+  %\typeout{ point two: (\the\@tempdima,\the\@tempdimb)}%
+  \pIIe@addtoGraph\pIIe@curveto@op
+}
+\newcommand*\pIIe@elliparc[7][0]{%
+  \@ovro #4\relax
+  \@ovri #5\relax
+  \iffalse%dim\@ovro=\@ovri
+    \pIIe@arc[#1]{#2}{#3}{#4}{#6}{#7}
+  \else
+    \ifdim \@ovro<\z@ \pIIe@badcircarg\else
+      \ifdim \@ovri<\z@ \pIIe@badcircarg\else
+        \@arclen #7\p@ \advance\@arclen -#6\p@
+        \ifdim \@arclen<\z@ \def\@tempsign{-}\else\def\@tempsign{}\fi
+        \ifdim \@tempsign\@arclen>720\p@
+          \PackageWarning {ellipse}{The arc angle is reduced to -720..720}%
+          \@whiledim \@tempsign\@arclen>720\p@ \do {\advance\@arclen-\@tempsign360\p@}%
+          \@tempdima #6\p@ \advance\@tempdima \@arclen
+          \edef\@angleend{\strip@pt\@tempdima}%
+          \pIIe@@elliparc{#1}{#2}{#3}{#6}{\@angleend}%
+        \else
+          \pIIe@@elliparc{#1}{#2}{#3}{#6}{#7}%
+        \fi
+      \fi
+    \fi
+  \fi
+}
+\newcommand*\pIIe@@elliparc[5]{%
+  \begingroup
+  \ifdim \@tempsign\@arclen>90\p@
+    \divide\@arclen 2%
+    \@tempdima #4\p@\advance\@tempdima by \@arclen
+    \edef\@anglemid{\strip@pt\@tempdima}%
+    \def\@tempa{\pIIe@@elliparc{#1}{#2}{#3}{#4}}%
+    \expandafter\@tempa\expandafter{\@anglemid}%
+    \def\@tempa{\pIIe@@elliparc{2}{#2}{#3}}%
+    \expandafter\@tempa\expandafter{\@anglemid}{#5}%
+  \else
+    \pIIe@elliparc@{#1}{#2}{#3}{#4}{#5}%
+  \fi
+  \endgroup
+}%
+
+\newcommand*\pIIeelliparc[7][0]{%
+  \@killglue
+  \pIIe@elliparc[#1]{#2\unitlength}{#3\unitlength}{#4\unitlength}{#5\unitlength}{#6}{#7}%
+  \ignorespaces%
+}
+\ifx\undefined\elliparc\else
+  \PackageWarning{ellipse}{\protect\elliparc\space is redefined}%
+\fi
+\let\elliparc\pIIeelliparc
+
+\newcommand*\pIIeearc
+  {\@ifstar{\@tempswatrue\pIIe@earc@}{\@tempswafalse\pIIe@earc@}}
+\newcommand*\pIIe@earc@[3][0,360]{\pIIe@earc@@(#1){#2}{#3}}
+\def\pIIe@earc@@(#1,#2)#3#4{%
+  \if@tempswa
+    \pIIe@moveto\z@\z@
+    \pIIe@elliparc{\z@}{\z@}{#3\unitlength}{#4\unitlength}{#1}{#2}%
+    \pIIe@closepath\pIIe@fillGraph
+  \else
+    \pIIe@elliparc[1]{\z@}{\z@}{#3\unitlength}{#4\unitlength}{#1}{#2}%
+    \pIIe@strokeGraph
+  \fi}
+\ifx\undefined\earc\else
+  \PackageWarning{ellipse}{\protect\earc\space is redefined}%
+\fi
+\let\earc\pIIeearc
+
+\newcommand*\pIIeellipse
+  {\@ifstar{\@tempswatrue\pIIe@earc@}{\@tempswafalse\pIIe@earc@}}
+\let\ellipse\pIIeellipse
+
+\endinput
+%%
+%% End of file `ellipse.sty'.

doc/utils/sphinx-config/latex/idxlayout.sty

@@ -0,0 +1,279 @@
+%%
+%% This is file `idxlayout.sty',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% idxlayout.dtx  (with options: `package')
+%% 
+%% Copyright (C) 2010--2012 by Thomas Titz <thomas.titz@chello.at>
+%% 
+%% Permission is granted to distribute and/or modify this work under the
+%% terms of the LaTeX Project Public License (LPPL), version 1.3c or
+%% later.
+%% 
+%% The LPPL maintenance status of this work is "maintained".
+%% 
+%% This work consists of the files idxlayout.dtx, idxlayout.ins and
+%% README and the derived files idxlayout.pdf and idxlayout.sty.
+%% 
+\NeedsTeXFormat{LaTeX2e}
+\ProvidesPackage{idxlayout}[2012/03/30 v0.4d Configurable index layout]
+\RequirePackage{etoolbox,kvoptions,multicol}
+\SetupKeyvalOptions{family=ila,prefix=ila@}
+\newcommand*{\ila@defradiokey}[3][]{%
+  \define@key{ila}{#2}[#1]{%
+    \ifcsname ila@#3@##1\endcsname
+      \csname ila@#3@##1\expandafter\endcsname
+    \else
+      \PackageError{idxlayout}{Unknown value ##1 for option #2}%
+    \fi
+  }%
+}
+\newcounter{idxcols}
+\define@key{ila}{columns}{\setcounter{idxcols}{#1}}
+\setkeys{ila}{columns=2}
+\@ifclassloaded{memoir}{%
+  \ifbool{onecolindex}{%
+    \setkeys{ila}{columns=1}%
+  }{%
+  }%
+  \appto{\onecolindex}{\setkeys{ila}{columns=1}}%
+  \appto{\twocolindex}{\setkeys{ila}{columns=2}}%
+}{%
+  \newlength{\indexcolsep}%
+  \setlength{\indexcolsep}{35\p@}%
+  \newlength{\indexrule}%
+  \setlength{\indexrule}{\z@}%
+}
+\define@key{ila}{columnsep}{\setlength{\indexcolsep}{#1}}
+\define@key{ila}{rule}{\setlength{\indexrule}{#1}}
+\DeclareBoolOption{unbalanced}
+\newlength{\ila@indentunit}
+\define@key{ila}{indentunit}{\setlength{\ila@indentunit}{#1}}
+\setkeys{ila}{indentunit=20\p@}
+\DeclareStringOption{hangindent}
+\DeclareStringOption{subindent}
+\DeclareStringOption{subsubindent}
+\renewcommand{\@idxitem}{\par\setlength{\hangindent}{\ila@hangindent}}
+\def\ila@it@abshang{%
+  \renewcommand*{\ila@hangindent}{2\ila@indentunit}%
+  \renewcommand*{\ila@subindent}{\ila@indentunit}%
+  \renewcommand*{\ila@subsubindent}{1.5\ila@indentunit}%
+  \renewcommand{\subitem}{\@idxitem\hspace*{\ila@subindent}}%
+  \renewcommand{\subsubitem}{\@idxitem\hspace*{\ila@subsubindent}}%
+}
+\def\ila@it@relhang{%
+  \renewcommand*{\ila@hangindent}{1.5\ila@indentunit}%
+  \renewcommand*{\ila@subindent}{\ila@indentunit}%
+  \renewcommand*{\ila@subsubindent}{2\ila@indentunit}%
+  \renewcommand{\subitem}{%
+    \par
+    \deflength{\hangindent}{\ila@hangindent + \ila@subindent}%
+    \hspace*{\ila@subindent}%
+  }%
+  \renewcommand{\subsubitem}{%
+    \par
+    \deflength{\hangindent}{\ila@hangindent + \ila@subsubindent}%
+    \hspace*{\ila@subsubindent}%
+  }%
+}
+\newcommand*{\indexsubsdelim}{; }
+\def\ila@it@singlepar{%
+  \renewcommand*{\ila@hangindent}{\ila@indentunit}%
+  \renewcommand{\subitem}{\unskip\indexsubsdelim}%
+  \renewcommand{\subsubitem}{\unskip\indexsubsdelim}%
+}
+\ila@defradiokey{itemlayout}{it}
+\setkeys{ila}{itemlayout=abshang}
+\newlength{\ila@initsep}
+\define@key{ila}{initsep}{\setlength{\ila@initsep}{#1}}
+\setkeys{ila}{initsep=10\p@ \@plus 5\p@ \@minus 3\p@}
+\DeclareStringOption[\ila@initsep]{notesep}
+\DeclareStringOption[80\p@]{minspace}
+\renewcommand{\indexspace}{\par\vspace{\ila@initsep}}
+\DeclareBoolOption{columnnote}
+\newcommand*{\indexfont}{}
+\def\ila@fo@current{\renewcommand*{\indexfont}{}}
+\def\ila@fo@normalsize{\renewcommand*{\indexfont}{\normalsize}}
+\def\ila@fo@small{\renewcommand*{\indexfont}{\small}}
+\def\ila@fo@footnotesize{\renewcommand*{\indexfont}{\footnotesize}}
+\ila@defradiokey{font}{fo}
+\setkeys{ila}{font=current}
+\newcommand*{\indexjustific}{}
+\def\ila@ju@standard{%
+  \renewcommand*{\indexjustific}{%
+    \setlength{\parindent}{\z@}%
+    \setlength{\parfillskip}{\z@ \@plus 1fil}%
+  }%
+}
+\def\ila@ju@raggedright{\renewcommand*{\indexjustific}{\raggedright}}
+\newcommand*{\ila@RaggedRight}{}
+\def\ila@ju@RaggedRight{%
+  \renewcommand*{\indexjustific}{\ila@RaggedRight}%
+}
+\AtEndPreamble{%
+  \IfFileExists{ragged2e.sty}{%
+    \RequirePackage{ragged2e}%
+    \renewcommand*{\ila@RaggedRight}{\RaggedRight}%
+  }{%
+    \PackageWarning{idxlayout}{%
+      Package ragged2e not available, therefore\MessageBreak
+      substituting command raggedright for RaggedRight\MessageBreak
+    }%
+    \renewcommand*{\ila@RaggedRight}{\raggedright}%
+  }%
+}
+\ila@defradiokey{justific}{ju}
+\setkeys{ila}{justific=standard}
+\newcommand{\ila@prenote}{}
+\newcommand{\setindexprenote}[1]{%
+  \def\ila@prenote{%
+    \begingroup#1\par\nobreak\endgroup
+    \vspace{\ila@notesep}%
+  }%
+}
+\newcommand*{\noindexprenote}{\let\ila@prenote\relax}
+\noindexprenote
+\newcommand*{\indexstheadcase}{\MakeUppercase}
+\newcommand*{\ila@classtype}{0}
+\@ifclassloaded{memoir}{%
+  \def\ila@classtype{2}%
+}{%
+  \ifundef{\KOMAClassName}{%
+  }{%
+    \def\ila@classtype{1}%
+  }%
+}
+\ifcase\ila@classtype\relax
+  \DeclareBoolOption{totoc}%
+  \def\ila@prologue{%
+    \ifundef{\chapter}{%
+      \section*{\indexname}%
+      \ifbool{ila@totoc}{%
+        \addcontentsline{toc}{section}{\indexname}%
+      }{%
+      }%
+    }{%
+      \chapter*{\indexname}%
+      \ifbool{ila@totoc}{%
+        \addcontentsline{toc}{chapter}{\indexname}%
+      }{%
+      }%
+    }%
+    \@mkboth{\indexstheadcase\indexname}{\indexstheadcase\indexname}%
+  }
+\or
+  \def\ila@tc@true{\KOMAoptions{index=totoc}}%
+  \def\ila@tc@false{\KOMAoptions{index=nottotoc}}%
+  \ila@defradiokey[true]{totoc}{tc}%
+  \providecommand{\MakeMarkcase}[1]{#1}%
+  \def\ila@prologue{%
+    \ifundef{\chapter}{%
+    }{%
+      \ifundef{\index@preamble}{%
+      }{%
+        \setchapterpreamble{\index@preamble}%
+      }%
+    }%
+    \idx@@heading{\indexname}%
+    \@mkboth{\MakeMarkcase{\indexname}}{\MakeMarkcase{\indexname}}%
+    \ifundef{\chapter}{%
+    }{%
+      \thispagestyle{\indexpagestyle}%
+    }%
+  }
+\or
+  \def\ila@tc@true{\boolfalse{noindexintoc}}%
+  \def\ila@tc@false{\booltrue{noindexintoc}}%
+  \ila@defradiokey[true]{totoc}{tc}%
+  \def\ila@prologue{%
+    \chapter*{\indexname}%
+    \ifbool{noindexintoc}{%
+    }{%
+      \addcontentsline{toc}{chapter}{\indexname}%
+    }%
+    \ifbool{artopt}{%
+    }{%
+      \thispagestyle{indextitlepagestyle}%
+    }%
+    \indexmark
+    \preindexhook
+  }
+\fi
+\@ifpackageloaded{index}{%
+  \@ifpackagelater{index}{2004/01/21}{%
+    \let\ila@packindadjust\relax
+  }{%
+    \def\ila@packindadjust{%
+      \edef\indexname{\the\@nameuse{idxtitle@\@indextype}}%
+      \ifdefempty{\index@prologue}{%
+      }{%
+        \setindexprenote{\index@prologue}%
+      }%
+    }%
+  }%
+}{%
+  \let\ila@packindadjust\relax
+}
+\ProcessKeyvalOptions*
+\newcommand*{\idxlayout}[1]{\setkeys{ila}{#1}}
+\renewenvironment{theindex}{%
+  \ifbool{@twocolumn}{%
+    \boolfalse{@restonecol}%
+    \onecolumn
+  }{%
+    \booltrue{@restonecol}%
+  }%
+  \setlength{\multicolsep}{\z@}%
+  \setlength{\columnsep}{\indexcolsep}%
+  \setlength{\columnseprule}{\indexrule}%
+  \ila@packindadjust
+  \def\ila@prologueplus{%
+    \ila@prologue
+    \indexfont
+    \ifbool{ila@columnnote}{%
+    }{%
+      \ila@prenote
+    }%
+  }%
+  \ifnumcomp{\theidxcols}{<}{\tw@}{%
+    \ila@prologueplus
+  }{%
+    \ifbool{ila@unbalanced}{%
+      \begin{multicols*}{\theidxcols}[\ila@prologueplus][\ila@minspace]%
+    }{%
+      \begin{multicols}{\theidxcols}[\ila@prologueplus][\ila@minspace]%
+    }%
+  }%
+  \setlength{\parskip}{\z@ \@plus 0.3\p@}%
+  \indexjustific
+  \ifundef{\chapter}{%
+    \ifundef{\index@preamble}{%
+    }{%
+      \index@preamble\par\nobreak
+    }%
+  }{%
+  }%
+  \ifbool{ila@columnnote}{%
+    \ila@prenote
+  }{%
+  }%
+  \let\item\@idxitem
+}{%
+  \ifnumcomp{\theidxcols}{<}{\tw@}{%
+  }{%
+    \ifbool{ila@unbalanced}{%
+      \end{multicols*}%
+    }{%
+      \end{multicols}%
+    }%
+  }%
+  \ifbool{@restonecol}{%
+  }{%
+    \twocolumn
+  }%
+}
+\endinput
+%%
+%% End of file `idxlayout.sty'.

doc/utils/sphinx-config/latex/p2e-pdftex.def

@@ -0,0 +1,41 @@
+%%
+%% This is file `p2e-pdftex.def',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% p2e-drivers.dtx  (with options: `pdftex')
+%% 
+%% Copyright (C) 2003-2016
+%% Rolf Niepraschk, Rolf.Niepraschk@gmx.de
+%% Hubert Gaesslein,
+%% Josef Tkadlec, j.tkadlec@email.cz
+%% 
+%% This work may be distributed and/or modified under the
+%% conditions of the LaTeX Project Public License, either version 1.3
+%% of this license or (at your option) any later version.
+%% The latest version of this license is in
+%%   http://www.latex-project.org/lppl.txt
+%% and version 1.3 or later is part of all distributions of LaTeX
+%% version 2003/12/01 or later.
+%% 
+%% This work has the LPPL maintenance status "author-maintained".
+%% 
+%% This work consists of all files listed in `manifest.txt'.
+%% 
+\ProvidesFile{p2e-pdftex.def}
+        [2016/02/05 v0.1u
+                          Driver-dependant file (RN,HjG,JT)]
+\begingroup
+  \@ifundefined{pdfoutput}{}{%
+    \ifnum\pdfoutput>0\relax
+      \gdef\pIIe@mode{2}
+    \fi
+  }
+\endgroup
+\ifcase\pIIe@mode\relax \or\or
+  \def\pIIe@code#1{\pdfliteral{ q #1 Q }}
+\fi
+\endinput
+%%
+%% End of file `p2e-pdftex.def'.

