Merge branch 'master' into plugin-loader

doc/src/Build_basics.rst

@@ -234,6 +234,8 @@ LAMMPS.
          cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
          # Building with Intel Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         # Building with Intel oneAPI Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
          # Building with LLVM/Clang Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
          # Building with PGI/Nvidia Compilers:
@@ -243,8 +245,10 @@ LAMMPS.
       provided that can be loaded with
       `-C ../cmake/presets/clang.cmake`.  Similarly,
       `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
-      should switch the compiler to the PGI compilers.
+      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
+      will switch to the LLVM based oneAPI Intel compilers,
+      and `-C ../cmake/presets/pgi.cmake`
+      will switch the compiler to the PGI compilers.
 
       In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts. By

doc/src/Build_extras.rst

@@ -128,9 +128,9 @@ CMake build
                                 # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
-   -D CUDPP_OPT=value           # optimization setting for GPU_API=cuda
-                                # enables CUDA Performance Primitives Optimizations, must be "no" for CUDA_MPS_SUPPORT=yes
-                                # value = yes (default) or no
+   -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
+                                # enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
+                                # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
    -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
@@ -230,11 +230,12 @@ GPU architectures as supported by the CUDA toolkit in use. This is done
 through using the "--gencode " flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
-To include CUDA performance primitives set the Makefile variable
-``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.
+To enable GPU binning via CUDA performance primitives set the Makefile variable
+``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.  This should **not** be used with
+most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you should **not** use
+``-DCUDA_PROXY``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 

doc/src/Howto_cmake.rst

@@ -411,10 +411,10 @@ interface (``ccmake`` or ``cmake-gui``).
 .. note::
 
    Using a preset to select a compiler package (``clang.cmake``,
-   ``gcc.cmake``, or ``intel.cmake``) are an exception to the option
-   of updating the configuration incrementally, as they will trigger
-   a reset of cached internal CMake settings and thus reset them to
-   their default values.
+   ``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
+   are an exception to the mechanism of updating the configuration incrementally,
+   as they will trigger a reset of cached internal CMake settings and thus
+   reset settings to their default values.
 
 Compilation and build targets
 -----------------------------

doc/src/Tools.rst

@@ -93,6 +93,7 @@ Miscellaneous tools
    * :ref:`i-pi <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
+   * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -641,6 +642,39 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 ----------
 
+.. _magic:
+
+Magic patterns for the "file" command
+-------------------------------------
+
+.. versionadded:: 10Mar2021
+
+The file ``magic`` contains patterns that are used by the
+`file program <https://en.wikipedia.org/wiki/File_(command)>`_
+available on most Unix-like operating systems which enables it
+to detect various LAMMPS files and print some useful information
+about them.  To enable these patterns, append or copy the contents
+of the file to either the file ``.magic`` in your home directory
+or (as administrator) to ``/etc/magic`` (for a system-wide
+installation).  Afterwards the ``file`` command should be able to
+detect most LAMMPS restarts, dump, data and log files. Examples:
+
+.. code-block:: bash
+
+   $ file *.*
+   dihedral-quadratic.restart:   LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
+   mol-pair-wf_cut.restart:      LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
+   atom.bin:                     LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
+   custom.bin:                   LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
+   bn1.lammpstrj:                LAMMPS text mode dump, First time step: 5000
+   data.fourmol:                 LAMMPS data file written by LAMMPS
+   pnc.data:                     LAMMPS data file written by msi2lmp
+   data.spce:                    LAMMPS data file written by TopoTools
+   B.data:                       LAMMPS data file written by OVITO
+   log.lammps:                   LAMMPS log file written by version 10 Feb 2021
+
+----------
+
 .. _matlab:
 
 matlab tool

doc/utils/sphinx-config/false_positives.txt

@@ -160,6 +160,7 @@ atwt
 augt
 AuO
 automagically
+Auvergne
 Avalos
 avalue
 aveforce
@@ -1740,6 +1741,7 @@ lwsock
 lx
 ly
 Lybrand
+lyon
 Lyulin
 lz
 Maaravi
@@ -3256,6 +3258,7 @@ Tz
 Tzou
 ub
 Uberuaga
+uca
 uChem
 uCond
 uef