doc/utils/sphinx-config/latex/pict2e.sty

@@ -0,0 +1,820 @@
+%%
+%% This is file `pict2e.sty',
+%% generated with the docstrip utility.
+%%
+%% The original source files were:
+%%
+%% pict2e.dtx  (with options: `package')
+%% 
+%% Copyright (C) 2003-2016
+%% Rolf Niepraschk, Rolf.Niepraschk@gmx.de
+%% Hubert Gaesslein,
+%% Josef Tkadlec, j.tkadlec@email.cz
+%% 
+%% This work may be distributed and/or modified under the
+%% conditions of the LaTeX Project Public License, either version 1.3
+%% of this license or (at your option) any later version.
+%% The latest version of this license is in
+%%   http://www.latex-project.org/lppl.txt
+%% and version 1.3 or later is part of all distributions of LaTeX
+%% version 2003/12/01 or later.
+%% 
+%% This work has the LPPL maintenance status "author-maintained".
+%% 
+%% This work consists of all files listed in `manifest.txt'.
+%% 
+\NeedsTeXFormat{LaTeX2e}[1999/12/01]
+\ProvidesPackage{pict2e}[2020/09/30 v0.4b Improved picture commands (HjG,RN,JT)]
+\edef\Gin@codes{%
+ \catcode`\noexpand\^^A\the\catcode`\^^A\relax
+ \catcode`\noexpand\"\the\catcode`\"\relax
+ \catcode`\noexpand\!\the\catcode`\!\relax
+ \catcode`\noexpand\:\the\catcode`\:\relax}
+\catcode`\^^A=\catcode`\%
+\@makeother\"%
+\@makeother\!%
+\@makeother\:%
+\def\@defaultunitsset#1#2#3{%
+  \@defaultunits#1\dimexpr#2#3\relax\relax\@nnil}
+\newcommand*\pIIe@mode{-1}
+\newcommand*\pIIe@code[1]{}
+\providecommand*\Gin@driver{}
+\newcommand*\pIIe@tempa{}
+\newcommand*\pIIe@tempb{}
+\newcommand*\pIIe@tempc{}
+\DeclareOption{dvips}{\def\Gin@driver{dvips.def}}
+\DeclareOption{xdvi}{\ExecuteOptions{dvips}}
+\DeclareOption{dvipdf}{\def\Gin@driver{dvipdf.def}}
+\DeclareOption{dvipdfm}{\def\Gin@driver{dvipdfm.def}}
+\DeclareOption{dvipdfmx}{\def\Gin@driver{dvipdfmx.def}}
+\DeclareOption{pdftex}{\def\Gin@driver{pdftex.def}}
+\DeclareOption{luatex}{\def\Gin@driver{luatex.def}}
+\DeclareOption{xetex}{\def\Gin@driver{xetex.def}}
+\DeclareOption{dvipsone}{\def\Gin@driver{dvipsone.def}}
+\DeclareOption{dviwindo}{\ExecuteOptions{dvipsone}}
+\DeclareOption{oztex}{\ExecuteOptions{dvips}}
+\DeclareOption{textures}{\def\Gin@driver{textures.def}}
+\DeclareOption{pctexps}{\def\Gin@driver{pctexps.def}}
+\DeclareOption{pctex32}{\def\Gin@driver{pctex32.def}}
+\DeclareOption{vtex}{\def\Gin@driver{vtex.def}}
+\DeclareOption{original}{\def\pIIe@mode{0}}
+\newif\ifpIIe@pdfliteral@ok
+\pIIe@pdfliteral@oktrue
+\ifx\pIIe@pdfliteral\@undefined
+  \ifx\pdfliteral\@undefined
+    \pIIe@pdfliteral@okfalse
+    \def\pIIe@pdfliteral#1{%
+      \PackageWarning{pict2e}{pdfliteral not supported}%
+    }%
+  \else
+    \let\pIIe@pdfliteral\pdfliteral
+  \fi
+\fi
+\def\pIIe@buttcap{%
+  \ifpIIe@pdfliteral@ok
+    \buttcap
+  \fi
+}
+\newcommand*\pIIe@FAL{1.52}%
+\newcommand*\pIIe@FAW{3.2}%
+\newcommand*\pIIe@CAW{1.5pt}%
+\newcommand*\pIIe@FAI{0.25}%
+\newcommand*\ltxarrows{%
+  \let\pIIe@vector=\pIIe@vector@ltx
+}
+\newcommand*\pstarrows{%
+  \let\pIIe@vector=\pIIe@vector@pst
+}
+\DeclareOption{ltxarrows}{\AtEndOfPackage{\ltxarrows}}
+\DeclareOption{pstarrows}{\AtEndOfPackage{\pstarrows}}
+\newcommand*\pIIe@debug@comment{}
+\DeclareOption{debug}{%
+  \def\pIIe@debug@comment{^^J^^J\@percentchar\space >>> pict2e <<<^^J}%
+  \begingroup
+    \@ifundefined{pdfcompresslevel}{}{\global\pdfcompresslevel\z@}%
+  \endgroup}
+\DeclareOption{hide}{\AtEndOfPackage{%
+  \let\pIIe@code\@gobble
+}}
+\DeclareOption*{\ExecuteOptions{original}}
+\ExecuteOptions{ltxarrows}
+\InputIfFileExists{pict2e.cfg}{}{}
+\ProcessOptions\relax
+\ifnum\pIIe@mode=\z@
+  \PackageInfo{pict2e}{Package option `original' requested}
+\else
+  \if!\Gin@driver!
+    \PackageError{pict2e}
+      {No driver specified at all}
+      {You should make a default driver option in a file\MessageBreak
+       pict2e.cfg\MessageBreak eg: \protect\ExecuteOptions{dvips}}%
+  \else
+    \PackageInfo{pict2e}{Driver file: \Gin@driver}
+    \@ifundefined{ver@\Gin@driver}{\input{\Gin@driver}}{}
+    \PackageInfo{pict2e}{Driver file for pict2e: p2e-\Gin@driver}
+    \InputIfFileExists{p2e-\Gin@driver}{}{%
+      \PackageError{pict2e}%
+        {Driver file ``p2e-\Gin@driver'' not found}%
+        {Q: Is the file properly installed? A: No!}}
+  \fi
+\fi
+\ifnum\pIIe@mode>\z@
+  \ifnum\pIIe@mode<\thr@@
+    \RequirePackage{trig}
+    \let\pIIe@oldline\line
+    \let\pIIe@old@sline\@sline
+    \let\pIIe@oldvector\vector
+    \let\pIIe@old@circle\@circle
+    \let\pIIe@old@dot\@dot
+    \let\pIIe@old@bezier\@bezier
+    \AtBeginDocument{%
+      \@ifundefined{@cbezier}{%
+        \def\pIIe@old@cbezier[#1](#2,#3)(#4,#5)(#6,#7)(#8,#9){}%
+        }{\let\pIIe@old@cbezier\@cbezier}}
+    \let\pIIe@oldoval\oval
+    \let\pIIe@old@oval\@oval
+    \newcommand*\OriginalPictureCmds{%
+      \let\@sline\pIIe@old@sline
+      \let\line\pIIe@oldline
+      \let\vector\pIIe@oldvector
+      \let\@circle\pIIe@old@circle
+      \let\@dot\pIIe@old@dot
+      \let\@bezier\pIIe@old@bezier
+      \let\@cbezier\pIIe@old@cbezier
+      \renewcommand*\oval[1][]{\pIIe@oldoval}%
+      \let\@oval\pIIe@old@oval
+    }
+  \else
+    \PackageError{pict2e}
+      {Unsupported mode (\pIIe@mode) specified}
+      {The driver you specified requested a mode\MessageBreak
+       not supported by this version of this package}
+  \fi
+\else
+  \ifnum\pIIe@mode<\z@
+    \PackageError{pict2e}
+      {No suitable driver specified}
+      {You should make a default driver option in a file\MessageBreak
+       pict2e.cfg\MessageBreak eg: \protect\ExecuteOptions{dvips}}
+  \fi
+\fi
+\ifnum\pIIe@mode>\z@
+  \ifcase\pIIe@mode\relax
+  \or
+    \newcommand*\pIIe@moveto@op{moveto}
+    \newcommand*\pIIe@lineto@op{lineto}
+    \newcommand*\pIIe@setlinewidth@op{setlinewidth}
+    \newcommand*\pIIe@stroke@op{stroke}
+    \newcommand*\pIIe@fill@op{fill}
+    \newcommand*\pIIe@curveto@op{curveto}
+    \newcommand*\pIIe@concat@op{concat}
+    \newcommand*\pIIe@closepath@op{closepath}
+  \or
+    \newcommand*\pIIe@moveto@op{m}
+    \newcommand*\pIIe@lineto@op{l}
+    \newcommand*\pIIe@setlinewidth@op{w}
+    \newcommand*\pIIe@stroke@op{S}
+    \newcommand*\pIIe@fill@op{f}
+    \newcommand*\pIIe@curveto@op{c}
+    \newcommand*\pIIe@concat@op{cm}
+    \newcommand*\pIIe@closepath@op{h}
+  \fi
+  \@ifdefinable\pIIe@GRAPH{\newtoks\pIIe@GRAPH}
+  \newcommand*\pIIe@addtoGraph[1]{%
+    \begingroup
+      \edef\x{\the\pIIe@GRAPH\space#1}%
+      \global\pIIe@GRAPH\expandafter{\x}%
+    \endgroup}
+  \newcommand*\pIIe@fillGraph{\begingroup \@tempswatrue\pIIe@drawGraph}
+  \newcommand*\pIIe@strokeGraph{\begingroup \@tempswafalse\pIIe@drawGraph}
+  \newcommand*\pIIe@drawGraph{%
+      \edef\x{\pIIe@debug@comment\space
+              \pIIe@scale@PTtoBP}%
+      \if@tempswa
+        \edef\y{\pIIe@fill@op}%
+      \else
+        \edef\x{\x\space
+          \strip@pt\@wholewidth\space\pIIe@setlinewidth@op
+          \pIIe@linecap\pIIe@linejoin\space}%
+        \edef\y{\pIIe@stroke@op}%
+      \fi
+      \expandafter\pIIe@code\expandafter{%
+        \expandafter\x\the\pIIe@GRAPH\space\y}%
+      \global\pIIe@GRAPH{}\xdef\pIIe@CPx{}\xdef\pIIe@CPy{}%
+    \endgroup}
+  \newcommand*\pIIe@CPx{} \newcommand*\pIIe@CPy{}
+  \newcommand*\pIIe@add@CP[2]{%
+    \begingroup
+      \@tempdima#1\xdef\pIIe@CPx{\the\@tempdima}%
+      \@tempdimb#2\xdef\pIIe@CPy{\the\@tempdimb}%
+      \pIIe@addtoGraph{\strip@pt\@tempdima\space\strip@pt\@tempdimb}%
+    \endgroup}
+  \newcommand*\pIIe@add@nums[2]{%
+    \begingroup
+      \@tempdima#1\relax
+      \@tempdimb#2\relax
+      \pIIe@addtoGraph{\strip@pt\@tempdima\space\strip@pt\@tempdimb}%
+    \endgroup}
+  \newcommand*\pIIe@add@num[1]{%
+    \begingroup
+      \@tempdima#1\relax
+      \pIIe@addtoGraph{\strip@pt\@tempdima}%
+    \endgroup}
+  \newcommand*\pIIe@PTtoBP{0.99626401 }
+  \ifcase\pIIe@mode\relax
+  \or
+    \newcommand*\pIIe@concat[6]{%
+      \begingroup
+        \pIIe@addtoGraph{[}%
+        \@tempdima#1\relax \@tempdimb#2\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#3\relax \@tempdimb#4\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#5\relax \@tempdimb#6\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \pIIe@addtoGraph{] \pIIe@concat@op}%
+      \endgroup}
+    \newcommand*\pIIe@translate[2]{\pIIe@add@nums{#1}{#2}\pIIe@addtoGraph{translate}}
+    \newcommand*\pIIe@rotate[1]{\pIIe@add@num{#1}\pIIe@addtoGraph{rotate}}
+    \newcommand*\pIIe@scale[2]{\pIIe@add@nums{#1}{#2}\pIIe@addtoGraph{scale}}
+    \newcommand*\pIIe@scale@PTtoBP{\pIIe@PTtoBP \pIIe@PTtoBP scale}
+  \or
+    \newcommand*\pIIe@concat[6]{%
+      \begingroup
+        \@tempdima#1\relax \@tempdimb#2\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#3\relax \@tempdimb#4\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#5\relax \@tempdimb#6\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \pIIe@addtoGraph\pIIe@concat@op
+      \endgroup}
+    \newcommand*\pIIe@translate[2]{\pIIe@concat\p@\z@\z@\p@{#1}{#2}}
+    \newcommand*\pIIe@rotate[1]{%
+      \begingroup
+        \@tempdima#1\relax
+        \edef\pIIe@tempa{\strip@pt\@tempdima}%
+        \CalculateSin\pIIe@tempa
+        \CalculateCos\pIIe@tempa
+        \edef\pIIe@tempb{\UseSin\pIIe@tempa}%
+        \edef\pIIe@tempc{\UseCos\pIIe@tempa}%
+        \pIIe@concat{\pIIe@tempc\p@}{\pIIe@tempb\p@}%
+          {-\pIIe@tempb\p@}{\pIIe@tempc\p@}\z@\z@
+      \endgroup}
+    \newcommand*\pIIe@scale[2]{\pIIe@concat{#1}\z@\z@{#2}\z@\z@}
+    \newcommand*\pIIe@scale@PTtoBP{\pIIe@PTtoBP 0 0 \pIIe@PTtoBP 0 0 \pIIe@concat@op}
+  \fi
+  \newcommand*\pIIe@moveto[2]{%
+    \pIIe@add@CP{#1}{#2}\pIIe@addtoGraph\pIIe@moveto@op}
+  \newcommand*\pIIe@lineto[2]{%
+    \pIIe@add@CP{#1}{#2}\pIIe@addtoGraph\pIIe@lineto@op}
+  \ifcase\pIIe@mode\relax
+  \or
+    \newcommand*\pIIe@rcurveto[6]{%
+      \begingroup
+        \@tempdima#1\relax \@tempdimb#2\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#3\relax \@tempdimb#4\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#5\relax \@tempdimb#6\relax
+        \pIIe@add@CP\@tempdima\@tempdimb
+        \pIIe@addtoGraph{rcurveto}%
+      \endgroup}
+  \or
+    \newcommand*\pIIe@rcurveto[6]{%
+      \begingroup
+        \@tempdima#1\advance\@tempdima\pIIe@CPx\relax
+        \@tempdimb#2\advance\@tempdimb\pIIe@CPy\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#3\advance\@tempdima\pIIe@CPx\relax
+        \@tempdimb#4\advance\@tempdimb\pIIe@CPy\relax
+        \pIIe@add@nums\@tempdima\@tempdimb
+        \@tempdima#5\advance\@tempdima\pIIe@CPx\relax
+        \@tempdimb#6\advance\@tempdimb\pIIe@CPy\relax
+        \pIIe@add@CP\@tempdima\@tempdimb
+        \pIIe@addtoGraph\pIIe@curveto@op
+      \endgroup}
+  \fi
+  \newcommand*\pIIe@curveto[6]{%
+    \begingroup
+      \@tempdima#1\relax \@tempdimb#2\relax
+      \pIIe@add@nums\@tempdima\@tempdimb
+      \@tempdima#3\relax \@tempdimb#4\relax
+      \pIIe@add@nums\@tempdima\@tempdimb
+      \@tempdima#5\relax \@tempdimb#6\relax
+      \pIIe@add@CP\@tempdima\@tempdimb
+      \pIIe@addtoGraph\pIIe@curveto@op
+    \endgroup}
+  \newcommand*\pIIe@closepath{\pIIe@addtoGraph\pIIe@closepath@op}
+  \newcommand*\pIIe@pyth[3]{%
+    \begingroup
+      \@tempdima=#1\relax
+      \ifnum\@tempdima<\z@\@tempdima=-\@tempdima\fi
+      \@tempdimb=#2\relax
+      \ifnum\@tempdimb<\z@\@tempdimb=-\@tempdimb\fi
+      \advance\@tempdimb\@tempdima
+      \ifnum\@tempdimb=\z@
+        \@tempdimc=\z@
+      \else
+        \multiply\@tempdima 8\relax
+        \pIIe@divide\@tempdima\@tempdimb\@tempdimc
+        \advance\@tempdimc -4pt
+        \multiply\@tempdimc 2
+        \edef\pIIe@tempa{\strip@pt\@tempdimc}%
+        \@tempdima=\pIIe@tempa\@tempdimc
+        \advance\@tempdima 64pt
+        \divide\@tempdima 2\relax
+        \@dashdim=7pt
+        \pIIe@@pyth\pIIe@@pyth\pIIe@@pyth
+        \edef\pIIe@tempa{\strip@pt\@dashdim}%
+        \@tempdimc=\pIIe@tempa\@tempdimb
+        \global\divide\@tempdimc 8
+      \fi
+      \edef\x{\endgroup#3=\the\@tempdimc}%
+    \x}
+  \newcommand*\pIIe@@pyth{%
+    \pIIe@divide\@tempdima\@dashdim\@tempdimc
+    \advance\@dashdim\@tempdimc
+    \divide\@dashdim\tw@}
+  \newcommand*\pIIe@divide[3]{%
+    \begingroup
+    \dimendef\Numer=254\relax \dimendef\Denom=252\relax
+    \countdef\Num=254\relax   \countdef\Den=252\relax
+    \countdef\I=250\relax     \countdef\Numb=248\relax
+    \Numer #1\relax \Denom #2\relax
+    \ifdim\Denom<\z@ \Denom -\Denom \Numer=-\Numer \fi
+    \ifdim\Numer<\z@ \def\sign{-}\Numer=-\Numer \else \def\sign{}\fi
+    \ifdim\Denom=\z@
+      \edef\Q{\strip@pt\maxdimen}%
+      \PackageWarning{pict2e}%
+        {Division by 0, \sign\strip@pt\maxdimen\space used}{}%
+    \else
+      \Num=\Numer \Den=\Denom
+      \Numb=\Num \divide\Numb\Den
+      \ifnum\Numb>16383
+        \edef\Q{\strip@pt\maxdimen}%
+        \PackageWarning{pict2e}%
+          {Division overflow, \sign\strip@pt\maxdimen\space used}{}%
+      \else
+        \edef\Q{\number\Numb.}%
+        \multiply \Numb\Den \advance\Num -\Numb
+        \I=6\relax
+        \@whilenum \I>\z@ \do{\pIIe@@divide\advance\I\m@ne}%
+      \fi
+    \fi
+    \edef\tempend{\noexpand\endgroup\noexpand#3=\sign\Q\p@}%
+    \tempend}
+  \def\pIIe@@divide{%
+    \@whilenum \Num>214748364 \do{\divide\Num\tw@ \divide\Den\tw@}%
+    \multiply \Num 10
+    \Numb=\Num \divide\Numb\Den
+    \edef\Q{\Q\number\Numb}%
+    \multiply \Numb\Den \advance \Num -\Numb
+    \ifnum\Num>\z@\else\I=0\fi}
+  \newcommand*\pIIe@checkslopeargsline[2]{%
+    \pIIe@checkslopeargs{#1}{#2}{16383}}
+  \newcommand*\pIIe@checkslopeargsvector[2]{%
+    \pIIe@checkslopeargs{#1}{#2}{1000}}
+  \newcommand*\pIIe@checkslopeargs[3]{%
+    \edef\@tempa{#1}\expandafter\pIIe@checkslopearg\@tempa.:{#3}%
+    \edef\@tempa{#2}\expandafter\pIIe@checkslopearg\@tempa.:{#3}%
+    \ifdim #1\p@=\z@ \ifdim #2\p@=\z@ \@badlinearg \fi\fi}
+  \def\pIIe@checkslopearg #1.#2:#3{%
+    \def\@tempa{#1}%
+    \ifx\@tempa\empty\def\@tempa{0}\fi
+    \ifx\@tempa\space\def\@tempa{0}\fi
+    \ifnum\ifnum\@tempa<\z@-\fi\@tempa>#3 \@badlinearg \fi}
+  \def\@badlinearg{\PackageError
+    {pict2e}{Bad \protect\line\space or \protect\vector\space argument}{}}
+  \def\line(#1,#2)#3{%
+    \begingroup
+    \pIIe@checkslopeargsline{#1}{#2}%
+    \@tempdima=#1pt\relax \@tempdimb=#2pt\relax
+    \@defaultunitsset\@linelen{#3}\unitlength
+    \ifdim\@linelen<\z@ \@badlinearg \else
+      \pIIe@sline
+      \pIIe@moveto\z@\z@
+      \pIIe@lineto\@xdim\@ydim
+      \pIIe@strokeGraph
+      \box\@tempboxa
+    \fi
+    \endgroup}
+  \newcommand*\pIIe@sline{%
+    \ifdim\@tempdima=\z@
+      \ifdim\@tempdimb<\z@\@linelen-\@linelen\fi
+      \@ydim=\@linelen
+      \@xdim=\z@
+    \else
+      \ifdim\@tempdima<\z@\@linelen-\@linelen\fi
+      \ifdim\@tempdimb=\z@
+        \@xdim=\@linelen
+        \@ydim=\z@
+      \else
+        \pIIe@divide\@tempdimb\@tempdima\dimen@
+        \@ydim=\strip@pt\dimen@\@linelen
+        \@xdim=\@linelen
+      \fi
+    \fi
+    \@ovxx=\ifnum\@xdim=\z@ \z@\else\@linelen\fi
+    \@ovyy=\ifnum\@ydim<\z@ \z@\else\@ydim\fi
+    \@ovdy=\ifnum\@ydim<\z@ -\@ydim\else\z@\fi
+    \setbox\@tempboxa\hbox{%
+      \vrule\@height \@ovyy \@depth \@ovdy \@width \z@
+      \vrule\@height \z@ \@depth \z@ \@width \@ovxx}}
+  \def\vector(#1,#2)#3{%
+    \begingroup
+    \pIIe@checkslopeargsvector{#1}{#2}%
+    \@tempdima=#1pt\relax \@tempdimb=#2pt\relax
+    \@defaultunitsset\@linelen{#3}\unitlength
+    \ifdim\@linelen<\z@ \@badlinearg \else
+      \pIIe@sline
+      \@defaultunitsset\@linelen{#3}\unitlength
+      \pIIe@pyth{\@tempdima}{\@tempdimb}\dimen@
+      \ifdim\@tempdima=\z@ \else
+        \ifdim\@tempdimb=\z@ \else
+          \pIIe@divide\dimen@{\@tempdima}\@xdim
+          \@linelen\strip@pt\@xdim\@linelen
+          \ifdim\@linelen<\z@\@linelen-\@linelen\fi
+        \fi
+      \fi
+      \pIIe@divide{\@tempdimb}\dimen@\@ydim
+      \pIIe@divide{\@tempdima}\dimen@\@xdim
+      \pIIe@concat\@xdim\@ydim{-\@ydim}\@xdim\z@\z@
+      \pIIe@vector
+      \pIIe@fillGraph
+      \box\@tempboxa
+    \fi
+    \endgroup}
+  \newcommand*\pIIe@vector{}
+  \newcommand*\pIIe@vector@ltx{%
+    \@ydim\pIIe@FAW\@wholewidth \advance\@ydim\pIIe@CAW\relax
+    \@ovxx\pIIe@FAL\@ydim
+    \@xdim\@linelen \advance\@xdim-\@ovxx
+    \divide\@ydim\tw@
+    \divide\@ovxx\tw@ \advance\@ovxx\@xdim
+    \@ovyy\@ydim
+    \divide\@ovyy\tw@ \advance\@ovyy-\pIIe@FAI\@ydim
+    \pIIe@bezier@QtoC\@linelen\@ovxx\@ovro
+    \pIIe@bezier@QtoC\z@\@ovyy\@ovri
+    \pIIe@bezier@QtoC\@xdim\@ovxx\@clnwd
+    \pIIe@bezier@QtoC\@ydim\@ovyy\@clnht
+    \pIIe@moveto\@linelen\z@
+    \pIIe@curveto\@ovro{-\@ovri}\@clnwd{-\@clnht}\@xdim{-\@ydim}%
+    \ifdim\@xdim>\z@
+      \pIIe@lineto\@xdim{-\@halfwidth}%
+      \pIIe@lineto\z@{-\@halfwidth}%
+      \pIIe@lineto\z@{\@halfwidth}%
+      \pIIe@lineto\@xdim{\@halfwidth}%
+    \fi
+    \pIIe@lineto\@xdim\@ydim
+    \pIIe@curveto\@clnwd\@clnht\@ovro\@ovri\@linelen\z@}
+  \newcommand*\pIIe@vector@pst{%
+    \@ydim\pIIe@FAW\@wholewidth \advance\@ydim\pIIe@CAW\relax
+    \@ovxx\pIIe@FAL\@ydim
+    \@xdim\@linelen \advance\@xdim-\@ovxx
+    \divide\@ydim\tw@
+    \@ovyy\@ydim \advance\@ovyy-\@halfwidth
+    \@ovdx\pIIe@FAI\@ovxx
+    \pIIe@divide\@ovdx\@ydim\@tempdimc
+    \@ovxx\strip@pt\@ovyy\@tempdimc
+    \advance\@ovxx\@xdim
+    \advance\@ovdx\@xdim
+    \pIIe@moveto\@linelen\z@
+    \pIIe@lineto\@xdim{-\@ydim}%
+    \ifdim\@xdim>\z@
+      \pIIe@lineto\@ovxx{-\@halfwidth}%
+      \pIIe@lineto\z@{-\@halfwidth}%
+      \pIIe@lineto\z@{\@halfwidth}%
+      \pIIe@lineto\@ovxx{\@halfwidth}%
+    \else
+      \pIIe@lineto\@ovdx\z@
+    \fi
+    \pIIe@lineto\@xdim\@ydim
+    \pIIe@lineto\@linelen\z@}
+    \def\@circle#1{\begingroup \@tempswafalse\pIIe@circ{#1}}
+    \def\@dot#1{\begingroup \@tempswatrue\pIIe@circ{#1}}
+  \newcommand*\pIIe@circ[1]{%
+      \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+      \ifdim\pIIe@tempdima<\z@ \pIIe@badcircarg \fi
+      \divide\pIIe@tempdima\tw@
+      \pIIe@circle\pIIe@tempdima
+      \if@tempswa \pIIe@fillGraph \else \buttcap \pIIe@strokeGraph \fi
+    \endgroup}
+  \newcommand*\pIIe@circle[1]{%
+    \pIIe@qcircle[1]\z@{#1}\pIIe@qcircle  \@ne{#1}%
+    \pIIe@qcircle  \tw@{#1}\pIIe@qcircle\thr@@{#1}\pIIe@closepath}
+  \newcommand*\pIIe@qcircle[3][0]{%
+    \begingroup
+      \@ovro#3\relax \@ovri0.55228474983\@ovro
+      \@tempdimc\@ovri \advance\@tempdimc-\@ovro
+      \ifnum#1>\z@ \@tempswatrue \else \@tempswafalse \fi
+      \ifcase#2\relax
+        \pIIe@@qcircle\@ovro\z@\z@\@ovri\@tempdimc\@ovro{-\@ovro}\@ovro
+      \or
+        \pIIe@@qcircle\z@\@ovro{-\@ovri}\z@{-\@ovro}\@tempdimc{-\@ovro}{-\@ovro}%
+      \or
+        \pIIe@@qcircle{-\@ovro}\z@\z@{-\@ovri}{-\@tempdimc}{-\@ovro}\@ovro{-\@ovro}%
+      \or
+        \pIIe@@qcircle\z@{-\@ovro}\@ovri\z@\@ovro{-\@tempdimc}\@ovro\@ovro
+      \fi
+    \endgroup}
+  \newcommand*\pIIe@@qcircle[8]{%
+    \if@tempswa\pIIe@moveto{#1}{#2}\fi \pIIe@rcurveto{#3}{#4}{#5}{#6}{#7}{#8}}
+  \newcommand*\pIIe@badcircarg{%
+    \PackageError{pict2e}%
+      {Illegal argument in \protect\circle(*), \protect\oval, \protect\arc(*) or
+      \protect\circlearc.}%
+      {The radius of a circle, dot, arc or oval corner must be greater than zero.}}%
+  \newcommand*\maxovalrad{20pt}
+  \newcommand*\pIIe@defaultUL[2]{%
+    \@defaultunitsset\pIIe@tempdima{#2}\unitlength
+    \edef#1{\the\pIIe@tempdima}}
+  \newcommand*\pIIe@def@UL{}
+  \def\pIIe@def@UL#1\relax#2#3{%
+    \edef#2{\the\dimen@}}
+  \newcommand*\pIIe@maxovalrad{}
+  \newcommand*\pIIe@oval{}
+  \def\pIIe@oval#1(#2,#3){\@ifnextchar[{\@oval(#2,#3)}{\@oval(#2,#3)[]}}
+  \renewcommand*\oval[1][\maxovalrad]{%
+    \begingroup \pIIe@defaultUL\pIIe@maxovalrad{#1}%
+      \ifdim\pIIe@maxovalrad<\z@ \pIIe@badcircarg \fi
+      \pIIe@oval}
+  \def\@oval(#1,#2)[#3]{%
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength \divide\pIIe@tempdima\tw@
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength \divide\pIIe@tempdimb\tw@
+    \pIIe@tempdimc \ifdim\pIIe@tempdimb>\pIIe@tempdima \pIIe@tempdima \else \pIIe@tempdimb \fi
+    \ifdim\pIIe@maxovalrad<\pIIe@tempdimc \pIIe@tempdimc\pIIe@maxovalrad\relax \fi
+    \pIIe@tempdimd\pIIe@tempdima \advance\pIIe@tempdimd-\pIIe@tempdimc
+    \pIIe@tempdime\pIIe@tempdimb \advance\pIIe@tempdime-\pIIe@tempdimc
+    \pIIe@get@quadrants{#3}%
+    \ifnum15=\@tempcnta \pIIe@buttcap \fi
+    \@tempswatrue
+    \ifnum9=\@tempcnta
+      \pIIe@qoval\z@{-\pIIe@tempdimb}{\pIIe@tempdimd}{-\pIIe@tempdimb}%
+        \thr@@\pIIe@tempdimc\pIIe@tempdima\z@
+      \@tempcnta\@ne
+    \fi
+    \pIIe@qoval\pIIe@tempdima\z@\pIIe@tempdima\pIIe@tempdime%
+      \z@\pIIe@tempdimc\z@\pIIe@tempdimb
+    \pIIe@qoval\z@\pIIe@tempdimb{-\pIIe@tempdimd}\pIIe@tempdimb%
+      \@ne\pIIe@tempdimc{-\pIIe@tempdima}\z@
+    \pIIe@qoval{-\pIIe@tempdima}\z@{-\pIIe@tempdima}{-\pIIe@tempdime}%
+      \tw@\pIIe@tempdimc\z@{-\pIIe@tempdimb}%
+    \pIIe@qoval\z@{-\pIIe@tempdimb}{\pIIe@tempdimd}{-\pIIe@tempdimb}%
+      \thr@@\pIIe@tempdimc\pIIe@tempdima\z@
+    \pIIe@strokeGraph
+    \endgroup}
+  \newcommand*\pIIe@qoval[8]{%
+    \ifodd\@tempcnta
+      \if@tempswa\pIIe@moveto{#1}{#2}\fi
+      \pIIe@lineto{#3}{#4}\pIIe@qcircle{#5}{#6}\pIIe@lineto{#7}{#8}%
+      \@tempswafalse
+    \else
+      \@tempswatrue
+    \fi
+    \divide\@tempcnta\tw@}
+  \newcommand*\pIIe@get@quadrants[1]{%
+    \@ovttrue \@ovbtrue \@ovltrue \@ovrtrue \@tempcnta\z@
+    \@tfor\reserved@a:=#1\do{\csname @ov\reserved@a false\endcsname}%
+    \if@ovr \if@ovb\@setfpsbit2\fi \if@ovt\@setfpsbit4\fi \fi
+    \if@ovl \if@ovb\@setfpsbit1\fi \if@ovt\@setfpsbit8\fi \fi}
+  \def\@bezier#1(#2,#3)(#4,#5)(#6,#7){%
+    \ifnum #1=\z@
+      \@killglue
+      \begingroup
+      \@defaultunitsset\pIIe@tempdima{#2}\unitlength
+      \@defaultunitsset\pIIe@tempdimb{#3}\unitlength
+      \@defaultunitsset\pIIe@tempdimc{#4}\unitlength
+      \@defaultunitsset\pIIe@tempdimd{#5}\unitlength
+      \@defaultunitsset\pIIe@tempdime{#6}\unitlength
+      \@defaultunitsset\pIIe@tempdimf{#7}\unitlength
+      \pIIe@bezier@QtoC\pIIe@tempdima\pIIe@tempdimc\@ovro
+      \pIIe@bezier@QtoC\pIIe@tempdimb\pIIe@tempdimd\@ovri
+      \pIIe@bezier@QtoC\pIIe@tempdime\pIIe@tempdimc\@clnwd
+      \pIIe@bezier@QtoC\pIIe@tempdimf\pIIe@tempdimd\@clnht
+      \pIIe@moveto\pIIe@tempdima\pIIe@tempdimb
+      \pIIe@curveto\@ovro\@ovri\@clnwd\@clnht\pIIe@tempdime\pIIe@tempdimf
+      \pIIe@strokeGraph
+      \endgroup
+      \ignorespaces
+    \else
+      \pIIe@old@bezier{#1}(#2,#3)(#4,#5)(#6,#7)
+    \fi}
+  \newcommand*\pIIe@bezier@QtoC[3]{%
+    \@tempdimc#1\relax      \advance\@tempdimc-#2\relax
+    \divide\@tempdimc\thr@@ \advance\@tempdimc #2\relax
+    #3\@tempdimc}
+  \ifx\undefined\@arclen \newdimen\@arclen \fi
+  \ifx\undefined\@arcrad \newdimen\@arcrad \fi
+  \ifx\undefined\pIIe@tempdima \newdimen\pIIe@tempdima \fi
+  \ifx\undefined\pIIe@tempdimb \newdimen\pIIe@tempdimb \fi
+  \ifx\undefined\pIIe@tempdimc \newdimen\pIIe@tempdimc \fi
+  \ifx\undefined\pIIe@tempdimd \newdimen\pIIe@tempdimd \fi
+  \ifx\undefined\pIIe@tempdime \newdimen\pIIe@tempdime \fi
+  \ifx\undefined\pIIe@tempdimf \newdimen\pIIe@tempdimf \fi
+  \newcommand*\pIIe@arc[6][0]{%
+    \@arcrad #4\relax
+    \ifdim \@arcrad<\z@ \pIIe@badcircarg \else
+      \@arclen #6\p@ \advance\@arclen -#5\p@
+      \ifdim \@arclen<\z@ \def\sign{-}\else\def\sign{}\fi
+      \ifdim \sign\@arclen>720\p@
+        \PackageWarning {pict2e}{The arc angle is reduced to -720..720}%
+        \@whiledim \sign\@arclen>720\p@ \do {\advance\@arclen-\sign360\p@}%
+        \@tempdima #5\p@ \advance\@tempdima \@arclen
+        \edef\@angleend{\strip@pt\@tempdima}%
+        \pIIe@@arc{#1}{#2}{#3}{#4}{#5}{\@angleend}%
+      \else
+        \pIIe@@arc{#1}{#2}{#3}{#4}{#5}{#6}%
+      \fi
+    \fi}
+  \newcommand*\pIIe@@arc[6]{%
+    \begingroup
+    \ifdim \sign\@arclen>90\p@
+      \divide\@arclen 2
+      \@tempdima #5\p@ \advance\@tempdima \@arclen
+      \edef\@anglemid{\strip@pt\@tempdima}%
+      \def\@temp{\pIIe@@arc{#1}{#2}{#3}{#4}{#5}}%
+      \expandafter\@temp\expandafter{\@anglemid}%
+      \def\@temp{\pIIe@@arc{2}{#2}{#3}{#4}}%
+      \expandafter\@temp\expandafter{\@anglemid}{#6}%
+    \else
+      \CalculateSin{#5}\CalculateCos{#5}%
+      \@tempdima\UseCos{#5}\@arcrad \advance\@tempdima #2\relax
+      \@tempdimb\UseSin{#5}\@arcrad \advance\@tempdimb #3\relax
+      \ifcase #1\relax
+          \pIIe@lineto\@tempdima\@tempdimb
+      \or \pIIe@moveto\@tempdima\@tempdimb
+      \or
+      \else \PackageWarning {pict2e}%
+            {Illegal obligatory argument in \protect\circlearc.}%
+      \fi
+      \@tempdimc\@arclen \divide\@tempdimc\@iv
+      \edef\@angle{\strip@pt\@tempdimc}\CalculateTan{\@angle}%
+      \@linelen\UseTan{\@angle}\@arcrad \@linelen4\@linelen \divide\@linelen\thr@@
+      \advance\@tempdima-\UseSin{#5}\@linelen
+      \advance\@tempdimb \UseCos{#5}\@linelen
+      \pIIe@add@nums\@tempdima\@tempdimb
+      \CalculateSin{#6}\CalculateCos{#6}%
+      \@tempdima \UseCos{#6}\@arcrad \advance\@tempdima #2\relax
+      \@tempdimb \UseSin{#6}\@arcrad \advance\@tempdimb #3\relax
+      \@tempdimc \UseSin{#6}\@linelen \advance\@tempdimc \@tempdima
+      \pIIe@tempdimd-\UseCos{#6}\@linelen \advance\pIIe@tempdimd \@tempdimb
+      \pIIe@add@nums\@tempdimc\pIIe@tempdimd
+      \pIIe@add@CP\@tempdima\@tempdimb
+      \pIIe@addtoGraph\pIIe@curveto@op
+    \fi
+    \endgroup}
+  \newcommand*\pIIearc
+    {\@ifstar{\@tempswatrue\pIIe@arc@}{\@tempswafalse\pIIe@arc@}}
+  \newcommand*\pIIe@arc@[2][0,360]{\pIIe@arc@@(#1){#2}}
+  \def\pIIe@arc@@(#1,#2)#3{%
+    \@defaultunitsset\pIIe@tempdima{#3}\unitlength
+    \if@tempswa
+      \pIIe@moveto\z@\z@
+      \pIIe@arc{\z@}{\z@}{\pIIe@tempdima}{#1}{#2}%
+      \pIIe@closepath\pIIe@fillGraph
+    \else
+      \pIIe@arc[1]{\z@}{\z@}{\pIIe@tempdima}{#1}{#2}%
+      \pIIe@strokeGraph
+    \fi}
+  \ifx\undefined\arc
+  \else
+      \PackageWarning{pict2e}{\protect\arc\space redefined}%
+  \fi
+  \let\arc\pIIearc
+  \let\lp@r( \let\rp@r)
+  \def\Line(#1,#2)(#3,#4){\polyline(#1,#2)(#3,#4)}
+  \def\polyline(#1,#2){%
+    \@killglue
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@moveto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \@ifnextchar\lp@r{\@polyline}{\PackageWarning{pict2e}%
+      {Polygonal lines require at least two vertices!}%
+    \ignorespaces}}
+  \def\@polyline(#1,#2){%
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@lineto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \@ifnextchar\lp@r{\@polyline}{\pIIe@strokeGraph\ignorespaces}}
+  \def\Vector(#1,#2)(#3,#4){\polyvector(#1,#2)(#3,#4)}
+  \def\polyvector(#1,#2){%
+    \@killglue
+    \@ifnextchar\lp@r{\begingroup\@polyvector(#1,#2)}{%
+      \PackageWarning{pict2e}%
+      {Polygonal vectors require at least two vertices!}\ignorespaces}}
+  \def\@polyvector(#1,#2)(#3,#4){%
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \@defaultunitsset\pIIe@tempdimc{#3}\unitlength
+    \@defaultunitsset\pIIe@tempdimd{#4}\unitlength
+    \advance\pIIe@tempdimc-\pIIe@tempdima \advance\pIIe@tempdimd-\pIIe@tempdimb
+    \ifdim\pIIe@tempdimc=\z@ \@linelen\pIIe@tempdimd \else
+      \ifdim\pIIe@tempdimd=\z@ \@linelen\pIIe@tempdimc \else
+        \pIIe@pyth\pIIe@tempdimc\pIIe@tempdimd\@linelen
+      \fi
+    \fi
+    \ifdim\@linelen<\z@ \@linelen-\@linelen\fi
+    \pIIe@divide{\pIIe@tempdimc}\@linelen\pIIe@tempdime
+    \pIIe@divide{\pIIe@tempdimd}\@linelen\pIIe@tempdimf
+    \pIIe@concat\pIIe@tempdime\pIIe@tempdimf{-\pIIe@tempdimf}\pIIe@tempdime\pIIe@tempdima\pIIe@tempdimb
+    \pIIe@vector \pIIe@fillGraph
+    \@ifnextchar\lp@r{\@polyvector(#3,#4)}{\endgroup\ignorespaces}}
+  \def\polygon{%
+    \@killglue
+    \@ifstar{\begingroup\@tempswatrue\@polygon}%
+      {\begingroup\@tempswafalse\@polygon}}
+  \def\@polygon(#1,#2){%
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@moveto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \@ifnextchar\lp@r{\@@polygon}{\PackageWarning{pict2e}%
+      {Polygons require at least two vertices!}%
+    \ignorespaces}}
+  \def\@@polygon(#1,#2){%
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@lineto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \@ifnextchar\lp@r{\@@polygon}{\pIIe@closepath
+      \if@tempswa\pIIe@fillGraph\else\pIIe@strokeGraph\fi
+      \endgroup
+      \ignorespaces}}
+  \def\moveto(#1,#2){%
+    \@killglue
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@moveto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \ignorespaces}
+  \def\lineto(#1,#2){%
+    \@killglue
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \pIIe@lineto{\pIIe@tempdima}{\pIIe@tempdimb}%
+    \ignorespaces}
+  \def\curveto(#1,#2)(#3,#4)(#5,#6){%
+    \@killglue
+    \@defaultunitsset\pIIe@tempdima{#1}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#2}\unitlength
+    \@defaultunitsset\pIIe@tempdimc{#3}\unitlength
+    \@defaultunitsset\pIIe@tempdimd{#4}\unitlength
+    \@defaultunitsset\pIIe@tempdime{#5}\unitlength
+    \@defaultunitsset\pIIe@tempdimf{#6}\unitlength
+    \pIIe@curveto{\pIIe@tempdima}{\pIIe@tempdimb}{\pIIe@tempdimc}%
+      {\pIIe@tempdimd}{\pIIe@tempdime}{\pIIe@tempdimf}%
+    \ignorespaces}
+  \newcommand*\circlearc[6][0]{%
+    \@killglue
+    \@defaultunitsset\pIIe@tempdima{#2}\unitlength
+    \@defaultunitsset\pIIe@tempdimb{#3}\unitlength
+    \@defaultunitsset\pIIe@tempdimc{#4}\unitlength
+    \pIIe@arc[#1]{\pIIe@tempdima}{\pIIe@tempdimb}{\pIIe@tempdimc}{#5}{#6}%
+    \ignorespaces}
+  \def\closepath{\pIIe@closepath}
+  \def\strokepath{\pIIe@strokeGraph}
+  \def\fillpath{\pIIe@fillGraph}
+  \ifcase\pIIe@mode\relax
+  \or
+    \newcommand*\pIIe@linecap@op{setlinecap}
+    \newcommand*\pIIe@linejoin@op{setlinejoin}
+  \or
+    \newcommand*\pIIe@linecap@op{J}
+    \newcommand*\pIIe@linejoin@op{j}
+  \fi
+  \def\pIIe@linecap{}
+  \def\pIIe@linejoin{}
+  \def\buttcap{\edef\pIIe@linecap{ 0 \pIIe@linecap@op}}
+  \def\roundcap{\edef\pIIe@linecap{ 1 \pIIe@linecap@op}}
+  \def\squarecap{\edef\pIIe@linecap{ 2 \pIIe@linecap@op}}
+  \def\miterjoin{\edef\pIIe@linejoin{ 0 \pIIe@linejoin@op}}
+  \def\roundjoin{\edef\pIIe@linejoin{ 1 \pIIe@linejoin@op}}
+  \def\beveljoin{\edef\pIIe@linejoin{ 2 \pIIe@linejoin@op}}
+  \AtBeginDocument{\@ifundefined{cbezier}{\newcommand}{\renewcommand}*%
+      \cbezier[2][0]{\pIIe@@cbezier[#1]#2}%
+    \@ifdefinable\pIIe@@cbezier{}%
+    \def\pIIe@@cbezier#1)#2(#3)#4(#5)#6({\@cbezier#1)(#3)(#5)(}%
+    \def\@cbezier[#1](#2,#3)(#4,#5)(#6,#7)(#8,#9){%
+      \@killglue
+      \@defaultunitsset\pIIe@tempdima{#2}\unitlength
+      \@defaultunitsset\pIIe@tempdimb{#3}\unitlength
+      \pIIe@moveto{\pIIe@tempdima}{\pIIe@tempdimb}%
+      \@defaultunitsset\pIIe@tempdima{#4}\unitlength
+      \@defaultunitsset\pIIe@tempdimb{#5}\unitlength
+      \@defaultunitsset\pIIe@tempdimc{#6}\unitlength
+      \@defaultunitsset\pIIe@tempdimd{#7}\unitlength
+      \@defaultunitsset\pIIe@tempdime{#8}\unitlength
+      \@defaultunitsset\pIIe@tempdimf{#9}\unitlength
+      \pIIe@curveto{\pIIe@tempdima}{\pIIe@tempdimb}{\pIIe@tempdimc}%
+        {\pIIe@tempdimd}{\pIIe@tempdime}{\pIIe@tempdimf}%
+      \pIIe@strokeGraph
+      \ignorespaces}%
+  }
+\else
+  \renewcommand*\oval[1][]{\pIIe@oldoval}
+  \newcommand*\maxovalrad{20pt}
+  \newcommand*\OriginalPictureCmds{}
+\fi
+\Gin@codes
+\let\Gin@codes\relax
+\endinput
+%%
+%% End of file `pict2e.sty'.

examples/PACKAGES/latboltz/toycar/in.toycar

@@ -457,9 +457,9 @@ mass *4 ${wheel_mass}
 variable dx equal 1.0
 variable density equal 0.001184
 
-neighbor 0.5 bin            
+neighbor 0.5 bin
 neigh_modify delay 0 every 1 check yes
-comm_modify cutoff 3.0     
+comm_modify cutoff 3.0
 
 pair_style lj/cut 1.2
 pair_coeff * * 0.0 0.0
@@ -474,7 +474,7 @@ reset_timestep 0
 #variable node_force equal "v_total_force / 178"
 #fix drag all addforce 0.0 0.0 0.0
 
-velocity all set 0.0 -7.5.0 0.0 units box
+velocity all set 0.0 -7.5 0.0 units box
 
 # viscosity of air is 0.0001847
 

examples/PACKAGES/pace/plugin/paceplugin.nsis

@@ -39,7 +39,7 @@ InstallDir "$LOCALAPPDATA\${PACEPLUGIN}"
 
 ShowInstDetails show
 ShowUninstDetails show
-SetCompressor lzma
+SetCompressor zlib
 
 !define MUI_ABORTWARNING
 

examples/PACKAGES/plumed/plugin/CMakeLists.txt

@@ -0,0 +1,59 @@
+# -*- CMake -*- build system for plugin examples.
+# The is meant to be used as a template for plugins that are
+# distributed independent from the LAMMPS package.
+##########################################
+
+cmake_minimum_required(VERSION 3.16)
+
+project(plumedplugin VERSION 1.0 LANGUAGES CXX)
+
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR})
+include(CheckIncludeFileCXX)
+include(LAMMPSInterfacePlugin)
+include(PLUMED)
+
+##########################
+# building the plugins
+
+add_library(plumedplugin MODULE plumedplugin.cpp ${LAMMPS_SOURCE_DIR}/PLUMED/fix_plumed.cpp)
+target_link_libraries(plumedplugin PRIVATE LAMMPS::PLUMED)
+target_link_libraries(plumedplugin PRIVATE lammps)
+target_include_directories(plumedplugin PRIVATE ${LAMMPS_SOURCE_DIR}/PLUMED)
+set_target_properties(plumedplugin PROPERTIES PREFIX "" SUFFIX ".so")
+
+# MacOS seems to need this
+if(CMAKE_SYSTEM_NAME STREQUAL Darwin)
+  set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-Wl,-undefined,dynamic_lookup")
+elseif(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+# tell CMake to export all symbols to a .dll on Windows with special case for MinGW cross-compilers
+  set_target_properties(plumedplugin PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS TRUE)
+  if(CMAKE_CROSSCOMPILING)
+    set_target_properties(plumedplugin  PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
+  endif()
+
+  get_lammps_version(${LAMMPS_SOURCE_DIR}/version.h LAMMPS_VERSION)
+  find_program(MAKENSIS_PATH makensis)
+  if(MAKENSIS_PATH)
+    execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_SOURCE_DIR}/lammps.ico
+      ${CMAKE_SOURCE_DIR}/lammps-text-logo-wide.bmp ${CMAKE_SOURCE_DIR}/plumedplugin.nsis
+      ${CMAKE_BINARY_DIR})
+    if(BUILD_MPI)
+      if(USE_MSMPI)
+        add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MSMPI plumedplugin.nsis
+          DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
+          BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MSMPI.exe)
+      else()
+        add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION}-MPI plumedplugin.nsis
+          DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
+          BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}-MPI.exe)
+      endif()
+    else()
+      add_custom_target(package ${MAKENSIS_PATH} -V1 -DVERSION=${LAMMPS_VERSION} plumedplugin.nsis
+        COMMAND ${CMAKE_COMMAND} -E echo ${PWD}
+        DEPENDS plumedplugin plumed_copy lammps.ico lammps-text-logo-wide.bmp plumedplugin.nsis
+        BYPRODUCTS LAMMPS-PLUMED-plugin-${LAMMPS_VERSION}.exe)
+    endif()
+  endif()
+else()
+  set_target_properties(plumedplugin PROPERTIES LINK_FLAGS "-rdynamic")
+endif()

examples/PACKAGES/plumed/plugin/LAMMPSInterfacePlugin.cmake

@@ -0,0 +1 @@
+../../../../cmake/Modules/LAMMPSInterfacePlugin.cmake

examples/PACKAGES/plumed/plugin/PLUMED.cmake

@@ -0,0 +1 @@
+../../../../cmake/Modules/Packages/PLUMED.cmake

examples/PACKAGES/plumed/plugin/README.txt

@@ -0,0 +1,2 @@
+This folder contains a loader and support files to build the PLUMED package as plugin.
+For more information please see: https://docs.lammps.org/Developer_plugins.html

examples/PACKAGES/plumed/plugin/plumedplugin.cpp

@@ -0,0 +1,28 @@
+
+#include "lammpsplugin.h"
+#include "version.h"
+
+#include "fix_plumed.h"
+
+using namespace LAMMPS_NS;
+
+static Fix *fix_plumed_creator(LAMMPS *lmp, int argc, char **argv)
+{
+  return new FixPlumed(lmp, argc, argv);
+}
+
+extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+{
+  lammpsplugin_t plugin;
+  lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+  // register plumed fix style
+  plugin.version = LAMMPS_VERSION;
+  plugin.style = "fix";
+  plugin.name = "plumed";
+  plugin.info = "Plumed2 plugin fix style v1.0";
+  plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)";
+  plugin.creator.v1 = (lammpsplugin_factory1 *) &fix_plumed_creator;
+  plugin.handle = handle;
+  (*register_plugin)(&plugin, lmp);
+}

examples/PACKAGES/plumed/plugin/plumedplugin.nsis

@@ -0,0 +1,172 @@
+#!Nsis Installer Command Script
+#
+# The following external defines are recognized:
+# ${VERSION} = YYYYMMDD
+
+!include "MUI2.nsh"
+!include "FileFunc.nsh"
+
+!define MUI_ICON "lammps.ico"
+!define MUI_UNICON "lammps.ico"
+!define MUI_HEADERIMAGE
+!define MUI_HEADERIMAGE_BITMAP "lammps-text-logo-wide.bmp"
+!define MUI_HEADERIMAGE_RIGHT
+
+Unicode true
+XPStyle on
+
+!include "LogicLib.nsh"
+!addplugindir "envvar/Plugins/x86-unicode"
+!include "x64.nsh"
+
+RequestExecutionLevel user
+
+!macro VerifyUserIsAdmin
+UserInfo::GetAccountType
+pop $0
+${If} $0 != "admin"
+  messageBox mb_iconstop "Administrator rights required!"
+  setErrorLevel 740 ;ERROR_ELEVATION_REQUIRED
+  quit
+${EndIf}
+!macroend
+
+!define PLUMEDPLUGIN "LAMMPS PLUMED Plugin ${VERSION}"
+OutFile "LAMMPS-PLUMED-plugin-${VERSION}.exe"
+
+Name "${PLUMEDPLUGIN}"
+InstallDir "$LOCALAPPDATA\${PLUMEDPLUGIN}"
+
+ShowInstDetails show
+ShowUninstDetails show
+SetCompressor zlib
+
+!define MUI_ABORTWARNING
+
+!insertmacro MUI_PAGE_DIRECTORY
+!insertmacro MUI_PAGE_INSTFILES
+
+!insertmacro MUI_UNPAGE_CONFIRM
+!insertmacro MUI_UNPAGE_INSTFILES
+
+!insertmacro MUI_LANGUAGE "English"
+
+function .onInit
+  # Determine if LAMMPS was already installed and check whether it was in 32-bit
+  # or 64-bit. Then look up path to uninstaller and offer to uninstall or quit
+  SetRegView 32
+  ReadRegDWORD $0 HKCU "Software\LAMMPS-PLUMED" "Bits"
+  SetRegView LastUsed
+  ${If} $0 == "32"
+    SetRegView 32
+  ${ElseIf} $0 == "64"
+    SetRegView 64
+  ${Else}
+    SetRegView 64
+  ${EndIf}
+  ClearErrors
+  ReadRegStr $R0 HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" "UninstallString"
+  SetRegView LastUsed
+  ${If} ${Errors}
+    DetailPrint "LAMMPS PLUMED plugin not (yet) installed"
+  ${Else}
+    MessageBox MB_YESNO "LAMMPS PLUMED plugin ($0 bit) is already installed. Uninstall existing version?" /SD IDYES IDNO Quit
+      Pop $R1
+      StrCmp $R1 2 Quit +1
+      Exec $R0
+    Quit:
+      Quit
+  ${EndIf}
+  setShellVarContext all
+functionEnd
+
+Section "${PLUMEDPLUGIN}" SecPlumedplugin
+  SectionIn RO
+  # Write LAMMPS installation bitness marker. Always use 32-bit registry view
+  SetRegView 32
+  IntFmt $0 "0x%08X" 64
+  WriteRegDWORD HKCU "Software\LAMMPS-PLUMED" "Bits" $0
+
+  # Switch to "native" registry view
+  SetRegView 64
+  SetShellVarContext current
+
+  SetOutPath "$INSTDIR"
+  CreateDirectory "$INSTDIR\patches"
+  CreateDirectory "$INSTDIR\bin"
+  File lammps.ico
+  File plumedplugin.so
+
+  SetOutPath "$INSTDIR\bin"
+  File plumed.exe
+
+  # Register Application and its uninstaller
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "DisplayName" "${PLUMEDPLUGIN}"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "Publisher" "The LAMMPS and PLUMED Developers"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "URLInfoAbout" "lammps.org"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "DisplayIcon" "$INSTDIR\lammps.ico"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "DisplayVersion" "${VERSION}"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "InstallLocation" "$INSTDIR"
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "UninstallString" "$\"$INSTDIR\uninstall.exe$\""
+  WriteRegStr HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "QuietUninstallString" "$\"$INSTDIR\uninstall.exe$\" /S"
+
+  ${GetSize} "$INSTDIR" "/S=0K" $0 $1 $2
+  IntFmt $0 "0x%08X" $0
+  WriteRegDWORD HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED" \
+                 "EstimatedSize" "$0"
+
+  # update path variables
+  EnVar::SetHKCU
+  # add plumed executable path
+  EnVar::AddValue "PATH" "$INSTDIR\bin"
+  # add to LAMMPS plugin search path
+  EnVar::AddValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
+  # add plumed2 patch files
+  EnVar::AddValue "PLUMED_ROOT" "$INSTDIR"
+
+  WriteUninstaller "$INSTDIR\Uninstall.exe"
+SectionEnd
+
+function un.onInit
+  SetShellVarContext current
+functionEnd
+
+Section "Uninstall"
+  # remove LAMMPS bitness/installation indicator always in 32-bit registry view
+  SetRegView 32
+  DeleteRegKey HKCU "Software\LAMMPS-PLUMED"
+
+  # unregister extension, and uninstall info
+  SetRegView 64
+  SetShellVarContext current
+  # unregister installation
+  DeleteRegKey HKCU "Software\Microsoft\Windows\CurrentVersion\Uninstall\LAMMPS-PLUMED"
+
+  # update path variables
+  EnVar::SetHKCU
+  # remove plumed executable path
+  EnVar::DeleteValue "PATH" "$INSTDIR\bin"
+  # remove entry from LAMMPS plugin search path
+  EnVar::DeleteValue "LAMMPS_PLUGIN_PATH" "$INSTDIR"
+  # remove plumed patch environment
+  EnVar::Delete "PLUMED_ROOT"
+
+  RMDir /r /REBOOTOK "$INSTDIR\patches"
+  RMDir /r /REBOOTOK "$INSTDIR\bin"
+  Delete /REBOOTOK "$INSTDIR\plumedplugin.so"
+  Delete /REBOOTOK "$INSTDIR\Uninstall.exe"
+  Delete /REBOOTOK "$INSTDIR\lammps.ico"
+  RMDir /REBOOTOK "$INSTDIR"
+SectionEnd
+
+# Local Variables:
+# mode: sh
+# End:

examples/meam/msmeam/library.msmeam

@@ -0,0 +1 @@
+../../../potentials/library.msmeam

fortran/lammps.f90

@@ -3633,7 +3633,7 @@ CONTAINS
 
     n = LEN_TRIM(f_string)
     ptr = lammps_malloc(n+1)
-    CALL C_F_POINTER(ptr, c_string, [1])
+    CALL C_F_POINTER(ptr, c_string, [n+1])
     DO i=1, n
         c_string(i) = f_string(i:i)
     END DO

lib/gpu/lal_base_amoeba.h

@@ -33,6 +33,7 @@
 
 //#define ASYNC_DEVICE_COPY
 
+#if 0
 #if !defined(USE_OPENCL) && !defined(USE_HIP)
 // temporary workaround for int2 also defined in cufft
 #ifdef int2
@@ -40,6 +41,7 @@
 #endif
 #include "cufft.h"
 #endif
+#endif
 
 namespace LAMMPS_AL {
 
@@ -313,10 +315,11 @@ class BaseAmoeba {
   virtual int fphi_mpole();
   virtual int polar_real(const int eflag, const int vflag) = 0;
 
-
+#if 0
   #if !defined(USE_OPENCL) && !defined(USE_HIP)
   cufftHandle plan;
   #endif
+#endif
   bool fft_plan_created;
 };
 

lib/linalg/lmp_f2c.h

@@ -19,141 +19,13 @@ typedef long int logical;
 typedef short int shortlogical;
 typedef char logical1;
 typedef char integer1;
-#ifdef INTEGER_STAR_8   /* Adjust for integer*8. */
-typedef long long longint;              /* system-dependent */
-typedef unsigned long long ulongint;    /* system-dependent */
-#define qbit_clear(a,b) ((a) & ~((ulongint)1 << (b)))
-#define qbit_set(a,b)   ((a) |  ((ulongint)1 << (b)))
-#endif
 
 #define TRUE_ (1)
 #define FALSE_ (0)
 
-/* Extern is for use with -E */
-#ifndef Extern
-#define Extern extern
-#endif
-
-/* I/O stuff */
-
-#ifdef f2c_i2
-/* for -i2 */
-typedef short flag;
-typedef short ftnlen;
-typedef short ftnint;
-#else
-typedef long int flag;
 typedef long int ftnlen;
-typedef long int ftnint;
-#endif
-
-/*external read, write*/
-typedef struct
-{       flag cierr;
-        ftnint ciunit;
-        flag ciend;
-        char *cifmt;
-        ftnint cirec;
-} cilist;
-
-/*internal read, write*/
-typedef struct
-{       flag icierr;
-        char *iciunit;
-        flag iciend;
-        char *icifmt;
-        ftnint icirlen;
-        ftnint icirnum;
-} icilist;
-
-/*open*/
-typedef struct
-{       flag oerr;
-        ftnint ounit;
-        char *ofnm;
-        ftnlen ofnmlen;
-        char *osta;
-        char *oacc;
-        char *ofm;
-        ftnint orl;
-        char *oblnk;
-} olist;
-
-/*close*/
-typedef struct
-{       flag cerr;
-        ftnint cunit;
-        char *csta;
-} cllist;
-
-/*rewind, backspace, endfile*/
-typedef struct
-{       flag aerr;
-        ftnint aunit;
-} alist;
-
-/* inquire */
-typedef struct
-{       flag inerr;
-        ftnint inunit;
-        char *infile;
-        ftnlen infilen;
-        ftnint	*inex;	/*parameters in standard's order*/
-        ftnint	*inopen;
-        ftnint	*innum;
-        ftnint	*innamed;
-        char	*inname;
-        ftnlen	innamlen;
-        char	*inacc;
-        ftnlen	inacclen;
-        char	*inseq;
-        ftnlen	inseqlen;
-        char 	*indir;
-        ftnlen	indirlen;
-        char	*infmt;
-        ftnlen	infmtlen;
-        char	*inform;
-        ftnint	informlen;
-        char	*inunf;
-        ftnlen	inunflen;
-        ftnint	*inrecl;
-        ftnint	*innrec;
-        char	*inblank;
-        ftnlen	inblanklen;
-} inlist;
-
 #define VOID void
 
-union Multitype {       /* for multiple entry points */
-        integer1 g;
-        shortint h;
-        integer i;
-        /* longint j; */
-        real r;
-        doublereal d;
-        complex c;
-        doublecomplex z;
-        };
-
-typedef union Multitype Multitype;
-
-/*typedef long int Long;*/      /* No longer used; formerly in Namelist */
-
-struct Vardesc {        /* for Namelist */
-        char *name;
-        char *addr;
-        ftnlen *dims;
-        int  type;
-        };
-typedef struct Vardesc Vardesc;
-
-struct Namelist {
-        char *name;
-        Vardesc **vars;
-        int nvars;
-        };
-typedef struct Namelist Namelist;
-
 #define abs(x) ((x) >= 0 ? (x) : -(x))
 #define dabs(x) (doublereal)abs(x)
 #define min(a,b) ((a) <= (b) ? (a) : (b))

lib/linalg/s_lmp_cat.cpp

@@ -4,7 +4,7 @@
 // concatenate two strings
 
 extern "C" {
-void s_lmp_cat(char *lp, char *rpp[], ftnint rnp[], ftnint *np, ftnlen ll)
+void s_lmp_cat(char *lp, char **rpp, integer *rnp, integer *np, ftnlen ll)
 {
     ftnlen i, nc;
     char *rp;

lib/plumed/Install.py

@@ -16,8 +16,10 @@ parser = ArgumentParser(prog='Install.py',
                         description="LAMMPS library build wrapper script")
 
 # settings
+# Note: must also adjust check for supported API versions in
+# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
 
-version = "2.8.2"
+version = "2.9.1"
 mode = "static"
 
 # help message
@@ -45,6 +47,10 @@ checksums = { \
         '2.7.6' : 'fb8c0ec10f97a9353eb123a5c4c35aa6', \
         '2.8.1' : '6bfe72ebdae63dc38a9ca27d9b0e08f8', \
         '2.8.2' : '599092b6a0aa6fff992612537ad98994', \
+        '2.8.3' : '76d23cd394eba9e6530316ed1184e219', \
+        '2.8.4' : '9f59c4f9bda86fe5bef19543c295a981', \
+        '2.9.0' : '661eabeebee05cf84bbf9dc23d7d5f46', \
+        '2.9.1' : 'c3b2d31479c1e9ce211719d40e9efbd7', \
         }
 
 # parse and process arguments

python/lammps/core.py

@@ -334,8 +334,8 @@ class lammps(object):
     if self.has_mpi_support:
       try:
         from mpi4py import __version__ as mpi4py_version
-        # tested to work with mpi4py versions 2 and 3
-        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
+        # tested to work with mpi4py versions 2, 3, and 4
+        self.has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4']
       except ImportError:
         # ignore failing import
         pass
@@ -361,7 +361,7 @@ class lammps(object):
         if not self.has_mpi_support:
           raise Exception('LAMMPS not compiled with real MPI library')
         if not self.has_mpi4py:
-          raise Exception('Python mpi4py version is not 2 or 3')
+          raise Exception('Python mpi4py version is not 2, 3, or 4')
         if self.MPI._sizeof(self.MPI.Comm) == sizeof(c_int):
           MPI_Comm = c_int
         else:
@@ -374,12 +374,16 @@ class lammps(object):
         narg = 0
         cargs = None
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*(narg+1))(*cmdargs)
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
           cargs[narg] = None
           self.lib.lammps_open.argtypes = [c_int, c_char_p*(narg+1), MPI_Comm, c_void_p]
         else:
@@ -395,12 +399,16 @@ class lammps(object):
           self.comm = self.MPI.COMM_WORLD
         self.opened = 1
         if cmdargs is not None:
-          cmdargs.insert(0,"lammps")
-          narg = len(cmdargs)
-          for i in range(narg):
-            if type(cmdargs[i]) is str:
-              cmdargs[i] = cmdargs[i].encode()
-          cargs = (c_char_p*(narg+1))(*cmdargs)
+          myargs = ["lammps".encode()]
+          narg = len(cmdargs) + 1
+          for arg in cmdargs:
+            if type(arg) is str:
+              myargs.append(arg.encode())
+            elif type(arg) is bytes:
+              myargs.append(arg)
+            else:
+              raise TypeError('Unsupported cmdargs type ', type(arg))
+          cargs = (c_char_p*(narg+1))(*myargs)
           cargs[narg] = None
           self.lib.lammps_open_no_mpi.argtypes = [c_int, c_char_p*(narg+1), c_void_p]
           self.lmp = c_void_p(self.lib.lammps_open_no_mpi(narg,cargs,None))

python/lammps/pylammps.py

@@ -192,11 +192,23 @@ class Atom(object):
   @property
   def mass(self):
     """
-    Return the atom mass
+    Return the atom mass as a per-atom property.
+    This returns either the per-type mass or the per-atom
+    mass (AKA 'rmass') depending on what is available with
+    preference for the per-atom mass.
+
+    .. versionchanged:: 2Aug2023_update_4
+
+       Support both per-type and per-atom masses. With
+       per-type return "mass[type[i]]" else return "rmass[i]".
+       Per-atom mass is preferred if available.
 
     :type: float
     """
-    return self.get("mass", self.index)
+    if self._pylmp.lmp.extract_setting('rmass_flag'):
+      return self.get("rmass", self.index)
+    else:
+      return self.get("mass", self.type)
 
   @property
   def radius(self):

src/ASPHERE/pair_ylz.cpp

@@ -300,6 +300,7 @@ double PairYLZ::init_one(int i, int j)
   zeta[j][i] = zeta[i][j];
   mu[j][i] = mu[i][j];
   beta[j][i] = beta[i][j];
+  cut[j][i] = cut[i][j];
 
   return cut[i][j];
 }
@@ -409,7 +410,7 @@ void PairYLZ::write_data_all(FILE *fp)
 {
   for (int i = 1; i <= atom->ntypes; i++)
     for (int j = i; j <= atom->ntypes; j++)
-      fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][i], sigma[i][i], cut[i][j],
+      fprintf(fp, "%d %d %g %g %g %g %g %g\n", i, j, epsilon[i][j], sigma[i][j], cut[i][j],
               zeta[i][j], mu[i][j], beta[i][j]);
 }
 

src/BODY/body_rounded_polyhedron.cpp

@@ -99,10 +99,9 @@ int BodyRoundedPolyhedron::nedges(AtomVecBody::Bonus *bonus)
 {
   int nvertices = bonus->ivalue[0];
   int nedges = bonus->ivalue[1];
-  //int nfaces = bonus->ivalue[2];
   if (nvertices == 1) return 0;
   else if (nvertices == 2) return 1;
-  return nedges; //(nvertices+nfaces-2); // Euler formula: V-E+F=2
+  return nedges;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -116,6 +115,9 @@ double *BodyRoundedPolyhedron::edges(AtomVecBody::Bonus *bonus)
 
 int BodyRoundedPolyhedron::nfaces(AtomVecBody::Bonus *bonus)
 {
+  int nvertices = bonus->ivalue[0];
+  if (nvertices < 3) return 0;
+
   return bonus->ivalue[2];
 }
 

src/COLLOID/pair_brownian.cpp

@@ -480,15 +480,18 @@ void PairBrownian::init_style()
   // are re-calculated at every step.
 
   flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style, "deform") == 0)
-      flagdeform = 1;
-    else if (strstr(modify->fix[i]->style, "wall") != nullptr) {
-      if (flagwall) error->all(FLERR, "Cannot use multiple fix wall commands with pair brownian");
-      flagwall = 1;    // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2;    // Moving walls exist
-    }
+  wallfix = nullptr;
+
+  if (modify->get_fix_by_style("^deform").size() > 0) flagdeform = 1;
+  auto fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair brownian");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair brownian", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   // set the isotropic constants depending on the volume fraction

src/COLLOID/pair_brownian_poly.cpp

@@ -349,17 +349,18 @@ void PairBrownianPoly::init_style()
   // are re-calculated at every step.
 
   flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"deform") == 0)
-      flagdeform = 1;
-    else if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      if (flagwall)
-        error->all(FLERR,
-                   "Cannot use multiple fix wall commands with pair brownian");
-      flagwall = 1; // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2; // Moving walls exist
-    }
+  wallfix = nullptr;
+
+  if (modify->get_fix_by_style("^deform").size() > 0) flagdeform = 1;
+  auto fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair brownian/poly");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair brownian/poly", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   // set the isotropic constants that depend on the volume fraction

src/COLLOID/pair_lubricate.cpp

@@ -560,21 +560,23 @@ void PairLubricate::init_style()
   // are re-calculated at every step.
 
   shearing = flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"deform") == 0) {
-      shearing = flagdeform = 1;
-      if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
-        error->all(FLERR,"Using pair lubricate with inconsistent "
-                   "fix deform remap option");
-    }
-    if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      if (flagwall)
-        error->all(FLERR,
-                   "Cannot use multiple fix wall commands with pair lubricate");
-      flagwall = 1; // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2; // Moving walls exist
-    }
+
+  auto fixes = modify->get_fix_by_style("^deform");
+  if (fixes.size() > 0) {
+    shearing = flagdeform = 1;
+    auto *myfix = dynamic_cast<FixDeform *>(fixes[0]);
+    if (myfix && (myfix->remapflag != Domain::V_REMAP))
+      error->all(FLERR,"Using pair lubricate with inconsistent fix deform remap option");
+  }
+  fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair lubricate");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair lubricate", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   // set the isotropic constants that depend on the volume fraction

src/COLLOID/pair_lubricateU.cpp

@@ -1792,18 +1792,18 @@ void PairLubricateU::init_style()
   // are re-calculated at every step.
 
   flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"deform") == 0)
-      flagdeform = 1;
-    else if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      if (flagwall)
-        error->all(FLERR,
-                   "Cannot use multiple fix wall commands with "
-                   "pair lubricateU");
-      flagwall = 1; // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2; // Moving walls exist
-    }
+  wallfix = nullptr;
+
+  if (modify->get_fix_by_style("^deform").size() > 0) flagdeform = 1;
+  auto fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair lubricateU");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair lubricateU", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   // set the isotropic constants depending on the volume fraction

src/COLLOID/pair_lubricateU_poly.cpp

@@ -1156,18 +1156,18 @@ void PairLubricateUPoly::init_style()
   // are re-calculated at every step.
 
   flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"deform") == 0)
-      flagdeform = 1;
-    else if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      if (flagwall)
-        error->all(FLERR,
-                   "Cannot use multiple fix wall commands with "
-                   "pair lubricateU");
-      flagwall = 1; // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2; // Moving walls exist
-    }
+  wallfix = nullptr;
+
+  if (modify->get_fix_by_style("^deform").size() > 0) flagdeform = 1;
+  auto fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair lubricateU/poly");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair lubricateU/poly", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   // set the isotropic constants depending on the volume fraction

src/COLLOID/pair_lubricate_poly.cpp

@@ -460,30 +460,23 @@ void PairLubricatePoly::init_style()
   // are re-calculated at every step.
 
   shearing = flagdeform = flagwall = 0;
-  for (int i = 0; i < modify->nfix; i++) {
-    if (strcmp(modify->fix[i]->style,"deform") == 0) {
-      shearing = flagdeform = 1;
-      if ((dynamic_cast<FixDeform *>(modify->fix[i]))->remapflag != Domain::V_REMAP)
-        error->all(FLERR,"Using pair lubricate with inconsistent "
-                   "fix deform remap option");
-    }
-    if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      if (flagwall)
-        error->all(FLERR,
-                   "Cannot use multiple fix wall commands with "
-                   "pair lubricate/poly");
-      flagwall = 1; // Walls exist
-      wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      if (wallfix->xflag) flagwall = 2; // Moving walls exist
-    }
 
-    if (strstr(modify->fix[i]->style,"wall") != nullptr) {
-      flagwall = 1; // Walls exist
-      if ((dynamic_cast<FixWall *>(modify->fix[i]))->xflag) {
-        flagwall = 2; // Moving walls exist
-        wallfix = dynamic_cast<FixWall *>(modify->fix[i]);
-      }
-    }
+  auto fixes = modify->get_fix_by_style("^deform");
+  if (fixes.size() > 0) {
+    shearing = flagdeform = 1;
+    auto *myfix = dynamic_cast<FixDeform *>(fixes[0]);
+    if (myfix && (myfix->remapflag != Domain::V_REMAP))
+      error->all(FLERR,"Using pair lubricate/poly with inconsistent fix deform remap option");
+  }
+  fixes = modify->get_fix_by_style("^wall");
+  if (fixes.size() > 1)
+    error->all(FLERR, "Cannot use multiple fix wall commands with pair lubricate/poly");
+  else if (fixes.size() == 1) {
+    wallfix = dynamic_cast<FixWall *>(fixes[0]);
+    if (!wallfix)
+      error->all(FLERR, "Fix {} is not compatible with pair lubricate/poly", fixes[0]->style);
+    flagwall = 1;
+    if (wallfix->xflag) flagwall = 2; // Moving walls exist
   }
 
   double vol_T;

src/DPD-MESO/fix_mvv_dpd.cpp

@@ -24,6 +24,7 @@
 #include "fix_mvv_dpd.h"
 
 #include "atom.h"
+#include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "update.h"
@@ -65,6 +66,11 @@ void FixMvvDPD::init()
   if (!atom->vest_flag)
     error->all(FLERR,"Fix mvv/dpd requires atom attribute vest e.g. from atom style mdpd");
 
+  // Cannot use vremap since its effects aren't propagated to vest
+  //   see RHEO or SPH packages for examples of patches
+  if (domain->deform_vremap)
+    error->all(FLERR, "Fix mvv/dpd cannot be used with velocity remapping");
+
   if (!force->pair_match("^mdpd",0) && !force->pair_match("^dpd",0)) {
     if (force->pair_match("^hybrid",0)) {
       if (!(force->pair_match("^mdpd",0,1) || force->pair_match("^dpd",0),1)) {

src/DPD-MESO/fix_mvv_edpd.cpp

@@ -33,6 +33,7 @@
 #include "fix_mvv_edpd.h"
 
 #include "atom.h"
+#include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "update.h"
@@ -73,6 +74,11 @@ void FixMvvEDPD::init()
 {
   if (!atom->edpd_flag) error->all(FLERR,"Fix mvv/edpd requires atom style edpd");
 
+  // Cannot use vremap since its effects aren't propagated to vest
+  //   see RHEO or SPH packages for examples of patches
+  if (domain->deform_vremap)
+    error->all(FLERR, "Fix mvv/edpd cannot be used with velocity remapping");
+
   if (!force->pair_match("^edpd",0)) {
     if (force->pair_match("^hybrid",0)) {
       if (!force->pair_match("^edpd",0,1)) {

src/DPD-MESO/fix_mvv_tdpd.cpp

@@ -29,6 +29,7 @@
 #include "fix_mvv_tdpd.h"
 
 #include "atom.h"
+#include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "update.h"
@@ -71,6 +72,11 @@ void FixMvvTDPD::init()
 {
   if (!atom->tdpd_flag) error->all(FLERR,"Fix mvv/tdpd requires atom style tdpd");
 
+  // Cannot use vremap since its effects aren't propagated to vest
+  //   see RHEO or SPH packages for examples of patches
+  if (domain->deform_vremap)
+    error->all(FLERR, "Fix mvv/tdpd cannot be used with velocity remapping");
+
   if (!force->pair_match("^tdpd",0)) {
     if (force->pair_match("^hybrid",0)) {
       if (!force->pair_match("^tdpd",0,1)) {

src/DPD-SMOOTH/fix_meso_move.cpp

@@ -350,7 +350,14 @@ void FixMesoMove::init () {
 }
 
 void FixMesoMove::setup_pre_force (int /*vflag*/) {
+
+  // Cannot use vremap since its effects aren't propagated to vest
+  //   see RHEO or SPH packages for examples of patches
+  if (domain->deform_vremap)
+    error->all(FLERR, "Fix meso/move cannot be used with velocity remapping");
+
   // set vest equal to v
+
   double **v = atom->v;
   double **vest = atom->vest;
   int *mask = atom->mask;

src/DPD-SMOOTH/fix_rigid_meso.cpp

@@ -29,11 +29,12 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_rigid_meso.h"
+
 #include "math_extra.h"
 #include "atom.h"
 #include "domain.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -92,6 +93,11 @@ void FixRigidMeso::setup (int vflag) {
     conjqm[ibody][2] *= 2.0;
     conjqm[ibody][3] *= 2.0;
   }
+
+  // Cannot use vremap since its effects aren't propagated to vest
+  //   see RHEO or SPH packages for examples of patches
+  if (domain->deform_vremap)
+    error->all(FLERR, "Fix rigid/meso cannot be used with velocity remapping");
 }
 
 /* ----------------------------------------------------------------------

src/EFF/fix_nh_eff.cpp

@@ -16,7 +16,6 @@
    Contributing author: Andres Jaramillo-Botero (Caltech)
 ------------------------------------------------------------------------- */
 
-
 #include "fix_nh_eff.h"
 
 #include "atom.h"
@@ -62,7 +61,7 @@ void FixNHEff::nve_v()
     if (mask[i] & groupbit) {
       if (abs(spin[i])==1) {
         dtfm = dtf / mass[type[i]];
-        ervel[i] = dtfm * erforce[i] / mefactor;
+        ervel[i] += dtfm * erforce[i] / mefactor;
       }
     }
   }
@@ -79,15 +78,26 @@ void FixNHEff::nve_x()
   FixNH::nve_x();
 
   double *eradius = atom->eradius;
+  double *erforce = atom->erforce;
   double *ervel = atom->ervel;
+  double *mass = atom->mass;
+  int *type = atom->type;
   int *spin = atom->spin;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
   if (igroup == atom->firstgroup) nlocal = atom->nfirst;
 
+  double mefactor = domain->dimension/4.0;
+  double dtfm;
+
   for (int i = 0; i < nlocal; i++)
-    if (mask[i] & groupbit)
-      if (abs(spin[i])==1) eradius[i] += dtv * ervel[i];
+    if (mask[i] & groupbit) {
+      dtfm = dtf / mass[type[i]];
+      if (abs(spin[i])==1) {
+        ervel[i] += dtfm * erforce[i] / mefactor;
+        eradius[i] += dtv * ervel[i];
+      }
+    }
 }
 
 /* ----------------------------------------------------------------------

src/ELECTRODE/fix_electrode_conp.cpp

@@ -494,7 +494,7 @@ void FixElectrodeConp::setup_post_neighbor()
     if (read_mat)
       read_from_file(input_file_mat, elastance, "elastance");
     else if (!read_inv) {
-      if (etypes_neighlists) neighbor->build_one(mat_neighlist, 0);
+      if (etypes_neighlists) neighbor->build_one(mat_neighlist);
       auto array_compute = std::unique_ptr<ElectrodeMatrix>(new ElectrodeMatrix(lmp, igroup, eta));
       array_compute->setup(tag_to_iele, pair, mat_neighlist);
       if (tfflag) { array_compute->setup_tf(tf_types); }

src/EXTRA-COMPUTE/compute_hexorder_atom.cpp

@@ -147,10 +147,8 @@ void ComputeHexOrderAtom::compute_peratom()
   }
 
   // invoke full neighbor list (will copy or build if necessary)
-  // on the first step of a run, set preflag to one in neighbor->build_one(...)
 
-  if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
-  else neighbor->build_one(list);
+  neighbor->build_one(list);
 
   inum = list->inum;
   ilist = list->ilist;

src/EXTRA-COMPUTE/compute_hma.cpp

@@ -291,8 +291,7 @@ void ComputeHMA::compute_vector()
       double *special_coul = force->special_coul;
       int newton_pair = force->newton_pair;
 
-      if (update->firststep == update->ntimestep) neighbor->build_one(list,1);
-      else neighbor->build_one(list);
+      neighbor->build_one(list);
       int inum = list->inum;
       int *ilist = list->ilist;
       int *numneigh = list->numneigh;

src/EXTRA-COMPUTE/compute_stress_cartesian.cpp

@@ -386,7 +386,7 @@ void ComputeStressCartesian::compute_array()
         if (tag[i] > tag[j]) {
           if ((tag[i] + tag[j]) % 2 == 0) continue;
         } else if (tag[i] < tag[j]) {
-          if ((tag[i] < tag[j]) % 2 == 1) continue;
+          if ((tag[i] + tag[j]) % 2 == 1) continue;
         }
       }
 

src/EXTRA-DUMP/dump_xtc.cpp

@@ -14,7 +14,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing authors: Naveen Michaud-Agrawal (Johns Hopkins U)
-                         open-source XDR routines from
+                         Open Source XDR based I/O routines from
                            Frans van Hoesel (https://www.rug.nl/staff/f.h.j.van.hoesel/)
                            are included in this file
                          Axel Kohlmeyer (Temple U)
@@ -35,27 +35,29 @@
 #include "output.h"
 #include "update.h"
 
+#include "xdr_compat.h"
+
 #include <climits>
 #include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-#define EPS 1e-5
-#define XTC_MAGIC 1995
+static constexpr double EPS = 1.0e-5;
+static constexpr int XTC_MAGIC = 1995;
 
 #define MYMIN(a,b) ((a) < (b) ? (a) : (b))
 #define MYMAX(a,b) ((a) > (b) ? (a) : (b))
 
-int xdropen(XDR *, const char *, const char *);
-int xdrclose(XDR *);
-void xdrfreebuf();
-int xdr3dfcoord(XDR *, float *, int *, float *);
+static int xdropen(XDR *, const char *, const char *);
+static int xdrclose(XDR *);
+static void xdrfreebuf();
+static int xdr3dfcoord(XDR *, float *, int *, float *);
 
 /* ---------------------------------------------------------------------- */
 
-DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
-  coords(nullptr)
+DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg)
+  : Dump(lmp, narg, arg), coords(nullptr), xd(nullptr)
 {
   if (narg != 5) error->all(FLERR,"Illegal dump xtc command");
   if (binary || compressed || multifile || multiproc)
@@ -68,6 +70,7 @@ DumpXTC::DumpXTC(LAMMPS *lmp, int narg, char **arg) : Dump(lmp, narg, arg),
   flush_flag = 0;
   unwrap_flag = 0;
   precision = 1000.0;
+  xd = new XDR;
 
   // allocate global array for atom coords
 
@@ -105,9 +108,10 @@ DumpXTC::~DumpXTC()
   memory->destroy(coords);
 
   if (me == 0) {
-    xdrclose(&xd);
+    xdrclose(xd);
     xdrfreebuf();
   }
+  delete xd;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -150,7 +154,8 @@ void DumpXTC::openfile()
 
   fp = nullptr;
   if (me == 0)
-    if (xdropen(&xd,filename,"w") == 0) error->one(FLERR,"Cannot open dump file");
+    if (xdropen(xd,filename,"w") == 0)
+      error->one(FLERR,"Cannot open XTC format dump file {}: {}", filename, utils::getsyserror());
 }
 
 /* ---------------------------------------------------------------------- */
@@ -176,11 +181,11 @@ void DumpXTC::write_header(bigint nbig)
   if (me != 0) return;
 
   int tmp = XTC_MAGIC;
-  xdr_int(&xd,&tmp);
-  xdr_int(&xd,&n);
-  xdr_int(&xd,&ntimestep);
+  xdr_int(xd,&tmp);
+  xdr_int(xd,&n);
+  xdr_int(xd,&ntimestep);
   float time_value = ntimestep * tfactor * update->dt;
-  xdr_float(&xd,&time_value);
+  xdr_float(xd,&time_value);
 
   // cell basis vectors
   if (domain->triclinic) {
@@ -192,18 +197,18 @@ void DumpXTC::write_header(bigint nbig)
     float xz = sfactor * domain->xz;
     float yz = sfactor * domain->yz;
 
-    xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
-    xdr_float(&xd,&xy  ); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
-    xdr_float(&xd,&xz  ); xdr_float(&xd,&yz  ); xdr_float(&xd,&zdim);
+    xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero);
+    xdr_float(xd,&xy  ); xdr_float(xd,&ydim); xdr_float(xd,&zero);
+    xdr_float(xd,&xz  ); xdr_float(xd,&yz  ); xdr_float(xd,&zdim);
   } else {
     float zero = 0.0;
     float xdim = sfactor * (domain->boxhi[0] - domain->boxlo[0]);
     float ydim = sfactor * (domain->boxhi[1] - domain->boxlo[1]);
     float zdim = sfactor * (domain->boxhi[2] - domain->boxlo[2]);
 
-    xdr_float(&xd,&xdim); xdr_float(&xd,&zero); xdr_float(&xd,&zero);
-    xdr_float(&xd,&zero); xdr_float(&xd,&ydim); xdr_float(&xd,&zero);
-    xdr_float(&xd,&zero); xdr_float(&xd,&zero); xdr_float(&xd,&zdim);
+    xdr_float(xd,&xdim); xdr_float(xd,&zero); xdr_float(xd,&zero);
+    xdr_float(xd,&zero); xdr_float(xd,&ydim); xdr_float(xd,&zero);
+    xdr_float(xd,&zero); xdr_float(xd,&zero); xdr_float(xd,&zdim);
   }
 }
 
@@ -328,7 +333,7 @@ double DumpXTC::memory_usage()
 
 void DumpXTC::write_frame()
 {
-  xdr3dfcoord(&xd,coords,&natoms,&precision);
+  xdr3dfcoord(xd,coords,&natoms,&precision);
 }
 
 // ----------------------------------------------------------------------
@@ -406,7 +411,7 @@ static int magicints[] = {
  |
  | xdropen - open xdr file
  |
- | This versions differs from xdrstdio_create, because I need to know
+ | This version differs from xdrstdio_create, because I need to know
  | the state of the file (read or write) so I can use xdr3dfcoord
  | in eigther read or write mode, and the file descriptor
  | so I can close the file (something xdr_destroy doesn't do).
@@ -1048,7 +1053,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
     }
     if (buf[1] != 0) buf[0]++;
     xdr_int(xdrs, &(buf[0])); /* buf[0] holds the length in bytes */
-    return errval * (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]));
+    return errval * (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]));
   } else {
 
     /* xdrs is open for reading */
@@ -1129,7 +1134,7 @@ int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
 
     if (xdr_int(xdrs, &(buf[0])) == 0)
       return 0;
-    if (xdr_opaque(xdrs, (caddr_t)&(buf[3]), (u_int)buf[0]) == 0)
+    if (xdr_opaque(xdrs, (char *)&(buf[3]), (unsigned int)buf[0]) == 0)
       return 0;
     buf[0] = buf[1] = buf[2] = 0;
 

src/EXTRA-DUMP/dump_xtc.h

@@ -21,8 +21,8 @@ DumpStyle(xtc,DumpXTC);
 #define LMP_DUMP_XTC_H
 
 #include "dump.h"
-#include "xdr_compat.h"
 
+struct XDR;
 namespace LAMMPS_NS {
 
 class DumpXTC : public Dump {
@@ -37,7 +37,7 @@ class DumpXTC : public Dump {
   float precision;    // user-adjustable precision setting
   float *coords;
   double sfactor, tfactor;    // scaling factors for positions and time unit
-  XDR xd;
+  XDR *xd;
 
   void init_style() override;
   int modify_param(int, char **) override;

src/EXTRA-DUMP/xdr_compat.cpp

@@ -1,54 +1,63 @@
-// clang-format off
 #include "xdr_compat.h"
+
 #include <cstdlib>
 #include <cstring>
 
-/* This file is needed for systems, that do not provide XDR support
- * in their system libraries. It was written for windows, but will
- * most probably work on other platforms too. better make sure you
- * test that the xtc files produced are ok before using it.
+/*
+ * This file contains an implementation of the Sun External Data Representation (XDR)
+ * routines.  They have been adapted specifically for the use with the LAMMPS xtc dump
+ * style to produce compressed trajectory files in the Gromacs XTC format.
  *
- * It is also needed on BG/L and Cray XT3/XT4 as we don't have
- * XDR support in the lightweight kernel runtimes either.
+ * The XDR sources are available under the BSD 3-clause license for example in
+ * the MIT Kerberos 5 distribution with the following copyright notice and license.
  *
- * This file contains the definitions for Sun External Data
- * Representation (XDR) headers and routines.
+ * @(#)xdr.h    2.2 88/07/29 4.0 RPCSRC
  *
- * Although the rest of LAMPPS is GPL, you can copy and use the XDR
- * routines in any way you want as long as you obey Sun's license:
+ * Copyright (c) 2010, Oracle America, Inc.
  *
- * Sun RPC is a product of Sun Microsystems, Inc. and is provided for
- * unrestricted use provided that this legend is included on all tape
- * media and as a part of the software program in whole or part.  Users
- * may copy or modify Sun RPC without charge, but are not authorized
- * to license or distribute it to anyone else except as part of a product or
- * program developed by the user.
+ * All rights reserved.
  *
- * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
- * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
- * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
  *
- * Sun RPC is provided with no support and without any obligation on the
- * part of Sun Microsystems, Inc. to assist in its use, correction,
- * modification or enhancement.
+ *     * Redistributions of source code must retain the above copyright
+ *       notice, this list of conditions and the following disclaimer.
  *
- * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
- * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
- * OR ANY PART THEREOF.
+ *     * Redistributions in binary form must reproduce the above copyright
+ *       notice, this list of conditions and the following disclaimer in
+ *       the documentation and/or other materials provided with the
+ *       distribution.
  *
- * In no event will Sun Microsystems, Inc. be liable for any lost revenue
- * or profits or other special, indirect and consequential damages, even if
- * Sun has been advised of the possibility of such damages.
+ *     * Neither the name of the "Oracle America, Inc." nor the names of
+ *       its contributors may be used to endorse or promote products
+ *       derived from this software without specific prior written permission.
  *
- * Sun Microsystems, Inc.
- * 2550 Garcia Avenue
- * Mountain View, California  94043
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
 #ifdef __cplusplus
 extern "C" {
 #endif
 
+#ifndef FALSE
+#define FALSE (0)
+#endif
+#ifndef TRUE
+#define TRUE (1)
+#endif
+
+#define BYTES_PER_XDR_UNIT (4)
+
 /*
  * for unit alignment
  */
@@ -58,19 +67,18 @@ static xdr_uint32_t xdr_swapbytes(xdr_uint32_t x)
 {
   xdr_uint32_t y;
   int i;
-  char *px=(char *)&x;
-  char *py=(char *)&y;
+  char *px = (char *) &x;
+  char *py = (char *) &y;
 
-  for (i=0;i<4;i++)
-    py[i]=px[3-i];
+  for (i = 0; i < 4; i++) py[i] = px[3 - i];
 
   return y;
 }
 
 static xdr_uint32_t xdr_htonl(xdr_uint32_t x)
 {
-  short s=0x0F00;
-  if (*((char *)&s)==(char)0x0F) {
+  short s = 0x0F00;
+  if (*((char *) &s) == (char) 0x0F) {
     /* bigendian, do nothing */
     return x;
   } else {
@@ -81,8 +89,8 @@ static xdr_uint32_t xdr_htonl(xdr_uint32_t x)
 
 static xdr_uint32_t xdr_ntohl(xdr_uint32_t x)
 {
-  short s=0x0F00;
-  if (*((char *)&s)==(char)0x0F) {
+  short s = 0x0F00;
+  if (*((char *) &s) == (char) 0x0F) {
     /* bigendian, do nothing */
     return x;
   } else {
@@ -91,221 +99,39 @@ static xdr_uint32_t xdr_ntohl(xdr_uint32_t x)
   }
 }
 
-
-/*
- * Free a data structure using XDR
- * Not a filter, but a convenient utility nonetheless
- */
-void
-xdr_free (xdrproc_t proc, char *objp)
-{
-  XDR x;
-
-  x.x_op = XDR_FREE;
-  (*proc) (&x, objp);
-}
-
-/*
- * XDR nothing
- */
-bool_t
-xdr_void (void)
-{
-  return TRUE;
-}
-
 /*
  * XDR integers
  */
-bool_t
-xdr_int (XDR *xdrs, int *ip)
+bool_t xdr_int(XDR *xdrs, int *ip)
 {
   xdr_int32_t l;
 
-  switch (xdrs->x_op)
-  {
+  switch (xdrs->x_op) {
+
     case XDR_ENCODE:
       l = (xdr_int32_t) (*ip);
-      return xdr_putint32 (xdrs, &l);
+      return xdr_putint32(xdrs, &l);
+      break;
 
     case XDR_DECODE:
-      if (!xdr_getint32 (xdrs, &l))
-          {
-            return FALSE;
-          }
+      if (!xdr_getint32(xdrs, &l)) return FALSE;
       *ip = (int) l;
+      return TRUE;
+      break;
 
     case XDR_FREE:
       return TRUE;
+      break;
   }
   return FALSE;
 }
 
-
-/*
- * XDR unsigned integers
- */
-bool_t
-xdr_u_int (XDR *xdrs, unsigned int *up)
-{
-  xdr_uint32_t l;
-
-  switch (xdrs->x_op)
-  {
-    case XDR_ENCODE:
-      l = (xdr_uint32_t) (*up);
-      return xdr_putuint32 (xdrs, &l);
-
-    case XDR_DECODE:
-      if (!xdr_getuint32 (xdrs, &l))
-          {
-            return FALSE;
-          }
-      *up = (unsigned int) l;
-
-    case XDR_FREE:
-      return TRUE;
-  }
-  return FALSE;
-}
-
-
-
-
-/*
- * XDR short integers
- */
-bool_t
-xdr_short (XDR *xdrs, short *sp)
-{
-  xdr_int32_t l;
-
-  switch (xdrs->x_op)
-    {
-    case XDR_ENCODE:
-      l = (xdr_int32_t) *sp;
-      return xdr_putint32 (xdrs, &l);
-
-    case XDR_DECODE:
-      if (!xdr_getint32 (xdrs, &l))
-        {
-          return FALSE;
-        }
-      *sp = (short) l;
-      return TRUE;
-
-    case XDR_FREE:
-      return TRUE;
-    }
-  return FALSE;
-}
-
-
-/*
- * XDR unsigned short integers
- */
-bool_t
-xdr_u_short (XDR *xdrs, unsigned short *usp)
-{
-  xdr_uint32_t l;
-
-  switch (xdrs->x_op)
-    {
-    case XDR_ENCODE:
-      l = (xdr_uint32_t) *usp;
-      return xdr_putuint32 (xdrs, &l);
-
-    case XDR_DECODE:
-      if (!xdr_getuint32 (xdrs, &l))
-        {
-          return FALSE;
-        }
-          *usp = (unsigned short) l;
-      return TRUE;
-
-    case XDR_FREE:
-      return TRUE;
-    }
-  return FALSE;
-}
-
-
-/*
- * XDR a char
- */
-bool_t
-xdr_char (XDR *xdrs, char *cp)
-{
-  int i;
-
-  i = (*cp);
-  if (!xdr_int (xdrs, &i))
-    {
-      return FALSE;
-    }
-  *cp = i;
-  return TRUE;
-}
-
-/*
- * XDR an unsigned char
- */
-bool_t
-xdr_u_char (XDR *xdrs, unsigned char *cp)
-{
-  unsigned int u;
-
-  u = (*cp);
-  if (!xdr_u_int (xdrs, &u))
-    {
-      return FALSE;
-    }
-  *cp = u;
-  return TRUE;
-}
-
-/*
- * XDR booleans
- */
-bool_t
-xdr_bool (XDR *xdrs, int *bp)
-{
-#define XDR_FALSE        ((xdr_int32_t) 0)
-#define XDR_TRUE        ((xdr_int32_t) 1)
-
-  xdr_int32_t lb;
-
-  switch (xdrs->x_op)
-    {
-    case XDR_ENCODE:
-      lb = *bp ? XDR_TRUE : XDR_FALSE;
-      return xdr_putint32 (xdrs, &lb);
-
-    case XDR_DECODE:
-      if (!xdr_getint32 (xdrs, &lb))
-        {
-          return FALSE;
-        }
-      *bp = (lb == XDR_FALSE) ? FALSE : TRUE;
-      return TRUE;
-
-    case XDR_FREE:
-      return TRUE;
-    }
-  return FALSE;
-#undef XDR_FALSE
-#undef XDR_TRUE
-}
-
-
-
 /*
  * XDR opaque data
  * Allows the specification of a fixed size sequence of opaque bytes.
  * cp points to the opaque object and cnt gives the byte length.
  */
-bool_t
-xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
+bool_t xdr_opaque(XDR *xdrs, char *cp, unsigned int cnt)
 {
   unsigned int rndup;
   static char crud[BYTES_PER_XDR_UNIT];
@@ -313,219 +139,61 @@ xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)
   /*
    * if no data we are done
    */
-  if (cnt == 0)
-    return TRUE;
+  if (cnt == 0) return TRUE;
 
   /*
    * round byte count to full xdr units
    */
   rndup = cnt % BYTES_PER_XDR_UNIT;
-  if (rndup > 0)
-    rndup = BYTES_PER_XDR_UNIT - rndup;
-
-  switch (xdrs->x_op)
-    {
-    case XDR_DECODE:
-      if (!xdr_getbytes (xdrs, cp, cnt))
-        {
-          return FALSE;
-        }
-      if (rndup == 0)
-        return TRUE;
-      return xdr_getbytes (xdrs, (char *)crud, rndup);
-
-    case XDR_ENCODE:
-      if (!xdr_putbytes (xdrs, cp, cnt))
-        {
-          return FALSE;
-        }
-      if (rndup == 0)
-        return TRUE;
-      return xdr_putbytes (xdrs, xdr_zero, rndup);
-
-    case XDR_FREE:
-      return TRUE;
-    }
-  return FALSE;
-}
-
-
-/*
- * XDR null terminated ASCII strings
- * xdr_string deals with "C strings" - arrays of bytes that are
- * terminated by a nullptr character.  The parameter cpp references a
- * pointer to storage; If the pointer is null, then the necessary
- * storage is allocated.  The last parameter is the max allowed length
- * of the string as specified by a protocol.
- */
-bool_t
-xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)
-{
-  char *sp = *cpp;        /* sp is the actual string pointer */
-  unsigned int size = 0;
-  unsigned int nodesize = 0;
-
-  /*
-   * first deal with the length since xdr strings are counted-strings
-   */
-  switch (xdrs->x_op)
-    {
-    case XDR_FREE:
-      if (sp == nullptr)
-        {
-          return TRUE;                /* already free */
-        }
-      /* fall through... */
-    case XDR_ENCODE:
-      if (sp == nullptr)
-            return FALSE;
-      size = strlen (sp);
-      break;
-    case XDR_DECODE:
-      break;
-    }
-
-  if (!xdr_u_int (xdrs, &size))
-    {
-      return FALSE;
-    }
-  if (size > maxsize)
-    {
-      return FALSE;
-    }
-  nodesize = size + 1;
-
-  /*
-   * now deal with the actual bytes
-   */
-  switch (xdrs->x_op)
-    {
-    case XDR_DECODE:
-      if (nodesize == 0)
-        {
-          return TRUE;
-        }
-      if (sp == nullptr)
-        *cpp = sp = (char *) malloc (nodesize);
-      if (sp == nullptr)
-        {
-          (void) fputs ("xdr_string: out of memory\n", stderr);
-          return FALSE;
-        }
-      sp[size] = 0;
-      /* fall into ... */
-
-    case XDR_ENCODE:
-      return xdr_opaque (xdrs, sp, size);
-
-    case XDR_FREE:
-      free (sp);
-      *cpp = nullptr;
-      return TRUE;
-    }
-  return FALSE;
-}
-
-
-
-/* Floating-point stuff */
-
-bool_t
-xdr_float(XDR *xdrs, float *fp)
-{
-        xdr_int32_t tmp;
-
-        switch (xdrs->x_op) {
-
-        case XDR_ENCODE:
-                tmp = *(xdr_int32_t *)fp;
-               return (xdr_putint32(xdrs, &tmp));
-
-                break;
-
-        case XDR_DECODE:
-                        if (xdr_getint32(xdrs, &tmp)) {
-                                *(xdr_int32_t *)fp = tmp;
-                                return (TRUE);
-                        }
-
-                break;
-
-        case XDR_FREE:
-                return (TRUE);
-        }
-        return (FALSE);
-}
-
-
-bool_t
-xdr_double(XDR *xdrs, double *dp)
-{
-
-  /* Windows and some other systems dont define double-precision
-   * word order in the header files, so unfortunately we have
-   * to calculate it!
-   */
-  static int LSW=-1; /* Least significant fp word */
-  int *ip;
-  xdr_int32_t tmp[2];
-
-  if (LSW<0) {
-    double x=0.987654321; /* Just a number */
-
-    /* Possible representations in IEEE double precision:
-     * (S=small endian, B=big endian)
-     *
-     * Byte order, Word order, Hex
-     *     S           S       b8 56 0e 3c dd 9a ef 3f
-     *     B           S       3c 0e 56 b8 3f ef 9a dd
-     *     S           B       dd 9a ef 3f b8 56 0e 3c
-     *     B           B       3f ef 9a dd 3c 0e 56 b8
-     */
-
-    unsigned char ix = *((char *)&x);
-
-    if (ix==0xdd || ix==0x3f)
-      LSW=1;  /* Big endian word order */
-    else if (ix==0xb8 || ix==0x3c)
-      LSW=0;  /* Small endian word order */
-    else { /* Catch strange errors */
-      printf("Error when detecting floating-point word order.\n"
-             "Do you have a non-IEEE system?\n"
-             "If possible, use the XDR libraries provided with your system,\n"
-             "instead of the Gromacs fallback XDR source.\n");
-      exit(0);
-    }
-  }
+  if (rndup > 0) rndup = BYTES_PER_XDR_UNIT - rndup;
 
   switch (xdrs->x_op) {
 
-  case XDR_ENCODE:
-    ip = (int *)dp;
-    tmp[0] = ip[!LSW];
-    tmp[1] = ip[LSW];
-    return (xdr_putint32(xdrs, tmp) &&
-               xdr_putint32(xdrs, tmp+1));
+    case XDR_DECODE:
+      if (!xdr_getbytes(xdrs, cp, cnt)) { return FALSE; }
+      if (rndup == 0) return TRUE;
+      return xdr_getbytes(xdrs, (char *) crud, rndup);
+      break;
 
-    break;
+    case XDR_ENCODE:
+      if (!xdr_putbytes(xdrs, cp, cnt)) { return FALSE; }
+      if (rndup == 0) return TRUE;
+      return xdr_putbytes(xdrs, xdr_zero, rndup);
+      break;
 
-  case XDR_DECODE:
-    ip = (int *)dp;
-    if (xdr_getint32(xdrs, tmp+!LSW) &&
-           xdr_getint32(xdrs, tmp+LSW)) {
-        ip[0] = tmp[0];
-        ip[1] = tmp[1];
-        return (TRUE);
-    }
-
-    break;
-
-  case XDR_FREE:
-    return (TRUE);
+    case XDR_FREE:
+      return TRUE;
+      break;
   }
-  return (FALSE);
+  return FALSE;
 }
 
+/* Floating-point stuff */
+
+bool_t xdr_float(XDR *xdrs, float *fp)
+{
+  xdr_int32_t tmp;
+
+  switch (xdrs->x_op) {
+
+    case XDR_ENCODE:
+      tmp = *(xdr_int32_t *) fp;
+      return (xdr_putint32(xdrs, &tmp));
+      break;
+
+    case XDR_DECODE:
+      if (xdr_getint32(xdrs, &tmp)) {
+        *(xdr_int32_t *) fp = tmp;
+        return TRUE;
+      }
+      break;
+
+    case XDR_FREE:
+      return TRUE;
+      break;
+  }
+  return FALSE;
+}
 
 /* Array routines */
 
@@ -539,55 +207,37 @@ xdr_double(XDR *xdrs, double *dp)
  * > elemsize: size of each element
  * > xdr_elem: routine to XDR each element
  */
-bool_t
-xdr_vector (XDR *xdrs, char *basep, unsigned int nelem,
-            unsigned int elemsize, xdrproc_t xdr_elem)
+bool_t xdr_vector(XDR *xdrs, char *basep, unsigned int nelem, unsigned int elemsize,
+                  xdrproc_t xdr_elem)
 {
-#define LASTUNSIGNED        ((unsigned int)0-1)
+#define LASTUNSIGNED ((unsigned int) 0 - 1)
   unsigned int i;
   char *elptr;
 
   elptr = basep;
-  for (i = 0; i < nelem; i++)
-    {
-      if (!(*xdr_elem) (xdrs, elptr, LASTUNSIGNED))
-        {
-          return FALSE;
-        }
-      elptr += elemsize;
-    }
+  for (i = 0; i < nelem; i++) {
+    if (!(*xdr_elem)(xdrs, elptr, LASTUNSIGNED)) { return FALSE; }
+    elptr += elemsize;
+  }
   return TRUE;
 #undef LASTUNSIGNED
 }
 
-
-
-static bool_t xdrstdio_getbytes (XDR *, char *, unsigned int);
-static bool_t xdrstdio_putbytes (XDR *, char *, unsigned int);
-static unsigned int xdrstdio_getpos (XDR *);
-static bool_t xdrstdio_setpos (XDR *, unsigned int);
-static xdr_int32_t *xdrstdio_inline (XDR *, int);
-static void xdrstdio_destroy (XDR *);
-static bool_t xdrstdio_getint32 (XDR *, xdr_int32_t *);
-static bool_t xdrstdio_putint32 (XDR *, xdr_int32_t *);
-static bool_t xdrstdio_getuint32 (XDR *, xdr_uint32_t *);
-static bool_t xdrstdio_putuint32 (XDR *, xdr_uint32_t *);
+static bool_t xdrstdio_getbytes(XDR *, char *, unsigned int);
+static bool_t xdrstdio_putbytes(XDR *, char *, unsigned int);
+static void xdrstdio_destroy(XDR *);
+static bool_t xdrstdio_getint32(XDR *, xdr_int32_t *);
+static bool_t xdrstdio_putint32(XDR *, xdr_int32_t *);
 
 /*
  * Ops vector for stdio type XDR
  */
-static const struct xdr_ops xdrstdio_ops =
-{
-  xdrstdio_getbytes,               /* deserialize counted bytes */
-  xdrstdio_putbytes,             /* serialize counted bytes */
-  xdrstdio_getpos,                /* get offset in the stream */
-  xdrstdio_setpos,                /* set offset in the stream */
-  xdrstdio_inline,                /* prime stream for inline macros */
-  xdrstdio_destroy,                /* destroy stream */
-  xdrstdio_getint32,        /* deserialize a int */
-  xdrstdio_putint32,        /* serialize a int */
-  xdrstdio_getuint32,        /* deserialize a int */
-  xdrstdio_putuint32                /* serialize a int */
+static const struct xdr_ops xdrstdio_ops = {
+    xdrstdio_getbytes, /* deserialize counted bytes */
+    xdrstdio_putbytes, /* serialize counted bytes */
+    xdrstdio_destroy,  /* destroy stream */
+    xdrstdio_getint32, /* deserialize a int */
+    xdrstdio_putint32, /* serialize a int */
 };
 
 /*
@@ -595,8 +245,7 @@ static const struct xdr_ops xdrstdio_ops =
  * Sets the xdr stream handle xdrs for use on the stream file.
  * Operation flag is set to op.
  */
-void
-xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)
+void xdrstdio_create(XDR *xdrs, FILE *file, enum xdr_op op)
 {
   xdrs->x_op = op;
   /* We have to add the const since the `struct xdr_ops' in `struct XDR'
@@ -611,104 +260,42 @@ xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)
  * Destroy a stdio xdr stream.
  * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create.
  */
-static void
-xdrstdio_destroy (XDR *xdrs)
+static void xdrstdio_destroy(XDR *xdrs)
 {
-  (void) fflush ((FILE *) xdrs->x_private);
+  (void) fflush((FILE *) xdrs->x_private);
   /* xx should we close the file ?? */
 }
 
-
-static bool_t
-xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)
+static bool_t xdrstdio_getbytes(XDR *xdrs, char *addr, unsigned int len)
 {
-  if ((len != 0) && (fread (addr, (int) len, 1,
-                            (FILE *) xdrs->x_private) != 1))
-    return FALSE;
+  if ((len != 0) && (fread(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE;
   return TRUE;
 }
 
-static bool_t
-xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)
+static bool_t xdrstdio_putbytes(XDR *xdrs, char *addr, unsigned int len)
 {
-  if ((len != 0) && (fwrite (addr, (int) len, 1,
-                             (FILE *) xdrs->x_private) != 1))
-    return FALSE;
+  if ((len != 0) && (fwrite(addr, (int) len, 1, (FILE *) xdrs->x_private) != 1)) return FALSE;
   return TRUE;
 }
 
-static unsigned int
-xdrstdio_getpos (XDR *xdrs)
-{
-  return (unsigned int) ftell ((FILE *) xdrs->x_private);
-}
-
-static bool_t
-xdrstdio_setpos (XDR *xdrs, unsigned int pos)
-{
-  return fseek ((FILE *) xdrs->x_private, (xdr_int32_t) pos, 0) < 0 ? FALSE : TRUE;
-}
-
-static xdr_int32_t *
-xdrstdio_inline (XDR * /*xdrs*/, int /*len*/)
-{
-  /*
-   * Must do some work to implement this: must ensure
-   * enough data in the underlying stdio buffer,
-   * that the buffer is aligned so that we can indirect through a
-   * long *, and stuff this pointer in xdrs->x_buf.  Doing
-   * a fread or fwrite to a scratch buffer would defeat
-   * most of the gains to be had here and require storage
-   * management on this buffer, so we don't do this.
-   */
-  return nullptr;
-}
-
-static bool_t
-xdrstdio_getint32 (XDR *xdrs, xdr_int32_t *ip)
+static bool_t xdrstdio_getint32(XDR *xdrs, xdr_int32_t *ip)
 {
   xdr_int32_t mycopy;
 
-  if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
-    return FALSE;
-  *ip = xdr_ntohl (mycopy);
+  if (fread((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE;
+  *ip = xdr_ntohl(mycopy);
   return TRUE;
 }
 
-static bool_t
-xdrstdio_putint32 (XDR *xdrs, xdr_int32_t *ip)
+static bool_t xdrstdio_putint32(XDR *xdrs, xdr_int32_t *ip)
 {
-  xdr_int32_t mycopy = xdr_htonl (*ip);
+  xdr_int32_t mycopy = xdr_htonl(*ip);
 
   ip = &mycopy;
-  if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
-    return FALSE;
+  if (fwrite((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1) return FALSE;
   return TRUE;
 }
 
-static bool_t
-xdrstdio_getuint32 (XDR *xdrs, xdr_uint32_t *ip)
-{
-        xdr_uint32_t mycopy;
-
-        if (fread ((char *) &mycopy, 4, 1, (FILE *) xdrs->x_private) != 1)
-                return FALSE;
-        *ip = xdr_ntohl (mycopy);
-        return TRUE;
-}
-
-static bool_t
-xdrstdio_putuint32 (XDR *xdrs, xdr_uint32_t *ip)
-{
-        xdr_uint32_t mycopy = xdr_htonl (*ip);
-
-        ip = &mycopy;
-        if (fwrite ((char *) ip, 4, 1, (FILE *) xdrs->x_private) != 1)
-                return FALSE;
-        return TRUE;
-}
-
 #ifdef __cplusplus
 }
 #endif
-

src/EXTRA-DUMP/xdr_compat.h

@@ -1,7 +1,7 @@
 #ifndef LMP_XDR_COMPAT_H
 #define LMP_XDR_COMPAT_H
 
-#include <climits>
+#include <cstdint>
 #include <cstdio>
 
 #ifdef __cplusplus
@@ -9,47 +9,53 @@ extern "C" {
 #endif
 
 /*
- * This file is needed for systems, that do not provide XDR support
- * in their system libraries. It was written for windows, but will
- * most probably work on other platforms too. better make sure you
- * test that the xtc files produced are ok before using it.
+ * This file contains the definitions for Sun External Data Representation (XDR).
+ * They have been adapted specifically for the use with the LAMMPS xtc dump style
+ * to produce compressed trajectory files in the Gromacs XTC format.
  *
- * It is also needed on BG/L, BG/P and Cray XT3/XT4/XT5 as we don't
- * have XDR support in the lightweight kernel runtimes either.
+ * The XDR sources are available under the BSD 3-clause license for example in
+ * the MIT Kerberos 5 distribution with the following copyright notice and license.
  *
- * This file contains the definitions for Sun External Data
- * Representation (XDR) headers and routines.
+ * @(#)xdr.h    2.2 88/07/29 4.0 RPCSRC
  *
- * Although the rest of LAMPPS is GPL, you can copy and use the XDR
- * routines in any way you want as long as you obey Sun's license:
- * Sun RPC is a product of Sun Microsystems, Inc. and is provided for
- * unrestricted use provided that this legend is included on all tape
- * media and as a part of the software program in whole or part.  Users
- * may copy or modify Sun RPC without charge, but are not authorized
- * to license or distribute it to anyone else except as part of a product or
- * program developed by the user.
+ * Copyright (c) 2010, Oracle America, Inc.
  *
- * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
- * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
- * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.
+ * All rights reserved.
  *
- * Sun RPC is provided with no support and without any obligation on the
- * part of Sun Microsystems, Inc. to assist in its use, correction,
- * modification or enhancement.
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
  *
- * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
- * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
- * OR ANY PART THEREOF.
+ *     * Redistributions of source code must retain the above copyright
+ *       notice, this list of conditions and the following disclaimer.
  *
- * In no event will Sun Microsystems, Inc. be liable for any lost revenue
- * or profits or other special, indirect and consequential damages, even if
- * Sun has been advised of the possibility of such damages.
+ *     * Redistributions in binary form must reproduce the above copyright
+ *       notice, this list of conditions and the following disclaimer in
+ *       the documentation and/or other materials provided with the
+ *       distribution.
  *
- * Sun Microsystems, Inc.
- * 2550 Garcia Avenue
- * Mountain View, California  94043
+ *     * Neither the name of the "Oracle America, Inc." nor the names of
+ *       its contributors may be used to endorse or promote products
+ *       derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED
+ * TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
+/* compatibility typedefs */
+typedef int bool_t;
+
+typedef int32_t xdr_int32_t;
+typedef uint32_t xdr_uint32_t;
+
 /*
  * Xdr operations.  XDR_ENCODE causes the type to be encoded into the
  * stream.  XDR_DECODE causes the type to be extracted from the stream.
@@ -57,44 +63,8 @@ extern "C" {
  * XDR_DECODE request.
  */
 
-typedef int bool_t;
-
-#if defined(_WIN32) || defined(__APPLE__) || defined(__FreeBSD__) || defined(__DragonFly__) || \
-    defined(__OpenBSD__) || defined(__NetBSD__) || (defined(__linux__) && !defined(__GLIBC_MINOR__))
-typedef char *caddr_t;
-typedef unsigned int u_int;
-#endif
-
-/*
- * Aninteger type that is 32 bits wide. Check if int,
- * long or short is 32 bits and die if none of them is :-)
- */
-#if (INT_MAX == 2147483647)
-typedef int xdr_int32_t;
-typedef unsigned int xdr_uint32_t;
-#elif (LONG_MAX == 2147483647L)
-typedef long xdr_int32_t;
-typedef unsigned long xdr_uint32_t;
-#elif (SHRT_MAX == 2147483647)
-typedef short xdr_int32_t;
-typedef unsigned short xdr_uint32_t;
-#else
-#error ERROR: No 32 bit wide integer type found!
-#endif
-
 enum xdr_op { XDR_ENCODE = 0, XDR_DECODE = 1, XDR_FREE = 2 };
 
-#ifndef FALSE
-#define FALSE (0)
-#endif
-#ifndef TRUE
-#define TRUE (1)
-#endif
-
-#define BYTES_PER_XDR_UNIT (4)
-/* Macro to round up to units of 4. */
-#define XDR_RNDUP(x) (((x) + BYTES_PER_XDR_UNIT - 1) & ~(BYTES_PER_XDR_UNIT - 1))
-
 /*
  * The XDR handle.
  * Contains operation which is being applied to the stream,
@@ -113,26 +83,16 @@ struct XDR {
 };
 
 struct xdr_ops {
+  /* get some bytes from XDR stream */
   bool_t (*x_getbytes)(XDR *__xdrs, char *__addr, unsigned int __len);
-  /* get some bytes from " */
+  /* put some bytes to XDR stream */
   bool_t (*x_putbytes)(XDR *__xdrs, char *__addr, unsigned int __len);
-  /* put some bytes to " */
-  unsigned int (*x_getpostn)(XDR *__xdrs);
-  /* returns bytes off from beginning */
-  bool_t (*x_setpostn)(XDR *__xdrs, unsigned int __pos);
-  /* lets you reposition the stream */
-  xdr_int32_t *(*x_inline)(XDR *__xdrs, int __len);
-  /* buf quick ptr to buffered data */
-  void (*x_destroy)(XDR *__xdrs);
   /* free privates of this xdr_stream */
+  void (*x_destroy)(XDR *__xdrs);
+  /* get a int from XDR stream */
   bool_t (*x_getint32)(XDR *__xdrs, xdr_int32_t *__ip);
-  /* get a int from underlying stream */
+  /* put a int to XDR stream */
   bool_t (*x_putint32)(XDR *__xdrs, xdr_int32_t *__ip);
-  /* put a int to " */
-  bool_t (*x_getuint32)(XDR *__xdrs, xdr_uint32_t *__ip);
-  /* get a unsigned int from underlying stream */
-  bool_t (*x_putuint32)(XDR *__xdrs, xdr_uint32_t *__ip);
-  /* put a int to " */
 };
 
 /*
@@ -151,53 +111,25 @@ typedef bool_t (*xdrproc_t)(XDR *, void *, ...);
  *
  * XDR          *xdrs;
  * xdr_int32_t  *int32p;
- * long         *longp;
- * char         *addr;
  * unsigned int  len;
- * unsigned int  pos;
  */
 
 #define xdr_getint32(xdrs, int32p) (*(xdrs)->x_ops->x_getint32)(xdrs, int32p)
-
 #define xdr_putint32(xdrs, int32p) (*(xdrs)->x_ops->x_putint32)(xdrs, int32p)
-
-#define xdr_getuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_getuint32)(xdrs, uint32p)
-
-#define xdr_putuint32(xdrs, uint32p) (*(xdrs)->x_ops->x_putuint32)(xdrs, uint32p)
-
 #define xdr_getbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_getbytes)(xdrs, addr, len)
-
 #define xdr_putbytes(xdrs, addr, len) (*(xdrs)->x_ops->x_putbytes)(xdrs, addr, len)
-
-#define xdr_getpos(xdrs) (*(xdrs)->x_ops->x_getpostn)(xdrs)
-
-#define xdr_setpos(xdrs, pos) (*(xdrs)->x_ops->x_setpostn)(xdrs, pos)
-
-#define xdr_inline(xdrs, len) (*(xdrs)->x_ops->x_inline)(xdrs, len)
-
 #define xdr_destroy(xdrs)                                            \
   do {                                                               \
     if ((xdrs)->x_ops->x_destroy) (*(xdrs)->x_ops->x_destroy)(xdrs); \
   } while (0)
 
 extern bool_t xdr_int(XDR *__xdrs, int *__ip);
-extern bool_t xdr_u_int(XDR *__xdrs, unsigned int *__ip);
-extern bool_t xdr_short(XDR *__xdrs, short *__ip);
-extern bool_t xdr_u_short(XDR *__xdrs, unsigned short *__ip);
-extern bool_t xdr_bool(XDR *__xdrs, int *__bp);
 extern bool_t xdr_opaque(XDR *__xdrs, char *__cp, unsigned int __cnt);
-extern bool_t xdr_string(XDR *__xdrs, char **__cpp, unsigned int __maxsize);
-extern bool_t xdr_char(XDR *__xdrs, char *__cp);
-extern bool_t xdr_u_char(XDR *__xdrs, unsigned char *__cp);
 extern bool_t xdr_vector(XDR *__xdrs, char *__basep, unsigned int __nelem, unsigned int __elemsize,
                          xdrproc_t __xdr_elem);
 extern bool_t xdr_float(XDR *__xdrs, float *__fp);
-extern bool_t xdr_double(XDR *__xdrs, double *__dp);
 extern void xdrstdio_create(XDR *__xdrs, FILE *__file, enum xdr_op __xop);
 
-/* free memory buffers for xdr */
-extern void xdr_free(xdrproc_t __proc, char *__objp);
-
 #ifdef __cplusplus
 }
 #endif

src/GRANULAR/fix_pour.cpp

@@ -701,7 +701,7 @@ void FixPour::pre_exchange()
   // rebuild atom map
 
   if (atom->map_style != Atom::MAP_NONE) {
-    if (success) atom->map_init();
+    atom->map_init();
     atom->map_set();
   }
 

src/INTEL/fix_nh_intel.cpp

@@ -26,6 +26,7 @@
 #include "memory.h"
 #include "modify.h"
 #include "neighbor.h"
+#include "respa.h"
 #include "update.h"
 
 #include <cmath>
@@ -339,8 +340,13 @@ void FixNHIntel::reset_dt()
 
   // If using respa, then remap is performed in innermost level
 
-  if (utils::strmatch(update->integrate_style,"^respa"))
+  if (utils::strmatch(update->integrate_style,"^respa")) {
+    auto respa_ptr = dynamic_cast<Respa *>(update->integrate);
+    if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style);
+    nlevels_respa = respa_ptr->nlevels;
+    step_respa = respa_ptr->step;
     dto = 0.5*step_respa[0];
+  }
 
   if (pstat_flag)
     pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);

src/INTEL/intel_intrinsics.h

@@ -123,7 +123,9 @@ struct vector_ops<double, KNC> {
     static fvec recip(const fvec &a) { return _mm512_recip_pd(a); }
     template<int scale>
     static void gather_prefetch_t0(const ivec &idx, bvec mask, const void *base) {
+#ifdef __AVX512PF__
       _mm512_mask_prefetch_i32gather_ps(idx, mask, base, scale, _MM_HINT_T0);
+#endif
     }
     template<int scale>
     static fvec gather(const fvec &from, bvec mask, const ivec &idx, const void *base) {
@@ -262,7 +264,9 @@ struct vector_ops<float, KNC> {
     static fvec recip(const fvec &a) { return _mm512_recip_ps(a); }
     template<int scale>
     static void gather_prefetch_t0(const ivec &idx, bvec mask, const void *base) {
+#ifdef __AVX512PF__
       _mm512_mask_prefetch_i32gather_ps(idx, mask, base, scale, _MM_HINT_T0);
+#endif
     }
     template<int scale>
     static fvec gather(const fvec &from, bvec mask, const ivec &idx, const void *base) {

src/INTEL/intel_intrinsics_airebo.h

@@ -639,8 +639,10 @@ public:
   AVEC_BINOP(-, sub)
 
   VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
+#ifdef __AVX512PF__
     _mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
                                       sizeof(FVEC_SCAL_T), _MM_HINT_T0);
+#endif
   }
 };
 
@@ -697,8 +699,10 @@ public:
   AVEC2_BINOP(-, sub)
 
   VEC_INLINE static void gather_prefetch0(const IVEC_NAME &a, void * mem) {
+#ifdef __AVX512PF__
     _mm512_mask_prefetch_i32gather_ps(a.val_, BVEC_NAME::full().val_, mem,
                                       sizeof(double), _MM_HINT_T0);
+#endif
   }
 };
 #endif

src/KOKKOS/atom_vec_kokkos.h

@@ -142,28 +142,6 @@ class AtomVecKokkos : virtual public AtomVec {
  public:
 
   #ifdef LMP_KOKKOS_GPU
-  template<class ViewType>
-  Kokkos::View<typename ViewType::data_type,
-               typename ViewType::array_layout,
-               LMPPinnedHostType,
-               Kokkos::MemoryTraits<Kokkos::Unmanaged> >
-  create_async_copy(const ViewType& src) {
-    typedef Kokkos::View<typename ViewType::data_type,
-                 typename ViewType::array_layout,
-                 typename std::conditional<
-                   std::is_same<typename ViewType::execution_space,LMPDeviceType>::value,
-                   LMPPinnedHostType,typename ViewType::memory_space>::type,
-                 Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
-    if (buffer_size == 0) {
-       buffer = Kokkos::kokkos_malloc<LMPPinnedHostType>(src.span());
-       buffer_size = src.span();
-    } else if (buffer_size < src.span()) {
-       buffer = Kokkos::kokkos_realloc<LMPPinnedHostType>(buffer,src.span());
-       buffer_size = src.span();
-    }
-    return mirror_type(buffer, src.d_view.layout());
-  }
-
   template<class ViewType>
   void perform_async_copy(ViewType& src, unsigned int space) {
     typedef Kokkos::View<typename ViewType::data_type,
@@ -173,11 +151,11 @@ class AtomVecKokkos : virtual public AtomVec {
                    LMPPinnedHostType,typename ViewType::memory_space>::type,
                  Kokkos::MemoryTraits<Kokkos::Unmanaged> > mirror_type;
     if (buffer_size == 0) {
-       buffer = Kokkos::kokkos_malloc<LMPPinnedHostType>(src.span()*sizeof(typename ViewType::value_type));
-       buffer_size = src.span();
-    } else if (buffer_size < src.span()) {
-       buffer = Kokkos::kokkos_realloc<LMPPinnedHostType>(buffer,src.span()*sizeof(typename ViewType::value_type));
-       buffer_size = src.span();
+      buffer_size = src.span() * sizeof(typename ViewType::value_type);
+      buffer = Kokkos::kokkos_malloc<LMPPinnedHostType>(buffer_size);
+    } else if (buffer_size < (src.span() * sizeof(typename ViewType::value_type))) {
+       buffer_size = src.span() * sizeof(typename ViewType::value_type);
+       buffer = Kokkos::kokkos_realloc<LMPPinnedHostType>(buffer, buffer_size);
     }
     mirror_type tmp_view((typename ViewType::value_type*)buffer, src.d_view.layout());
 

src/KOKKOS/domain_kokkos.cpp

@@ -22,8 +22,7 @@
 
 using namespace LAMMPS_NS;
 
-#define BIG   1.0e20
-#define SMALL 1.0e-4
+static constexpr double BIG = 1.0e20;
 
 /* ---------------------------------------------------------------------- */
 
@@ -81,6 +80,11 @@ public:
 void DomainKokkos::reset_box()
 {
   // perform shrink-wrapping
+
+  // nothing to do for empty systems
+
+  if (atom->natoms == 0) return;
+
   // compute extent of atoms on this proc
   // for triclinic, this is done in lamda space
 

src/LATBOLTZ/fix_lb_fluid.cpp

@@ -220,9 +220,11 @@ FixLbFluid::FixLbFluid(LAMMPS *lmp, int narg, char **arg) :
 
   // Flags for fix references (i.e. quantities accessible via f_ID[n]
   vector_flag = 1;
+  extvector = 0;
   size_vector = 5;
 
   scalar_flag = 1;
+  extscalar = 0;
 
   int iarg = 6;
   while (iarg < narg) {

src/MACHDYN/compute_smd_vol.cpp

@@ -25,13 +25,14 @@
 
 #include "compute_smd_vol.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -39,12 +40,12 @@ using namespace LAMMPS_NS;
 
 ComputeSMDVol::ComputeSMDVol(LAMMPS *lmp, int narg, char **arg) :
                 Compute(lmp, narg, arg) {
-        if (narg != 3)
-                error->all(FLERR, "Illegal compute smd/volume command");
+        if (narg != 3) error->all(FLERR, "Illegal compute smd/volume command");
         if (atom->vfrac_flag != 1)
-                error->all(FLERR, "compute smd/volume command requires atom_style with density (e.g. smd)");
+          error->all(FLERR, "compute smd/volume command requires atom_style with density (e.g. smd)");
 
         scalar_flag = 1;
+        extscalar = 1;
         peratom_flag = 1;
         size_peratom_cols = 0;
 

src/MACHDYN/fix_smd_integrate_tlsph.cpp

@@ -24,15 +24,18 @@
  ------------------------------------------------------------------------- */
 
 #include "fix_smd_integrate_tlsph.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "pair.h"
+#include "update.h"
+
 #include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "error.h"
-#include "pair.h"
-#include "comm.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
@@ -115,6 +118,11 @@ void FixSMDIntegrateTlsph::init() {
         dtv = update->dt;
         dtf = 0.5 * update->dt * force->ftm2v;
         vlimitsq = vlimit * vlimit;
+
+        // Cannot use vremap since its effects aren't propagated to vest
+        //   see RHEO or SPH packages for examples of patches
+        if (domain->deform_vremap)
+          error->all(FLERR, "Fix smd/integrate_tlsph cannot be used with velocity remapping");
 }
 
 /* ----------------------------------------------------------------------

src/MACHDYN/fix_smd_integrate_ulsph.cpp

@@ -24,15 +24,18 @@
  ------------------------------------------------------------------------- */
 
 #include "fix_smd_integrate_ulsph.h"
+
+#include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
+#include "force.h"
+#include "pair.h"
+#include "update.h"
+
 #include <cmath>
 #include <cstring>
 #include <Eigen/Eigen>
-#include "atom.h"
-#include "comm.h"
-#include "force.h"
-#include "update.h"
-#include "error.h"
-#include "pair.h"
 
 using namespace Eigen;
 using namespace LAMMPS_NS;
@@ -144,6 +147,11 @@ void FixSMDIntegrateUlsph::init() {
         dtv = update->dt;
         dtf = 0.5 * update->dt * force->ftm2v;
         vlimitsq = vlimit * vlimit;
+
+        // Cannot use vremap since its effects aren't propagated to vest
+        //   see RHEO or SPH packages for examples of patches
+        if (domain->deform_vremap)
+          error->all(FLERR, "Fix smd/integrate_ulsph cannot be used with velocity remapping");
 }
 
 /* ----------------------------------------------------------------------

src/MC/fix_bond_create.cpp

@@ -408,15 +408,15 @@ void FixBondCreate::post_integrate()
   int *mask = atom->mask;
   int *type = atom->type;
 
-  if (constrainflag) {
-    // communicate partner and 1-2 special neighbors
-    // to correctly handle angle constraints
+  // communicate partner and 1-2 special neighbors
+  // to correctly handle angle constraints
 
+  if (constrainflag) {
     commflag = 3;
     comm->forward_comm(this);
   }
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/MC/fix_bond_swap.cpp

@@ -229,7 +229,7 @@ void FixBondSwap::post_integrate()
   type = atom->type;
   x = atom->x;
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
   inum = list->inum;
   ilist = list->ilist;
   numneigh = list->numneigh;

src/MEAM/meam.h

@@ -17,7 +17,7 @@
 #include <cmath>
 #include <string>
 
-constexpr int maxelt = 5;
+constexpr int maxelt = 8;
 
 namespace LAMMPS_NS {
 class Memory;

src/MEAM/pair_meam.cpp

@@ -550,14 +550,14 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
 
   std::shared_ptr<PotentialFileReader> reader;
 
-  if (comm->me == 0) { reader = std::make_shared<PotentialFileReader>(lmp, userfile, "MEAM"); }
+  if (comm->me == 0) reader = std::make_shared<PotentialFileReader>(lmp, userfile, "MEAM");
 
   // read settings
   // pass them one at a time to MEAM package
   // match strings to list of corresponding ints
   char *line = nullptr;
   char buffer[MAXLINE];
-
+  int lineno = 0;
   while (true) {
     int which;
     int nindex, index[3];
@@ -565,6 +565,7 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
     int nline;
     if (comm->me == 0) {
       line = reader->next_line();
+      ++lineno;
       if (line == nullptr) {
         nline = -1;
       } else
@@ -584,20 +585,32 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
     for (which = 0; which < nkeywords; which++)
       if (keyword == keywords[which]) break;
     if (which == nkeywords)
-      error->all(FLERR, "Keyword {} in MEAM parameter file not recognized", keyword);
+      error->all(FLERR, "Keyword {} in MEAM parameter file {}:{} not recognized", keyword,
+                 userfile, lineno);
 
-    nindex = nparams - 2;
-    for (int i = 0; i < nindex; i++) index[i] = values.next_int() - 1;
+    try {
+      nindex = nparams - 2;
+      for (int i = 0; i < nindex; i++) index[i] = values.next_int() - 1;
+    } catch (std::exception &e) {
+      error->all(FLERR, "Error parsing MEAM parameter file {}:{}: {}", userfile, lineno, e.what());
+    }
 
     // map lattce_meam value to an integer
     if (which == 4) {
       std::string lattice_type = values.next_string();
       lattice_t latt;
       if (!MEAM::str_to_lat(lattice_type, false, latt))
-        error->all(FLERR, "Unrecognized lattice type in MEAM parameter file: {}", lattice_type);
+        error->all(FLERR, "Unrecognized lattice type {} in MEAM parameter file {}:{}",
+                   lattice_type, userfile, lineno);
       value = latt;
-    } else
-      value = values.next_double();
+    } else {
+      try {
+        value = values.next_double();
+      } catch (std::exception &e) {
+        error->all(FLERR, "Error parsing MEAM parameter file {}:{}: {}", userfile, lineno,
+                   e.what());
+      }
+    }
 
     // pass single setting to MEAM package
 
@@ -607,7 +620,8 @@ void PairMEAM::read_user_meam_file(const std::string &userfile)
       const char *descr[] = {"has an unknown error", "is out of range (please report a bug)",
                              "expected more indices", "has out of range element index"};
       if ((errorflag < 0) || (errorflag > 3)) errorflag = 0;
-      error->all(FLERR, "Error in MEAM parameter file: keyword {} {}", keyword, descr[errorflag]);
+      error->all(FLERR, "Error in MEAM parameter file {}:{}: keyword {} {}", userfile, lineno,
+                 keyword, descr[errorflag]);
     }
   }
 }

src/MISC/fix_ipi.cpp

@@ -48,6 +48,7 @@ using namespace FixConst;
 #ifndef _WIN32
 #include <netdb.h>
 #include <netinet/in.h>
+#include <netinet/tcp.h>
 #include <sys/socket.h>
 #include <sys/types.h>
 #include <sys/un.h>
@@ -78,7 +79,7 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
    error: pointer to a LAMMPS Error object
 */
 {
-  int ai_err;
+  int ai_err,flagNagle;
 
 #ifdef _WIN32
   error->one(FLERR, "i-PI socket implementation requires UNIX environment");
@@ -100,6 +101,11 @@ static void open_socket(int &sockfd, int inet, int port, char *host, Error *erro
     sockfd = socket(res->ai_family, res->ai_socktype, res->ai_protocol);
     if (sockfd < 0) error->one(FLERR, "Error creating socket for fix ipi");
 
+    // set TCP_NODELAY=1 to disable Nagle's algorithm as it slows down the small transactions for i-PI
+    flagNagle = 1;
+    int result_TCP = setsockopt(sockfd, IPPROTO_TCP, TCP_NODELAY, (char *)&flagNagle, sizeof(int));
+    if (result_TCP < 0) { perror("Error setting TCP_NODELAY"); }
+
     // makes connection
     if (connect(sockfd, res->ai_addr, res->ai_addrlen) < 0)
       error->one(FLERR, "Error opening INET socket: wrong port or server unreachable");
@@ -182,6 +188,7 @@ FixIPI::FixIPI(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), irregul
   master = (comm->me == 0) ? 1 : 0;
   inet = 1;
   reset_flag = 0;
+  firsttime = 1;
 
   int iarg = 5;
   while (iarg < narg) {
@@ -247,6 +254,7 @@ void FixIPI::init()
     ipisock = 0;
   // TODO: should check for success in socket opening,
   // but the current open_socket routine dies brutally if unsuccessful
+
   // tell lammps we have assigned a socket
   socketflag = 1;
 
@@ -363,17 +371,40 @@ void FixIPI::initial_integrate(int /*vflag*/)
   // has to be be done before invoking Irregular::migrate_atoms()
   //   since it requires atoms be inside simulation box
 
+  // folds atomic coordinates close to the origin
   if (domain->triclinic) domain->x2lamda(atom->nlocal);
   domain->pbc();
   domain->reset_box();
-  if (domain->triclinic) domain->lamda2x(atom->nlocal);
-
   // move atoms to new processors via irregular()
   // only needed if migrate_check() says an atom moves to far
-  if (domain->triclinic) domain->x2lamda(atom->nlocal);
   if (irregular->migrate_check()) irregular->migrate_atoms();
   if (domain->triclinic) domain->lamda2x(atom->nlocal);
 
+  // ensures continuity of trajectories relative to the
+  // snapshot at neighbor list creation, minimizing the
+  // number of neighbor list updates
+  auto xhold = neighbor->get_xhold();
+  if (xhold != NULL && !firsttime) {
+    // don't wrap if xhold is not used in the NL, or the
+    // first call (because the NL is initialized from the
+    // data file that might have nothing to do with the
+    // current structure
+    for (int i = 0; i < nlocal; i++) {
+      if (mask[i] & groupbit) {
+        auto delx = x[i][0] - xhold[i][0];
+        auto dely = x[i][1] - xhold[i][1];
+        auto delz = x[i][2] - xhold[i][2];
+
+        domain->minimum_image(delx, dely, delz);
+
+        x[i][0] = xhold[i][0] + delx;
+        x[i][1] = xhold[i][1] + dely;
+        x[i][2] = xhold[i][2] + delz;
+      }
+    }
+  }
+  firsttime = 0;
+
   // check if kspace solver is used
   if (reset_flag && kspace_flag) {
     // reset kspace, pair, angles, ... b/c simulation box might have changed.
@@ -452,6 +483,7 @@ void FixIPI::final_integrate()
   retstr[0]=0;
 
   if (master) {
+    // check for new messages
     while (true) {
       readbuffer(ipisock, header, MSGLEN, error); header[MSGLEN]=0;
 
@@ -464,6 +496,7 @@ void FixIPI::final_integrate()
       error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
 
     if (strcmp(header,"GETFORCE    ") == 0)  {
+      // return force and energy data
       writebuffer(ipisock,"FORCEREADY  ",MSGLEN, error);
       writebuffer(ipisock,(char*) &pot,8, error);
       writebuffer(ipisock,(char*) &nat,4, error);
@@ -478,5 +511,3 @@ void FixIPI::final_integrate()
 
   hasdata=0;
 }
-
-

src/MISC/fix_ipi.h

@@ -42,6 +42,7 @@ class FixIPI : public Fix {
   long bsize;
   int kspace_flag;
   int reset_flag;
+  int firsttime;
 
  private:
   class Irregular *irregular;

src/OPENMP/fix_omp.cpp

@@ -167,6 +167,10 @@ void FixOMP::init()
   // adjust number of data objects when the number of OpenMP
   // threads has been changed somehow
   const int nthreads = comm->nthreads;
+#if defined(_OPENMP)
+  // make certain threads are initialized correctly. avoids segfaults with LAMMPS-GUI
+  if (nthreads != omp_get_max_threads()) omp_set_num_threads(nthreads);
+#endif
   if (_nthr != nthreads) {
     if (comm->me == 0)
       utils::logmesg(lmp,"Re-init OPENMP for {} OpenMP thread(s)\n", nthreads);
@@ -226,7 +230,8 @@ void FixOMP::init()
   check_hybrid = 0;                                                     \
   if (force->name) {                                                    \
     if ( (strcmp(force->name ## _style,"hybrid") == 0) ||               \
-         (strcmp(force->name ## _style,"hybrid/overlay") == 0) )        \
+         (strcmp(force->name ## _style,"hybrid/overlay") == 0) ||       \
+         (strcmp(force->name ## _style,"hybrid/scaled") == 0) )         \
       check_hybrid=1;                                                   \
     if (force->name->suffix_flag & Suffix::OMP) {                       \
       last_force_name = (const char *) #name;                           \

src/OPENMP/reaxff_forces_omp.cpp

@@ -155,7 +155,7 @@ namespace ReaxFF {
 /* ---------------------------------------------------------------------- */
 
   static void Validate_ListsOMP(reax_system *system, reax_list **lists,
-                         int step, int n, int N, int numH)
+                         int step, int N, int numH)
   {
     int comp, Hindex;
     reax_list *bonds, *hbonds;
@@ -195,7 +195,7 @@ namespace ReaxFF {
 #if defined(_OPENMP)
 #pragma omp for schedule(guided)
 #endif
-        for (int i = 0; i < n; ++i) {
+        for (int i = 0; i < N; ++i) {
           Hindex = system->my_atoms[i].Hindex;
           if (Hindex > -1) {
             system->my_atoms[i].num_hbonds =
@@ -457,8 +457,7 @@ namespace ReaxFF {
     workspace->realloc.num_bonds = num_bonds;
     workspace->realloc.num_hbonds = num_hbonds;
 
-    Validate_ListsOMP(system, lists, data->step,
-                      system->n, system->N, system->numH);
+    Validate_ListsOMP(system, lists, data->step, system->N, system->numH);
   }
 
 /* ---------------------------------------------------------------------- */

src/PLUMED/fix_plumed.cpp

@@ -77,9 +77,9 @@ FixPlumed::FixPlumed(LAMMPS *lmp, int narg, char **arg) :
 
   int api_version=0;
   p->cmd("getApiVersion",&api_version);
-  if ((api_version < 5) || (api_version > 9))
+  if ((api_version < 5) || (api_version > 10))
     error->all(FLERR,"Incompatible API version for PLUMED in fix plumed. "
-               "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x are tested and supported.");
+               "Only Plumed 2.4.x, 2.5.x, 2.6.x, 2.7.x, 2.8.x, 2.9.x are tested and supported.");
 
 #if !defined(MPI_STUBS)
   // If the -partition option is activated then enable

src/PYTHON/fix_python_invoke.cpp

@@ -105,6 +105,13 @@ void FixPythonInvoke::end_of_step()
 
 /* ---------------------------------------------------------------------- */
 
+void FixPythonInvoke::setup(int vflag)
+{
+  if (selected_callback == POST_FORCE) post_force(vflag);
+}
+
+/* ---------------------------------------------------------------------- */
+
 void FixPythonInvoke::post_force(int vflag)
 {
   if (update->ntimestep % nevery != 0) return;

src/PYTHON/fix_python_invoke.h

@@ -30,6 +30,7 @@ class FixPythonInvoke : public Fix {
   FixPythonInvoke(class LAMMPS *, int, char **);
   ~FixPythonInvoke() override;
   int setmask() override;
+  void setup(int) override;
   void end_of_step() override;
   void post_force(int) override;
 

src/QEQ/fix_qeq_shielded.cpp

@@ -55,29 +55,53 @@ void FixQEqShielded::init()
 
   neighbor->add_request(this, NeighConst::REQ_FULL);
 
-  int ntypes = atom->ntypes;
+  const int ntypes = atom->ntypes;
   memory->create(shld, ntypes + 1, ntypes + 1, "qeq:shielding");
 
   init_shielding();
 
-  int i;
-  for (i = 1; i <= ntypes; i++) {
-    if (gamma[i] == 0.0) error->all(FLERR, "Invalid param file for fix qeq/shielded");
+  // check if valid parameters for all atom types in the fix group are provided
+  const int *type = atom->type;
+  const int *mask = atom->mask;
+  int tmp = 0, tmp_all = 0;
+  for (int i = 0; i < nlocal; ++i) {
+    if (mask[i] & groupbit) {
+      if (gamma[type[i]] == 0.0)
+        tmp = type[i];
+    }
   }
+  MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+  if (tmp_all)
+    error->all(FLERR, "Invalid QEq parameters for atom type {} provided", tmp_all);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixQEqShielded::extract_reax()
 {
+  const int nlocal = atom->nlocal;
+  const int *mask = atom->mask;
+  const int *type = atom->type;
+
   Pair *pair = force->pair_match("^reax..", 0);
   if (pair == nullptr) error->all(FLERR, "No pair reaxff for fix qeq/shielded");
-  int tmp;
+  int tmp, tmp_all;
   chi = (double *) pair->extract("chi", tmp);
   eta = (double *) pair->extract("eta", tmp);
   gamma = (double *) pair->extract("gamma", tmp);
-  if (chi == nullptr || eta == nullptr || gamma == nullptr)
-    error->all(FLERR, "Fix qeq/shielded could not extract params from pair reaxff");
+  if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
+    error->all(FLERR, "Fix qeq/shielded could not extract all QEq parameters from pair reaxff");
+
+  tmp = tmp_all = 0;
+  for (int i = 0; i < nlocal; ++i) {
+    if (mask[i] & groupbit) {
+      if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
+        tmp = type[i];
+    }
+  }
+  MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+  if (tmp_all)
+    error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
 }
 
 // clang-format off

src/REACTION/fix_bond_react.cpp

@@ -919,7 +919,7 @@ void FixBondReact::post_integrate()
   tagint *tag = atom->tag;
   int *type = atom->type;
 
-  neighbor->build_one(list,1);
+  neighbor->build_one(list);
 
   // here we define a full special list
   // may need correction for unusual special bond settings

src/REAXFF/fix_qeq_reaxff.cpp

@@ -205,24 +205,42 @@ int FixQEqReaxFF::setmask()
 
 void FixQEqReaxFF::pertype_parameters(char *arg)
 {
+  const int nlocal = atom->nlocal;
+  const int *mask = atom->mask;
+  const int *type = atom->type;
+
   // match either new keyword "reaxff" or old keyword "reax/c"
   if (utils::strmatch(arg,"^reax..$")) {
     reaxflag = 1;
     Pair *pair = force->pair_match("^reax..",0);
     if (!pair) error->all(FLERR,"No reaxff pair style for fix qeq/reaxff");
 
-    int tmp;
+    int tmp, tmp_all;
     chi = (double *) pair->extract("chi",tmp);
     eta = (double *) pair->extract("eta",tmp);
     gamma = (double *) pair->extract("gamma",tmp);
-    if (chi == nullptr || eta == nullptr || gamma == nullptr)
-      error->all(FLERR, "Fix qeq/reaxff could not extract params from pair reaxff");
+    if ((chi == nullptr) || (eta == nullptr) || (gamma == nullptr))
+      error->all(FLERR, "Fix qeq/reaxff could not extract all QEq parameters from pair reaxff");
+    tmp = tmp_all = 0;
+    for (int i = 0; i < nlocal; ++i) {
+      if (mask[i] & groupbit) {
+        if ((chi[type[i]] == 0.0) && (eta[type[i]] == 0.0) && (gamma[type[i]] == 0.0))
+          tmp = type[i];
+      }
+    }
+    MPI_Allreduce(&tmp, &tmp_all, 1, MPI_INT, MPI_MAX, world);
+    if (tmp_all)
+      error->all(FLERR, "No QEq parameters for atom type {} provided by pair reaxff", tmp_all);
     return;
+  } else if (platform::file_is_readable(arg)) {
+    ; // arg is readable file. will read below
+  } else {
+    error->all(FLERR, "Unknown fix qeq/reaxff keyword {}", arg);
   }
 
   reaxflag = 0;
-  const int ntypes = atom->ntypes;
 
+  const int ntypes = atom->ntypes;
   memory->create(chi,ntypes+1,"qeq/reaxff:chi");
   memory->create(eta,ntypes+1,"qeq/reaxff:eta");
   memory->create(gamma,ntypes+1,"qeq/reaxff:gamma");

src/REAXFF/fix_reaxff_bonds.cpp

@@ -44,6 +44,7 @@ FixReaxFFBonds::FixReaxFFBonds(LAMMPS *lmp, int narg, char **arg) :
   ntypes = atom->ntypes;
   nmax = atom->nmax;
   compressed = 0;
+  first_flag = true;
 
   nevery = utils::inumeric(FLERR,arg[3],false,lmp);
 
@@ -94,7 +95,10 @@ int FixReaxFFBonds::setmask()
 
 void FixReaxFFBonds::setup(int /*vflag*/)
 {
-  end_of_step();
+  // only print output during setup() at the very beginning
+  // to avoid duplicate outputs when using multiple run statements
+  if (first_flag) end_of_step();
+  first_flag = false;
 }
 
 /* ---------------------------------------------------------------------- */

src/REAXFF/fix_reaxff_bonds.h

@@ -41,6 +41,7 @@ class FixReaxFFBonds : public Fix {
   tagint **neighid;
   double **abo;
   FILE *fp;
+  bool first_flag;
 
   void allocate();
   void destroy();

src/REAXFF/pair_reaxff.cpp

@@ -691,24 +691,28 @@ void *PairReaxFF::extract(const char *str, int &dim)
 {
   dim = 1;
   if (strcmp(str,"chi") == 0 && chi) {
+    chi[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) chi[i] = api->system->reax_param.sbp[map[i]].chi;
       else chi[i] = 0.0;
     return (void *) chi;
   }
   if (strcmp(str,"eta") == 0 && eta) {
+    eta[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) eta[i] = api->system->reax_param.sbp[map[i]].eta;
       else eta[i] = 0.0;
     return (void *) eta;
   }
   if (strcmp(str,"gamma") == 0 && gamma) {
+    gamma[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) gamma[i] = api->system->reax_param.sbp[map[i]].gamma;
       else gamma[i] = 0.0;
     return (void *) gamma;
    }
    if (strcmp(str,"bcut_acks2") == 0 && bcut_acks2) {
+    bcut_acks2[0] = 0.0;
     for (int i = 1; i <= atom->ntypes; i++)
       if (map[i] >= 0) bcut_acks2[i] = api->system->reax_param.sbp[map[i]].bcut_acks2;
       else bcut_acks2[i] = 0.0;

src/REPLICA/neb.cpp

@@ -200,7 +200,7 @@ void NEB::run()
   if (me == 0)
     color = 0;
   else
-    color = 1;
+    color = MPI_UNDEFINED;
   MPI_Comm_split(uworld, color, 0, &roots);
 
   auto fixes = modify->get_fix_by_style("^neb$");
@@ -610,17 +610,20 @@ void NEB::open(char *file)
 void NEB::print_status()
 {
   double fnorm2 = sqrt(update->minimize->fnorm_sqr());
-  double fmaxreplica;
-  MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots);
   double fnorminf = update->minimize->fnorm_inf();
-  double fmaxatom;
-  MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots);
+  double fmaxreplica = 0.0;
+  double fmaxatom = 0.0;
 
-  if (print_mode == VERBOSE) {
-    freplica = new double[nreplica];
-    MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots);
-    fmaxatomInRepl = new double[nreplica];
-    MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots);
+  if (me == 0) {
+    MPI_Allreduce(&fnorm2, &fmaxreplica, 1, MPI_DOUBLE, MPI_MAX, roots);
+    MPI_Allreduce(&fnorminf, &fmaxatom, 1, MPI_DOUBLE, MPI_MAX, roots);
+
+    if (print_mode == VERBOSE) {
+      freplica = new double[nreplica];
+      MPI_Allgather(&fnorm2, 1, MPI_DOUBLE, &freplica[0], 1, MPI_DOUBLE, roots);
+      fmaxatomInRepl = new double[nreplica];
+      MPI_Allgather(&fnorminf, 1, MPI_DOUBLE, &fmaxatomInRepl[0], 1, MPI_DOUBLE, roots);
+    }
   }
 
   double one[7];
@@ -705,7 +708,7 @@ void NEB::print_status()
       fflush(universe->ulogfile);
     }
   }
-  if (print_mode == VERBOSE) {
+  if ((me == 0) && (print_mode == VERBOSE)) {
     delete[] freplica;
     delete[] fmaxatomInRepl;
   }

src/RIGID/fix_rigid_small.cpp

@@ -2160,7 +2160,7 @@ void FixRigidSmall::setup_bodies_static()
     xgc = body[ibody].xgc;
     double delta[3];
     MathExtra::sub3(xgc,xcm,delta);
-    domain->minimum_image(delta);
+    domain->minimum_image_big(delta);
     MathExtra::transpose_matvec(ex,ey,ez,delta,body[ibody].xgc_body);
     MathExtra::add3(xcm,delta,xgc);
   }

src/RIGID/fix_shake.cpp

@@ -371,7 +371,9 @@ void FixShake::init()
   // if rRESPA, find associated fix that must exist
   // could have changed locations in fix list since created
   // set ptrs to rRESPA variables
+  // set respa to 0 if verlet is used and to 1 otherwise
 
+  respa = 0;
   fix_respa = nullptr;
   if (utils::strmatch(update->integrate_style,"^respa")) {
     if (update->whichflag > 0) {
@@ -379,10 +381,12 @@ void FixShake::init()
       if (fixes.size() > 0) fix_respa = dynamic_cast<FixRespa *>(fixes.front());
       else error->all(FLERR,"Run style respa did not create fix RESPA");
     }
-    auto respa_style = dynamic_cast<Respa *>(update->integrate);
-    nlevels_respa = respa_style->nlevels;
-    loop_respa = respa_style->loop;
-    step_respa = respa_style->step;
+    auto respa_ptr = dynamic_cast<Respa *>(update->integrate);
+    if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style);
+    respa = 1;
+    nlevels_respa = respa_ptr->nlevels;
+    loop_respa = respa_ptr->loop;
+    step_respa = respa_ptr->step;
   }
 
   // set equilibrium bond distances
@@ -473,18 +477,22 @@ void FixShake::setup(int vflag)
       next_output = (ntimestep/output_every)*output_every + output_every;
   } else next_output = -1;
 
-  // set respa to 0 if verlet is used and to 1 otherwise
-
-  if (utils::strmatch(update->integrate_style,"^verlet"))
-    respa = 0;
-  else
-    respa = 1;
-
   if (!respa) {
     dtv     = update->dt;
     dtfsq   = 0.5 * update->dt * update->dt * force->ftm2v;
     if (!rattle) dtfsq = update->dt * update->dt * force->ftm2v;
   } else {
+    auto respa_ptr = dynamic_cast<Respa *>(update->integrate);
+    if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style);
+    if (update->whichflag > 0) {
+      auto fixes = modify->get_fix_by_style("^RESPA");
+      if (fixes.size() > 0) fix_respa = dynamic_cast<FixRespa *>(fixes.front());
+      else error->all(FLERR,"Run style respa did not create fix RESPA");
+    }
+    respa = 1;
+    nlevels_respa = respa_ptr->nlevels;
+    loop_respa = respa_ptr->loop;
+    step_respa = respa_ptr->step;
     dtv = step_respa[0];
     dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
     dtf_inner = dtf_innerhalf;
@@ -3123,7 +3131,14 @@ void FixShake::reset_dt()
     dtv = update->dt;
     if (rattle) dtfsq   = 0.5 * update->dt * update->dt * force->ftm2v;
     else dtfsq = update->dt * update->dt * force->ftm2v;
+    respa = 0;
   } else {
+    auto respa_ptr = dynamic_cast<Respa *>(update->integrate);
+    if (!respa_ptr) error->all(FLERR, "Failure to access Respa style {}", update->integrate_style);
+    respa = 1;
+    nlevels_respa = respa_ptr->nlevels;
+    loop_respa = respa_ptr->loop;
+    step_respa = respa_ptr->step;
     dtv = step_respa[0];
     dtf_innerhalf = 0.5 * step_respa[0] * force->ftm2v;
     if (rattle) dtf_inner = dtf_innerhalf;

src/SPH/compute_sph_e_atom.cpp

@@ -13,13 +13,15 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_sph_e_atom.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -31,7 +33,7 @@ ComputeSPHEAtom::ComputeSPHEAtom(LAMMPS *lmp, int narg, char **arg) :
   if (narg != 3)
     error->all(FLERR,"Number of arguments for compute sph/e/atom command != 3");
   if (atom->esph_flag != 1)
-    error->all(FLERR,"Compute sph/e/atom command requires atom_style sph)");
+    error->all(FLERR,"Compute sph/e/atom requires atom attribute energy, e.g. in atom_style sph");
 
   peratom_flag = 1;
   size_peratom_cols = 0;
@@ -51,12 +53,11 @@ ComputeSPHEAtom::~ComputeSPHEAtom()
 
 void ComputeSPHEAtom::init()
 {
-
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"evector/atom") == 0) count++;
+    if (strcmp(modify->compute[i]->style,"sph/e/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute evector/atom");
+    error->warning(FLERR,"More than one compute sph/e/atom");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -78,14 +79,13 @@ void ComputeSPHEAtom::compute_peratom()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit) {
-              evector[i] = esph[i];
-      }
-      else {
-              evector[i] = 0.0;
-      }
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      evector[i] = esph[i];
+    } else {
+      evector[i] = 0.0;
     }
+  }
 }
 
 /* ----------------------------------------------------------------------

src/SPH/compute_sph_rho_atom.cpp

@@ -13,13 +13,15 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_sph_rho_atom.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -30,8 +32,7 @@ ComputeSPHRhoAtom::ComputeSPHRhoAtom(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg != 3) error->all(FLERR,"Illegal compute sph/rho/atom command");
   if (atom->rho_flag != 1)
-    error->all(FLERR,"Compute sph/rho/atom command requires atom_style sph");
-
+    error->all(FLERR, "Compute sph/rho/atom requires atom attribute density, e.g. in atom_style sph");
   peratom_flag = 1;
   size_peratom_cols = 0;
 
@@ -50,12 +51,11 @@ ComputeSPHRhoAtom::~ComputeSPHRhoAtom()
 
 void ComputeSPHRhoAtom::init()
 {
-
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"rhoVector/atom") == 0) count++;
+    if (strcmp(modify->compute[i]->style,"sph/rho/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute rhoVector/atom");
+    error->warning(FLERR,"More than one compute sph/rho/atom");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -73,20 +73,17 @@ void ComputeSPHRhoAtom::compute_peratom()
     vector_atom = rhoVector;
   }
 
-  // compute kinetic energy for each atom in group
-
   double *rho = atom->rho;
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit) {
-              rhoVector[i] = rho[i];
-      }
-      else {
-              rhoVector[i] = 0.0;
-      }
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      rhoVector[i] = rho[i];
+    } else {
+      rhoVector[i] = 0.0;
     }
+  }
 }
 
 /* ----------------------------------------------------------------------

src/SPH/compute_sph_t_atom.cpp

@@ -13,13 +13,15 @@
 ------------------------------------------------------------------------- */
 
 #include "compute_sph_t_atom.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
-#include "modify.h"
 #include "comm.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "modify.h"
+#include "update.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -31,7 +33,7 @@ ComputeSPHTAtom::ComputeSPHTAtom(LAMMPS *lmp, int narg, char **arg) :
   if (narg != 3)
     error->all(FLERR,"Number of arguments for compute sph/t/atom command != 3");
   if ((atom->esph_flag != 1) || (atom->cv_flag != 1))
-    error->all(FLERR,"Compute sph/t/atom command requires atom_style sph");
+    error->all(FLERR, "Compute sph/t/atom requires atom attributes energy and specific heat, e.g. in atom_style sph");
 
   peratom_flag = 1;
   size_peratom_cols = 0;
@@ -51,12 +53,11 @@ ComputeSPHTAtom::~ComputeSPHTAtom()
 
 void ComputeSPHTAtom::init()
 {
-
   int count = 0;
   for (int i = 0; i < modify->ncompute; i++)
-    if (strcmp(modify->compute[i]->style,"meso/t/atom") == 0) count++;
+    if (strcmp(modify->compute[i]->style,"sph/t/atom") == 0) count++;
   if (count > 1 && comm->me == 0)
-    error->warning(FLERR,"More than one compute meso/t/atom");
+    error->warning(FLERR,"More than one compute sph/t/atom");
 }
 
 /* ---------------------------------------------------------------------- */
@@ -79,16 +80,15 @@ void ComputeSPHTAtom::compute_peratom()
   int *mask = atom->mask;
   int nlocal = atom->nlocal;
 
-    for (int i = 0; i < nlocal; i++) {
-      if (mask[i] & groupbit) {
-              if (cv[i] > 0.0) {
-                      tvector[i] = esph[i] / cv[i];
-              }
-      }
-      else {
-              tvector[i] = 0.0;
+  for (int i = 0; i < nlocal; i++) {
+    if (mask[i] & groupbit) {
+      if (cv[i] > 0.0) {
+        tvector[i] = esph[i] / cv[i];
       }
+    } else {
+      tvector[i] = 0.0;
     }
+  }
 }
 
 /* ----------------------------------------------------------------------

src/SPH/fix_sph.cpp

@@ -13,10 +13,13 @@
  ------------------------------------------------------------------------- */
 
 #include "fix_sph.h"
+
 #include "atom.h"
+#include "comm.h"
+#include "domain.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
-#include "error.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -24,11 +27,10 @@ using namespace FixConst;
 /* ---------------------------------------------------------------------- */
 
 FixSPH::FixSPH(LAMMPS *lmp, int narg, char **arg) :
-  Fix(lmp, narg, arg) {
-
-  if ((atom->esph_flag != 1) || (atom->rho_flag != 1))
-    error->all(FLERR,
-        "Fix sph command requires atom_style with both energy and density");
+  Fix(lmp, narg, arg)
+{
+  if ((atom->esph_flag != 1) || (atom->rho_flag != 1) || (atom->vest_flag != 1))
+    error->all(FLERR, "Fix sph requires atom attributes energy, density, and velocity estimates, e.g. in atom_style sph");
 
   if (narg != 3)
     error->all(FLERR,"Illegal number of arguments for fix sph command");
@@ -38,7 +40,8 @@ FixSPH::FixSPH(LAMMPS *lmp, int narg, char **arg) :
 
 /* ---------------------------------------------------------------------- */
 
-int FixSPH::setmask() {
+int FixSPH::setmask()
+{
   int mask = 0;
   mask |= INITIAL_INTEGRATE;
   mask |= FINAL_INTEGRATE;
@@ -48,13 +51,20 @@ int FixSPH::setmask() {
 
 /* ---------------------------------------------------------------------- */
 
-void FixSPH::init() {
+void FixSPH::init()
+{
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
 }
 
+/* ---------------------------------------------------------------------- */
+
 void FixSPH::setup_pre_force(int /*vflag*/)
 {
+  remap_v_flag = domain->deform_vremap;
+  if (remap_v_flag && (!comm->ghost_velocity))
+    error->all(FLERR, "Fix sph requires ghost atoms store velocity when deforming with remap v");
+
   // set vest equal to v
   double **v = atom->v;
   double **vest = atom->vest;
@@ -76,7 +86,8 @@ void FixSPH::setup_pre_force(int /*vflag*/)
  allow for both per-type and per-atom mass
  ------------------------------------------------------------------------- */
 
-void FixSPH::initial_integrate(int /*vflag*/) {
+void FixSPH::initial_integrate(int /*vflag*/)
+{
   // update v and x and rho and e of atoms in group
 
   double **x = atom->x;
@@ -112,9 +123,16 @@ void FixSPH::initial_integrate(int /*vflag*/) {
       rho[i] += dtf * drho[i]; // ... and density
 
       // extrapolate velocity for use with velocity-dependent potentials, e.g. SPH
-      vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
-      vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
-      vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
+      // if velocities are remapped, perform this extrapolation after communication
+      if (remap_v_flag) {
+        vest[i][0] = dtfm * f[i][0];
+        vest[i][1] = dtfm * f[i][1];
+        vest[i][2] = dtfm * f[i][2];
+      } else {
+        vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
+        vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
+        vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
+      }
 
       v[i][0] += dtfm * f[i][0];
       v[i][1] += dtfm * f[i][1];
@@ -129,8 +147,33 @@ void FixSPH::initial_integrate(int /*vflag*/) {
 
 /* ---------------------------------------------------------------------- */
 
-void FixSPH::final_integrate() {
+void FixSPH::pre_force(int /*vflag*/)
+{
+  // if velocities are remapped, calculate estimates here
+  // note that vest currently stores dtfm * force
+  if (!remap_v_flag) return;
 
+  double **v = atom->v;
+  double **vest = atom->vest;
+  int *mask = atom->mask;
+  int nlocal = atom->nlocal;
+  if (igroup == atom->firstgroup)
+    nlocal = atom->nfirst;
+
+  int nall = nlocal + atom->nghost;
+  for (int i = 0; i < nall; i++) {
+    if (mask[i] & groupbit) {
+      vest[i][0] += v[i][0];
+      vest[i][1] += v[i][1];
+      vest[i][2] += v[i][2];
+    }
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixSPH::final_integrate()
+{
   // update v, rho, and e of atoms in group
 
   double **v = atom->v;
@@ -169,7 +212,8 @@ void FixSPH::final_integrate() {
 
 /* ---------------------------------------------------------------------- */
 
-void FixSPH::reset_dt() {
+void FixSPH::reset_dt()
+{
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
 }